diff --git a/BRAINSABC/CMakeLists.txt b/BRAINSABC/CMakeLists.txt new file mode 100644 index 00000000..2ed73439 --- /dev/null +++ b/BRAINSABC/CMakeLists.txt @@ -0,0 +1,41 @@ +project(BRAINSABC) +set(LOCAL_PROJECT_NAME BRAINSABC) +cmake_minimum_required(VERSION 2.8) +cmake_policy(VERSION 2.8) + +enable_testing() +include(CTest) + +find_package(BRAINSCommonLib NO_MODULE REQUIRED) +include(${BRAINSCommonLib_USE_FILE}) + +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/PreventInSourceBuilds.cmake) +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBuildMacros.cmake) +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMMacroBuildCLI.cmake) +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBRAINS3BuildMacros.cmake) +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/IJMacros.txt) + +### +SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib) +SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib) +SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin) +SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin) +link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}) + +if(NOT ITK_FOUND) + find_package(ITK REQUIRED) + include(${ITK_USE_FILE}) +endif(NOT ITK_FOUND) + +#----------------------------------------------------------------------------- +# Output directories. +# +#SETOPTIONALDEBUGIMAGEVIEWER() + +### +add_subdirectory(brainseg) + +if(1) + add_subdirectory(TestSuite) +endif(1) + diff --git a/BRAINSABC/CTestConfig.cmake b/BRAINSABC/CTestConfig.cmake new file mode 100644 index 00000000..5801c7b1 --- /dev/null +++ b/BRAINSABC/CTestConfig.cmake @@ -0,0 +1,14 @@ +## This file should be placed in the root directory of your project. +## Then modify the CMakeLists.txt file in the root directory of your +## project to incorporate the testing dashboard. +## # The following are required to uses Dart and the Cdash dashboard +## enable_testing() +## include(CTest) +set(CTEST_PROJECT_NAME "BRAINSABC") +set(CTEST_NIGHTLY_START_TIME "00:00:00 EST") + +set(CTEST_DROP_METHOD "http") +set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu") +set(CTEST_DROP_LOCATION "/CDash/submit.php?project=BRAINSABC") +set(CTEST_DROP_SITE_CDASH TRUE) +set(CTEST_TEST_TIMEOUT 3600) ## Set timeout to one hour for now. There is a lot of work to be done. diff --git a/BRAINSABC/TestSuite/AtlasPVDefinition.xml.md5 b/BRAINSABC/TestSuite/AtlasPVDefinition.xml.md5 new file mode 100644 index 00000000..1881159a --- /dev/null +++ b/BRAINSABC/TestSuite/AtlasPVDefinition.xml.md5 @@ -0,0 +1 @@ +24d6e8d67a2fa417853e1b86449c8cfb diff --git a/BRAINSABC/TestSuite/BRAINSABCTest.cxx b/BRAINSABC/TestSuite/BRAINSABCTest.cxx new file mode 100644 index 00000000..8d7d3f65 --- /dev/null +++ b/BRAINSABC/TestSuite/BRAINSABCTest.cxx @@ -0,0 +1,23 @@ +// +//A test driver to append the +//itk image processing test +//commands to an +//the SEM compatibile program +// +#if defined(_MSC_VER) +#pragma warning ( disable : 4786 ) +#endif + +#ifdef WIN32 +#define MODULE_IMPORT __declspec(dllimport) +#else +#define MODULE_IMPORT +#endif + +extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []); + +int BRAINSABCTest(int argc, char** argv) +{ + return ModuleEntryPoint(argc, argv); +} + diff --git a/BRAINSABC/TestSuite/BlendImageFilterTest.cxx b/BRAINSABC/TestSuite/BlendImageFilterTest.cxx new file mode 100644 index 00000000..f1fca5c2 --- /dev/null +++ b/BRAINSABC/TestSuite/BlendImageFilterTest.cxx @@ -0,0 +1,54 @@ +#include "itkImage.h" +#include "itkBlendImageFilter.h" +#include "itkRandomImageSource.h" +#include "itkImageRegionConstIterator.h" +#include "vnl/vnl_math.h" + +int main(int, char * *) +{ + typedef itk::Image ImageType; + + std::cout << "Create input image using RandomImageSource" << std::endl; + ImageType::Pointer images[2]; + for( unsigned i = 0; i < 2; i++ ) + { + typedef itk::RandomImageSource SourceType; + SourceType::Pointer source = SourceType::New(); + ImageType::SizeValueType size[2] = {64, 64}; + source->SetSize( size ); + source->SetMin(0.0); + source->SetMax(1.0); + source->Update(); + images[i] = source->GetOutput(); + } + typedef itk::BlendImageFilter + BlendImageFilterType; + BlendImageFilterType::Pointer filter = + BlendImageFilterType::New(); + filter->SetInput1(images[0]); + filter->SetInput2(images[1]); + filter->SetBlend1(0.2); + filter->SetBlend2(0.8); + filter->Update(); + ImageType::Pointer blendImage = filter->GetOutput(); + itk::ImageRegionConstIterator + it1(images[0], + images[0]->GetLargestPossibleRegion() ), + it2(images[1], + images[1]->GetLargestPossibleRegion() ), + itBlend(blendImage, + blendImage->GetLargestPossibleRegion() ); + for( ; !it1.IsAtEnd() && !it2.IsAtEnd() && !itBlend.IsAtEnd(); + ++it1, ++it2, ++itBlend ) + { + float blend = (it1.Get() * 0.2) + (it2.Get() * 0.8); + if( vcl_fabs(blend - itBlend.Get() ) > 0.0001 ) + { + std::cerr << "Expected " << blend << " found " << itBlend.Get() + << std::endl; + exit(1); + } + } + exit(0); +} + diff --git a/BRAINSABC/TestSuite/CMakeLists.txt b/BRAINSABC/TestSuite/CMakeLists.txt new file mode 100644 index 00000000..0be1d5f3 --- /dev/null +++ b/BRAINSABC/TestSuite/CMakeLists.txt @@ -0,0 +1,60 @@ +list(APPEND ExternalData_URL_TEMPLATES + # Local data store populated by the ITK pre-commit hook + "file:///${CMAKE_SOURCE_DIR}/.ExternalData/%(algo)/%(hash)" + # Data published by Iowa Psychiatry web interface + "http://www.psychiatry.uiowa.edu/users/brainstestdata/ctestdata/%(algo)/%(hash)" + + # Data published by MIDAS + "http://midas.kitware.com/api/rest/midas.bitstream.by.hash?hash=%(hash)&algorithm=%(algo)" + + # Data published by developers using git-gerrit-push. + "http://www.itk.org/files/ExternalData/%(algo)/%(hash)" + ) + +# Tell ExternalData commands to transform raw files to content links. +# TODO: Condition this feature on presence of our pre-commit hook. +set(ExternalData_LINK_CONTENT MD5) +include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/ExternalData.cmake) + +include_directories( + ${BRAINSABC_SOURCE_DIR}/brainseg + ${BRAINSABC_SOURCE_DIR}/common + ${BRAINSABC_BINARY_DIR}/brainseg +) + + + +MakeTestDriverFromSEMTool(BRAINSABC BRAINSABCTest.cxx) + +ExternalData_add_test( FetchData NAME BRAINSABCLongTest + COMMAND ${LAUNCH_EXE} $ + --compare DATA{test_data/refResults/labels.nii.gz} + ${CMAKE_CURRENT_BINARY_DIR}/labels.nii.gz + --compareIntensityTolerance 1 + --compareRadiusTolerance 1 + --compareNumberOfPixelsTolerance 10000 + BRAINSABCTest + --inputVolumes DATA{test_data/small_ISO_T1_REP0.nii.gz} --inputVolumes DATA{test_data/small_ISO_T2_REP0.nii.gz} + --outputVolumes ${CMAKE_CURRENT_BINARY_DIR}/T1_cleaned.nii.gz,${CMAKE_CURRENT_BINARY_DIR}/T2_cleaned.nii.gz + --outputLabels ${CMAKE_CURRENT_BINARY_DIR}/labels.nii.gz + --outputDirtyLabels ${CMAKE_CURRENT_BINARY_DIR}/dirty_labels.nii.gz + --posteriorTemplate ${CMAKE_CURRENT_BINARY_DIR}/POST_%s.nii.gz + --inputVolumeTypes T1,T2 + --filterIteration 3 + --maxIterations 2 + --maxBiasDegree 2 + --debuglevel 0 + --outputFormat NIFTI + --outputDir ${CMAKE_CURRENT_BINARY_DIR} + --gridSize 5,3,4 + --atlasDefinition ${CMAKE_CURRENT_BINARY_DIR}/../../src/bin/Atlas/Atlas_20110607/AtlasPVDefinition.xml +) +set_tests_properties(BRAINSABCLongTest PROPERTIES TIMEOUT 6500) + +if(0) # This should be restored after fixing. +add_executable(BlendImageFilterTest BlendImageFilterTest.cxx) +target_link_libraries(BlendImageFilterTest ${ITK_LIBRARIES}) +ExternalData_add_test( FetchData NAME BlendImageFilterTest COMMAND ${LAUNCH_EXE} $ ) +endif() + +ExternalData_Add_Target( FetchData ) # Name of data management target diff --git a/BRAINSABC/TestSuite/simpleEM.cxx b/BRAINSABC/TestSuite/simpleEM.cxx new file mode 100644 index 00000000..a1d9c638 --- /dev/null +++ b/BRAINSABC/TestSuite/simpleEM.cxx @@ -0,0 +1,347 @@ +#include "simpleEMCLP.h" + +#include + +#include "itkCastImageFilter.h" +#include "itkImage.h" +#include "itkImageFileWriter.h" +#include "itkImageFileReader.h" +#include "itkLinearInterpolateImageFunction.h" +#include "itkNumericTraits.h" +#include "itkMultiplyImageFilter.h" +#include "itkResampleImageFilter.h" +#include "itkRescaleIntensityImageFilter.h" +#include "itkVersion.h" +#include "AtlasCropImageSource.h" + +#include + +// Use manually instantiated classes for the big program chunks +// #define MU_MANUAL_INSTANTIATION +#include "EMSegmentationFilter.h" +#include "itkLargestForegroundFilledMaskImageFilter.h" + +// #undef MU_MANUAL_INSTANTIATION + +#include "filterFloatImages.h" + +#include +#include +#include + +#include +// template +template +int simpleRunEMS( std::string t1Volume, + std::string t2Volume, + std::string pdVolume, + std::string templateVolume, + int maxIteration, + std::string OutputFileNamePrefix, + std::vector & priorsList, + std::vector & priorsWeightList, + bool warp, + int degreeOfBiasFieldCorrection, + double likelihoodTolerance) +{ + int status = -1; + // PARSE_ARGS; + /** read parameters **/ + /** - read target input images **/ + std::string T1FileName(t1Volume); + std::string T2FileName(t2Volume); + std::string PDFileName(pdVolume); + + typedef itk::Image FloatImageType; + typedef itk::Image ByteImageType; + typedef itk::Image ShortImageType; + + typedef FloatImageType::Pointer FloatImagePointer; + typedef ByteImageType::Pointer ByteImagePointer; + typedef ShortImageType::Pointer ShortImagePointer; + + typedef itk::Image InputImageType; + typedef itk::ImageFileReader InputImageReaderType; + typedef itk::RescaleIntensityImageFilter RescaleImageFilterType; + typedef typename InputImageType::Pointer InputImagePointer; + + typedef itk::ImageFileReader templateReaderType; + typename templateReaderType::Pointer templateReader = templateReaderType::New(); + templateReader->SetFileName(templateVolume); + templateReader->Update(); + std::vector images; + + /* IMAGES MUST BE Non-Negative or the results will fail. */ + std::vector inputImageFilenames; + if( T1FileName == "" ) + { + std::cerr << " T1 file is missing, other modality will be used as a reference image.\n "; + } + else + { + typename InputImageReaderType::Pointer inputReaderT1 = InputImageReaderType::New(); + inputReaderT1->SetFileName(T1FileName); + inputImageFilenames.push_back(T1FileName); + inputReaderT1->Update(); + typename RescaleImageFilterType::Pointer rescalerT1 = RescaleImageFilterType::New(); + // Set the upper limit to 4096 in the case of floating point data. + const inputPixelType outMin = 0; + const inputPixelType outMax + = ( vcl_numeric_limits::max() > 4096 ) ? 4096 : vcl_numeric_limits::max(); + rescalerT1->SetOutputMinimum(outMin); + rescalerT1->SetOutputMaximum(outMax); + rescalerT1->SetInput( inputReaderT1->GetOutput() ); + rescalerT1->Update(); + images.push_back( rescalerT1->GetOutput() ); + } + + if( T2FileName == "" ) + { + std::cerr << " T2 file is missing.\n "; + } + else + { + typename InputImageReaderType::Pointer inputReaderT2 = InputImageReaderType::New(); + inputReaderT2->SetFileName(T2FileName); + inputImageFilenames.push_back(T2FileName); + inputReaderT2->Update(); + typename RescaleImageFilterType::Pointer rescalerT2 = RescaleImageFilterType::New(); + // Set the upper limit to 4096 in the case of floating point data. + const inputPixelType outMin = 0; + const inputPixelType outMax + = ( vcl_numeric_limits::max() > 4096 ) ? 4096 : vcl_numeric_limits::max(); + rescalerT2->SetOutputMinimum(outMin); + rescalerT2->SetOutputMaximum(outMax); + rescalerT2->SetInput( inputReaderT2->GetOutput() ); + rescalerT2->Update(); + images.push_back( rescalerT2->GetOutput() ); + } + + if( PDFileName == "" ) + { + std::cerr << " PD file is missing.\n "; + } + else + { + typename InputImageReaderType::Pointer inputReaderPD = InputImageReaderType::New(); + inputReaderPD->SetFileName(PDFileName); + inputImageFilenames.push_back(PDFileName); + inputReaderPD->Update(); + typename RescaleImageFilterType::Pointer rescalerPD = RescaleImageFilterType::New(); + // Set the upper limit to 4096 in the case of floating point data. + const inputPixelType outMin = 0; + const inputPixelType outMax + = ( vcl_numeric_limits::max() > 4096 ) ? 4096 : vcl_numeric_limits::max(); + rescalerPD->SetOutputMinimum(outMin); + rescalerPD->SetOutputMaximum(outMax); + rescalerPD->SetInput( inputReaderPD->GetOutput() ); + rescalerPD->Update(); + images.push_back( rescalerPD->GetOutput() ); + } + if( T1FileName == "" && T2FileName == "" && PDFileName == "" ) + { + std::cerr << " We need at lease one or more target image.\n"; + status = -1; + return status; + } + // Compute the brain outline in order to cut images later after bias + // correction + const unsigned int closingSize = 7; + const float otsuPercentileThreshold = 0.01; + // typename InputImageType::Pointer HeadOutlineMaskImage = + // FindLargestForgroundFilledMask( images[0], + // otsuPercentileThreshold, closingSize ); + typedef itk::LargestForegroundFilledMaskImageFilter LFFMaskFilterType; + typename LFFMaskFilterType::Pointer LFF = LFFMaskFilterType::New(); + LFF->SetInput(images[0]); + LFF->SetOtsuPercentileThreshold(otsuPercentileThreshold); + LFF->SetClosingSize(closingSize); + LFF->Update(); + typename InputImageType::Pointer HeadOutlineMaskImage = LFF->GetOutput(); + + std::cerr << " Following image will be used as a reference target image \n"; + std::cerr << " Input Image 1:: " << images[0]->GetLargestPossibleRegion().GetSize() << std::endl; + + /** - read atlas images **/ + /* atlas should have list of atlas for interest and background */ + /* and those atlas should including prior weight. */ + std::vector PriorsList(priorsList); + std::vector PriorWeights(priorsWeightList); + + typedef itk::Image PriorImageType; + typedef itk::ImageFileReader PriorImageReaderType; + typedef typename PriorImageType::Pointer PriorImagePointer; + + std::vector priors; + + if( PriorsList.size() != PriorWeights.size() ) + { + std::cerr << " Number of List of Prior Image should be same to the Prior Weights List\n"; + status = -1; + return status; + } + + std::vector priorImageFileNames; + if( PriorsList.empty() ) + { + std::cerr << " There is no prior image at all, we need at least one image\n"; + status = -1; + return status; + } + else + { + for( unsigned int i = 0; i < PriorsList.size(); i++ ) + { + typename PriorImageReaderType::Pointer priorReader = PriorImageReaderType::New(); + std::string name = PriorsList.at(i); + priorReader->SetFileName( name ); + priorImageFileNames.push_back(name); + priorReader->Update(); + priors.push_back( priorReader->GetOutput() ); + std::cout << " Prior List :: " << i << " :: " << name << "\n"; + } + } + + typedef EMSegmentationFilter SegFilterType; + typename SegFilterType::VectorType priorweights( PriorWeights.size() ); + for( unsigned int i = 0; i < PriorWeights.size(); i++ ) + { + priorweights[i] = PriorWeights.at(i); + } + + std::cerr << "Start segmentation...\n"; + + typename SegFilterType::Pointer segfilter = SegFilterType::New(); + segfilter->DebugOn(); + + // HACK: Need for loop around this + std::vector templateImageList; + templateImageList.clear(); + + templateImageList.push_back( templateReader->GetOutput() ); + + segfilter->SetTemplateImages( templateImageList ); + segfilter->SetInputImages( images ); + segfilter->SetPriors( priors ); + segfilter->SetMaximumIterations( maxIteration ); + segfilter->SetPriorWeights(priorweights); + segfilter->SetMaxBiasDegree(degreeOfBiasFieldCorrection); + if( likelihoodTolerance > 0.0 ) // override the default only if provided. + { + segfilter->SetLikelihoodTolerance(likelihoodTolerance); + } + if( warp ) + { + segfilter->DoWarpingOn(); + } + else + { + segfilter->DoWarpingOff(); + } + segfilter->Update(); + + // Write the labels + std::cerr << "Writing labels...\n"; + { + typedef itk::ImageFileWriter OutputWriterType; + OutputWriterType::Pointer writer = OutputWriterType::New(); + + writer->SetInput( segfilter->GetOutput() ); + writer->UseCompressionOn(); + std::string fn = std::string(OutputFileNamePrefix + "_labels.nii.gz"); + writer->SetFileName( fn.c_str() ); + writer->Update(); + } + + // Write the secondary outputs + if( true ) + { + std::cerr << "Writing filtered and bias corrected images...\n"; + std::vector imgset = segfilter->GetCorrected(); + for( unsigned i = 0; i < imgset.size(); i++ ) + { + typedef itk::CastImageFilter CasterType; + typename CasterType::Pointer caster = CasterType::New(); + typename itk::MultiplyImageFilter::Pointer multiplyFilter + = itk::MultiplyImageFilter::New(); + multiplyFilter->SetInput1(imgset[i]); + multiplyFilter->SetInput2(HeadOutlineMaskImage); + + caster->SetInput( multiplyFilter->GetOutput() ); + caster->Update(); + std::string fn = std::string(inputImageFilenames[i] + "_corrected.nii.gz"); + + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + + writer->SetInput( caster->GetOutput() ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + + // Short posteriors + std::cerr << "Writing posterior images...\n"; + std::vector probset = segfilter->GetShortPosteriors(); + for( unsigned int i = 0; i < ( probset.size() - 3 ); i++ ) + { + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + writer->SetInput( probset[i] ); + writer->SetFileName(priorImageFileNames[i] + "_posterior.nii.gz"); + writer->UseCompressionOn(); + writer->Update(); + } + } + return status; +} + +int main(int argc, char *argv[]) +{ + PARSE_ARGS; + int status = -1; + status + = simpleRunEMS(t1Volume, + t2Volume, + pdVolume, + templateVolume, + maxIteration, + OutputFileNamePrefix, + priorsList, + priorsWeightList, + warp, + degreeOfBiasFieldCorrection, + likelihoodTolerance ); + /* + if(inputPixelType=="double") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, maxIteration , + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="short") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="ushort") status = + simpleRunEMS(t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="int") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="uint") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="long") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="float") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else if( inputPixelType=="uchar") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + else( inputPixelType=="char") status = + simpleRunEMS( t1Volume, t2Volume, pdVolume, templateVolume, + OutputFileNamePrefix, priorsList, priorsWeightList, warp , degreeOfBiasFieldCorrection ); + */ + return status; +} + diff --git a/BRAINSABC/TestSuite/simpleEM.xml b/BRAINSABC/TestSuite/simpleEM.xml new file mode 100644 index 00000000..9c2893c2 --- /dev/null +++ b/BRAINSABC/TestSuite/simpleEM.xml @@ -0,0 +1,143 @@ + + + UNC + simpleEM + Atlas-based tissue segmentation method + + + + + + t1Volume + t1Volume + T1 Volume + + + input + + + t2Volume + t2Volume + T2 Volume + + + input + + + pdVolume + pdVolume + PD Volume + + + input + + + + + + templateVolume + templateVolume + template Volume + + + input + + + priorsList + priorsList + number of input should same to the number of priorsList + + + + priorsWeightList + priorsWeightList + number of input should same to the number of priorsList + + + + likelihoodTolerance + likelihoodTolerance + a convergence parameter (0 indicates take the default from the EMSegmentationFilter constructor.) + 0.0 + + + + + + warp + warp + + false + input + + + degreeOfBiasFieldCorrection + degreeOfBiasFieldCorrection + + 4 + input + + + maxIteration + maxIteration + + 100 + input + + + + + + OutputFileNamePrefix + + BRAINSABC + input + + + inputPixelType + inputPixelType + + Input Type + uchar + usigned char + short + unsigned short + int + unsigned int + long + float + double + + + outputPixelType + outputPixelType + + Input Type + uchar + unsigbed char + short + unsigned short + int + unsigned int + long + float + double + + + priorPixelType + priorPixelType + + prior Type + float + unsigbed char + short + unsigned short + int + unsigned int + long + float + double + + + + diff --git a/BRAINSABC/TestSuite/test_data/000517510_000517510_lmks.fcsv.md5 b/BRAINSABC/TestSuite/test_data/000517510_000517510_lmks.fcsv.md5 new file mode 100644 index 00000000..1ff420c4 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/000517510_000517510_lmks.fcsv.md5 @@ -0,0 +1 @@ +91e369151012a32934b6218189a6d15d \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/EMS-Param.xml.md5 b/BRAINSABC/TestSuite/test_data/EMS-Param.xml.md5 new file mode 100644 index 00000000..b202439b --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/EMS-Param.xml.md5 @@ -0,0 +1 @@ +f2d6f5a91deed770db64bc7204ec4be2 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/EMS.log.md5 b/BRAINSABC/TestSuite/test_data/EMS.log.md5 new file mode 100644 index 00000000..f1c2b835 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/EMS.log.md5 @@ -0,0 +1 @@ +b6a47cf38e7e46f9f8496155546f0d60 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/EMS.xml.md5 b/BRAINSABC/TestSuite/test_data/EMS.xml.md5 new file mode 100644 index 00000000..9c735149 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/EMS.xml.md5 @@ -0,0 +1 @@ +2a39f7a4ce55aecb1c491f54ad9ad493 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/FAST_logger.log.md5 b/BRAINSABC/TestSuite/test_data/FAST_logger.log.md5 new file mode 100644 index 00000000..c1c73cc4 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/FAST_logger.log.md5 @@ -0,0 +1 @@ +aa78504cd5f2401582b90346e42502c3 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/ISO_T1_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/ISO_T1_REP0.nii.gz.md5 new file mode 100644 index 00000000..be2f9f39 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/ISO_T1_REP0.nii.gz.md5 @@ -0,0 +1 @@ +67793308fc0d9fe80a6baf917a60cfb4 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/ISO_T1_REP0_to_template_EMS.bspline.md5 b/BRAINSABC/TestSuite/test_data/ISO_T1_REP0_to_template_EMS.bspline.md5 new file mode 100644 index 00000000..07348b24 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/ISO_T1_REP0_to_template_EMS.bspline.md5 @@ -0,0 +1 @@ +927ddcdf4ab6048c041c4610d00789be \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/ISO_T1_REP1.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/ISO_T1_REP1.nii.gz.md5 new file mode 100644 index 00000000..9fca1b93 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/ISO_T1_REP1.nii.gz.md5 @@ -0,0 +1 @@ +9f074e4025a2054bf85a5d0c23d9ff2f \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/ISO_T2_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/ISO_T2_REP0.nii.gz.md5 new file mode 100644 index 00000000..cc88b9f3 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/ISO_T2_REP0.nii.gz.md5 @@ -0,0 +1 @@ +d66e002dedb39db3062f364c7cf84cd4 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/T1_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/T1_REP0.nii.gz.md5 new file mode 100644 index 00000000..3ef1095b --- /dev/null +++ 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end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nii.gz.md5 new file mode 100644 index 00000000..47ce210e --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nii.gz.md5 @@ -0,0 +1 @@ +822f9b0f90bda6605933ace6502c8a4a \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..0fe0aec1 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_labels_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +37f384e7bb117dc5fef7527440da40d4 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior0_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior0_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..dd3436fe --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior0_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +4eeb4bf5e5bb00072f5a6d8b2686f03b \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior1_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior1_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..89b58b73 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior1_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +7da5c82116eeceb5e7b290732c8b6e69 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior2_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior2_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..fe65748b --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_posterior2_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +79d40e6226122822d848683bea798ca1 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_registered_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_registered_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..c60a57cf --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_registered_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +aa81874f49d7e74b229f9729959f800f \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_template_affine_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_template_affine_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..23a90117 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP0_template_affine_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ 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a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP1_registered_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP1_registered_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..2bb5a4c1 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T1_REP1_registered_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +43a6cdbeff841b1f69db1c97ea90555a \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_corrected_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_corrected_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..20ec1df7 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_corrected_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +03348131aa6626e2d6a795c433efa439 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_registered_BRAINSABC.nrrd.md5 b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_registered_BRAINSABC.nrrd.md5 new file mode 100644 index 00000000..e743b63a --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/refResults/small_ISO_T2_REP0_registered_BRAINSABC.nrrd.md5 @@ -0,0 +1 @@ +51ba4d6ed6c93a7c6a80d0b431febf92 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/run_test.sh.md5 b/BRAINSABC/TestSuite/test_data/run_test.sh.md5 new file mode 100644 index 00000000..d5e9a582 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/run_test.sh.md5 @@ -0,0 +1 @@ +22ea386f7bc25e4c623631ac3e9f8cd4 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0.nii.gz.md5 new file mode 100644 index 00000000..8ad149f9 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0.nii.gz.md5 @@ -0,0 +1 @@ +f5376fed7ace5288f354a400f78b63c1 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T1_REP1_EMS.affine.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T1_REP1_EMS.affine.md5 new file mode 100644 index 00000000..3fef45b2 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T1_REP1_EMS.affine.md5 @@ -0,0 +1 @@ +bcf7ac034b51a40c2a566074f7d7ac0d \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T2_REP0_EMS.affine.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T2_REP0_EMS.affine.md5 new file mode 100644 index 00000000..b4c00b6f --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_small_ISO_T2_REP0_EMS.affine.md5 @@ -0,0 +1 @@ +e99fc06cd42c0f718b1ebac784e5a6c8 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.affine.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.affine.md5 new file mode 100644 index 00000000..b27cdef1 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.affine.md5 @@ -0,0 +1 @@ +aca942f1ae529e13b55ec0abe8c3809c \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.bspline.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.bspline.md5 new file mode 100644 index 00000000..c00db168 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP0_to_template_EMS.bspline.md5 @@ -0,0 +1 @@ +85f0d61e57edcf3e8632ad6a94c2059f \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP1.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP1.nii.gz.md5 new file mode 100644 index 00000000..527fff79 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T1_REP1.nii.gz.md5 @@ -0,0 +1 @@ +1efd6c51ce6846d04cd882778ae5982c \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_ISO_T2_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_ISO_T2_REP0.nii.gz.md5 new file mode 100644 index 00000000..89cbc50e --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_ISO_T2_REP0.nii.gz.md5 @@ -0,0 +1 @@ +29e6f3bda04965df586bdd37e16c3979 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_T1_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_T1_REP0.nii.gz.md5 new file mode 100644 index 00000000..a35c43cc --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_T1_REP0.nii.gz.md5 @@ -0,0 +1 @@ +5597e9dc203ffe689de3c0cc50cfee78 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_T1_REP0_to_template_EMS.bspline.md5 b/BRAINSABC/TestSuite/test_data/small_T1_REP0_to_template_EMS.bspline.md5 new file mode 100644 index 00000000..9f24d39d --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_T1_REP0_to_template_EMS.bspline.md5 @@ -0,0 +1 @@ +1b5da6351f561587eb7e40edc6929952 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_T1_REP1.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_T1_REP1.nii.gz.md5 new file mode 100644 index 00000000..ea1e1bc4 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_T1_REP1.nii.gz.md5 @@ -0,0 +1 @@ +e94dcbc50400f911f328c218b4de7c83 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/small_T2_REP0.nii.gz.md5 b/BRAINSABC/TestSuite/test_data/small_T2_REP0.nii.gz.md5 new file mode 100644 index 00000000..915907bb --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/small_T2_REP0.nii.gz.md5 @@ -0,0 +1 @@ +b7099ae59aedc0b7e5a9411d0e0368b1 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/test.sh.md5 b/BRAINSABC/TestSuite/test_data/test.sh.md5 new file mode 100644 index 00000000..b62d693b --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/test.sh.md5 @@ -0,0 +1 @@ +002e8928393b89364e40fc9b515f9b99 \ No newline at end of file diff --git a/BRAINSABC/TestSuite/test_data/tmp_load.b2.md5 b/BRAINSABC/TestSuite/test_data/tmp_load.b2.md5 new file mode 100644 index 00000000..03cdb214 --- /dev/null +++ b/BRAINSABC/TestSuite/test_data/tmp_load.b2.md5 @@ -0,0 +1 @@ +99d28a03ddc239d339d148ba7a41e2ed \ No newline at end of file diff --git a/BRAINSABC/brainseg/AtlasCropImageSource.h b/BRAINSABC/brainseg/AtlasCropImageSource.h new file mode 100644 index 00000000..4f5b86b7 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasCropImageSource.h @@ -0,0 +1,122 @@ +// +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Generate cropped images using ROI obtained from probabilities +// +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 11/2003 + +#ifndef __AtlasCropImageSource_h +#define __AtlasCropImageSource_h + +#include "itkObject.h" + +#include + +/** \class AtlasCropImageSource + */ +template +class AtlasCropImageSource : public itk::Object +{ +public: + + /** Standard class typedefs. */ + typedef AtlasCropImageSource Self; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** The dimension of the image. */ + itkStaticConstMacro(ImageDimension, unsigned int, + TInputImage::ImageDimension); + + // Image types + typedef TInputImage InputImageType; + typedef typename TInputImage::Pointer InputImagePointer; + typedef typename TInputImage::IndexType InputImageIndexType; + typedef typename TInputImage::OffsetType InputImageOffsetType; + typedef typename TInputImage::PixelType InputImagePixelType; + typedef typename TInputImage::PointType InputImagePointType; + typedef typename TInputImage::RegionType InputImageRegionType; + typedef typename TInputImage::SizeType InputImageSizeType; + typedef typename TInputImage::SpacingType InputImageSpacingType; + + typedef TProbabilityImage ProbabilityImageType; + typedef typename ProbabilityImageType::Pointer ProbabilityImagePointer; + typedef typename ProbabilityImageType::IndexType ProbabilityImageIndexType; + typedef typename ProbabilityImageType::OffsetType ProbabilityImageOffsetType; + typedef typename ProbabilityImageType::PixelType ProbabilityImagePixelType; + typedef typename ProbabilityImageType::RegionType ProbabilityImageRegionType; + typedef typename ProbabilityImageType::SizeType ProbabilityImageSizeType; + typedef typename ProbabilityImageType::SpacingType ProbabilityImageSpacingType; + + typedef std::vector ProbabilityImageList; + + typedef struct + { + InputImageIndexType offset; + InputImageSizeType cropped_size; + InputImageSizeType original_size; + } CropInfoType; + + // Set/get output image padding, in mm + itkGetMacro(Padding, double); + itkSetMacro(Padding, double); + + bool CheckBounds(); + + void UseProbabilities(ProbabilityImageList probs); + + // Create new images (either cropped or padded) + InputImagePointer Restore(InputImagePointer img); + + InputImagePointer Crop(InputImagePointer img); + + // Crop region information + void SetCropInfo(const CropInfoType & info) + { + m_CropInfo = info; + } + + const CropInfoType & GetCropInfo() + { + return m_CropInfo; + } + + // For debugging, generate slabs in last dim with top and bottom parts removed + itkSetMacro(SlabMode, bool); + itkGetConstMacro(SlabMode, bool); + itkBooleanMacro(SlabMode); +protected: + + AtlasCropImageSource(); + ~AtlasCropImageSource() + { + } + + double m_Padding; + + InputImageIndexType m_LowerBound; + InputImageIndexType m_UpperBound; + + InputImagePointType m_InputOrigin; + InputImagePointType m_CropOrigin; + + InputImageSizeType m_OriginalSize; + + CropInfoType m_CropInfo; + + bool m_SlabMode; +}; + +#ifndef MU_MANUAL_INSTANTIATION +#include "AtlasCropImageSource.txx" +#endif + +#endif diff --git a/BRAINSABC/brainseg/AtlasCropImageSource.txx b/BRAINSABC/brainseg/AtlasCropImageSource.txx new file mode 100644 index 00000000..67e1575b --- /dev/null +++ b/BRAINSABC/brainseg/AtlasCropImageSource.txx @@ -0,0 +1,291 @@ +#ifndef __AtlasCropImageSource_txx +#define __AtlasCropImageSource_txx + +#include "itkImageRegionIteratorWithIndex.h" + +#include "AtlasCropImageSource.h" + +template +AtlasCropImageSource +::AtlasCropImageSource() +{ + m_Padding = 8.0; + + m_LowerBound.Fill(0); + m_UpperBound.Fill(0); + + m_OriginalSize.Fill(0); + + m_SlabMode = false; +} + +template +bool +AtlasCropImageSource +::CheckBounds() +{ + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + if( m_LowerBound[i] > m_UpperBound[i] ) + { + return false; + } + } + + InputImageSizeType croppedSize; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + croppedSize[i] = m_UpperBound[i] - m_LowerBound[i] + 1; + } + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + if( croppedSize[i] > m_OriginalSize[i] ) + { + return false; + } + } + + return true; +} + +template +void +AtlasCropImageSource +::UseProbabilities(ProbabilityImageList probs) +{ + if( probs.size() == 0 ) + { + itkExceptionMacro(<< "Need at least one class probability image"); + } + + ProbabilityImageSizeType size + = probs[0]->GetLargestPossibleRegion().size(); + + ProbabilityImageSpacingType spacing + = probs[0]->GetSpacing(); + // Make sure all class probabilities have the same space + for( unsigned int i = 1; i < probs.size(); i++ ) + { + ProbabilityImageSizeType othersize + = probs[i]->GetLargestPossibleRegion().size(); + if( size != othersize ) + { + itkExceptionMacro(<< "Probability list size mismatch"); + } + } + + // Transform padding to voxel counts + InputImageOffsetType padding; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + padding[i] = (unsigned int)vcl_floor(m_Padding / spacing[i] + 0.5); + } + // Make sure padding is sensible + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + if( (long)size[i] <= padding[i] ) + { + itkExceptionMacro( + << "Bounding box padding larger than or equal to image size"); + } + } + + // Save size info + m_OriginalSize = size; + // Initial bounds: whole image + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + m_LowerBound[i] = size[i] - 1; + m_UpperBound[i] = 0; + } + + // Go through image and update bounds + typedef itk::ImageRegionIteratorWithIndex + IteratorType; + + IteratorType it( probs[0], probs[0]->GetLargestPossibleRegion() ); + + it.GoToBegin(); + while( !it.IsAtEnd() ) + { + ProbabilityImageIndexType ind = it.GetIndex(); + + double sumProb = 0; + for( unsigned int i = 0; i < probs.size(); i++ ) + { + sumProb += probs[i]->GetPixel(ind); + } + + if( sumProb > 0 ) + { + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + if( ind[i] < m_LowerBound[i] ) + { + m_LowerBound[i] = ind[i]; + } + if( ind[i] > m_UpperBound[i] ) + { + m_UpperBound[i] = ind[i]; + } + } + } + + ++it; + } + + // Only generate a slab? + if( m_SlabMode ) + { + long len + = m_UpperBound[ImageDimension - 1] - m_LowerBound[ImageDimension - 1] + 1; + long offt = (long)( 0.2 * len ); + m_LowerBound[ImageDimension - 1] += offt; + m_UpperBound[ImageDimension - 1] -= offt; + } + // Enlarge/pad bounding box + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + if( m_LowerBound[i] > padding[i] ) + { + m_LowerBound[i] -= padding[i]; + } + else + { + m_LowerBound[i] = 0; + } + + if( m_UpperBound[i] < ( (long)size[i] - 1 - padding[i] ) ) + { + m_UpperBound[i] += padding[i]; + } + else + { + m_UpperBound[i] = size[i] - 1; + } + } + + // Store origin information + m_InputOrigin = probs[0]->GetOrigin(); + probs[0]->TransformIndexToPhysicalPoint(m_LowerBound, m_CropOrigin); + + // m_CropInfo.offset = + // m_CropInfo.size = +} + +template +typename AtlasCropImageSource +::InputImagePointer +AtlasCropImageSource +::Restore(InputImagePointer img) +{ + if( !this->CheckBounds() ) + { + itkExceptionMacro(<< "Invalid bounds"); + } + + InputImageSizeType size = img->GetLargestPossibleRegion().size(); + + InputImageSizeType croppedSize; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + croppedSize[i] = m_UpperBound[i] - m_LowerBound[i] + 1; + } + + if( size != croppedSize ) + { + itkExceptionMacro(<< "Input size does not match size of cropped image"); + } + + InputImageRegionType region; + region.SetSize(m_OriginalSize); + + InputImagePointer output = InputImageType::New(); + output->CopyInformation(img); + // Adjust origin + output->SetOrigin(m_InputOrigin); + output->SetRegions(region); + output->Allocate(); + output->FillBuffer(0); + + InputImageOffsetType offt; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + offt[i] = m_LowerBound[i]; + } + + typedef itk::ImageRegionIteratorWithIndex IteratorType; + + IteratorType inIt( img, img->GetLargestPossibleRegion() ); + + inIt.GoToBegin(); + while( !inIt.IsAtEnd() ) + { + InputImageIndexType ind = inIt.GetIndex(); + + output->SetPixel( ind + offt, inIt.Get() ); + + ++inIt; + } + + return output; +} + +template +typename AtlasCropImageSource +::InputImagePointer +AtlasCropImageSource +::Crop(InputImagePointer img) +{ + if( !this->CheckBounds() ) + { + itkExceptionMacro(<< "Invalid bounds"); + } + + InputImageSizeType size = img->GetLargestPossibleRegion().size(); + + if( size != m_OriginalSize ) + { + itkExceptionMacro(<< "Input size does not match size of probability images"); + } + + InputImageSizeType croppedSize; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + croppedSize[i] = m_UpperBound[i] - m_LowerBound[i] + 1; + } + + InputImageRegionType cropRegion; + cropRegion.SetSize(croppedSize); + + InputImagePointer output = InputImageType::New(); + output->CopyInformation(img); + // Adjust origin + output->SetOrigin(m_CropOrigin); + output->SetRegions(cropRegion); + output->Allocate(); + + InputImageOffsetType offt; + for( unsigned int i = 0; i < ImageDimension; i++ ) + { + offt[i] = m_LowerBound[i]; + } + + typedef itk::ImageRegionIteratorWithIndex IteratorType; + + IteratorType outIt(output, cropRegion); + + outIt.GoToBegin(); + while( !outIt.IsAtEnd() ) + { + InputImageIndexType ind = outIt.GetIndex(); + + outIt.Set( img->GetPixel(ind + offt) ); + + ++outIt; + } + + return output; +} + +#endif diff --git a/BRAINSABC/brainseg/AtlasDefinition.cxx b/BRAINSABC/brainseg/AtlasDefinition.cxx new file mode 100644 index 00000000..929b2906 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasDefinition.cxx @@ -0,0 +1,384 @@ +#include "AtlasDefinition.h" +#include +#include +#include +#include + +namespace // anon +{ +extern "C" +{ +void +start(void *data, const char *el, const char * *) +{ + // std::cerr << "Start, El = (" + // << el + // << ")"; + // std::cerr << " Attributes = ("; + // for(unsigned i = 0; attr[i] != 0; i+= 2) + // { + // if(i > 0) std::cerr << ","; + // std::cerr << attr[i] << "=" << attr[i+1]; + // } + // std::cerr << ")" << std::endl; + AtlasDefinition *_this = reinterpret_cast( data ); + + _this->XMLStart(el); +} + +void +end(void *data, const char *el) +{ + // std::cerr << "End, El = (" + // << el + // << ")" << std::endl; + AtlasDefinition *_this = reinterpret_cast( data ); + + _this->XMLEnd(el); +} + +void +charhandler(void *data, const char *txt, int txtlen) +{ + // std::cerr << "Char data = ("; + // for(unsigned i = 0; i < txtlen; i++) + // { + // std::cerr << txt[i]; + // } + // std::cerr << ")" << std::endl; + char *buf = new char[txtlen + 1]; + int i; + for( i = 0; i < txtlen; i++ ) + { + buf[i] = txt[i]; + } + buf[i] = '\0'; + AtlasDefinition *_this = reinterpret_cast( data ); + _this->XMLChar(buf); + delete[] buf; +} + +} +} +#if 0 +const char *AtlasDefinition::tissueTypes[] = + { + "WM", + "GM", + "BGM", + "CSF", + "VB", + "NOTCSF", + "NOTGM", + "NOTVB", + "NOTWM", + "AIR", + 0 + }; +#endif + +AtlasDefinition::AtlasDefinition() : + m_LastWeight(0.0), + m_LastLower(0.0), + m_LastUpper(0.0), + m_LastGaussianClusterCount(0), + m_LastLabelCode(0), + m_LastUseForBias(0), + m_LastIsForegroundPrior(0) +{ + this->m_TissueTypes.resize(0); +} + +const AtlasDefinition::TissueTypeVector & +AtlasDefinition::TissueTypes() +{ + if( this->m_TissueTypes.size() == 0 ) + { + for( PriorMapType::const_iterator it = this->m_PriorMap.begin(); + it != this->m_PriorMap.end(); + ++it ) + { + this->m_TissueTypes.push_back(it->first); + } + } + return this->m_TissueTypes; +} + +void +AtlasDefinition::XMLStart(const char *el) +{ + std::string El(el); + + this->m_XMLElementStack.push_back(El); + if( El == "Prior" ) + { + this->m_LastPriorBounds.clear(); + } +} + +void +AtlasDefinition::XMLEnd(const char *el) +{ + std::string El(el); + const char *start = this->m_LastXMLString.c_str(); + char * last; + + // pop the current element name off the stack. + this->m_XMLElementStack.pop_back(); + + if( El == "Atlas" ) + { + return; // final element + } + const std::string ContainingElement = this->m_XMLElementStack.back(); + if( El == "filename" ) + { + this->m_LastFilename = this->m_LastXMLString; + } + else if( El == "type" ) + { + if( ContainingElement == "Prior" ) + { + this->m_LastPriorType = this->m_LastXMLString; + } + else + { + this->m_LastType = this->m_LastXMLString; + } + } + else if( El == "AtlasImage" ) + { + this->m_TemplateVolumes[this->m_LastType] = this->m_LastFilename; + } + else if( El == "Weight" ) + { + double w = strtod(start, &last); + if( start == (const char *)last ) + { + std::cerr << "Bad Weight given " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastWeight = w; + } + else if( El == "lower" ) + { + double l = strtod(start, &last); + if( start == (const char *)last ) + { + std::cerr << "Bad lower bound " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastLower = l; + } + else if( El == "upper" ) + { + double u = strtod(start, &last); + if( start == (const char *)last ) + { + std::cerr << "Bad upper bound " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastUpper = u; + } + else if( El == "GaussianClusterCount" ) + { + int GCC = strtol(start, &last, 10); + if( start == (const char *)last ) + { + std::cerr << "Bad GaussianClusterCount given " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastGaussianClusterCount = GCC; + } + else if( El == "LabelCode" ) + { + int GCC = strtol(start, &last, 10); + if( start == (const char *)last ) + { + std::cerr << "Bad LabelCode given " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastLabelCode = GCC; + } + else if( El == "UseForBias" ) + { + int UFB = strtol(start, &last, 10); + if( start == (const char *)last ) + { + std::cerr << "Bad UseForBias given " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastUseForBias = UFB; + } + else if( El == "IsForegroundPrior" ) + { + int UFB = strtol(start, &last, 10); + if( start == (const char *)last ) + { + std::cerr << "Bad IsForegroundPrior given " << this->m_LastXMLString + << std::endl; + throw; + } + this->m_LastIsForegroundPrior = UFB; + } + else if( El == "BrainMask" ) + { + this->m_TemplateBrainMask = this->m_LastFilename; + } + else if( El == "HeadRegion" ) + { + this->m_TemplateHeadRegion = this->m_LastFilename; + } + else if( El == "Prior" ) + { + Prior curPrior; + curPrior.SetFilename(this->m_LastFilename); + curPrior.SetWeight(this->m_LastWeight); + curPrior.SetGaussianClusterCount(this->m_LastGaussianClusterCount); + curPrior.SetLabelCode(this->m_LastLabelCode); + curPrior.SetUseForBias(this->m_LastUseForBias); + curPrior.SetIsForegroundPrior(this->m_LastIsForegroundPrior); + curPrior.SetBoundsList(this->m_LastPriorBounds); + this->m_PriorMap[this->m_LastPriorType] = curPrior; + } + else if( El == "bounds" ) + { + BoundsType & curBounds = this->m_LastPriorBounds[this->m_LastType]; + curBounds.SetLower(this->m_LastLower); + curBounds.SetUpper(this->m_LastUpper); + } + else + { + std::cerr << "Unhandled XML Element type " << El << std::endl; + throw; + } +} + +void +AtlasDefinition::XMLChar(const char *buf) +{ + this->m_LastXMLString = buf; +} + +void +AtlasDefinition::InitFromXML(const std::string & XMLFilename) +{ + std::ifstream xmlFile(XMLFilename.c_str(), + std::ifstream::in); + + if( !xmlFile.good() ) + { + throw; + } + xmlFile.seekg(static_cast( 0 ), + std::ios_base::end); + std::streampos fSize( xmlFile.tellg() ); + xmlFile.seekg(static_cast( 0 ), + std::ios_base::beg); + XML_Parser parser = XML_ParserCreate(0); + XML_SetUserData( parser, static_cast( this ) ); + XML_SetElementHandler(parser, start, end); + XML_SetCharacterDataHandler(parser, charhandler); + char *filebuf = new char[fSize]; + if( filebuf == NULL ) + { + throw; + } + xmlFile.read(filebuf, fSize); + if( !xmlFile.good() ) + { + delete[] filebuf; + throw; + } + xmlFile.close(); + if( XML_Parse(parser, filebuf, fSize, 1) == 0 ) + { + delete[] filebuf; + std::cerr << "XML File parsing error" << std::endl; + throw; + } + delete[] filebuf; +} + +void +AtlasDefinition::DebugPrint() +{ + std::cout << "" << std::endl; + for( TemplateMap::iterator it + = m_TemplateVolumes.begin(); + it != m_TemplateVolumes.end(); + ++it ) + { + std::cout << " " << std::endl + << " " << it->first << "" << std::endl + << " " << it->second << "" << std::endl + << " " << std::endl; + } + + std::cout << " " << std::endl + << " " + << m_TemplateBrainMask + << "" << std::endl + << " " << std::endl; + + std::cout << " " << std::endl + << " " + << m_TemplateHeadRegion + << "" << std::endl + << " " << std::endl; + for( PriorMapType::iterator it + = m_PriorMap.begin(); + it != m_PriorMap.end(); + ++it ) + { + std::cout << " " << std::endl + << " " + << it->first + << "" << std::endl + << " " + << it->second.GetFilename() + << "" << std::endl + << " " + << it->second.GetWeight() + << "" << std::endl + << " " + << it->second.GetGaussianClusterCount() + << "" << std::endl + << " " + << it->second.GetLabelCode() + << "" << std::endl + << " " + << it->second.GetUseForBias() + << "" << std::endl + << " " + << it->second.GetIsForegroundPrior() + << "" << std::endl; + const BoundsMapType & curBounds = it->second.GetBoundsList(); + for( BoundsMapType::const_iterator it2 + = curBounds.begin(); + it2 != curBounds.end(); + ++it2 ) + { + std::cout << " " << std::endl + << " " + << it2->first + << "" << std::endl + << " " + << it2->second.GetLower() + << "" << std::endl + << " " + << it2->second.GetUpper() + << "" << std::endl + << " " << std::endl; + } + std::cout << " " << std::endl; + } + std::cout << "" << std::endl; +} + diff --git a/BRAINSABC/brainseg/AtlasDefinition.h b/BRAINSABC/brainseg/AtlasDefinition.h new file mode 100644 index 00000000..b8ea6a67 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasDefinition.h @@ -0,0 +1,361 @@ +#ifndef __AtlasDefinition_h +#define __AtlasDefinition_h + +#include +#include +#include +#include +#include + +/** \class AtlasDefiniton */ +class AtlasDefinition +{ +public: + // static const char * tissueTypes[]; + typedef std::vector TissueTypeVector; + typedef std::map TemplateMap; + typedef std::vector FloatVector; + typedef std::vector IntVector; + /** \class BoundsType */ + class BoundsType + { + public: + BoundsType() : m_Low(0), m_High(0) + { + } + + void SetLower(const double v) + { + m_Low = v; + } + + double GetLower() const + { + return m_Low; + } + + void SetUpper(const double v) + { + m_High = v; + } + + double GetUpper() const + { + return m_High; + } + + void Print(void) const + { + std::cout << "RANGE: [" << m_Low << "," << m_High << "]" << std::endl; + } + + private: + double m_Low; + double m_High; + }; + typedef std::map BoundsMapType; + + AtlasDefinition(); + void InitFromXML(const std::string & XMLFilename); + + void DebugPrint(); + + const TemplateMap & GetTemplateVolumes() const + { + return m_TemplateVolumes; + } + + const std::string & GetTemplateBrainMask() const + { + return m_TemplateBrainMask; + } + + const std::string & GetTemplateHeadRegion() const + { + return m_TemplateHeadRegion; + } + + std::string GetPriorFilename(const std::string & tissueType) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING TISSUE TYPE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetFilename(); + } + + double GetWeight(const std::string & tissueType) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING TISSUE TYPE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetWeight(); + } + + int GetGaussianClusterCount(const std::string & tissueType) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING TISSUE TYPE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetGaussianClusterCount(); + } + + int GetLabelCode(const std::string & tissueType) const + { + //HACK: All the get functions need review to remove duplicate code. + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING LABEL CODE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetLabelCode(); + } + + int GetUseForBias(const std::string & tissueType) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING TISSUE TYPE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetUseForBias(); + } + + bool GetIsForegroundPrior(const std::string & tissueType) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING IsForegroungPrior IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetIsForegroundPrior(); + } + + const BoundsType & GetBounds(const std::string & tissueType, + const std::string & Modality) const + { + if( m_PriorMap.find(tissueType) == m_PriorMap.end() ) + { + std::cout << "MISSING TISSUE TYPE IN ATLAS: " << tissueType << std::endl; + throw; + } + PriorMapType::const_iterator mit = m_PriorMap.find(tissueType); + if( mit == m_PriorMap.end() ) + { + // HACK: Should throw and exception here with line number and file + std::cout << "ERROR: Invalid tissueType requested in GetPriorFilename" << std::endl; + throw; + } + return mit->second.GetBounds(Modality); + } + + double GetLow(const std::string & tissueType, + const std::string & Modality) const + { + return this->GetBounds(tissueType, Modality).GetLower(); + } + + double GetHigh(const std::string & tissueType, + const std::string & Modality) const + { + return this->GetBounds(tissueType, Modality).GetUpper(); + } + + const TissueTypeVector & TissueTypes(); + + void XMLStart(const char *el); + + void XMLEnd(const char *el); + + void XMLChar(const char *buf); + +private: + TemplateMap m_TemplateVolumes; + std::string m_TemplateBrainMask; + std::string m_TemplateHeadRegion; + TissueTypeVector m_TissueTypes; + class Prior + { + public: + Prior() : + m_Weight(0.0), + m_GaussianClusterCount(0), + m_LabelCode(0), + m_UseForBias(false), + m_IsForegroundPrior(false) + { + } + + const std::string & GetFilename() const + { + return m_Filename; + } + + void SetFilename(const std::string & s) + { + m_Filename = s; + } + + double GetWeight() const + { + return m_Weight; + } + + void SetWeight(double x) + { + m_Weight = x; + } + + int GetGaussianClusterCount() const + { + return m_GaussianClusterCount; + } + + void SetGaussianClusterCount(int i) + { + m_GaussianClusterCount = i; + } + + int GetLabelCode() const + { + return m_LabelCode; + } + + void SetLabelCode(const int i) + { + m_LabelCode = i; + } + + int GetUseForBias() const + { + return m_UseForBias; + } + + void SetUseForBias(const bool i) + { + m_UseForBias = i; + } + + int GetIsForegroundPrior() const + { + return m_IsForegroundPrior; + } + + void SetIsForegroundPrior(const bool i) + { + m_IsForegroundPrior = i; + } + + const BoundsType & GetBounds(const std::string & Modality) const + { + BoundsMapType::const_iterator bit= m_BoundsMap.find(Modality); + if(bit == m_BoundsMap.end() ) + { + std::cout << "MISSING MODALIITY TYPE IN ATLAS: " << Modality << std::endl; + throw; + } + + return bit->second; + } + + void SetBounds(const std::string & Modality, const BoundsType & b) + { + this->m_BoundsMap[Modality] = b; + } + + void SetBounds(const std::string & Modality, double lower, double upper) + { + BoundsType b; + + b.SetLower(lower); + b.SetUpper(upper); + this->SetBounds(Modality, b); + } + + void SetBoundsList(BoundsMapType & boundsMap) + { + this->m_BoundsMap = boundsMap; + } + + const BoundsMapType & GetBoundsList() const + { + return this->m_BoundsMap; + } + + private: + std::string m_Filename; + double m_Weight; + int m_GaussianClusterCount; + int m_LabelCode; + bool m_UseForBias; + bool m_IsForegroundPrior; + BoundsMapType m_BoundsMap; + }; + typedef std::map PriorMapType; + PriorMapType m_PriorMap; + // + // XML Parsing variables + std::string m_LastXMLString; + std::string m_LastPriorType; + std::string m_LastFilename; + std::string m_LastType; + std::list m_XMLElementStack; + double m_LastWeight, + m_LastLower, + m_LastUpper; + + int m_LastGaussianClusterCount; + int m_LastLabelCode; + bool m_LastUseForBias; + bool m_LastIsForegroundPrior; + BoundsMapType m_LastPriorBounds; +}; + +#endif // AtlasDefinition_h diff --git a/BRAINSABC/brainseg/AtlasRegistrationMethod.h b/BRAINSABC/brainseg/AtlasRegistrationMethod.h new file mode 100644 index 00000000..0b5bf564 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasRegistrationMethod.h @@ -0,0 +1,195 @@ +// +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Registration of a dataset to an atlas using affine transformation and +// MI image match metric +// +// Only for 3D! +// +// Given a list of filenames for atlas template and probabilities along with +// the dataset, this class generate images that are in the space of the first +// image (all data and probability images). +// +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 10/2003 + +#ifndef __AtlasRegistrationMethod_h +#define __AtlasRegistrationMethod_h + +#include "itkAffineTransform.h" +#include "itkArray.h" +#include "itkImage.h" +#include "itkObject.h" + +#include + +#include "itkAffineTransform.h" +#include "BRAINSFitHelper.h" + +#include + +/** \class AtlasRegistrationMethod + */ +template +class AtlasRegistrationMethod : public itk::Object +{ +public: + + /** Standard class typedefs. */ + typedef AtlasRegistrationMethod Self; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + // Image types + typedef itk::Image OutputImageType; + typedef typename OutputImageType::Pointer OutputImagePointer; + typedef typename OutputImageType::IndexType OutputImageIndexType; + typedef typename OutputImageType::OffsetType OutputImageOffsetType; + typedef typename OutputImageType::PixelType OutputImagePixelType; + typedef typename OutputImageType::SizeType OutputImageSizeType; + typedef typename OutputImageType::RegionType OutputImageRegionType; + + typedef itk::Image ProbabilityImageType; + typedef typename ProbabilityImageType::Pointer ProbabilityImagePointer; + typedef typename ProbabilityImageType::IndexType ProbabilityImageIndexType; + typedef typename ProbabilityImageType::OffsetType ProbabilityImageOffsetType; + typedef typename ProbabilityImageType::PixelType ProbabilityImagePixelType; + typedef typename ProbabilityImageType::SizeType ProbabilityImageSizeType; + typedef typename ProbabilityImageType::RegionType ProbabilityImageRegionType; + + typedef itk::Image InternalImageType; + typedef typename InternalImageType::Pointer InternalImagePointer; + typedef typename InternalImageType::IndexType InternalImageIndexType; + typedef typename InternalImageType::OffsetType InternalImageOffsetType; + typedef typename InternalImageType::PixelType InternalImagePixelType; + typedef typename InternalImageType::RegionType InternalImageRegionType; + typedef typename InternalImageType::SizeType InternalImageSizeType; + + typedef itk::Image ByteImageType; + typedef typename ByteImageType::Pointer ByteImagePointer; + typedef typename ByteImageType::IndexType ByteImageIndexType; + typedef typename ByteImageType::OffsetType ByteImageOffsetType; + typedef typename ByteImageType::PixelType ByteImagePixelType; + typedef typename ByteImageType::RegionType ByteImageRegionType; + typedef typename ByteImageType::SizeType ByteImageSizeType; + + typedef std::vector ProbabilityImageList; + typedef std::vector OutputImageList; + + typedef itk::Array FlagArrayType; + + void SetSuffix(std::string suffix); + + itkGetConstMacro(OutputDebugDir, std::string); + itkSetMacro(OutputDebugDir, std::string); + + void SetAtlasOriginalImageList(std::vector & NewAtlasList); + + void SetIntraSubjectOriginalImageList(std::vector & NewImageList); + + // itkSetMacro( IntraSubjectTransformFileNames, std::vector ); + itkSetMacro( AtlasToSubjectTransformFileName, std::string ); + + void SetIntraSubjectTransformFileNames(std::vector userlist) + { + m_IntraSubjectTransformFileNames = userlist; + } + + void RegisterImages(); + + GenericTransformType::Pointer GetAtlasToSubjectTransform() + { + return m_AtlasToSubjectTransform; + } + + std::vector GetIntraSubjectTransforms() + { + return m_IntraSubjectTransforms; + } + + // Set/Get the Debugging level for filter verboseness + itkSetMacro(DebugLevel, unsigned int); + itkGetMacro(DebugLevel, unsigned int); + + itkGetMacro(UseNonLinearInterpolation, bool); + itkSetMacro(UseNonLinearInterpolation, bool); + + void Update(); + + void SetAtlasLinearTransformChoice(const std::string & c) + { + m_AtlasLinearTransformChoice = c; + } + + void SetImageLinearTransformChoice(const std::string & c) + { + m_ImageLinearTransformChoice = c; + } + + void SetWarpGrid(const unsigned int gx, const unsigned int gy, const unsigned int gz) + { + m_WarpGrid.resize(3); m_WarpGrid[0] = gx; m_WarpGrid[1] = gy; m_WarpGrid[2] = gz; + } + + // Get and set the input volume image types. i.e. T1 or T2 or PD + void SetInputVolumeTypes(const std::vector & newInputVolumeTypes) + { + this->m_InputVolumeTypes = newInputVolumeTypes; + } + + std::vector GetInputVolumeTypes(void) const + { + return this->m_InputVolumeTypes; + } + +protected: + + AtlasRegistrationMethod(); + ~AtlasRegistrationMethod(); + + OutputImagePointer CopyOutputImage(InternalImagePointer img); + + ProbabilityImagePointer CopyProbabilityImage(InternalImagePointer img); + +private: + + std::string m_Suffix; + std::string m_OutputDebugDir; + + // ByteImagePointer m_AtlasOriginalMask; + std::vector m_AtlasOriginalImageList; + std::vector m_IntraSubjectOriginalImageList; + ByteImagePointer m_InputImageTissueRegion; + ImageMaskPointer m_InputSpatialObjectTissueRegion; + + std::vector m_WarpGrid; + std::vector m_IntraSubjectTransformFileNames; + std::string m_AtlasToSubjectTransformFileName; + + std::vector m_InputVolumeTypes; + + GenericTransformType::Pointer m_AtlasToSubjectTransform; + std::vector m_IntraSubjectTransforms; + + bool m_UseNonLinearInterpolation; + bool m_DoneRegistration; + bool m_Modified; + + std::string m_AtlasLinearTransformChoice; + std::string m_ImageLinearTransformChoice; + + unsigned int m_DebugLevel; +}; + +#ifndef MU_MANUAL_INSTANTIATION +#include "AtlasRegistrationMethod.txx" +#endif + +#endif diff --git a/BRAINSABC/brainseg/AtlasRegistrationMethod.txx b/BRAINSABC/brainseg/AtlasRegistrationMethod.txx new file mode 100644 index 00000000..82f902d5 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasRegistrationMethod.txx @@ -0,0 +1,772 @@ +#ifndef __AtlasRegistrationMethod_txx +#define __AtlasRegistrationMethod_txx + +#include "itkAffineTransform.h" +#include "itkBSplineInterpolateImageFunction.h" +#include "itkImageFileReader.h" +#include "itkImageRegionIterator.h" +#include "itkImageRegionIteratorWithIndex.h" +#include "itkLinearInterpolateImageFunction.h" +#include "itkNearestNeighborInterpolateImageFunction.h" +#include "itkResampleImageFilter.h" +#include "itkRescaleIntensityImageFilter.h" + +// MI registration module +#include "AtlasRegistrationMethod.h" +#include "RegistrationParameters.h" + +#include "vnl/vnl_math.h" + +#include "Log.h" + +#include +#include +#include + +#include "itkBRAINSROIAutoImageFilter.h" + +GenericTransformType::Pointer MakeRigidIdentity(void) +{ + // Also append identity matrix for each image + VersorRigid3DTransformType::Pointer rigidIdentity = VersorRigid3DTransformType::New(); + + rigidIdentity->SetIdentity(); + GenericTransformType::Pointer genericTransform = NULL; + genericTransform = rigidIdentity.GetPointer(); + return genericTransform; +} + +template +AtlasRegistrationMethod +::AtlasRegistrationMethod() : m_WarpGrid(3, 0), + m_UseNonLinearInterpolation(true), + m_DoneRegistration(false), + m_Modified(false), + m_AtlasLinearTransformChoice("Affine"), + m_ImageLinearTransformChoice("Rigid"), + m_DebugLevel(0) +{ + m_InputImageTissueRegion = NULL; + m_InputSpatialObjectTissueRegion = NULL; +} + +template +AtlasRegistrationMethod +::~AtlasRegistrationMethod() +{ + m_IntraSubjectTransforms.clear(); +} + +template +void +AtlasRegistrationMethod +::SetSuffix(std::string suffix) +{ + m_Suffix = suffix; + m_Modified = true; +} + +template +void +AtlasRegistrationMethod +::SetAtlasOriginalImageList(std::vector & NewAtlasList) +{ + m_AtlasOriginalImageList = NewAtlasList; + m_AtlasToSubjectTransform = MakeRigidIdentity(); + m_DoneRegistration = false; + m_Modified = true; +} + +template +void +AtlasRegistrationMethod +::SetIntraSubjectOriginalImageList(std::vector & NewIntraSubjectOriginalImageList) +{ + muLogMacro(<< "Set Intrasubject original image list" << std::endl); + + const unsigned int numIntraSubjectOriginalImages = NewIntraSubjectOriginalImageList.size(); + if( numIntraSubjectOriginalImages == 0 ) + { + itkExceptionMacro(<< "No images specified"); + } + + m_IntraSubjectOriginalImageList = NewIntraSubjectOriginalImageList; + m_AtlasToSubjectTransform = MakeRigidIdentity(); + // Clear previous transforms + m_IntraSubjectTransforms.clear(); + m_IntraSubjectTransforms.resize(numIntraSubjectOriginalImages); + for( unsigned int i = 0; i < numIntraSubjectOriginalImages; i++ ) + { // Also append identity matrix for each image + GenericTransformType::Pointer transform = MakeRigidIdentity(); + m_IntraSubjectTransforms[i] = transform; + } + m_DoneRegistration = false; + m_Modified = true; +} + +template +void +AtlasRegistrationMethod +::Update() +{ + muLogMacro(<< "Update" << std::endl); + + if( m_Modified ) + { + m_DoneRegistration = false; + } + + if( m_Modified || !m_DoneRegistration ) + { + this->RegisterImages(); + } + + m_Modified = false; + +} + +template +void +AtlasRegistrationMethod +::RegisterImages() +{ + muLogMacro(<< "RegisterImages" << std::endl); + + const std::string suffixstr = (m_Suffix.length() != 0) ? std::string("_") + m_Suffix : std::string(""); + + { + for( unsigned int i = 1; i < m_IntraSubjectOriginalImageList.size(); i++ ) + { + if( itksys::SystemTools::FileExists( this->m_IntraSubjectTransformFileNames[i].c_str() ) ) + { + try + { + muLogMacro( + << "Reading transform from file: " << this->m_IntraSubjectTransformFileNames[i] << "." << std::endl); + m_IntraSubjectTransforms[i] = itk::ReadTransformFromDisk(this->m_IntraSubjectTransformFileNames[i]); + } + catch( ... ) + { + muLogMacro( + << "Failed to read transform file caused exception." << this->m_IntraSubjectTransformFileNames[i] + << std::endl ); + exit(-1); + } + } + else if( m_ImageLinearTransformChoice == "Identity" ) + { + muLogMacro(<< "Registering (Identity) image " << i + 1 << " to first image." << std::endl); + m_IntraSubjectTransforms[i] = MakeRigidIdentity(); + } + else + { + typedef itk::BRAINSFitHelper HelperType; + HelperType::Pointer intraSubjectRegistrationHelper = HelperType::New(); + intraSubjectRegistrationHelper->SetNumberOfSamples(500000); + intraSubjectRegistrationHelper->SetNumberOfHistogramBins(50); + std::vector numberOfIterations(1); + numberOfIterations[0] = 1500; + intraSubjectRegistrationHelper->SetNumberOfIterations(numberOfIterations); + // + // + // + // intraSubjectRegistrationHelper->SetMaximumStepLength(maximumStepSize); + intraSubjectRegistrationHelper->SetTranslationScale(1000); + intraSubjectRegistrationHelper->SetReproportionScale(1.0); + intraSubjectRegistrationHelper->SetSkewScale(1.0); + // Register each intrasubject image mode to first image + intraSubjectRegistrationHelper->SetFixedVolume(m_IntraSubjectOriginalImageList[0]); + // TODO: Find way to turn on histogram equalization for same mode images + intraSubjectRegistrationHelper->SetMovingVolume(m_IntraSubjectOriginalImageList[i]); + { + muLogMacro( << "Generating MovingImage Mask (Intrasubject " << i << ")" << std::endl ); + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_IntraSubjectOriginalImageList[i]); + ROIFilter->SetDilateSize(3); // Only use a very small non-tissue + // region outside of head during initial + // runnings + ROIFilter->Update(); + ByteImageType::Pointer movingMaskImage = ROIFilter->GetOutput(); + intraSubjectRegistrationHelper->SetMovingBinaryVolume(ROIFilter->GetSpatialObjectROI() ); + if( this->m_DebugLevel > 7 ) + { + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->UseCompressionOn(); + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "IntraSubject_MovingMask_" << i << ".nii.gz" << std::ends; + std::string fn = oss.str(); + + writer->SetInput( movingMaskImage ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + } + } + { + if( m_InputImageTissueRegion.IsNull() || m_InputSpatialObjectTissueRegion.IsNull() ) // + // + // Delayed + // + // until + // + // first + // + // use, + // + // but + // + // only + // + // create + // + // it + // + // once. + { + muLogMacro( << "Generating FixedImage Mask (Intrasubject)" << std::endl ); + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_IntraSubjectOriginalImageList[0]); + ROIFilter->SetDilateSize(3); // Only use a very small non-tissue + // region outside of head during + // initial runnings + ROIFilter->Update(); + m_InputImageTissueRegion = ROIFilter->GetOutput(); + m_InputSpatialObjectTissueRegion = ROIFilter->GetSpatialObjectROI(); + if( this->m_DebugLevel > 7 ) + { + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->UseCompressionOn(); + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "IntraSubject_FixedMask_" << 0 << ".nii.gz" << std::ends; + std::string fn = oss.str(); + + writer->SetInput( m_InputImageTissueRegion ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + } + } + intraSubjectRegistrationHelper->SetFixedBinaryVolume(m_InputSpatialObjectTissueRegion); + } + if( m_ImageLinearTransformChoice == "Rigid" ) + { + muLogMacro(<< "Registering (Rigid) image " << i << " to first image." << std::endl); + std::vector minimumStepSize(1); + minimumStepSize[0] = 0.00005; + intraSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(1); + transformType[0] = "Rigid"; + intraSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_ImageLinearTransformChoice == "Affine" ) + { + muLogMacro(<< "Registering (Affine) image " << i << " to first image." << std::endl); + std::vector minimumStepSize(4); + minimumStepSize[0] = 0.00005; + minimumStepSize[1] = 0.005; + minimumStepSize[2] = 0.005; + minimumStepSize[3] = 0.005; + intraSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(4); + transformType[0] = "Rigid"; + transformType[1] = "ScaleVersor3D"; + transformType[2] = "ScaleSkewVersor3D"; + transformType[3] = "Affine"; + intraSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_ImageLinearTransformChoice == "BSpline" ) + { + muLogMacro(<< "Registering (BSpline) image " << i << " to first subject image." << std::endl); + std::vector minimumStepSize(5); + minimumStepSize[0] = 0.00005; + minimumStepSize[1] = 0.005; + minimumStepSize[2] = 0.005; + minimumStepSize[3] = 0.005; + minimumStepSize[4] = 0.005; + intraSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(5); + transformType[0] = "Rigid"; + transformType[1] = "ScaleVersor3D"; + transformType[2] = "ScaleSkewVersor3D"; + transformType[3] = "Affine"; + transformType[4] = "BSpline"; + intraSubjectRegistrationHelper->SetTransformType(transformType); + std::vector splineGridSize(3); + splineGridSize[0] = this->m_WarpGrid[0]; + splineGridSize[1] = this->m_WarpGrid[1]; + splineGridSize[2] = this->m_WarpGrid[2]; + intraSubjectRegistrationHelper->SetSplineGridSize(splineGridSize); + intraSubjectRegistrationHelper->SetMaxBSplineDisplacement(6.0); // + // Setting + // max + // + // displace + // + // + // + // intraSubjectRegistrationHelper->SetUseExplicitPDFDerivativesMode(useExplicitPDFDerivativesMode); + // + // + // + // intraSubjectRegistrationHelper->SetUseCachingOfBSplineWeightsMode(useCachingOfBSplineWeightsMode); + } + // + // + // + // intraSubjectRegistrationHelper->SetBackgroundFillValue(backgroundFillValue); + // NOT VALID When using initializeTransformMode + // + // + // intraSubjectRegistrationHelper->SetCurrentGenericTransform(currentGenericTransform); + // intraSubjectRegistrationHelper->SetUseWindowedSinc(useWindowedSinc); + const std::string initializeTransformMode("useCenterOfHeadAlign"); + intraSubjectRegistrationHelper->SetInitializeTransformMode(initializeTransformMode); + intraSubjectRegistrationHelper->SetMaskInferiorCutOffFromCenter(65.0); // + // + // maskInferiorCutOffFromCenter); + m_IntraSubjectTransforms[i] = NULL; + intraSubjectRegistrationHelper->SetCurrentGenericTransform(m_IntraSubjectTransforms[i]); + if( this->m_DebugLevel > 9 ) + { + static unsigned int IntraSubjectRegistration = 0; + std::stringstream ss; + ss << std::setw(3) << std::setfill('0') << IntraSubjectRegistration; + intraSubjectRegistrationHelper->PrintCommandLine(true, std::string("IntraSubjectRegistration") + ss.str() ); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + IntraSubjectRegistration++; + } + intraSubjectRegistrationHelper->StartRegistration(); + const unsigned int actualIterations = intraSubjectRegistrationHelper->GetActualNumberOfIterations(); + muLogMacro( << "Registration tool " << actualIterations << " iterations." << std::endl ); + m_IntraSubjectTransforms[i] = intraSubjectRegistrationHelper->GetCurrentGenericTransform(); + // Write out intermodal matricies + { + muLogMacro(<< "Writing " << this->m_IntraSubjectTransformFileNames[i] << "." << std::endl); + WriteTransformToDisk(m_IntraSubjectTransforms[i], this->m_IntraSubjectTransformFileNames[i]); + } + } + } + } + + // Now register the atlas to the subject + { + // TODO: Need to make this register all the atlas filenames to all the + // reference images. + // Should probably do it in reverse order. + if( itksys::SystemTools::FileExists( this->m_AtlasToSubjectTransformFileName.c_str() ) ) + { + try + { + muLogMacro(<< "Reading " << this->m_AtlasToSubjectTransformFileName << "." << std::endl); + m_AtlasToSubjectTransform = itk::ReadTransformFromDisk(this->m_AtlasToSubjectTransformFileName); + // Note: No need to write this transform to disk + } + catch( ... ) + { + muLogMacro( + << "Failed to read transform file caused exception." << this->m_AtlasToSubjectTransformFileName << std::endl ); + exit(-1); + } + } + else if( m_AtlasLinearTransformChoice == "Identity" ) + { + muLogMacro(<< "Registering (Identity) atlas to first image." << std::endl); + m_AtlasToSubjectTransform = MakeRigidIdentity(); + // Note: No need to write this transform to disk + } + else // continue; + { + if( ( m_AtlasOriginalImageList.size() != m_IntraSubjectTransforms.size() ) || + ( m_AtlasOriginalImageList.size() != m_IntraSubjectOriginalImageList.size() ) ) + { + muLogMacro( << "ERROR: atlas and template image list sizes do not match. " << std::endl ); + muLogMacro( << "m_AtlasOriginalImageList.size() = " << m_AtlasOriginalImageList.size() << std::endl ); + muLogMacro( << "m_IntraSubjectTransforms.size() = " << m_IntraSubjectTransforms.size() << std::endl ); + muLogMacro( + << "m_IntraSubjectOriginalImageList.size() = " << m_IntraSubjectOriginalImageList.size() << std::endl ); + exit(-1); + } + muLogMacro(<< "Registering all atlas images to first subject." << std::endl); + for( unsigned int atlasIter = 0; atlasIter < m_AtlasOriginalImageList.size(); atlasIter++ ) + { + typedef itk::BRAINSFitHelper HelperType; + HelperType::Pointer atlasToSubjectRegistrationHelper = HelperType::New(); + atlasToSubjectRegistrationHelper->SetNumberOfSamples(500000); + atlasToSubjectRegistrationHelper->SetNumberOfHistogramBins(50); + std::vector numberOfIterations(1); + numberOfIterations[0] = 1500; + atlasToSubjectRegistrationHelper->SetNumberOfIterations(numberOfIterations); + // + // + // + // atlasToSubjectRegistrationHelper->SetMaximumStepLength(maximumStepSize); + atlasToSubjectRegistrationHelper->SetTranslationScale(1000); + atlasToSubjectRegistrationHelper->SetReproportionScale(1.0); + atlasToSubjectRegistrationHelper->SetSkewScale(1.0); + // Register all atlas images to first image + { + muLogMacro( + << "Registering atlas " << atlasIter << " of " << m_AtlasOriginalImageList.size() << " to subject image " + << atlasIter << "." << std::endl); + InternalImageType::Pointer currentWarpedIntraSubject = NULL; + // NOTE: This is to save memory, so just resample the images as needed + // to avoid keeping an extra copy of them + if( atlasIter == 0 ) + { // First subject image does not need to be resampled + currentWarpedIntraSubject = m_IntraSubjectOriginalImageList[0]; + } + else + { // All other subject images must be resampled + typedef itk::ResampleImageFilter ResampleType; + typedef ResampleType::Pointer ResamplePointer; + + ResamplePointer resampler = ResampleType::New(); + resampler->SetInput(m_IntraSubjectOriginalImageList[atlasIter]); + resampler->SetTransform(m_IntraSubjectTransforms[atlasIter]); + resampler->SetOutputParametersFromImage(m_IntraSubjectOriginalImageList[0]); + resampler->SetDefaultPixelValue(0); + resampler->Update(); + currentWarpedIntraSubject = resampler->GetOutput(); + } + atlasToSubjectRegistrationHelper->SetFixedVolume(currentWarpedIntraSubject); + std::string preprocessMovingString(""); +#if 0 // def __EXAMINE_EFFECTS_OF_HISTOGRAM_MATCHING__ + // TODO: Just turn histogram matching off at this point. + // histogram matching often help in the registration for difficult + // cases + // Need to find some way to quantify how much it helps/hurts. + // Changed so FLAIR doesn't get histogram matched to non-existing + // atlas + const bool histogramMatch = false; + // const bool + // histogramMatch=(m_InputVolumeTypes[atlasIter]=="FLAIR")?false:true; + + // const bool histogramMatch=true;//Setting histogram matching to true + if( histogramMatch ) + { + typedef itk::HistogramMatchingImageFilter HistogramMatchingFilterType; + HistogramMatchingFilterType::Pointer histogramfilter + = HistogramMatchingFilterType::New(); + + histogramfilter->SetInput( m_AtlasOriginalImageList[atlasIter] ); + histogramfilter->SetReferenceImage( currentWarpedIntraSubject ); + + histogramfilter->SetNumberOfHistogramLevels( 128 ); + histogramfilter->SetNumberOfMatchPoints( 2 ); + histogramfilter->ThresholdAtMeanIntensityOn(); + histogramfilter->Update(); + InternalImageType::Pointer equalizedMovingImage = histogramfilter->GetOutput(); + if( equalizedMovingImage->GetLargestPossibleRegion().GetSize() != + m_AtlasOriginalImageList[atlasIter]->GetLargestPossibleRegion().GetSize() ) + { + itkExceptionMacro(<< "Histogram equalized image has wrong size." ); + } + preprocessMovingString = "histogram equalized "; + atlasToSubjectRegistrationHelper->SetMovingVolume(equalizedMovingImage); + if( this->m_DebugLevel > 7 ) + { + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + writer->UseCompressionOn(); + + std::string fn = + this->m_OutputDebugDir + std::string("AtlasPostHistogram_") + ".nii.gz"; + + writer->SetInput( equalizedMovingImage ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + exit( -1 ); + } + } + else +#endif + { + atlasToSubjectRegistrationHelper->SetMovingVolume(m_AtlasOriginalImageList[atlasIter]); + } + { + muLogMacro( << "Generating MovingImage Mask (Atlas " << atlasIter << ")" << std::endl ); + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_AtlasOriginalImageList[atlasIter]); + ROIFilter->SetDilateSize(1); // Only use a very small non-tissue + // region outside of head during + // initial runnings + ROIFilter->Update(); + atlasToSubjectRegistrationHelper->SetMovingBinaryVolume(ROIFilter->GetSpatialObjectROI() ); + if( this->m_DebugLevel > 7 ) + { + ByteImageType::Pointer movingMaskImage = ROIFilter->GetOutput(); + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->UseCompressionOn(); + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "Atlas_MovingMask_" << atlasIter << ".nii.gz" << std::ends; + std::string fn = oss.str(); + + writer->SetInput( movingMaskImage ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + } + } + { + muLogMacro( << "Generating FixedImage Mask (Atlas)" << std::endl ); + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_IntraSubjectOriginalImageList[0]); + ROIFilter->SetDilateSize(1); // Only use a very small non-tissue + // region outside of head during + // initial runnings + ROIFilter->Update(); + atlasToSubjectRegistrationHelper->SetFixedBinaryVolume(ROIFilter->GetSpatialObjectROI() ); + if( this->m_DebugLevel > 7 ) + { + ByteImageType::Pointer fixedMaskImage = ROIFilter->GetOutput(); + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->UseCompressionOn(); + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "SubjectForAtlas_FixedMask_" << 0 << ".nii.gz" << std::ends; + std::string fn = oss.str(); + + writer->SetInput( fixedMaskImage ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + } + } + if( m_AtlasLinearTransformChoice == "Rigid" ) + { + muLogMacro( + << "Registering (Rigid) " << preprocessMovingString << "atlas(" << atlasIter << ") to template(" + << atlasIter << ") image." << std::endl); + const unsigned int regLevels = (atlasIter == 0) ? 1 : 1; + std::vector minimumStepSize(regLevels); + std::vector transformType(regLevels); + if( atlasIter == 0 ) + { + minimumStepSize[1] = 0.0025; + transformType[0] = "Rigid"; + } + else + { + minimumStepSize[0] = 0.0025; + transformType[0] = "Rigid"; + } + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_AtlasLinearTransformChoice == "Affine" ) + { + muLogMacro( + << "Registering (Affine) " << preprocessMovingString << "atlas(" << atlasIter << ") to template(" + << atlasIter << ") image." << std::endl); + const unsigned int regLevels = (atlasIter == 0) ? 4 : 1; + std::vector minimumStepSize(regLevels); + std::vector transformType(regLevels); + if( atlasIter == 0 ) + { + minimumStepSize[0] = 0.0025; + minimumStepSize[1] = 0.0025; + minimumStepSize[2] = 0.0025; + minimumStepSize[3] = 0.0025; + transformType[0] = "Rigid"; + transformType[1] = "ScaleVersor3D"; + transformType[2] = "ScaleSkewVersor3D"; + transformType[3] = "Affine"; + } + else + { + minimumStepSize[0] = 0.0025; + transformType[0] = "Affine"; + } + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_AtlasLinearTransformChoice == "BSpline" ) + { + muLogMacro( + << "Registering (BSpline) " << preprocessMovingString << "atlas(" << atlasIter << ") to template(" + << atlasIter << ") image." << std::endl); + const unsigned int regLevels = (atlasIter == 0) ? 5 : 1; + std::vector minimumStepSize(regLevels); + std::vector transformType(regLevels); + if( atlasIter == 0 ) + { + minimumStepSize[0] = 0.0025; + minimumStepSize[1] = 0.0025; + minimumStepSize[2] = 0.0025; + minimumStepSize[3] = 0.0025; + minimumStepSize[4] = 0.0025; + transformType[0] = "Rigid"; + transformType[1] = "ScaleVersor3D"; + transformType[2] = "ScaleSkewVersor3D"; + transformType[3] = "Affine"; + transformType[4] = "BSpline"; + } + else + { + minimumStepSize[0] = 0.0025; + transformType[0] = "BSpline"; + } + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + std::vector splineGridSize(3); + splineGridSize[0] = this->m_WarpGrid[0]; + splineGridSize[1] = this->m_WarpGrid[1]; + splineGridSize[2] = this->m_WarpGrid[2]; + atlasToSubjectRegistrationHelper->SetSplineGridSize(splineGridSize); + atlasToSubjectRegistrationHelper->SetMaxBSplineDisplacement(6.0); // + // + // Setting + // + // max + // + // displace + } + if( atlasIter == 0 ) + { + // + // + // + // atlasToSubjectRegistrationHelper->SetBackgroundFillValue(backgroundFillValue); + // + // + // + // atlasToSubjectRegistrationHelper->SetUseWindowedSinc(useWindowedSinc); + // TODO: Need to make external/internal variable inside + // StartRegistration that + // changes a variable to set the initialization mode + // "useCenterOfHeadAlign" works well for brain images, but + // will break + // algorithm for many other segmentation types. + const std::string initializeTransformMode("useCenterOfHeadAlign"); + atlasToSubjectRegistrationHelper->SetInitializeTransformMode(initializeTransformMode); + atlasToSubjectRegistrationHelper->SetMaskInferiorCutOffFromCenter(65.0); // + // + // maskInferiorCutOffFromCenter); + this->m_AtlasToSubjectTransform = NULL; + } + else + { + const std::string initializeTransformMode("Off"); + atlasToSubjectRegistrationHelper->SetInitializeTransformMode(initializeTransformMode); + } + atlasToSubjectRegistrationHelper->SetCurrentGenericTransform(m_AtlasToSubjectTransform); + if( this->m_DebugLevel > 9 && m_AtlasToSubjectTransform.IsNotNull() ) + { + muLogMacro( << "PRE_ASSIGNMENT" << atlasIter << " " ); // << + // + // transformType[0] + // << " + // first of + // " << + // + // transformType.size() + // << + // + // + // std::endl + // ); + muLogMacro( + << __FILE__ << " " << __LINE__ << " " << m_AtlasToSubjectTransform->GetFixedParameters() << std::endl ); + muLogMacro( + << __FILE__ << " " << __LINE__ << " " << m_AtlasToSubjectTransform->GetParameters() << std::endl ); + } + if( this->m_DebugLevel > 9 ) + { + static unsigned int originalAtlasToSubject = 0; + std::stringstream ss; + ss << std::setw(3) << std::setfill('0') << originalAtlasToSubject; + atlasToSubjectRegistrationHelper->PrintCommandLine(true, std::string("AtlasToSubject") + ss.str() ); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + originalAtlasToSubject++; + } + atlasToSubjectRegistrationHelper->StartRegistration(); + const unsigned int actualIterations = atlasToSubjectRegistrationHelper->GetActualNumberOfIterations(); + muLogMacro( << "Registration tool " << actualIterations << " iterations." << std::endl ); + m_AtlasToSubjectTransform = atlasToSubjectRegistrationHelper->GetCurrentGenericTransform(); + if( this->m_DebugLevel > 9 ) + { + muLogMacro( << "POST_ASSIGNMENT" << atlasIter << " " ); // << + // + // transformType[0] + // << " + // first + // of " << + // + // transformType.size() + // << + // + // + // std::endl + // ); + muLogMacro( + << __FILE__ << " " << __LINE__ << " " << m_AtlasToSubjectTransform->GetFixedParameters() << std::endl ); + muLogMacro( + << __FILE__ << " " << __LINE__ << " " << m_AtlasToSubjectTransform->GetParameters() << std::endl ); + } + } + } + { + muLogMacro(<< "Writing " << this->m_AtlasToSubjectTransformFileName << "." << std::endl); + WriteTransformToDisk(m_AtlasToSubjectTransform, this->m_AtlasToSubjectTransformFileName); + } + } + } + m_DoneRegistration = true; +} + +template +typename AtlasRegistrationMethod +::ProbabilityImagePointer +AtlasRegistrationMethod +::CopyProbabilityImage( + typename AtlasRegistrationMethod + ::InternalImagePointer img) +{ + + muLogMacro(<< "CopyProbabilityImage" << std::endl); + + ProbabilityImagePointer outimg = ProbabilityImageType::New(); + outimg->CopyInformation(img); + outimg->SetRegions(img->GetLargestPossibleRegion() ); + outimg->Allocate(); + + typedef itk::ImageRegionIterator InternalIteratorType; + InternalIteratorType inputIter(img, img->GetLargestPossibleRegion() ); + + typedef itk::ImageRegionIterator + ProbabilityIteratorType; + ProbabilityIteratorType outputIter(outimg, + outimg->GetLargestPossibleRegion() ); + + inputIter.GoToBegin(); + outputIter.GoToBegin(); + + while( !inputIter.IsAtEnd() ) + { + double p = inputIter.Get(); + if( p < 0.0 ) + { + p = 0.0; + } + outputIter.Set(static_cast(p) ); + ++inputIter; + ++outputIter; + } + + return outimg; +} + +#endif diff --git a/BRAINSABC/brainseg/AtlasRegistrationMethod_float+float.cxx b/BRAINSABC/brainseg/AtlasRegistrationMethod_float+float.cxx new file mode 100644 index 00000000..b0561789 --- /dev/null +++ b/BRAINSABC/brainseg/AtlasRegistrationMethod_float+float.cxx @@ -0,0 +1,3 @@ +#include "AtlasRegistrationMethod.txx" + +template class AtlasRegistrationMethod; diff --git a/BRAINSABC/brainseg/BRAINSABC.cxx b/BRAINSABC/brainseg/BRAINSABC.cxx new file mode 100644 index 00000000..8c1d7a4e --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABC.cxx @@ -0,0 +1,1382 @@ +#include "itkOutputWindow.h" +#include "itkTextOutput.h" +#include "itkTimeProbe.h" +#include +#include +#include +#include +#include +#include + +#include "itkNormalizedCorrelationImageToImageMetric.h" +#include "itkCastImageFilter.h" +#include "itkImage.h" +#include "itkImageFileWriter.h" +#include "itkLinearInterpolateImageFunction.h" +#include "itkWindowedSincInterpolateImageFunction.h" +#include "itkNumericTraits.h" +#include "itkRescaleIntensityImageFilter.h" +#include "itkVersion.h" +#include "itksys/SystemTools.hxx" +#include "PrettyPrintTable.h" +#include "DenoiseFiltering.h" + +typedef itk::Image FloatImageType; +typedef itk::Image ByteImageType; +typedef itk::Image ShortImageType; + +typedef FloatImageType::Pointer FloatImagePointer; +typedef ByteImageType::Pointer ByteImagePointer; +typedef ShortImageType::Pointer ShortImagePointer; + +#include "mu.h" +#include "EMSParameters.h" +#include "AtlasDefinition.h" +#include +#include "Log.h" + +#include + +#include +#include +#include + +#include + +#include +#include "BRAINSABCCLP.h" +#include "BRAINSThreadControl.h" + +// Use manually instantiated classes for the big program chunks +#define MU_MANUAL_INSTANTIATION +#include "EMSegmentationFilter.h" +#include "AtlasRegistrationMethod.h" +#undef MU_MANUAL_INSTANTIATION + +// From an inputVector create an outputVector that only contains the unique +// elements. +template +T RemoveDuplicates(T & origVect, const std::vector & dupsList) +{ + T outVector(0); + + outVector.reserve(origVect.size() ); + for( size_t inlist = 0; inlist < origVect.size(); inlist++ ) + { + if( dupsList[inlist] == false ) + { + outVector.push_back(origVect[inlist]); + } + } + return outVector; +} + +// +// Get a version of the filename that does not include the preceeding path, or +// the image file extensions. +static std::string GetStripedImageFileNameExtension(const std::string & ImageFileName) +{ + std::vector ExtensionsToRemove(6); + ExtensionsToRemove[0] = ".gz"; + ExtensionsToRemove[1] = ".nii"; + ExtensionsToRemove[2] = ".hdr"; + ExtensionsToRemove[3] = ".img"; + ExtensionsToRemove[4] = ".gipl"; + ExtensionsToRemove[5] = ".nrrd"; + + std::string returnString = itksys::SystemTools::GetFilenameName( ImageFileName ); + for( size_t s = 0; s < ExtensionsToRemove.size(); s++ ) + { + size_t rfind_location = returnString.rfind(ExtensionsToRemove[s]); + if( ( rfind_location != std::string::npos ) + && ( rfind_location == ( returnString.size() - ExtensionsToRemove[s].size() ) ) + ) + { + returnString.replace(rfind_location, ExtensionsToRemove[s].size(), ""); + } + } + return returnString; +} + +static FloatImageType::Pointer CopyOutputImage(FloatImageType::Pointer img ) +{ + // muLogMacro(<< "CopyOutputImage" << std::endl ); + + FloatImageType::Pointer outimg = FloatImageType::New(); + + outimg->CopyInformation(img); + outimg->SetRegions( img->GetLargestPossibleRegion() ); + outimg->Allocate(); + + typedef itk::ImageRegionIterator InternalIteratorType; + InternalIteratorType inputIter( img, img->GetLargestPossibleRegion() ); + + typedef itk::ImageRegionIterator OutputIteratorType; + OutputIteratorType outputIter( outimg, outimg->GetLargestPossibleRegion() ); + + inputIter.GoToBegin(); + outputIter.GoToBegin(); + + while( !inputIter.IsAtEnd() ) + { + outputIter.Set( static_cast( inputIter.Get() ) ); + ++inputIter; + ++outputIter; + } + + return outimg; +} + +// ///// +// +// +// +static std::vector ResampleImageList( + const std::string & resamplerInterpolatorType, + const std::vector & inputImageList, + const std::vector & intraSubjectTransforms) +{ + // Clear image list + std::vector outputImageList; + outputImageList.clear(); + outputImageList.resize( inputImageList.size() ); + outputImageList[0] = CopyOutputImage(inputImageList[0]); + + const FloatImageType::PixelType outsideFOVCode = vnl_huge_val( static_cast( 1.0f ) ); + // Resample the other images + for( unsigned int i = 1; i < inputImageList.size(); i++ ) + { + muLogMacro(<< "Resampling input image " << i + 1 << "." << std::endl); + typedef itk::ResampleImageFilter ResampleType; + typedef ResampleType::Pointer ResamplePointer; + ResamplePointer resampler = ResampleType::New(); + resampler->SetInput(inputImageList[i]); + resampler->SetTransform(intraSubjectTransforms[i]); + + if( resamplerInterpolatorType == "BSpline" ) + { + typedef itk::BSplineInterpolateImageFunction + SplineInterpolatorType; + + // Spline interpolation, only available for input images, not + // atlas + SplineInterpolatorType::Pointer splineInt + = SplineInterpolatorType::New(); + splineInt->SetSplineOrder(5); + resampler->SetInterpolator(splineInt); + } + else if( resamplerInterpolatorType == "WindowedSinc" ) + { + typedef itk::ConstantBoundaryCondition + BoundaryConditionType; + static const unsigned int WindowedSincHammingWindowRadius = 5; + typedef itk::Function::HammingWindowFunction< + WindowedSincHammingWindowRadius, double, double> WindowFunctionType; + typedef itk::WindowedSincInterpolateImageFunction + WindowedSincInterpolatorType; + WindowedSincInterpolatorType::Pointer windowInt + = WindowedSincInterpolatorType::New(); + resampler->SetInterpolator(windowInt); + } + else // Default to m_UseNonLinearInterpolation == "Linear" + { + typedef itk::LinearInterpolateImageFunction + LinearInterpolatorType; + LinearInterpolatorType::Pointer linearInt + = LinearInterpolatorType::New(); + resampler->SetInterpolator(linearInt); + } + + resampler->SetDefaultPixelValue(outsideFOVCode); + resampler->SetOutputParametersFromImage(inputImageList[0]); + resampler->Update(); + + // Zero the mask region outside FOV and also the intensities with + // outside + // FOV code + typedef itk::ImageRegionIterator InternalIteratorType; + + FloatImageType::Pointer tmp = resampler->GetOutput(); + InternalIteratorType tmpIt( tmp, tmp->GetLargestPossibleRegion() ); + + // HACK: We can probably remove the mask generation from here. + // The FOV mask, regions where intensities in all channels do not + // match FOV code + ByteImageType::Pointer intraSubjectFOVIntersectionMask = NULL; + intraSubjectFOVIntersectionMask = ByteImageType::New(); + intraSubjectFOVIntersectionMask->CopyInformation(inputImageList[0]); + intraSubjectFOVIntersectionMask->SetRegions( inputImageList[0]->GetLargestPossibleRegion() ); + intraSubjectFOVIntersectionMask->Allocate(); + intraSubjectFOVIntersectionMask->FillBuffer(1); + typedef itk::ImageRegionIterator MaskIteratorType; + MaskIteratorType maskIt( intraSubjectFOVIntersectionMask, + intraSubjectFOVIntersectionMask->GetLargestPossibleRegion() ); + maskIt.GoToBegin(); + tmpIt.GoToBegin(); + while( !maskIt.IsAtEnd() ) + { + if( tmpIt.Get() == outsideFOVCode ) // Voxel came from outside + // the original FOV during + // registration, so + // invalidate it. + { + maskIt.Set(0); // Set it as an invalid voxel in + // intraSubjectFOVIntersectionMask + tmpIt.Set(0); // Set image intensity value to zero. + } + ++maskIt; + ++tmpIt; + } + + // Add the image + outputImageList[i] = CopyOutputImage(tmp); + } + return outputImageList; +} + +static void RescaleFunctionLocal( std::vector & localList) +{ + for( unsigned int i = 0; i < localList.size(); i++ ) + { + typedef itk::RescaleIntensityImageFilter + RescaleType; + RescaleType::Pointer rescaler = RescaleType::New(); + rescaler->SetOutputMinimum(1); + rescaler->SetOutputMaximum(MAX_IMAGE_OUTPUT_VALUE); +#define INPLACE_RESCALER 0 // HACK Test this out +#if defined( INPLACE_RESCALER ) + rescaler->SetInPlace(true); +#endif + FloatImageType::Pointer tmp = localList[i]; + rescaler->SetInput(tmp); + rescaler->Update(); +#if defined( INPLACE_RESCALER ) + localList[i] = rescaler->GetOutput(); +#else + FloatImageType::SizeType size = localList[0]->GetLargestPossibleRegion().GetSize(); + + FloatImagePointer rImg = rescaler->GetOutput(); + FloatImageType::IndexType ind; + // T.O.D.O. This could be done in-place using the -inplace flag of the + // rescaleImageIntensityFilter. + { +#pragma omp parallel for + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + tmp->SetPixel( currIndex, rImg->GetPixel(ind) ); + } + } + } + } +#endif + } +} + +static std::vector FindDuplicateImages(const std::vector candidateSameImageList ) +{ + const double THREASHOLD_CUTOFF = 0.999; // Images with higher correlation are + + // considered duplicate. + + typedef itk::IdentityTransform IDTYPE; + IDTYPE::Pointer myID = IDTYPE::New(); + typedef itk::LinearInterpolateImageFunction InterpType; + InterpType::Pointer myInterp = InterpType::New(); + + std::vector isDuplicated(candidateSameImageList.size(), false); + for( unsigned int start = 0; start < candidateSameImageList.size(); start++ ) + { + for( unsigned int q = start + 1; q < candidateSameImageList.size(); q++ ) + { + typedef itk::NormalizedCorrelationImageToImageMetric NormalizerType; + NormalizerType::Pointer myNormalizer = NormalizerType::New(); + myNormalizer->SetFixedImage(candidateSameImageList[start]); + myNormalizer->SetMovingImage(candidateSameImageList[q]); + myNormalizer->SetTransform(myID); + myNormalizer->SetFixedImageRegion( candidateSameImageList[start]->GetBufferedRegion() ); + myInterp->SetInputImage(candidateSameImageList[q]); + myNormalizer->SetInterpolator(myInterp); + myNormalizer->Initialize(); + const double correlationValue = vcl_abs(myNormalizer->GetValue(myID->GetParameters() ) ); + std::cout << "Correlation value between image " << start + << " and image " << q << ": " << correlationValue << std::endl; + if( correlationValue > THREASHOLD_CUTOFF ) + { + isDuplicated[q] = true; + } + } + } + for( unsigned int q = 0; q < candidateSameImageList.size(); q++ ) + { + std::cout << "Removing highly correlated image " << static_cast(isDuplicated[q]) << std::endl; + } + return isDuplicated; +} + +int main(int argc, char * *argv) +{ + PARSE_ARGS; + BRAINSUtils::SetThreadCount(numberOfThreads); + + // TODO: Need to figure out how to conserve memory better during the running + // of this application: itk::DataObject::GlobalReleaseDataFlagOn(); + itk::OutputWindow::SetInstance( itk::TextOutput::New() ); + + typedef EMSegmentationFilter SegFilterType; + + // Check the parameters for valid values + bool AllSimpleParameterChecksValid = true; + if( maxIterations < 1 ) + { + muLogMacro( << "Warning: " + << "--maxIterations set to 0, so only initialization with priors will be completed." << std::endl ); + } + if( inputVolumes.size() == 0 ) + { + muLogMacro( << "ERROR: " + << "Must specify --inputVolumes" << std::endl ); + AllSimpleParameterChecksValid = false; + } + if(outputVolumes.size() != 1 && outputVolumes.size() != inputVolumes.size()) + { + std::cerr << inputVolumes.size() << " images in input volumeslist, but " + << outputVolumes.size() << " names in output volumes list" + << "OR it must be exactly 1, and be the template for writing files." + << std::endl; + exit(1); + } + if( inputVolumeTypes.size() != inputVolumes.size() ) + { + muLogMacro( << "ERROR: " + << "--inputVolumeTypes and --inputVolumes must" + << " have the same number of elements" << std::endl ); + AllSimpleParameterChecksValid = false; + } + if( atlasDefinition == "" ) + { + muLogMacro( << "Error: " + << "--atlasDefinition required" + << std::endl ); + AllSimpleParameterChecksValid = false; + } + if( outputDir == "" ) + { + muLogMacro( << "ERROR: " + << "outputDir must be specified" << std::endl ); + AllSimpleParameterChecksValid = false; + } + if( AllSimpleParameterChecksValid == false ) + { + muLogMacro( << "ERROR: Commanline arguments are not valid." << std::endl ); + GENERATE_ECHOARGS; + exit(-1); + } + AtlasDefinition atlasDefinitionParser; + try + { + atlasDefinitionParser.InitFromXML(atlasDefinition); + } + catch( ... ) + { + muLogMacro( << "Error reading Atlas Definition from " + << atlasDefinition + << std::endl ); + exit(1); + } + ; + atlasDefinitionParser.DebugPrint(); + // Create and start a new timer (for the whole process) + // EMSTimer* timer = new EMSTimer(); + itk::TimeProbe timer; + timer.Start(); + + // Directory separator string + std::string separator = std::string("/"); + // separator[0] = MU_DIR_SEPARATOR; // always a '/' -- windows can handle + // that fine... + + // Make sure last character in output directory string is a separator + if( outputDir[outputDir.size() - 1] != '/' /* MU_DIR_SEPARATOR */ ) + { + outputDir += separator; + } + + // Create the output directory, stop if it does not exist + // if(!mu::create_dir(outputDir.c_str())) + if( !itksys::SystemTools::MakeDirectory( outputDir.c_str() ) ) + { + muLogMacro( << "ERROR: Could not create requested output directory " << outputDir << std::endl ); + exit(-1); + } + + // Set up the logger + { + const std::string logfn = outputDir + defaultSuffix + ".log"; + ( mu::Log::GetInstance() )->EchoOn(); + ( mu::Log::GetInstance() )->SetOutputFileName( logfn.c_str() ); + } + + // Set up suffix string for images + std::string fmt = outputFormat; + std::string outext = ".mha"; + if( itksys::SystemTools::Strucmp(fmt.c_str(), "Nrrd") == 0 ) + { + outext = ".nrrd"; + } + else if( itksys::SystemTools::Strucmp(fmt.c_str(), "Meta") == 0 ) + { + outext = ".mha"; + } + else if( itksys::SystemTools::Strucmp(fmt.c_str(), "NIFTI") == 0 ) + { + outext = ".nii.gz"; + } + else + { + muLogMacro(<< "WARNING: output format unrecognized, using Meta format\n"); + } + const std::string suffstr + = std::string("_") + std::string(defaultSuffix) + outext; + const std::string metasuffstr + = std::string("_") + std::string(defaultSuffix) + std::string(".mha"); + + muLogMacro(<< "mu::brainseg\n"); + muLogMacro(<< "========================================\n"); + muLogMacro(<< "Program compiled on: " << __DATE__ << std::endl ); + muLogMacro(<< std::endl ); + + muLogMacro( + << "Hans J. Johnson - hans-johnson@uiowa.edu, has made significant" + << " edits to this front end of the BRAINSABC system.\n"); + muLogMacro( + << "Original application was written by Marcel Prastawa - " + << "prastawa@sci.utah.edu, and is maintained as a separate program.\n"); + muLogMacro(<< "This software is provided for research purposes only\n"); + muLogMacro(<< std::endl ); + + muLogMacro(<< "Using ITK version " + << itk::Version::GetITKMajorVersion() << "." + << itk::Version::GetITKMinorVersion() << "." + << itk::Version::GetITKBuildVersion() << std::endl ); + muLogMacro(<< std::endl ); + + // Write input parameters + muLogMacro(<< "=== Parameters ===\n"); + muLogMacro(<< "Suffix: " << defaultSuffix << std::endl ); + muLogMacro(<< "Output Directory: " << outputDir << std::endl ); + muLogMacro(<< "Output Format: " << outputFormat << std::endl ); + muLogMacro(<< "Input images: \n"); + muLogMacro( + << "Non-linear filtering, method: " << filterMethod << ", " + << filterIteration + << " iterations, dt = " << filterTimeStep << std::endl ); + + const AtlasDefinition::TissueTypeVector & PriorNames + = atlasDefinitionParser.TissueTypes(); + + PrettyPrintTable AtlasDefTable; + AtlasDefTable.add(0, 0, "Prior Names"); + AtlasDefTable.add(0, 1, ": ["); + AtlasDefTable.add(0, PriorNames.size() + 2 + 1, "]"); + SegFilterType::VectorType priorsWeightList; + priorsWeightList.set_size( PriorNames.size() ); + AtlasDefTable.add(1, 0, "Prior weight scales"); + AtlasDefTable.add(1, 1, ": ["); + AtlasDefTable.add(1, PriorNames.size() + 2 + 1, "]"); + + unsigned int currentRow = 0; + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + AtlasDefTable.add(currentRow, 2 + pwi, PriorNames[pwi]); + } + + currentRow++; + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + priorsWeightList[pwi] = atlasDefinitionParser.GetWeight(PriorNames[pwi]); + AtlasDefTable.add(currentRow, 2 + pwi, priorsWeightList[pwi], "%4.2f"); + } + + currentRow++; + SegFilterType::IntVectorType priorLabelCodeVector; + priorLabelCodeVector.set_size( PriorNames.size() ); + AtlasDefTable.add(currentRow, 0, "Prior Label Codes"); + AtlasDefTable.add(currentRow, 1, ": ["); + AtlasDefTable.add(currentRow, PriorNames.size() + 2 + 1, "]"); + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + priorLabelCodeVector[pwi] = atlasDefinitionParser.GetLabelCode(PriorNames[pwi]); + AtlasDefTable.add(currentRow, 2 + pwi, priorLabelCodeVector[pwi], "%d"); + } + + currentRow++; + SegFilterType::BoolVectorType priorIsForegroundPriorVector; + priorIsForegroundPriorVector.resize( PriorNames.size() ); + AtlasDefTable.add(currentRow, 0, "Prior IsForeground"); + AtlasDefTable.add(currentRow, 1, ": ["); + AtlasDefTable.add(currentRow, PriorNames.size() + 2 + 1, "]"); + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + priorIsForegroundPriorVector[pwi] = atlasDefinitionParser.GetIsForegroundPrior(PriorNames[pwi]); + AtlasDefTable.add(currentRow, 2 + pwi, priorIsForegroundPriorVector[pwi], "%d"); + } + + currentRow++; + SegFilterType::IntVectorType priorGaussianClusterCountVector; + priorGaussianClusterCountVector.set_size( PriorNames.size() ); + AtlasDefTable.add(currentRow, 0, "Prior Clusters"); + AtlasDefTable.add(currentRow, 1, ": ["); + AtlasDefTable.add(currentRow, PriorNames.size() + 2 + 1, "]"); + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + priorGaussianClusterCountVector[pwi] = atlasDefinitionParser.GetGaussianClusterCount(PriorNames[pwi]); + AtlasDefTable.add(currentRow, 2 + pwi, priorGaussianClusterCountVector[pwi], "%d"); + } + + currentRow++; + SegFilterType::BoolVectorType priorUseForBiasVector; + priorUseForBiasVector.resize( PriorNames.size() ); + AtlasDefTable.add(currentRow, 0, "Prior For Bias"); + AtlasDefTable.add(currentRow, 1, ": ["); + AtlasDefTable.add(currentRow, PriorNames.size() + 2 + 1, "]"); + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + priorUseForBiasVector[pwi] = atlasDefinitionParser.GetUseForBias(PriorNames[pwi]); + AtlasDefTable.add(currentRow, 2 + pwi, priorUseForBiasVector[pwi], "%d"); + } + + { // Print out the ranges. + currentRow++; + for( unsigned int pwi = 0; pwi < PriorNames.size(); pwi++ ) + { + std::map temp_range_List; + for( unsigned int tt = 0; tt < inputVolumeTypes.size(); tt++ ) + { + AtlasDefTable.add(currentRow + tt * 2 + 0, 0, std::string(inputVolumeTypes[tt]) + std::string(" Lower") ); + AtlasDefTable.add(currentRow + tt * 2 + 0, 1, ": ["); + AtlasDefTable.add(currentRow + tt * 2 + 0, PriorNames.size() + 2 + 1, "]"); + + AtlasDefTable.add(currentRow + tt * 2 + 1, 0, std::string(inputVolumeTypes[tt]) + std::string(" Upper") ); + AtlasDefTable.add(currentRow + tt * 2 + 1, 1, ": ["); + AtlasDefTable.add(currentRow + tt * 2 + 1, PriorNames.size() + 2 + 1, "]"); + + temp_range_List[inputVolumeTypes[tt]] = atlasDefinitionParser.GetBounds(PriorNames[pwi], inputVolumeTypes[tt]); + AtlasDefTable.add(currentRow + tt * 2 + 0, 2 + pwi, temp_range_List[inputVolumeTypes[tt]].GetLower(), "%4.2f"); + AtlasDefTable.add(currentRow + tt * 2 + 1, 2 + pwi, temp_range_List[inputVolumeTypes[tt]].GetUpper(), "%4.2f"); + } + } + } + + { + std::ostringstream oss; + AtlasDefTable.Print(oss); + muLogMacro( << oss.str() ); + } + muLogMacro( + << "Max bias polynomial degree: " << maxBiasDegree << std::endl ); + muLogMacro(<< "Atlas warping: " << !atlasWarpingOff << std::endl ); + muLogMacro( + << "Atlas warp spline grid size: " << gridSize[0] << " X " + << gridSize[1] << " X " + << gridSize[2] << std::endl ); + muLogMacro(<< std::endl ); + muLogMacro(<< "=== Start ===\n"); + muLogMacro(<< "Registering images using affine transform...\n"); + + GenericTransformType::Pointer atlasToSubjectPreSegmentationTransform = NULL; + + std::vector atlasOriginalImageList; + ByteImagePointer atlasBrainMask; + { // Read template images needed for atlas registration + // muLogMacro(<< "Read template mask"); + const std::string templateMask = atlasDefinitionParser.GetTemplateBrainMask(); + if( templateMask.size() < 1 ) + { + muLogMacro( << "No template mask specified" << std::endl ); + exit(-1); + } + typedef itk::ImageFileReader ReaderType; + typedef ReaderType::Pointer ReaderPointer; + { + muLogMacro( << "Reading mask : " << templateMask << "...\n"); + + ReaderPointer imgreader = ReaderType::New(); + imgreader->SetFileName( templateMask.c_str() ); + + try + { + imgreader->Update(); + } + catch( ... ) + { + muLogMacro( << "ERROR: Could not read image " << templateMask << "." << std::endl ); + exit(-1); + } + atlasBrainMask = imgreader->GetOutput(); + } + } + + std::vector intraSubjectRegisteredImageList; + std::vector intraSubjectRegisteredRawImageList; + std::vector priorfnlist; + std::vector templateVolumes( inputVolumeTypes.size() ); + for( unsigned int q = 0; q < inputVolumeTypes.size(); q++ ) + { + const AtlasDefinition::TemplateMap & tm = atlasDefinitionParser.GetTemplateVolumes(); + AtlasDefinition::TemplateMap::const_iterator ti = tm.find(inputVolumeTypes[q]); + if(ti != tm.end() ) + { + std::string temp = ti->second; + std::cerr << "STATUS: Atlas image of type: " << inputVolumeTypes[q] << " added with filename: " << temp << std::endl; + templateVolumes[q] = temp; + } + else + { + std::cerr << "ERROR: Atlas image of type: " << inputVolumeTypes[q] << " not found in xml file." << std::endl; + throw; + } + } + + std::vector duplicatesFound; + { + typedef AtlasRegistrationMethod AtlasRegType; + AtlasRegType::Pointer atlasreg = AtlasRegType::New(); + + if( debuglevel > 0 ) + { + atlasreg->DebugOn(); + atlasreg->SetDebugLevel(debuglevel); + } + + atlasreg->SetSuffix(defaultSuffix); + // Compute list of file names for the atlasOriginalPriors + for( unsigned int q = 0; q < PriorNames.size(); q++ ) + { + priorfnlist.push_back( atlasDefinitionParser.GetPriorFilename( PriorNames[q] ) ); + } + { + std::vector intraSubjectRawImageList; + intraSubjectRawImageList.clear(); + intraSubjectRawImageList.resize(inputVolumes.size(), 0); + std::vector intraSubjectNoiseRemovedImageList; + intraSubjectNoiseRemovedImageList.clear(); + intraSubjectNoiseRemovedImageList.resize(inputVolumes.size(), 0); + { // StartOriginalImagesList + const std::string suffixstr = ""; + { // Read subject images needed for atlas registration + // muLogMacro(<< "Read subject images"); + if( inputVolumes.size() < 1 ) + { + muLogMacro( << "No data images specified" << std::endl ); + exit(-1); + } + + typedef itk::ImageFileReader ReaderType; + typedef ReaderType::Pointer ReaderPointer; + + std::vector intraSubjectTransformFileNames( inputVolumes.size() ); + for( unsigned int i = 0; i < inputVolumes.size(); i++ ) + { + muLogMacro( + << "Reading image " << i + 1 << ": " << inputVolumes[i] << "...\n"); + + ReaderPointer imgreader = ReaderType::New(); + imgreader->SetFileName( inputVolumes[i].c_str() ); + + try + { + imgreader->Update(); + } + catch( ... ) + { + muLogMacro( << "ERROR: Could not read image " << inputVolumes[i] << "." << std::endl ); + exit(-1); + } + // Initialize with file read in + FloatImageType::Pointer typewiseEqualizedToFirstImage = imgreader->GetOutput(); +#if 0 // This needs more testing. + // Now go looking to see if this image type has already been found, + // and equalize to the first image of this type if found. + for( unsigned int prevImageIndex = 0; prevImageIndex < i; prevImageIndex++ ) + { + if( inputVolumeTypes[i] == inputVolumeTypes[prevImageIndex] ) + // If it matches a previous found image type, + // then histogram equalize + { + muLogMacro( << "Equalizing image (" << i << ") to image (" << prevImageIndex << ")" << std::endl ); + typedef itk::HistogramMatchingImageFilter HistogramMatchingFilterType; + HistogramMatchingFilterType::Pointer histogramfilter + = HistogramMatchingFilterType::New(); + + histogramfilter->SetInput( imgreader->GetOutput() ); + histogramfilter->SetReferenceImage( intraSubjectNoiseRemovedImageList[prevImageIndex] ); + + histogramfilter->SetNumberOfHistogramLevels( 128 ); + histogramfilter->SetNumberOfMatchPoints( 16 ); + // histogramfilter->ThresholdAtMeanIntensityOn(); + histogramfilter->Update(); + // Overwrite if necessary. + typewiseEqualizedToFirstImage = histogramfilter->GetOutput(); + break; + } + } +#endif + + // Normalize Image Intensities: + muLogMacro( << "Standardizing Intensities: ...\n" ); + intraSubjectRawImageList[i] = StandardizeMaskIntensity( + typewiseEqualizedToFirstImage, + NULL, + 0.0005, 1.0 - 0.0005, + 1, 0.95 * MAX_IMAGE_OUTPUT_VALUE, + 0, MAX_IMAGE_OUTPUT_VALUE); + muLogMacro( << "done.\n" ); +#if 1 + { + std::vector unused_gridSize; + intraSubjectNoiseRemovedImageList[i] = + DenoiseFiltering(intraSubjectRawImageList[i], filterMethod, filterIteration, + filterTimeStep, + unused_gridSize); + if( debuglevel > 1 ) + { + // DEBUG: This code is for debugging purposes only; + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream template_index_stream(""); + template_index_stream << i; + const std::string fn = outputDir + "/DENOISED_INDEX_" + template_index_stream.str() + ".nii.gz"; + writer->SetInput(intraSubjectNoiseRemovedImageList[i]); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } +#else + intraSubjectNoiseRemovedImageList[i] = intraSubjectRawImageList[i]; +#endif + intraSubjectTransformFileNames[i] = outputDir + + GetStripedImageFileNameExtension(inputVolumes[i]) + std::string( + "_to_") + + GetStripedImageFileNameExtension(inputVolumes[0]) + suffixstr + + std::string(".mat"); + } + atlasreg->SetIntraSubjectOriginalImageList(intraSubjectNoiseRemovedImageList); + atlasreg->SetIntraSubjectTransformFileNames(intraSubjectTransformFileNames); + } + + { // Read template images needed for atlas registration + // muLogMacro(<< "Read template images"); + if( templateVolumes.size() < 1 ) + { + muLogMacro( << "No data images specified" << std::endl ); + exit(-1); + } + + typedef itk::ImageFileReader ReaderType; + typedef ReaderType::Pointer ReaderPointer; + + atlasOriginalImageList.clear(); + atlasOriginalImageList.resize(templateVolumes.size(), 0); + for( unsigned int atlasIndex = 0; atlasIndex < templateVolumes.size(); atlasIndex++ ) + { + //KENT: HACK: This currently just checks one previous location in the list to + // determine if the image was already loaded, It should check the + // entire list and avoid loading duplicate images into the list + // of atlas images. + if( ( atlasIndex > 0 ) && ( templateVolumes[atlasIndex] == templateVolumes[atlasIndex - 1] ) ) + { // If they are the same name, then just use same reference + muLogMacro( + << "Referencing previous image " << atlasIndex + 1 << ": " << templateVolumes[atlasIndex] << "...\n"); + atlasOriginalImageList[atlasIndex] = atlasOriginalImageList[atlasIndex - 1]; + } + else + { + muLogMacro( + << "Reading image " << atlasIndex + 1 << ": " << templateVolumes[atlasIndex] << "...\n"); + + ReaderPointer imgreader = ReaderType::New(); + imgreader->SetFileName( templateVolumes[atlasIndex].c_str() ); + + try + { + imgreader->Update(); + } + catch( ... ) + { + muLogMacro( << "ERROR: Could not read image " << templateVolumes[atlasIndex] << "." << std::endl ); + exit(-1); + } + + muLogMacro( << "Standardizing Intensities: ..." ); + FloatImagePointer img_i = StandardizeMaskIntensity( + imgreader->GetOutput(), + atlasBrainMask, + 0.0005, 1.0 - 0.0005, + 1, 0.95 * MAX_IMAGE_OUTPUT_VALUE, + 0, MAX_IMAGE_OUTPUT_VALUE); + muLogMacro( << "done." << std::endl ); + atlasOriginalImageList[atlasIndex] = img_i; + if( debuglevel > 7 ) + { + typedef itk::ImageFileWriter FloatWriterType; + FloatWriterType::Pointer writer = FloatWriterType::New(); + + std::stringstream write_atlas_index_stream(""); + write_atlas_index_stream << atlasIndex; + const std::string fn + = outputDir + std::string("RenormalizedAtlasTemplate_") + write_atlas_index_stream.str() + suffstr; + + writer->SetInput(atlasOriginalImageList[atlasIndex] ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + } + } + atlasreg->SetAtlasOriginalImageList(atlasOriginalImageList); + atlasreg->SetInputVolumeTypes(inputVolumeTypes); + const std::string atlasTransformFileName = outputDir + + GetStripedImageFileNameExtension(templateVolumes[0]) + + std::string("_to_") + + GetStripedImageFileNameExtension(inputVolumes[0]) + suffixstr + + std::string("PreSegmentation.mat"); + atlasreg->SetAtlasToSubjectTransformFileName(atlasTransformFileName); + } + + // atlasreg->SetOutputDebugDir(outputDir); + + if( !( ( atlasToSubjectTransformType.compare("Identity") == 0 ) + || ( atlasToSubjectTransformType.compare("Rigid") == 0 ) + || ( atlasToSubjectTransformType.compare("Affine") == 0 ) + || ( atlasToSubjectTransformType.compare("BSpline") == 0 ) ) + ) + { + muLogMacro( + "ERROR: Invalid atlasToSubjectTransformType specified" << atlasToSubjectTransformType << std::endl); + exit(-1); + } + + if( !( ( subjectIntermodeTransformType.compare("Identity") == 0 ) + || ( subjectIntermodeTransformType.compare("Rigid") == 0 ) + || ( subjectIntermodeTransformType.compare("Affine") == 0 ) + || ( subjectIntermodeTransformType.compare("BSpline") == 0 ) ) + ) + { + muLogMacro( + "ERROR: Invalid subjectIntermodeTransformType specified" << subjectIntermodeTransformType << std::endl); + exit(-1); + } + + atlasreg->SetAtlasLinearTransformChoice(atlasToSubjectTransformType); + atlasreg->SetImageLinearTransformChoice(subjectIntermodeTransformType); + + atlasreg->SetWarpGrid( + gridSize[0], + gridSize[1], + gridSize[2]); + muLogMacro(<< "Registering and resampling images..." << std::endl); + // EMSTimer* regtimer = new EMSTimer(); + // muLogMacro(<< "Registration took " << + // regtimer->GetElapsedHours() << " hours, "); + // muLogMacro(<< regtimer->GetElapsedMinutes() << " minutes, "); + // muLogMacro(<< regtimer->GetElapsedSeconds() << " seconds\n"); + // delete regtimer; + itk::TimeProbe regtimer; + regtimer.Start(); + atlasreg->SetOutputDebugDir(outputDir); + atlasreg->Update(); + regtimer.Stop(); + itk::RealTimeClock::TimeStampType elapsedTime + = regtimer.GetTotal(); + muLogMacro(<< "Registration took " << elapsedTime << " " << regtimer.GetUnit() << std::endl); + + std::vector intraSubjectTransforms = atlasreg->GetIntraSubjectTransforms(); + + // ::ResampleImages() + { + // muLogMacro(<< "ResampleImages"); + + // Define the internal reader type + typedef itk::ResampleImageFilter ResampleType; + typedef ResampleType::Pointer ResamplePointer; + + intraSubjectRegisteredImageList = + ResampleImageList(resamplerInterpolatorType, intraSubjectNoiseRemovedImageList, + intraSubjectTransforms); + intraSubjectRegisteredRawImageList = ResampleImageList(resamplerInterpolatorType, intraSubjectRawImageList, + intraSubjectTransforms); + assert( intraSubjectRegisteredImageList.size() == intraSubjectNoiseRemovedImageList.size() ); + assert( intraSubjectRegisteredImageList.size() == intraSubjectRawImageList.size() ); + intraSubjectNoiseRemovedImageList.clear(); + intraSubjectRawImageList.clear(); + } // End registering data + + { + // Now check that the intraSubjectNoiseRemovedImageList has positive + // definite covariance matrix. + // The algorithm is not stable if the covariance matrix is not + // positive definite, and this + // occurs when two or more of the images are linearly dependant (i.e. + // nearly the same image). + duplicatesFound = FindDuplicateImages(intraSubjectRegisteredImageList); + for( size_t q = 0; q < duplicatesFound.size(); q++ ) + { + if( duplicatesFound[q] == true ) + { + std::cout << "WARNING: Found images that were very highly correlated." << std::endl; + std::cout << "WARNING: Removing image " << inputVolumes[q] << " from further processing" << std::endl; + std::cout << "WARNING:" << std::endl; + } + } + } + } // EndOriginalImagesList + + atlasToSubjectPreSegmentationTransform = atlasreg->GetAtlasToSubjectTransform(); + if( debuglevel > 9 ) + { // NOTE THIS IS REALLY ANNOYING FOR LARGE BSPLINE REGISTRATIONS! + muLogMacro( << __FILE__ << " " << __LINE__ << " " << atlasToSubjectPreSegmentationTransform->GetFixedParameters( + ) << std::endl ); + muLogMacro( + << __FILE__ << " " << __LINE__ << " " << atlasToSubjectPreSegmentationTransform->GetParameters() << std::endl ); + } + if( debuglevel > 4 ) + { + // Write the registered template and images + if( !writeLess ) + { + muLogMacro(<< "Writing registered template...\n"); + + typedef itk::ResampleImageFilter ResampleType; + typedef ResampleType::Pointer ResamplePointer; + ResamplePointer resampler = ResampleType::New(); + + resampler->SetInput(atlasOriginalImageList[0]); + resampler->SetTransform(atlasToSubjectPreSegmentationTransform); + + resampler->SetOutputParametersFromImage(intraSubjectRegisteredRawImageList[0]); + resampler->SetDefaultPixelValue(0); + resampler->Update(); + typedef itk::CastImageFilter + ShortRescaleType; + ShortRescaleType::Pointer rescaler = ShortRescaleType::New(); + rescaler->SetInput( resampler->GetOutput() ); + rescaler->Update(); + + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + + std::string fn + = outputDir + std::string("AtlasToSubjectInitialization_") + suffstr; + + writer->SetInput( rescaler->GetOutput() ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + for( unsigned int i = 0; i < intraSubjectRegisteredRawImageList.size(); i++ ) + { + typedef itk::RescaleIntensityImageFilter + ShortRescaleType; + + ShortRescaleType::Pointer rescaler = ShortRescaleType::New(); + rescaler->SetOutputMinimum(0); + rescaler->SetOutputMaximum(MAX_IMAGE_OUTPUT_VALUE); + rescaler->SetInput(intraSubjectRegisteredRawImageList[i]); + rescaler->Update(); + + std::string fn + = outputDir + GetStripedImageFileNameExtension( ( inputVolumes[i] ) ) + + std::string("_registered") + suffstr; + + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + + writer->SetInput( rescaler->GetOutput() ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + } + } + } // end atlas reg block + + { + // Now based on the duplicates found, update input lists to only use unique + // images + intraSubjectRegisteredImageList = RemoveDuplicates(intraSubjectRegisteredImageList, duplicatesFound); + intraSubjectRegisteredRawImageList = RemoveDuplicates(intraSubjectRegisteredRawImageList, duplicatesFound); + inputVolumes = RemoveDuplicates(inputVolumes, duplicatesFound); + inputVolumeTypes = RemoveDuplicates(inputVolumeTypes, duplicatesFound); + } + + muLogMacro(<< "Rescale intensity of filtered images...\n"); + { + + RescaleFunctionLocal(intraSubjectRegisteredImageList); + RescaleFunctionLocal(intraSubjectRegisteredRawImageList); + } + // Start the segmentation process. + for( unsigned int segmentationLevel = 0; segmentationLevel < 1; segmentationLevel++ ) + { +#if 0 + // Prior Names + // Prior Names : [ AIR GM BGM CSF NOTCSF NOTGM NOTVB NOTWM VB + // WM ] + // Prior weight scales : [ 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 + // 1.00 0.50 ] + // Prior Label Codes : [ 0 2 3 4 6 7 9 8 5 + // 1 ] + std::map > ParentLabels; + // Air + ParentLabels[100].push_back(0); + // GM-BGM-NOTGM + ParentLabels[101].push_back(2); + ParentLabels[101].push_back(3); + ParentLabels[101].push_back(7); + // CSF-NOTCSF + ParentLabels[102].push_back(4); + ParentLabels[102].push_back(6); + // WM-NOTWM + ParentLabels[103].push_back(1); + ParentLabels[103].push_back(8); + // VB-NOTVB + ParentLabels[104].push_back(5); + ParentLabels[104].push_back(9); + + std::map ParentLabelNames; + for( + std::map >::const_iterator plIter = ParentLabels.begin(); + plIter != ParentLabels.end(); plIter++ ) + { + std::string combinedName = ""; + bool firstpass = true; + for( + std::vector::const_iterator vIter = plIter->second.begin(); + vIter != plIter->second.end(); vIter++ ) + { + if( firstpass ) + { + firstpass = false; + } + else + { + combinedName += "-"; + } + combinedName += PriorNames[*vIter]; + } + ParentLabelNames[plIter->first] = combinedName; + } + +#endif + + SegFilterType::Pointer segfilter = SegFilterType::New(); + // __MAX__PROBS + { + std::vector atlasOriginalPriors( PriorNames.size() ); + for( unsigned int i = 0; i < PriorNames.size(); i++ ) + { + typedef itk::ImageFileReader ReaderType; + typedef ReaderType::Pointer ReaderPointer; + ReaderPointer priorReader = ReaderType::New(); + priorReader->SetFileName( atlasDefinitionParser.GetPriorFilename(PriorNames[i]) ); + priorReader->Update(); + FloatImageType::Pointer temp = priorReader->GetOutput(); + atlasOriginalPriors[i] = temp; + } + segfilter->SetPriors(atlasOriginalPriors); + } + { + SegFilterType::RangeDBType myRanges; + for( unsigned int q = 0; q < PriorNames.size(); q++ ) + { + std::map temp_range_List; + for( unsigned int tt = 0; tt < inputVolumeTypes.size(); tt++ ) + { + temp_range_List[inputVolumeTypes[tt]] = atlasDefinitionParser.GetBounds(PriorNames[q], inputVolumeTypes[tt]); + } + myRanges[PriorNames[q]] = temp_range_List; + } + segfilter->SetTissueTypeThresholdMapsRange(myRanges); + segfilter->SetPriorNames(PriorNames); + } + + // //Static component that does not depend on priors-consolidation. + muLogMacro(<< "Start segmentation...\n"); + segfilter->SetOutputDebugDir(outputDir); + + if( debuglevel > 0 ) + { + segfilter->DebugOn(); + segfilter->SetDebugLevel(debuglevel); + } + + segfilter->SetInputImages(intraSubjectRegisteredImageList); + segfilter->SetRawInputImages(intraSubjectRegisteredRawImageList); + segfilter->SetInputVolumeTypes(inputVolumeTypes); + + segfilter->SetMaximumIterations( maxIterations ); + segfilter->SetOriginalAtlasImages(atlasOriginalImageList); + segfilter->SetTemplateBrainMask(atlasBrainMask); + segfilter->SetTemplateGenericTransform(atlasToSubjectPreSegmentationTransform); + + segfilter->SetPriorWeights(priorsWeightList); + segfilter->SetPriorLabelCodeVector(priorLabelCodeVector); + segfilter->SetPriorUseForBiasVector(priorUseForBiasVector); + segfilter->SetPriorIsForegroundPriorVector(priorIsForegroundPriorVector); + + segfilter->SetMaxBiasDegree(maxBiasDegree); + +#if 0 + // THIS ACTAULLY NEEDS TO BE USED FOR ONLY DOING THE FINAL ITERATION OF THE + // SEGMENTATION PROCESS AND SKIPPING MOST OF EMLoop + // If this "Post" transform is given, then jump over the looping, and + // warp priors,do estimates, and bias correct in one step. + { + ReadGenericTransform; + + segfilter->SetTemplateGenericTransform(); + // Turn off warping, and just use the input given from disk. + } +#endif + + if( !atlasWarpingOff ) + { + segfilter->UpdateTransformationOn(); + } + else + { + segfilter->UpdateTransformationOff(); + } + segfilter->SetWarpGrid( + gridSize[0], + gridSize[1], + gridSize[2]); + + segfilter->Update(); + + std::vector names = inputVolumes; + // Write the secondary outputs + if( !writeLess ) + { + muLogMacro(<< "Writing filtered and bias corrected images...\n"); + // std::vector imgset = segfilter->GetCorrected(); + std::vector imgset = segfilter->GetRawCorrected(); + std::vector outFileNames; + if(outputVolumes.size() == 1) + { + outFileNames.resize(imgset.size()); + for( unsigned i = 0; i < imgset.size(); i++ ) + { + char buf[8192]; + sprintf(buf,outputVolumes[0].c_str(),inputVolumeTypes[i].c_str(),i); + outFileNames[i] = buf; + } + } + else if( outputVolumes.size() != imgset.size()) + { + std::cerr << imgset.size() << " images in filter output, but " + << outputVolumes.size() << " names in output volumes list" + << std::endl; + exit(1); + } + else + { + outFileNames=outputVolumes; + } + + for( unsigned i = 0; i < imgset.size(); i++ ) + { + // typedef itk::RescaleIntensityImageFilter ShortRescaleType; + typedef itk::CastImageFilter CasterType; + CasterType::Pointer caster = CasterType::New(); + + caster->SetInput(imgset[i]); + caster->Update(); + // std::string fn + // = outputDir + GetStripedImageFileNameExtension(names[i]) + std::string("_corrected") + // + suffstr; + + typedef itk::ImageFileWriter ShortWriterType; + ShortWriterType::Pointer writer = ShortWriterType::New(); + + writer->SetInput( caster->GetOutput() ); + writer->SetFileName(outFileNames[i]); + writer->UseCompressionOn(); + writer->Update(); + } + } + + // Write warped template and bspline trafo + if( !atlasWarpingOff ) + { + std::vector WarpedAtlasList = segfilter->GenerateWarpedAtlasImages(); + for( unsigned int index = 0; index < WarpedAtlasList.size(); index++ ) + { + typedef itk::RescaleIntensityImageFilter + ByteRescaleType; + + ByteRescaleType::Pointer rescaler = ByteRescaleType::New(); + rescaler->SetOutputMinimum(0); + rescaler->SetOutputMaximum(255); + rescaler->SetInput(WarpedAtlasList[index]); + rescaler->Update(); + + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + + const std::string fn = outputDir + + GetStripedImageFileNameExtension(templateVolumes[index]) + std::string("_to_") + + GetStripedImageFileNameExtension( ( inputVolumes[0] ) ) + + std::string("_warped") + std::string(".nii.gz"); + + muLogMacro(<< "Writing warped template images... " << fn << std::endl ); + writer->SetInput( rescaler->GetOutput() ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + if(atlasToSubjectTransform != "") + { + /* HACK Remove this completely + const std::string postSegmentationTransformFileName = outputDir + + GetStripedImageFileNameExtension(templateVolumes[0]) + + std::string("_to_") + + GetStripedImageFileNameExtension( ( inputVolumes[0] ) ) + + std::string("_") + defaultSuffix + "_PostSegmentation.mat"; + */ + const std::string postSegmentationTransformFileName=atlasToSubjectTransform; + // + // NOTE: Aliasing of smart-pointers up the polymorphic tree OK here + // because + // the primary + // smart pointer is gaunteed to exists during lifespan of all aliases. + muLogMacro(<< "Writing final atlas to subject template... " << postSegmentationTransformFileName << std::endl ); + GenericTransformType::Pointer atlasToSubjectPostSegmentationTransform = segfilter->GetTemplateGenericTransform(); + WriteTransformToDisk(atlasToSubjectPostSegmentationTransform, postSegmentationTransformFileName); + // TODO: Need to write a short circuit so that if this final transform + // filename exists, it will just read it in and use it directly + // without doing all the iterations. + } + } + + // Write the labels + muLogMacro(<< "Writing labels...\n"); + { + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + + writer->SetInput( segfilter->GetOutput() ); + std::string fn; + if(outputLabels == "") + { + fn = outputDir; + fn += GetStripedImageFileNameExtension(names[0]); + fn += std::string("_DirtyLabels"); + fn += suffstr; + } + else + { + fn = outputDirtyLabels; + } + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + { + typedef itk::ImageFileWriter ByteWriterType; + ByteWriterType::Pointer writer = ByteWriterType::New(); + + std::string fn; + if(outputLabels == "") + { + fn = outputDir; + fn += GetStripedImageFileNameExtension(names[0]); + fn += std::string("_labels"); + fn += suffstr; + } + else + { + fn = outputLabels; + } + + writer->SetInput( segfilter->GetCleanedOutput() ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + try + { + writer->Update(); + } + catch( itk::ExceptionObject & e ) + { + muLogMacro( << e << std::endl ); + return -1; + } + catch( std::exception & e ) + { + muLogMacro( << "Exception: " << e.what() << std::endl ); + return -1; + } + catch( std::string & s ) + { + muLogMacro( << "Exception: " << s << std::endl ); + return -1; + } + catch( ... ) + { + muLogMacro( << "Unknown exception" << std::endl ); + muLogMacro( << "failed to write image " << fn << std::endl ); + return -1; + } + } + // Write final Posteriors + { + // NOTE : Priors and Posteriors should correspond, so use the PriorNames + // to get the names. + for( unsigned int probabilityIndex = 0; probabilityIndex < PriorNames.size(); probabilityIndex++ ) + { + std::string fn; + if(posteriorTemplate == "") + { + fn = outputDir; + fn += GetStripedImageFileNameExtension(names[0]); + fn += "_POSTERIOR_"; + fn += PriorNames[probabilityIndex]; + fn += suffstr; + } + else + { + char buf[8192]; + sprintf(buf,posteriorTemplate.c_str(), + PriorNames[probabilityIndex].c_str()); + fn = buf; + } + typedef itk::ImageFileWriter FloatWriterType; + FloatWriterType::Pointer writer = FloatWriterType::New(); + + FloatImageType::Pointer currPosterior = segfilter->GetPosteriors()[probabilityIndex]; + writer->SetInput( currPosterior ); + writer->SetFileName( fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + } + } + timer.Stop(); + muLogMacro(<< "All segmentation processes took " << timer.GetTotal() << " " << timer.GetUnit() << std::endl ); + return 0; +} + diff --git a/BRAINSABC/brainseg/BRAINSABC.xml b/BRAINSABC/brainseg/BRAINSABC.xml new file mode 100644 index 00000000..3d62943b --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABC.xml @@ -0,0 +1,271 @@ + + + + BRAINS.Classify + BRAINSABC + Atlas-based tissue segmentation method. This is an algorithmic extension of work done by XXXX at UNC and Utah XXXX need more description here. + + + + + + Input parameters + + + inputVolumes + + inputVolumes + i + input + The list of input image files to be segmented. + + + atlasDefinition + + atlasDefinition + input + + Contains all parameters for Atlas + + + + + inputVolumeTypes + + The list of input image types corresponding to the inputVolumes. + inputVolumeTypes + + + + outputDir + + + outputDir + output + Ouput directory + + + + + atlasToSubjectTransformType + + atlasToSubjectTransformType + What type of linear transform type do you want to use to register the atlas to the reference subject image. + ID + Rigid + Affine + BSpline + Affine + + + atlasToSubjectTransform + + The trasform from atlas to the subject + atlasToSubjectTransform + output + + + subjectIntermodeTransformType + + subjectIntermodeTransformType + What type of linear transform type do you want to use to register the atlas to the reference subject image. + ID + Rigid + Affine + BSpline + Rigid + + + + + Output filename specifications + + outputVolumes + + outputVolumes + output + %s_corrected_%d.nii.gz + Corrected Output Images: should specify the same number of images as inputVolume, if only one element is given, then it is used as a file pattern where %s is replaced by the imageVolumeType, and %d by the index list location. + + + + outputLabels + + outputLabels + output + + Output Label Image + + + + outputDirtyLabels + + outputDirtyLabels + output + + Output Dirty Label Image + + + + posteriorTemplate + + posteriorTemplate + POST_%s.nii.gz + filename template for Posterior output files + + + + + Advanced parameters for the creation of the segmentation file + + + outputFormat + outputFormat + Output format + NIFTI + Meta + Nrrd + NIFTI + + + + resamplerInterpolatorType + interpolationMode + Type of interpolation to be used when applying transform to moving volume. Options are Linear, NearestNeighbor, BSpline, WindowedSinc, or ResampleInPlace. The ResampleInPlace option will create an image with the same discrete voxel values and will adjust the origin and direction of the physical space interpretation. + BSpline + NearestNeighbor + WindowedSinc + Linear + ResampleInPlace + BSpline + + + maxIterations + Filter iterations + + maxIterations + 40 + + 1 + 100 + 1 + + + + + + medianFilterSize + medianFilterSize + + The radius for the optional MedianImageFilter preprocessing in all 3 directions. + 0,0,0 + + + filterIteration + Filter iterations + + filterIteration + 5 + + 0 + 50 + 1 + + + + filterTimeStep + Filter time step + + filterTimeStep + 0.0625 + + 0 + 0.5 + 0.01 + + + + filterMethod + + filterMethod + Filter method for preprocessing of registration + None + CurvatureFlow + GradientAnisotropicDiffusion + Median + None + + + + maxBiasDegree + Maximum bias degree + + maxBiasDegree + 4 + + 0 + 20 + 1 + + + + + atlasWarpingOff + false + + atlasWarpingOff + Deformable registration of atlas to subject + + + gridSize + Grid size for atlas warping with BSplines + + gridSize + 5,5,5 + + + + + + + + defaultSuffix + + s + defaultSuffix + BRAINSABC + + + + + + + Options + + debuglevel + + Display debug messages, and produce debug intermediate results. 0=OFF, 1=Minimal, 10=Maximum debugging. + debuglevel + 0 + + + + writeLess + + Does not write posteriors and filtered, bias corrected images + writeLess + false + + + + + + numberOfThreads + numberOfThreads + + Explicitly specify the maximum number of threads to use. + -1 + + + + diff --git a/BRAINSABC/brainseg/BRAINSABCUtilities.cxx b/BRAINSABC/brainseg/BRAINSABCUtilities.cxx new file mode 100644 index 00000000..442ac05f --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABCUtilities.cxx @@ -0,0 +1,98 @@ +#include "BRAINSABCUtilities.h" +/***************************** + * Now call the instantiations + */ +#include "BRAINSABCUtilities.txx" +#include "LLSBiasCorrector.h" + +template std::vector DuplicateImageList( + const std::vector & ); + +template std::vector DuplicateImageList( + const std::vector & ); + +template void ComputeLabels( std::vector &, std::vector &, + vnl_vector &, ByteImageType::Pointer &, + ByteImageType::Pointer &, + ByteImageType::Pointer & ); + +template void NormalizeProbListInPlace(std::vector & ); + +template void ZeroNegativeValuesInPlace( std::vector & ); + +std::vector CorrectBias( + const unsigned int degree, + const unsigned int CurrentEMIteration, + const std::vector & + CandidateRegions, + const std::vector & + inputImages, + const ByteImageType::Pointer currentBrainMask, + const ByteImageType::Pointer currentTissueMask, + const std::vector & probImages, + const std::vector & probUseForBias, + const FloatingPrecision sampleSpacing, + const int DebugLevel, + const std::string& OutputDebugDir + ) +{ + std::vector correctedImages(inputImages.size() ); + if( degree == 0 ) + { + muLogMacro(<< "Skipping Bias correction, polynomial degree = " << degree << std::endl); + return inputImages; + } + muLogMacro(<< "Bias correction, polynomial degree = " << degree << std::endl); + + // Perform bias correction + const unsigned int numClasses = probImages.size(); + std::vector biasPosteriors; + std::vector biasCandidateRegions; + biasPosteriors.clear(); + biasCandidateRegions.clear(); + { + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + const unsigned iprior = iclass; + if( probUseForBias[iprior] == 1 ) + { + // Focus only on FG classes, more accurate if bg classification is bad + // but sacrifices accuracy in border regions (tend to overcorrect) + biasPosteriors.push_back(probImages[iclass]); + biasCandidateRegions.push_back(CandidateRegions[iclass]); + } + } + } + + itk::TimeProbe BiasCorrectorTimer; + BiasCorrectorTimer.Start(); + typedef LLSBiasCorrector BiasCorrectorType; + typedef BiasCorrectorType::Pointer BiasCorrectorPointer; + + BiasCorrectorPointer biascorr = BiasCorrectorType::New(); + biascorr->SetMaxDegree(degree); + // biascorr->SetMaximumBiasMagnitude(5.0); + // biascorr->SetSampleSpacing(2.0*SampleSpacing); + biascorr->SetSampleSpacing(1); + biascorr->SetWorkingSpacing(sampleSpacing); + biascorr->SetForegroundBrainMask(currentBrainMask); + biascorr->SetAllTissueMask(currentTissueMask); + biascorr->SetProbabilities(biasPosteriors, biasCandidateRegions); + biascorr->SetDebugLevel(DebugLevel); + biascorr->SetOutputDebugDir(OutputDebugDir); + + if( DebugLevel > 0 ) + { + biascorr->DebugOn(); + } + + biascorr->SetInputImages(inputImages); + correctedImages = biascorr->CorrectImages(CurrentEMIteration); + + BiasCorrectorTimer.Stop(); + itk::RealTimeClock::TimeStampType elapsedTime = BiasCorrectorTimer.GetTotal(); + muLogMacro(<< "Computing BiasCorrection took " << elapsedTime << " " << BiasCorrectorTimer.GetUnit() << std::endl); + + return correctedImages; +} + diff --git a/BRAINSABC/brainseg/BRAINSABCUtilities.h b/BRAINSABC/brainseg/BRAINSABCUtilities.h new file mode 100644 index 00000000..f29ae939 --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABCUtilities.h @@ -0,0 +1,106 @@ +/** + * This file is to make some smaller compilation units to help improve compilation performance. + */ +#ifndef __BRAINSABCUtilities__h__ +#define __BRAINSABCUtilities__h__ + +#include "Log.h" +#include +#include + +#include +#include +#include + +#include + +#include +#include + +// The 200805 OpenMPv3.0 specificaiton allows unsigned iterators +#if defined(_OPENMP) +#define LOCAL_USE_OPEN_MP +#endif + +#if defined(LOCAL_USE_OPEN_MP) && (_OPENMP < 200805) +typedef int LOOPITERTYPE; +#else +typedef unsigned int LOOPITERTYPE; +#endif + +// vnl_math_isnan(value) || vnl_math_isinf(value) ) +#if 1 // Runtime performance penalty that can be used to find faulty code + // during debugging. +#define CHECK_NAN( XXXTESTXXX, srcfile, srcline ) \ + { \ + if( !vnl_math_isfinite( XXXTESTXXX ) ) \ + { \ + std::cout << "Found " << XXXTESTXXX << " at " << srcfile << " " << srcline << std::endl; \ + /*exit(-1);*/ \ + } \ + } +#else +#define CHECK_NAN( XXXTESTXXX, srcfile, srcline ) \ + { } +#endif + +typedef double FloatingPrecision; +typedef itk::Image ByteImageType; +typedef itk::Image FloatImageType; +typedef FloatImageType::Pointer FloatImagePointerType; +typedef itk::Image ShortImageType; + +typedef itk::Image CorrectIntensityImageType; + +/** A utiliy class for holding statistical information + * for all image channels for a given tissue class type + */ +class RegionStats +{ +public: + typedef vnl_matrix MatrixType; + typedef vnl_matrix_inverse MatrixInverseType; + typedef vnl_vector VectorType; + + RegionStats() : m_Means(), m_Covariance(), m_Weighting(0.0) + { + } + + void resize(const unsigned int numChannels) + { + this->m_Covariance = MatrixType(numChannels, numChannels); + this->m_Means.set_size(numChannels); + } + + VectorType m_Means; // One measure per image channel type; + MatrixType m_Covariance; // Matrix of covariances of class by image + // channel + FloatingPrecision m_Weighting; // The strength of this class. +}; + +#include "BRAINSABCUtilities.txx" + +// External Templates to improve compilation times. +extern std::vector CorrectBias( + const unsigned int degree, const unsigned int CurrentEMIteration, + const std::vector & CandidateRegions, + const std::vector & inputImages, const ByteImageType::Pointer currentBrainMask, + const ByteImageType::Pointer currentForegroundMask, const std::vector & probImages, + const std::vector & probUseForBias, const FloatingPrecision sampleSpacing, const int DebugLevel, const std::string& OutputDebugDir); + +extern template class std::vector DuplicateImageList( + const std::vector & ); + +extern template std::vector DuplicateImageList( + const std::vector & ); + +extern template void ComputeLabels( std::vector &, std::vector &, + vnl_vector &, ByteImageType::Pointer &, + ByteImageType::Pointer &, + ByteImageType::Pointer & ); + +extern template void NormalizeProbListInPlace(std::vector & ); + +extern template void ZeroNegativeValuesInPlace( std::vector & ); + +#endif // __BRAINSABCUtilities__h__ diff --git a/BRAINSABC/brainseg/BRAINSABCUtilities.txx b/BRAINSABC/brainseg/BRAINSABCUtilities.txx new file mode 100644 index 00000000..7b2c1869 --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABCUtilities.txx @@ -0,0 +1,294 @@ +#ifndef __BRAINSABCUtilities__txx__ +#define __BRAINSABCUtilities__txx__ + +#include "ExtractSingleLargestRegion.h" + +template +void ZeroNegativeValuesInPlace(std::vector & priors) +{ + const unsigned int numPriors = priors.size(); + + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + // First copy value, and set negative values to zero. + for( LOOPITERTYPE iprior = 0; iprior < (LOOPITERTYPE)numPriors; iprior++ ) + { + for( itk::ImageRegionIterator priorIter(priors[iprior], + priors[iprior]->GetLargestPossibleRegion() ); + !priorIter.IsAtEnd(); ++priorIter ) + { + typename TProbabilityImage::PixelType inputValue(priorIter.Get() ); + if( inputValue < 0.0 ) + { + priorIter.Set(0.0); + } + } + } + } +} + +template +void NormalizeProbListInPlace(std::vector & ProbList) +{ + const unsigned int numProbs = ProbList.size(); + + const typename TProbabilityImage::SizeType size = ProbList[0]->GetLargestPossibleRegion().GetSize(); + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + FloatingPrecision sumPrior = 0.0; + for( unsigned int iprior = 0; iprior < numProbs; iprior++ ) + { + sumPrior += ProbList[iprior]->GetPixel(currIndex); + } + if( sumPrior < 1e-20 ) + { + const FloatingPrecision averageValue = 1.0 / static_cast(numProbs); + for( unsigned int iprior = 0; iprior < numProbs; iprior++ ) + { + ProbList[iprior]->SetPixel(currIndex, averageValue); + } + } + else + { + const FloatingPrecision invSumPrior = 1.0 / sumPrior; + for( unsigned int iprior = 0; iprior < numProbs; iprior++ ) + { + const FloatingPrecision normValue = ProbList[iprior]->GetPixel(currIndex) * invSumPrior; + CHECK_NAN(normValue, __FILE__, __LINE__); + ProbList[iprior]->SetPixel(currIndex, normValue); + } + } + } + } + } + } +} + +// Labeling using maximum a posteriori, also do brain stripping using +// mathematical morphology and connected component +template +void ComputeLabels( + std::vector & Posteriors, + std::vector & PriorIsForegroundPriorVector, + vnl_vector & PriorLabelCodeVector, + typename ByteImageType::Pointer & NonAirRegion, + typename ByteImageType::Pointer & DirtyLabels, + typename ByteImageType::Pointer & CleanedLabels) +{ + muLogMacro(<< "ComputeLabels" << std::endl ); + itk::TimeProbe ComputeLabelsTimer; + ComputeLabelsTimer.Start(); + + const unsigned int numClasses = Posteriors.size(); + const typename TProbabilityImage::RegionType region = Posteriors[0]->GetLargestPossibleRegion(); + + DirtyLabels = ByteImageType::New(); + DirtyLabels->CopyInformation(Posteriors[0]); + DirtyLabels->SetRegions(region); + DirtyLabels->Allocate(); + DirtyLabels->FillBuffer(0); + + typename ByteImageType::Pointer foregroundMask = ByteImageType::New(); + foregroundMask->CopyInformation(Posteriors[0]); + foregroundMask->SetRegions(region); + foregroundMask->Allocate(); + foregroundMask->FillBuffer(0); + + const typename ByteImageType::SizeType size = DirtyLabels->GetLargestPossibleRegion().GetSize(); + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + if( NonAirRegion->GetPixel(currIndex) == 0 ) // If outside the tissue + // region, then set to + // zero vIndex! + { + // TODO: May want to specify this explicitly in the XML file for + // the proper background value + DirtyLabels->SetPixel(currIndex, 0); // This is implied by the + // FillBuffer(0) above; + continue; + } + + FloatingPrecision maxPosteriorClassValue = Posteriors[0]->GetPixel(currIndex); + unsigned int indexMaxPosteriorClassValue = 0; + for( unsigned int iclass = 1; iclass < numClasses; iclass++ ) + { + const FloatingPrecision currentPosteriorClassValue = Posteriors[iclass]->GetPixel(currIndex); + if( currentPosteriorClassValue > maxPosteriorClassValue ) + { + maxPosteriorClassValue = currentPosteriorClassValue; + indexMaxPosteriorClassValue = iclass; + } + } + + { + bool fgflag = PriorIsForegroundPriorVector[indexMaxPosteriorClassValue]; + unsigned int label = PriorLabelCodeVector[indexMaxPosteriorClassValue]; + // Only use non-zero probabilities and foreground classes + if( !fgflag || ( maxPosteriorClassValue < 0.001 ) ) + { + fgflag = false; // If priors are zero or negative, then set the + // fgflag back to false + } + DirtyLabels->SetPixel(currIndex, label); + foregroundMask->SetPixel(currIndex, fgflag); + } + } + } + } + } + // + // CleanedLabels=ExtractSingleLargestRegionFromMask(foregroundMask,2,2,1,DirtyLabels); + CleanedLabels = ExtractSingleLargestRegionFromMask(foregroundMask, 0, 0, 0, DirtyLabels); + ComputeLabelsTimer.Stop(); + itk::RealTimeClock::TimeStampType elapsedTime = + ComputeLabelsTimer.GetTotal(); + muLogMacro(<< "Computing Labels took " << elapsedTime << " " << ComputeLabelsTimer.GetUnit() << std::endl); +} + +template +std::vector +DuplicateImageList(const std::vector & inputList) +{ + std::vector outputList(inputList.size() ); + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + for( LOOPITERTYPE i = 0; i < (LOOPITERTYPE)inputList.size(); i++ ) + { + typename itk::ImageDuplicator::Pointer myDuplicator + = itk::ImageDuplicator::New(); + myDuplicator->SetInputImage(inputList[i]); + myDuplicator->Update(); + outputList[i] = myDuplicator->GetOutput(); + } + } + return outputList; +} + +#if 0 +template +void WinnerTakesAll(std::vector & listOfImages) +{ + itk::ImageRegionIteratorWithIndex it(listOfImages[0], listOfImages[0]->GetLargestPossibleRegion() ); + while( !it.IsAtEnd() ) + { + const typename ImageType::IndexType currIndex = it.GetIndex(); + unsigned int currMaxIndex = 0; + typename ImageType::PixelType currMax = listOfImages[0]->GetPixel(currIndex); + typename ImageType::PixelType sum = currMax; + listOfImages[0]->SetPixel(currIndex, 0); + for( unsigned int im = 1; im < listOfImages.size(); im++ ) + { + const typename ImageType::PixelType currValue = listOfImages[im]->GetPixel(currIndex); + sum += currValue; + if( currValue > currMax ) + { + currMax = currValue; + currMaxIndex = im; + } + listOfImages[im]->SetPixel(currIndex, 0); + } + listOfImages[currMaxIndex]->SetPixel(currIndex, sum); + ++it; + } + + return; +} + +#endif + +template +typename ByteImageType::Pointer ComputeForegroundProbMask( + const std::vector & probList, const std::vector & IsForegroundPriorVector ) +{ + muLogMacro(<< "ComputeForegroundProbMask" << std::endl ); + const unsigned int numPriors = probList.size(); + typename ByteImageType::Pointer currForegroundMask = ByteImageType::New(); + currForegroundMask->CopyInformation(probList[0]); + currForegroundMask->SetRegions(probList[0]->GetLargestPossibleRegion() ); + currForegroundMask->Allocate(); + + const typename TProbabilityImage::SizeType size = probList[0]->GetLargestPossibleRegion().GetSize(); + const typename ByteImageType::PixelType insideMaskValue = 1; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + FloatingPrecision tmp = 0.0; + for( unsigned int iprior = 0; iprior < numPriors; iprior++ ) + { + const bool fgflag = IsForegroundPriorVector[iprior]; + if( fgflag == true ) + { + tmp += probList[iprior]->GetPixel(currIndex); + } + } + if( tmp > 0.5 ) // Only include if the sum of the non-background + // priors are greater than 50 % + { + currForegroundMask->SetPixel(currIndex, static_cast(insideMaskValue) ); + } + else + { + currForegroundMask->SetPixel(currIndex, 0); + } + } + } + } + } +#if 0 + { + // Pre-Dilate mask + typedef itk::BinaryBallStructuringElement StructElementType; + typedef + itk::BinaryDilateImageFilter DilateType; + + StructElementType structel; + structel.SetRadius(1); + structel.CreateStructuringElement(); + + typename DilateType::Pointer dil = DilateType::New(); + dil->SetDilateValue(50); + dil->SetKernel(structel); + dil->SetInput(currForegroundMask); + + dil->Update(); + + ByteImagePointer dilmask = dil->GetOutput(); + // a simple assignment is probably sufficient, test both ways? + currForegroundMask = CopyImage(dilmask); + } +#endif + return currForegroundMask; +} + +#endif // __BRAINSABCUtilities__txx__ diff --git a/BRAINSABC/brainseg/BRAINSABCimple.xml b/BRAINSABC/brainseg/BRAINSABCimple.xml new file mode 100644 index 00000000..b5ea6f79 --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSABCimple.xml @@ -0,0 +1,15 @@ + + + + BRAINSABCimple + + + Simple Versiont of itkEM for plug in other registration. + + + + NEED TO ADD + Regina . + + + diff --git a/BRAINSABC/brainseg/BRAINSCleanMask.cxx b/BRAINSABC/brainseg/BRAINSCleanMask.cxx new file mode 100644 index 00000000..b193a92f --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSCleanMask.cxx @@ -0,0 +1,73 @@ +#include "CleanBrainLabelMap.h" +#include "itkIO.h" +#include "BRAINSCleanMaskCLP.h" +#include "BRAINSThreadControl.h" + +int main(int argc, char * *argv) +{ + PARSE_ARGS; + BRAINSUtils::SetThreadCount(numberOfThreads); + if( inputVolume == "" ) + { + std::cerr << "No input volume name given" << std::endl; + return 1; + } + if( outputVolume == "" ) + { + std::cerr << "No output volume name given" << std::endl; + return 1; + } + + typedef itk::Image ImageType; + + ImageType::Pointer input; + try + { + input = itkUtil::ReadImage(inputVolume); + } + catch( itk::ExceptionObject & e ) + { + std::cerr << "error reading " << inputVolume << std::endl + << e << std::endl; + return 1; + } + catch( ... ) + { + std::cerr << "Unable to open " << inputVolume << std::endl; + exit(1); + } + ImageType::Pointer output; + try + { + output = CleanBrainLabelMap(input); + } + catch( itk::ExceptionObject & e ) + { + std::cerr << e << std::endl; + return 1; + } + catch( ... ) + { + std::cerr << "Error during processing of " + << inputVolume << std::endl; + return 1; + } + + try + { + itkUtil::WriteImage(output, outputVolume); + } + catch( itk::ExceptionObject & e ) + { + std::cerr << "error writing " << inputVolume << std::endl + << e << std::endl; + return 1; + } + catch( ... ) + { + std::cerr << "Unable to write " << outputVolume << std::endl; + return 1; + } + return 0; +} + diff --git a/BRAINSABC/brainseg/BRAINSCleanMask.xml b/BRAINSABC/brainseg/BRAINSCleanMask.xml new file mode 100644 index 00000000..12e56247 --- /dev/null +++ b/BRAINSABC/brainseg/BRAINSCleanMask.xml @@ -0,0 +1,39 @@ + + + + BRAINS.Classify + BRAINSCleanMask + Cleans up a mask image by filling any holes + + + + + + inputVolume + + --inputVolume + i + input + The mask image to be cleaned up. + + + outputVolume + + --outputVolume + o + output + The cleaned mask image. + + + + + + numberOfThreads + numberOfThreads + + Explicitly specify the maximum number of threads to use. + -1 + + + + diff --git a/BRAINSABC/brainseg/CMakeLists.txt b/BRAINSABC/brainseg/CMakeLists.txt new file mode 100644 index 00000000..13b61e05 --- /dev/null +++ b/BRAINSABC/brainseg/CMakeLists.txt @@ -0,0 +1,103 @@ + +#mark_as_advanced(USE_DEBUG_IMAGE_VIEWER) +#if( USE_DEBUG_IMAGE_VIEWER ) +# if(NOT KWWidgets_SOURCE_DIR) +# find_package(KWWidgets REQUIRED) +# include(${KWWidgets_USE_FILE}) +# endif(NOT KWWidgets_SOURCE_DIR) +# add_definitions(-DUSE_DEBUG_IMAGE_VIEWER) +# find_path(DEBUG_IMAGE_VIEWER_INCLUDE_DIR DebugImageViewerClient.h ${CMAKE_INSTALL_PREFIX}/include) +# include_directories(${DEBUG_IMAGE_VIEWER_INCLUDE_DIR}) +#endif( USE_DEBUG_IMAGE_VIEWER ) + +include_directories( + ${BRAINSABC_SOURCE_DIR}/brainseg + ${BRAINSABC_SOURCE_DIR}/common +) +# ${CMAKE_CURRENT_SOURCE_DIR}/../qhull + +set(QHULL_SRCS + ../qhull/user.c + ../qhull/global.c + ../qhull/stat.c + ../qhull/io.c + ../qhull/geom2.c + ../qhull/poly2.c + ../qhull/merge.c + ../qhull/qhull.c + ../qhull/geom.c + ../qhull/poly.c + ../qhull/qset.c + ../qhull/mem.c + QHullMSTClusteringProcess.cxx + ) + +set(BRAINSABCCOMMONLIB_SRCS + ../common/Log.cxx + EMSParameters.h + EMSParameters.cxx + EMSegmentationFilter.h + EMSegmentationFilter.txx + EMSegmentationFilter_float+float.cxx + AtlasRegistrationMethod_float+float.cxx + AtlasDefinition.cxx + filterFloatImages.h + ExtractSingleLargestRegion.cxx + ExtractSingleLargestRegion.h + BRAINSABCUtilities.cxx + BRAINSABCUtilities.h +) + +set(CLP BRAINSABC) +if(0) # Build against Slicer + ## Include the Slicer macro for setting up default locations! + SlicerMacroBuildCLI( + NAME ${CLP} + LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h + TARGET_LIBRARIES BRAINSCommonLib ${ITK_LIBRARIES} ${OPTIONAL_DEBUG_LINK_LIBRARIES} + CLI_SHARED_LIBRARY_WRAPPER_CXX ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx + VERBOSE + ) +else() + SEMMacroBuildCLI( + NAME ${CLP} + LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h + TARGET_LIBRARIES BRAINSCommonLib ${ITK_LIBRARIES} ${OPTIONAL_DEBUG_LINK_LIBRARIES} + CLI_SHARED_LIBRARY_WRAPPER_CXX ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx + ADDITIONAL_SRCS ${BRAINSABCCOMMONLIB_SRCS} + VERBOSE + ) +endif() + + +if(0) + +set(${CLP}_SOURCE BRAINSABC.cxx ) +set(BRAINSABC_PRIMARY_SOURCE ${BRAINSABC_SOURCE_DIR}/brainseg/BRAINSABCPrimary.cxx) +CONFIGUREBRAINSORSLICERPROPERTIES(${CLP} BRAINSABCPrimary.xml "${${CLP}_SOURCE}" "${BRAINSABC_PRIMARY_SOURCE}" "BRAINSABCPrimary" "") +add_dependencies(BRAINSABCCOMMONLIB BRAINSABCPrimaryCLP.h) ## Needed to create proper library dependancies when building parallel +target_link_libraries( ${CLP} BRAINSABCCOMMONLIB) + + + + +set(CLP ESLR) +set(${CLP}_SOURCE ${CLP}.cxx ) +CONFIGUREBRAINSORSLICERPROPERTIES(${CLP} ${CLP}.xml "${${CLP}_SOURCE}" "" "main" "") +target_link_libraries( ${CLP} BRAINSABCCOMMONLIB ) + +set(CLP GenerateLabelMapFromProbabilityMap) +set(${CLP}_SOURCE ${CLP}.cxx ) +CONFIGUREBRAINSORSLICERPROPERTIES(${CLP} ${CLP}.xml "${${CLP}_SOURCE}" "" "main" "") +target_link_libraries( ${CLP} ${ITK_LIBRARIES}) + +## A utility program +add_executable(StandardizeMaskIntensity StandardizeMaskIntensity.cxx) +target_link_libraries(StandardizeMaskIntensity ${ITK_LIBRARIES}) + +set(CLP BRAINSCleanMask) +set(${CLP}_SOURCE ${CLP}.cxx) +CONFIGUREBRAINSORSLICERPROPERTIES(${CLP} ${CLP}.xml "${${CLP}_SOURCE}" "" "main" "") +target_link_libraries( ${CLP} ${ITK_LIBRARIES}) + +endif() diff --git a/BRAINSABC/brainseg/ComputeDistributions.h b/BRAINSABC/brainseg/ComputeDistributions.h new file mode 100644 index 00000000..b702c3be --- /dev/null +++ b/BRAINSABC/brainseg/ComputeDistributions.h @@ -0,0 +1,231 @@ +#ifndef __ComputeDistributions__h_ +#define __ComputeDistributions__h_ + +#include + +#define EXPP(x) vcl_exp( ( x ) ) +#define LOGP(x) vcl_log( ( x ) ) + +typedef itk::Image ByteImageType; + +template +void +CombinedComputeDistributions( const std::vector & SubjectCandidateRegions, + const std::vector & InputImagesList, + const std::vector & PosteriorsList, + std::vector & ListOfClassStatistics, // + // + // This + // + // is + // + // an + // + // output! + const unsigned int DebugLevel, + const bool logConvertValues + ) +{ + const LOOPITERTYPE numChannels = InputImagesList.size(); + const LOOPITERTYPE numClasses = PosteriorsList.size(); + + ListOfClassStatistics.clear(); + ListOfClassStatistics.resize(numClasses); + for( LOOPITERTYPE iclass = 0; iclass < numClasses; iclass++ ) + { + ListOfClassStatistics[iclass].resize(numChannels); + } + + typename TInputImage::SizeType size + = PosteriorsList[0]->GetLargestPossibleRegion().GetSize(); + + // Compute sum of posteriors for each class +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE iclass = 0; iclass < numClasses; iclass++ ) + { + const typename TProbabilityImage::ConstPointer currentProbImage = PosteriorsList[iclass].GetPointer(); + const typename ByteImageType::ConstPointer currentCandidateRegion = SubjectCandidateRegions[iclass].GetPointer(); + double tmp = 1e-20; // NOTE: vnl_math:eps is too small vnl_math::eps; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for reduction(+:tmp) default(shared) +#endif + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + if( currentCandidateRegion->GetPixel(currIndex) ) + { + const double currentProbValue = currentProbImage->GetPixel(currIndex); + tmp = tmp + currentProbValue; + } + } + } + } + } + ListOfClassStatistics[iclass].m_Weighting = tmp; + } + // Compute the means weighted by the probability of each value. + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE iclass = 0; iclass < (LOOPITERTYPE)numClasses; iclass++ ) + { + const typename TProbabilityImage::ConstPointer currentProbImage = PosteriorsList[iclass].GetPointer(); + const typename ByteImageType::ConstPointer currentCandidateRegion = + SubjectCandidateRegions[iclass].GetPointer(); + for( LOOPITERTYPE ichan = 0; ichan < numChannels; ichan++ ) + { + double muSum = 0.0; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) reduction(+:muSum) +#endif + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + if( currentCandidateRegion->GetPixel(currIndex) ) + { + const double currentProbValue = currentProbImage->GetPixel(currIndex); + const double currentInputValue = InputImagesList[ichan]->GetPixel(currIndex); + if( logConvertValues ) + { + muSum += currentProbValue * LOGP(currentInputValue); + } + else + { + muSum += currentProbValue * ( currentInputValue ); + } + } + } + } + } + } + ListOfClassStatistics[iclass].m_Means[ichan] = ( muSum ) / ( ListOfClassStatistics[iclass].m_Weighting ); + } + } + } + + // Compute the covariances + std::vector oldCovariances(ListOfClassStatistics.size() ); + if( (LOOPITERTYPE)oldCovariances.size() != numClasses ) + { + oldCovariances.clear(); + oldCovariances.resize(numClasses); + for( LOOPITERTYPE iclass = 0; iclass < numClasses; iclass++ ) + { + MatrixType C(numChannels, numChannels); + C.set_identity(); + C *= 1e-10; + oldCovariances[iclass] = C; + } + } + else // Copy from previous version. + { + for( LOOPITERTYPE iclass = 0; iclass < numClasses; iclass++ ) + { + oldCovariances[iclass] = ListOfClassStatistics[iclass].m_Covariance; + } + } + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE iclass = 0; iclass < (LOOPITERTYPE)numClasses; iclass++ ) + { + const typename TProbabilityImage::ConstPointer currentProbImage = PosteriorsList[iclass].GetPointer(); + const typename ByteImageType::ConstPointer currentCandidateRegion = + SubjectCandidateRegions[iclass].GetPointer(); + MatrixType covtmp(numChannels, numChannels, 0.0); + for( LOOPITERTYPE r = 0; r < numChannels; r++ ) + { + const double mu1 = ListOfClassStatistics[iclass].m_Means[r]; + typename TInputImage::Pointer img1 = InputImagesList[r]; + for( LOOPITERTYPE c = r; c < numChannels; c++ ) + { + const double mu2 = ListOfClassStatistics[iclass].m_Means[c]; + typename TInputImage::Pointer img2 = InputImagesList[c]; + double var = 0.0; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) reduction(+:var) +#endif + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const typename TInputImage::IndexType currIndex = {{ii, jj, kk}}; + if( currentCandidateRegion->GetPixel(currIndex) ) + { + const double currentProbValue = currentProbImage->GetPixel(currIndex); + if( logConvertValues ) + { + const double diff1 = LOGP( static_cast( img1->GetPixel(currIndex) ) ) - mu1; + const double diff2 = LOGP( static_cast( img2->GetPixel(currIndex) ) ) - mu2; + var += currentProbValue * ( diff1 * diff2 ); + } + else + { + const double diff1 = ( static_cast( img1->GetPixel(currIndex) ) ) - mu1; + const double diff2 = ( static_cast( img2->GetPixel(currIndex) ) ) - mu2; + var += currentProbValue * ( diff1 * diff2 ); + } + } + } + } + } + } + var /= ListOfClassStatistics[iclass].m_Weighting; + + // Adjust diagonal, to make sure covariance is pos-def + if( r == c ) + { + var += 1e-20; + } + + // Assign value to the covariance matrix (symmetric) + covtmp(r, c) = var; + covtmp(c, r) = var; + } + } + { + ListOfClassStatistics[iclass].m_Covariance = covtmp; + } + } // end covariance loop + } + if( DebugLevel > 5 ) + { + for( LOOPITERTYPE iclass = 0; iclass < (LOOPITERTYPE)numClasses; iclass++ ) + { + muLogMacro( + << "DEBUG USING NEW COVARIANCES: " << iclass << "\n" << ListOfClassStatistics[iclass].m_Covariance << std::endl ); + } + } + if( DebugLevel > 9 ) + { + std::cout << "=================================================" << std::endl; + for( LOOPITERTYPE iclass = 0; iclass < (LOOPITERTYPE)numClasses; iclass++ ) + { + for( LOOPITERTYPE ichan = 0; ichan < numChannels; ichan++ ) + { + muLogMacro( << "DEBUG MEAN " << ichan << " : " << iclass << " : \n" + << ListOfClassStatistics[iclass].m_Means[ichan] << " \n" << std::endl ); + } + muLogMacro( << "DEBUG Covariances: " << iclass << "\n" << ListOfClassStatistics[iclass].m_Covariance << std::endl ); + } + } +} + +#endif // __ComputeDistributions__h__ diff --git a/BRAINSABC/brainseg/DenoiseFiltering.h b/BRAINSABC/brainseg/DenoiseFiltering.h new file mode 100644 index 00000000..b2a1482d --- /dev/null +++ b/BRAINSABC/brainseg/DenoiseFiltering.h @@ -0,0 +1,127 @@ +#ifndef __DenoiseFiltering_h +#define __DenoiseFiltering_h + +#include "itkCurvatureFlowImageFilter.h" +#include "itkGradientAnisotropicDiffusionImageFilter.h" + +// TODO: BRAINSFit currently has an option for doing a median filter to remove +// noise, +// this should be expanded to allow for a richer set of pre-filter +// denoising operations +// such as the anisotropic diffusion denoising options. +// This should be made into a strategy pattern class that is dynamically +// selectable at runtime. +// + +template +// TODO: Input and outputs should be templated separately? +typename TInputImageType::Pointer DenoiseFiltering( + typename TInputImageType::Pointer img, + const std::string PrefilteringMethod, // Select the type of denoising to + // do + const unsigned int PrefilteringIterations, // Only used in AD and CF + const double PrefilteringTimeStep, // Only used in AD and CF + const std::vector // gridSize //Only used in median + // filtering + ) +{ + + typename TInputImageType::Pointer denoisedImage = NULL; + if( PrefilteringMethod.compare("GradientAnisotropicDiffusion") == 0 && PrefilteringIterations > 0 ) + { + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "Prefiltering with " << PrefilteringMethod << " (Iters=" << PrefilteringIterations + << ",TimeStep=" << PrefilteringTimeStep << ") gridSize=(" << ")" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + typedef itk::GradientAnisotropicDiffusionImageFilter AnisoFilterType; + typename AnisoFilterType::Pointer anisofilt = AnisoFilterType::New(); + + anisofilt->SetInput(img); + anisofilt->SetConductanceParameter(1); + anisofilt->SetNumberOfIterations(PrefilteringIterations); + anisofilt->SetTimeStep(PrefilteringTimeStep); + anisofilt->Update(); + + denoisedImage = anisofilt->GetOutput(); + } + else if( PrefilteringMethod.compare("CurvatureFlow") == 0 && PrefilteringIterations > 0 ) + { + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "Prefiltering with " << PrefilteringMethod << " (Iters=" << PrefilteringIterations + << ",TimeStep=" << PrefilteringTimeStep << ") gridSize=(" << ")" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^" << std::endl; + typedef itk::CurvatureFlowImageFilter CurvatureFilterType; + typename CurvatureFilterType::Pointer cfilt = CurvatureFilterType::New(); + cfilt->SetInput(img); + cfilt->SetNumberOfIterations(PrefilteringIterations); + cfilt->SetTimeStep(PrefilteringTimeStep); + cfilt->Update(); + + denoisedImage = cfilt->GetOutput(); + } + else if( PrefilteringMethod.compare("MedianFilter") == 0 ) + { + // TODO: Kent put a median filter in here, with filter radius equal to 1. + } + + if( denoisedImage.IsNotNull() ) + { + return denoisedImage; + } + // else No filtering. + return img; +} + +#if 0 +< !--Standard options for the denoising phase of a program-- > +< integer - vector > +< name > medianFilterSize +< longflag > medianFilterSize +< label > Median Filter Size +< description > The radius for the optional MedianImageFilter preprocessing in all 3 directions.< / description > +< default > 0, 0, 0 < / default > +< / integer - vector > +< integer > +< name > filterIteration +< description > Filter iterations +< label > Filter Iterations +< longflag > filterIteration +< default > 10 < / default > +< constraints > +< minimum > 0 < / minimum > +< maximum > 50 < / maximum > +< step > 1 < / step > +< / constraints > +< / integer > +< float > +< name > filterTimeStep +< description > Filter time step +< label > Filter Time Step +< longflag > filterTimeStep +< default > 0.01 < / default > +< constraints > +< minimum > 0 < / minimum > +< maximum > 0.5 < / maximum > +< step > 0.01 < / step > +< / constraints > +< / float > +< string - enumeration > +< name > filterMethod +< label > Filter Method +< longflag > filterMethod +< description > Filter method for preprocessing of registration +< element > None +< element > CurvatureFlow +< element > GradientAnisotropicDiffusion +< element > Median +< default > None +< / string - enumeration > +#endif + +#endif diff --git a/BRAINSABC/brainseg/EMSParameters.cxx b/BRAINSABC/brainseg/EMSParameters.cxx new file mode 100644 index 00000000..54489e35 --- /dev/null +++ b/BRAINSABC/brainseg/EMSParameters.cxx @@ -0,0 +1,154 @@ +#include "EMSParameters.h" + +#include "itksys/SystemTools.hxx" + +EMSParameters +::EMSParameters() +{ + m_Suffix = ""; + + m_AtlasDirectory = ""; + + m_AtlasOrientation = "RAI"; + + m_DoAtlasWarp = true; + + m_OutputDirectory = ""; + m_OutputFormat = "Meta"; + + m_Images.clear(); + m_ImageOrientations.clear(); + + m_FilterMethod = "CurvatureFlow"; + m_FilterIterations = 1; + m_FilterTimeStep = 0.01; + + m_MaxBiasDegree = 4; + + m_AtlasWarpGridX = 5; + m_AtlasWarpGridY = 5; + m_AtlasWarpGridZ = 5; + + m_Prior1 = 1.0; + m_Prior2 = 1.0; + m_Prior3 = 1.0; + m_Prior4 = 1.0; + + m_AtlasLinearMapType = "BSpline"; + m_ImageLinearMapType = "Rigid"; +} + +EMSParameters +::~EMSParameters() +{ +} + +void +EMSParameters +::AddImage(std::string s, std::string orient) +{ + m_Images.push_back(s); + m_ImageOrientations.push_back(orient); +} + +void +EMSParameters +::ClearImages() +{ + m_Images.clear(); + m_ImageOrientations.clear(); +} + +bool +EMSParameters +::CheckValues() const +{ + if( m_Suffix.length() == 0 ) + { + std::cerr << "Invalid Suffix length" << std::endl; + return false; + } + + if( m_AtlasDirectory.length() == 0 ) + { + std::cerr << "Invalid Atlas Directory" << std::endl; + return false; + } + + if( m_OutputDirectory.length() == 0 ) + { + std::cerr << "Invalid OutputDirectory" << std::endl; + return false; + } + + bool validFormat = false; + if( itksys::SystemTools::Strucmp(m_OutputFormat.c_str(), "Analyze") == 0 ) + { + validFormat = true; + } + if( itksys::SystemTools::Strucmp(m_OutputFormat.c_str(), "GIPL") == 0 ) + { + validFormat = true; + } + if( itksys::SystemTools::Strucmp(m_OutputFormat.c_str(), "Nrrd") == 0 ) + { + validFormat = true; + } + if( itksys::SystemTools::Strucmp(m_OutputFormat.c_str(), "Meta") == 0 ) + { + validFormat = true; + } + if( itksys::SystemTools::Strucmp(m_OutputFormat.c_str(), "NIFTI") == 0 ) + { + validFormat = true; + } + + if( !validFormat ) + { + std::cerr << "No valid image format defined." << std::endl; + return false; + } + + if( m_Images.empty() ) + { + std::cerr << "Images not defined." << std::endl; + return false; + } + + return true; +} + +void +EMSParameters +::PrintSelf(std::ostream & os, itk::Indent) const +{ + os << "Suffix = " << m_Suffix << std::endl; + os << "Atlas directory = " << m_AtlasDirectory << std::endl; + os << "Atlas orientation = " << m_AtlasOrientation << std::endl; + os << "Output directory = " << m_OutputDirectory << std::endl; + os << "Output format = " << m_OutputFormat << std::endl; + os << "Images:" << std::endl; + for( unsigned int k = 0; k < m_Images.size(); k++ ) + { + os << " " << m_Images[k] << " --- " << m_ImageOrientations[k] << std::endl; + } + os << "Filter iterations = " << m_FilterIterations << std::endl; + os << "Filter time step = " << m_FilterTimeStep << std::endl; + os << "Max bias degree = " << m_MaxBiasDegree << std::endl; + os << "Prior 1 = " << m_Prior1 << std::endl; + os << "Prior 2 = " << m_Prior2 << std::endl; + os << "Prior 3 = " << m_Prior3 << std::endl; + os << "Prior 4 = " << m_Prior4 << std::endl; + if( m_DoAtlasWarp ) + { + os << "Atlas warping, grid = " + << m_AtlasWarpGridX << "x" + << m_AtlasWarpGridY << "x" + << m_AtlasWarpGridZ << std::endl; + } + else + { + os << "No atlas warping..." << std::endl; + } +} + diff --git a/BRAINSABC/brainseg/EMSParameters.h b/BRAINSABC/brainseg/EMSParameters.h new file mode 100644 index 00000000..35907d4e --- /dev/null +++ b/BRAINSABC/brainseg/EMSParameters.h @@ -0,0 +1,132 @@ +#ifndef __EMSParameters_h +#define __EMSParameters_h + +#include "itkObject.h" +#include "itkObjectFactory.h" + +#include +#include + +#include + +/** + * \class EMSParameters + */ +class EMSParameters : public itk::Object +{ +public: + + typedef EMSParameters Self; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + itkNewMacro(Self); + + // Make sure all values are OK + virtual bool CheckValues() const; + + virtual void PrintSelf(std::ostream & os, itk::Indent) const; + + itkGetConstMacro(Suffix, std::string); + itkSetMacro(Suffix, std::string); + + itkGetConstMacro(AtlasDirectory, std::string); + itkSetMacro(AtlasDirectory, std::string); + + itkGetConstMacro(AtlasOrientation, std::string); + itkSetMacro(AtlasOrientation, std::string); + + itkGetConstMacro(DoAtlasWarp, bool); + itkSetMacro(DoAtlasWarp, bool); + + itkGetConstMacro(OutputDirectory, std::string); + itkSetMacro(OutputDirectory, std::string); + + itkGetConstMacro(OutputFormat, std::string); + itkSetMacro(OutputFormat, std::string); + + void AddImage(std::string s, std::string orientation); + + void ClearImages(); + + std::vector GetImages() + { + return m_Images; + } + + std::vector GetImageOrientations() + { + return m_ImageOrientations; + } + + itkGetConstMacro(FilterMethod, std::string); + itkSetMacro(FilterMethod, std::string); + + itkGetConstMacro(FilterIterations, unsigned int); + itkSetMacro(FilterIterations, unsigned int); + + itkGetConstMacro(FilterTimeStep, float); + itkSetMacro(FilterTimeStep, float); + + itkGetConstMacro(MaxBiasDegree, unsigned int); + itkSetMacro(MaxBiasDegree, unsigned int); + + itkGetConstMacro(AtlasWarpGridX, unsigned int); + itkSetMacro(AtlasWarpGridX, unsigned int); + itkGetConstMacro(AtlasWarpGridY, unsigned int); + itkSetMacro(AtlasWarpGridY, unsigned int); + itkGetConstMacro(AtlasWarpGridZ, unsigned int); + itkSetMacro(AtlasWarpGridZ, unsigned int); + + itkGetConstMacro(Prior1, float); + itkSetMacro(Prior1, float); + itkGetConstMacro(Prior2, float); + itkSetMacro(Prior2, float); + itkGetConstMacro(Prior3, float); + itkSetMacro(Prior3, float); + itkGetConstMacro(Prior4, float); + itkSetMacro(Prior4, float); + + itkGetConstMacro(AtlasLinearMapType, std::string); + itkSetMacro(AtlasLinearMapType, std::string); + + itkGetConstMacro(ImageLinearMapType, std::string); + itkSetMacro(ImageLinearMapType, std::string); +protected: + + EMSParameters(); + ~EMSParameters(); + + std::string m_Suffix; + + std::string m_AtlasDirectory; + std::string m_AtlasOrientation; + + bool m_DoAtlasWarp; + + unsigned int m_AtlasWarpGridX; + unsigned int m_AtlasWarpGridY; + unsigned int m_AtlasWarpGridZ; + + std::string m_OutputDirectory; + std::string m_OutputFormat; + + std::vector m_Images; + std::vector m_ImageOrientations; + + std::string m_FilterMethod; + unsigned int m_FilterIterations; + float m_FilterTimeStep; + + unsigned int m_MaxBiasDegree; + + float m_Prior1; + float m_Prior2; + float m_Prior3; + float m_Prior4; + + std::string m_AtlasLinearMapType; + std::string m_ImageLinearMapType; +}; + +#endif diff --git a/BRAINSABC/brainseg/EMSegmentationFilter.h b/BRAINSABC/brainseg/EMSegmentationFilter.h new file mode 100644 index 00000000..030610a7 --- /dev/null +++ b/BRAINSABC/brainseg/EMSegmentationFilter.h @@ -0,0 +1,324 @@ +// +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Atlas based segmentation using the Expectation Maximization algorithm +// +// Designed for 3D MRI originally inspired by prastawa@cs.unc.edu 3/2004 +// +// Van Leemput K, Maes F, Vandermeulen D, Suetens P. Automated model based +// tissue classification of MR images of the brain. IEEE TMI 1999; 18:897-908. +// +// +// +// ////////////////////////////////////////////////////////////////////////////// +#ifndef __EMSegmentationFilter_h +#define __EMSegmentationFilter_h + +#include "BRAINSABCUtilities.h" + +class AtlasDefinition; + +/** + * \class EMSegmentationFilter + */ +template +class EMSegmentationFilter : public itk::ProcessObject +{ +public: + + // Standard class typedefs + typedef EMSegmentationFilter Self; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + // Method for creation through the object factory + itkNewMacro(Self); + + // The dimension of the image we're working with + itkStaticConstMacro(ImageDimension, unsigned int, + TInputImage::ImageDimension); + + typedef typename std::map > RangeDBType; + // Image types + typedef TInputImage InputImageType; + typedef typename TInputImage::Pointer InputImagePointer; + typedef typename TInputImage::IndexType InputImageIndexType; + typedef typename TInputImage::OffsetType InputImageOffsetType; + typedef typename TInputImage::PixelType InputImagePixelType; + typedef typename TInputImage::RegionType InputImageRegionType; + typedef typename TInputImage::SizeType InputImageSizeType; + typedef typename TInputImage::SpacingType InputImageSpacingType; + + typedef typename ByteImageType::Pointer ByteImagePointer; + typedef typename ByteImageType::IndexType ByteImageIndexType; + typedef typename ByteImageType::OffsetType ByteImageOffsetType; + typedef typename ByteImageType::PixelType ByteImagePixelType; + typedef typename ByteImageType::RegionType ByteImageRegionType; + typedef typename ByteImageType::SizeType ByteImageSizeType; + + typedef itk::Image ShortImageType; + typedef typename ShortImageType::Pointer ShortImagePointer; + typedef typename ShortImageType::IndexType ShortImageIndexType; + typedef typename ShortImageType::OffsetType ShortImageOffsetType; + typedef typename ShortImageType::PixelType ShortImagePixelType; + typedef typename ShortImageType::RegionType ShortImageRegionType; + typedef typename ShortImageType::SizeType ShortImageSizeType; + + typedef TProbabilityImage ProbabilityImageType; + typedef typename ProbabilityImageType::Pointer ProbabilityImagePointer; + typedef typename ProbabilityImageType::IndexType ProbabilityImageIndexType; + typedef typename ProbabilityImageType::OffsetType ProbabilityImageOffsetType; + typedef typename ProbabilityImageType::PixelType ProbabilityImagePixelType; + typedef typename ProbabilityImageType::RegionType ProbabilityImageRegionType; + typedef typename ProbabilityImageType::SizeType ProbabilityImageSizeType; + typedef typename ProbabilityImageType::SpacingType ProbabilityImageSpacingType; + + typedef vnl_vector VectorType; + typedef vnl_vector IntVectorType; + typedef std::vector BoolVectorType; + typedef vnl_matrix MatrixType; + typedef vnl_matrix_inverse MatrixInverseType; + + typedef BSplineTransformType::Pointer BSplineTransformPointer; + + // Set/Get the maximum polynomial degree of the bias field estimate + itkSetMacro(MaxBiasDegree, unsigned int); + itkGetMacro(MaxBiasDegree, unsigned int); + // + // Set/Get the Debugging level for filter verboseness + itkSetMacro(DebugLevel, unsigned int); + itkGetMacro(DebugLevel, unsigned int); + + itkSetMacro(BiasLikelihoodTolerance, FloatingPrecision); + itkGetMacro(BiasLikelihoodTolerance, FloatingPrecision); + + itkSetMacro(OutputDebugDir, std::string); + itkGetMacro(OutputDebugDir, std::string); + + itkSetMacro(LikelihoodTolerance, FloatingPrecision); + itkGetMacro(LikelihoodTolerance, FloatingPrecision); + + itkSetMacro(MaximumIterations, unsigned int); + itkGetMacro(MaximumIterations, unsigned int); + + itkSetMacro(SampleSpacing, FloatingPrecision); + itkGetMacro(SampleSpacing, FloatingPrecision); + + void SetInputImages(const std::vector & newInputImages); + + void SetRawInputImages(const std::vector & newInputImages); + + void SetOriginalAtlasImages(const std::vector & newTemplateImages); + + // + // itkGetMacro(WarpedAtlasImages,std::vector); + std::vector GenerateWarpedAtlasImages(void); + + itkSetMacro(TemplateBrainMask, ByteImagePointer); + itkGetMacro(TemplateBrainMask, ByteImagePointer); + + // Get and set the input volume image types. i.e. T1 or T2 or PD + void SetInputVolumeTypes(const std::vector & newInputVolumeTypes) + { + this->m_InputVolumeTypes = newInputVolumeTypes; + } + + std::vector GetInputVolumeTypes(void) const + { + return this->m_InputVolumeTypes; + } + + void SetPriors(std::vector probs); + + void SetPriorWeights(VectorType w); + + IntVectorType GetPriorLabelCodeVector( void ) const + { + return m_PriorLabelCodeVector; + } + + void SetPriorLabelCodeVector(IntVectorType n); + + BoolVectorType GetPriorUseForBiasVector( void ) const + { + return m_PriorUseForBiasVector; + } + + void SetPriorUseForBiasVector(const BoolVectorType& n); + + BoolVectorType GetPriorIsForegroundPriorVector( void ) const + { + return m_PriorIsForegroundPriorVector; + } + + void SetPriorIsForegroundPriorVector(const BoolVectorType& n); + + void SetPriorNames(const std::vector & newPriorNames) + { + this->m_PriorNames = newPriorNames; + } + + std::vector GetPriorNames(void) const + { + return this->m_PriorNames; + } + + ByteImagePointer GetOutput(void); + + ByteImagePointer GetCleanedOutput(void); + + std::vector GetPosteriors(); + + std::vector GetCorrected(); + + std::vector GetRawCorrected(); + + void Update(); + + itkGetMacro(AtlasTransformType, std::string); + itkSetMacro(AtlasTransformType, std::string); + + // Standard ITK style get/set macros for DoWarp + itkGetMacro(UpdateTransformation, bool); + itkSetMacro(UpdateTransformation, bool); + itkBooleanMacro(UpdateTransformation); + + /* For backwards compatibility */ + /* + void WarpingOn() { this->SetDoWarp(true); } + void WarpingOff() { this->SetDoWarp(false); } + */ + + itkGetMacro(TemplateGenericTransform, GenericTransformType::Pointer); + itkSetMacro(TemplateGenericTransform, GenericTransformType::Pointer); + + void SetWarpGrid(unsigned int gx, unsigned int gy, unsigned int gz) + { + m_WarpGrid[0] = gx; + m_WarpGrid[1] = gy; + m_WarpGrid[2] = gz; + this->Modified(); + } + + void SetTissueTypeThresholdMapsRange(const RangeDBType & newRangeDB) + { + this->m_TissueTypeThresholdMapsRange = newRangeDB; + this->Modified(); + } + +protected: + + EMSegmentationFilter(void); + ~EMSegmentationFilter(void); + + void CheckInput(void); + + FloatingPrecision ComputeLogLikelihood(void) const; + + void EMLoop(void); + + void UpdateTransformation(const unsigned int CurrentEMIteration); + + std::vector UpdateIntensityBasedClippingOfPriors( + const unsigned int CurrentEMIteration, const std::vector &intensityList, + std::vector &WarpedPriorsList, typename ByteImageType::Pointer NonAirRegion); + + std::vector ForceToOne( + const unsigned int CurrentEMIteration, const std::vector &intensityList, + std::vector &WarpedPriorsList, typename ByteImageType::Pointer NonAirRegion); +private: + + void WritePartitionTable(const unsigned int CurrentEMIteration) const; + + void WriteDebugLabels(const unsigned int CurrentEMIteration) const; + + void WriteDebugHeadRegion(const unsigned int CurrentEMIteration) const; + + void WriteDebugPosteriors(const unsigned int CurrentEMIteration) const; + + void WriteDebugBlendClippedPriors(const unsigned int CurrentEMIteration) const; + + void WriteDebugWarpedAtlasPriors(const unsigned int CurrentEMIteration) const; + + void WriteDebugWarpedAtlasImages(const unsigned int CurrentEMIteration) const; + + void WriteDebugForegroundMask(const ByteImageType::Pointer & currForegroundMask, + const unsigned int CurrentEMIteration) const; + + void WriteDebugCorrectedImages(const std::vector & correctImageList, + const unsigned int CurrentEMIteration ) const; + + unsigned int ComputePriorLookupTable(void); + + void InitializePosteriors(void); + + std::vector m_WarpedPriors; + std::vector m_OriginalSpacePriors; + std::vector m_Posteriors; + + std::string m_AtlasTransformType; + + // Variable set if the inputs are modified + std::vector m_InputImages; + std::vector m_RawInputImages; + std::vector m_CorrectedImages; + std::vector m_RawCorrectedImages; + std::vector m_InputVolumeTypes; + + ByteImagePointer m_TemplateBrainMask; + std::vector m_OriginalAtlasImages; + std::vector m_WarpedAtlasImages; + + // final output + ByteImagePointer m_DirtyLabels; + ByteImagePointer m_CleanedLabels; + + // exclude region from outside image space created by warping an all ones + // image with zero default value, anded across images + ByteImagePointer m_NonAirRegion; + + FloatingPrecision m_SampleSpacing; + + unsigned int m_MaxBiasDegree; + FloatingPrecision m_BiasLikelihoodTolerance; + FloatingPrecision m_LikelihoodTolerance; + unsigned int m_MaximumIterations; + + VectorType m_PriorWeights; + bool m_PriorWeightsSet; + + IntVectorType m_PriorLabelCodeVector; + bool m_PriorLabelCodeVectorSet; + + BoolVectorType m_PriorUseForBiasVector; + bool m_PriorUseForBiasVectorSet; + + BoolVectorType m_PriorIsForegroundPriorVector; + bool m_PriorIsForegroundPriorVectorSet; + + std::vector m_PriorsBackgroundValues; + + std::string m_OutputDebugDir; + + std::vector m_ListOfClassStatistics; + + bool m_UpdateTransformation; + unsigned int m_DebugLevel; + + GenericTransformType::Pointer m_TemplateGenericTransform; + unsigned int m_WarpGrid[3]; + + FloatingPrecision m_WarpLikelihoodTolerance; + bool m_UpdateRequired; + + std::vector m_PriorNames; + std::vector m_ClassToPriorMapping; + RangeDBType m_TissueTypeThresholdMapsRange; +}; + +#ifndef MU_MANUAL_INSTANTIATION +#include "EMSegmentationFilter.txx" +#endif + +#endif diff --git a/BRAINSABC/brainseg/EMSegmentationFilter.txx b/BRAINSABC/brainseg/EMSegmentationFilter.txx new file mode 100644 index 00000000..215d84c9 --- /dev/null +++ b/BRAINSABC/brainseg/EMSegmentationFilter.txx @@ -0,0 +1,1839 @@ +#ifndef __EMSegmentationFilter_txx +#define __EMSegmentationFilter_txx + +#include +#include +#include +#include + +#include +#include + +#include "itkAddImageFilter.h" +#include "itkBSplineDownsampleImageFilter.h" +#include "itkBinaryBallStructuringElement.h" +#include "itkBinaryDilateImageFilter.h" +#include "itkBinaryErodeImageFilter.h" +#include "itkBinaryThresholdImageFilter.h" +#include "itkBlendImageFilter.h" +#include "itkConnectedComponentImageFilter.h" +#include "itkDiscreteGaussianImageFilter.h" +#include "itkHistogramMatchingImageFilter.h" +#include "itkImageDuplicator.h" +#include "itkImageRegionConstIterator.h" +#include "itkImageRegionIterator.h" +#include "itkMinimumMaximumImageCalculator.h" +#include "itkMultiModeHistogramThresholdBinaryImageFilter.h" +#include "itkMultiplyImageFilter.h" +#include "itkNumericTraits.h" +#include "itkRelabelComponentImageFilter.h" +#include "itkResampleImageFilter.h" +// #include "itkMersenneTwisterRandomVariateGenerator.h" + +#include "vnl/algo/vnl_determinant.h" +#include "vnl/vnl_math.h" + +#include "itkBRAINSROIAutoImageFilter.h" +#include "BRAINSFitBSpline.h" +#include "BRAINSFitUtils.h" + +// #include "QHullMSTClusteringProcess.h" +#include "AtlasDefinition.h" +#include "EMSegmentationFilter.h" +#include "ExtractSingleLargestRegion.h" +#include "PrettyPrintTable.h" +#include "ComputeDistributions.h" + +template +EMSegmentationFilter +::EMSegmentationFilter() +{ + + m_DirtyLabels = NULL; + m_CleanedLabels = NULL; + + m_SampleSpacing = 2.0; + + // Bias + m_MaxBiasDegree = 4; + m_BiasLikelihoodTolerance = 1e-2; + // NOTE: warp tol needs to be <= bias tol + m_WarpLikelihoodTolerance = 1e-3; + + // EM convergence parameters + m_LikelihoodTolerance = 1e-5; + m_MaximumIterations = 40; + + m_PriorWeights = VectorType(0); + m_PriorWeightsSet = false; + + // m_PriorGaussianClusterCountVector = IntVectorType(0); + // m_PriorGaussianClusterCountVectorSet=false; + + m_PriorLabelCodeVector = IntVectorType(0); + m_PriorLabelCodeVectorSet = false; + + m_PriorUseForBiasVector = BoolVectorType(0); + m_PriorUseForBiasVectorSet = false; + + m_PriorIsForegroundPriorVector = BoolVectorType(false); + m_PriorIsForegroundPriorVectorSet = false; + + m_PriorsBackgroundValues.resize(0); + + m_WarpedPriors.clear(); + m_OriginalSpacePriors.clear(); + m_Posteriors.clear(); + + m_InputImages.clear(); + m_RawInputImages.clear(); + m_CorrectedImages.clear(); + m_RawCorrectedImages.clear(); + m_InputVolumeTypes.clear(); + + m_TemplateBrainMask = NULL; + m_OriginalAtlasImages.clear(); + m_WarpedAtlasImages.clear(); + + m_OutputDebugDir = ""; + // m_PriorLookupTable = IntVectorType(0); + + m_NonAirRegion = 0; + + m_AtlasTransformType = "BSpline"; + + m_UpdateTransformation = false; + + m_DebugLevel = 0; + + m_TemplateGenericTransform = NULL; + + m_WarpGrid[0] = 5; + m_WarpGrid[1] = 5; + m_WarpGrid[2] = 5; + + m_UpdateRequired = true; + + this->m_PriorNames.clear(); + // m_ClassToPriorMapping.clear(); +} + +template +EMSegmentationFilter +::~EMSegmentationFilter() +{ +} + +template +void +EMSegmentationFilter +::CheckInput() +{ + if( m_WarpedPriors.size() < 1 ) + { + itkExceptionMacro(<< "Must have one or more class probabilities" << std::endl ); + } + + if( m_PriorWeightsSet == false ) + { + itkExceptionMacro(<< "The PriorWeights were not set." << std::endl ); + } + if( m_PriorLabelCodeVectorSet == false ) + { + itkExceptionMacro(<< "The PriorLabelCodeVector was not set." << std::endl ); + } + if( m_PriorUseForBiasVectorSet == false ) + { + itkExceptionMacro(<< "The PriorUseForBiasVector was not set." << std::endl ); + } + if( m_PriorIsForegroundPriorVectorSet == false ) + { + itkExceptionMacro(<< "The PriorIsForegroundPriorVector was not set." << std::endl ); + } + + if( m_WarpedPriors.size() != m_PriorWeights.size() ) + { + itkExceptionMacro(<< "The PriorWeights vector size must match the number of priors listed." << std::endl ); + } + if( m_WarpedPriors.size() != m_PriorLabelCodeVector.size() ) + { + itkExceptionMacro(<< "The PriorLabelCodeVector vector size must match the number of priors listed." << std::endl ); + } + if( m_WarpedPriors.size() != m_PriorUseForBiasVector.size() ) + { + itkExceptionMacro(<< "The PriorUseForBiasVector vector size must match the number of priors listed." << std::endl ); + } + if( m_WarpedPriors.size() != m_PriorIsForegroundPriorVector.size() ) + { + itkExceptionMacro( + << "The PriorIsForegroundPriorVector vector size must match the number of priors listed." << std::endl ); + } + + if( m_MaximumIterations == 0 ) + { + itkWarningMacro(<< "Maximum iterations set to zero" << std::endl ); + } + + if( m_InputImages.empty() ) + { + itkExceptionMacro(<< "No input images" << std::endl ); + } + + { + const InputImageSizeType size = m_InputImages[0]->GetLargestPossibleRegion().GetSize(); + for( unsigned i = 1; i < m_InputImages.size(); i++ ) + { + if( m_InputImages[i]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "InputImage [" << i << "] has invalid dimension: only supports 3D images" << std::endl ); + } + const InputImageSizeType isize = m_InputImages[i]->GetLargestPossibleRegion().GetSize(); + if( size != isize ) + { + itkExceptionMacro( + << "Image data [" << i << "] 3D size mismatch " << size << " != " << isize << "." << std::endl ); + } + } + for( unsigned i = 0; i < m_WarpedPriors.size(); i++ ) + { + if( m_WarpedPriors[i]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "Warped Prior [" << i << "] has invalid dimension: only supports 3D images" << std::endl ); + } + const ProbabilityImageSizeType psize = m_WarpedPriors[i]->GetLargestPossibleRegion().GetSize(); + if( size != psize ) + { + itkExceptionMacro( + << "Warped prior [" << i << "] and atlas data 3D size mismatch" << size << " != " << psize << "." + << std::endl ); + } + } + } + + { + const InputImageSizeType atlasSize = m_OriginalAtlasImages[0]->GetLargestPossibleRegion().GetSize(); + for( unsigned i = 1; i < m_OriginalAtlasImages.size(); i++ ) + { + if( m_OriginalAtlasImages[i]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "Atlas Image [" << i << "] has invalid dimension: only supports 3D images" << std::endl ); + } + const InputImageSizeType asize = m_OriginalAtlasImages[i]->GetLargestPossibleRegion().GetSize(); + if( atlasSize != asize ) + { + itkExceptionMacro( + << "Image data [" << i << "] 3D size mismatch " << atlasSize << " != " << asize << "." << std::endl ); + } + } + for( unsigned i = 0; i < m_OriginalSpacePriors.size(); i++ ) + { + if( m_OriginalSpacePriors[i]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "Prior [" << i << "] has invalid dimension: only supports 3D images" << std::endl ); + } + const ProbabilityImageSizeType psize = m_OriginalSpacePriors[i]->GetLargestPossibleRegion().GetSize(); + if( atlasSize != psize ) + { + itkExceptionMacro( + << "Normalized prior [" << i << "] and atlas 3D size mismatch" << atlasSize << " != " << psize << "." + << std::endl ); + } + } + } +} + +template +void +EMSegmentationFilter +::SetInputImages(const std::vector & newInputImages) +{ + + muLogMacro(<< "SetInputImages" << std::endl); + + if( newInputImages.size() == 0 ) + { + itkExceptionMacro(<< "No input images" << std::endl ); + } + + m_InputImages = newInputImages; + + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetRawInputImages(const std::vector & newInputImages) +{ + + muLogMacro(<< "SetRawInputImages" << std::endl); + + if( newInputImages.size() == 0 ) + { + itkExceptionMacro(<< "No input images" << std::endl ); + } + + m_RawInputImages = newInputImages; + + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetOriginalAtlasImages(const std::vector & newAtlasImages) +{ + muLogMacro(<< "SetAtlasImages" << std::endl); + + if( newAtlasImages.size() == 0 ) + { + itkExceptionMacro(<< "No template images" << std::endl ); + } + m_OriginalAtlasImages = newAtlasImages; + + this->Modified(); + m_UpdateRequired = true; +} + +template +void EMSegmentationFilter +::WriteDebugPosteriors(const unsigned int ComputeIterationID) const +{ + + if( this->m_DebugLevel > 9 ) + { + // write out posteriors + const unsigned int numPosteriors = this->m_Posteriors.size(); + const unsigned int write_posteriors_level = ComputeIterationID; // DEBUG: + // This + // code is + // for + // debugging + // purposes + // only; + std::stringstream write_posteriors_level_stream(""); + write_posteriors_level_stream << write_posteriors_level; + for( unsigned int iprob = 0; iprob < numPosteriors; iprob++ ) + { + typedef itk::ImageFileWriter ProbabilityImageWriterType; + typename ProbabilityImageWriterType::Pointer writer = ProbabilityImageWriterType::New(); + + std::stringstream template_index_stream(""); + template_index_stream << iprob; + const std::string fn = this->m_OutputDebugDir + "/POSTERIOR_INDEX_" + template_index_stream.str() + "_" + + this->m_PriorNames[iprob] + "_LEVEL_" + write_posteriors_level_stream.str() + ".nii.gz"; + + muLogMacro(<< "Writing posterior images... " << fn << std::endl); + writer->SetInput(m_Posteriors[iprob]); + writer->SetFileName(fn); + writer->UseCompressionOn(); + writer->Update(); + } + } + return; +} + +template +void +EMSegmentationFilter +::SetPriors(std::vector priors) +{ + muLogMacro(<< "Set and Normalize for segmentation." << std::endl); + // Need to normalize priors before getting started. + this->m_OriginalSpacePriors = priors; + ZeroNegativeValuesInPlace(this->m_OriginalSpacePriors); + NormalizeProbListInPlace(this->m_OriginalSpacePriors); + this->m_OriginalSpacePriors = priors; + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetPriorWeights(VectorType w) +{ + muLogMacro(<< "SetPriorWeights" << std::endl); + + if( w.size() != m_OriginalSpacePriors.size() ) + { + itkExceptionMacro(<< "Number of prior weights invalid" << w.size() << " != " << m_OriginalSpacePriors.size() ); + } + for( unsigned i = 0; i < w.size(); i++ ) + { + if( w[i] == 0.0 ) + { + itkExceptionMacro(<< "Prior weight " << i << " is zero" << std::endl ); + } + } + + m_PriorWeights = w; + m_PriorWeightsSet = true; + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetPriorLabelCodeVector(IntVectorType ng) +{ + muLogMacro(<< "SetPriorLabelCodeVector" << std::endl ); + if( ng.size() == 0 ) + { + itkExceptionMacro(<< "Number of clusters info invalid" << std::endl ); + } + const unsigned int numPriors = m_WarpedPriors.size(); + for( unsigned int i = 0; i < numPriors; i++ ) + { + if( ng[i] == 0 ) + { + itkExceptionMacro(<< "PriorLabelCode" << i << " is zero" << std::endl ); + } + } + m_PriorLabelCodeVector = ng; + m_PriorLabelCodeVectorSet = true; + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetPriorUseForBiasVector(const BoolVectorType& ng) +{ + muLogMacro(<< "SetPriorUseForBiasVector" << std::endl ); + if( ng.size() == 0 ) + { + itkExceptionMacro(<< "Vector size for PriorUseForBiasVector info invalid" << std::endl ); + } + const unsigned int numPriors = m_WarpedPriors.size(); + for( unsigned int i = 0; i < numPriors; i++ ) + { + if( ng[i] != 0 && ng[i] != 1 ) + { + itkExceptionMacro(<< "PriorUseForBiasVector" << i << " can only be 0 or 1" << std::endl ); + } + } + m_PriorUseForBiasVector = ng; + m_PriorUseForBiasVectorSet = true; + this->Modified(); + m_UpdateRequired = true; +} + +template +void +EMSegmentationFilter +::SetPriorIsForegroundPriorVector(const BoolVectorType& ng) +{ + muLogMacro(<< "SetPriorIsForegroundPriorVector" << std::endl ); + if( ng.size() == 0 ) + { + itkExceptionMacro(<< "Vector size for PriorIsForegroundPriorVector info invalid" << std::endl ); + } + const unsigned int numPriors = m_WarpedPriors.size(); + for( unsigned int i = 0; i < numPriors; i++ ) + { + if( ng[i] != 0 && ng[i] != 1 ) + { + itkExceptionMacro(<< "PriorIsForegroundPriorVector" << i << " can only be 0 or 1" << std::endl ); + } + } + m_PriorIsForegroundPriorVector = ng; + m_PriorIsForegroundPriorVectorSet = true; + this->Modified(); + m_UpdateRequired = true; +} + +template +typename EMSegmentationFilter:: +ByteImagePointer +EMSegmentationFilter +::GetCleanedOutput(void) +{ + // TODO: This assumes that GetOutput was already called. This should be made + // more intelligent + return m_CleanedLabels; +} + +template +typename EMSegmentationFilter:: +ByteImagePointer +EMSegmentationFilter +::GetOutput(void) +{ + this->Update(); + return m_DirtyLabels; +} + +template +std::vector< + typename EMSegmentationFilter:: + ProbabilityImagePointer> +EMSegmentationFilter +::GetPosteriors() +{ + return m_Posteriors; +} + +template +std::vector::InputImagePointer> +EMSegmentationFilter +::GetCorrected() +{ + return m_CorrectedImages; +} + +template +std::vector::InputImagePointer> +EMSegmentationFilter +::GetRawCorrected() +{ + return m_RawCorrectedImages; +} + +template +void +CheckLoopAgainstFilterOutput + (typename EMSegmentationFilter::ByteImageType::Pointer & loopImg, + typename EMSegmentationFilter::ByteImageType::Pointer & filterImg) +{ + typedef typename EMSegmentationFilter::ByteImageType + ByteImageType; + + typedef typename itk::ImageRegionConstIterator IterType; + + IterType maskIter(loopImg, loopImg->GetLargestPossibleRegion() ); + IterType dilIter(filterImg, filterImg->GetLargestPossibleRegion() ); + unsigned int count = 0; + for( maskIter.Begin(), dilIter.Begin(); + !maskIter.IsAtEnd() && !dilIter.IsAtEnd(); ++maskIter, ++dilIter ) + { + if( maskIter.Value() != dilIter.Value() ) + { + std::cerr << "mask = " << static_cast(maskIter.Value() ) + << " dilated = " << static_cast(dilIter.Value() ) + << " at vIndex " << maskIter.GetIndex() + << std::endl; + count++; + } + } + if( count == 0 ) + { + muLogMacro( << "DEBUG: Filter output same as after loop output!" << std::endl); + } +} + +namespace +{ +template +typename ImageType::Pointer +CopyImage(const typename ImageType::Pointer & input ) +{ + typedef itk::ImageDuplicator ImageDupeType; + typename ImageDupeType::Pointer MyDuplicator = ImageDupeType::New(); + MyDuplicator->SetInputImage(input); + MyDuplicator->Update(); + return MyDuplicator->GetOutput(); +} + +} + +template +std::vector ComputeDistributions( + const std::vector & SubjectCandidateRegions, + const std::vector & probAllDistributions, + const std::vector & intensityImages, + const unsigned int DebugLevel) +{ + muLogMacro(<< "Computing Distributions" << std::endl ); + const std::vector & probabilityMaps = probAllDistributions; + + std::vector outputStats; + typedef vnl_matrix MatrixType; + + CombinedComputeDistributions(SubjectCandidateRegions, intensityImages, + probabilityMaps, + outputStats, + DebugLevel, + false); + + return outputStats; +} + +static double ComputeCovarianceDeterminant( const vnl_matrix & currCovariance) +{ + const FloatingPrecision detcov = vnl_determinant(currCovariance); + + if( detcov <= 0.0 ) + { + itkGenericExceptionMacro( + << "Determinant of covariance " + << " is <= 0.0 (" << detcov << "), covariance matrix:" << std::endl + << currCovariance + << + "\n\n\n This is indicative of providing two images that are related only through a linear depenancy\n" + << + "at least two images are so close in their ratio of values that a degenerate covariance matrix\n" + << "would result, thus making an unstable calculation\n\n\n"); + } + return detcov; +} + +template +typename TProbabilityImage::Pointer +ComputeOnePosterior( + const FloatingPrecision priorScale, + const typename TProbabilityImage::Pointer prior, + const vnl_matrix currCovariance, + const vnl_vector currMeans, + const std::vector & intensityImages + ) +{ + typedef vnl_matrix MatrixType; + typedef vnl_matrix_inverse MatrixInverseType; + + const unsigned numChannels = currMeans.size(); + const FloatingPrecision detcov = ComputeCovarianceDeterminant(currCovariance); + + // Normalizing constant for the Gaussian + const FloatingPrecision denom = + vcl_pow(2 * vnl_math::pi, numChannels / 2.0) * vcl_sqrt(detcov) + vnl_math::eps; + const FloatingPrecision invdenom = 1.0 / denom; + CHECK_NAN(invdenom, __FILE__, __LINE__); + MatrixType invcov = MatrixInverseType(currCovariance); + + typename TProbabilityImage::Pointer post = TProbabilityImage::New(); + post->CopyInformation(prior); + post->SetRegions(prior->GetLargestPossibleRegion() ); + post->Allocate(); + + const typename TProbabilityImage::SizeType size = post->GetLargestPossibleRegion().GetSize(); + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for +#endif + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const typename TProbabilityImage::IndexType currIndex = {{ii, jj, kk}}; + // At a minimum, every class has at least a 0.001% chance of being + // true no matter what. + // I realize that this small value makes the priors equal slightly + // larger than 100%, but everything + // is renormalized anyway, so it is not really that big of a deal as + // long as the main priors for + // the desired class is significantly higher than 1%. + const typename TProbabilityImage::PixelType minPriorValue = 0.0; + const typename TProbabilityImage::PixelType priorValue = (prior->GetPixel(currIndex) + minPriorValue); + { + MatrixType X(numChannels, 1); + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + X(ichan, 0) = + intensityImages[ichan]->GetPixel(currIndex) - currMeans[ichan]; + } + + const MatrixType Y = invcov * X; + FloatingPrecision mahalo = 0.0; + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + mahalo += X(ichan, 0) * Y(ichan, 0); + } + + // Note: This is the maximum likelyhood estimate as described in + // formula at bottom of + // http://en.wikipedia.org/wiki/Maximum_likelihood_estimation + const FloatingPrecision likelihood = vcl_exp(-0.5 * mahalo) * invdenom; + + const typename TProbabilityImage::PixelType currentPosterior = + static_cast( (priorScale * priorValue * likelihood) ); + post->SetPixel(currIndex, currentPosterior); + } + } + } + } + } + return post; +} + +template +std::vector +ComputePosteriors(const std::vector & Priors, + const vnl_vector & PriorWeights, + const std::vector & IntensityImages, + std::vector & ListOfClassStatistics) +{ + // Compute initial distribution parameters + muLogMacro(<< "ComputePosteriors" << std::endl ); + itk::TimeProbe ComputePosteriorsTimer; + ComputePosteriorsTimer.Start(); + + const unsigned int numClasses = Priors.size(); + muLogMacro(<< "Computing posteriors at full resolution" << std::endl); + + const typename TProbabilityImage::SizeType size = Priors[0]->GetLargestPossibleRegion().GetSize(); + std::vector Posteriors; + Posteriors.resize(numClasses); + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + const FloatingPrecision priorScale = PriorWeights[iclass]; + CHECK_NAN(priorScale, __FILE__, __LINE__); + + Posteriors[iclass] = ComputeOnePosterior( + priorScale, + Priors[iclass], + ListOfClassStatistics[iclass].m_Covariance, + ListOfClassStatistics[iclass].m_Means, + IntensityImages + ); + + } // end class loop + + ComputePosteriorsTimer.Stop(); + itk::RealTimeClock::TimeStampType elapsedTime = + ComputePosteriorsTimer.GetTotal(); + muLogMacro(<< "Computing Posteriors took " << elapsedTime << " " << ComputePosteriorsTimer.GetUnit() << std::endl); + return Posteriors; + +} + +template +void +EMSegmentationFilter +::WriteDebugLabels(const unsigned int CurrentEMIteration) const +{ + if( this->m_DebugLevel > 6 ) + { + // write out labels + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + { + typedef itk::ImageFileWriter LabelImageWriterType; + typename LabelImageWriterType::Pointer writer = LabelImageWriterType::New(); + + const std::string fn = this->m_OutputDebugDir + "/LABELS_LEVEL_" + CurrentEMIteration_stream.str() + ".nii.gz"; + + muLogMacro(<< "Writing label images... " << fn << std::endl); + writer->SetInput(m_CleanedLabels); + writer->SetFileName(fn); + writer->UseCompressionOn(); + writer->Update(); + } + } + if( this->m_DebugLevel > 6 ) + { + // write out labels + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + { + typedef itk::ImageFileWriter LabelImageWriterType; + typename LabelImageWriterType::Pointer writer = LabelImageWriterType::New(); + + const std::string fn = this->m_OutputDebugDir + "/LABELSDIRTY_LEVEL_" + CurrentEMIteration_stream.str() + + ".nii.gz"; + + muLogMacro(<< "Writing label images... " << fn << std::endl); + writer->SetInput(m_DirtyLabels); + writer->SetFileName(fn); + writer->UseCompressionOn(); + writer->Update(); + } + } +} + +template +void +EMSegmentationFilter +::WriteDebugCorrectedImages(const std::vector & correctImageList, + const unsigned int CurrentEMIteration ) const +{ + if( this->m_DebugLevel > 8 ) + { // DEBUG: This code is for debugging purposes only; + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + for( unsigned int vIndex = 0; vIndex < correctImageList.size(); vIndex++ ) + { + { // DEBUG: This code is for debugging purposes only; + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream template_index_stream(""); + template_index_stream << vIndex; + const std::string fn = this->m_OutputDebugDir + "/CORRECTED_INDEX_" + template_index_stream.str() + "_LEVEL_" + + CurrentEMIteration_stream.str() + ".nii.gz"; + writer->SetInput(correctImageList[vIndex]); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } + } +} + +template +FloatingPrecision +EMSegmentationFilter +::ComputeLogLikelihood() const +{ + const InputImageSizeType size = m_Posteriors[0]->GetLargestPossibleRegion().GetSize(); + const unsigned int computeInitialNumClasses = m_Posteriors.size(); + FloatingPrecision logLikelihood = 0.0; + + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for reduction(+:logLikelihood) +#endif + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + FloatingPrecision tmp = 1e-20; + for( unsigned int iclass = 0; iclass < computeInitialNumClasses; iclass++ ) + { + if( this->m_PriorIsForegroundPriorVector[iclass] ) // We should + // probably only + // compute the + // foreground. + { + tmp += m_Posteriors[iclass]->GetPixel(currIndex); + } + } + logLikelihood = logLikelihood + vcl_log(tmp); + } + } + } + } + return logLikelihood; +} + +/** + * \param referenceImage is the image to be used for defining the tissueRegion of iterest. + * \param safetyRegion is the amount to dilate so that there is not such a tight region. + */ +template +typename TByteImage::Pointer +ComputeTissueRegion(const typename TInputImage::Pointer referenceImage, const unsigned int safetyRegion) +{ + typedef itk::BRAINSROIAutoImageFilter ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(referenceImage); + ROIFilter->SetDilateSize(safetyRegion); // Create a very tight fitting tissue + // region here. + ROIFilter->Update(); + typename TByteImage::Pointer tissueRegion = ROIFilter->GetOutput(); + return tissueRegion; +} + +template +void +EMSegmentationFilter +::WriteDebugHeadRegion(const unsigned int CurrentEMIteration) const +{ + if( this->m_DebugLevel > 7 ) + { + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + { // DEBUG: This code is for debugging purposes only; + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + const std::string fn = this->m_OutputDebugDir + "/HEAD_REGION_LEVEL_" + CurrentEMIteration_stream.str() + + ".nii.gz"; + writer->SetInput( this->m_NonAirRegion ); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } +} + +template +std::vector +WarpImageList(const std::vector & originalList, + const typename TInputImage::Pointer referenceOutput, + const std::vector & backgroundValues, + const GenericTransformType::Pointer warpTransform) +{ + if( originalList.size() != backgroundValues.size() ) + { + std::cout << "ERROR: originalList and backgroundValues arrays sizes do not match" << std::endl; + exit(-1); + } + std::vector warpedList(originalList.size() ); + + typedef itk::ResampleImageFilter ResamplerType; + { + for( unsigned int vIndex = 0; vIndex < originalList.size(); vIndex++ ) + { + typename ResamplerType::Pointer warper = ResamplerType::New(); + warper->SetInput(originalList[vIndex]); + warper->SetTransform(warpTransform); + + // warper->SetInterpolator(linearInt); // Default is linear + warper->SetOutputParametersFromImage(referenceOutput); + warper->SetDefaultPixelValue(backgroundValues[vIndex]); + warper->Update(); + warpedList[vIndex] = warper->GetOutput(); + } + } + return warpedList; +} + +template +void +EMSegmentationFilter +::WriteDebugWarpedAtlasImages(const unsigned int CurrentEMIteration) const +{ + std::stringstream CurrentEMIteration_stream(""); + + CurrentEMIteration_stream << CurrentEMIteration; + if( this->m_DebugLevel > 9 ) + { + for( unsigned int vIndex = 0; vIndex < this->m_WarpedAtlasImages.size(); vIndex++ ) + { + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream template_index_stream(""); + template_index_stream << vIndex; + const std::string fn = this->m_OutputDebugDir + "/WARPED_ATLAS_INDEX_" + template_index_stream.str() + + "_LEVEL_" + CurrentEMIteration_stream.str() + ".nii.gz"; + writer->SetInput(m_WarpedAtlasImages[vIndex]); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } +} + +template +std::vector +EMSegmentationFilter +::GenerateWarpedAtlasImages(void) +{ + // TODO: Need to make this cleaner. + std::vector backgroundValues(m_OriginalAtlasImages.size() ); + std::fill(backgroundValues.begin(), backgroundValues.end(), 0); + this->m_WarpedAtlasImages = + WarpImageList(this->m_OriginalAtlasImages, this->m_InputImages[0], backgroundValues, + this->m_TemplateGenericTransform); + return m_WarpedAtlasImages; +} + +template +std::vector +EMSegmentationFilter +::UpdateIntensityBasedClippingOfPriors(const unsigned int CurrentEMIteration, + const std::vector & intensityList, + std::vector & WarpedPriorsList, + typename ByteImageType::Pointer ForegroundBrainRegion) +{ + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // For each intensityList, get it's type, and then create an "anded mask of + // candidate regions" + // using the table from BRAINSMultiModeHistogramThresholder. + std::vector subjectCandidateRegions; + subjectCandidateRegions.resize(WarpedPriorsList.size() ); + { // StartValid Regions Section +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE i = 0; i < (LOOPITERTYPE)WarpedPriorsList.size(); i++ ) + { + typename ByteImageType::Pointer probThreshImage = NULL; + { + typedef itk::BinaryThresholdImageFilter ProbThresholdType; + typename ProbThresholdType::Pointer probThresh = ProbThresholdType::New(); + probThresh->SetInput( WarpedPriorsList[i] ); + probThresh->SetInsideValue(1); + probThresh->SetOutsideValue(0); + probThresh->SetLowerThreshold(0.05); // Need greater than 1 in 20 + // chance of being this structure + // from the spatial probabilities + probThresh->SetUpperThreshold(1e200); // No upper limit needed, values + // should be between 0 and 1 + probThresh->Update(); + probThreshImage = probThresh->GetOutput(); + if( this->m_DebugLevel > 9 ) + { + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + // Write the subject candidate regions + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "CANDIDIDATE_PROBTHRESH_" << this->m_PriorNames[i] << "_LEVEL_" + << CurrentEMIteration_stream.str() << ".nii.gz" << std::ends; + std::string fn = oss.str(); + muLogMacro( << "Writing Subject Candidate Region." << fn << std::endl ); + muLogMacro( << std::endl ); + + typedef itk::ImageFileWriter ByteWriterType; + typename ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->SetInput(probThreshImage); + writer->SetFileName(fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + } + + const unsigned int numberOfModes = intensityList.size(); + typedef typename itk::MultiModeHistogramThresholdBinaryImageFilter ThresholdRegionFinderType; + typename ThresholdRegionFinderType::ThresholdArrayType QuantileLowerThreshold(numberOfModes); + typename ThresholdRegionFinderType::ThresholdArrayType QuantileUpperThreshold(numberOfModes); + typename ThresholdRegionFinderType::Pointer thresholdRegionFinder = ThresholdRegionFinderType::New(); + // TODO: Need to define PortionMaskImage from deformed probspace + thresholdRegionFinder->SetBinaryPortionImage(ForegroundBrainRegion); + for( LOOPITERTYPE modeIndex = 0; modeIndex < (LOOPITERTYPE)numberOfModes; modeIndex++ ) + { + thresholdRegionFinder->SetInput(modeIndex, intensityList[modeIndex]); + const std::string imageType = this->m_InputVolumeTypes[modeIndex]; + const std::string priorType = this->m_PriorNames[i]; + if( m_TissueTypeThresholdMapsRange[priorType].find(imageType) == m_TissueTypeThresholdMapsRange[priorType].end() ) + { + muLogMacro( + << "NOT FOUND:" << "[" << priorType << "," << imageType << "]: [" << 0.00 << "," << 1.00 << "]" + << std::endl); + QuantileLowerThreshold.SetElement(modeIndex, 0.00); + QuantileUpperThreshold.SetElement(modeIndex, 1.00); + } + else + { + const float lower = m_TissueTypeThresholdMapsRange[priorType][imageType].GetLower(); + const float upper = m_TissueTypeThresholdMapsRange[priorType][imageType].GetUpper(); + muLogMacro( << "[" << priorType << "," << imageType << "]: [" << lower << "," << upper << "]" << std::endl); + QuantileLowerThreshold.SetElement(modeIndex, lower); + QuantileUpperThreshold.SetElement(modeIndex, upper); + m_TissueTypeThresholdMapsRange[priorType][imageType].Print(); + } + } + // Assume upto (2*0.025)% of intensities are noise that corrupts the image + // min/max values + thresholdRegionFinder->SetLinearQuantileThreshold(0.025); + thresholdRegionFinder->SetQuantileLowerThreshold(QuantileLowerThreshold); + thresholdRegionFinder->SetQuantileUpperThreshold(QuantileUpperThreshold); + // thresholdRegionFinder->SetInsideValue(1); + // thresholdRegionFinder->SetOutsideValue(0);//Greatly reduce the value to + // zero. + thresholdRegionFinder->Update(); + if( this->m_DebugLevel > 8 ) + { + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + // Write the subject candidate regions + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "CANDIDIDATE_INTENSITY_REGION_" << this->m_PriorNames[i] << "_LEVEL_" + << CurrentEMIteration_stream.str() << ".nii.gz" << std::ends; + std::string fn = oss.str(); + muLogMacro( << "Writing Subject Candidate Region." << fn << std::endl ); + muLogMacro( << std::endl ); + + typedef itk::ImageFileWriter ByteWriterType; + typename ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->SetInput(thresholdRegionFinder->GetOutput() ); + writer->SetFileName(fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + + // Now multiply the warped priors by the subject candidate regions. + typename itk::MultiplyImageFilter::Pointer multFilter = + itk::MultiplyImageFilter::New(); + multFilter->SetInput1( probThreshImage ); + multFilter->SetInput2( thresholdRegionFinder->GetOutput() ); + multFilter->Update(); + subjectCandidateRegions[i] = multFilter->GetOutput(); + } // End loop over all warped priors + + { // Ensure that every candidate region has some value + const unsigned int candiateVectorSize = subjectCandidateRegions.size(); + itk::ImageRegionIteratorWithIndex + firstCandidateIter(subjectCandidateRegions[0], subjectCandidateRegions[0]->GetLargestPossibleRegion() ); + const size_t AllZeroCounts = 0; + while( !firstCandidateIter.IsAtEnd() ) + { + const typename ByteImageType::IndexType myIndex = firstCandidateIter.GetIndex(); + bool AllPixelsAreZero = true; + size_t AllZeroCounts = 0; +// unsigned int maxPriorRegionIndex = 0; + typename TProbabilityImage::PixelType maxProbValue = WarpedPriorsList[0]->GetPixel(myIndex); + for( unsigned int k = 0; ( k < candiateVectorSize ) && AllPixelsAreZero; k++ ) + { + const typename ByteImageType::PixelType value = subjectCandidateRegions[k]->GetPixel(myIndex); + if( value > 0 ) + { + AllPixelsAreZero = false; + } + typename TProbabilityImage::PixelType currValue = WarpedPriorsList[k]->GetPixel(myIndex); + if( currValue > maxProbValue ) + { + maxProbValue = currValue; +// maxPriorRegionIndex = k; + } + } + if( AllPixelsAreZero ) // If all candidate regions are zero, then force + // to most likely background value. + { + AllZeroCounts++; + for( unsigned int k = 0; k < candiateVectorSize; k++ ) + { + if( this->m_PriorIsForegroundPriorVector[k] == false ) + { + subjectCandidateRegions[k]->SetPixel(myIndex, 1); + WarpedPriorsList[k]->SetPixel(myIndex, 0.05); + } + } + } + ++firstCandidateIter; + } + + if( AllZeroCounts != 0 ) + { + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "Locations with no candidate regions specified!" << AllZeroCounts << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + std::cout << "^^^^^^^^^^^^^^^^" << std::endl; + } + } + if( this->m_DebugLevel > 5 ) + { + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + for( unsigned int i = 0; i < subjectCandidateRegions.size(); i++ ) + { + // Write the subject candidate regions + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "CANDIDIDATE_FINAL" << this->m_PriorNames[i] << "_LEVEL_" + << CurrentEMIteration_stream.str() << ".nii.gz" << std::ends; + std::string fn = oss.str(); + muLogMacro( << "Writing Subject Candidate Region." << fn << std::endl ); + muLogMacro( << std::endl ); + + typedef itk::ImageFileWriter ByteWriterType; + typename ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->SetInput(subjectCandidateRegions[i]); + writer->SetFileName(fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } + } + } // END Valid regions section + + return subjectCandidateRegions; +} + +template +std::vector +EMSegmentationFilter +::ForceToOne(const unsigned int, const std::vector &, + std::vector & WarpedPriorsList, + typename ByteImageType::Pointer ) +{ + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // ################################################################# + // For each intensityList, get it's type, and then create an "anded mask of + // candidate regions" + // using the table from BRAINSMultiModeHistogramThresholder. + std::vector subjectCandidateRegions; + subjectCandidateRegions.resize(WarpedPriorsList.size() ); + { // StartValid Regions Section +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE i = 0; i < (LOOPITERTYPE)WarpedPriorsList.size(); i++ ) + { + subjectCandidateRegions[i] = ByteImageType::New(); + subjectCandidateRegions[i]->CopyInformation(WarpedPriorsList[i].GetPointer() ); + subjectCandidateRegions[i]->SetRegions( WarpedPriorsList[i]->GetLargestPossibleRegion() ); + subjectCandidateRegions[i]->Allocate(); + subjectCandidateRegions[i]->FillBuffer(1); + } + } // END Valid regions section + + return subjectCandidateRegions; +} + +// ReturnBlendedProbList can be the same as one of the inputs! +template +void BlendPosteriorsAndPriors(const double blendPosteriorPercentage, + const std::vector & ProbList1, + const std::vector & ProbList2, + std::vector & ReturnBlendedProbList) +{ + for( unsigned int k = 0; k < ProbList2.size(); k++ ) + { + std::cout << "Start Blending Prior:" << k << std::endl; + typename TProbabilityImage::Pointer multInputImage = ProbList2[k]; + // BLEND Posteriors and Priors Here: + // It is important to keep the warped priors as at least a small component + // of this part + // of the algorithm, because otherwise single pixels that exactly match the + // mean of the + // NOT* regions will become part of those NOT* regions regardless of spatial + // locations. + // std::cout << "\n\nWarpedPriors[" << k << "] \n" << ProbList2[k] << + // std::endl; + if( + ( ProbList1.size() == ProbList2.size() ) + && ProbList1.size() > k + && ProbList1[k].IsNotNull() + && ( blendPosteriorPercentage > 0.01 ) // Need to blend at more than 1%, + // else just skip it + ) + { + // Really we need to use a heirarchial approach to solving this problem. + // It is not sufficient to have these heuristics + // break things apart artificially. + std::cout << "\nBlending Priors with Posteriors with formula: " << (blendPosteriorPercentage) + << "*Posterior + " << (1.0 - blendPosteriorPercentage) << "*Prior" << std::endl; + typedef itk::BlendImageFilter BlenderType; + typename BlenderType::Pointer myBlender = BlenderType::New(); + myBlender->SetInput1(ProbList1[k]); + myBlender->SetInput2(ProbList2[k]); + myBlender->SetBlend1(blendPosteriorPercentage); + myBlender->SetBlend2(1.0 - blendPosteriorPercentage); + myBlender->Update(); + multInputImage = myBlender->GetOutput(); + } + else + { + std::cout << "Not Blending Posteriors into Priors" << std::endl; + multInputImage = ProbList2[k]; + } +#if 1 + ReturnBlendedProbList[k] = multInputImage; +#else + // Now multiply the warped priors by the subject candidate regions. + typename itk::MultiplyImageFilter::Pointer multFilter = + itk::MultiplyImageFilter::New(); + multFilter->SetInput1(multInputImage); + multFilter->SetInput2(candidateRegions[k]); + multFilter->Update(); + ReturnBlendedProbList[k] = multFilter->GetOutput(); + std::cout << "Stop Blending Prior:" << k << std::endl; +#endif + } +} + +template +void +EMSegmentationFilter +::WriteDebugWarpedAtlasPriors(const unsigned int CurrentEMIteration) const +{ + std::stringstream CurrentEMIteration_stream(""); + + CurrentEMIteration_stream << CurrentEMIteration; + if( this->m_DebugLevel > 9 ) + { + for( unsigned int vIndex = 0; vIndex < this->m_WarpedPriors.size(); vIndex++ ) + { + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream template_index_stream(""); + template_index_stream << this->m_PriorNames[vIndex]; + const std::string fn = this->m_OutputDebugDir + "/WARPED_PRIOR_" + template_index_stream.str() + "_LEVEL_" + + CurrentEMIteration_stream.str() + ".nii.gz"; + writer->SetInput(m_WarpedPriors[vIndex]); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } + +} + +template +void +EMSegmentationFilter +::WriteDebugBlendClippedPriors( const unsigned int CurrentEMIteration) const +{ + std::stringstream CurrentEMIteration_stream(""); + + CurrentEMIteration_stream << CurrentEMIteration; + if( this->m_DebugLevel > 9 ) + { // DEBUG: This code is for debugging purposes only; + for( unsigned int k = 0; k < m_WarpedPriors.size(); k++ ) + { + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream prior_index_stream(""); + prior_index_stream << k; + // const std::string fn = this->m_OutputDebugDir + + // + // "PRIOR_INDEX_"+prior_index_stream.str()+"_LEVEL_"+CurrentEMIteration_stream.str()+".nii.gz"; + const std::string fn = this->m_OutputDebugDir + "BLENDCLIPPED_PRIOR_INDEX_" + this->m_PriorNames[k] + "_LEVEL_" + + CurrentEMIteration_stream.str() + ".nii.gz"; + writer->SetInput(m_WarpedPriors[k]); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + } +} + +template +void +EMSegmentationFilter +::UpdateTransformation(const unsigned int /*CurrentEMIteration*/) +{ + muLogMacro(<< "Updating Warping with transform type: " << m_AtlasTransformType << std::endl ); + if( m_UpdateTransformation == false ) + { + muLogMacro( + << "WARNING: WARNING: WARNING: WARNING: Doing warping even though it was turned off from the command line" + << std::endl); + } + for( unsigned int vIndex = 0; vIndex < m_OriginalAtlasImages.size() && vIndex < m_CorrectedImages.size(); vIndex++ ) + { + typedef itk::BRAINSFitHelper HelperType; + HelperType::Pointer atlasToSubjectRegistrationHelper = HelperType::New(); + atlasToSubjectRegistrationHelper->SetNumberOfSamples(500000); + atlasToSubjectRegistrationHelper->SetNumberOfHistogramBins(50); + std::vector numberOfIterations(1); + numberOfIterations[0] = 1500; + atlasToSubjectRegistrationHelper->SetNumberOfIterations(numberOfIterations); + // atlasToSubjectRegistrationHelper->SetMaximumStepLength(maximumStepSize); + atlasToSubjectRegistrationHelper->SetTranslationScale(1000); + atlasToSubjectRegistrationHelper->SetReproportionScale(1.0); + atlasToSubjectRegistrationHelper->SetSkewScale(1.0); + // + // + // + // atlasToSubjectRegistrationHelper->SetBackgroundFillValue(backgroundFillValue); + // NOT VALID When using initializeTransformMode + // + // + // atlasToSubjectRegistrationHelper->SetCurrentGenericTransform(currentGenericTransform); + // + // + // + // atlasToSubjectRegistrationHelper->SetMaskInferiorCutOffFromCenter(maskInferiorCutOffFromCenter); + // atlasToSubjectRegistrationHelper->SetUseWindowedSinc(useWindowedSinc); + // Register each intrasubject image mode to first image + atlasToSubjectRegistrationHelper->SetFixedVolume(m_CorrectedImages[vIndex]); + // Register all atlas images to first image + { + if( false /* m_AtlasTransformType == ID_TRANSFORM */ ) + { + muLogMacro(<< "Registering (Identity) atlas to first image." << std::endl); + // TODO: m_AtlasToSubjectTransform = MakeRigidIdentity(); + } + else // continue; + { + std::string preprocessMovingString(""); + // const bool histogramMatch=true;//Setting histogram matching to true + + // Setting histogram matching to false because it appears to have been + // causing problems for some images. + const bool histogramMatch = false; + if( histogramMatch ) + { + typedef itk::HistogramMatchingImageFilter HistogramMatchingFilterType; + typename HistogramMatchingFilterType::Pointer histogramfilter + = HistogramMatchingFilterType::New(); + + histogramfilter->SetInput( m_OriginalAtlasImages[vIndex] ); + histogramfilter->SetReferenceImage( m_CorrectedImages[vIndex] ); + + histogramfilter->SetNumberOfHistogramLevels( 50 ); + histogramfilter->SetNumberOfMatchPoints( 10 ); + histogramfilter->ThresholdAtMeanIntensityOn(); + histogramfilter->Update(); + typename InputImageType::Pointer equalizedMovingImage = histogramfilter->GetOutput(); + atlasToSubjectRegistrationHelper->SetMovingVolume(equalizedMovingImage); + preprocessMovingString = "histogram equalized "; + } + else + { + atlasToSubjectRegistrationHelper->SetMovingVolume(m_OriginalAtlasImages[vIndex]); + preprocessMovingString = ""; + } + { + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_OriginalAtlasImages[vIndex]); + ROIFilter->SetDilateSize(10); + ROIFilter->Update(); + atlasToSubjectRegistrationHelper->SetMovingBinaryVolume(ROIFilter->GetSpatialObjectROI() ); + } + { + typedef itk::BRAINSROIAutoImageFilter > ROIAutoType; + typename ROIAutoType::Pointer ROIFilter = ROIAutoType::New(); + ROIFilter->SetInput(m_CorrectedImages[vIndex]); + ROIFilter->SetDilateSize(10); + ROIFilter->Update(); + atlasToSubjectRegistrationHelper->SetFixedBinaryVolume(ROIFilter->GetSpatialObjectROI() ); + } + // KENT TODO: Need to expose the transform type to the command line + // --AtlasTransformType [Rigid|Affine|BSpline], defaults to BSpline. + if( m_AtlasTransformType == "Rigid" ) + { + muLogMacro( + << "Registering (Rigid) " << preprocessMovingString << "atlas(" << vIndex << ") to template(" << vIndex + << ") image." << std::endl); + std::vector minimumStepSize(1); + minimumStepSize[0] = 0.005; // NOTE: 0.005 for between subject + // registration is probably about the + // limit. + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(1); + transformType[0] = "Rigid"; + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_AtlasTransformType == "Affine" ) + { + muLogMacro( + << "Registering (Affine) " << preprocessMovingString << "atlas(" << vIndex << ") to template(" << vIndex + << ") image." << std::endl); + std::vector minimumStepSize(1); + minimumStepSize[0] = 0.0025; + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(1); + transformType[0] = "Affine"; + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + } + else if( m_AtlasTransformType == "BSpline" ) + { + muLogMacro( + << "Registering (BSpline) " << preprocessMovingString << "atlas(" << vIndex << ") to template(" << vIndex + << ") image." << std::endl); + std::vector minimumStepSize(1); + minimumStepSize[0] = 0.0025; + atlasToSubjectRegistrationHelper->SetMinimumStepLength(minimumStepSize); + std::vector transformType(1); + transformType[0] = "BSpline"; + atlasToSubjectRegistrationHelper->SetTransformType(transformType); + std::vector splineGridSize(3); + splineGridSize[0] = m_WarpGrid[0]; + splineGridSize[1] = m_WarpGrid[1]; + splineGridSize[2] = m_WarpGrid[2]; + atlasToSubjectRegistrationHelper->SetSplineGridSize(splineGridSize); + atlasToSubjectRegistrationHelper->SetMaxBSplineDisplacement(6.0); // + // Setting + // + // max + // + // displace + } + atlasToSubjectRegistrationHelper->SetCurrentGenericTransform(m_TemplateGenericTransform); + if( this->m_DebugLevel > 9 ) + { + static unsigned int atlasToSubjectCounter = 0; + std::stringstream ss; + ss << std::setw(3) << std::setfill('0') << atlasToSubjectCounter; + atlasToSubjectRegistrationHelper->PrintCommandLine(true, std::string("AtlasToSubjectUpdate") + ss.str() ); + muLogMacro( << __FILE__ << " " << __LINE__ << " " << std::endl ); + atlasToSubjectCounter++; + } + atlasToSubjectRegistrationHelper->StartRegistration(); + unsigned int actualIterations = atlasToSubjectRegistrationHelper->GetActualNumberOfIterations(); + muLogMacro( << "Registration tool " << actualIterations << " iterations." << std::endl ); +#if 0 // ERROR: This is not working correctly, because the proper number of + // iterations is not reportd by the optimizer. + while( actualIterations == 0 ) + { + double newGradientTolerance = atlasToSubjectRegistrationHelper->GetProjectedGradientTolerance() * 0.1; + atlasToSubjectRegistrationHelper->SetProjectedGradientTolerance(newGradientTolerance); + muLogMacro( << "Reducing Gradient Tolerance to " << newGradientTolerance << std::endl ); + atlasToSubjectRegistrationHelper->StartRegistration(); + actualIterations = atlasToSubjectRegistrationHelper->GetActualNumberOfIterations(); + muLogMacro( << "Registration tool " << actualIterations << " iterations." << std::endl ); + } + +#endif + m_TemplateGenericTransform = atlasToSubjectRegistrationHelper->GetCurrentGenericTransform(); + } + } + } +} + +template +void +EMSegmentationFilter +::WritePartitionTable(const unsigned int CurrentEMIteration) const +{ + const unsigned int numChannels = this->m_CorrectedImages.size(); + const unsigned int numPriors = this->m_WarpedPriors.size(); + + muLogMacro(<< "\n\nEM iteration " << CurrentEMIteration << std::endl); + muLogMacro(<< "---------------------" << std::endl); + PrettyPrintTable EMIterationTable; + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + EMIterationTable.add(0, ichan + 2, this->m_InputVolumeTypes[ichan]); + } + for( unsigned int iclass = 0; iclass < numPriors; iclass++ ) + { + EMIterationTable.add(iclass + 1, 0, std::string("Class ") + this->m_PriorNames[iclass] + " mean "); + EMIterationTable.add(iclass + 1, 1, std::string(": ") ); + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + EMIterationTable.add(iclass + 1, ichan + 2, this->m_ListOfClassStatistics[iclass].m_Means[ichan], "%8.2f"); + } + } + { + std::ostringstream oss; + EMIterationTable.Print(oss); + muLogMacro( << oss.str() ); + } +} + +template +void +EMSegmentationFilter +::WriteDebugForegroundMask(const ByteImageType::Pointer & currForgroundBrainMask, + const unsigned int CurrentEMIteration) const +{ + std::stringstream CurrentEMIteration_stream(""); + + CurrentEMIteration_stream << CurrentEMIteration; + typedef itk::ImageFileWriter WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + const std::string fn = this->m_OutputDebugDir + "/MASK_LEVEL_" + CurrentEMIteration_stream.str() + ".nii.gz"; + writer->SetInput(currForgroundBrainMask); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl ); +} + +template +void +EMSegmentationFilter +::Update() +{ + if( m_UpdateRequired ) + { + + // TODO: This should be filled out from the XML file eventually + this->m_PriorsBackgroundValues.resize(this->m_OriginalSpacePriors.size() ); + std::fill(this->m_PriorsBackgroundValues.begin(), this->m_PriorsBackgroundValues.end(), 0); + { + // HACK: In the XML file, each prior should also specify the default + // background value + // to be used during the warping process. + // For AIR, it should be 1.0, for all others is should be 0.0 + // + const LOOPITERTYPE HACK_AIR_INDEX = 0; + m_PriorsBackgroundValues[HACK_AIR_INDEX] = 1; + } + + this->EMLoop(); + m_UpdateRequired = false; + } +} + +/** + * The EMLoop is the global algorithmic framework for + * completing the iterative parts of the processing. + */ + +template +void +EMSegmentationFilter +::EMLoop() +{ + if( this->m_TemplateGenericTransform.IsNull() ) + { + std::cout << "ERROR: Must suppply an intial transformation!" << std::endl; + exit(-1); + } + + this->m_NonAirRegion = ComputeTissueRegion(this->m_InputImages[0], 3); + if( this->m_DebugLevel > 9 ) + { + this->WriteDebugHeadRegion(0); + } + + this->m_WarpedPriors = + WarpImageList(this->m_OriginalSpacePriors, this->m_InputImages[0], + this->m_PriorsBackgroundValues, + this->m_TemplateGenericTransform); + if( this->m_DebugLevel > 9 ) + { + this->WriteDebugWarpedAtlasPriors(0); + std::vector backgroundValues(m_OriginalAtlasImages.size() ); + std::fill(backgroundValues.begin(), backgroundValues.end(), 0); + this->m_WarpedAtlasImages = + WarpImageList(this->m_OriginalAtlasImages, this->m_InputImages[0], backgroundValues, + this->m_TemplateGenericTransform); + this->WriteDebugWarpedAtlasImages(0); + } + typename ByteImageType::Pointer + currForgroundBrainMask = ComputeForegroundProbMask(this->m_WarpedPriors, + this->m_PriorIsForegroundPriorVector); + if( this->m_DebugLevel > 9 ) + { + WriteDebugForegroundMask(currForgroundBrainMask, 0); + } + + std::vector SubjectCandidateRegions = this->UpdateIntensityBasedClippingOfPriors( + 0, this->m_InputImages, this->m_WarpedPriors, currForgroundBrainMask); + { + BlendPosteriorsAndPriors(0.0, this->m_WarpedPriors, this->m_WarpedPriors, this->m_WarpedPriors); + NormalizeProbListInPlace(this->m_WarpedPriors); + if( this->m_DebugLevel > 9 ) + { + this->WriteDebugBlendClippedPriors(0); + } + } + + // NOTE: Labels are only needed if debugging them. + ComputeLabels(this->m_WarpedPriors, this->m_PriorIsForegroundPriorVector, + this->m_PriorLabelCodeVector, this->m_NonAirRegion, this->m_DirtyLabels, + this->m_CleanedLabels); + this->WriteDebugLabels(0); + this->m_ListOfClassStatistics.resize(0); // Reset this to empty for debugging + // purposes to induce failures when + // being re-used. + this->m_CorrectedImages = + CorrectBias(1, 0, SubjectCandidateRegions, this->m_InputImages, this->m_CleanedLabels, this->m_NonAirRegion, + this->m_WarpedPriors, this->m_PriorUseForBiasVector, this->m_SampleSpacing, this->m_DebugLevel, + this->m_OutputDebugDir); + WriteDebugCorrectedImages(this->m_CorrectedImages, 0); +#if 0 // This is probably overkill since the update of NonAirRegion is likely + // not making much in changes at this level of bias correction! Otsu + // works well even in hightly biased images + this->m_NonAirRegion = ComputeTissueRegion(this->m_CorrectedImages[0], 0); + if( this->m_DebugLevel > 5 ) + { + this->WriteDebugHeadRegion(0); + } +#endif + this->m_ListOfClassStatistics = + ComputeDistributions(SubjectCandidateRegions, this->m_WarpedPriors, + this->m_CorrectedImages, + this->m_DebugLevel); + this->WritePartitionTable(0); + { + // Now check that the intraSubjectOriginalImageList has positive definite + // covariance matrix. + // The algorithm is not stable if the covariance matrix is not positive + // definite, and this + // occurs when two or more of the images are linearly dependant (i.e. nearly + // the same image). + for( unsigned int q = 0; q < this->m_ListOfClassStatistics.size(); q++ ) + { + try + { + ComputeCovarianceDeterminant( this->m_ListOfClassStatistics[q].m_Covariance ); + } + catch( ... ) + { + std::cerr << "ERROR:\nERROR:\nERROR:\nERROR:" + << + " Linearly dependant input images detected. Please remove the images in the above table that show very similar values images." + << "ERROR:\nERROR:\nERROR:\nERROR:" << std::endl; + exit(-1); + } + } + } + + this->CheckInput(); + + // FloatingPrecision logLikelihood = vnl_huge_val(1.0); + FloatingPrecision logLikelihood = 1.0 / vnl_math::eps; + FloatingPrecision deltaLogLikelihood = 1.0; + + unsigned int biasdegree = 0; + + // EM loop + bool converged = false; + double priorWeighting = 1.00; // NOTE: This turns off blending of + // posteriors and priors when set to 1.0, + // thus short-circuting the system. + unsigned int CurrentEMIteration = 1; + while( !converged && ( CurrentEMIteration <= m_MaximumIterations ) ) + { + // Recompute posteriors, not at full resolution + this->m_Posteriors = + ComputePosteriors(this->m_WarpedPriors, this->m_PriorWeights, + this->m_CorrectedImages, + this->m_ListOfClassStatistics); + NormalizeProbListInPlace(this->m_Posteriors); + this->WriteDebugPosteriors(CurrentEMIteration); + ComputeLabels(this->m_Posteriors, this->m_PriorIsForegroundPriorVector, + this->m_PriorLabelCodeVector, this->m_NonAirRegion, this->m_DirtyLabels, + this->m_CleanedLabels); + this->WriteDebugLabels(CurrentEMIteration); + this->m_CorrectedImages = + CorrectBias(this->m_MaxBiasDegree, CurrentEMIteration, SubjectCandidateRegions, this->m_InputImages, + this->m_CleanedLabels, this->m_NonAirRegion, this->m_Posteriors, this->m_PriorUseForBiasVector, + this->m_SampleSpacing, this->m_DebugLevel, + this->m_OutputDebugDir); + WriteDebugCorrectedImages(this->m_CorrectedImages, CurrentEMIteration); + this->m_ListOfClassStatistics.resize(0); // Reset this to empty for + // debugging purposes to induce + // failures when being re-used. + this->m_ListOfClassStatistics = + ComputeDistributions(SubjectCandidateRegions, this->m_Posteriors, + this->m_CorrectedImages, + this->m_DebugLevel); + this->WritePartitionTable(CurrentEMIteration); + + // Now update transformation and estimates of probability regions based on + // current knowledge. + { + this->UpdateTransformation(CurrentEMIteration); // This changes the class + // value of + // + // m_TemplateGenericTransform. + this->m_WarpedPriors = + WarpImageList(this->m_OriginalSpacePriors, this->m_InputImages[0], + this->m_PriorsBackgroundValues, + this->m_TemplateGenericTransform); + if( this->m_DebugLevel > 9 ) + { + this->WriteDebugWarpedAtlasPriors(CurrentEMIteration); + std::vector backgroundValues(m_OriginalAtlasImages.size() ); + std::fill(backgroundValues.begin(), backgroundValues.end(), 0); + this->m_WarpedAtlasImages = + WarpImageList(this->m_OriginalAtlasImages, this->m_InputImages[0], backgroundValues, + this->m_TemplateGenericTransform); + this->WriteDebugWarpedAtlasImages(CurrentEMIteration); + } + SubjectCandidateRegions = this->ForceToOne(CurrentEMIteration, this->m_CorrectedImages, this->m_WarpedPriors, + this->m_CleanedLabels); + { + BlendPosteriorsAndPriors(1.0 - priorWeighting, this->m_Posteriors, this->m_WarpedPriors, + this->m_WarpedPriors); + priorWeighting *= priorWeighting; + NormalizeProbListInPlace(this->m_WarpedPriors); + this->WriteDebugBlendClippedPriors(CurrentEMIteration); + } + } + + FloatingPrecision prevLogLikelihood = ( logLikelihood < vnl_math::eps ) ? vnl_math::eps : logLikelihood; + // Compute log-likelihood and normalize posteriors + logLikelihood = this->ComputeLogLikelihood(); + muLogMacro(<< "log(likelihood) = " << logLikelihood << std::endl); + // TODO: move to before prevL update + deltaLogLikelihood = vcl_fabs( (logLikelihood - prevLogLikelihood) / prevLogLikelihood); + // (logLikelihood - prevLogLikelihood) / vcl_fabs(prevLogLikelihood); + CHECK_NAN(deltaLogLikelihood, __FILE__, __LINE__); + muLogMacro( + << "delta vcl_log(likelihood) = " << deltaLogLikelihood << " Convergence Tolerance: " + << m_WarpLikelihoodTolerance << std::endl); + + // Convergence check + converged = (CurrentEMIteration >= m_MaximumIterations) + // Ignore jumps in the vcl_log likelihood + // || + // (deltaLogLikelihood < 0) + || + ( (deltaLogLikelihood < m_LikelihoodTolerance) + && + (biasdegree == m_MaxBiasDegree) ); + + CurrentEMIteration++; + const float biasIncrementInterval = (m_MaximumIterations / (m_MaxBiasDegree + 1) ); + CHECK_NAN(biasIncrementInterval, __FILE__, __LINE__); + // Bias correction + if( m_MaxBiasDegree > 0 ) + { + if( ( + (deltaLogLikelihood < m_BiasLikelihoodTolerance) + || ( CurrentEMIteration > (biasdegree + 1) * biasIncrementInterval) ) + && + (biasdegree < m_MaxBiasDegree) + ) + { + biasdegree++; + } + } + } // end EM loop + + muLogMacro(<< "Done computing posteriors with " << CurrentEMIteration << " iterations" << std::endl); + + this->m_Posteriors = + ComputePosteriors(this->m_WarpedPriors, this->m_PriorWeights, + this->m_CorrectedImages, + this->m_ListOfClassStatistics); + NormalizeProbListInPlace(this->m_Posteriors); + this->WriteDebugPosteriors(CurrentEMIteration + 100); + ComputeLabels(this->m_Posteriors, this->m_PriorIsForegroundPriorVector, + this->m_PriorLabelCodeVector, this->m_NonAirRegion, this->m_DirtyLabels, + this->m_CleanedLabels); + this->WriteDebugLabels(CurrentEMIteration + 100); + + // Bias correction at full resolution, still using downsampled images + // for computing the bias field coeficients + if( m_MaxBiasDegree > 0 ) + { + this->m_CorrectedImages = + CorrectBias(biasdegree, CurrentEMIteration + 100, SubjectCandidateRegions, this->m_InputImages, + this->m_CleanedLabels, this->m_NonAirRegion, this->m_Posteriors, this->m_PriorUseForBiasVector, + this->m_SampleSpacing, this->m_DebugLevel, + this->m_OutputDebugDir); + WriteDebugCorrectedImages(this->m_CorrectedImages, CurrentEMIteration + 100); + this->m_ListOfClassStatistics.resize(0); // Reset this to empty for + // debugging purposes to induce + // failures when being re-used. + this->m_ListOfClassStatistics = + ComputeDistributions(SubjectCandidateRegions, this->m_Posteriors, + this->m_CorrectedImages, + this->m_DebugLevel); +#if 0 // This is probably overkill since the update of NonAirRegion is likely + // not making much in changes at this level of bias correction! Otsu + // works well even in hightly biased images + this->m_NonAirRegion = ComputeTissueRegion(this->m_CorrectedImages[0], 0); + if( this->m_DebugLevel > 9 ) + { + this->WriteDebugHeadRegion(0); + } +#endif + this->m_RawCorrectedImages = + CorrectBias(biasdegree, CurrentEMIteration + 100, SubjectCandidateRegions, this->m_RawInputImages, + this->m_CleanedLabels, this->m_NonAirRegion, this->m_Posteriors, this->m_PriorUseForBiasVector, + this->m_SampleSpacing, this->m_DebugLevel, + this->m_OutputDebugDir); + } + this->m_ListOfClassStatistics.resize(0); // Reset this to empty for debugging + // purposes to induce failures when + // being re-used. + this->m_ListOfClassStatistics = + ComputeDistributions(SubjectCandidateRegions, this->m_Posteriors, + this->m_CorrectedImages, + this->m_DebugLevel); + this->WritePartitionTable(0 + 100); +} + +#endif diff --git a/BRAINSABC/brainseg/EMSegmentationFilter_float+float.cxx b/BRAINSABC/brainseg/EMSegmentationFilter_float+float.cxx new file mode 100644 index 00000000..4fbc9920 --- /dev/null +++ b/BRAINSABC/brainseg/EMSegmentationFilter_float+float.cxx @@ -0,0 +1,7 @@ +#include "EMSegmentationFilter.txx" + +#include "itkImage.h" + +typedef itk::Image FloatImageType; + +template class EMSegmentationFilter; diff --git a/BRAINSABC/brainseg/EMSplitPriorMST.h b/BRAINSABC/brainseg/EMSplitPriorMST.h new file mode 100644 index 00000000..633f9dd3 --- /dev/null +++ b/BRAINSABC/brainseg/EMSplitPriorMST.h @@ -0,0 +1,393 @@ +#if 0 +#ifndef __EMSplitPriorMST_h +#define __EMSplitPriorMST_h +template +void +EMSegmentationFilter +::SplitPriorMST(unsigned int /*iprior*/) +{ + exit(-1); +#if 0 + const unsigned int numChannels = m_InputImages.size(); + const unsigned int numPriors = m_WarpedPriors.size(); + + if( iprior >= numPriors ) + { + itkExceptionMacro(<< "Invalid prior index"); + } + + if( m_PriorGaussianClusterCountVector[iprior] == 1 ) + { + return; // No split necessary + } + + unsigned int numClasses = 0; + for( unsigned int i = 0; i < numPriors; i++ ) + { + numClasses += m_PriorGaussianClusterCountVector[i]; + } + + muLogMacro(<< "Splitting distributions for prior " << iprior + 1 << " (MST)\n"); + + InputImageSizeType size + = m_InputImages[0]->GetLargestPossibleRegion().GetSize(); + + ProbabilityImagePointer probImg = m_WarpedPriors[iprior]; + + // Find max prob + double maxP = 0.0; + { + // #pragma omp parallel for + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + if( m_CurrentIterationForegroundMask->GetPixel(currIndex) == 0 ) + { + continue; + } + if( probImg->GetPixel(currIndex) > maxP ) + { + maxP = probImg->GetPixel(currIndex); + } + } + } + } + } + + // Select uniqueClassAverageSamples by thresholding prior with value above tau + const double tau = 0.85 * maxP; + muLogMacro(<< "Sampling with threshold tau = " << tau << "\n"); + + unsigned int numPossibleSamples = 0; + { + // #pragma omp parallel for + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + if( m_CurrentIterationForegroundMask->GetPixel(currIndex) == 0 ) + { + continue; + } + if( probImg->GetPixel(currIndex) >= tau ) + { + numPossibleSamples++; + } + } + } + } + } + + // Make a mapping of unique type names to a list of corresponding corrected + // images indicies + // The uniqueClassAverageSamples should only have dimension of the number of + // unique class types, + // and not the total number of images being corrected. + std::map > uniqueClassMappings; + { + for( unsigned int u = 0; u < m_InputVolumeTypes.size(); u++ ) + { + uniqueClassMappings[m_InputVolumeTypes[u]].push_back(u); + } + } + // Sample selection mask + std::vector uniqueClassAverageSamples; + std::vector uniqueClassAverageIndicies; + size_t numSamples = numPossibleSamples; + { + std::vector selectMask(numPossibleSamples); + for( unsigned int i = 0; i < numPossibleSamples; i++ ) + { + selectMask[i] = 0; + } + + if( numSamples > 50000 ) + { + numSamples = 50000; + } + + muLogMacro(<< " Selecting " << numSamples << " / " << numPossibleSamples << "\n"); + + itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer + rng( itk::Statistics::MersenneTwisterRandomVariateGenerator::New() ); + static unsigned int rngInitializer = 0; + rng->Initialize(rngInitializer); + rngInitializer++; + + if( numSamples < numPossibleSamples ) + { + unsigned int c = 0; + while( c < numSamples ) + { + const unsigned int which = (unsigned int) + rng->GetIntegerVariate(numPossibleSamples - 1); + if( selectMask[which] != 0 ) + { + continue; + } + selectMask[which] = 1; + c++; + } + } + else + { + for( unsigned int i = 0; i < numSamples; i++ ) + { + selectMask[i] = 1; + } + } + + uniqueClassAverageSamples.clear(); + uniqueClassAverageSamples.reserve(numSamples); + uniqueClassAverageIndicies.clear(); + uniqueClassAverageIndicies.reserve(numSamples); + + muLogMacro(<< " Finding uniqueClassAverageSamples...\n"); + + // Compute the muAccumulator + { + const size_t numUniqueClassMappings = uniqueClassMappings.size(); + unsigned int selectMaskIndex = 0; + { + // #pragma omp parallel for + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + if( ( m_CurrentIterationForegroundMask->GetPixel(currIndex) == 0 ) || + ( probImg->GetPixel(currIndex) < tau ) ) + { + continue; + } + + if( selectMask[selectMaskIndex] != 0 ) + { + QHullMSTClusteringProcess::VertexType x(numUniqueClassMappings); + unsigned int uniqueIndex = 0; + for( std::map >::const_iterator mi = uniqueClassMappings.begin(); + mi != uniqueClassMappings.end(); + mi++ ) + { + const std::list & currentListOfImages = mi->second; + const double invCurrentListSize = 1.0 + / ( static_cast( currentListOfImages.size() ) ); + x[uniqueIndex] = 0.0; + for( std::list::const_iterator li = currentListOfImages.begin(); + li != currentListOfImages.end(); + li++ + ) + { + const typename TInputImage::PixelType currPixel = this->m_CorrectedImages[*li]->GetPixel(currIndex); + x[uniqueIndex] += currPixel * invCurrentListSize; + } + uniqueIndex++; + } + uniqueClassAverageSamples.push_back(x); + uniqueClassAverageIndicies.push_back(currIndex); + } + ++selectMaskIndex; + } + } + } + } + } + } + + muLogMacro(<< " Create MST...\n"); + + QHullMSTClusteringProcess mstProc; + mstProc.SetInputVertices(uniqueClassAverageSamples); + mstProc.SortOn(); + + muLogMacro(<< " Allocate maps...\n"); + + // TODO: Make this an std::vector + unsigned int *mapOfSamplesIntoCluster = new unsigned int[numSamples]; + { + for( double T = 2.0; T > 0; T -= 0.01 ) + { + if( T < 1.0 ) + { + itkExceptionMacro(<< "Failed clustering prior " << iprior + 1); + } + muLogMacro(<< " MST clustering, T = " << T << "\n"); + const unsigned int numClusters = mstProc.GetClusters(mapOfSamplesIntoCluster, T); + + if( numClusters < m_PriorGaussianClusterCountVector[iprior] ) + { + continue; + } + + // Check cluster sizes + bool sizeOK = true; + for( unsigned int currentPriorSubClassCluster = 0; + currentPriorSubClassCluster < m_PriorGaussianClusterCountVector[iprior]; + currentPriorSubClassCluster++ ) + { + unsigned int numSamplesInSubClassCluster = 0; + for( unsigned int i = 0; i < numSamples; i++ ) + { + if( mapOfSamplesIntoCluster[i] == currentPriorSubClassCluster ) + { + numSamplesInSubClassCluster++; + } + } + if( numSamplesInSubClassCluster < 10 ) // TODO: Determine what this + // does? + { + sizeOK = false; + } + } + if( sizeOK ) + { + break; + } + } + } + // TODO: Should be able to clear uniqueClassAverageSamples here. + // =============Clustering Done + + // Find beginning class index for this prior + unsigned int istart = 0; + for( unsigned int j = 0; j < iprior; j++ ) + { + istart += m_PriorGaussianClusterCountVector[j]; + } + // Use the largest clusters to estimate the Gaussian parameters + for( unsigned int currentPriorSubClassCluster = 0; + currentPriorSubClassCluster < m_PriorGaussianClusterCountVector[iprior]; + currentPriorSubClassCluster++ ) + { + const unsigned int iclass = istart + currentPriorSubClassCluster; + + unsigned int numSamplesInSubClassCluster = 0; + for( unsigned int i = 0; i < numSamples; i++ ) + { + if( mapOfSamplesIntoCluster[i] == currentPriorSubClassCluster ) + { + numSamplesInSubClassCluster++; + } + } + + muLogMacro(<< " Estimating Gaussian parameters for prior " << iprior + 1 << ":class " << iclass + 1); + muLogMacro(<< " with " << numSamplesInSubClassCluster << " uniqueClassAverageSamples\n"); + + QHullMSTClusteringProcess::VertexType muAccumulator( m_InputVolumeTypes.size() ); + std::fill( muAccumulator.begin(), muAccumulator.end(), 0.0F ); + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + muAccumulator[ichan] = 0.0; + for( unsigned int i = 0; i < numSamples; i++ ) + { + if( mapOfSamplesIntoCluster[i] == currentPriorSubClassCluster ) + { + const typename TInputImage::PixelType currPixel + = this->m_CorrectedImages[ichan]->GetPixel(uniqueClassAverageIndicies[i]); + muAccumulator[ichan] += currPixel; + } + } + muAccumulator[ichan] /= static_cast( numSamplesInSubClassCluster ); + this->m_ListOfClassStatistics[iclass].m_Means[ichan] = muAccumulator[ichan]; + } + // Compute symmetric covariance matrix. + MatrixType tmpSubClassSampleCovarianceBetweenChannels(numChannels, numChannels); + for( unsigned int channel1Index = 0; channel1Index < numChannels; channel1Index++ ) + { + const double channel1mu = this->m_ListOfClassStatistics[iclass].m_Means[channel1Index]; + for( unsigned int channel2Index = channel1Index; channel2Index < numChannels; channel2Index++ ) + { + const double channel2mu = this->m_ListOfClassStatistics[iclass].m_Means[channel2Index]; + double tmpSubClassClusterCovarianceBetweenChannels12 = 0.0; + for( unsigned int i = 0; i < numSamples; i++ ) + { + if( mapOfSamplesIntoCluster[i] == currentPriorSubClassCluster ) + { + const typename TInputImage::PixelType channel1Pixel + = this->m_CorrectedImages[channel1Index]->GetPixel(uniqueClassAverageIndicies[i]); + const double diff1 = static_cast( channel1Pixel ) - channel1mu; + + const typename TInputImage::PixelType channel2Pixel + = this->m_CorrectedImages[channel2Index]->GetPixel(uniqueClassAverageIndicies[i]); + const double diff2 = static_cast( channel2Pixel ) - channel2mu; + tmpSubClassClusterCovarianceBetweenChannels12 += ( diff1 * diff2 ); + } + } + tmpSubClassClusterCovarianceBetweenChannels12 + /= ( static_cast( numSamplesInSubClassCluster ) - 1.0 + vnl_math::eps ); + if( channel1Index == channel2Index ) + { + tmpSubClassClusterCovarianceBetweenChannels12 += 1e-20; + } + + tmpSubClassSampleCovarianceBetweenChannels(channel1Index, + channel2Index) = tmpSubClassClusterCovarianceBetweenChannels12; + tmpSubClassSampleCovarianceBetweenChannels(channel2Index, + channel1Index) = tmpSubClassClusterCovarianceBetweenChannels12; + } + } + // Scale the covariance up a bit for softer initialization + tmpSubClassSampleCovarianceBetweenChannels *= 1.2; + this->m_ListOfClassStatistics[iclass].m_Covariance = tmpSubClassSampleCovarianceBetweenChannels; + } + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + const double detcov = vnl_determinant(this->m_ListOfClassStatistics[iclass].m_Covariance); + if( detcov <= 0.0 ) + { + itkExceptionMacro(<< "Determinant of covariance for class " << iclass + << " is <= 0.0 (" << detcov << "), covariance matrix:\n" + << this->m_ListOfClassStatistics[iclass].m_Covariance); + } + } + + uniqueClassAverageSamples.clear(); + uniqueClassAverageIndicies.clear(); // Free the memory. + + delete[] mapOfSamplesIntoCluster; + + // Special case for background, always set the "darkest" mean + // to be the last and set it to zero + if( iprior == ( numPriors - 1 ) ) + { + unsigned int imin = istart; + double minm = this->m_ListOfClassStatistics[istart].m_Means.squared_magnitude(); + for( unsigned int currentPriorSubClassCluster = 1; + currentPriorSubClassCluster < m_PriorGaussianClusterCountVector[iprior]; + currentPriorSubClassCluster++ ) + { + unsigned int iclass = istart + currentPriorSubClassCluster; + double mag = this->m_ListOfClassStatistics[iclass].m_Means.squared_magnitude(); + if( mag < minm ) + { + imin = iclass; + minm = mag; + } + } + + if( imin != ( numClasses - 1 ) ) + { + muLogMacro( + << " Replacing " << this->m_ListOfClassStatistics[imin].m_Means << " with zero\n"); + VectorType v = this->m_ListOfClassStatistics[numClasses - 1].m_Means; + this->m_ListOfClassStatistics[imin].m_Means = v; + } + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + this->m_ListOfClassStatistics[numClasses - 1].m_Means[ichan] = 0; + } + } +#endif +} + +#endif +#endif diff --git a/BRAINSABC/brainseg/ESLR.cxx b/BRAINSABC/brainseg/ESLR.cxx new file mode 100644 index 00000000..aaf08ab4 --- /dev/null +++ b/BRAINSABC/brainseg/ESLR.cxx @@ -0,0 +1,58 @@ +#include "ESLRCLP.h" +#include "BRAINSThreadControl.h" +#include "ExtractSingleLargestRegion.h" + +#include + +#include "itkImageFileWriter.h" +#include "itkImageFileReader.h" + +int main(int argc, char *argv[]) +{ + PARSE_ARGS; + BRAINSUtils::SetThreadCount(numberOfThreads); + + typedef itk::Image ByteImageType; + typedef itk::ImageFileReader ReaderType; + + ReaderType::Pointer myReader = ReaderType::New(); + myReader->SetFileName(inputVolume); + myReader->Update(); + ByteImageType::Pointer myDirtyRegion = myReader->GetOutput(); + + ByteImageType::Pointer myCleanRegion + = ExtractSingleLargestRegion(low, high, openingSize, closingSize, safetySize, myDirtyRegion); + + if( preserveOutside == true ) // For values outside the specified range, + // preserve those values. + { + std::cout << "PRESERVING OUTSIDE VALUES" << std::endl; + itk::ImageRegionConstIterator dit( myDirtyRegion, myDirtyRegion->GetLargestPossibleRegion() ); + itk::ImageRegionIterator cit( myCleanRegion, myCleanRegion->GetLargestPossibleRegion() ); + dit.GoToBegin(); + cit.GoToBegin(); + while( ( !cit.IsAtEnd() ) && ( !dit.IsAtEnd() ) ) + { + if( ( dit.Get() < low ) || ( dit.Get() > high ) ) // Outside of cleaning + // range, then + // preserve old value + { + cit.Set( dit.Get() ); + } + ++cit; + ++dit; + } + } + + typedef itk::ImageFileWriter OutputWriterType; + OutputWriterType::Pointer writer = OutputWriterType::New(); + + writer->SetInput( myCleanRegion ); + writer->UseCompressionOn(); + const std::string fn = std::string(outputVolume); + writer->SetFileName( fn.c_str() ); + writer->Update(); + + return 0; +} + diff --git a/BRAINSABC/brainseg/ESLR.xml b/BRAINSABC/brainseg/ESLR.xml new file mode 100644 index 00000000..ed07a836 --- /dev/null +++ b/BRAINSABC/brainseg/ESLR.xml @@ -0,0 +1,80 @@ + + + BRAINS.Segmentation + ESLR + From a range of label map values, extract the largest contiguous region of those labels + + + + + + inputVolume + inputVolume + Input Label Volume + + + input + + + outputVolume + outputVolume + Output Label Volume + + + output + + + low + low + The lower bound of the labels to be used. + + 1 + + + high + high + The higher bound of the labels to be used. + + 5 + + + closingSize + closingSize + The closing size for hole filling. + + 2 + + + openingSize + openingSize + The opening size for hole filling. + + 2 + + + safetySize + safetySize + The safetySize size for the clipping region. + + 1 + + + preserveOutside + preserveOutside + For values outside the specified range, preserve those values. + + false + + + + + + numberOfThreads + numberOfThreads + + Explicitly specify the maximum number of threads to use. + -1 + + + + diff --git a/BRAINSABC/brainseg/ExtractSingleLargestRegion.cxx b/BRAINSABC/brainseg/ExtractSingleLargestRegion.cxx new file mode 100644 index 00000000..cf68da61 --- /dev/null +++ b/BRAINSABC/brainseg/ExtractSingleLargestRegion.cxx @@ -0,0 +1,132 @@ +#include "itkBinaryBallStructuringElement.h" +#include "itkBinaryDilateImageFilter.h" +#include "itkBinaryErodeImageFilter.h" + +#include +#include +#include +#include "itkMultiplyImageFilter.h" +#include "ExtractSingleLargestRegion.h" + +itk::Image::Pointer +ExtractSingleLargestRegionFromMask(itk::Image::Pointer Mask, + const int openingSize, const int closingSize, const int safetySize, + itk::Image::Pointer inputLabelImage) +{ + typedef itk::Image ByteImageType; + typedef itk::BinaryBallStructuringElement StructElementType; + typedef + itk::BinaryDilateImageFilter DilateType; + typedef itk::BinaryErodeImageFilter ErodeType; + typedef itk::ConnectedComponentImageFilter > FilterType; + + ByteImageType::Pointer errodedImage = Mask; + if( openingSize > 0 ) + { + // Binary Erode + StructElementType openStruct; + openStruct.SetRadius(openingSize); + openStruct.CreateStructuringElement(); + ErodeType::Pointer erode = ErodeType::New(); + erode->SetErodeValue(1); + erode->SetKernel(openStruct); + erode->SetInput(Mask); + erode->Update(); + errodedImage = erode->GetOutput(); + } + + FilterType::Pointer labelConnectedComponentsFilter = FilterType::New(); + // SimpleFilterWatcher watcher(labelConnectedComponentsFilter); + // watcher.QuietOn(); + labelConnectedComponentsFilter->SetInput( errodedImage ); + + typedef itk::RelabelComponentImageFilter, ByteImageType> RelabelType; + RelabelType::Pointer relabel = RelabelType::New(); + relabel->SetInput( labelConnectedComponentsFilter->GetOutput() ); + try + { + relabel->Update(); + } + catch( itk::ExceptionObject & excep ) + { + std::cerr << "Relabel: exception caught !" << std::endl; + std::cerr << excep << std::endl; + } + + typedef itk::BinaryThresholdImageFilter BinaryThresholdFilter; + BinaryThresholdFilter::Pointer labelThreshold = BinaryThresholdFilter::New(); + labelThreshold->SetInput( relabel->GetOutput() ); + labelThreshold->SetInsideValue(1); + labelThreshold->SetOutsideValue(0); + labelThreshold->SetLowerThreshold(1); // Only the largest label + labelThreshold->SetUpperThreshold(1); // Only the largest label + labelThreshold->Update(); + + ByteImageType::Pointer largestLabel = labelThreshold->GetOutput(); + + ByteImageType::Pointer dilateImage = largestLabel; + if( closingSize > 0 ) + { + // Dilate mask + StructElementType closeStruct; + closeStruct.SetRadius(openingSize + closingSize); + closeStruct.CreateStructuringElement(); + DilateType::Pointer dil = DilateType::New(); + dil->SetDilateValue(1); + dil->SetKernel(closeStruct); + dil->SetInput( largestLabel ); + dil->Update(); + dilateImage = dil->GetOutput(); + } + + ByteImageType::Pointer safetyImage = dilateImage; + const int finalOpeningSize = ( closingSize - safetySize ) > 0 ? ( closingSize - safetySize ) : 0; + if( finalOpeningSize > 0 ) + { + // Binary Erode + StructElementType remainderStruct; + remainderStruct.SetRadius(finalOpeningSize); + remainderStruct.CreateStructuringElement(); + ErodeType::Pointer finalErode = ErodeType::New(); + finalErode->SetErodeValue(1); + finalErode->SetKernel(remainderStruct); + finalErode->SetInput( dilateImage ); + finalErode->Update(); + safetyImage = finalErode->GetOutput(); + } + + typedef itk::MultiplyImageFilter multFilter; + multFilter::Pointer myMult1 = multFilter::New(); + myMult1->SetInput1( safetyImage ); + myMult1->SetInput2( Mask ); + myMult1->Update(); + + typedef itk::MultiplyImageFilter multFilter; + multFilter::Pointer myMult2 = multFilter::New(); + myMult2->SetInput1( myMult1->GetOutput() ); + myMult2->SetInput2(inputLabelImage); + myMult2->Update(); + return myMult2->GetOutput(); +} + +itk::Image::Pointer +ExtractSingleLargestRegion(const unsigned char threshold_low, const unsigned char threshold_high, + const int openingSize, const int closingSize, const int safetySize, + itk::Image::Pointer inputLabelImage) +{ + typedef itk::Image ByteImageType; + typedef itk::BinaryThresholdImageFilter BinaryThresholdFilter; + BinaryThresholdFilter::Pointer threshold = BinaryThresholdFilter::New(); + threshold->SetInput(inputLabelImage); + threshold->SetInsideValue(1); + threshold->SetOutsideValue(0); + threshold->SetLowerThreshold(threshold_low); + threshold->SetUpperThreshold( threshold_high ); + threshold->Update(); + + return ExtractSingleLargestRegionFromMask( + threshold->GetOutput(), openingSize, closingSize, safetySize, inputLabelImage); +} + diff --git a/BRAINSABC/brainseg/ExtractSingleLargestRegion.h b/BRAINSABC/brainseg/ExtractSingleLargestRegion.h new file mode 100644 index 00000000..43038501 --- /dev/null +++ b/BRAINSABC/brainseg/ExtractSingleLargestRegion.h @@ -0,0 +1,23 @@ +#ifndef __ExtractSingleLargestRegion_h +#define __ExtractSingleLargestRegion_h + +#include "itkImage.h" + +extern itk::Image::Pointer ExtractSingleLargestRegionFromMask(itk::Image::Pointer Mask, const int openingSize, + const int closingSize, const int safetySize, + itk::Image + ::Pointer inputLabelImage); + +extern +itk::Image::Pointer ExtractSingleLargestRegion(const unsigned char threshold_low, + const unsigned char threshold_high, + const int openingSize, const int closingSize, + const int safetySize, + itk::Image + ::Pointer inputLabelImage); + +#endif // ExtractSingleLargestRegion_h diff --git a/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.cxx b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.cxx new file mode 100644 index 00000000..67b4a3d3 --- /dev/null +++ b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.cxx @@ -0,0 +1,133 @@ +/* + * Author : Eun Young (Regina) Kim + */ + +#include "itkImage.h" +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" +#include "itkImageRegionIterator.h" +#include + +#include "GenerateLabelMapFromProbabilityMapCLP.h" +#include "BRAINSThreadControl.h" + +/* + * main function + */ + +int +main(int argc, char *argv[]) +{ + PARSE_ARGS; + BRAINSUtils::SetThreadCount(numberOfThreads); + if( inputVolumes.size() < 1 ) + { + std::cerr << argv[0] << ": Missing required probability maps" + << std::cerr; + exit(1); + + } + + const unsigned int numberOfProbabilityMaps = inputVolumes.size(); + + // + // Define Image Type + // + typedef float ProbabilityMapPixelType; + const unsigned int Dimension = 3; + typedef itk::Image ProbabilityMapImageType; + + // + // Label Index should start from zero and increasing order. + // + + // + // read in images + // + + std::vector probabilityImages( numberOfProbabilityMaps ); + for( unsigned int indexInputImages = 0; + indexInputImages < numberOfProbabilityMaps; + indexInputImages++ ) + { + std::cout << "- Read image::" + << inputVolumes[indexInputImages] + << std::endl; + typedef itk::ImageFileReader ProbabilityImageReaderType; + + ProbabilityImageReaderType::Pointer probabilityReader = ProbabilityImageReaderType::New(); + + probabilityReader->SetFileName( inputVolumes[indexInputImages] ); + probabilityReader->Update(); + + probabilityImages[indexInputImages] = probabilityReader->GetOutput(); + } + + // + // crerate empty label maps + // + std::cout << "Create Label Map" << std::endl; + typedef unsigned int LabelMapPixelType; + typedef itk::Image LabelMapImageType; + + LabelMapImageType::Pointer labelImage = LabelMapImageType::New(); + + std::cerr << "here" << __FILE__ << " " << __LINE__ << std::endl; + std::cerr << " ProbImage: " << probabilityImages[0] << std::endl; + labelImage->CopyInformation( probabilityImages[0] ); + std::cerr << "here" << __FILE__ << " " << __LINE__ << std::endl; + labelImage->SetRegions( probabilityImages[0]->GetLargestPossibleRegion() ); + std::cerr << "here" << __FILE__ << " " << __LINE__ << std::endl; + labelImage->Allocate(); + std::cerr << "here" << __FILE__ << " " << __LINE__ << std::endl; + labelImage->FillBuffer(0); + std::cerr << "here" << __FILE__ << " " << __LINE__ << std::endl; + + std::cout << "start iteration " << std::endl; + // + // Iterate Images + // + typedef itk::ImageRegionIterator IteratorType; + + IteratorType probabilityIterator( probabilityImages[0], + probabilityImages[0]->GetLargestPossibleRegion() ); + + typedef itk::ImageRegionIterator LabelIteratorType; + LabelIteratorType labelIterator( labelImage, labelImage->GetLargestPossibleRegion() ); + for( probabilityIterator.GoToBegin(), labelIterator.GoToBegin(); + !probabilityIterator.IsAtEnd(); + ++probabilityIterator, ++labelIterator ) + { + ProbabilityMapPixelType max = probabilityIterator.Get(); + LabelMapPixelType label = 0; + for( unsigned int indexInputImages = 1; indexInputImages < numberOfProbabilityMaps; + indexInputImages++ ) + { + ProbabilityMapPixelType pixelValue = + probabilityImages[indexInputImages]->GetPixel( probabilityIterator.GetIndex() ); + if( pixelValue > max ) + { + max = pixelValue; + label = indexInputImages; + } + } + + labelIterator.Set( label ); + + } + + // + // Image Writer + // + typedef itk::ImageFileWriter LabelWriterType; + + LabelWriterType::Pointer labelWriter = LabelWriterType::New(); + + labelWriter->SetFileName( outputLabelVolume ); + labelWriter->SetInput( labelImage ); + + labelWriter->Update(); + + return 0; +} + diff --git a/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml new file mode 100644 index 00000000..0f15cf10 --- /dev/null +++ b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml @@ -0,0 +1,47 @@ + + + BRAINS.Utilities + Write Out Image Intensities + + + For Analysis + + 0.1 + + + University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu + + + + + + + inputVolumes + inputVolumes + The Input probaiblity images to be computed for lable maps + input + + + + + + outputLabelVolume + outputLabelVolume + The Input binary image for region of interest + input + + + + + + + + + numberOfThreads + numberOfThreads + + Explicitly specify the maximum number of threads to use. + -1 + + + diff --git a/BRAINSABC/brainseg/LLSBiasCorrector.h b/BRAINSABC/brainseg/LLSBiasCorrector.h new file mode 100644 index 00000000..23794585 --- /dev/null +++ b/BRAINSABC/brainseg/LLSBiasCorrector.h @@ -0,0 +1,185 @@ +// +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Bias field estimation using linear least squares polynomial fitting. +// Requires input image intensities and probability estimates for each voxel. +// +// Corrections are done either on subsampled grid or full resolution. +// This is designed to be run iteratively. Corrections should not be +// accumulated. Always use original image as the input, otherwise may get +// strange results. +// +// Van Leemput K, Maes F, Vandermeulen D, Suetens P. Automated model based +// bias field correction of MR images of the brain. IEEE TMI 1999; 18:885-896. +// +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 3/2004 + +#ifndef __LLSBiasCorrector_h +#define __LLSBiasCorrector_h + +#include "itkImage.h" +#include "itkObject.h" + +#include "vnl/vnl_matrix.h" +#include "vnl/vnl_vector.h" +#include "vnl/algo/vnl_matrix_inverse.h" +#include "vnl/algo/vnl_qr.h" +#include "vnl/algo/vnl_svd.h" + +#include +/** \class LLSBiasCorrector + */ +template +class LLSBiasCorrector : public itk::Object +{ +public: + + /** Standard class typedefs. */ + typedef LLSBiasCorrector Self; + typedef itk::SmartPointer Pointer; + typedef itk::SmartPointer ConstPointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** The dimension of the image. */ + itkStaticConstMacro(ImageDimension, unsigned int, + TInputImage::ImageDimension); + + // Image types + typedef TInputImage InputImageType; + typedef typename TInputImage::Pointer InputImagePointer; + typedef typename TInputImage::IndexType InputImageIndexType; + typedef typename TInputImage::PixelType InputImagePixelType; + typedef typename TInputImage::RegionType InputImageRegionType; + typedef typename TInputImage::SizeType InputImageSizeType; + typedef typename TInputImage::SpacingType InputImageSpacingType; + + typedef itk::Image ByteImageType; + typedef typename ByteImageType::Pointer ByteImagePointer; + typedef typename ByteImageType::IndexType ByteImageIndexType; + typedef typename ByteImageType::OffsetType ByteImageOffsetType; + typedef typename ByteImageType::PixelType ByteImagePixelType; + typedef typename ByteImageType::RegionType ByteImageRegionType; + typedef typename ByteImageType::SizeType ByteImageSizeType; + + typedef TProbabilityImage ProbabilityImageType; + typedef typename ProbabilityImageType::Pointer ProbabilityImagePointer; + typedef typename ProbabilityImageType::IndexType ProbabilityImageIndexType; + typedef typename ProbabilityImageType::PixelType ProbabilityImagePixelType; + typedef typename ProbabilityImageType::RegionType ProbabilityImageRegionType; + typedef typename ProbabilityImageType::SizeType ProbabilityImageSizeType; + + typedef itk::Image InternalImageType; + typedef InternalImageType::Pointer InternalImagePointer; + typedef InternalImageType::IndexType InternalImageIndexType; + typedef InternalImageType::PixelType InternalImagePixelType; + typedef InternalImageType::RegionType InternalImageRegionType; + typedef InternalImageType::SizeType InternalImageSizeType; + + typedef double ScalarType; + + typedef vnl_matrix MatrixType; + typedef vnl_vector VectorType; + + typedef vnl_matrix_inverse MatrixInverseType; + typedef vnl_qr MatrixQRType; + typedef vnl_svd MatrixSVDType; + + // The maximum polynomial degree of the bias field estimate + void SetMaxDegree(unsigned int); + + itkGetMacro(MaxDegree, unsigned int); + + // Spacing for determining voxels in LLS + void SetSampleSpacing(double s); + + itkGetMacro(SampleSpacing, double); + + // Spacing for determining which voxels need to be updated + // if correction is not done at full resolution + itkSetMacro(WorkingSpacing, double); + itkGetMacro(WorkingSpacing, double); + + // Bias field max magnitude + // itkSetMacro(MaximumBiasMagnitude, double); + // itkGetMacro(MaximumBiasMagnitude, double); + + void Initialize(); + + itkSetObjectMacro(AllTissueMask, ByteImageType); + itkGetConstObjectMacro(AllTissueMask, ByteImageType); + + void SetForegroundBrainMask(ByteImageType *mask); + + void SetInputImages(const std::vector & inputs) + { + this->m_InputImages = inputs; + this->Modified(); + } + + void SetProbabilities(const std::vector & probs, + const std::vector & candidateRegions); + + void SetListOfClassStatistics(const std::vector & regionStats); + + // Set/Get the Debugging level for filter verboseness + itkSetMacro(DebugLevel, unsigned int); + itkGetMacro(DebugLevel, unsigned int); + + // Set/Get the Debugging level for filter verboseness + itkSetMacro(OutputDebugDir, std::string); + itkGetMacro(OutputDebugDir, std::string); + // Correct input images and write it to the designated output + // fullRes flag selects whether to correct whole image or just grid points + // defined by WorkingSpacing + std::vector CorrectImages(const unsigned int CurrentIterationID); + +protected: + + LLSBiasCorrector(); + ~LLSBiasCorrector(); + + void CheckInputs(); + + void ComputeDistributions(); + +private: + + std::vector m_InputImages; + std::vector m_ValidIndicies; + ByteImagePointer m_ForegroundBrainMask; + ByteImagePointer m_AllTissueMask; + + std::vector m_BiasPosteriors; + std::vector m_CandidateRegions; + + unsigned int m_DebugLevel; + std::string m_OutputDebugDir; + + unsigned int m_MaxDegree; + + double m_SampleSpacing; + double m_WorkingSpacing; + + // double m_MaximumBiasMagnitude; + + std::vector m_ListOfClassStatistics; + MatrixType m_Basis; + + // Coordinate scaling and offset, computed from input probabilities + // for preconditioning the polynomial basis equations + double m_XMu[3]; + double m_XStd[3]; +}; + +#ifndef MU_MANUAL_INSTANTIATION +#include "LLSBiasCorrector.txx" +#endif + +#endif diff --git a/BRAINSABC/brainseg/LLSBiasCorrector.txx b/BRAINSABC/brainseg/LLSBiasCorrector.txx new file mode 100644 index 00000000..f71040a9 --- /dev/null +++ b/BRAINSABC/brainseg/LLSBiasCorrector.txx @@ -0,0 +1,867 @@ +#ifndef __LLSBiasCorrector_txx +#define __LLSBiasCorrector_txx + +#include +#include +#include +#include + +#include "Log.h" +#include "StandardizeMaskIntensity.h" +#include "LLSBiasCorrector.h" +#include "vnl/vnl_math.h" + +#include "ComputeDistributions.h" + +#define USE_HALF_RESOLUTION 1 +#define MIN_SKIP_SIZE 2 + +// Use the normal equation? Less accurate, but requires much less memory +#define LLSBIAS_USE_NORMAL_EQUATION 1 +// +// +// ////////////////////////////////////////////////////////////////////////////// +#define mypow(a, b) vcl_pow( ( a ), static_cast(b) ) +// +// +// ////////////////////////////////////////////////////////////////////////////// + +template +LLSBiasCorrector +::LLSBiasCorrector() +{ + m_InputImages.clear(); + + m_MaxDegree = 4; + + m_DebugLevel = 0; + m_OutputDebugDir = ""; + m_SampleSpacing = 4.0; + m_WorkingSpacing = 1.0; + + // m_MaximumBiasMagnitude = .1; + + m_XMu[0] = 0.0; + m_XMu[1] = 0.0; + m_XMu[2] = 0.0; + + m_XStd[0] = 1.0; + m_XStd[1] = 1.0; + m_XStd[2] = 1.0; +} + +template +LLSBiasCorrector +::~LLSBiasCorrector() +{ + m_ForegroundBrainMask = 0; +} + +template +void +LLSBiasCorrector +::CheckInputs() +{ + // if (m_MaxDegree == 0) + // itkExceptionMacro(<< "Max bias degree is zero" << std::endl ); + + if( m_InputImages.size() == 0 ) + { + itkExceptionMacro(<< "No input image specified" << std::endl ); + } + + if( m_InputImages[0]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "Input dimension invalid: only supports 3D images" << std::endl ); + } + + if( m_BiasPosteriors.size() < 1 ) + { + itkExceptionMacro(<< "Must have one or more class probabilities" << std::endl ); + } + + const InputImageSizeType size = m_InputImages[0]->GetLargestPossibleRegion().GetSize(); + for( unsigned int i = 1; i < m_InputImages.size(); i++ ) + { + const InputImageSizeType size_i = m_InputImages[i]->GetLargestPossibleRegion().GetSize(); + if( size != size_i ) + { + itkExceptionMacro(<< "Image sizes do not match" << std::endl ); + } + } + for( unsigned int i = 0; i < m_BiasPosteriors.size(); i++ ) + { + if( m_BiasPosteriors[i]->GetImageDimension() != 3 ) + { + itkExceptionMacro(<< "Probability [" << i << "] has invalid dimension: only supports 3D images" << std::endl ); + } + const ProbabilityImageSizeType psize = m_BiasPosteriors[i]->GetLargestPossibleRegion().GetSize(); + if( size[0] != psize[0] || size[1] != psize[1] || size[2] != psize[2] ) + { + itkExceptionMacro(<< "Image data and probabilities 3D size mismatch" << std::endl ); + } + } +} + +template +void +LLSBiasCorrector +::ComputeDistributions() +{ + muLogMacro(<< "LLSBiasCorrector: Computing means and variances..." << std::endl ); + + std::vector ClassProbabilityWeightings; + CombinedComputeDistributions(this->m_CandidateRegions, m_InputImages, + m_BiasPosteriors, + this->m_ListOfClassStatistics, // + // + // This + // + // is + // + // an + // + // output! + this->m_DebugLevel, + true); +} + +template +void +LLSBiasCorrector +::SetListOfClassStatistics(const std::vector & regionStats) +{ + this->m_ListOfClassStatistics = regionStats; +} + +template +void +LLSBiasCorrector +::SetMaxDegree(unsigned int n) +{ + muLogMacro(<< "SetMaxDegree" << std::endl ); + + m_MaxDegree = n; + + // NOTE: update basis equations, Need to call the Initialize in order to + // update + // the basis equations. + if( !m_ForegroundBrainMask.IsNull() ) + { + this->Initialize(); + } +#if 1 // HACK + if( m_BiasPosteriors.size() > 0 ) + { + this->SetProbabilities(m_BiasPosteriors, this->m_CandidateRegions); + } +#endif +} + +template +void +LLSBiasCorrector +::SetSampleSpacing(double s) +{ + muLogMacro(<< "SetSampleSpacing" << std::endl ); + + m_SampleSpacing = s; + +#if 1 // HACK + if( m_BiasPosteriors.size() > 0 ) + { + this->SetProbabilities(m_BiasPosteriors, this->m_CandidateRegions); + } +#endif + // NOTE: update basis equations, Need to call the Initialize in order to + // update + // the basis equations. + if( m_ForegroundBrainMask.IsNotNull() ) + { + this->Initialize(); + } +} + +template +void +LLSBiasCorrector +::SetForegroundBrainMask(ByteImageType *mask) +{ + m_ForegroundBrainMask = mask; + this->Initialize(); +} + +template +void +LLSBiasCorrector +::Initialize() +{ + const InputImageSizeType size + = m_ForegroundBrainMask->GetLargestPossibleRegion().GetSize(); + + // Compute skips along each dimension +#ifdef USE_HALF_RESOLUTION // Need to do full scale to prevent checkerboard + // images from being created + InputImageSpacingType spacing = m_ForegroundBrainMask->GetSpacing(); + unsigned int skips[3]; + skips[0] = (unsigned int)( m_SampleSpacing / spacing[0] ); + skips[1] = (unsigned int)( m_SampleSpacing / spacing[1] ); + skips[2] = (unsigned int)( m_SampleSpacing / spacing[2] ); + + if( skips[0] < MIN_SKIP_SIZE ) + { + skips[0] = MIN_SKIP_SIZE; + } + if( skips[1] < MIN_SKIP_SIZE ) + { + skips[1] = MIN_SKIP_SIZE; + } + if( skips[2] < MIN_SKIP_SIZE ) + { + skips[2] = MIN_SKIP_SIZE; + } + muLogMacro(<< "Sample skips: " << skips[0] << " x " << skips[1] << " x " << skips[2] << std::endl); +#else + const unsigned int skips[3] = {1, 1, 1}; +#endif + + const unsigned int numCoefficients + = ( m_MaxDegree + 1 ) * ( m_MaxDegree + 2 ) / 2 * ( m_MaxDegree + 3 ) / 3; + + // Number of pixels with non-zero weights, downsampled + unsigned numEquations = 0; + m_ValidIndicies.reserve(size[2] * size[1] * size[0] / (8 * skips[0] * skips[1] * skips[2]) ); // + // + // Assume + // + // that + // + // only + // + // 0.125 + // + // of + // + // the + // + // image + // + // is + // + // part + // + // of + // + // mask + m_ValidIndicies.resize(0); + { + // Not parallizable! ORDER IS IMPORTANT //#pragma omp parallel for + // reduction(+:numEquations) default(shared) + for( long kk = 0; kk < (long)size[2]; kk += skips[2] ) + { + for( long jj = 0; jj < (long)size[1]; jj += skips[1] ) + { + for( long ii = 0; ii < (long)size[0]; ii += skips[0] ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + if( m_ForegroundBrainMask->GetPixel(currIndex) != 0 ) + { + m_ValidIndicies.push_back(currIndex); + // numEquations++; + } + } + } + } + } + numEquations = m_ValidIndicies.size(); + muLogMacro(<< "Linear system size = " << numEquations << " x " << numCoefficients << std::endl); + + // Make sure that number of equations >= number of unknowns + if( numEquations < numCoefficients ) + { + std::cout << size << std::endl; + itkExceptionMacro(<< "Number of unknowns exceed number of equations:" << numEquations << " < " << numCoefficients); + } + + // Create basis matrix + + muLogMacro(<< "Computing polynomial basis functions..." << std::endl ); + + m_Basis.set_size(numEquations, numCoefficients); + + { + // Coordinate scaling and offset parameters + unsigned long long int local_XMu_x = 0; + unsigned long long int local_XMu_y = 0; + unsigned long long int local_XMu_z = 0; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) reduction(+:local_XMu_x,local_XMu_y,local_XMu_z) +#endif + for( long kk = 0; kk < numEquations; kk++ ) + { + const ProbabilityImageIndexType & currIndex = m_ValidIndicies[kk]; + local_XMu_x += currIndex[0]; + local_XMu_y += currIndex[1]; + local_XMu_z += currIndex[2]; + } + } + const double invNumEquations = 1.0 / static_cast(numEquations); + m_XMu[0] = static_cast(local_XMu_x) * invNumEquations; + m_XMu[1] = static_cast(local_XMu_y) * invNumEquations; + m_XMu[2] = static_cast(local_XMu_z) * invNumEquations; + } + + { + double local_XStd_x = 0.0; + double local_XStd_y = 0.0; + double local_XStd_z = 0.0; + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) reduction(+:local_XStd_x,local_XStd_y,local_XStd_z) +#endif + for( long kk = 0; kk < numEquations; kk++ ) + { + const ProbabilityImageIndexType & currIndex = m_ValidIndicies[kk]; + const double diff0 = static_cast(currIndex[0]) - m_XMu[0]; + local_XStd_x += diff0 * diff0; + const double diff1 = static_cast(currIndex[1]) - m_XMu[1]; + local_XStd_y += diff1 * diff1; + const double diff2 = static_cast(currIndex[2]) - m_XMu[2]; + local_XStd_z += diff2 * diff2; + } + } + m_XStd[0] = vcl_sqrt(local_XStd_x / numEquations); + m_XStd[1] = vcl_sqrt(local_XStd_y / numEquations); + m_XStd[2] = vcl_sqrt(local_XStd_z / numEquations); + } + + { + // Row and column indices + // Fill in polynomial basis values +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( long r = 0; r < numEquations; r++ ) + { + const ProbabilityImageIndexType & currIndex = m_ValidIndicies[r]; + unsigned int c = 0; + for( unsigned int order = 0; order <= m_MaxDegree; order++ ) + { + for( unsigned int xorder = 0; xorder <= order; xorder++ ) + { + for( unsigned int yorder = 0; yorder <= ( order - xorder ); yorder++ ) + { + const int zorder = order - xorder - yorder; + + const double xc = ( currIndex[0] - m_XMu[0] ) / m_XStd[0]; + const double yc = ( currIndex[1] - m_XMu[1] ) / m_XStd[1]; + const double zc = ( currIndex[2] - m_XMu[2] ) / m_XStd[2]; + + m_Basis(r, c) + = mypow(xc, xorder) * mypow(yc, yorder) * mypow(zc, zorder); + c++; + } + } + } + } + } +} + +template +void +LLSBiasCorrector +::SetProbabilities(const std::vector & probs, + const std::vector & candidateRegions ) +{ + muLogMacro(<< "SetProbabilities" << std::endl ); + + if( probs.size() < 1 ) + { + itkExceptionMacro(<< "Need one or more probabilities" << std::endl ); + } + if( probs.size() != candidateRegions.size() ) + { + itkExceptionMacro(<< "Probabilities and CandidateRegions size must be the same." << std::endl ); + } + for( unsigned int i = 0; i < probs.size(); i++ ) + { + if( probs[i].IsNull() ) + { + itkExceptionMacro(<< "One of input probabilities not initialized" << std::endl ); + } + } + for( unsigned int i = 0; i < candidateRegions.size(); i++ ) + { + if( candidateRegions[i].IsNull() ) + { + itkExceptionMacro(<< "One of input candidate regions is not initialized" << std::endl ); + } + } + m_BiasPosteriors = probs; + m_CandidateRegions = candidateRegions; +} + +template +std::vector +LLSBiasCorrector +::CorrectImages(const unsigned int CurrentIterationID) +{ + muLogMacro(<< "Correct Images" << std::endl ); + itk::TimeProbe CorrectImagesTimer; + CorrectImagesTimer.Start(); + // Verify input + this->CheckInputs(); + + const InputImageSizeType size = m_InputImages[0]->GetLargestPossibleRegion().GetSize(); + + // Compute means and variances + this->ComputeDistributions(); + +#ifdef USE_HALF_RESOLUTION + // Compute skips along each dimension + InputImageSpacingType spacing = m_InputImages[0]->GetSpacing(); + + unsigned int sampleofft[3]; + sampleofft[0] = (unsigned int)vcl_floor(m_SampleSpacing / spacing[0]); + sampleofft[1] = (unsigned int)vcl_floor(m_SampleSpacing / spacing[1]); + sampleofft[2] = (unsigned int)vcl_floor(m_SampleSpacing / spacing[2]); + + if( sampleofft[0] < MIN_SKIP_SIZE ) + { + sampleofft[0] = MIN_SKIP_SIZE; + } + if( sampleofft[1] < MIN_SKIP_SIZE ) + { + sampleofft[1] = MIN_SKIP_SIZE; + } + if( sampleofft[2] < MIN_SKIP_SIZE ) + { + sampleofft[2] = MIN_SKIP_SIZE; + } + + muLogMacro( + << "Sample offsets: " << sampleofft[0] << " x " << sampleofft[1] << " x " << sampleofft[2] << std::endl); +#else + const unsigned int sampleofft[3] = {1, 1, 1}; +#endif + +#ifdef USE_HALF_RESOLUTION // Need more accurate value the downsampling was + // causing images with zeros to be produced, and the + // bspline registrations were not doing very much + // because of this. + unsigned int workingofft[3]; + workingofft[0] = (unsigned int)vcl_floor(m_WorkingSpacing / spacing[0]); + workingofft[1] = (unsigned int)vcl_floor(m_WorkingSpacing / spacing[1]); + workingofft[2] = (unsigned int)vcl_floor(m_WorkingSpacing / spacing[2]); + + if( workingofft[0] < MIN_SKIP_SIZE ) + { + workingofft[0] = MIN_SKIP_SIZE; + } + if( workingofft[1] < MIN_SKIP_SIZE ) + { + workingofft[1] = MIN_SKIP_SIZE; + } + if( workingofft[2] < MIN_SKIP_SIZE ) + { + workingofft[2] = MIN_SKIP_SIZE; + } + muLogMacro( + << "Working offsets: " << workingofft[0] << " x " << workingofft[1] << " x " << workingofft[2] << std::endl); +#else + // const unsigned int workingofft[3] ={ {1,1,1} }; +#endif + + const unsigned int numChannels = m_InputImages.size(); + const unsigned int numClasses = m_BiasPosteriors.size(); + + /* if m_MaxDegree = 4/3/2, then this is 35/20/10 */ + const unsigned int numCoefficients + = ( m_MaxDegree + 1 ) * ( m_MaxDegree + 2 ) / 2 * ( m_MaxDegree + 3 ) / 3; + + muLogMacro(<< numClasses << " classes\n" << std::endl ); + muLogMacro(<< numCoefficients << " coefficients\n" << std::endl ); + + /* compute inverse matrix for each tissue type */ + muLogMacro(<< "Computing inverse covars...\n" << std::endl ); + std::vector invCovars; + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + invCovars.push_back( MatrixInverseType(this->m_ListOfClassStatistics[iclass].m_Covariance) ); + } + + // Create matrices and vectors + // lhs = replicated basis polynomials for each channel, weighted by inv cov + // rhs = difference image between original and reconstructed mean image + + muLogMacro(<< "Creating matrices for LLS..." << std::endl ); + + const unsigned int numEquations = m_Basis.rows(); /* since m_Basis is [numEqu * + 35 ] matrix */ + + muLogMacro( + << numEquations << " equations, " << numCoefficients << " coefficients" << std::endl ); + + // Compute orthogonal transpose component of basis + muLogMacro(<< "Computing ortho part of basis" << std::endl ); +#if 1 + // Note: vnl_qr gives Q mxm and R mxn for A mxn + + MatrixType basisT; + { + MatrixQRType qr(m_Basis); + + // Get economy size R (square) + MatrixType R(numCoefficients, numCoefficients, 0); + + { + MatrixType Rfull = qr.R(); /* right triangular matrix */ + for( unsigned int r = 0; r < numCoefficients; r++ ) + { + for( unsigned int c = r; c < numCoefficients; c++ ) + { + R(r, c) = Rfull(r, c); + } + } + // Rfull.set_size(1, 1); + } + // NOTE: to get mxn Q from vnl_qr, Q'*Q = id nxn + basisT = m_Basis * MatrixInverseType(R); + } + basisT.inplace_transpose(); // basisT = Q' +#else + // Do this instead for ordinary weighted LSQ + MatrixType basisT = m_Basis.transpose(); +#endif + +#if LLSBIAS_USE_NORMAL_EQUATION + MatrixType lhs(numCoefficients * numChannels, numCoefficients * numChannels); + + MatrixType rhs(numCoefficients * numChannels, 1); + +#else + MatrixType lhs(numEquations * numChannels, numCoefficients * numChannels); + + MatrixType rhs(numEquations * numChannels, 1); + +#endif + + muLogMacro(<< "Fill rhs" << std::endl ); + rhs.fill(0.0); + + { + // Compute ratio between original and flat image, weighted using posterior + // probability and inverse covariance + for( LOOPITERTYPE ichan = 0; ichan < (LOOPITERTYPE) numChannels; ichan++ ) + { + MatrixType R_i(numEquations, 1, 0.0); + for( unsigned int jchan = 0; jchan < numChannels; jchan++ ) + { + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( long eq = 0; eq < numEquations; eq++ ) + { + const ProbabilityImageIndexType & currIndex = m_ValidIndicies[eq]; + // Compute reconstructed intensity, weighted by prob * invCov + double sumW = DBL_EPSILON; + double recon = 0; + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + const MatrixType & invCov = invCovars[iclass]; + const double w = m_BiasPosteriors[iclass]->GetPixel(currIndex) + * invCov(ichan, jchan); + sumW += w; + recon += w * this->m_ListOfClassStatistics[iclass].m_Means[jchan]; + } + recon /= sumW; + + const double bias = LOGP( m_InputImages[jchan]->GetPixel(currIndex) ) - recon; + R_i(eq, 0) += sumW * bias; + } + } + } // for jchan + +#if LLSBIAS_USE_NORMAL_EQUATION + R_i = basisT * R_i; + for( unsigned int row = 0; row < numCoefficients; row++ ) + { + rhs(ichan * numCoefficients + row, 0) = R_i(row, 0); + } +#else + for( unsigned int row = 0; row < numEquations; row++ ) + { + rhs(ichan * numEquations + row, 0) = R_i(row, 0); + } +#endif + } // for ichan + } + + muLogMacro(<< "Fill lhs" << std::endl ); + + // Compute LHS using replicated basis entries, weighted using posterior + // probability and inverse covariance + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE ichan = 0; ichan < (LOOPITERTYPE)numChannels; ichan++ ) + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( LOOPITERTYPE jchan = 0; jchan < (LOOPITERTYPE)numChannels; jchan++ ) + { + MatrixType Wij_A(numEquations, numCoefficients, 0.0); + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for shared(Wij_A) // default(shared) +#endif + for( long eq = 0; eq < numEquations; eq++ ) + { + const ProbabilityImageIndexType & currIndex = m_ValidIndicies[eq]; + double sumW = DBL_EPSILON; + for( unsigned int iclass = 0; iclass < numClasses; iclass++ ) + { + const MatrixType & invCov = invCovars[iclass]; + double w = m_BiasPosteriors[iclass]->GetPixel(currIndex) + * invCov(ichan, jchan); + sumW += w; + } + for( unsigned int col = 0; col < numCoefficients; col++ ) + { + Wij_A(eq, col) = sumW * m_Basis(eq, col); + } + } + } + +#if LLSBIAS_USE_NORMAL_EQUATION + MatrixType lhs_ij = basisT * Wij_A; + for( unsigned int row = 0; row < numCoefficients; row++ ) + { + for( unsigned int col = 0; col < numCoefficients; col++ ) + { + lhs(row + ichan * numCoefficients, col + jchan * numCoefficients) + = lhs_ij(row, col); + } + } +#else + for( unsigned int row = 0; row < numEquations; row++ ) + { + for( unsigned int col = 0; col < numCoefficients; col++ ) + { + lhs(row + ichan * numEquations, col + jchan * numCoefficients) + = Wij_A(row, col); + } + } +#endif + } // for jchan + } // for ichan + } + + muLogMacro(<< "Solve " << lhs.rows() << " x " << lhs.columns() << std::endl); + + // Use VNL to solve linear system + MatrixType coeffs; + { + // MatrixQRType qr(lhs); + // coeffs = qr.solve(rhs); + // SVD more expensive, should be more accurate + MatrixSVDType svd(lhs); + + svd.zero_out_absolute(1e-8); + coeffs = svd.solve(rhs); + } +#if 1 + if( !std::isfinite( (double)coeffs[0][0]) ) + { + std::cout + << "\ncoeffs: \n" << coeffs + // << "\nlhs_ij: \n" << lhs_ij + << "\nbasisT: \n" << basisT + // << "\nWij_A: \n" << Wij_A + << "\nlhs: \n" << lhs + << "\nrhs: \n" << rhs + << std::endl; + exit(-1); + } +#endif + // Clear memory for the basis transpose + basisT.set_size(0, 0); + + if( this->m_DebugLevel > 9 ) + { + muLogMacro(<< "Bias field coeffs after LLS:" << std::endl << coeffs); + } + + // Remove bias + muLogMacro(<< "Correcting input images..." << std::endl ); + + std::vector outputs(numChannels); + for( unsigned int ichan = 0; ichan < numChannels; ichan++ ) + { + outputs[ichan] = InternalImageType::New(); + outputs[ichan]->CopyInformation(this->m_InputImages[ichan]); + outputs[ichan]->SetRegions( this->m_InputImages[ichan]->GetLargestPossibleRegion() ); + outputs[ichan]->Allocate(); + outputs[ichan]->FillBuffer(0); + + // Compute the vcl_log transformed bias field + InternalImagePointer biasIntensityScaleFactor = InternalImageType::New(); + biasIntensityScaleFactor->CopyInformation(this->m_InputImages[ichan]); + biasIntensityScaleFactor->SetRegions( this->m_InputImages[ichan]->GetLargestPossibleRegion() ); + biasIntensityScaleFactor->Allocate(); + biasIntensityScaleFactor->FillBuffer(0); + + double maxBiasInForegroundMask = vcl_numeric_limits::min(); + double minBiasInForegroundMask = vcl_numeric_limits::max(); + + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for shared(maxBiasInForegroundMask,minBiasInForegroundMask) default(shared) +#endif + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + double logFitValue = 0.0; + unsigned int c = ichan * numCoefficients; + for( unsigned int order = 0; order <= m_MaxDegree; order++ ) + { + for( unsigned int xorder = 0; xorder <= order; xorder++ ) + { + for( unsigned int yorder = 0; yorder <= ( order - xorder ); yorder++ ) + { + const int zorder = order - xorder - yorder; + + const double xc = ( currIndex[0] - m_XMu[0] ) / m_XStd[0]; + const double yc = ( currIndex[1] - m_XMu[1] ) / m_XStd[1]; + const double zc = ( currIndex[2] - m_XMu[2] ) / m_XStd[2]; + + const double poly + = mypow(xc, xorder) * mypow(yc, yorder) * mypow(zc, zorder); + + // logFitValue += coeffs[c] * poly; + logFitValue += coeffs(c, 0) * poly; + c++; + } + } + } + + const ByteImagePixelType maskValue = m_ForegroundBrainMask->GetPixel(currIndex); + /* NOTE: For regions listed as background, clamp the outputs[ichan] + */ + if( vnl_math_isnan(logFitValue) || vnl_math_isinf(logFitValue) ) + { + std::cout << "WARNING: Bad Scale Value Computed!" << std::endl; + logFitValue = 0.0; + } + const double multiplicitiveBiasCorrectionFactor = 1.0 / EXPP(logFitValue); + if( maskValue != 0 ) + { + if( multiplicitiveBiasCorrectionFactor > maxBiasInForegroundMask ) + { + maxBiasInForegroundMask = multiplicitiveBiasCorrectionFactor; + } + if( multiplicitiveBiasCorrectionFactor < minBiasInForegroundMask ) + { + minBiasInForegroundMask = multiplicitiveBiasCorrectionFactor; + } + } + biasIntensityScaleFactor->SetPixel(currIndex, (InternalImagePixelType)multiplicitiveBiasCorrectionFactor); + } // for currIndex[0] + } + } + } + std::cout << "Foreground Mask Bias Correction MIN: " << minBiasInForegroundMask << " MAX: " + << maxBiasInForegroundMask << std::endl; + // Correct image using (clamped) bias field) + { +#if defined(LOCAL_USE_OPEN_MP) +#pragma omp parallel for default(shared) +#endif + for( long kk = 0; kk < (long)size[2]; kk++ ) + { + for( long jj = 0; jj < (long)size[1]; jj++ ) + { + for( long ii = 0; ii < (long)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + double multiplicitiveBiasCorrectionFactor = biasIntensityScaleFactor->GetPixel( + currIndex); + if( multiplicitiveBiasCorrectionFactor > maxBiasInForegroundMask ) // + // + // CLAMP + { + multiplicitiveBiasCorrectionFactor = maxBiasInForegroundMask; + biasIntensityScaleFactor->SetPixel(currIndex, (InternalImagePixelType) multiplicitiveBiasCorrectionFactor ); + } + else if( multiplicitiveBiasCorrectionFactor < minBiasInForegroundMask ) // + // + // CLAMP + { + multiplicitiveBiasCorrectionFactor = minBiasInForegroundMask; + biasIntensityScaleFactor->SetPixel(currIndex, (InternalImagePixelType) multiplicitiveBiasCorrectionFactor ); + } + if( ( this->m_AllTissueMask->GetPixel(currIndex) == 0 ) ) + { + // Now clamp intensities outside the probability mask region to + // the min and + // max of inside the mask region. + outputs[ichan]->SetPixel(currIndex, 0 ); + } + else + { + const double originalPixelValue = m_InputImages[ichan]->GetPixel(currIndex); + const double correctedPixelValue = originalPixelValue * multiplicitiveBiasCorrectionFactor; + outputs[ichan]->SetPixel(currIndex, (InputImagePixelType)correctedPixelValue); + } + } // for currIndex[0] + } + } + } + + { + std::cout << "Standardizing Bias Corrected Intensities: ..."; + outputs[ichan] + = StandardizeMaskIntensity( + outputs[ichan], + this->m_ForegroundBrainMask, + 0.0005, 1.0 - 0.0005, + 1, 0.95 * MAX_IMAGE_OUTPUT_VALUE, + 0, MAX_IMAGE_OUTPUT_VALUE); + std::cout << "done." << std::endl; + } + if( this->m_DebugLevel > 7 ) + { // DEBUG: This code is for debugging purposes only; + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + std::stringstream CurrentIterationID_stream(""); + CurrentIterationID_stream << CurrentIterationID; + std::stringstream template_index_stream(""); + template_index_stream << ichan; + const std::string fn = this->m_OutputDebugDir + "/BIAS_INDEX_" + template_index_stream.str() + "_LEVEL_" + + CurrentIterationID_stream.str() + ".nii.gz"; + writer->SetInput(biasIntensityScaleFactor); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl); + } + // + } // for ichan + // Remove internal references to input images when done + m_InputImages.clear(); + CorrectImagesTimer.Stop(); + itk::RealTimeClock::TimeStampType elapsedTime = CorrectImagesTimer.GetTotal(); + muLogMacro(<< "Correcting Images took " << elapsedTime << " " << CorrectImagesTimer.GetUnit() << std::endl); + return outputs; +} + +#endif diff --git a/BRAINSABC/brainseg/MSTEdge.h b/BRAINSABC/brainseg/MSTEdge.h new file mode 100644 index 00000000..a72ed380 --- /dev/null +++ b/BRAINSABC/brainseg/MSTEdge.h @@ -0,0 +1,41 @@ +#ifndef __MSTEdge_h +#define __MSTEdge_h + +/** \class MSTEdge + */ +class MSTEdge +{ +public: + + // Pair of graph vertex indices + unsigned int i; + unsigned int j; + + // Distance between the vertices + float dist; + + MSTEdge() + { + this->i = 0; this->j = 0; this->dist = 0; + } + + ~MSTEdge() + { + } + + const MSTEdge & operator=(const MSTEdge & e) + { + this->i = e.i; + this->j = e.j; + this->dist = e.dist; + return *this; + } + + bool operator<(const MSTEdge & e) const + { + return this->dist < e.dist; + } + +}; + +#endif diff --git a/BRAINSABC/brainseg/QHullMSTClusteringProcess.cxx b/BRAINSABC/brainseg/QHullMSTClusteringProcess.cxx new file mode 100644 index 00000000..5693dc10 --- /dev/null +++ b/BRAINSABC/brainseg/QHullMSTClusteringProcess.cxx @@ -0,0 +1,443 @@ +#include "Heap.h" +#include "QHullMSTClusteringProcess.h" + +#include + +#include +#include +#include + +extern "C" +{ +#include "qhull.h" +#include "mem.h" +#include "qset.h" +} + +#define BUF_SIZE 2048 +#define QHULL_COMMAND "qhull d QJ Tv " +// #define QHULL_COMMAND "qhull d QJ " + +/** + * \class MSTCluster + * For sorting cluster maps based on size (descending) + */ +class MSTCluster +{ +public: + unsigned int map; + unsigned int size; + + MSTCluster() + { + this->map = 0; this->size = 0; + } + + ~MSTCluster() + { + } + + inline MSTCluster & operator=(const MSTCluster & c) + { + this->map = c.map; this->size = c.size; return *this; + } + + inline bool operator<(const MSTCluster & c) const + { + return this->size > c.size; + } + +}; + +QHullMSTClusteringProcess +::QHullMSTClusteringProcess() +{ + m_NumberOfVertices = 0; + + m_MSTEdges = 0; + + m_NodeAverages = 0; + + m_SortFlag = false; +} + +QHullMSTClusteringProcess +::~QHullMSTClusteringProcess() +{ + delete[] m_MSTEdges; + delete[] m_NodeAverages; +} + +void +QHullMSTClusteringProcess +::SetInputVertices(const VertexList & vlist) +{ + delete[] m_MSTEdges; + delete[] m_NodeAverages; + + m_NumberOfVertices = vlist.size(); + if( m_NumberOfVertices == 0 ) + { + return; + } + + const unsigned int dim = vlist[0].size(); + + // Allocate memory to store elements of the list + // coordT *points = (coordT*) + // malloc((dim+1)*m_NumberOfVertices*sizeof(coordT)); + coordT *const points = new coordT[( dim + 1 ) * m_NumberOfVertices]; + // Store each coordinate in an array element + for( unsigned int k = 0; k < m_NumberOfVertices; k++ ) + { + const VertexType v = vlist[k]; + const long pos = k * ( dim + 1 ); +#if 1 + double sumS = 0; + for( unsigned int j = 0; j < dim; j++ ) + { + points[pos + j] = v[j]; + sumS += v[j] * v[j]; + } + points[pos + dim] = sumS; +#else + points[pos + dim] = 0.0; +#endif + } + + // Call out to qhull library to compute DeLaunay triangulation + qh_init_A(stdin, stdout, stderr, 0, NULL); + const int exitcode = setjmp(qh errexit); + + // Compute Delaunay triangulation and insert it to heap + Heap delaunayHeap; + if( !exitcode ) + { + char options[BUF_SIZE]; + // Add extra options here + strcpy(options, QHULL_COMMAND); + + qh_initflags(options); + qh_setdelaunay(dim + 1, m_NumberOfVertices, points); + qh_init_B(points, m_NumberOfVertices, dim + 1, False); + qh_qhull(); + qh_check_output(); + + facetT *facet; + long numfacets = 0; + FORALLfacets + { + if( !facet->upperdelaunay ) + { + numfacets++; + } + } + + vertexT * vertex; + vertexT * *vertexp; + // Insert DT edges to heap + FORALLfacets + { + if( !facet->upperdelaunay ) + { + std::vector ids; + ids.resize(dim + 1); + FOREACHvertex_(facet->vertices) + { + ids.push_back( qh_pointid(vertex->point) ); + } + for( unsigned int s = 0; s < ids.size(); s++ ) + { + for( unsigned int t = s + 1; t < ids.size(); t++ ) + { + MSTEdge e; + e.i = ids[s]; + e.j = ids[t]; + const VertexType dij = vlist[e.i] - vlist[e.j]; + e.dist = dij.squared_magnitude(); + delaunayHeap.Insert(e); + } + } + } + } + } + delete[] points; + + // Free allocated memory + qh NOerrexit = True; + qh_freeqhull(False); + int curlong, totlong; + qh_memfreeshort(&curlong, &totlong); + if( curlong || totlong ) + { + std::cerr << "qhull internal warning (main): did not free " << totlong + << "bytes of long memory (" << curlong << "pieces)" << std::endl; + throw "QHull error"; + } + + // Map vertex to set (tree) it belongs to, for cycle test + unsigned int *const treeMap = new unsigned int[m_NumberOfVertices]; + for( unsigned int i = 0; i < m_NumberOfVertices; i++ ) + { + treeMap[i] = i; + } + + // Number of edges in MST + unsigned int edgeCount = 0; + + // Build MST using Kruskal's algorithm + // + // Edges added in ascending order + m_MSTEdges = new MSTEdge[m_NumberOfVertices - 1]; + while( !delaunayHeap.IsEmpty() ) + { + MSTEdge minEdge = delaunayHeap.ExtractMinimum(); + + const unsigned int a = minEdge.i; + const unsigned int b = minEdge.j; + + const unsigned int map1 = treeMap[a]; + const unsigned int map2 = treeMap[b]; + + // Skip if they belong to the same tree (will form cycle) + if( map1 == map2 ) + { + continue; + } + // Merge trees + for( unsigned int k = 0; k < m_NumberOfVertices; k++ ) + { + if( treeMap[k] == map2 ) + { + treeMap[k] = map1; + } + } + m_MSTEdges[edgeCount] = minEdge; + edgeCount++; + + // See if a tree is formed already + if( edgeCount == ( m_NumberOfVertices - 1 ) ) + { + break; + } + } + + delete[] treeMap; + if( edgeCount != ( m_NumberOfVertices - 1 ) ) + { + std::cerr << "MST construction failed, E != (V-1)" << std::endl; + throw "MST construction failed, E != (V-1)"; + } + + m_NodeAverages = new float[m_NumberOfVertices]; + // Compute node averages + for( unsigned int k = 0; k < m_NumberOfVertices; k++ ) + { + m_NodeAverages[k] = 0.0; + } + + unsigned int *const countArray = new unsigned int[m_NumberOfVertices]; + for( unsigned int k = 0; k < m_NumberOfVertices; k++ ) + { + countArray[k] = 0; + } + + { + std::vector > nodeDistances; + nodeDistances.resize(m_NumberOfVertices + 1); + for( unsigned int i = 0; i <= m_NumberOfVertices + 1; i++ ) + { + std::vector dlist; + nodeDistances.push_back(dlist); + } + for( unsigned int k = 0; k < ( m_NumberOfVertices - 1 ); k++ ) + { + const unsigned int a = m_MSTEdges[k].i; + const unsigned int b = m_MSTEdges[k].j; + + m_NodeAverages[a] += m_MSTEdges[k].dist; + countArray[a]++; + + m_NodeAverages[b] += m_MSTEdges[k].dist; + countArray[b]++; + + nodeDistances[a].push_back(m_MSTEdges[k].dist); + nodeDistances[b].push_back(m_MSTEdges[k].dist); + } + for( unsigned int k = 0; k < m_NumberOfVertices; k++ ) + { + // Use mean OR... + // if (countArray[k] != 0) + // m_NodeAverages[k] /= countArray[k]; + // Median instead? + if( countArray[k] != 0 ) + { + m_NodeAverages[k] + = heapMedian( nodeDistances[k], nodeDistances[k].size() ); + } + } + } + delete[] countArray; +} + +unsigned int +QHullMSTClusteringProcess +::GetClusters(unsigned int *treeMap, float T) +{ + // Get number of vertices and edges + const unsigned int v = m_NumberOfVertices; + const unsigned int e = v - 1; + + // Allocate edge break flag array + unsigned char *const breakArray = new unsigned char[e]; + for( unsigned int k = 0; k < e; k++ ) + { + breakArray[k] = 0; + } + + // Break edges + unsigned int numBroken = 0; + for( unsigned int i = 0; i < v; i++ ) + { + const float thres = T * m_NodeAverages[i]; + // Break the coinciding long edges + for( unsigned int k = 0; k < e; k++ ) + { + if( breakArray[k] != 0 ) + { + continue; + } + + const unsigned int a = m_MSTEdges[k].i; + const unsigned int b = m_MSTEdges[k].j; + const bool incident = ( i == a ) || ( i == b ); + + // Never break zero length edges + if( incident && ( m_MSTEdges[k].dist > thres ) ) + { + breakArray[k] = 1; + numBroken++; + } + } + } + + if( numBroken == 0 ) + { + std::cerr << "No edges broken" << std::endl; + delete[] breakArray; + // TODO: FIXME: + // return whole tree with same label + return 0; + } + // Figure out distinct trees, merge connected vertices + for( unsigned int k = 0; k < v; k++ ) + { + treeMap[k] = k; + } + for( unsigned int i = 0; i < v; i++ ) + { + unsigned int map1 = treeMap[i]; + // Check incident edges + for( unsigned int j = 0; j < e; j++ ) + { + if( breakArray[j] != 0 ) + { + continue; + } + + const unsigned int a = m_MSTEdges[j].i; + const unsigned int b = m_MSTEdges[j].j; + const bool incident = ( i == a ) || ( i == b ); + + if( !incident ) + { + continue; + } + + // Get the map of the other id + unsigned int map2 = treeMap[b]; + if( i == b ) + { + map2 = treeMap[a]; + } + if( map1 == map2 ) + { + continue; + } + for( unsigned int k = 0; k < v; k++ ) + { + if( treeMap[k] == map2 ) + { + treeMap[k] = map1; + } + } + } // for neighbors + } // for i + + delete[] breakArray; + + if( !m_SortFlag ) + { + return numBroken + 1; + } + + // + // Sort the cluster maps based on cluster size (descending) + // Cluster 0 is the largest cluster + // + + // Obtain cluster info + MSTCluster *const clusters = new MSTCluster[v]; + unsigned int numNonZero = 0; + for( unsigned int i = 0; i < v; i++ ) + { + clusters[i].map = i; + unsigned int s = 0; + for( unsigned int j = 0; j < v; j++ ) + { + if( treeMap[j] == i ) + { + s++; + } + } + if( s > 0 ) + { + numNonZero++; + } + clusters[i].size = s; + } + + Heap heap; + heap.Allocate(numNonZero); + for( unsigned int i = 0; i < v; i++ ) + { + if( clusters[i].size != 0 ) + { + heap.Insert(clusters[i]); + } + } + + delete[] clusters; + + unsigned int *const sortedMap = new unsigned int[v]; + for( unsigned int i = 0; i < numNonZero; i++ ) + { + const MSTCluster c = heap.ExtractMinimum(); + const unsigned int m = c.map; + for( unsigned int j = 0; j < v; j++ ) + { + if( treeMap[j] == m ) + { + sortedMap[j] = i; + } + } + } + for( unsigned int i = 0; i < v; i++ ) + { + treeMap[i] = sortedMap[i]; + } + + delete[] sortedMap; + return numBroken + 1; +} + diff --git a/BRAINSABC/brainseg/QHullMSTClusteringProcess.h b/BRAINSABC/brainseg/QHullMSTClusteringProcess.h new file mode 100644 index 00000000..33983994 --- /dev/null +++ b/BRAINSABC/brainseg/QHullMSTClusteringProcess.h @@ -0,0 +1,73 @@ +// +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Clustering using Minimum Spanning Tree edge breaking +// MST constructed using Delaunay triangulation followed by Kruskal's algorithm +// (best for sparse graphs) +// +// Designed to be used iteratively +// +// Follows the heuristic described in: +// Cocosco, C.A., Zijdenbos, A.P., Evans, A.C.: A fully automatic and robust +// brain MRI tissue classification method. Medical Image Analysis 7 (2003) +// 513-527 +// +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 5/2008 + +#ifndef __QHullMSTClusteringProcess_h +#define __QHullMSTClusteringProcess_h + +#include +#include "MSTEdge.h" + +#include "vnl/vnl_vector.h" +/** + * \class QHullMSTClusteringProcess + */ +class QHullMSTClusteringProcess +{ +public: + + QHullMSTClusteringProcess(); + ~QHullMSTClusteringProcess(); + + typedef vnl_vector VertexType; + typedef MSTEdge EdgeType; + + typedef std::vector VertexList; + + void SetInputVertices(const VertexList & l); + + // Break edges with threshold value T, and then cluster based on MST edge + // connectivity + // + // Returns the number of clusters and fills the cluster map array + unsigned int GetClusters(unsigned int *maps, float T); + + inline void SortOn() + { + m_SortFlag = true; + } + + inline void SortOff() + { + m_SortFlag = false; + } + +private: + + unsigned int m_NumberOfVertices; + + MSTEdge *m_MSTEdges; + + float *m_NodeAverages; + + bool m_SortFlag; +}; + +#endif diff --git a/BRAINSABC/brainseg/RegistrationParameters.h b/BRAINSABC/brainseg/RegistrationParameters.h new file mode 100644 index 00000000..d76845b8 --- /dev/null +++ b/BRAINSABC/brainseg/RegistrationParameters.h @@ -0,0 +1,64 @@ +#if 0 +/******************************************************************************* + Common point for the registration parameters + + Sequence of parameters for affine: + Translation x, y, z + Rotation x, y, z + Scaling x, y, z + Skew x, y, z + ***************************************************************************** */ + +#ifndef _RegistrationParameters_h +#define _RegistrationParameters_h + +#define MU_REGISTER_MAJORVER "2" +#define MU_REGISTER_MINORVER "0a" + +// +// Line search steps +// + +#define MU_AFFINE_STEP_TRANSLATE 10.0 +#define MU_AFFINE_STEP_ROTATE 0.1 +#define MU_AFFINE_STEP_SCALE 0.1 +#define MU_AFFINE_STEP_SKEW 0.01 + +// +// Optimization order +// + +// Translation, rotation, scale, then skew + +#define MU_AFFINE_ORDER0 0 +#define MU_AFFINE_ORDER1 1 +#define MU_AFFINE_ORDER2 2 +#define MU_AFFINE_ORDER3 3 +#define MU_AFFINE_ORDER4 4 +#define MU_AFFINE_ORDER5 5 +#define MU_AFFINE_ORDER6 6 +#define MU_AFFINE_ORDER7 7 +#define MU_AFFINE_ORDER8 8 +#define MU_AFFINE_ORDER9 9 +#define MU_AFFINE_ORDER10 10 +#define MU_AFFINE_ORDER11 11 + +/* +// Translation, scale, rotation, then skew + +#define MU_AFFINE_ORDER0 0 +#define MU_AFFINE_ORDER1 1 +#define MU_AFFINE_ORDER2 2 +#define MU_AFFINE_ORDER3 6 +#define MU_AFFINE_ORDER4 7 +#define MU_AFFINE_ORDER5 8 +#define MU_AFFINE_ORDER6 3 +#define MU_AFFINE_ORDER7 4 +#define MU_AFFINE_ORDER8 5 +#define MU_AFFINE_ORDER9 9 +#define MU_AFFINE_ORDER10 10 +#define MU_AFFINE_ORDER11 11 +*/ + +#endif +#endif diff --git a/BRAINSABC/brainseg/StandardizeMaskIntensity.cxx b/BRAINSABC/brainseg/StandardizeMaskIntensity.cxx new file mode 100644 index 00000000..b7aeb174 --- /dev/null +++ b/BRAINSABC/brainseg/StandardizeMaskIntensity.cxx @@ -0,0 +1,58 @@ +#include "StandardizeMaskIntensity.h" +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" + +int main( int argc, char *argv[] ) +{ + typedef itk::Image ImageType; + typedef itk::Image MaskImageType; + + typedef itk::ImageFileReader ReaderType; + + ReaderType::Pointer imageReader = ReaderType::New(); + imageReader->SetFileName(argv[1]); + imageReader->Update(); + ImageType::Pointer image = imageReader->GetOutput(); + + MaskImageType::Pointer mask = NULL; // itkUtil::ReadImage( + // argv[2] ); + if( argc == 4 ) + { + typedef itk::ImageFileReader MaskReaderType; + MaskReaderType::Pointer maskReader = MaskReaderType::New(); + maskReader->SetFileName(argv[3]); + maskReader->Update(); + mask = maskReader->GetOutput(); + } + + const double lFract = 0.00005; + const double uFract = 1.0 - lFract; + const ImageType::PixelType lTarget = 1; + const ImageType::PixelType uTarget = 0.95 * MAX_IMAGE_OUTPUT_VALUE; + const ImageType::PixelType clipMin = 0; + const ImageType::PixelType clipMax = MAX_IMAGE_OUTPUT_VALUE; + + ImageType::Pointer result = StandardizeMaskIntensity(image, + mask, + lFract, + uFract, + lTarget, + uTarget, + clipMin, + clipMax); + + if( result.IsNull() ) + { + return 2; + } + + typedef itk::ImageFileWriter FloatWriterType; + FloatWriterType::Pointer writer = FloatWriterType::New(); + + writer->SetInput(result); + writer->SetFileName(argv[2]); + writer->UseCompressionOn(); + writer->Update(); + return 0; +} + diff --git a/BRAINSABC/brainseg/StandardizeMaskIntensity.h b/BRAINSABC/brainseg/StandardizeMaskIntensity.h new file mode 100644 index 00000000..24f507d0 --- /dev/null +++ b/BRAINSABC/brainseg/StandardizeMaskIntensity.h @@ -0,0 +1,134 @@ +#ifndef __StandardizeMaskIntensity_h +#define __StandardizeMaskIntensity_h +#include "itkMinimumMaximumImageCalculator.h" +#include "itkLabelStatisticsImageFilter.h" +#include "itkHistogram.h" +#include "itkIntensityWindowingImageFilter.h" +#include "itkThresholdImageFilter.h" +#include "itkNumericTraits.h" + +#define MAX_IMAGE_OUTPUT_VALUE 4096 + +/* * * * * + * StandardizeMaskIntensity trims the upper and lower fractions of the histogram inside the mask + * based on tail size fractions uFract and lFract, respectively. Then, using these histogram-based + * upper and lower bounds, it rescales the signal interval they represent to an interval marked by + * the target upper and lower values, and clips the output image signal to an interval that encloses + * the target interval. + * + * Uses Review Statistics Histogram's Quantile method. IntensityWindowingImageFilter clips to the + * same bounds it scales to as lowerQuantileValue target, so lowerQuantileValue little univariate extrapolation was done (see block comment). + * + * * * * */ +template +typename ImageType::Pointer StandardizeMaskIntensity( + typename ImageType::Pointer image, + typename LabelImageType::Pointer mask, + const double lFract, + const double uFract, + const typename ImageType::PixelType lowerPeggedValue, + const typename ImageType::PixelType upperPeggedValue, + const typename ImageType::PixelType clipMin, + const typename ImageType::PixelType clipMax) +{ + // the asserts, if you want them, go like this: + // ImageType::PixelType is scalar. + // 0.0 <= lFract < uFract <= 1.0 + // clipMin <= lowerPeggedValue < upperPeggedValue <= clipMax + + typedef typename itk::MinimumMaximumImageCalculator MinimumMaximumImageCalculator; + typename MinimumMaximumImageCalculator::Pointer wholeStatistics = MinimumMaximumImageCalculator::New(); + wholeStatistics->SetImage(image); + wholeStatistics->Compute(); + typename ImageType::PixelType imgMin = wholeStatistics->GetMinimum(); + typename ImageType::PixelType imgMax = wholeStatistics->GetMaximum(); + + int numBins = vnl_math_rnd(imgMax - imgMin + 1); + if( numBins < 256 ) + { + numBins = 256; + } + if( numBins > MAX_IMAGE_OUTPUT_VALUE ) + { + numBins = MAX_IMAGE_OUTPUT_VALUE; + } + + const typename LabelImageType::PixelType maskInteriorLabel = 1; + typename LabelImageType::Pointer internalMask; + if( mask.IsNull() ) + { + internalMask = LabelImageType::New(); + internalMask->CopyInformation(image); + internalMask->SetRegions( image->GetLargestPossibleRegion() ); + internalMask->Allocate(); + internalMask->FillBuffer(maskInteriorLabel); + } + else + { + typename itk::ThresholdImageFilter::Pointer thresholdFilter + = itk::ThresholdImageFilter::New(); + + thresholdFilter->SetInput(mask); + thresholdFilter->ThresholdAbove(1); // Values less than or equal to are set + // to OutsideValue + thresholdFilter->SetOutsideValue(maskInteriorLabel); + thresholdFilter->Update(); + internalMask = thresholdFilter->GetOutput(); + } + + typedef typename itk::LabelStatisticsImageFilter LabelStatisticsImageFilter; + typename LabelStatisticsImageFilter::Pointer maskedStatistics = LabelStatisticsImageFilter::New(); + maskedStatistics->SetInput(image); // i.clipMin., image. + maskedStatistics->SetLabelInput(internalMask); + maskedStatistics->UseHistogramsOn(); + maskedStatistics->SetHistogramParameters(numBins, imgMin, imgMax); + maskedStatistics->Update(); + typename LabelStatisticsImageFilter::HistogramType::Pointer hist = + maskedStatistics->GetHistogram( maskInteriorLabel ); + if( hist.IsNull() ) + { + std::cout << "TODO: THIS SHOULD BE AN EXCEPTION" + << "histogram had no value for label " + << __FILE__ << " " << __LINE__ << " " << maskInteriorLabel << std::endl; + exit(-1); + } + + // Remark: Since itk's filter uses the same bounds to scale and to clip, + // and since the clipping bounds are outside (surrounding) the scaling + // bounds, we need to compute adjustedWindowMaxForClipping and + // adjustedWindowMinForClipping + // to fake out ITK developers and get both + // jobs done at once. Fortunately, we may use itkHistogram's Quantile + // routine: + typedef typename itk::IntensityWindowingImageFilter IntensityWindowingImageFilter; + typename IntensityWindowingImageFilter::Pointer intensityMapper = IntensityWindowingImageFilter::New(); + intensityMapper->SetInput( maskedStatistics->GetOutput() ); // i.clipMin., + // image. + // NOTE: The math below is to extend the range to the clipping region. + // + // + typedef typename itk::NumericTraits::ScalarRealType Real; + const Real lowerQuantileValue = hist->Quantile(0, lFract); + const Real upperQuantileValue = hist->Quantile(0, uFract); + { + const Real windowSlope = ( upperPeggedValue - lowerPeggedValue ) / ( upperQuantileValue - lowerQuantileValue ); + const Real windowIntercept = ( upperPeggedValue - ( upperQuantileValue * windowSlope ) ); + const typename ImageType::PixelType adjustedWindowMinForClipping = ( clipMin - windowIntercept ) / ( windowSlope ); + const typename ImageType::PixelType adjustedWindowMaxForClipping = ( clipMax - windowIntercept ) / ( windowSlope ); + + std::cout << "Quantile: [" << lowerQuantileValue << "," << upperQuantileValue << "];" + << " Pegged: [" << lowerPeggedValue << "," << upperPeggedValue << "]." << std::endl; + std::cout << "Mapping Window: [" << adjustedWindowMinForClipping << "," << adjustedWindowMaxForClipping << "]" + << " to [" << clipMin << "," << clipMax << "]." << std::endl; + intensityMapper->SetWindowMinimum(adjustedWindowMinForClipping); + intensityMapper->SetWindowMaximum(adjustedWindowMaxForClipping); + intensityMapper->SetOutputMinimum(clipMin); + intensityMapper->SetOutputMaximum(clipMax); + } + intensityMapper->Update(); + typename ImageType::Pointer remappedImage = intensityMapper->GetOutput(); + remappedImage->DisconnectPipeline(); + return remappedImage; +} + +#endif // __StandardizeMaskIntensity_h diff --git a/BRAINSABC/brainseg/filterFloatImages.cxx b/BRAINSABC/brainseg/filterFloatImages.cxx new file mode 100644 index 00000000..65edc5bd --- /dev/null +++ b/BRAINSABC/brainseg/filterFloatImages.cxx @@ -0,0 +1,55 @@ +#include "itkCurvatureFlowImageFilter.h" + +#include "itkGradientAnisotropicDiffusionImageFilter.h" + +#include "filterFloatImages.h" + +void +filterFloatImages( + std::vector::Pointer> & images, + std::string & method, + unsigned int iters, + double dt) +{ + typedef itk::Image FloatImageType; + + if( method.compare("GradientAnisotropicDiffusion") == 0 ) + { + std::cout << "Gradient Anisotropic Diffusion" << std::endl; + typedef itk::GradientAnisotropicDiffusionImageFilter + + AnisoFilterType; + for( unsigned i = 0; i < images.size(); i++ ) + { + AnisoFilterType::Pointer anisofilt = AnisoFilterType::New(); + + // if (debugflag) + // anisofilt->DebugOn(); + + anisofilt->SetNumberOfIterations(iters); + anisofilt->SetTimeStep(dt); + anisofilt->SetInput(images[i]); + anisofilt->Update(); + images[i] = anisofilt->GetOutput(); + } + } + // else if? Default is curvature flow + else + { + std::cout << "K flow" << std::endl; + typedef itk::CurvatureFlowImageFilter + CurvatureFilterType; + for( unsigned int k = 0; k < images.size(); k++ ) + { + CurvatureFilterType::Pointer cfilt = CurvatureFilterType::New(); + + cfilt->SetNumberOfIterations(iters); + cfilt->SetTimeStep(dt); + cfilt->SetInput(images[k]); + cfilt->Update(); + + images[k] = cfilt->GetOutput(); + } + } +} + diff --git a/BRAINSABC/brainseg/filterFloatImages.h b/BRAINSABC/brainseg/filterFloatImages.h new file mode 100644 index 00000000..f2a82f1a --- /dev/null +++ b/BRAINSABC/brainseg/filterFloatImages.h @@ -0,0 +1,13 @@ +#ifndef __filterFloatImages_h +#define -_filterFloatImages_h + +#include "itkImage.h" + +#include + +#include + +void filterFloatImages(std::vector::Pointer> & images, std::string & method, unsigned int iters, + double dt); + +#endif diff --git a/BRAINSABC/brainseg/itkBlendImageFilter.h b/BRAINSABC/brainseg/itkBlendImageFilter.h new file mode 100644 index 00000000..9c824a1a --- /dev/null +++ b/BRAINSABC/brainseg/itkBlendImageFilter.h @@ -0,0 +1,111 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#ifndef __itkBlendImageFilter_h +#define __itkBlendImageFilter_h + +#include "itkImageToImageFilter.h" + +namespace itk +{ +/** \class BlendImageFilter + * \brief Blend 2 images based using weights for each images + */ +template +class ITK_EXPORT BlendImageFilter : public ImageToImageFilter +{ +public: + /** Standard class typedefs. */ + typedef BlendImageFilter Self; + typedef ImageToImageFilter Superclass; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(BlendImageFilter, ImageToImageFilter); + + /** Some convenient typedefs. */ + typedef TInputImage InputImageType; + typedef typename InputImageType::Pointer InputImagePointer; + typedef typename InputImageType::RegionType InputImageRegionType; + typedef typename InputImageType::PixelType InputImagePixelType; + + typedef TOutputImage OutputImageType; + typedef typename OutputImageType::Pointer OutputImagePointer; + typedef typename OutputImageType::RegionType OutputImageRegionType; + typedef typename OutputImageType::PixelType OutputImagePixelType; + + /** ImageDimension enumeration */ + itkStaticConstMacro(InputImageDimension, unsigned int, + TInputImage::ImageDimension); + itkStaticConstMacro(OutputImageDimension, unsigned int, + TOutputImage::ImageDimension); + + /** Input and output images must be the same dimension, or the output's + dimension must be one less than that of the input. */ +#ifdef ITK_USE_CONCEPT_CHECKING + /** Begin concept checking */ + itkConceptMacro( ImageDimensionCheck, + ( Concept::SameDimension ) ); + /** End concept checking */ +#endif + + /** Set the blend amounts for each input image. + * set before the update of the filter. + */ + itkGetConstMacro(Blend1, double); + itkSetMacro(Blend1, double); + itkGetConstMacro(Blend2, double); + itkSetMacro(Blend2, double); + + void SetInput1(const TInputImage *image1) + { + this->SetNthInput(0, const_cast(image1) ); + } + + void SetInput2(const TInputImage *image2) + { + this->SetNthInput(1, const_cast(image2) ); + } + +protected: + BlendImageFilter(); + virtual ~BlendImageFilter() + { + } + + void PrintSelf(std::ostream & os, Indent indent) const; + + void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, int threadId); + +private: + BlendImageFilter(const Self &); // purposely not implemented + void operator=(const Self &); // purposely not implemented + + double m_Blend1, m_Blend2; +}; +} // end namespace itk + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkBlendImageFilter.txx" +#endif + +#endif diff --git a/BRAINSABC/brainseg/itkBlendImageFilter.txx b/BRAINSABC/brainseg/itkBlendImageFilter.txx new file mode 100644 index 00000000..b58ed206 --- /dev/null +++ b/BRAINSABC/brainseg/itkBlendImageFilter.txx @@ -0,0 +1,88 @@ +/*========================================================================= + * + * Copyright Insight Software Consortium + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + *=========================================================================*/ +#ifndef __itkBlendImageFilter_txx +#define __itkBlendImageFilter_txx + +#include "itkBlendImageFilter.h" +#include "itkImageRegionIterator.h" +#include "itkProgressReporter.h" + +namespace itk +{ +/** + * Constructor + */ +template +BlendImageFilter +::BlendImageFilter() : m_Blend1(1.0), m_Blend2(1.0) +{ +} + +/** + * GenerateData Performs the accumulation + */ +template +void +BlendImageFilter +::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, + int threadId) +{ + // We use dynamic_cast since inputs are stored as DataObjects. The + // ImageToImageFilter::GetInput(int) always returns a pointer to a + // TInputImage so it cannot be used for the second input. + InputImagePointer inputPtr1 = dynamic_cast(this->ProcessObject::GetInput(0) ); + InputImagePointer inputPtr2 = dynamic_cast(this->ProcessObject::GetInput(1) ); + OutputImagePointer outputPtr = dynamic_cast(this->GetOutput(0) ); + + ImageRegionIterator inputIt1(inputPtr1, outputRegionForThread); + ImageRegionIterator inputIt2(inputPtr2, outputRegionForThread); + + ImageRegionIterator outputIt(outputPtr, outputRegionForThread); + + ProgressReporter progress( this, threadId, outputRegionForThread.GetNumberOfPixels() ); + + inputIt1.GoToBegin(); + inputIt2.GoToBegin(); + outputIt.GoToBegin(); + + while( !inputIt1.IsAtEnd() ) + { + double acc = static_cast(inputIt1.Get() ) * this->m_Blend1; + acc += static_cast(inputIt2.Get() ) * this->m_Blend2; + outputIt.Set( static_cast(acc) ); + ++inputIt2; + ++inputIt1; + ++outputIt; + progress.CompletedPixel(); // potential exception thrown here + } + +} + +template +void +BlendImageFilter::PrintSelf(std::ostream & os, Indent indent) const +{ + Superclass::PrintSelf(os, indent); + + os << indent << "Blend1: " << this->m_Blend1 << std::endl; + os << indent << "Blend2: " << this->m_Blend2 << std::endl; +} + +} // end namespace itk + +#endif diff --git a/BRAINSABC/brainseg/normalA-30.xml b/BRAINSABC/brainseg/normalA-30.xml new file mode 100644 index 00000000..497416cd --- /dev/null +++ b/BRAINSABC/brainseg/normalA-30.xml @@ -0,0 +1,24 @@ + + + +normalA-30 +C:/Work/Data/Atlas +RAI +C:/Work/Output/normalA-30 +GIPL + + C:/Work/Data/NormalA Dataset/NormalA-030/Series09_t1_mprage_ax.mha + RAI + + + C:/Work/Data/NormalA Dataset/NormalA-030/Series08_t2_tra_1mm_128images_0_gap.mha + RAI + +0 +0.001 +4 +1.3 +1 +0.8 +1 + diff --git a/BRAINSABC/brainseg/oldCode.cxx b/BRAINSABC/brainseg/oldCode.cxx new file mode 100644 index 00000000..a12a3567 --- /dev/null +++ b/BRAINSABC/brainseg/oldCode.cxx @@ -0,0 +1,236 @@ + { + // TODO: Investigate if a small gaussian filter is needed here after + // clipping. +#if 0 + if( 0 ) + { + typename itk::DiscreteGaussianImageFilter::Pointer gaussianFilter = + itk::DiscreteGaussianImageFilter::New(); + gaussianFilter->SetInput(WarpedPriorsList[i]); + typename itk::DiscreteGaussianImageFilter::ArrayType MySigmas; + for( size_t s = 0; s < MySigmas.Size(); s++ ) + { // Make it 115% of the voxel spacings + // #MySigmas[s]=1.10*WarpedPriorsList[k]->GetSpacing()[s]; + MySigmas[s] = 1.5 * WarpedPriorsList[i]->GetSpacing()[s]; + } + gaussianFilter->SetVariance( MySigmas ); + const FloatingPrecision MaximumError = 0.01; // Copied from example. + gaussianFilter->SetMaximumError( MaximumError ); + gaussianFilter->Update(); + smoothProbImage = gaussianFilter->GetOutput(); + } + if( this->m_DebugLevel > 5 ) + { + std::stringstream CurrentEMIteration_stream(""); + CurrentEMIteration_stream << CurrentEMIteration; + // Write the subject candidate regions + + std::ostringstream oss; + oss << this->m_OutputDebugDir << "CANDIDIDATE_PROB_" << this->m_PriorNames[i] << "_LEVEL_" + << CurrentEMIteration_stream.str() << ".nii.gz" << std::ends; + std::string fn = oss.str(); + muLogMacro( << "Writing Subject Candidate Region." << fn << std::endl ); + muLogMacro( << std::endl ); + + typedef itk::ImageFileWriter ByteWriterType; + typename ByteWriterType::Pointer writer = ByteWriterType::New(); + writer->SetInput(smoothProbImage); + writer->SetFileName(fn.c_str() ); + writer->UseCompressionOn(); + writer->Update(); + } +#endif + } + +/** +*/ +template +typename ByteImageType::Pointer +EMSegmentationFilter +::ExtractNonAirRegion(const unsigned int /*CurrentIterationID*/, + const typename TProbabilityImage::Pointer & BackgroundPrior ) +{ + ByteImageType::Pointer NonBackground; + + { + typedef itk::ResampleImageFilter + ByteResamplerType; + muLogMacro(<< " Computing non-air region ." << std::endl); + + typedef itk::BinaryThresholdImageFilter ProbThresholdType; + typename ProbThresholdType::Pointer probNonAirRegion = ProbThresholdType::New(); + probNonAirRegion->SetInput( BackgroundPrior ); + probNonAirRegion->SetInsideValue(1); + probNonAirRegion->SetOutsideValue(0); + probNonAirRegion->SetLowerThreshold(-1.0e10); + probNonAirRegion->SetUpperThreshold(0.99); // Set the uppper threshold to + // 99% of image + probNonAirRegion->Update(); + NonBackground = probNonAirRegion->GetOutput(); + } + + return NonBackground; +} + +typename ByteImageType::Pointer ComputeForegroundProbMask( + const std::vector & probList, const BoolVectorType & IsForegroundPriorVector); + +template +typename ByteImageType::Pointer +EMSegmentationFilter +::ComputeForegroundProbMask(const std::vector & probList, + const BoolVectorType & IsForegroundPriorVector ) +{ + + muLogMacro(<< "ComputeForegroundProbMask" << std::endl ); + + const unsigned int numPriors = probList.size(); + + typename ByteImageType::Pointer currForegroundMask = ByteImageType::New(); + currForegroundMask->CopyInformation(probList[0]); + currForegroundMask->SetRegions(probList[0]->GetLargestPossibleRegion() ); + currForegroundMask->Allocate(); + + const ProbabilityImageSizeType size = probList[0]->GetLargestPossibleRegion().GetSize(); + const typename ByteImageType::PixelType insideMaskValue = 100; + + { +#pragma omp parallel for + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + FloatingPrecision tmp = 0.0; + for( unsigned int iprior = 0; iprior < numPriors; iprior++ ) + { + const bool fgflag = IsForegroundPriorVector[iprior]; + if( fgflag == true ) + { + tmp += probList[iprior]->GetPixel(currIndex); + } + } + if( tmp > 0.005 ) // Only include if the sum of the non-background + // priors are greater than 1/2 of 1 percent chance + { + currForegroundMask->SetPixel(currIndex, static_cast(insideMaskValue) ); + } + else + { + currForegroundMask->SetPixel(currIndex, 0); + } + } + } + } + } +#if 1 + { + // Pre-Dilate mask + typedef itk::BinaryBallStructuringElement StructElementType; + typedef + itk::BinaryDilateImageFilter DilateType; + + StructElementType structel; + structel.SetRadius(1); + structel.CreateStructuringElement(); + + typename DilateType::Pointer dil = DilateType::New(); + dil->SetDilateValue(50); + dil->SetKernel(structel); + dil->SetInput(currForegroundMask); + + dil->Update(); + + ByteImagePointer dilmask = dil->GetOutput(); + // a simple assignment is probably sufficient, test both ways? + currForegroundMask = CopyImage(dilmask); + } +#endif + +#if 0 + { // Now clip to the filed of view + if( m_NonAirRegion.IsNotNull() ) + { + if( size != m_NonAirRegion->GetLargestPossibleRegion().GetSize() ) + { + itkExceptionMacro( + << "NonAirRegion mask size mismatch " << size << " != " + << m_NonAirRegion->GetLargestPossibleRegion().GetSize() << " ." << std::endl ); + } + + unsigned long count = 0; + { +#pragma omp parallel for reduction(+:count) + for( LOOPITERTYPE kk = 0; kk < (LOOPITERTYPE)size[2]; kk++ ) + { + for( LOOPITERTYPE jj = 0; jj < (LOOPITERTYPE)size[1]; jj++ ) + { + for( LOOPITERTYPE ii = 0; ii < (LOOPITERTYPE)size[0]; ii++ ) + { + const ProbabilityImageIndexType currIndex = {{ii, jj, kk}}; + if( ( m_NonAirRegion->GetPixel(currIndex) == 0) ) + { + currForegroundMask->SetPixel(currIndex, 0); + } + else + { + count = count + 1; + } + } + } + } + } + muLogMacro( + << "DEBUG: Warped TemplateBrainMask size " << count << " of " << size[0] * size[1] * size[2] << std::endl); + } +#if 1 + { + // Dilate mask + typedef itk::BinaryBallStructuringElement StructElementType; + typedef + itk::BinaryDilateImageFilter DilateType; + + StructElementType structel; + structel.SetRadius(1); + structel.CreateStructuringElement(); + + typename DilateType::Pointer dil = DilateType::New(); + dil->SetDilateValue(25); + dil->SetKernel(structel); + dil->SetInput(currForegroundMask); + + dil->Update(); + + ByteImagePointer dilmask = dil->GetOutput(); + currForegroundMask = CopyImage(dilmask); + } +#endif + } +#endif + + if( this->m_DebugLevel > 5 ) + { // DEBUG: This code is for + // debugging purposes only; + unsigned int write_corrected_level = 0; // DEBUG: This code is for + // debugging purposes only; + std::stringstream write_corrected_level_stream(""); + write_corrected_level_stream << write_corrected_level; + { // DEBUG: This code is for debugging purposes only; + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + const std::string fn = this->m_OutputDebugDir + "/MASK_LEVEL_" + write_corrected_level_stream.str() + ".nii.gz"; + writer->SetInput(currForegroundMask); + writer->SetFileName(fn.c_str() ); + writer->Update(); + muLogMacro( << "DEBUG: Wrote image " << fn << std::endl ); + } + } + return currForegroundMask; +} + diff --git a/BRAINSABC/common/Heap.h b/BRAINSABC/common/Heap.h new file mode 100644 index 00000000..24cddd49 --- /dev/null +++ b/BRAINSABC/common/Heap.h @@ -0,0 +1,81 @@ +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Binary heap using arrays +// +// Element type must have: default constructor, copy ctor, operator=, operator< +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 9/2003 + +#ifndef __Heap_h +#define __Heap_h + +#include + +/** + * \class Heap + */ +template +class Heap +{ +public: + + Heap(); + Heap(const Heap & h); + ~Heap(); + + Heap & operator=(const Heap & h); + + void Allocate(unsigned int size); + + inline void Clear() + { + m_Elements.clear(); + } + + T ExtractMinimum(); + + inline unsigned int GetNumberOfElements() + { + return m_Elements.size(); + } + + void Insert(const T & e); + + bool IsEmpty(); + + T * GetElements() + { + return m_Elements.GetRawArray(); + } + + void UpdateElementAt(unsigned int i); + +private: + + std::vector m_Elements; + + void PreserveHeapOrder(); + +}; + +// Get the first k sorted elements using heap sort +template +T * heapFirstK(std::vector & array, unsigned int n, unsigned int k); + +// Get the k-th element using heap sort +template +T heapKthElement(std::vector & array, unsigned int n, unsigned int k); + +// Get median using heap sort +template +T heapMedian(std::vector & array, unsigned int n); + +#ifndef MU_MANUAL_INSTANTIATION +#include "Heap.txx" +#endif + +#endif diff --git a/BRAINSABC/common/Heap.txx b/BRAINSABC/common/Heap.txx new file mode 100644 index 00000000..4c79e458 --- /dev/null +++ b/BRAINSABC/common/Heap.txx @@ -0,0 +1,265 @@ +#ifndef __Heap_txx +#define __Heap_txx + +#include "Heap.h" + +#include "muException.h" + +// Macros to convert binary tree traversal to array access +// Tree root is 1 +#define HEAP_PARENT(x) ( ( x ) / 2 ) +#define HEAP_LEFT(x) ( 2 * ( x ) ) +#define HEAP_RIGHT(x) ( 2 * ( x ) + 1 ) + +template +Heap +::Heap() +{ +} + +template +Heap +::Heap(const Heap & h) +{ + m_Elements = h.m_Elements; +} + +template +Heap +::~Heap() +{ +} + +template +Heap & +Heap +::operator =( const Heap & h ) +{ + m_Elements = h.m_Elements; +} + +template +void +Heap +::Allocate(unsigned int size) +{ + m_Elements.resize(size); +} + +template +T +Heap +::ExtractMinimum() +{ + if( this->IsEmpty() ) + { + muExceptionMacro(<< "[Heap::ExtractMinimum] Heap is empty"); + } + + T minElem = m_Elements[0]; + + unsigned int last = m_Elements.size() - 1; + + m_Elements[0] = m_Elements[last]; + m_Elements.pop_back(); + + this->PreserveHeapOrder(); + + return minElem; +} + +template +bool +Heap +::IsEmpty() +{ + return m_Elements.empty(); +} + +template +void +Heap +::Insert(const T & e) +{ + m_Elements.push_back(e); + + unsigned int i = m_Elements.size(); + + while( ( i > 1 ) && ( e < m_Elements[HEAP_PARENT(i) - 1] ) ) + { + m_Elements[i - 1] = m_Elements[HEAP_PARENT(i) - 1]; + i = HEAP_PARENT(i); + } + + m_Elements[i - 1] = e; +} + +template +void +Heap +::PreserveHeapOrder() +{ + unsigned int numElements = m_Elements.size(); + + unsigned int current; + unsigned int left; + unsigned int right; + unsigned int smallest; + + // Start at root node + current = 1; + + do + { + left = HEAP_LEFT(current); + right = HEAP_RIGHT(current); + + smallest = current; + + if( ( left <= numElements ) + && + ( m_Elements[left - 1] < m_Elements[smallest - 1] ) ) + { + smallest = left; + } + + if( ( right <= numElements ) + && + ( m_Elements[right - 1] < m_Elements[smallest - 1] ) ) + { + smallest = right; + } + + if( smallest == current ) + { + break; + } + + T temp = m_Elements[current - 1]; + m_Elements[current - 1] = m_Elements[smallest - 1]; + m_Elements[smallest - 1] = temp; + + current = smallest; + } + while( true ); +} + +template +void +Heap +::UpdateElementAt(unsigned int i) +{ + unsigned int loc = i + 1; + + // Root update + if( loc == 1 ) + { + this->PreserveHeapOrder(); + } + + // + // Find new location while swapping values between parent-child + // + + // Loop until we reach root or until the element is in the right order + // relative to parent + while( + ( loc > 1 ) + && + ( m_Elements[loc - 1] < m_Elements[HEAP_PARENT(loc) - 1] ) ) + { + // Swap parent and current + T t = m_Elements[HEAP_PARENT(loc) - 1]; + m_Elements[HEAP_PARENT(loc) - 1] = m_Elements[loc - 1]; + m_Elements[loc - 1] = t; + + // Process parent at next iteration + loc = HEAP_PARENT(loc); + } +} + +template +T * +heapFirstK(std::vector & array, unsigned int n, unsigned int k) +{ + if( k >= n ) + { + return 0; + } + T *firstk = new T[k]; + + Heap heap; + heap.Allocate(n); + for( unsigned int i = 0; i < n; i++ ) + { + heap.Insert(array[i]); + } + for( unsigned int i = 0; i < k; i++ ) + { + firstk[i] = heap.ExtractMinimum(); + } + + return firstk; +} + +template +T +heapKthElement(std::vector & array, unsigned int n, unsigned int k) +{ + if( k >= n ) + { + return array[n - 1]; + } + + Heap heap; + heap.Allocate(n); + for( unsigned int i = 0; i < n; i++ ) + { + heap.Insert(array[i]); + } + // Throw away first k-1 values + for( unsigned int i = 0; i < k; i++ ) + { + heap.ExtractMinimum(); + } + + return heap.ExtractMinimum(); +} + +template +T +heapMedian(std::vector & array, unsigned int n) +{ + if( n == 0 ) + { + return 0; + } + + if( n == 1 ) + { + return array[0]; + } + + if( n == 2 ) + { + return ( array[0] + array[1] ) / 2; + } + + if( ( n % 2 ) == 0 ) + { + unsigned int k = ( n / 2 ) + 1; + + T *tmp = heapFirstK(array, n, k); + T mid = ( tmp[k - 2] + tmp[k - 1] ) / 2; + + delete[] tmp; + + return mid; + } + else + { + return heapKthElement(array, n, ( n + 1 ) / 2); + } +} + +#endif diff --git a/BRAINSABC/common/Log.cxx b/BRAINSABC/common/Log.cxx new file mode 100644 index 00000000..eedb5de4 --- /dev/null +++ b/BRAINSABC/common/Log.cxx @@ -0,0 +1,102 @@ +#include "Log.h" + +#include "muException.h" + +namespace mu +{ +Log * +Log +::GetInstance() +{ + // Allow only one instance + static Log instance; + + return &instance; +} + +Log +::Log() +{ + m_EchoFlag = true; + m_OutputFileName = ""; +} + +Log +::~Log() +{ + this->CloseFile(); +} + +Log +::Log(const Log & l) +{ + m_EchoFlag = l.m_EchoFlag; + m_OutputFileName = l.m_OutputFileName; +} + +void +Log +::CloseFile() +{ + if( m_Output.is_open() ) + { + m_Output.close(); + } +} + +void +Log +::SetOutputFileName(const char *s) +{ + if( m_Output.is_open() ) + { + m_Output.close(); + } + + m_Output.open(s); + + if( m_Output.fail() ) + { + muExceptionMacro( + << "[Log::SetOutputFileName] Failed to open " << s); + } +} + +void +Log +::SetOutputFileName(const std::string & s) +{ + this->SetOutputFileName( s.c_str() ); +} + +void +Log +::WriteString(const char *s) +{ + if( s == NULL ) + { + std::cout << "[Log::WriteString] NULL argument" << std::endl << std::flush; + return; + } + + if( m_Output.good() ) + { + m_Output << s; + m_Output.flush(); + } + + if( m_EchoFlag ) + { + std::cout << s; + (std::cout).flush(); + } +} + +void +Log +::WriteString(const std::string & s) +{ + this->WriteString( s.c_str() ); +} + +} // namespace mu diff --git a/BRAINSABC/common/Log.h b/BRAINSABC/common/Log.h new file mode 100644 index 00000000..cb76a781 --- /dev/null +++ b/BRAINSABC/common/Log.h @@ -0,0 +1,76 @@ +// +// ////////////////////////////////////////////////////////////////////////////// +// +// Handles log messages to terminal and disk, follows singleton pattern +// +// +// ////////////////////////////////////////////////////////////////////////////// + +// prastawa@cs.unc.edu 2/2004 + +#ifndef __Log_h +#define __Log_h + +#include +#include +#include +#include + +namespace mu +{ +/** \class Log + */ +class Log +{ +public: + + static Log * GetInstance(); + + void CloseFile(); + + // Enable / disable writes to terminal + inline void EchoOn() + { + m_EchoFlag = true; + } + inline void EchoOff() + { + m_EchoFlag = false; + } + + void SetOutputFileName(const char *s); + + void SetOutputFileName(const std::string & s); + + void WriteString(const char *s); + + void WriteString(const std::string & s); + + std::ofstream & GetFileObject() + { + return m_Output; + } +private: + + // Restrict access to constructors + Log(); + ~Log(); + Log(const Log & l); + + bool m_EchoFlag; + + std::ofstream m_Output; + + std::string m_OutputFileName; +}; +} // namespace mu + +// Allows declarations such as: muLogMacro(<< "Message: " << 1.1234); +#define muLogMacro(x) \ + { \ + std::ostringstream outss; \ + outss << "" x << std::ends; \ + ( mu::Log::GetInstance() )->WriteString( outss.str().c_str() ); \ + } + +#endif diff --git a/BRAINSABC/common/mu.h b/BRAINSABC/common/mu.h new file mode 100644 index 00000000..8f915107 --- /dev/null +++ b/BRAINSABC/common/mu.h @@ -0,0 +1,17 @@ +// Include all mu relevant headers + +#ifndef __mu_h +#define __mu_h + +// Platform specific stuff +#ifdef __CYGWIN__ +#include "muCygwin.h" +#endif + +// Convenience macros +#include "muMacros.h" + +// Utility functions +#include "muUtils.h" + +#endif diff --git a/BRAINSABC/common/muCygwin.h b/BRAINSABC/common/muCygwin.h new file mode 100644 index 00000000..73cc49ad --- /dev/null +++ b/BRAINSABC/common/muCygwin.h @@ -0,0 +1,47 @@ +// Include this file before including stuff from mu + +#ifndef __muCygwin_h +#define __muCygwin_h + +#include "itkMacro.h" +#include +#include + +// Cygwin exception handling work-around +#undef itkExceptionMacro +#define itkExceptionMacro(x) \ + { \ + std::cerr << "Exception: " x << std::endl; \ + std::cerr << "Possibly crashing about now..." << std::endl; \ + throw "exc"; \ + } + +// TODO wrap main so that uncaught exception does not crash program +#define MU_DEFINE_MAIN \ + int \ + main(int argc, char * *argv) \ + { \ + int r = 0; \ + try \ + { \ + r = _mu_main(argc, argv); \ + } \ + catch( itk::ExceptionObject & e ) \ + { \ + std::cerr << e << std::endl; \ + return -1; \ + } \ + catch( std::exception & e ) \ + { \ + std::cerr << "Exception: " << e.what() << std::endl; \ + return -1; \ + } \ + catch( char *s ) \ + { \ + std::cerr << "Exception: " << s << std::endl; \ + return -1; \ + } \ + return r; \ + } + +#endif diff --git a/BRAINSABC/common/muException.h b/BRAINSABC/common/muException.h new file mode 100644 index 00000000..e01b2bd3 --- /dev/null +++ b/BRAINSABC/common/muException.h @@ -0,0 +1,68 @@ +#ifndef __muException_h +#define __muException_h + +#include +#include +#include + +#include "Log.h" + +namespace mu +{ +/** \class Exception + */ +class Exception : public std::exception +{ +public: + + Exception() + throw ( ) + { + m_Message = ""; + } + ~Exception() + throw ( ) + { + } + + void SetMessage(const char *s) + { + m_Message = s; + } + + void Print(std::ostream & os) const + { + os << m_Message << std::endl; + } + + const char * what() const + throw ( ) + { + return m_Message.c_str(); + } + +protected: + + std::string m_Message; +}; +} // namespace mu + +inline std::ostream & operator<<(std::ostream & os, mu::Exception & e) +{ + ( &e )->Print(os); + return os; +} + +#define muExceptionMacro(x) \ + { \ + muLogMacro( << "mu::Exception, in " << __FILE__ << " line " << __LINE__; \ + std::cerr << "\n" x << "\n"); \ + std::stringstream oss; \ + oss << "mu::Exception, in " << __FILE__ << " line " << __LINE__; \ + oss << "\n" x << std::ends; \ + mu::Exception e; \ + e.SetMessage( oss.str().c_str() ); \ + throw e; \ + } + +#endif diff --git a/BRAINSABC/common/muMacros.h b/BRAINSABC/common/muMacros.h new file mode 100644 index 00000000..e3545626 --- /dev/null +++ b/BRAINSABC/common/muMacros.h @@ -0,0 +1,46 @@ +#ifndef __muMacros_h +#define __muMacros_h + +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" + +#include +#include + +#define muEcho(varname) \ + std::cout << #varname << " = " << varname << std::flush << std::endl; + +#define muStringMacro(strname, s) \ + std::string strname; \ + { \ + std::ostringstream outss; \ + outss << "" s << std::ends; \ + strname = outss.str(); \ + } + +#define muSelfFilterMacro(filter, obj) \ + { \ + filter->SetInput(obj); \ + iterator copy \ + } + +#define muReadMacro(type, filename, image) \ + { \ + typedef itk::ImageFileReader ReaderType; \ + typename ReaderType::Pointer reader = ReaderType::New(); \ + reader->SetFileName(filename); \ + reader->Update(); \ + image = reader->GetOutput(); \ + } + +#define muWriteMacro(type, filename, image) \ + { \ + typedef itk::ImageFileWriter WriterType; \ + typename WriterType::Pointer writer = WriterType::New(); \ + writer->UseCompressionOn(); \ + writer->SetFileName(filename); \ + writer->SetInput(image); \ + writer->Update(); \ + } + +#endif diff --git a/BRAINSABC/common/muUtils.h b/BRAINSABC/common/muUtils.h new file mode 100644 index 00000000..7ccca7c0 --- /dev/null +++ b/BRAINSABC/common/muUtils.h @@ -0,0 +1,66 @@ +// Simple utility functions + +#ifndef __muUtils_h +#define __muUtils_h + +#include "itkImageFileReader.h" +#include "itkImageFileWriter.h" + +#include "muException.h" + +#include + +#define muAlloc(n, T) muAlloc_func(n, __FILE__, __LINE__) + +template +T * +muAlloc_func(unsigned int n, const char *s, int line) +{ + T *array = new T[n]; + + if( array == NULL ) + { + muExceptionMacro(<< "muAlloc: Failed at " << s << ": " << line); + } + return array; +} + +template +typename TImage::Pointer +readImage(const char *fn) +{ + typedef itk::ImageFileReader ReaderType; + typename ReaderType::Pointer reader = ReaderType::New(); + + reader->SetFileName(fn); + reader->Update(); + + return reader->GetOutput(); +} + +template +void +writeImage(const char *fn, const TImage *ip) +{ + typedef itk::ImageFileWriter WriterType; + typename WriterType::Pointer writer = WriterType::New(); + writer->UseCompressionOn(); + + writer->SetFileName(fn); + writer->SetInput(ip); + + writer->Update(); +} + +// template +// void +// writeImageAsByte +// { +// typedef itk::Cast +// typedef itk::ImageFileWriter WriterType; +// } + +// void +// writeImageAsShort + +#endif diff --git a/BRAINSABC/common/testexc.cxx b/BRAINSABC/common/testexc.cxx new file mode 100644 index 00000000..4153dda7 --- /dev/null +++ b/BRAINSABC/common/testexc.cxx @@ -0,0 +1,17 @@ +#include "muException.h" + +int main() +{ + try + { + muExceptionMacro(<< "FOO"); + } + catch( mu::Exception & e ) + { + std::cerr << e << std::endl; + return -1; + } + + return 0; +} + diff --git a/BRAINSABC/common/testheap.cxx b/BRAINSABC/common/testheap.cxx new file mode 100644 index 00000000..7a8350e8 --- /dev/null +++ b/BRAINSABC/common/testheap.cxx @@ -0,0 +1,89 @@ +#include "Heap.h" + +#include + +class WrapInt +{ +public: + WrapInt() + { + v = 0; + } + WrapInt(int i) + { + v = i; + } + bool operator<(const WrapInt & w) const + { + return this->v < w.v; + } + WrapInt & operator=(const WrapInt & w) + { + this->v = w.v; return *this; + } + int v; +}; + +int main() +{ + Heap heap; + + heap.Insert( WrapInt(3) ); + heap.Insert( WrapInt(99) ); + heap.Insert( WrapInt(-1) ); + heap.Insert( WrapInt(7) ); + heap.Insert( WrapInt(21) ); + heap.Insert( WrapInt(-9) ); + heap.Insert( WrapInt(30) ); + heap.Insert( WrapInt(5) ); + + std::cout << "Heap size = " << heap.GetNumberOfElements() << std::endl; + + unsigned int origSize = heap.GetNumberOfElements(); + for( unsigned int i = 0; i < origSize; i++ ) + { + WrapInt mm = heap.ExtractMinimum(); + std::cout << mm.v << " :: "; + } + std::cout << std::endl; + + Heap heapf; + + heapf.Insert(9.9); + heapf.Insert(-2.5); + heapf.Insert(8.5); + heapf.Insert(3.0); + heapf.Insert(7.0); + heapf.Insert(-1.0); + heapf.Insert(6.0); + + origSize = heapf.GetNumberOfElements(); + for( unsigned int i = 0; i < origSize; i++ ) + { + std::cout << heapf.ExtractMinimum() << " :: "; + } + std::cout << std::endl; + + double x[] = {7.1, 2.4, -1.2, 12.1, 50.1, 1.9}; + + std::cout << "x = "; + for( unsigned int i = 0; i < 6; i++ ) + { + std::cout << x[i] << ", "; + } + std::cout << std::endl; + + std::cout << "x median = " << heapMedian(x, 6) << std::endl; + std::cout << "x largest = " << heapKthElement(x, 6, 5) << std::endl; + + double *x3 = heapFirstK(x, 6, 3); + std::cout << "x3 = "; + for( unsigned int i = 0; i < 3; i++ ) + { + std::cout << x3[i] << ", "; + } + std::cout << std::endl; + + return 0; +} + diff --git a/BRAINSABC/common/testmacro.cxx b/BRAINSABC/common/testmacro.cxx new file mode 100644 index 00000000..f63f7a5e --- /dev/null +++ b/BRAINSABC/common/testmacro.cxx @@ -0,0 +1,26 @@ +#include +#include +#include + +#define muDisplayMacro(varname) \ + std::cout << #varname << " = " << varname << std::endl; + +#define muStringMacro(strname, s) \ + std::string strname; \ + { \ + std::ostringstream outss; \ + outss << "" s << std::ends; \ + strname = outss.str(); \ + } + +int main() +{ + int x = 10; + std::string s = "abcfoo"; + + muDisplayMacro(x); + muDisplayMacro(s); + + return 0; +} + diff --git a/BRAINSABC/notes.BRAINSABC b/BRAINSABC/notes.BRAINSABC new file mode 100644 index 00000000..046aacf0 --- /dev/null +++ b/BRAINSABC/notes.BRAINSABC @@ -0,0 +1,85 @@ +Hello Martin and Marcel, + +We are stating to have some success with BRAINSABC (EMSegmentation.h to be more precise) program. We are working on creating a new set of atlases and using diffeomorphic demons to do the registration. The initial results are very promising! + +I've now committed the clean compiling code for BRAINSABC. There is a dashboard at: http://testing.psychiatry.uiowa.edu/CDash/index.php?project=BRAINSABC. Currently I do not have nightly dashboards, or multiple platforms being built. I'll work on that as we build more fine grained tests. + [hjohnson@hans-uiowa BRAINSABC]$ diff -Naur log_orig_code.log log_post_cvs_3.log + --- log_orig_code.log 2009-02-16 18:50:05.000000000 -0600 + +++ log_post_cvs_3.log 2009-02-17 20:04:07.000000000 -0600 + @@ -12,7 +12,7 @@ + Test timeout computed to be: 1500 + mu::brainseg + ======================================== + -Program compiled on: Feb 16 2009 + +Program compiled on: Feb 17 2009 + + Using ITK version 3.10.2 + + @@ -51,7 +51,7 @@ + Cropping images based on atlas priors... + Non-linear filtering of registered images... + K flow + -Non-linear filtering took 0 hours, 0 minutes, 0 seconds + +Non-linear filtering took 0 hours, 0 minutes, 1 seconds + Rescale intensity of filtered cropped images... + Start segmentation... + Splitting distributions with same prior + @@ -1805,7 +1805,7 @@ + Writing labels... + Writing filtered and bias corrected images... + Writing posterior images... + -All segmentation processes took 0 hours, 16 minutes, 24 seconds + +All segmentation processes took 0 hours, 15 minutes, 25 seconds + small_ISO_T1_REP1_corrected_EMS.nrrd + -- Process completed + Passed + +There are also some comments that are added in areas where more testing needs to be done, or where the code was not immediately clear to me or the graduate student (Regina) who is working on an implementation that will work well on our data. + +===== +I've added a file in BRAINSABC called buildBRAINSABC.sh which downloads the necessary files (ITK/VTK/fltk), creates ../BRAINSABC-COMPILE directory, configures and compiles BRAINSABC all by itself. You should be able to cd into the BRAINSABC directory and type "./buildBRAINSABC.sh" and it will download ITK/VTK/fltk configure and build them in optimized mode for your platform. Alternatively, a debuggable version can be built with "./buildBRAINSABC.sh DEBUG", or a profileable version with "./buildBRAINSABC.sh PROFILE". All these can be built from the same source tree, and across multiple platforms (assuming share storage between nodes). + +I've added a reference atlas to be used with BRAINSABC. + +I've added a few small test images and a reference data set (takes 11minutes to test on my MacBook Air). + +I've added SlicerExecutionModel directory to BRAINSABC so that Slicer is not needed in order to build BRAINSABC. + +===== +There seems to be a minor configuration problem on your CVS server: +cvs update: cannot open /home/cvsprivateuser/.cvsignore: Permission denied +===== +These are just random comments and sugestions about how I think that NeuroLib building could be easier. I have many of these implemented in my local builds, but some of them would involve major change in how this is built, so I'm not prepared to commit them to the cvs repository. Some of these changes were, however, necessary to get mriWatcher to build with the private version of BRAINSABC and the BUILD_TESTING turned on only for those two packages. + +I've had a little success in build all of NeuroLib, but there were several stumbling blocks in NeuroLib's CMakeLists.txt configurations. + 1) The logic to turn components on/off is very complex + a) If BUILD_TESTING is ON, then and it tries to build EVERYTHING, even if you do not have the necessary supporting libraries (i.e. QT), This prevents you from building and testing only a small subset of the NeuroLib packages. + b) There are mulitple "SUBDIRS" commands in CMake for the same directory, but they depend on different logic flags, so even if you explicitly request that a tool that depends on QT is not built, but turn BUILD_TESTING on, then it is built anyway. + 2) There are some CMakeLists.txt files with out PROJECT() tags + 3) the public and private versions of BRAINSABC have conflicting target names that must be unique across all projects (i.e. brainseg is a library in the public version, and is an executable in the private version). + 4) NeuroLib/Testing/Applications/CMakeLists.txt has tests for programs that may or may not be built from the NeuroLib/Applications tree. I would move the test into CMakeLists unit that actually builds the tested executable. This has the added advantage of simplifying the conditional build logic from the CMakeLists.txt. + 5) The file CMake/qtSetup.cmake appears to have many paths hardcoded for a particular install location (non of which worked for my lab). + I replace the original 137 lines of logic with: + FIND_PACKAGE(QT3 REQUIRED) + OPTION(QT_WRAP_CPP "QT_WRAP_CPP." ON) + OPTION(QT_WRAP_UI "QT_WRAP_UI. " ON) + and mriWatcher built immediately after that. + 6) Many of the CMake/*Setup.cmake files have standard FIND_PACKAGE() commands from cmake (fltk, fftw, vtk, boost, glut...), and it would be easier to build against these standard packages in our lab if the standard cmake FIND_PACKAGE commands were used. + 7) There a many aliased variables, for example COMPILE_SHAPE and NeuroLib_COMPILE_SHAPE + OPTION(COMPILE_SHAPE "Compile Shape Library" ON) + SET(NeuroLib_COMPILE_SHAPE ${COMPILE_SHAPE}) + MARK_AS_ADVANCED(COMPILE_SHAPE) + One of these variables is not needed, and it would be easier to follow which variable controls adding subdirectories and other actions. + 8) The USE_ITK_LIB and USE_VTK_LIB seem like they should be removed completely (and perhaps others). It is my opinion that each sub-component should know what libraries they depend on, and when those sub-components are requested for building, then there dependancies are found. For example, if you choose COMPILE_SHAPE=ON, then the LAPACK LIBRARIES are required, and cmake requires them before continuing. + + +Thanks for all your help. I look forward to continued collaborations. + +Hans + + + + + + + diff --git a/BRAINSABC/qhull/CMakeLists.txt b/BRAINSABC/qhull/CMakeLists.txt new file mode 100644 index 00000000..5a60858e --- /dev/null +++ b/BRAINSABC/qhull/CMakeLists.txt @@ -0,0 +1,43 @@ +project(qhull_lib) + +find_package(VTK) +if(VTK_FOUND) + include(${USE_VTK_FILE}) +else(VTK_FOUND) + message(FATAL_ERROR "VTK not found. Please set VTK_DIR.") +endif(VTK_FOUND) + +set(VTK_LIBRARIES + vtkCommon + vtkFiltering + vtkImaging + vtkGraphics + vtkGenericFiltering + vtkIO +) + +include_directories( + ${VTK_INCLUDE_DIRS} +# ${CMAKE_CURRENT_SOURCE_DIR}/../basicimg + ${CMAKE_CURRENT_SOURCE_DIR}/../common +) + +add_executable(testqh + testqh.cxx + vtkQhullDelaunay3D.cxx + user.c + global.c + stat.c + io.c + geom2.c + poly2.c + merge.c + qhull.c + geom.c + poly.c + qset.c + mem.c +) + + +target_link_libraries(testqh ${VTK_LIBRARIES}) diff --git a/BRAINSABC/qhull/Changes.txt b/BRAINSABC/qhull/Changes.txt new file mode 100644 index 00000000..c71571ab --- /dev/null +++ b/BRAINSABC/qhull/Changes.txt @@ -0,0 +1,1085 @@ + +.............This file lists all changes to qhull and rbox..................... + +qhull 2009.1 2009/06/11 + +This is a maintenance release done by Rafael Laboissiere . + + - src/rbox.c (main): Avoid problems of evaluation order when + pre-incrementing arguments of strtod + - src/io.c (qh_produce_output), src/stat.c (qh_initstatistics): Use %lu + instead of %d in the format string for arguments of type size_t + - html/qhull.man, html/rbox.man: Fix several syntax, macros, and hyphen + problems in man pages + - The Autotools files have been generated with modern version of autoconf (2.63), + automake/aclocal (1.10.2), and libtool (2.2.6) + - Some character issues in the man pages are fixed + +qhull 2003.1 2003/12/30 + + - Updated Qhull citation with page numbers. + - Project: constructing Voronoi diagram + - Project: computing Voronoi volumes + - identity function may drop points. The following lens distribution drops 52 of 102 points of its points + rbox 100 L1e5 | tee r | qconvex FV n | qhalf Fp | cat - r | /bin/sort -n > x + - offsetted points will add intersection points + rbox 1000 s O2 t | tee r | qconvex FV n | qhalf Fp | cat - r | /bin/sort -n | tail + +New Features: + - Add Maple output ('FM') for 2-d and 3-d convex hulls [T. Abraham] + +Bug Fixes and Code Changes: + - Fixed qh_findbest() for upperdelaunay facets w/o better, lower neighbors + For library users and some qhull users [A. Cutti, E. Milloti, K. Sun] + - Preserved qhmem.ferr in qh_memfreeshort() for library users + - Removed 'static' from qh_compare... for io.h and merge.h [V. Brumberg] + +Documentation: + - Add warning to findDelaunay() and qh_in.htm about tricoplanar facets + - Noted Edelsbrunner's Geometry & Topology for Mesh Generation [qh-impre.htm] + - Noted Gartner's Miniball algorithm [qh_impre.htm] + - Noted Veron and Leon's shape preserving simplification [qh_impre.htm] + +qhull 2003.1 2003/12/19 + +Bug Fixes: + - Reversed coordinate order for qh.ATinfinity in qh_projectinput [V. Brumberg] + This effects: + Qhull library 'd' or 'v' users with 'Qz' and unequal coordinate ranges. + qdelaunay/qvoronoi users with 'Qbk:0Bk:0', 'Qz', and unequal coordinate ranges + +Changes to code: + - Replaced qh_VERSION with qh_version in global.c [B. Pearlmutter] + The previous techniques were either clumsy or caused compiler errors + - Removed unused variables from qh_findbest and qh_findbestnew [B. Pearlmutter] + - Note that qh.TESTpoints was added in 2002.1 for tsearch implementation + +Changes to distribution: + - Added Unix distribution including Debian files [R. Laboissiere] + The previous Unix distribution is now the source distribution + - Added rpm distribution [L. Mazet] + - Investigated generation of Win32 dll. Need to define a C++ interface. + +Changes to documentation: + - Moved Qhull to www.qhull.org (geom.umn.edu is not available) + - The Geometry Center is archived at http://www.geom.uiuc.edu + - Reviewed introduction to each program + Triangulated output ('Qt') is more accurate than joggled input ('QJ') + qdelaunay is 'qhull d Qbb' [C. Ulbrich] + qvoronoi is 'qhull v Qbb' + Added example of non-simplicial intersection to halfspace intersections + - Added warning about using the Qhull library. + - Added qhull timings to When to use Qhull [C. Ulbrich] + - Reorganized the home page index and the manual index + - Moved qh-home.htm to index.htm + +Changes to examples + - Fixed options for eg/eg.t23.voronoi.imprecise [B. Pearlmutter] + + +qhull 2002.1 2002/8/20 + +Changes to distribution: + - Set up savannah.nongnu.org/projects/qhull/ [R. Laboissiere] + - Set up www.thesa.com as a backup + - Added qh-get.htm, a local copy of the download page + - Added Visual C++ interface to Qhull, qhull_interface.cpp [K. Erleben] + - Use HTTP instead of FTP for downloading Qhull + - Renamed qhull-1.0.sit.hqx + +Bug fixes: + - Fixed sign of coefficients for cdd halfspaces ('FD','Fd') [T. Abraham] + +Changes to code: + - Replace qh_version with qh_VERSION in qhull.h. + Allows shared libraries and single point of definition + - Added qh.TESTpoints for future implementation of tsearch + +Changes to build + - Makefile.txt works under cygwin + - Added Make-config.sh to create a Debian build [R. Laboissiere] + - Added .exe to Makefile.txt#clean. + - In README, use -fno-strict-aliasing with gcc-2.95.1 [Karas, Krishnaswami] + - Fixed chmod in Makefile.txt [B. Karas] + +Documentation updates + - Documented input options for each program [A. Montesinos] + - FAQ: "How to get the radii of the empty spheres for Voronoi vertices" + +URL updates: + - Changed official URL from locate/qhull to software/qhull + - Changed URLs from relative to absolute in qh-home.htm and qh-get.htm + - Added URL for Newsgroup: comp.soft-sys.matlab + - Added URL for GNU Octave + - Added URLs for Google and Google Groups + - Replaced qhull_mail.html and qhull_bug.html with mailto links. + - Removed URL for Computational Geometry Tribune + - Changed URL for locate/cglist to software/cglist + - Used site relative links for qh-home.htm + +qhull 3.1 2001/10/04 + +New features + - Added option 'Qt' to triangulate non-simplicial facets + - Added option 'TI file' to input data from file + - Added option 'Q10' to prevent special processing for narrow distributions + e.g., RBOX 1000 L100000 s G1e-6 t1001803691 | QHULL Tv Q10 + - Tried to compute Voronoi volumes ('Pv'). Requires dual face graph--not easy + See Clarkson's hull program for code. + +Changes to options + - Added numtricoplanars to 'Fs'. Number of good, triangulated facets for 'Qt' + - Added Zdelvertextot to 'Fs'. If non-zero and Delaunay, input is degenerate + - Qhull command ('FQ') may be repeated. + - If 'TPn' and 'TWn' defined, trace the addition of point 'n' + otherwise continue tracing (previously it stopped in 4-d) + - Removed 'Ft' from qdelaunay. Use 'Qt o' or 'qhull d QJ Qt' instead. + For non-simplicial regions, 'Ft' does not satisify the Delaunay property. + - If 'Po' or 'TVn', qhull checks outer planes. Use 'Q5' to turn off. + - If 'T4', print facet lists and check polygon after adding each point + +Corrections to code + - rbox: allow 'c' and 'd' with 's r', meshes, etc. + - qh_findbest: redesigned as directed search. qh_findbesthorizon for coplanar + qh_findbest is faster for many distributions + - qh_findbestnew: redesigned to search horizon of coplanar best newfacets + needed for distributions with a sharp edge, + e.g., rbox 1000 s Z1 G1e-13 | qhull Tv + - qh_findbest/qh_findbestnew: search neighbors of better horizon facets + was needed for RBOX 1000 s Z1 G1e-13 t996564279 | qhull Tv + and RBOX 1000 s W1e-13 P0 t996547055 | QHULL d Qbb Qc Tv + - qh_findbest with noupper: could return an upperdelaunay facet if dist>qh.MINoutside. + - qh_findbestnew: allow facet->upperdelaunay if dist > qh.MINoutside + - qh_partitioncoplanar: call qh_partitionpoint if outside and perpendicular + for distributions with a sharp edge + - qh_partitionvisible: report precision error if all newfacets degenerate. + was needed for RBOX 1000 s W1e-13 t995138628 | QHULL d + - qh_createsimplex: clears qh.num_visible, may be non-zero with 'TRn QJ' + +Changes to prompts, warnings, and statistics + - For Delaunay & Voronoi, 's' reports deleted vertices due to facet merging. + They were incorrectly reported as nearly incident points. + - Warn if recompute centrum after constructing hull + - Simplified narrow hull warning and print all digits of cosine. + A narrow hull may lead to a point outside of the hull. + - Print total vertices deleted instead of ave. per iteration (Zdelvertextot) + - Improved tracing for qh_partitionpoint and qh_partitioncoplanar + - Added number of distance tests for checking outer planes (qh_check_maxout) + - Simplified "qhull precision error: Only n facets remain." + - Included 'TRn' in the causes of a premature exit + +Changes to documentation + - README.txt: Added quickstart instructions for Visual C++ + - rbox: Added example of edge of narrow lens, rbox 1000 L100000 s G1e-6 + - Added cross references between options 'o' and 'p'. + - qh-eg.html: added examples comparing 'Qt', 'QJ', and neither 'Qt' nor 'QJ' + eg.15a.surface, eg.15b.triangle, eg.17a.delaunay.2, etc. + - Reorganized and enhanced discussion of precision problems in qh_impre.htm + - Fixed spelling errors [K. Briggs] + - Fixed link errors, validated HTML, and spell checked [HomeSite] + - Removed unnecessary #TOP links + - Added source links to the qh-quick.htm's header and footer + - qh-geom.htm, qh-poly.htm: add links to Voronoi functions in io.c + - src/index.htm: Added how to search qhull.h for qhull options + - qvoronoi.htm/qdelaun.htm: 'Fc' and 'FN' includes deleted vertices + +Changes to URLs + - Added http://www.voronoi.com and http://www.magic-software.com + +Changes to code + - qh_qhull: if 'TVn' or 'TCn' do not call qh_check_maxout and qh_nearcoplanar + - reviewed time profile. Qhull is slower. Optimized qh_findbestnew() + - qh_addpoint: Added warning note about avoiding a local minimum + - qh_checkpolygon: report qh.facet_next error if NARROWhull & dist>MINoutside + - qh_findbest: renamed "newfacets" parameter to "isnewfacets" since it is boolT + - qh_findbest/qh_findbestnew: testhorizon even if !MERGING + Otherwise qhull c D6 | qhull Q0 Tv assigns coplanar points + - qh_resetlists: add qh_RESETvisible for qh_triangulate + - qh_findbest: search better facets first. Rewritten. + - qh_findbest: increased minminsearch, always check coplanar facets. + See: RBOX 1000 s Z1 G1e-13 t996564279 | QHULL Tv + - qh_findbestnew: report precision error for deleted cones [rare event] + e.g.: RBOX 1000 s W1e-13 P0 t1001034076 | QHULL d Qbb Qc Tv + - qh_findbesthorizon: search horizon of qh.coplanarset. New. + - qh_findbestsharp: replaced with qh_sharpnewfacets followed by qh_findbestnew + - qh_partitionpoint, Delaunay sites can not be inside. Otherwise points may + be outside upperDelaunay facets yet not near-inside Delaunay facets + See: RBOX s 1000 t993602376 | QHULL C-1e-3 d Qbb FA Tv + - qh_partitioncoplanar: call qh_findbest/qh_findbestnew with qh DELAUNAY + - qh_printlists: format long lines + - qh_printvertex: format long lines + - user.h: tightened qh_WARNnarrow and qh_MAXnarrow. Do not see problems + until they are -1.0. + - user.h: defined qh_DISToutside, qh_SEARCHdist, and qh_USEfindbestnew + - qh_checkfacet: in 3-d, allow #ridges > #vertices. Can get a vertex twice + in a ridge list, e.g, RBOX 1000 s W1e-13 t995849315 D2 | QHULL d Tc Tv + +Changes to FAQ + - Recommended use of triangulated output ('Qt') + +Changes to distribution + - Recompiled in Visual C++ 5.0 with optimization (as was version 2.6) + - q_test: Added bad cases for Qhull and tests for new features + +Changes to Qhull library + - Added qh_triangulate() to poly2.c. It triangulates the output. + - Added option 'Q11' to copy normals and recompute centrums for tricoplanar facets + 'FP' may not print the nearest vertex for coplanar points + Use option 'Q11' when adding points after qh_triangulate() + +qhull 3.0 2001/02/11 + +Changes to distribution + - added qconvex, qdelaunay, qhalf, and qvoronoi + - added qhull-interface.cpp on calling Qhull from C++ [K. Erleben] + - renamed to qhull3.0/. + - added eg/, html/, and src/ directories + +Changes to URLs + - MathLab6 qhull: convhulln, delaunayn, griddatan, tsearchn, vororoin [Z. You] + - Wolfram Research wrote a Mathematica interface for qdelaunay [Hinton] + - Geomview moved from www.geom.umn.edu to www.geomview.org [M. Phillips} + - added URLs for tcsh and cygwin to README.txt + +Changes to documentation + - reorganized table of contents and renamed qh-man.htm to index.htm + - wrote program documentation, dropped qh-opt.htm and qh-optv.htm + - added quick reference, qh-quick.htm + - reorganized qh-rbox.htm and renamed it to rbox.htm + - split up qh-c.htm for quick navigation + +Corrections to code + - fixed type of arg for error message in qh_initqhull_globals [N. Max] + - fixed incorrect initialization of qh MINdenom_1 for scalepoints + - fixed drop dim for 'H Qbk:0Bk:0'. Added qh.feasible_point to qh_projectinput + - qh_WARNnarrow is angle between facet normals. Negate for warning message. + - statistics for Wangle/etc. concerns facet normals. Reworded [E. Voth] + - fixed error message for 'FC v' + - report cospherical points if Delaunay and error in qh_scalelast() + +Changes to code + - turn on Pg if (QVn or QGn) and not (Qg or PG) + - turn on Qc if format option 'Fc', 'FP', or 'Gp' (removes warning) + - removed last good facet unless ONLYgood ('Qg'). + - added count of non-simplicial or merged facets to 'FS' + - added count of non-simplicial facets to 's' (OK if #vertices==dim) + - added Znonsimplicial and Znowsimplicial to 'Ts' + - allow Mathematica output of dual polytope for halfspace intersection + - added qh_checkflags to globals.c for multiple front ends + - qh_initqhull_globals sets qh.MERGING if qh.MERGEexact + - removed hashentryT. It is no longer used. + +Changes to prompts and warnings + - reorganized prompts + - reorganized synopsis for rbox.c + - print warning if 'Fc' or 'FP' with 'd QJ'. Coincident points are unlikely. + - ignore warning if options 'v i Pp'. qvoronoi users may need Delaunay tri. + - reworded warning if 'Pg' and 'QVn' is not a vertex. + - reworded warning for 'Qx Tv', qh_check_points() in poly2.c + - if 'Pp', turn off warning for 'Qbb' without 'd' or 'v' + - in qh_printsummary() of Voronoi and Delaunay, distinguish QVn, QGn, Pdn, PDn + +Changes to FAQ + - added FAQ item for nearly flat Delaunay triangles [Z. You] + - added FAQ item for area and volume [R. Konatham] + - added FAQ item for Voronoi diagram of a square [J. Yong] + - edited FAQ item on point location in Delaunay triangles [Z. You] + - added FAQ item on nearly flat Delaunay triangles [Dehghani] + - added FAQ item about halfspace intersection [V. Tyberghein] + - added FAQ item for missing ridges [M. Schmidt] + - added FAQ item about qh_call_qhull [R. Snyder] + - added FAQ item about memory statistics [Masi] + - added FAQ item on meshing non-convex objects + - added FAQ item on MATLAB and Mathematica interface + +qhull 2.6 1999/04/19 + - fixed memory overwrite (no effect) in qh_initstatistics() [K. Ford] + - added zdoc11 to qh-stat.h#ZZdef for !qh_KEEPstatistics [K. Ford] + - enhanced qh_initqhull_globals() test of qh_RANDOMint and qh_RANDOMmax + - added debugging option to always return qh_RANDOMmax from qh_rand() + - fixed option 'Qr', qh_initialvertices(), to allow a broken qh_rand() + fixed option 'Qr', qh_nextfurthest(), to allow narrow hulls + Option 'Qr' simulates the random incremental algorithm for convex hulls + - added note that qh.num_outside includes coplanar points for narrow hulls + - added FAQ items for triangles/ridges of 3-d Delaunay triangulation[P. Kumar] + - added FAQ item about on-line processing with the Qhull library [O. Skare] + - changed name of option 'Error-roundoff' to 'Distance-roundoff' + +qhull 2.6 1998/12/30 + - for the unbounded rays of the Voronoi diagram, use a large box [Schmidt] + e.g., 'rbox P4,4,4 P4,2,4 P2,4,4 P4,4,2 10 | qhull v Fv' fails for point 0 + while 'rbox P4,4,4 P4,2,4 P2,4,4 P4,4,2 10 c G5 | qhull v Fv' is OK. + - fixed qh_new_qhull() to use outfile/errfile instead of stdout/stderr [Ford] + - clarified COPYING.txt for use in other programs [Archer] + - improved qh_readpoints() error message for incorrect point count. + - added FAQ item for closest triangle to a point [Sminchisescu & Heijting] + - added FAQ item for is a point outside of a facet [Beardsley] + - added FAQ item for visiting facets of the Delaunay triangulation [Heijting] + - added link to Erickson's Computational Geometry Software + - added link to Sharman's HTML version of the comp.graphics.algorithms FAQ + - added link to Owen's Meshing Research Corner + - added note to 'd' about quadratic size of 'rbox 100 l | qhull d' [Kumar] + - added 'about a point' to mentions of halfspace intersection + - added request to qh-in.htm to compute largest empty circle [Hase] + - the DOS window in Windows NT is better than the DOS window in Windows 95 + - removed obsolete qh_findfacet() from qh-c.htm [Sminchisescu] + +qhull 2.6 1998/8/12 + new and modified features + - rbox: added option Mn,m,r to generate a rotated lattice or mesh + - rbox: report error if more than one of 'l', 'x', 'L', 's', or 'M' + + Qhull library changes + - added qh_new_qhull() to user.c for calling qhull() from a program [D. Zwick] + rewrote user_eg.c to use qh_new_qhull(). Added qh_QHpointer example. + - added qh_CLOCKtype 2 in user.h to call times() for CPU time [B. Hemkemeier] + - renamed set.c/set.h to avoid conflict with STL's set.h [G. van den Bergen] + can also use '#include ' for Qhull library + + fixed errors + - fixed qh_init_B() to call qh_initqhull_mem() once only [D. Zwick] + This only effects Qhull library users of qh_QHpointer. + - fixed qh_mergecycle_all() to check for redundant vertices [J. Nagle] + e.g., 'rbox M3,4 64 | qhull Qc' should report 8 vertices & 48 coplanars + - fixed gmcoord initialization in qh_setfacetplane() for qh.RANDOMdist + - turn off qh.RANDOMdist during qh_printfacetheader() + - fixed error messages for unknown option flags + + documentation changes + - added note to FAQ on the Voronoi diagram of cospherical points [H. Hase] + - added note to 'Qu' on furthest-site Delaunay triangulation via convex hull + - added note to 'QJ' about coplanar points on the convex hull of the input + - added note that 'o' and 'FN' list Voronoi regions in site id order [Arvind] + - added links to Fukuda's introduction to convex hulls, etc. [H. Hase] + - added .c and .h source files to web distribution and qh-c.htm [J. Sands] + - documented qh_ZEROdelaunay. Delaunay and Voronoi diagrams do not include + facets that are coplanar with the convex hull of the input sites. + + modified code + - replaced computed minnorm in qh_sethyperplane_det with distance test + - removed 'qh rand_seed' since random number generator is independent of qhull + - dropt 'qhull-PPC.sit.bin' from the distribution (out-of-date) [M. Harris] + +qhull 2.5 1998/5/4 + + fixed errors + - removed zero-area Delaunay triangles and furthest-site triangles [I. Beichl] + Zero-area triangles occur for points coplanar with the input's convex hull. + - replaced qh.MINnorm with computed minnorm in qh_sethyperplane_det [J. Nagle] + qh.MINnorm was incorrect for the convex hull of the "teapot" example. + Qhull runs 0-20% slower in 3-d and 4-d. + - allow 'Qg' with furthest-site Delaunay triangulation (may be faster) + - removed extra space in definition of FOREACHmerge_() for Alpha cc [R. LeRoy] + - fixed innerouter type in qh_printvdiagram2 [does not effect code, R. Adams] + + documentation changes + - to browse qh-c.htm, set MIME type of .c and .h files to text/html + - added example of 3-d Delaunay triangulation to q-faq.htm + - added Delaunay and Voronoi examples to qh-optv.htm + +qhull 2.5 1998/2/4 + - added option 'v Fi' for separating hyperplanes of bounded Voronoi regions + - added option 'v Fo' for separating hyperplanes of unbounded Voronoi regions + - option 'Pp' turns off the warning, "initial hull is narrow" + - fixed partial, 3-d Voronoi diagrams (i.e., 'v Fv QVn Tc') + - fixed missing statistics in qh_allstat* [T. Johnson] + - rearranged qh_printvdiagram. Use qh_eachvoronoi to iterate Voronoi ridges. + - added qh_check_points to qh-math.c + +qhull 2.5 1998/1/28 + - added option 'Fv' to print the Voronoi diagram + - added rbox option 'x' to generate random points in a simplex + - added rbox option 'y' to generate a simplex and random points + - added rbox option 'On' to offset the output + - add unpacking instructions to README.txt + - updated discussion of forced output, 'Po' + - sorted the options alphabetically + - removed __STDC__ check from qhull.h for VisualC++ + - moved qh_markvoronoi from qh_printvoronoi and cleared facet->seen flags + - added facet->seen2 flag for 'Fv' + +qhull 2.5 1998/1/16 + - fixed initialization of qh.last_low on restart of 'd QJ' + - renamed qh_JOGGLEmax to qh_JOGGLEmaxincrease + - updated URL for Fukuda's cdd program + +qhull 2.5 1998/1/12 + +New or modified features + - added option 'Fx' to print vertices by point id [G. Harris, T. McClendon] + in 2-d, the vertices are printed in counter-clockwise order + for Delaunay triangl., 'Fx' lists the extreme points of the input sites + - added option 'QJ' to randomly joggle input instead of merging facets + - added option 'TO file' to output results to a file. Needed for Windows95. + - added option 'TRn' to rerun Qhull n times. Use to collect joggle statistics + +Corrections + - fixed 2-d facet orientation for 'i' and 'o' outputs + - for Mathematica 2.2 ('m') changed %10.8g to %16.8f [A. Zhaxybayev] + - fixed incorrect warning for 'QV0 Qg' in qh_initbuild [B. Wythoff] + - fixed unaccessible statistic if !qh_KEEPstatistics for Wnewvertexmax + - fixed overestimate of qh ONEmerge for point sets outside of + first quadrant and far from the origin + - fixed overestimate of 'Qbb' for point sets far from the origin + - fixed potential overestimate of qh DISTround under 'Qbb' + - fixed 'p' printing coplanar points of unselected facets + - fixed 'Ft' printing centrums unnecessarily in 2-d + +Changes to documentation + - wrote internal design documentation (qh-c.htm) + - started frequently asked questions (qh-faq.htm) + - added a section on joggled input to qh-impre.htm + - added joggle example to qh-eg.htm (eg.15.joggle) + - changed q_eg to use 'QJ' instead of 'Q0' were appropriate + - added an example to each of the main options + - added examples to rbox.htm + - added examples to the synopsis + - added a reference to Mucke, et al ['96], Fast randomized point location ... + - added code for printing Delaunay triangles to qh-in.htm [A. Tsui] + - options 'Pdk' and 'PDk' do not drop on equality + +Improvements to the code + - reviewed warning messages for Qhull options in qh_initflags + - added warning to 's' if premature exit from 'TCn' or 'TVn' + - 's' prints max distance above/below only if qh.MERGING + - reduced maxoutside in qh_check_bestdist/qh_check_points for 'Rn' + - in post-merging, rebuild centrums of large facets that become small + - lowered cutoff for coplanar facets for ischeckmax/qh_findbest + - removed qh_check_maxout for 'Wn Q0' + - reset tracing after 'TPn' adds point in 4-d and higher + +Changes for the Qhull library + - changed qh_setdelaunay to call qh_scalelast if used with 'Qbb' or 'QJ' + Delaunay callers to qh_findbestfacet, qh_addpoint, or qh_findfacet_all + should always use qh_setdelaunay as in user_eg.c + - defined qh.outside_err to check points against a given epsilon [E. Voth] + - added header to user_eg.c to avoid its incorporation into qhull [C. Begnis] + - added qh_nearcoplanar() calls to user_eg.c + only needed if use 'QJ' + - expanded __STDC__ warning message in qhull.h [C. Begnis] + - renamed qh maxmaxcoord to qh MAXabs_coord + - replaced qh MAXlowcoord with qh MAXabs_coord + - random seed ('QR-n') is reset in qh_initqhull_globals after testing + - replaced 'FO' options "_max-coord/_min-coord" with "_max-width"/qh.MAXwidth + +Other changes to Qhull functions + - report error for !bestfacet in qh_findbest (it shouldn't happen) [H. Meuret] + - set newbest in qh_findbest only if bestfacet updated + - renamed facet parameter for qh_findbest + - added maxdist argument to qh_checkpoint + - moved 'FO' output after qh_partitionall + - separated qh_initbuild from qh_qhull + - reinitialize globals modified by qh_buildhull + - moved initialization of qh.GOODvertexp & qh.GOODpointp to qh_initbuild + - separated qh_nearcoplanar from qh_check_maxout + - separated qh_geomplanes from qh_printfacet2geom, etc. + - separated qh_freebuild from qh_freeqhull + - separated qh_outerinner from io.c to return outer and inner planes + - separated qh_distround and qh_detroundoff from qh_maxmin + + +qhull 2.4 97/4/2 + +New or modified features + - made 'C-0' and 'Qx' default options. Use 'Q0' to not handle roundoff errors + - removed point-at-infinity from Delaunay/Voronoi. + you no longer need to use 'Qu PDk' + - added 'Qz' to add a point-at-infinity to Delaunay and Voronoi constructions + - added published version of qhull article in ACM Trans Math Software + - ported qhull to Windows95 under Visual C++ and Borland C++ + - added 'Ft' for triangulation by adding the centrums of non-simplicial facets + - added 'Gt' to display 3-d Delaunay triangulations with a transparent hull + - changed definition of coplanar point in output to qh min_vertex (see 'Qc') + it was qh MAXcoplanar ('Un') [could make vertices non-coplanar] + - automatically set 'Qi' for options 'd Qc' and 'v Qc'. + - reworded summary ('s') for Delaunay/Voronoi/halfspace. + use 'Fs' and 'FS' for summary statistics. + - for summary 's' of Delaunay/Voronoi, display number of coplanars for facets + if none, display total number of coplanars (i.e., non-vertices) + - input comment is first non-numeric text (previously limited to header) + - added input warning if use 'Qbb' without 'd' or 'v' + - 'Q3' can not be followed with a numeric option + +Corrections + - fixed qh_partitioncoplanar() to not drop interior points if 'Qi' is used + - fixed 'FP d' to report distance in point set instead of paraboloid + - fixed qh_findbest() to search all coplanar facets for qh_check_maxout() + +Changes to documentation + - added example eg.17f.delaunay.3 to show a triangulation of cospherical sites + - split up qh-opt.htm into multiple pieces + - split off qh-in.htm for Qhull internals + - renamed .html files to .htm for Windows95 + - rewrote qh-optv.htm on Delaunay triangulation and Voronoi vertices + - added 'man' pages qhull.txt and rbox.txt. These list all the options + - removed 'txt' versions of html files + - added note to 'PDk' about avoiding a 'd' option immediately after a float + - under option 'd', display the triangulation with 'GrD3', not 'GnrD3' + +Changes to the Qhull library + - added 'format' argument to qh_printfacetNvertex_nonsimplicial() in io.c + - removed C++ type errors [J. Stern, S. Marino] + - created SETelemt, SETfirstt, etc. for specifying data types. + - use SETelem,etc. for assignments. + - changed setT.maxsize to 'int' to prevent type conversion warnings + - changed FOREACH.. to a comma expression for better code and less warning + - changed qh.vertex_visit and .visit_id to unsigned int to prevent warnings + - changed clock() to qh_CPUclock (user.h) + - qh_init_B() and qh_readpoints() do not set qh.ATinfinity for Delaunay tri. + - qh_setvoronoi_all() sets upper Delaunay facets if qh.UPPERdelaunay is set + - qh_nearvertex() returns distance in dim-1 for qh.DELAUNAY + - removed MSDOS path from qhull_command. Spaces in Win95 tripped qh_setflags + - removed memory.h from qhull_a.h. memset,etc. should be in strings.h + - split qh_prompt into pieces for Visual C++ + - added note to qh_addpoint that coordinates can not be deallocated + - added Baker '89 to constrained Delaunay diagrams under Enhancements + please let me know if you try this + - added request for unbounded Voronoi rays to Enhancements + please let me know if you try this + +qhull V2.3 96/6/5 + - fixed total area of Delaunay triangulation. [A. Enge] + It should ignore facets on the upper-envelope. + - if 'd Qu FA', the total area is summed over the upper-Delaunay triangles + - fixed sign of area for Delaunay triangulations. + - fixed cdd input format for Delaunay triangulation. [A. Enge] + - for cdd input, allow feasible point for halfspaces. + - warning if cdd output format for centrums, halfspace intersections, or OFF. + - print '0' for area ('Fa') if area is not computed for a facet + - option 'QR-n' sets random number seed to n without rotating input + - fixed qh_findbest() to retest coplanar and flipped facets after a restart + - for 'd Qu Ts' collects angle statistics for upper Delaunay facets + + Changes to the Qhull library + - expanded user_eg.c for incremental constructions and Delaunay triangulation + - added discussion of incremental construction to qh_man.html#library + - WARNING: The default value of qh ATinfinity was changed from True to False. + A new flag, qh UPPERdelaunay, was defined for 'Qu'. + Please set qh ATinfinity if you explicitly add the point "at-infinity" + Please set qh ATinfinity if you explicitly call qh_projectinput. + Please set qh UPPERdelaunay if you explicitly cleared qh ATinfinity. + Other users do not need to change their code. + Now you can build a Delaunay triangulation without creating a point + "at-infinity". This removes a potential, hard-to-understand error. + qh_readpoints sets qh ATinfinity for options 'd' or 'v' without 'Qu'. + qh_initB sets qh ATinfinity for qh PROJECTdelaunay w/o qh UPPERdelaunay. + qh_projectinput adds a point "at-infinity" only if qh ATinfinity is set. + - added qh_setdelaunay to geom2.c to project points to paraboloid + - added qh_findbestfacet() to poly2.c to replace qh_findfacet() + - removed procedure qh_findfacet(). It does not always work. + - removed NULL option for facet in qh_addpoint(). It does not always work. + - added noupper parameter to qh_findbest. + - added search of upperdelaunay facets to qh_findbest() + - allowed qh_findbest() to start with a flipped or upperdelaunay facet + - removed qh_nonupper() -- it is no longer needed + - allow space at end of options + - fixed qh_projectinput for furthest-site Delaunay (qh PROJECTdelaunay 'd Qu') + - added voids to procedure declarations with empty parameter lists + +qhull V2.3 96/3/25 + - fixed missing qh_check_maxout when coplanar points and no merged facets. + - fixed qh_freeqhull/allmem (e.g., if qh_NOmem) [only custom code] [E. Voth] + - fixed qh_freeqhull to free qh interior_point [E. Voth] + - fixed main() to free all of memory if qh_NOmem. Include "mem.h" [E. Voth] + - reset f.newcycle link in qh_mergecycle_all [E. Voth] + - fixed false error if 'Tc', coplanar points, and a narrow hull + - turn off 'Rn' when computing statistics, checking code, or tracing code + - removed ={0} from global.c and stat.c to reduce compiler warnings + - changed Makefile dependences to $(HFILES) for all but unix.o, set.o, mem.o + - pulled out qh_printpointid and reordered qh_pointid [E. Voth] + - removed some compiler warnings + - moved 'FO' print of options to just before qh_buildhull + - changed 'FO' to list difference from -1 for _narrow-hull + +qhull V2.2 96/2/15 + - detect narrow initial hulls (cosine of min angle < qh_MAXnarrow in user.h). + Write warning if cosine < qh_WARNnarrow in user.h. If narrow (qh NARROWhull), + partition coplanar points as outside points and delay coplanar test to end. + Needed for RBOX 1000 L100000 s G1e-6 t995127886 | QHULL Tv + See 'limitations' in qh-impre.html for further discussion. + - corrected some confusions between 'FV' and 'Fv' in qh-opt.html + - fixed initialization error for small Voronoi diagrams (e.g., [0,0], [1,0], [0,1]) [J. Velez] + - fixed bad return from qh_mindiff in geom2.c + - for initial hull, first process facet with furthest outside point (qh_furthestnext) + - added facet->notfurthest flag for recomputing furthest point + - added check for __STDC__ (needs ANSI C) [E. Voth] + - reduced warning messages from [E. Voth]. e[1] in setT still reports a warning. + - added a cube to the discussion of option 'v' (Voronoi) in qh-opt.html [J. Velez] + - added notes about adjacent vertices to "Calling Qhull" in qh-man.html [R. Lewis & J. Velez] + - added note about 'lines closer' when viewing 3-d Delaunay triangulations [P. Kallberg] + - added option 'Q9' to always process furthest of furthest outside points. + - removed option 'Pp' from q_eg and qh-eg.html. + +qhull V2.2 95/12/28 + - added option 'Qbb' to scale the last coordinate to [0,m] (max prev coord). + This reduces roundoff errors for Delaunay triangulations with integer coordinates. + - changed option 'Qu d' to print out the furthest-site Delaunay triangulation + Use options 'Qu d PD2' to compute the normal 2-d Delaunay triangulation without + the point at infinity. + - added notes to the documentation of option 'd' + - added notes to limitations of how Qhull handles imprecision + - added warning if options 'FP', 'Fc', or 'Gp' without option 'Qc' or 'Qi' + - added note to options 'PDk:n' and 'Pdk:n' that closest facet is returned if none match + - added check that 'Qbk' and 'QBk' does not invert paraboloid for 'd' + - added notes that qh_findfacet and qh_addpoint require lifted points for Delaunay triangulations + - fixed 'rbox s 5000 W1e-13 D2 | qhull d Qcu C-0 Qbb' + - fixed option 'QbB' (qh SCALEpoints was not set) + - fixed minor confusion between 'Gc' (print centrums) and 'Gp' (print points) + - rewrote qh_findbestnew for upper convex hull, Delaunay facets + - changed option name for 'Gp' from 'Gcoplanar' to 'Gpoints' + - changed "nearest" facet for 'Pdk' to threshold - normal + - reworked qh GOODclosest for 'Qg' + - added note that 'Qg' does not always work + - recorded option 'C-0' as "_zero-merge" in option 'FO' + - refined qh DISTround in qh_maxmin/geom2.c for Delaunay triangulations + +qhull V2.2 95/12/4 + - Version 2.2 fixes an important bug in computing Delaunay triangulations + and convex hulls with edges sharper than ninety degrees. The problem + occurs when processing a point at a sharp edge. A directed search can + not be used for partitioning because one side may hide facets from the + other side. The new lens-shaped distribution for rbox demonstrates the + problem. For example, 'rbox 100 L3 G0.5 s | qhull Tv' fails for Version 2.1. + O. Schramm found the bug when computing the Delaunay triangulation of points + near an outside edge. + + I rewrote qh_findbest and related functions. Qh_findbest + uses an exhaustive test for sharp edges (qh_findbest_sharp). + Qh_findbest avoids the upper convex hull of Delaunay triangulations. + + Options 'd' and 'v' no longer assign coplanar points to the upper convex hull. + + Qh_check_maxout tests near-inside points. It ignores fully inside points. + When done, it removes near-inside points from the coplanar sets. + + If you use qh_addpoint or qh_findbest, please review the function headers. + They do not work for lens-shaped hulls for arbitrary facets. They do work for + Delaunay triangulations. + + Changes to options for V2.2 + - added 'Qu' for computing the furthest-site Delaunay triangulation (upper hull) + and furthest-site Voronoi vertices. + - added 'FP' to print nearest vertex for coplanar points + - added coplanar count to 'Fs' and 's' + - added number of similar points to summary for Delaunay/Voronoi + - Option 'Qc' is no longer necessary when merging. + - 'o' format for Voronoi vertices ('v') generates "0" lines for similar points + - 'QRn' for Delaunay ('d' or 'v') now rotates about the Z axis (see qh_init_B). + Otherwise Qhull does not identify the upper hull + - removed option 'Qa' for "all points outside". In V2.1 it was automatically + set for 'd'. Even though it was a bad idea, it revealed the above bug. + - for option list ('FO'), added version, values for one-merge, maxpos, maxneg, + and near-inside, and flags for zero-centrum + - optimized 'C-0' and 'Qx'. These options ("zero-centrum") test vertices + instead of centrums for adjacent simplicial facets. + - if 'Tv', report number of points that are not verified due to qh_findbest + - Option 'Q8' ignores near-inside points. + + rbox 95/12/3 + - added lens distribution ('Ln') It may be used with 's', 'r', 'Wn', and 'Gn' + - removed default point count except for the test case, 'Dn' + - divided main() of rbox.c into sections + + Documentation changes for V2.2 + - added examples for lens distribution and furthest-site Delaunay triangulation + and renumbered the examples for q_eg + - described facet orientation in 'data structure' section [P. Soikkonen] + - added notes to qh-man.html/"What to do if something goes wrong" + - added note about using 'Tv' to verify the results [O. Schramm] + - expanded definition of f_r in Performance section [S. Grundmann] + - noted that Geomview display of a Voronoi diagram adds extra edges + for unbounded Voronoi cells + - rewrote error "convexity constraints may be too strong" [D. Newland] + - added limitations section to "Imprecision in Qhull" + - added note about zero-area facets to 'Imprecise convex hulls' in qh-impre.html + - added note to 'Qi' that it does not retain coplanar points + - added note that option 'Q5' may be used if outer planes are not needed + - added note to README.txt about Irix 5.1 [C. Goudeseune] + - added code fragment for visiting Voronoi vertices to "Calling Qhull" [M. Downes] + - added note about qh_addpoint() to "Calling Qhull" [M. Downes] + + Errors fixed for V2.2 + - use qh_sethyperplane_gauss if 3-d or 4-d norm is less than qh MINnorm + - count Zcentrumtests if qh_NOstat + - reversed sign convention for qh_sethyperplane_gauss + it was opposite to qh_sethyperplane_det + this effects qh_determinant and qh_detsimplex + - fixed error in qh_findgood_all with multiple restrictions, e.g., 'QVn Pdk' + - fixed call to qh_clearcenters for qh_produce_output + - in qh_errexit, report p0 if last furthest point + + Changes for users of the Qhull library + - user code needs to define qh_version (see user_eg.c) + - merged initialization code into qh_init_A and qh_init_B [M. Mazzario] + old code works as before. + qh_initflags also sets qh qhull_command for qh_initthresholds + redid initialization for user_eg.c + - simplified user_eg.c. It computes the convex hull of a cube. + - added qh_setvoronoi_all in poly2.c to compute Voronoi centers + added related note to call_qhull + - added qh_findfacet to use in place of qh_findbest + - added qh_nearvertex to return nearest vertex in facet to point + - redid notes on multiple, concurrent calls in call_qhull/user.c + - changed BoolT to unsigned int (prevent implicit enum conversion warnings) + - added upperdelaunay to facetT. It indicates a facet of the upper convex hull. + - converted qhull-PPC.sit for CodeWarrior 7 + + Code changes for V2.2 + - simplified calls to setjmp() for Cray J916 [Salazar & Velez] + - replaced fprintf(fp,string) with fputs in io.c + - 'qh num_coplanar' removed (too expensive and not used). + - added numcoplanars to qh_countfacets() + - added min norm to qh_normalize2(). qh_normalize() wasn't changed + - removed type casts from qh_point and qh_pointid [Salazar & Velez] + - account for roundoff error in detecting upper convex hull (qh ANGLEround). + - post merging uses qh_findbestnew for partitioning + - qh_findbestnew for qh_partitioncoplanar goes to best facet + - 'Qm' always processes points above the upper hull of a Delaunay triangulation + - GOODvertex initialized with qh_findbestnew instead of qh_findbest + - for 'v', qh_facetcenter returns furthest-neighbor vertex if 'Qu' + - added test for qh feasible_point if use 'Fp' and qh_sethalfspace_all + - reviewed Sugihara's algorithm for topologically robust beneath-beyond + - on error, report if qhull in post-merging or has completed + - if tracing, option 'FO' and qhull command always printed + - added current furthest point ("during p%d") to 'T-1' events + - added 'TWn' tracing for vertices of new facets (qh_setfacetplane) + - added 'TWn' tracing for vertices in an output facet (qh_check_maxout) + - reorganized split between poly/poly2.c and geom/geom2.c + - reordered object files in Makefile + +qhull V2.1 95/9/25 + - converted qhull.man to html format, many edits + - referenced Shewchuk's triangle program and Schneiders' Mesh Generation page + - added option 'Qa' to force all points outside + automatically set for "precise" Delaunay or Voronoi [Salazar & Velez] + it is turned off by merging, 'Wn', 'Qc' or 'Qi' + - added coplanar points to option 'FN' + - moved option 'FO' to include default precision options + - changed default random number generator to qh_rand in geom2.c (user.h) + + other code changes + - fixed option comment Pdrop-facets-dim-less, Qbound-dim-low, QbBound-unit-box + - defined ptr_intT for converting 64-bit ptrs to 'unsigned long' [D. Bremner] + - defined setelemT to distinguish actual size from pointers [D. Bremner] + use either e[...].p or e[...].i (user-level code should use set.h macros) + - changed %x to %p in format statements for pointers [D. Bremner] + - added test of REALmax,etc. to qh_maxmin [H. Poulard] + - added type parameter to qh_memalloc_() macro for type conversion + - added type conversion to qh_memalloc() calls where missing + - added type conversion to calls into set.c that return void* + + other documentation changes: + - new URLs for graphics images + - fixed comment for facetT.neighbors in qhull.h [P. Soikkonen] + - changed recommendations for precision errors in qh_printhelp_degenerate() + - added recommendation for 'V0' (facet is visible if distance >= 0) + - added note about 'long double' to user.h [S. Grundmann] + - added note about zero area Delaunay triangles for the 'v' option + - added note about locating Delaunay triangles to option 'd' [A. Curtis] + - added note that coplanar vertices correspond to duplicate points for 'd' + - added note about option 'd' automatically setting 'PDk' (lower convex hull) + - added note about precision errors to option 'd' [many users] + - added note about qh_findbest() to the Qhull library section [L. Lai] + - 'make install' renames qhull.man to qhull.1 for Unix [M. Phillips] + - renamed README, etc. to *.txt to match WWW conventions [D. Cervone] + +qhull V2.1 7/10/95 + - in 2-d, 'v o' lists the vertex at infinity in order [R. Critchlow] + - it used to always list the vertex at infinity ("0") first + - rewrote description of 'v' option (Voronoi vertices and 2-d diagrams) + - added 'PFn' for printing facets whose area is at least 'n' [D. Holland] + - prefixed 'Q',etc. to the 'Q',etc. options in the long help prompt + - fixed references to 'Fv' and 'FV' options under option 'Hn,n,n' + - updated reference to cdd, + - in set.c, added some missing type coercions for qhmem.tempstack + +qhull V2.1 6/12/95 + - replaced qhull.ps with qhull-2.ps (paper submitted to ACM TOMS) + - use BUFSIZ for setvbuf for Power Macintosh + - number of good facets printed if QVn, QGn, Pd, or PD + - added Makefile for Borland C++ 4.02 with Win32 [D. Zwick] + - added note to Enhancements section of qhull.1 about constrained + Delaunay triangulations [T. Rasanen] + +qhull V2.1 6/7/95 + - fixed qh_facetarea_simplex() for non-simplicial facets [L. Schramm] + - fixed cast in qh_point and qh_pointid for 64-bit architectures + - fixed URL for Amenta's list of computational geometry software + - fixed cast in qh_meminitbuffers for qhmem.freelists + - added test for !qh half_space in qh readpoints + - clarified options for qh_printhelp_singular() + - discussed non-simplicial facet area under option 'Fa' in qhull.1 + +qhull V2.1 6/3/95 + - home page for Qhull and new descriptions for the Qhull examples + http://www.qhull.org + - changed SIOUX buffering for Power Macintosh. It runs fast now. + added a project file for Metrowerk's C + - note in README about compiling qhull on the PC + +qhull V2.1 beta 5/15/95 + + ======= main changes ======== + - added halfspace intersection ('Hn,n,n') + - facet merging is better, especially for high dimensions + - added 'Qx' for exact merges of coplanar points and precision faults + - facet merging is faster, especially for high dimensions. + e.g., convex hull of the 8-d hypercube is seven times faster + - added 'F' output formats for printing each aspect of the convex hull + - format 'Fa' computes facet areas, total area, and total volume + - format 'FO' writes a descriptive list of selected options to stderr + - moved all customization options to user.h + - changed the default precision to 'double' since it's needed for Delaunay. + using 'float' is faster and takes less space (REALfloat in user.h) + - option 'Qm' is no longer important for facet merging + - removed need for 'Qs' by selecting initial simplex with pos. determinants + - renamed 'Qv' to 'Q7' since virtual memory does not work well for qhull + - Qhull is available for the Power Mac (no graphical output) + + ====== other new and modified options =========== + - changed default MINvisible ('Vn') to a multiple of premerge_centrum ('C-n') + - added 'Un' option to set width of facet for coplanar points. + This replaces the previous rules for determining coplanar points. + - changed default MINoutside ('Wn') to twice MINvisible ('Vn') + - Geomview output adjusts point radii for MINvisible 'Vn' + - the input format allows the number of points to precede the dimension + - options 'v' 'd' 'FAn' and 'FMn' record good facets ('Pg') + - added 'Fd' and 'FD' options for homogeneous coordinates in cdd format + - in rbox, added 'h' flag to generate homogeneous coordinates in cdd format + - option 'PAn' prints out the n facets with the largest area + - option 'PMn' prints out the n facets with the most merges + - option 'Po' under tracing ('Tn') no longer tries to write erroneous facets + - option 'TCn' only prints the old 'visible' facets for 'f' + - 'TFn' reports intermediate results when post-merging + - option 'Ts' with option 'TFn' prints intermediate statistics + - the message for 'Tv' reports if it is checking outer planes + - 'Tz' sends stderr output to stdout + - added 'Q1' to ignore angle when sorting merges (merges are worse) + - added 'Q2' to not perform merges in independent sets (merges are worse) + - added 'Q3' to not remove redundant vertices (faster) + - added 'Q4' to avoid merges of old facets into new facets (does worse) + - added 'Q5' to skip qh_check_maxout (faster, but less accurate) + - added 'Q6' to skip pre-merge of concave and coplanar facets + - added 'Qv' for testing vertex neighbors for convexity (needs merge option) + - added warning if mix Geomview output with other outputs ('Po' turns off) + - options 'o v' for 3-d and higher sort the Voronoi vertices by index + + ======= documentation ======= + - rewrote the introduction and precision sections + - added a section on performance + - added an example on halfspace intersection + - installed examples of Qhull in + + + ======= Makefile, user.h, and messages ======= + - Makefile calls ./qhull, ./rbox, and prints short prompt for qhull + - added new statistics, e.g., for buildhull + - changed default qh_RANDOMtype to RAND_MAX with rand() + - added comment about numeric overflow to printhelp_singular + - reorganized the code to improve locality of reference + - option in mem.h (qh_NOmem) to turn off memory management in qhull + - option in user.h (qh_NOtrace) to turn off tracing in qhull + - option in user.h (qh_NOmerge) to turn off merging in qhull. + - use this instead of redefining qh_merge_nonconvex in user.c + - simplified user_eg.c. See qh_call_qhull() in user.c for the full version + + ======== bug fixes ============ + - fixed error in number of points for 'rbox 100 r' (odd distribution) + - fixed performance error in qh_degen_redundant_neighbors + - qh_partitionpoint now sets facet->maxoutside for first outside point + - fixed performance error in partitioning when merging a large, regular cone + - removed memory leak in qh_appendmergeset + - removed double free of qh line under errors in qh_readinput() + - forcing output on error ('Po') fixed for options 'n' 'o' 'i' 's' + - fixed optimization error on HP machines [fprintf(... *p++)] + + ======== changes to qhull.h for user code ======= + - qh_collectstatistics and qh_printstatistics removed from qhull.h. + should use qh_printallstatistics instead + - qh_findbest uses boolT for newfacets + - added qh_findbestnew for non-simplicial facets. qh_findbest is + too slow in this case since it needs to look at many nearly coplanar + facets. + - renamed qh_voronoi/qh_centrum to qh_ASvoronoi, qh_AScentrum + - changed facet->id to 32-bits, added new flags for merging + - added facet->f for facet pointers while merging and for facet area + - added dfacet/dvertex for printing facets/vertices while debugging + - added qh_produce_output and qh_printsummary + + ======== changes to code ========== + - moved qh_setfacetplane from qh_makenewfacets to qh_makenewplanes + - added qh_setfree2, qh_setcompact, and qh_setduplicate to set.c + - qh_findgooddist returns list of visible facets instead of setting global + - in qh_check_maxout, inside points may be added to coplanar list. + - qh_findbestnew used for qh_partitionall. It is faster. + - in qh_findbest, changed searchdist to MINvisible+max_outside+DISTround. + MINvisible is the default MAXcoplanar. + - cleaned up list management via qh_resetlists + - uses facet->dupridge to indicate duplicated ridges instead of ->seen + - qh_buildtracing records CPU time relative to qh hulltime instead of 0 + + ========== changes to merging ======= + - many performance improvements, especially in high-d. + - when merging, qh_findbest and qh_findbestnew stops search at qh_DISToutside + - vertex neighbors delayed until first merge + - post merges reported every TFn/2 merges + - vertex merging turned off in 7-d and higher (lots of work, no benefit). + vertex merging moved to qh_qhull_postmerging in 6-d. + - replaced qh min_vertex with MAXcoplanar for determining coplanarity + - pick closest facets to merge in duplicate ridge instead of flip/flip + (see qh_matchduplicates in poly2.c) + - optimize merge of simplex into a facet + - optimize merge of a "samecycle" of facets into a coplanar horizon facet + - cleaned up qh_forcedmerges/qh_flippedmerges and removed facet->newmerge + - rewrote qh_merge_degenredundant with separate queue + - qh_facetdegen replaced by facet->degenredun + - flipped neighbors no longer merged in preference to flip/non-flip pairs + - removed angle argument from qh_merge_degenredundant and qh_mergefacet + only used for tracing + - getmergeset_initial had extra test of neighbor->simplicial + - ridge->nonconvex is now set on only one ridge between non-convex facets + - moved centrum deletion to qh_updatetested + - qh_isnewmerge(facet) changed to facet->newmerge (removed NEWmerges) + - qh_findbestneighbor reports correct distance even if testcentrum + - added hull_dim factor to qh_BESTcentrum + - removed horizon preference in qh_merge_nonconvex (qh AVOIDold) + - facet->keepcentrum if qh WIDEfacet or qh_MAXnewcentrum extra vertices + +qhull V2.02 1/25/95 + - rbox 'z' prints integer coordinates, use 'Bn' to change range + - fixed rare bug in qh_check_maxout when qh_bestfacet returns NULL + - fixed performance bug in findbestneighbor, should be + BESTnonconvex + - renamed 'notgood' flag in 'f' option to 'notG' flag (caused confusion) + - changed qh.hulltime to (unsigned) to prevent negative CPU times + - added random perturbations to qh_getangle under the 'Rn' option + - reviewed the documentation and enhancement list + - added discussion of how to intersect halfspaces using qhull + - replaced expression that caused incorrect code under an old version of gcc + - added buffer after qh.errexit in case 'jmp_buf' has the wrong size + - rewrote qh_printhelp_singular for lower-dimensional inputs + - rewrote qh_printhelp_degenerate + - added options for qh_RANDOMint in qhull_a.h + - changed time format for 'TFn' to %02d + +qhull V2.01 6/20/94 + - fixed bug in qh_matchnewfacets that occured when memory alignment makes + facet->neighbors larger than necessary. + - fixed bug in computing worst-case simplicial merge of angle coplanar + facets (ONEmerge). This decreases (...x) in printsummary. + +qhull V2.01 6/17/94 + - added recommendation for 'Qcm' to documentation and help prompts + - added an input warning to qh_check_points ('Tv') if coplanars and no 'Qc' + - qh_partitionpoint: always counts coplanar partitions (Zcoplanarpart) + - rewrote qh_printhelp_degenerate to emphasize option 'C-0' + - For Geomview output, roundoff is not needed when printing the inner and + outer planes. This improves Geomview output for the 'Rn' option. + - For Geomview output without coplanar points or vertices, qh_GEOMepislon + is not needed. This removes the edge gap when displaying a Voronoi cell. + - For Geomview output 'Gp', direct vertices to the interior point + instead of the arithmetic center of the displayed vertices. + +qhull V2.01 6/11/94 + - if pre-merge, 'Qf' is automatically set. Otherwise an outside point may + be dropt by qh_findbest(). This slows down partitioning. + - always use 'Qc' if merging and all facet->maxoutside's must be right. + Otherwise distributions with many coplanar points may occassionally + miss a coplanar point for a facet. This is because qh_findbest, when + called by qh_check_maxout, can become stuck at a local maximum if + the search is started at an arbitrary facet. With 'Qc', the search + is started from a coplanar facet. For example, + rbox 1000 W8e-6 t | qhull C-0 Tv + will (rarely) report that a facet->minoutside is incorrect + - option 'Pp' turns off "Verifying" message for 'Tv' + - added qh_copynonconvex to qh_renameridgevertex (fixes rare error) + - 'rbox tn' sets random seed to n + - 'rbox t' reports random seed in comment line + - qh_errexit reports rbox_command | qhull_command and 'QR' random seed + - added additional tracing to bestdist and setfacetplane + - in qh_checkconvex, need to test coplanar against 0 instead of -DISTround + - in qh_checkconvex, always test centrums if merging. The opposite + vertex of a simplicial facet may be coplanar since a vertex of + a simplicial facet may be above the facet's hyperplane. + - fixed error handling in qh_checkconvex when merging + - in qh_printsummary, one merge ratio not printed if less than 'Wn' + - documented that 'Tv' verifies all facet->maxoutside + +qhull V2.01 6/2/94 + - 's' prints summary to stderr + - multiple output formats printed in order to stdout + - added statistic for worst-case distance for merging simplicial facets + can not hope for a better "max distance above/below facet" + print factor for "max distance.."/"merge simplicial" in printsummary + - fixed error in scaling input with min/max reversed ('Qb0:1B0:-1') + - fixed error in scaling if project & Delaunay & scale ('d Qb0:0B1:0b2:0') + - user_eg.c: qh_delpoint removed since it does not always work + - user_eg.c now works for either convex hull or Delaunay triangulation + - added PROJECTdelaunay for Delaunay triangulations and Voronoi diagrams + with libqhull.a and user_eg.c + - user_eg.c: if project or scale input, need to copy points + - user_eg.c: default just defines main, added fprintf's for qh_errprint etc. + - qh_gausselim: a 0 pivot no longer zeros the rest of the array, + need the remaining elements for area computation + - qh_qhull: restore cos_max, centrum_radius at end of POSTmerging + - qh_checkflipped with !allerror is >=0.0 instead of >0.0 + - removed -Wall from gcc due to unnecesssary "warning: implicit declaration" + - renamed 'new' variables and fields to allow compilation by g++ + - added README notes on C++, and "size isn't known" + - updated manual on 'Qg' with coplanar facets and no merging ('rbox c D7') + 'Qg Pg' and 'Pg' produce different results because of precision problems + +Converting from qhull 1.01 to qhull 2.00 + - 'qhull An' is now 'qhull Wn' + option 'Wn Po' is faster but it doesn't check coplanars + - 'qhull g' is now 'qhull G', and the output formats are different + - 'qhull c' is now 'qhull Tc' + - 'qhull f' is now 'qhull Qf' + - 'qhull o' is now 'qhull Po' + - 'qhull b' is now always done + - qhull and rbox now use floats, change REALfloat in qhull.h for doubles + - qhull 2.00 fixes several initialization errors and performanace errors + e.g., "singular input" on data with lots of 0 coordinates + - 'rbox b' is now 'rbox c G0.48' + - all rbox distributions are now scaled to a 0.5 box (use 'Bn' to change) + - rbox now adds a comment line. This may be removed by 'rbox n' + - 'rbox r s Z G' no longer includes the positive pole + - no changes to the Macintosh version + +qhull V2.00 5/23/94 + - if force output ('Po'), facet->maxoutside= 'Wn' since coplanars not updated + convexity checked if precision problems or verify ('Tv') + - if merging, new facets always checked for flipped orientation + - a facet is visible (findhorizon) under 'Qm' if distance > max_vertex + - if using 'Qm' then min. outside is max_vertex instead of max_outside + - default is random()/srandom() in qhull_a.h, checked in initqhull_globals + - created internal strtod since strtod may skip spacing after number + - removed lower bound (1.0) for qh maxmaxcoord + - divzero needs to handle 0/0 and large/small + - decreased size of precise vertices + - need to initialize qh MINdenom_1 for scalepoints + - added factor of qh maxmaxcoord into DISTround (needed for offset) + - 'Rn' perturbs distance computations by random +/-n + - check_points needs an extra DISTround to get from precise point to computed + - rewrote some of the IMPRECISION section in qhull.man + - added the input format to the qhull prompt + - moved include files to qhull_a.h since some compilers do not use float.h + - added qhull.1 and rbox.1 since SGI does not ship nroff + - reduced cutoff for printpointvect + - use time for qhull random seed only if QR0 or QR-1 + - radius of vertices and coplanar points determined by pre-merge values + +qhull V2.00 5/12/94 + - facet2point (io.c) used vertex0 instead of vertex1 + - can't print visible facets after cone is attached + - shouldn't check output after STOPcone (TCn) + - statistic 'Wminvertex' and 'Wmaxoutside' only if MERGING or APPROXhull + - 'make doc' uses lineprinter format for paging + - warning if Gpv in 4-d + +qhull V2.b05 5/9/94 + - decreased size of precise vertices + - precise facets in 2-d print hyperplanes + - accounted for GOODpoint in printsummary + - added IMPRECISION section to qhull.man + - 'Qg' does work in 7-d unless there's many coplanar facets + diff --git a/BRAINSABC/qhull/Makefile.am b/BRAINSABC/qhull/Makefile.am new file mode 100644 index 00000000..47d8dcde --- /dev/null +++ b/BRAINSABC/qhull/Makefile.am @@ -0,0 +1,97 @@ +### Makefile.am for the qhull package (src) +### Author: Rafael Laboissiere +### Created: Mon Dec 3 21:36:21 CET 2001 + +### Shared Library + +# to: +lib_LTLIBRARIES = libqhull.la + +# from: +libqhull_la_SOURCES = \ + user.c \ + global.c \ + stat.c \ + io.c \ + geom2.c \ + poly2.c \ + merge.c \ + qhull.c \ + geom.c \ + poly.c \ + qset.c \ + mem.c + +# how: +libqhull_la_LDFLAGS = -version-info 5:0:0 -lm + +### Utility programs + +# to: +bin_PROGRAMS = qhull rbox qconvex qdelaunay qvoronoi qhalf + +# from: +qhull_SOURCES = unix.c +rbox_SOURCES = rbox.c +qconvex_SOURCES = qconvex.c +qdelaunay_SOURCES = qdelaun.c +qvoronoi_SOURCES = qvoronoi.c +qhalf_SOURCES = qhalf.c + +# how: +qhull_LDADD = libqhull.la +rbox_LDADD = libqhull.la +qconvex_LDADD = libqhull.la +qdelaunay_LDADD = libqhull.la +qvoronoi_LDADD = libqhull.la +qhalf_LDADD = libqhull.la + +### Include files + +pkginclude_HEADERS = \ + geom.h \ + mem.h \ + poly.h \ + qhull_a.h \ + stat.h \ + io.h \ + merge.h \ + qhull.h \ + qset.h \ + user.h + + +### Example programs + +# to: +docdir = $(prefix)/share/doc/$(PACKAGE) +examplesdir = $(docdir)/examples + +# which: +examples_DATA = \ + user_eg.c \ + user_eg2.c \ + qhull_interface.cpp \ + Makefile.txt \ + Mborland + +doc_DATA = \ + Changes.txt \ + index.htm \ + qh-geom.htm \ + qh-globa.htm \ + qh-io.htm \ + qh-mem.htm \ + qh-merge.htm \ + qh-poly.htm \ + qh-qhull.htm \ + qh-set.htm \ + qh-stat.htm \ + qh-user.htm + + +### Extra files to be included in the tarball + +EXTRA_DIST = \ + $(doc_DATA) \ + $(examples_DATA) diff --git a/BRAINSABC/qhull/Makefile.in b/BRAINSABC/qhull/Makefile.in new file mode 100644 index 00000000..999463d6 --- /dev/null +++ b/BRAINSABC/qhull/Makefile.in @@ -0,0 +1,697 @@ +# Makefile.in generated by automake 1.7.9 from Makefile.am. +# @configure_input@ + +# Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 +# Free Software Foundation, Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +### Makefile.am for the qhull package (src) +### Author: Rafael Laboissiere +### Created: Mon Dec 3 21:36:21 CET 2001 + +### Shared Library + +srcdir = @srcdir@ +top_srcdir = @top_srcdir@ +VPATH = @srcdir@ +pkgdatadir = $(datadir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +top_builddir = .. + +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +INSTALL = 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+bin_PROGRAMS = qhull rbox qconvex qdelaunay qvoronoi qhalf + +# from: +qhull_SOURCES = unix.c +rbox_SOURCES = rbox.c +qconvex_SOURCES = qconvex.c +qdelaunay_SOURCES = qdelaun.c +qvoronoi_SOURCES = qvoronoi.c +qhalf_SOURCES = qhalf.c + +# how: +qhull_LDADD = libqhull.la +rbox_LDADD = libqhull.la +qconvex_LDADD = libqhull.la +qdelaunay_LDADD = libqhull.la +qvoronoi_LDADD = libqhull.la +qhalf_LDADD = libqhull.la + + +### Include files +pkginclude_HEADERS = \ + geom.h \ + mem.h \ + poly.h \ + qhull_a.h \ + stat.h \ + io.h \ + merge.h \ + qhull.h \ + qset.h \ + user.h + + +### Example programs + +# to: +docdir = $(prefix)/share/doc/$(PACKAGE) +examplesdir = $(docdir)/examples + +# which: +examples_DATA = \ + user_eg.c \ + user_eg2.c \ + qhull_interface.cpp \ + Makefile.txt \ + Mborland + + +doc_DATA = \ + Changes.txt \ + index.htm \ + qh-geom.htm \ + qh-globa.htm \ + qh-io.htm \ + qh-mem.htm \ + qh-merge.htm \ + qh-poly.htm \ + qh-qhull.htm \ + qh-set.htm \ + qh-stat.htm \ + qh-user.htm + 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distclean-generic \ + distclean-libtool distclean-tags + +dvi: dvi-am + +dvi-am: + +info: info-am + +info-am: + +install-data-am: install-docDATA install-examplesDATA \ + install-pkgincludeHEADERS + +install-exec-am: install-binPROGRAMS install-libLTLIBRARIES + +install-info: install-info-am + +install-man: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -rf ./$(DEPDIR) + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-compile mostlyclean-generic \ + mostlyclean-libtool + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-binPROGRAMS uninstall-docDATA \ + uninstall-examplesDATA uninstall-info-am \ + uninstall-libLTLIBRARIES uninstall-pkgincludeHEADERS + +.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \ + clean-generic clean-libLTLIBRARIES clean-libtool ctags \ + distclean distclean-compile distclean-generic distclean-libtool \ + distclean-tags distdir dvi dvi-am info info-am install \ + install-am install-binPROGRAMS install-data install-data-am \ + install-docDATA install-examplesDATA install-exec \ + install-exec-am install-info install-info-am \ + install-libLTLIBRARIES install-man install-pkgincludeHEADERS \ + install-strip installcheck installcheck-am installdirs \ + maintainer-clean maintainer-clean-generic mostlyclean \ + mostlyclean-compile mostlyclean-generic mostlyclean-libtool pdf \ + pdf-am ps ps-am tags uninstall uninstall-am \ + uninstall-binPROGRAMS uninstall-docDATA uninstall-examplesDATA \ + uninstall-info-am uninstall-libLTLIBRARIES \ + uninstall-pkgincludeHEADERS + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/BRAINSABC/qhull/Makefile.txt b/BRAINSABC/qhull/Makefile.txt new file mode 100644 index 00000000..5d5f8d8d --- /dev/null +++ b/BRAINSABC/qhull/Makefile.txt @@ -0,0 +1,191 @@ +# Unix Makefile for qhull and rbox +# +# see README.txt +# the Unix distribution contains a configure Makefile +# +# make to produce qhull qconvex qdelaunay qhalf qvoronoi rbox +# make qvoronoi to produce qvoronoi (etc.) +# make qhullx to produce qhull qconvex etc. w/o using libqhull.a +# make doc to print documentation +# make install to copy qhull, rbox, qhull.1, rbox.1 to BINDIR, MANDIR +# make new to rebuild qhull and rbox from source +# +# make printall to print all files +# make user_eg to produce user_eg +# make user_eg2 to produce user_eg2 +# make clean to remove object files and core +# make cleanall to remove all generated files +# +# PRINTMAN -- command for printing manual pages +# PRINTC -- command for printing C files +# BINDIR -- directory where to copy executables +# MANDIR -- directory where to copy manual pages +# CC -- ANSI C or C++ compiler +# CCOPTS1 - options used to compile .c files +# CCOPTS2 -- options used to link .o files +# +# CFILES -- .c files for printing +# HFILES -- .h files for printing +# DFILES -- documentation files +# MFILES -- man pages and html files +# TFILES -- .txt versions of html html files +# FILES -- all other files +# OBJS -- specifies the object files of libqhull.a +# +BINDIR = /usr/local/bin +MANDIR = /usr/local/man/man1 + +# if you do not have enscript, try a2ps or just use lpr. The files are text. +PRINTMAN = enscript -2rl +PRINTC = enscript -2r +# PRINTMAN = lpr +# PRINTC = lpr + +#for Gnu's gcc compiler -O2 for optimization, -g for debugging, -Wall for check +# +CC = gcc +CCOPTS1 = -O2 -ansi + +# for Sun's cc compiler, -fast or O2 for optimization, -g for debugging, -Xc for ANSI +#CC = cc +#CCOPTS1 = -Xc -v -fast + +# for Silicon Graphics cc compiler, -O2 for optimization, -g for debugging +#CC = cc +#CCOPTS1 = -ansi -O2 + +# for Next cc compiler with fat executable +#CC = cc +#CCOPTS1 = -ansi -O2 -arch m68k -arch i386 -arch hppa + +# for loader, ld +CCOPTS2 = $(CCOPTS1) + +# OBJS in execution frequency order. CFILES after qhull.c are alphabetical +OBJS = user.o global.o stat.o io.o geom2.o poly2.o \ + merge.o qhull.o geom.o poly.o qset.o mem.o + +CFILES= unix.c qhull.c geom.c geom2.c global.c io.c mem.c merge.c poly.c \ + poly2.c qset.c stat.c user.c qconvex.c qdelaun.c qhalf.c qvoronoi.c +HFILES= user.h qhull.h qhull_a.h geom.h io.h mem.h merge.h poly.h qset.h stat.h +TXTFILES= ../Announce.txt ../REGISTER.txt ../COPYING.txt ../README.txt Changes.txt +DOCFILES= ../html/rbox.txt ../html/qhull.txt +FILES= Makefile rbox.c user_eg.c ../eg/q_test ../eg/q_egtest ../eg/q_eg +HTMFILES= qhull.man rbox.man qh-in.htm qh-optg.htm qh-optt.htm qh-optp.htm \ + index.htm qh-quick.htm qh-impre.htm qh-eg.htm \ + qh-optc.htm qh-opto.htm qh-optf.htm qh-optq.htm \ + qh-c.htm qh-faq.htm qhull.htm qconvex.htm qdelaun.htm \ + qh-geom.htm qh-globa.htm qh-io.htm qh-mem.htm qh-merge.htm \ + qh-poly.htm qh-qhull.htm qh-set.htm qh-stat.htm qh-user.htm \ + qdelau_f.htm qhalf.htm qvoronoi.htm qvoron_f.htm rbox.htm + +all: rbox qconvex qdelaunay qhalf qvoronoi qhull + +unix.o: qhull.h user.h mem.h +qconvex.o: qhull.h user.h mem.h +qdelaun.o: qhull.h user.h mem.h +qhalf.o: qhull.h user.h mem.h +qvoronoi.o: qhull.h user.h mem.h +qhull.o: $(HFILES) +geom.o: $(HFILES) +geom2.o: $(HFILES) +global.o: $(HFILES) +io.o: $(HFILES) +mem.o: mem.h +merge.o: $(HFILES) +poly.o: $(HFILES) +poly2.o: $(HFILES) +qset.o: qset.h mem.h +stat.o: $(HFILES) +user.o: $(HFILES) + +.c.o: + $(CC) -c $(CCOPTS1) $< + +clean: + rm -f *.o ../core qconvex qdelaunay qhalf qvoronoi qhull libqhull.a \ + *.exe + +cleanall: clean + rm -f *~ ../rbox ../qhull ../qhalf ../qconvex ../qdelaunay ../qhalf\ + ../qvoronoi ../user_eg ../user_eg2 ../*.exe >/dev/null + +doc: + $(PRINTMAN) $(TXTFILES) $(DOCFILES) + +install: all + cp ../qconvex $(BINDIR)/qconvex + cp ../qdelaunay $(BINDIR)/qdelaunay + cp ../qhalf $(BINDIR)/qhalf + cp ../qhull $(BINDIR)/qhull + cp ../qvoronoi $(BINDIR)/qvoronoi + cp ../rbox $(BINDIR)/rbox + cp ../html/qhull.man $(MANDIR)/qhull.1 + cp ../html/rbox.man $(MANDIR)/rbox.1 + +new: cleanall all + +printall: doc printh printc printf + +printh: + $(PRINTC) $(HFILES) + +printc: + $(PRINTC) $(CFILES) + +printf: + $(PRINTC) $(FILES) + +libqhull.a: $(OBJS) + @echo if 'ar' or 'ranlib' fails, try 'make qhullx' + ar r libqhull.a $(OBJS) + @echo the next line may need to be removed. + -test -x /bin/ranlib -o -x /usr/bin/ranlib && ranlib libqhull.a + +# don't use ../qconvex. Does not work on Red Hat Linux +qconvex: qconvex.o libqhull.a + $(CC) -o qconvex $(CCOPTS2) qconvex.o -L. -lqhull -lm + cp qconvex .. + +qdelaunay: qdelaun.o libqhull.a + $(CC) -o qdelaunay $(CCOPTS2) qdelaun.o -L. -lqhull -lm + cp qdelaunay .. + +qhalf: qhalf.o libqhull.a + $(CC) -o qhalf $(CCOPTS2) qhalf.o -L. -lqhull -lm + cp qhalf .. + +qvoronoi: qvoronoi.o libqhull.a + $(CC) -o qvoronoi $(CCOPTS2) qvoronoi.o -L. -lqhull -lm + cp qvoronoi .. + +qhull: unix.o libqhull.a + $(CC) -o qhull $(CCOPTS2) unix.o -L. -lqhull -lm + cp qhull .. + -chmod +x ../eg/q_test ../eg/q_eg ../eg/q_egtest + -cd ..; ./rbox D4 | ./qhull + +# compile qhull without using libqhull.a +qhullx: qconvex.o qdelaun.o qhalf.o qvoronoi.o unix.o $(OBJS) + $(CC) -o qconvex $(CCOPTS2) qconvex.o $(OBJS) -lm + $(CC) -o qdelaunay $(CCOPTS2) qdelaun.o $(OBJS) -lm + $(CC) -o qhalf $(CCOPTS2) qhalf.o $(OBJS) -lm + $(CC) -o qvoronoi $(CCOPTS2) qvoronoi.o $(OBJS) -lm + $(CC) -o qhull $(CCOPTS2) unix.o $(OBJS) -lm + cp qconvex qdelaunay qhalf qvoronoi qhull .. + -chmod +x ../eg/q_test ../eg/q_eg ../eg/q_egtest + -cd ..; ./rbox D4 | ./qhull + +rbox: rbox.o + $(CC) -o rbox rbox.o $(CCOPTS2) -lm + cp rbox .. + +user_eg: user_eg.o libqhull.a + $(CC) -o user_eg $(CCOPTS2) user_eg.o -L. -lqhull -lm + cp user_eg .. + +user_eg2: user_eg2.o libqhull.a + $(CC) -o user_eg2 $(CCOPTS2) user_eg2.o -L. -lqhull -lm + cp user_eg2 .. + +# end of Makefile diff --git a/BRAINSABC/qhull/geom.c b/BRAINSABC/qhull/geom.c new file mode 100644 index 00000000..1fa97194 --- /dev/null +++ b/BRAINSABC/qhull/geom.c @@ -0,0 +1,1507 @@ +/*
  ---------------------------------
+
+  geom.c
+  geometric routines of qhull
+
+  see qh-geom.htm and geom.h
+
+  copyright (c) 1993-2003 The Geometry Center
+
+  infrequent code goes into geom2.c
+*/
+
+#include "qhull_a.h"
+
+/*---------------------------------
+
+  qh_distplane( point, facet, dist )
+  return distance from point to facet
+
+  returns:
+  dist
+  if qh.RANDOMdist, joggles result
+
+  notes:
+  dist > 0 if point is above facet (i.e., outside)
+  does not error (for sortfacets)
+
+  see:
+  qh_distnorm in geom2.c
+*/
+void qh_distplane(pointT *point, facetT *facet, realT *dist)
+{
+  coordT *normal = facet->normal, *coordp, randr;
+  int     k;
+
+  switch( qh hull_dim )
+    {
+    case 2:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1];
+      break;
+    case 3:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2];
+      break;
+    case 4:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2] + point[3] * normal[3];
+      break;
+    case 5:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2] + point[3]
+        * normal[3] + point[4] * normal[4];
+      break;
+    case 6:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2] + point[3]
+        * normal[3] + point[4] * normal[4] + point[5] * normal[5];
+      break;
+    case 7:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2] + point[3]
+        * normal[3] + point[4] * normal[4] + point[5] * normal[5] + point[6] * normal[6];
+      break;
+    case 8:
+      *dist = facet->offset + point[0] * normal[0] + point[1] * normal[1] + point[2] * normal[2] + point[3]
+        * normal[3] + point[4] * normal[4] + point[5] * normal[5] + point[6] * normal[6] + point[7] * normal[7];
+      break;
+    default:
+      *dist = facet->offset;
+      coordp = point;
+      for( k = qh hull_dim; k--; )
+        {
+        *dist += *coordp++ **normal++;
+        }
+      break;
+    }
+  zinc_(Zdistplane);
+  if( !qh RANDOMdist && qh IStracing < 4 )
+    {
+    return;
+    }
+  if( qh RANDOMdist )
+    {
+    randr = qh_RANDOMint;
+    *dist += (2.0 * randr / qh_RANDOMmax - 1.0)
+      * qh RANDOMfactor * qh MAXabs_coord;
+    }
+  if( qh IStracing >= 4 )
+    {
+    fprintf(qh ferr, "qh_distplane: ");
+    fprintf(qh ferr, qh_REAL_1, *dist);
+    fprintf(qh ferr, "from p%d to f%d\n", qh_pointid(point), facet->id);
+    }
+  return;
+} /* distplane */
+
+/*---------------------------------
+
+  qh_findbest( point, startfacet, bestoutside, qh_ISnewfacets, qh_NOupper, dist, isoutside, numpart )
+  find facet that is furthest below a point
+  for upperDelaunay facets
+  returns facet only if !qh_NOupper and clearly above
+
+  input:
+  starts search at 'startfacet' (can not be flipped)
+  if !bestoutside (qh_ALL), stops at qh.MINoutside
+
+  returns:
+  best facet (reports error if NULL)
+  early out if isoutside defined and bestdist > qh.MINoutside
+  dist is distance to facet
+  isoutside is true if point is outside of facet
+  numpart counts the number of distance tests
+
+  see also:
+  qh_findbestnew()
+
+  notes:
+  If merging (testhorizon), searches horizon facets of coplanar best facets because
+  after qh_distplane, this and qh_partitionpoint are the most expensive in 3-d
+  avoid calls to distplane, function calls, and real number operations.
+  caller traces result
+  Optimized for outside points.   Tried recording a search set for qh_findhorizon.
+  Made code more complicated.
+
+  when called by qh_partitionvisible():
+  indicated by qh_ISnewfacets
+  qh.newfacet_list is list of simplicial, new facets
+  qh_findbestnew set if qh_sharpnewfacets returns True (to use qh_findbestnew)
+  qh.bestfacet_notsharp set if qh_sharpnewfacets returns False
+
+  when called by qh_findfacet(), qh_partitionpoint(), qh_partitioncoplanar(),
+  qh_check_bestdist(), qh_addpoint()
+  indicated by !qh_ISnewfacets
+  returns best facet in neighborhood of given facet
+  this is best facet overall if dist > -   qh.MAXcoplanar
+  or hull has at least a "spherical" curvature
+
+  design:
+  initialize and test for early exit
+  repeat while there are better facets
+  for each neighbor of facet
+  exit if outside facet found
+  test for better facet
+  if point is inside and partitioning
+  test for new facets with a "sharp" intersection
+  if so, future calls go to qh_findbestnew()
+  test horizon facets
+*/
+facetT * qh_findbest(pointT *point, facetT *startfacet,
+                     boolT bestoutside, boolT isnewfacets, boolT noupper,
+                     realT *dist, boolT *isoutside, int *numpart)
+{
+  realT        bestdist = -REALmax / 2 /* avoid underflow */;
+  facetT *     facet, *neighbor, * *neighborp;
+  facetT *     bestfacet = NULL, *lastfacet = NULL;
+  int          oldtrace = qh IStracing;
+  unsigned int visitid = ++qh visit_id;
+  int          numpartnew = 0;
+  boolT        testhorizon = True; /* needed if precise, e.g., rbox c D6 | qhull
+                                     Q0 Tv */
+
+  zinc_(Zfindbest);
+  if( qh IStracing >= 3 || (qh TRACElevel && qh TRACEpoint >= 0 && qh TRACEpoint == qh_pointid(point) ) )
+    {
+    if( qh TRACElevel > qh IStracing )
+      {
+      qh IStracing = qh TRACElevel;
+      }
+    fprintf(qh ferr, "qh_findbest: point p%d starting at f%d isnewfacets? %d, unless %d exit if > %2.2g\n",
+            qh_pointid(point), startfacet->id, isnewfacets, bestoutside, qh MINoutside);
+    fprintf(qh ferr, "  testhorizon? %d noupper? %d", testhorizon, noupper);
+    fprintf(qh ferr, "  Last point added was p%d.", qh furthest_id);
+    fprintf(qh ferr, "  Last merge was #%d.  max_outside %2.2g\n", zzval_(Ztotmerge), qh max_outside);
+    }
+  if( isoutside )
+    {
+    *isoutside = True;
+    }
+  if( !startfacet->flipped )    /* test startfacet */
+    {
+    *numpart = 1;
+    qh_distplane(point, startfacet, dist);   /* this code is duplicated below */
+    if( !bestoutside && *dist >= qh MINoutside
+        && (!startfacet->upperdelaunay || !noupper) )
+      {
+      bestfacet = startfacet;
+      goto LABELreturn_best;
+      }
+    bestdist = *dist;
+    if( !startfacet->upperdelaunay )
+      {
+      bestfacet = startfacet;
+      }
+    }
+  else
+    {
+    *numpart = 0;
+    }
+  startfacet->visitid = visitid;
+  facet = startfacet;
+  while( facet )
+    {
+    trace4( (qh ferr, "qh_findbest: neighbors of f%d, bestdist %2.2g f%d\n",
+             facet->id, bestdist, getid_(bestfacet) ) );
+    lastfacet = facet;
+    FOREACHneighbor_(facet) {
+      if( !neighbor->newfacet && isnewfacets )
+        {
+        continue;
+        }
+      if( neighbor->visitid == visitid )
+        {
+        continue;
+        }
+      neighbor->visitid = visitid;
+      if( !neighbor->flipped )    /* code duplicated above */
+        {
+        (*numpart)++;
+        qh_distplane(point, neighbor, dist);
+        if( *dist > bestdist )
+          {
+          if( !bestoutside && *dist >= qh MINoutside
+              && (!neighbor->upperdelaunay || !noupper) )
+            {
+            bestfacet = neighbor;
+            goto LABELreturn_best;
+            }
+          if( !neighbor->upperdelaunay )
+            {
+            bestfacet = neighbor;
+            bestdist = *dist;
+            break; /* switch to neighbor */
+            }
+          else if( !bestfacet )
+            {
+            bestdist = *dist;
+            break; /* switch to neighbor */
+            }
+          } /* end of *dist>bestdist */
+        }   /* end of !flipped */
+      }     /* end of FOREACHneighbor */
+    facet = neighbor;  /* non-NULL only if *dist>bestdist */
+    } /* end of while facet (directed search) */
+
+  if( isnewfacets )
+    {
+    if( !bestfacet )
+      {
+      bestdist = -REALmax / 2;
+      bestfacet = qh_findbestnew(point, startfacet->next, &bestdist, bestoutside, isoutside, &numpartnew);
+      testhorizon = False; /* qh_findbestnew calls qh_findbesthorizon */
+      }
+    else if( !qh findbest_notsharp && bestdist < -qh DISTround )
+      {
+      if( qh_sharpnewfacets() )
+        {
+        /* seldom used, qh_findbestnew will retest all facets */
+        zinc_(Zfindnewsharp);
+        bestfacet = qh_findbestnew(point, bestfacet, &bestdist, bestoutside, isoutside, &numpartnew);
+        testhorizon = False; /* qh_findbestnew calls qh_findbesthorizon */
+        qh findbestnew = True;
+        }
+      else
+        {
+        qh findbest_notsharp = True;
+        }
+      }
+    }
+  if( !bestfacet )
+    {
+    bestfacet = qh_findbestlower(lastfacet, point, &bestdist, numpart);
+    }
+  if( testhorizon )
+    {
+    bestfacet = qh_findbesthorizon(!qh_IScheckmax, point, bestfacet, noupper, &bestdist, &numpartnew);
+    }
+  *dist = bestdist;
+  if( isoutside && bestdist < qh MINoutside )
+    {
+    *isoutside = False;
+    }
+LABELreturn_best:
+  zadd_(Zfindbesttot, *numpart);
+  zmax_(Zfindbestmax, *numpart);
+  (*numpart) += numpartnew;
+  qh IStracing = oldtrace;
+  return bestfacet;
+}  /* findbest */
+
+/*---------------------------------
+
+  qh_findbesthorizon( qh_IScheckmax, point, startfacet, qh_NOupper, &bestdist, &numpart )
+  search coplanar and better horizon facets from startfacet/bestdist
+  ischeckmax turns off statistics and minsearch update
+  all arguments must be initialized
+  returns (ischeckmax):
+  best facet
+  returns (!ischeckmax):
+  best facet that is not upperdelaunay
+  allows upperdelaunay that is clearly outside
+  returns:
+  bestdist is distance to bestfacet
+  numpart -- updates number of distance tests
+
+  notes:
+  no early out -- use qh_findbest() or qh_findbestnew()
+  Searches coplanar or better horizon facets
+
+  when called by qh_check_maxout() (qh_IScheckmax)
+  startfacet must be closest to the point
+  Otherwise, if point is beyond and below startfacet, startfacet may be a local minimum
+  even though other facets are below the point.
+  updates facet->maxoutside for good, visited facets
+  may return NULL
+
+  searchdist is qh.max_outside + 2 * DISTround
+  + max( MINvisible('Vn'), MAXcoplanar('Un'));
+  This setting is a guess.  It must be at least max_outside + 2*DISTround
+  because a facet may have a geometric neighbor across a vertex
+
+  design:
+  for each horizon facet of coplanar best facets
+  continue if clearly inside
+  unless upperdelaunay or clearly outside
+  update best facet
+*/
+facetT * qh_findbesthorizon(boolT ischeckmax, pointT* point, facetT *startfacet, boolT noupper, realT *bestdist,
+                            int *numpart)
+{
+  facetT *     bestfacet = startfacet;
+  realT        dist;
+  facetT *     neighbor, * *neighborp, *facet;
+  facetT *     nextfacet = NULL; /* optimize last facet of coplanarset */
+  int          numpartinit = *numpart, coplanarset_size;
+  unsigned int visitid = ++qh visit_id;
+  boolT        newbest = False;       /* for tracing */
+  realT        minsearch, searchdist; /* skip facets that are too far from point
+                                        */
+
+  if( !ischeckmax )
+    {
+    zinc_(Zfindhorizon);
+    }
+  else
+    {
+#if qh_MAXoutside
+    if( (!qh ONLYgood || startfacet->good) && *bestdist > startfacet->maxoutside )
+      {
+      startfacet->maxoutside = *bestdist;
+      }
+#endif
+    }
+  searchdist = qh_SEARCHdist; /* multiple of qh.max_outside and precision
+                                constants */
+  minsearch = *bestdist - searchdist;
+  if( ischeckmax )
+    {
+    /* Always check coplanar facets.  Needed for RBOX 1000 s Z1 G1e-13
+      t996564279 | QHULL Tv */
+    minimize_(minsearch, -searchdist);
+    }
+  coplanarset_size = 0;
+  facet = startfacet;
+  while( True )
+    {
+    trace4( (qh ferr,
+             "qh_findbesthorizon: neighbors of f%d bestdist %2.2g f%d ischeckmax? %d noupper? %d minsearch %2.2g searchdist %2.2g\n",
+             facet->id, *bestdist, getid_(bestfacet), ischeckmax, noupper,
+             minsearch, searchdist) );
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid == visitid )
+        {
+        continue;
+        }
+      neighbor->visitid = visitid;
+      if( !neighbor->flipped )
+        {
+        qh_distplane(point, neighbor, &dist);
+        (*numpart)++;
+        if( dist > *bestdist )
+          {
+          if( !neighbor->upperdelaunay || ischeckmax || (!noupper && dist >= qh MINoutside) )
+            {
+            bestfacet = neighbor;
+            *bestdist = dist;
+            newbest = True;
+            if( !ischeckmax )
+              {
+              minsearch = dist - searchdist;
+              if( dist > *bestdist + searchdist )
+                {
+                zinc_(Zfindjump); /* everything in qh.coplanarset at least
+                                    searchdist below */
+                coplanarset_size = 0;
+                }
+              }
+            }
+          }
+        else if( dist < minsearch )
+          {
+          continue; /* if ischeckmax, dist can't be positive */
+          }
+#if qh_MAXoutside
+        if( ischeckmax && dist > neighbor->maxoutside )
+          {
+          neighbor->maxoutside = dist;
+          }
+#endif
+        } /* end of !flipped */
+      if( nextfacet )
+        {
+        if( !coplanarset_size++ )
+          {
+          SETfirst_(qh coplanarset) = nextfacet;
+          SETtruncate_(qh coplanarset, 1);
+          }
+        else
+          {
+          qh_setappend(&qh coplanarset, nextfacet); /* Was needed for RBOX 1000 s W1e-13 P0 t996547055 | QHULL d Qbb Qc Tv
+              and RBOX 1000 s Z1 G1e-13 t996564279 | qhull Tv  */
+          }
+        }
+      nextfacet = neighbor;
+      } /* end of EACHneighbor */
+    facet = nextfacet;
+    if( facet )
+      {
+      nextfacet = NULL;
+      }
+    else if( !coplanarset_size )
+      {
+      break;
+      }
+    else if( !--coplanarset_size )
+      {
+      facet = SETfirst_(qh coplanarset);
+      SETtruncate_(qh coplanarset, 0);
+      }
+    else
+      {
+      facet = (facetT *)qh_setdellast(qh coplanarset);
+      }
+    } /* while True, for each facet in qh.coplanarset */
+
+  if( !ischeckmax )
+    {
+    zadd_(Zfindhorizontot, *numpart - numpartinit);
+    zmax_(Zfindhorizonmax, *numpart - numpartinit);
+    if( newbest )
+      {
+      zinc_(Zparthorizon);
+      }
+    }
+  trace4( (qh ferr, "qh_findbesthorizon: newbest? %d bestfacet f%d bestdist %2.2g\n", newbest, getid_(bestfacet),
+           *bestdist) );
+  return bestfacet;
+}  /* findbesthorizon */
+
+/*---------------------------------
+
+  qh_findbestnew( point, startfacet, dist, isoutside, numpart )
+  find best newfacet for point
+  searches all of qh.newfacet_list starting at startfacet
+  searches horizon facets of coplanar best newfacets
+  searches all facets if startfacet == qh.facet_list
+  returns:
+  best new or horizon facet that is not upperdelaunay
+  early out if isoutside and not 'Qf'
+  dist is distance to facet
+  isoutside is true if point is outside of facet
+  numpart is number of distance tests
+
+  notes:
+  Always used for merged new facets (see qh_USEfindbestnew)
+  Avoids upperdelaunay facet unless (isoutside and outside)
+
+  Uses qh.visit_id, qh.coplanarset.
+  If share visit_id with qh_findbest, coplanarset is incorrect.
+
+  If merging (testhorizon), searches horizon facets of coplanar best facets because
+  a point maybe coplanar to the bestfacet, below its horizon facet,
+  and above a horizon facet of a coplanar newfacet.  For example,
+  rbox 1000 s Z1 G1e-13 | qhull
+  rbox 1000 s W1e-13 P0 t992110337 | QHULL d Qbb Qc
+
+  qh_findbestnew() used if
+  qh_sharpnewfacets -- newfacets contains a sharp angle
+  if many merges, qh_premerge found a merge, or 'Qf' (qh.findbestnew)
+
+  see also:
+  qh_partitionall() and qh_findbest()
+
+  design:
+  for each new facet starting from startfacet
+  test distance from point to facet
+  return facet if clearly outside
+  unless upperdelaunay and a lowerdelaunay exists
+  update best facet
+  test horizon facets
+*/
+facetT * qh_findbestnew(pointT *point, facetT *startfacet,
+                        realT *dist, boolT bestoutside, boolT *isoutside, int *numpart)
+{
+  realT        bestdist = -REALmax / 2;
+  facetT *     bestfacet = NULL, *facet;
+  int          oldtrace = qh IStracing, i;
+  unsigned int visitid = ++qh visit_id;
+  realT        distoutside = 0.0;
+  boolT        isdistoutside;      /* True if distoutside is defined */
+  boolT        testhorizon = True; /* needed if precise, e.g., rbox c D6 | qhull
+                                     Q0 Tv */
+
+  if( !startfacet )
+    {
+    if( qh MERGING )
+      {
+      fprintf(
+        qh ferr,
+        "qhull precision error (qh_findbestnew): merging has formed and deleted a cone of new facets.  Can not continue.\n");
+      }
+    else
+      {
+      fprintf(qh ferr, "qhull internal error (qh_findbestnew): no new facets for point p%d\n",
+              qh furthest_id);
+      }
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  zinc_(Zfindnew);
+  if( qh BESToutside || bestoutside )
+    {
+    isdistoutside = False;
+    }
+  else
+    {
+    isdistoutside = True;
+    distoutside = qh_DISToutside; /* multiple of qh.MINoutside & qh.max_outside,
+                                    see user.h */
+    }
+  if( isoutside )
+    {
+    *isoutside = True;
+    }
+  *numpart = 0;
+  if( qh IStracing >= 3 || (qh TRACElevel && qh TRACEpoint >= 0 && qh TRACEpoint == qh_pointid(point) ) )
+    {
+    if( qh TRACElevel > qh IStracing )
+      {
+      qh IStracing = qh TRACElevel;
+      }
+    fprintf(qh ferr, "qh_findbestnew: point p%d facet f%d. Stop? %d if dist > %2.2g\n",
+            qh_pointid(point), startfacet->id, isdistoutside, distoutside);
+    fprintf(qh ferr, "  Last point added p%d visitid %d.",  qh furthest_id, visitid);
+    fprintf(qh ferr, "  Last merge was #%d.\n", zzval_(Ztotmerge) );
+    }
+  /* visit all new facets starting with startfacet, maybe qh facet_list */
+  for( i = 0, facet = startfacet; i < 2; i++, facet = qh newfacet_list )
+    {
+    FORALLfacet_(facet) {
+      if( facet == startfacet && i )
+        {
+        break;
+        }
+      facet->visitid = visitid;
+      if( !facet->flipped )
+        {
+        qh_distplane(point, facet, dist);
+        (*numpart)++;
+        if( *dist > bestdist )
+          {
+          if( !facet->upperdelaunay || *dist >= qh MINoutside )
+            {
+            bestfacet = facet;
+            if( isdistoutside && *dist >= distoutside )
+              {
+              goto LABELreturn_bestnew;
+              }
+            bestdist = *dist;
+            }
+          }
+        } /* end of !flipped */
+      }   /* FORALLfacet from startfacet or qh newfacet_list */
+    }
+  if( testhorizon || !bestfacet )
+    {
+    bestfacet = qh_findbesthorizon(!qh_IScheckmax, point, bestfacet ? bestfacet : startfacet,
+                                   !qh_NOupper, &bestdist, numpart);
+    }
+  *dist = bestdist;
+  if( isoutside && *dist < qh MINoutside )
+    {
+    *isoutside = False;
+    }
+LABELreturn_bestnew:
+  zadd_(Zfindnewtot, *numpart);
+  zmax_(Zfindnewmax, *numpart);
+  trace4( (qh ferr, "qh_findbestnew: bestfacet f%d bestdist %2.2g\n", getid_(bestfacet), *dist) );
+  qh IStracing = oldtrace;
+  return bestfacet;
+}  /* findbestnew */
+
+/* ============ hyperplane functions -- keep code together [?] ============ */
+
+/*---------------------------------
+
+  qh_backnormal( rows, numrow, numcol, sign, normal, nearzero )
+  given an upper-triangular rows array and a sign,
+  solve for normal equation x using back substitution over rows U
+
+  returns:
+  normal= x
+
+  if will not be able to divzero() when normalized (qh.MINdenom_2 and qh.MINdenom_1_2),
+  if fails on last row
+  this means that the hyperplane intersects [0,..,1]
+  sets last coordinate of normal to sign
+  otherwise
+  sets tail of normal to [...,sign,0,...], i.e., solves for b= [0...0]
+  sets nearzero
+
+  notes:
+  assumes numrow == numcol-1
+
+  see Golub & van Loan 4.4-9 for back substitution
+
+  solves Ux=b where Ax=b and PA=LU
+  b= [0,...,0,sign or 0]  (sign is either -1 or +1)
+  last row of A= [0,...,0,1]
+
+  1) Ly=Pb == y=b since P only permutes the 0's of   b
+
+  design:
+  for each row from end
+  perform back substitution
+  if near zero
+  use qh_divzero for division
+  if zero divide and not last row
+  set tail of normal to 0
+*/
+void qh_backnormal(realT * *rows, int numrow, int numcol, boolT sign,
+                   coordT *normal, boolT *nearzero)
+{
+  int     i, j;
+  coordT *normalp, *normal_tail, *ai, *ak;
+  realT   diagonal;
+  boolT   waszero;
+  int     zerocol = -1;
+
+  normalp = normal + numcol - 1;
+  *normalp-- = (sign ? -1.0 : 1.0);
+  for( i = numrow; i--; )
+    {
+    *normalp = 0.0;
+    ai = rows[i] + i + 1;
+    ak = normalp + 1;
+    for( j = i + 1; j < numcol; j++ )
+      {
+      *normalp -= *ai++ **ak++;
+      }
+    diagonal = (rows[i])[i];
+    if( fabs_(diagonal) > qh MINdenom_2 )
+      {
+      *(normalp--) /= diagonal;
+      }
+    else
+      {
+      waszero = False;
+      *normalp = qh_divzero(*normalp, diagonal, qh MINdenom_1_2, &waszero);
+      if( waszero )
+        {
+        zerocol = i;
+        *(normalp--) = (sign ? -1.0 : 1.0);
+        for( normal_tail = normalp + 2; normal_tail < normal + numcol; normal_tail++ )
+          {
+          *normal_tail = 0.0;
+          }
+        }
+      else
+        {
+        normalp--;
+        }
+      }
+    }
+  if( zerocol != -1 )
+    {
+    zzinc_(Zback0);
+    *nearzero = True;
+    trace4( (qh ferr, "qh_backnormal: zero diagonal at column %d.\n", i) );
+    qh_precision("zero diagonal on back substitution");
+    }
+} /* backnormal */
+
+/*---------------------------------
+
+  qh_gausselim( rows, numrow, numcol, sign )
+  Gaussian elimination with partial pivoting
+
+  returns:
+  rows is upper triangular (includes row exchanges)
+  flips sign for each row exchange
+  sets nearzero if pivot[k] < qh.NEARzero[k], else clears it
+
+  notes:
+  if nearzero, the determinant's sign may be incorrect.
+  assumes numrow <= numcol
+
+  design:
+  for each row
+  determine pivot and exchange rows if necessary
+  test for near zero
+  perform gaussian elimination step
+*/
+void qh_gausselim(realT * *rows, int numrow, int numcol, boolT *sign, boolT *nearzero)
+{
+  realT *ai, *ak, *rowp, *pivotrow;
+  realT  n, pivot, pivot_abs = 0.0, temp;
+  int    i, j, k, pivoti, flip = 0;
+
+  *nearzero = False;
+  for( k = 0; k < numrow; k++ )
+    {
+    pivot_abs = fabs_( (rows[k])[k]);
+    pivoti = k;
+    for( i = k + 1; i < numrow; i++ )
+      {
+      if( (temp = fabs_( (rows[i])[k]) ) > pivot_abs )
+        {
+        pivot_abs = temp;
+        pivoti = i;
+        }
+      }
+    if( pivoti != k )
+      {
+      rowp = rows[pivoti];
+      rows[pivoti] = rows[k];
+      rows[k] = rowp;
+      *sign ^= 1;
+      flip ^= 1;
+      }
+    if( pivot_abs <= qh NEARzero[k] )
+      {
+      *nearzero = True;
+      if( pivot_abs == 0.0 )     /* remainder of column == 0 */
+        {
+        if( qh IStracing >= 4 )
+          {
+          fprintf(qh ferr, "qh_gausselim: 0 pivot at column %d. (%2.2g < %2.2g)\n", k, pivot_abs, qh DISTround);
+          qh_printmatrix(qh ferr, "Matrix:", rows, numrow, numcol);
+          }
+        zzinc_(Zgauss0);
+        qh_precision("zero pivot for Gaussian elimination");
+        goto LABELnextcol;
+        }
+      }
+    pivotrow = rows[k] + k;
+    pivot = *pivotrow++;  /* signed value of pivot, and remainder of row */
+    for( i = k + 1; i < numrow; i++ )
+      {
+      ai = rows[i] + k;
+      ak = pivotrow;
+      n = (*ai++) / pivot;   /* divzero() not needed since |pivot| >= |*ai| */
+      for( j = numcol - (k + 1); j--; )
+        {
+        *ai++ -= n * *ak++;
+        }
+      }
+LABELnextcol:
+    ;
+    }
+  wmin_(Wmindenom, pivot_abs);  /* last pivot element */
+  if( qh IStracing >= 5 )
+    {
+    qh_printmatrix(qh ferr, "qh_gausselem: result", rows, numrow, numcol);
+    }
+} /* gausselim */
+
+/*---------------------------------
+
+  qh_getangle( vect1, vect2 )
+  returns the dot product of two vectors
+  if qh.RANDOMdist, joggles result
+
+  notes:
+  the angle may be > 1.0 or < -1.0 because of roundoff errors
+
+*/
+realT qh_getangle(pointT *vect1, pointT *vect2)
+{
+  realT angle = 0, randr;
+  int   k;
+  for( k = qh hull_dim; k--; )
+    {
+    angle += *vect1++ **vect2++;
+    }
+  if( qh RANDOMdist )
+    {
+    randr = qh_RANDOMint;
+    angle += (2.0 * randr / qh_RANDOMmax - 1.0)
+      * qh RANDOMfactor;
+    }
+  trace4( (qh ferr, "qh_getangle: %2.2g\n", angle) );
+  return angle;
+} /* getangle */
+
+/*---------------------------------
+
+  qh_getcenter( vertices )
+  returns arithmetic center of a set of vertices as a new point
+
+  notes:
+  allocates point array for center
+*/
+pointT * qh_getcenter(setT *vertices)
+{
+  int      k;
+  pointT * center, *coord;
+  vertexT *vertex, * *vertexp;
+  int      count = qh_setsize(vertices);
+
+  if( count < 2 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_getcenter): not defined for %d points\n", count);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  center = (pointT *)qh_memalloc(qh normal_size);
+  for( k = 0; k < qh hull_dim; k++ )
+    {
+    coord = center + k;
+    *coord = 0.0;
+    FOREACHvertex_(vertices)
+    * coord += vertex->point[k];
+    *coord /= count;
+    }
+  return center;
+} /* getcenter */
+
+/*---------------------------------
+
+  qh_getcentrum( facet )
+  returns the centrum for a facet as a new point
+
+  notes:
+  allocates the centrum
+*/
+pointT * qh_getcentrum(facetT *facet)
+{
+  realT   dist;
+  pointT *centrum, *point;
+
+  point = qh_getcenter(facet->vertices);
+  zzinc_(Zcentrumtests);
+  qh_distplane(point, facet, &dist);
+  centrum = qh_projectpoint(point, facet, dist);
+  qh_memfree(point, qh normal_size);
+  trace4( (qh ferr, "qh_getcentrum: for f%d, %d vertices dist= %2.2g\n",
+           facet->id, qh_setsize(facet->vertices), dist) );
+  return centrum;
+} /* getcentrum */
+
+/*---------------------------------
+
+  qh_getdistance( facet, neighbor, mindist, maxdist )
+  returns the maxdist and mindist distance of any vertex from neighbor
+
+  returns:
+  the max absolute value
+
+  design:
+  for each vertex of facet that is not in neighbor
+  test the distance from vertex to neighbor
+*/
+realT qh_getdistance(facetT *facet, facetT *neighbor, realT *mindist, realT *maxdist)
+{
+  vertexT *vertex, * *vertexp;
+  realT    dist, maxd, mind;
+
+  FOREACHvertex_(facet->vertices)
+  vertex->seen = False;
+  FOREACHvertex_(neighbor->vertices)
+  vertex->seen = True;
+  mind = 0.0;
+  maxd = 0.0;
+  FOREACHvertex_(facet->vertices) {
+    if( !vertex->seen )
+      {
+      zzinc_(Zbestdist);
+      qh_distplane(vertex->point, neighbor, &dist);
+      if( dist < mind )
+        {
+        mind = dist;
+        }
+      else if( dist > maxd )
+        {
+        maxd = dist;
+        }
+      }
+    }
+  *mindist = mind;
+  *maxdist = maxd;
+  mind = -mind;
+  if( maxd > mind )
+    {
+    return maxd;
+    }
+  else
+    {
+    return mind;
+    }
+} /* getdistance */
+
+/*---------------------------------
+
+  qh_normalize( normal, dim, toporient )
+  normalize a vector and report if too small
+  does not use min norm
+
+  see:
+  qh_normalize2
+*/
+void qh_normalize(coordT *normal, int dim, boolT toporient)
+{
+  qh_normalize2( normal, dim, toporient, NULL, NULL);
+} /* normalize */
+
+/*---------------------------------
+
+  qh_normalize2( normal, dim, toporient, minnorm, ismin )
+  normalize a vector and report if too small
+  qh.MINdenom/MINdenom1 are the upper limits for divide overflow
+
+  returns:
+  normalized vector
+  flips sign if !toporient
+  if minnorm non-NULL,
+  sets ismin if normal < minnorm
+
+  notes:
+  if zero norm
+  sets all elements to sqrt(1.0/dim)
+  if divide by zero (divzero ())
+  sets largest element to   +/-1
+  bumps Znearlysingular
+
+  design:
+  computes norm
+  test for minnorm
+  if not near zero
+  normalizes normal
+  else if zero norm
+  sets normal to standard value
+  else
+  uses qh_divzero to normalize
+  if nearzero
+  sets norm to direction of maximum value
+*/
+void qh_normalize2(coordT *normal, int dim, boolT toporient,
+                   realT *minnorm, boolT *ismin)
+{
+  int    k;
+  realT *colp, *maxp, norm = 0, temp, *norm1, *norm2, *norm3;
+  boolT  zerodiv;
+
+  norm1 = normal + 1;
+  norm2 = normal + 2;
+  norm3 = normal + 3;
+  if( dim == 2 )
+    {
+    norm = sqrt( (*normal) * (*normal) + (*norm1) * (*norm1) );
+    }
+  else if( dim == 3 )
+    {
+    norm = sqrt( (*normal) * (*normal) + (*norm1) * (*norm1) + (*norm2) * (*norm2) );
+    }
+  else if( dim == 4 )
+    {
+    norm = sqrt( (*normal) * (*normal) + (*norm1) * (*norm1) + (*norm2) * (*norm2)
+                 + (*norm3) * (*norm3) );
+    }
+  else if( dim > 4 )
+    {
+    norm = (*normal) * (*normal) + (*norm1) * (*norm1) + (*norm2) * (*norm2)
+      + (*norm3) * (*norm3);
+    for( k = dim - 4, colp = normal + 4; k--; colp++ )
+      {
+      norm += (*colp) * (*colp);
+      }
+    norm = sqrt(norm);
+    }
+  if( minnorm )
+    {
+    if( norm < *minnorm )
+      {
+      *ismin = True;
+      }
+    else
+      {
+      *ismin = False;
+      }
+    }
+  wmin_(Wmindenom, norm);
+  if( norm > qh MINdenom )
+    {
+    if( !toporient )
+      {
+      norm = -norm;
+      }
+    *normal /= norm;
+    *norm1 /= norm;
+    if( dim == 2 )
+      {
+      ; /* all done */
+      }
+    else if( dim == 3 )
+      {
+      *norm2 /= norm;
+      }
+    else if( dim == 4 )
+      {
+      *norm2 /= norm;
+      *norm3 /= norm;
+      }
+    else if( dim > 4 )
+      {
+      *norm2 /= norm;
+      *norm3 /= norm;
+      for( k = dim - 4, colp = normal + 4; k--; )
+        {
+        *colp++ /= norm;
+        }
+      }
+    }
+  else if( norm == 0.0 )
+    {
+    temp = sqrt(1.0 / dim);
+    for( k = dim, colp = normal; k--; )
+      {
+      *colp++ = temp;
+      }
+    }
+  else
+    {
+    if( !toporient )
+      {
+      norm = -norm;
+      }
+    for( k = dim, colp = normal; k--; colp++ )   /* k used below */
+      {
+      temp = qh_divzero(*colp, norm, qh MINdenom_1, &zerodiv);
+      if( !zerodiv )
+        {
+        *colp = temp;
+        }
+      else
+        {
+        maxp = qh_maxabsval(normal, dim);
+        temp = ( (*maxp * norm >= 0.0) ? 1.0 : -1.0);
+        for( k = dim, colp = normal; k--; colp++ )
+          {
+          *colp = 0.0;
+          }
+        *maxp = temp;
+        zzinc_(Znearlysingular);
+        trace0( (qh ferr, "qh_normalize: norm=%2.2g too small during p%d\n",
+                 norm, qh furthest_id) );
+        return;
+        }
+      }
+    }
+} /* normalize */
+
+/*---------------------------------
+
+  qh_projectpoint( point, facet, dist )
+  project point onto a facet by dist
+
+  returns:
+  returns a new point
+
+  notes:
+  if dist= distplane(point,facet)
+  this projects point to hyperplane
+  assumes qh_memfree_() is valid for normal_size
+*/
+pointT * qh_projectpoint(pointT *point, facetT *facet, realT dist)
+{
+  pointT *newpoint, *np, *normal;
+  size_t  normsize = qh normal_size; int k;
+  void * *freelistp; /* used !qh_NOmem */
+
+  qh_memalloc_(normsize, freelistp, newpoint, pointT);
+  np = newpoint;
+  normal = facet->normal;
+  for( k = qh hull_dim; k--; )
+    {
+    *(np++) = *point++ - dist * *normal++;
+    }
+  return newpoint;
+} /* projectpoint */
+
+/*---------------------------------
+
+  qh_setfacetplane( facet )
+  sets the hyperplane for a facet
+  if qh.RANDOMdist, joggles hyperplane
+
+  notes:
+  uses global buffers qh.gm_matrix and qh.gm_row
+  overwrites facet->normal if already defined
+  updates Wnewvertex if PRINTstatistics
+  sets facet->upperdelaunay if upper envelope of Delaunay triangulation
+
+  design:
+  copy vertex coordinates to qh.gm_matrix/gm_row
+  compute determinate
+  if nearzero
+  recompute determinate with gaussian elimination
+  if nearzero
+  force outside orientation by testing interior point
+*/
+void qh_setfacetplane(facetT *facet)
+{
+  pointT * point;
+  vertexT *vertex, * *vertexp;
+  int      k, i, oldtrace = 0;
+  size_t   normsize = qh normal_size;
+  realT    dist;
+  void * * freelistp; /* used !qh_NOmem */
+  coordT * coord, *gmcoord;
+  pointT * point0 = SETfirstt_(facet->vertices, vertexT)->point;
+  boolT    nearzero = False;
+
+  zzinc_(Zsetplane);
+  if( !facet->normal )
+    {
+    qh_memalloc_(normsize, freelistp, facet->normal, coordT);
+    }
+  if( facet == qh tracefacet )
+    {
+    oldtrace = qh IStracing;
+    qh IStracing = 5;
+    fprintf(qh ferr, "qh_setfacetplane: facet f%d created.\n", facet->id);
+    fprintf(qh ferr, "  Last point added to hull was p%d.", qh furthest_id);
+    if( zzval_(Ztotmerge) )
+      {
+      fprintf(qh ferr, "  Last merge was #%d.", zzval_(Ztotmerge) );
+      }
+    fprintf(qh ferr, "\n\nCurrent summary is:\n");
+    qh_printsummary(qh ferr);
+    }
+  if( qh hull_dim <= 4 )
+    {
+    i = 0;
+    if( qh RANDOMdist )
+      {
+      gmcoord = qh gm_matrix;
+      FOREACHvertex_(facet->vertices) {
+        qh gm_row[i++] = gmcoord;
+
+        coord = vertex->point;
+        for( k = qh hull_dim; k--; )
+          {
+          *(gmcoord++) = *coord++ *qh_randomfactor();
+          }
+        }
+      }
+    else
+      {
+      FOREACHvertex_(facet->vertices)
+      qh gm_row[i++] = vertex->point;
+      }
+    qh_sethyperplane_det(qh hull_dim, qh gm_row, point0, facet->toporient,
+                         facet->normal, &facet->offset, &nearzero);
+    }
+  if( qh hull_dim > 4 || nearzero )
+    {
+    i = 0;
+    gmcoord = qh gm_matrix;
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->point != point0 )
+        {
+        qh gm_row[i++] = gmcoord;
+        coord = vertex->point;
+        point = point0;
+        for( k = qh hull_dim; k--; )
+          {
+          *(gmcoord++) = *coord++ - *point++;
+          }
+        }
+      }
+    qh gm_row[i] = gmcoord;  /* for areasimplex */
+    if( qh RANDOMdist )
+      {
+      gmcoord = qh gm_matrix;
+      for( i = qh hull_dim - 1; i--; )
+        {
+        for( k = qh hull_dim; k--; )
+          {
+          *(gmcoord++) *= qh_randomfactor();
+          }
+        }
+      }
+    qh_sethyperplane_gauss(qh hull_dim, qh gm_row, point0, facet->toporient,
+                           facet->normal, &facet->offset, &nearzero);
+    if( nearzero )
+      {
+      if( qh_orientoutside(facet) )
+        {
+        trace0( (qh ferr, "qh_setfacetplane: flipped orientation after testing interior_point during p%d\n",
+                 qh furthest_id) );
+        /* this is part of using Gaussian Elimination.  For example in 5-d
+           1 1 1 1 0
+           1 1 1 1 1
+           0 0 0 1 0
+           0 1 0 0 0
+           1 0 0 0 0
+           norm= 0.38 0.38 -0.76 0.38 0
+           has a determinate of 1, but g.e. after subtracting pt. 0 has
+           0's in the diagonal, even with full pivoting.  It does work
+           if you subtract pt. 4 instead. */
+        }
+      }
+    }
+  facet->upperdelaunay = False;
+  if( qh DELAUNAY )
+    {
+    if( qh UPPERdelaunay )       /* matches qh_triangulate_facet and
+                                   qh.lower_threshold in qh_initbuild */
+      {
+      if( facet->normal[qh hull_dim - 1] >= qh ANGLEround * qh_ZEROdelaunay )
+        {
+        facet->upperdelaunay = True;
+        }
+      }
+    else
+      {
+      if( facet->normal[qh hull_dim - 1] > -qh ANGLEround * qh_ZEROdelaunay )
+        {
+        facet->upperdelaunay = True;
+        }
+      }
+    }
+  if( qh PRINTstatistics || qh IStracing || qh TRACElevel || qh JOGGLEmax < REALmax )
+    {
+    qh old_randomdist = qh RANDOMdist;
+    qh RANDOMdist = False;
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->point != point0 )
+        {
+        boolT istrace = False;
+        zinc_(Zdiststat);
+        qh_distplane(vertex->point, facet, &dist);
+        dist = fabs_(dist);
+        zinc_(Znewvertex);
+        wadd_(Wnewvertex, dist);
+        if( dist > wwval_(Wnewvertexmax) )
+          {
+          wwval_(Wnewvertexmax) = dist;
+          if( dist > qh max_outside )
+            {
+            qh max_outside = dist; /* used by qh_maxouter() */
+            if( dist > qh TRACEdist )
+              {
+              istrace = True;
+              }
+            }
+          }
+        else if( -dist > qh TRACEdist )
+          {
+          istrace = True;
+          }
+        if( istrace )
+          {
+          fprintf(
+            qh ferr,
+            "qh_setfacetplane: ====== vertex p%d (v%d) increases max_outside to %2.2g for new facet f%d last p%d\n",
+            qh_pointid(vertex->point), vertex->id, dist, facet->id, qh furthest_id);
+          qh_errprint("DISTANT", facet, NULL, NULL, NULL);
+          }
+        }
+      }
+    qh RANDOMdist = qh old_randomdist;
+    }
+  if( qh IStracing >= 3 )
+    {
+    fprintf(qh ferr, "qh_setfacetplane: f%d offset %2.2g normal: ",
+            facet->id, facet->offset);
+    for( k = 0; k < qh hull_dim; k++ )
+      {
+      fprintf(qh ferr, "%2.2g ", facet->normal[k]);
+      }
+    fprintf(qh ferr, "\n");
+    }
+  if( facet == qh tracefacet )
+    {
+    qh IStracing = oldtrace;
+    }
+} /* setfacetplane */
+
+/*---------------------------------
+
+  qh_sethyperplane_det( dim, rows, point0, toporient, normal, offset, nearzero )
+  given dim X dim array indexed by rows[], one row per point,
+  toporient (flips all signs),
+  and point0 (any row)
+  set normalized hyperplane equation from oriented simplex
+
+  returns:
+  normal (normalized)
+  offset (places point0 on the hyperplane)
+  sets nearzero if hyperplane not through points
+
+  notes:
+  only defined for dim == 2..4
+  rows[] is not modified
+  solves det(P-V_0, V_n-V_0, ..., V_1-V_0)=0, i.e. every point is on hyperplane
+  see Bower & Woodworth, A programmer's geometry, Butterworths 1983.
+
+  derivation of 3-d minnorm
+  Goal: all vertices V_i within qh.one_merge of hyperplane
+  Plan: exactly translate the facet so that V_0 is the origin
+  exactly rotate the facet so that V_1 is on the x-axis and y_2=0.
+  exactly rotate the effective perturbation to only effect n_0
+  this introduces a factor of sqrt(3)
+  n_0 = ((y_2-y_0)*(z_1-z_0) - (z_2-z_0)*(y_1-y_0)) / norm
+  Let M_d be the max coordinate difference
+  Let M_a be the greater of M_d and the max abs. coordinate
+  Let u be machine roundoff and distround be max error for distance computation
+  The max error for n_0 is sqrt(3) u M_a M_d / norm.  n_1 is approx. 1 and n_2 is approx. 0
+  The max error for distance of V_1 is sqrt(3) u M_a M_d M_d / norm.  Offset=0 at origin
+  Then minnorm = 1.8 u M_a M_d M_d / qh.ONEmerge
+  Note that qh.one_merge is approx. 45.5 u M_a and norm is usually about M_d M_d
+
+  derivation of 4-d minnorm
+  same as above except rotate the facet so that V_1 on x-axis and w_2, y_3, w_3=0
+  [if two vertices fixed on x-axis, can rotate the other two in yzw.]
+  n_0 = det3_(...) = y_2 det2_(z_1, w_1, z_3, w_3) = - y_2 w_1 z_3
+  [all other terms contain at least two factors nearly zero.]
+  The max error for n_0 is sqrt(4) u M_a M_d M_d / norm
+  Then minnorm = 2 u M_a M_d M_d M_d / qh.ONEmerge
+  Note that qh.one_merge is approx. 82 u M_a and norm is usually about M_d M_d M_d
+*/
+void qh_sethyperplane_det(int dim, coordT * *rows, coordT *point0,
+                          boolT toporient, coordT *normal, realT *offset, boolT *nearzero)
+{
+  realT   maxround, dist;
+  int     i;
+  pointT *point;
+
+  if( dim == 2 )
+    {
+    normal[0] = dY(1, 0);
+    normal[1] = dX(0, 1);
+    qh_normalize2(normal, dim, toporient, NULL, NULL);
+    *offset = -(point0[0] * normal[0] + point0[1] * normal[1]);
+    *nearzero = False;  /* since nearzero norm => incident points */
+    }
+  else if( dim == 3 )
+    {
+    normal[0] = det2_(dY(2, 0), dZ(2, 0),
+                      dY(1, 0), dZ(1, 0) );
+    normal[1] = det2_(dX(1, 0), dZ(1, 0),
+                      dX(2, 0), dZ(2, 0) );
+    normal[2] = det2_(dX(2, 0), dY(2, 0),
+                      dX(1, 0), dY(1, 0) );
+    qh_normalize2(normal, dim, toporient, NULL, NULL);
+    *offset = -(point0[0] * normal[0] + point0[1] * normal[1]
+                + point0[2] * normal[2]);
+    maxround = qh DISTround;
+    for( i = dim; i--; )
+      {
+      point = rows[i];
+      if( point != point0 )
+        {
+        dist = *offset + (point[0] * normal[0] + point[1] * normal[1]
+                          + point[2] * normal[2]);
+        if( dist > maxround || dist < -maxround )
+          {
+          *nearzero = True;
+          break;
+          }
+        }
+      }
+    }
+  else if( dim == 4 )
+    {
+    normal[0] = -det3_(dY(2, 0), dZ(2, 0), dW(2, 0),
+                       dY(1, 0), dZ(1, 0), dW(1, 0),
+                       dY(3, 0), dZ(3, 0), dW(3, 0) );
+    normal[1] =   det3_(dX(2, 0), dZ(2, 0), dW(2, 0),
+                        dX(1, 0), dZ(1, 0), dW(1, 0),
+                        dX(3, 0), dZ(3, 0), dW(3, 0) );
+    normal[2] = -det3_(dX(2, 0), dY(2, 0), dW(2, 0),
+                       dX(1, 0), dY(1, 0), dW(1, 0),
+                       dX(3, 0), dY(3, 0), dW(3, 0) );
+    normal[3] =   det3_(dX(2, 0), dY(2, 0), dZ(2, 0),
+                        dX(1, 0), dY(1, 0), dZ(1, 0),
+                        dX(3, 0), dY(3, 0), dZ(3, 0) );
+    qh_normalize2(normal, dim, toporient, NULL, NULL);
+    *offset = -(point0[0] * normal[0] + point0[1] * normal[1]
+                + point0[2] * normal[2] + point0[3] * normal[3]);
+    maxround = qh DISTround;
+    for( i = dim; i--; )
+      {
+      point = rows[i];
+      if( point != point0 )
+        {
+        dist = *offset + (point[0] * normal[0] + point[1] * normal[1]
+                          + point[2] * normal[2] + point[3] * normal[3]);
+        if( dist > maxround || dist < -maxround )
+          {
+          *nearzero = True;
+          break;
+          }
+        }
+      }
+    }
+  if( *nearzero )
+    {
+    zzinc_(Zminnorm);
+    trace0( (qh ferr, "qh_sethyperplane_det: degenerate norm during p%d.\n", qh furthest_id) );
+    zzinc_(Znearlysingular);
+    }
+} /* sethyperplane_det */
+
+/*---------------------------------
+
+  qh_sethyperplane_gauss( dim, rows, point0, toporient, normal, offset, nearzero )
+  given (dim-1) X dim array of rows[i]= V_{i+1} - V_0 (point0)
+  set normalized hyperplane equation from oriented simplex
+
+  returns:
+  normal (normalized)
+  offset (places point0 on the hyperplane)
+
+  notes:
+  if nearzero
+  orientation may be incorrect because of incorrect sign flips in gausselim
+  solves [V_n-V_0,...,V_1-V_0, 0 .. 0 1] * N == [0 .. 0 1]
+  or [V_n-V_0,...,V_1-V_0, 0 .. 0 1] * N == [0]
+  i.e., N is normal to the hyperplane, and the unnormalized
+  distance to [0 .. 1] is either 1 or   0
+
+  design:
+  perform gaussian elimination
+  flip sign for negative values
+  perform back substitution
+  normalize result
+  compute offset
+*/
+void qh_sethyperplane_gauss(int dim, coordT * *rows, pointT *point0,
+                            boolT toporient, coordT *normal, coordT *offset, boolT *nearzero)
+{
+  coordT *pointcoord, *normalcoef;
+  int     k;
+  boolT   sign = toporient, nearzero2 = False;
+
+  qh_gausselim(rows, dim - 1, dim, &sign, nearzero);
+  for( k = dim - 1; k--; )
+    {
+    if( (rows[k])[k] < 0 )
+      {
+      sign ^= 1;
+      }
+    }
+  if( *nearzero )
+    {
+    zzinc_(Znearlysingular);
+    trace0( (qh ferr, "qh_sethyperplane_gauss: nearly singular or axis parallel hyperplane during p%d.\n",
+             qh furthest_id) );
+    qh_backnormal(rows, dim - 1, dim, sign, normal, &nearzero2);
+    }
+  else
+    {
+    qh_backnormal(rows, dim - 1, dim, sign, normal, &nearzero2);
+    if( nearzero2 )
+      {
+      zzinc_(Znearlysingular);
+      trace0( (qh ferr, "qh_sethyperplane_gauss: singular or axis parallel hyperplane at normalization during p%d.\n",
+               qh furthest_id) );
+      }
+    }
+  if( nearzero2 )
+    {
+    *nearzero = True;
+    }
+  qh_normalize2(normal, dim, True, NULL, NULL);
+  pointcoord = point0;
+  normalcoef = normal;
+  *offset = -(*pointcoord++ **normalcoef++);
+  for( k = dim - 1; k--; )
+    {
+    *offset -= *pointcoord++ **normalcoef++;
+    }
+} /* sethyperplane_gauss */
+
diff --git a/BRAINSABC/qhull/geom.h b/BRAINSABC/qhull/geom.h
new file mode 100644
index 00000000..45c213f9
--- /dev/null
+++ b/BRAINSABC/qhull/geom.h
@@ -0,0 +1,225 @@
+/*
  ---------------------------------
+
+  geom.h
+    header file for geometric routines
+
+   see qh-geom.htm and geom.c
+
+   copyright (c) 1993-2003 The Geometry Center
+*/
+
+#ifndef qhDEFgeom
+#define qhDEFgeom 1
+
+/* ============ -macros- ======================== */
+
+/*----------------------------------
+
+  fabs_(a)
+    returns the absolute value of a
+*/
+#define fabs_( a ) ( ( ( a ) < 0 ) ? -( a ) : ( a ) )
+
+/*----------------------------------
+
+  fmax_(a,b)
+    returns the maximum value of a and b
+*/
+#define fmax_( a, b )  ( ( a ) < ( b ) ? ( b ) : ( a ) )
+
+/*----------------------------------
+
+  fmin_(a,b)
+    returns the minimum value of a and b
+*/
+#define fmin_( a, b )  ( ( a ) > ( b ) ? ( b ) : ( a ) )
+
+/*----------------------------------
+
+  maximize_(maxval, val)
+    set maxval to val if val is greater than maxval
+*/
+#define maximize_( maxval, val ) {if( ( maxval ) < ( val ) ) {( maxval ) = ( val ); }}
+
+/*----------------------------------
+
+  minimize_(minval, val)
+    set minval to val if val is less than minval
+*/
+#define minimize_( minval, val ) {if( ( minval ) > ( val ) ) {( minval ) = ( val ); }}
+
+/*----------------------------------
+
+  det2_(a1, a2,
+        b1, b2)
+
+    compute a 2-d determinate
+*/
+#define det2_( a1, a2, b1, b2 ) ( ( a1 ) * ( b2 ) - ( a2 ) * ( b1 ) )
+
+/*----------------------------------
+
+  det3_(a1, a2, a3,
+       b1, b2, b3,
+       c1, c2, c3)
+
+    compute a 3-d determinate
+*/
+#define det3_( a1, a2, a3, b1, b2, b3, c1, c2, c3 )                     \
+  ( ( a1 ) * det2_( b2, b3, c2, c3 )                                    \
+    - ( b1 ) * det2_( a2, a3, c2, c3 ) + ( c1 ) * det2_( a2, a3, b2, b3 ) )
+
+/*----------------------------------
+
+  dX( p1, p2 )
+  dY( p1, p2 )
+  dZ( p1, p2 )
+
+    given two indices into rows[],
+
+    compute the difference between X, Y, or Z coordinates
+*/
+#define dX( p1, p2 )  ( *( rows[p1] ) - *( rows[p2] ) )
+#define dY( p1, p2 )  ( *( rows[p1] + 1 ) - *( rows[p2] + 1 ) )
+#define dZ( p1, p2 )  ( *( rows[p1] + 2 ) - *( rows[p2] + 2 ) )
+#define dW( p1, p2 )  ( *( rows[p1] + 3 ) - *( rows[p2] + 3 ) )
+
+/*============= prototypes in alphabetical order, infrequent at end ======= */
+
+void    qh_backnormal(realT * *rows, int numrow, int numcol, boolT sign, coordT *normal, boolT *nearzero);
+
+void  qh_distplane(pointT *point, facetT *facet, realT *dist);
+
+facetT * qh_findbest(pointT *point, facetT *startfacet, boolT bestoutside, boolT isnewfacets, boolT noupper,
+                     realT *dist, boolT *isoutside,
+                     int *numpart);
+
+facetT * qh_findbesthorizon(boolT ischeckmax, pointT *point, facetT *startfacet, boolT noupper, realT *bestdist,
+                            int *numpart);
+
+facetT * qh_findbestnew(pointT *point, facetT *startfacet, realT *dist, boolT bestoutside, boolT *isoutside,
+                        int *numpart);
+
+void  qh_gausselim(realT * *rows, int numrow, int numcol, boolT *sign, boolT *nearzero);
+
+realT   qh_getangle(pointT *vect1, pointT *vect2);
+
+pointT * qh_getcenter(setT *vertices);
+
+pointT * qh_getcentrum(facetT *facet);
+
+realT   qh_getdistance(facetT *facet, facetT *neighbor, realT *mindist, realT *maxdist);
+
+void    qh_normalize(coordT *normal, int dim, boolT toporient);
+
+void    qh_normalize2(coordT *normal, int dim, boolT toporient, realT *minnorm, boolT *ismin);
+
+pointT * qh_projectpoint(pointT *point, facetT *facet, realT dist);
+
+void    qh_setfacetplane(facetT *newfacets);
+
+void  qh_sethyperplane_det(int dim, coordT * *rows, coordT *point0, boolT toporient, coordT *normal, realT *offset,
+                           boolT *nearzero);
+
+void  qh_sethyperplane_gauss(int dim, coordT * *rows, pointT *point0, boolT toporient, coordT *normal, coordT *offset,
+                             boolT *nearzero);
+
+boolT   qh_sharpnewfacets(void);
+
+/*========= infrequently used code in geom2.c =============*/
+
+coordT * qh_copypoints(coordT *points, int numpoints, int dimension);
+
+void qh_crossproduct(int dim, realT vecA[3], realT vecB[3], realT vecC[3]);
+realT   qh_determinant(realT * *rows, int dim, boolT *nearzero);
+
+realT   qh_detjoggle(pointT *points, int numpoints, int dimension);
+
+void    qh_detroundoff(void);
+
+realT   qh_detsimplex(pointT *apex, setT *points, int dim, boolT *nearzero);
+
+realT   qh_distnorm(int dim, pointT *point, pointT *normal, realT *offsetp);
+
+realT   qh_distround(int dimension, realT maxabs, realT maxsumabs);
+
+realT   qh_divzero(realT numer, realT denom, realT mindenom1, boolT *zerodiv);
+
+realT   qh_facetarea(facetT *facet);
+
+realT   qh_facetarea_simplex(int dim, coordT *apex, setT *vertices, vertexT *notvertex,  boolT toporient,
+                             coordT *normal,
+                             realT *offset);
+
+pointT * qh_facetcenter(setT *vertices);
+
+facetT * qh_findgooddist(pointT *point, facetT *facetA, realT *distp, facetT * *facetlist);
+
+void    qh_getarea(facetT *facetlist);
+
+boolT   qh_gram_schmidt(int dim, realT * *rows);
+
+boolT   qh_inthresholds(coordT *normal, realT *angle);
+
+void    qh_joggleinput(void);
+
+realT  * qh_maxabsval(realT *normal, int dim);
+
+setT   * qh_maxmin(pointT *points, int numpoints, int dimension);
+
+realT   qh_maxouter(void);
+
+void    qh_maxsimplex(int dim, setT *maxpoints, pointT *points, int numpoints, setT * *simplex);
+
+realT   qh_minabsval(realT *normal, int dim);
+
+int     qh_mindiff(realT *vecA, realT *vecB, int dim);
+
+boolT   qh_orientoutside(facetT *facet);
+
+void    qh_outerinner(facetT *facet, realT *outerplane, realT *innerplane);
+
+coordT  qh_pointdist(pointT *point1, pointT *point2, int dim);
+
+void    qh_printmatrix(FILE *fp, const char *string, realT * *rows, int numrow, int numcol);
+
+void    qh_printpoints(FILE *fp, const char *string, setT *points);
+
+void    qh_projectinput(void);
+
+void  qh_projectpoints(signed char *project, int n, realT *points, int numpoints, int dim, realT *newpoints, int newdim);
+
+int     qh_rand( void);
+
+void    qh_srand( int seed);
+
+realT   qh_randomfactor(void);
+
+void    qh_randommatrix(realT *buffer, int dim, realT * *row);
+
+void    qh_rotateinput(realT * *rows);
+
+void    qh_rotatepoints(realT *points, int numpoints, int dim, realT * *rows);
+
+void    qh_scaleinput(void);
+
+void    qh_scalelast(coordT *points, int numpoints, int dim, coordT low, coordT high, coordT newhigh);
+
+void  qh_scalepoints(pointT *points, int numpoints, int dim, realT *newlows, realT *newhighs);
+
+boolT   qh_sethalfspace(int dim, coordT *coords, coordT * *nextp, coordT *normal, coordT *offset, coordT *feasible);
+
+coordT * qh_sethalfspace_all(int dim, int count, coordT *halfspaces, pointT *feasible);
+
+pointT * qh_voronoi_center(int dim, setT *points);
+
+#endif /* qhDEFgeom */
diff --git a/BRAINSABC/qhull/geom2.c b/BRAINSABC/qhull/geom2.c
new file mode 100644
index 00000000..3bfa678c
--- /dev/null
+++ b/BRAINSABC/qhull/geom2.c
@@ -0,0 +1,2600 @@
+/*
  ---------------------------------
+
+
+  geom2.c
+  infrequently used geometric routines of qhull
+
+  see qh-geom.htm and geom.h
+
+  copyright (c) 1993-2003 The Geometry Center
+
+  frequently used code goes into geom.c
+*/
+
+#include "qhull_a.h"
+
+/*================== functions in alphabetic order ============*/
+
+/*---------------------------------
+
+  qh_copypoints( points, numpoints, dimension)
+  return malloc'd copy of points
+*/
+coordT * qh_copypoints(coordT *points, int numpoints, int dimension)
+{
+  size_t  size;
+  coordT *newpoints;
+
+  size = numpoints * dimension * sizeof(coordT);
+  if( !(newpoints = (coordT *)malloc(size) ) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory to copy %d points\n",
+            numpoints);
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  memcpy( (char *)newpoints, (char *)points, size);
+  return newpoints;
+} /* copypoints */
+
+/*---------------------------------
+
+  qh_crossproduct( dim, vecA, vecB, vecC )
+  crossproduct of 2 dim vectors
+  C= A x B
+
+  notes:
+  from Glasner, Graphics Gems I, p. 639
+  only defined for dim==3
+*/
+void qh_crossproduct(int dim, realT vecA[3], realT vecB[3], realT vecC[3])
+{
+
+  if( dim == 3 )
+    {
+    vecC[0] =   det2_(vecA[1], vecA[2],
+                      vecB[1], vecB[2]);
+    vecC[1] = -det2_(vecA[0], vecA[2],
+                     vecB[0], vecB[2]);
+    vecC[2] =   det2_(vecA[0], vecA[1],
+                      vecB[0], vecB[1]);
+    }
+} /* vcross */
+
+/*---------------------------------
+
+  qh_determinant( rows, dim, nearzero )
+  compute signed determinant of a square matrix
+  uses qh.NEARzero to test for degenerate matrices
+
+  returns:
+  determinant
+  overwrites rows and the matrix
+  if dim == 2 or 3
+  nearzero iff determinant < qh NEARzero[dim-1]
+  (not quite correct, not critical)
+  if dim >= 4
+  nearzero iff diagonal[k] < qh NEARzero[k]
+*/
+realT qh_determinant(realT * *rows, int dim, boolT *nearzero)
+{
+  realT det = 0;
+  int   i;
+  boolT sign = False;
+
+  *nearzero = False;
+  if( dim < 2 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_determinate): only implemented for dimension >= 2\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  else if( dim == 2 )
+    {
+    det = det2_(rows[0][0], rows[0][1],
+                rows[1][0], rows[1][1]);
+    if( fabs_(det) < qh NEARzero[1] )  /* not really correct, what should this
+                                         be? */
+      {
+      *nearzero = True;
+      }
+    }
+  else if( dim == 3 )
+    {
+    det = det3_(rows[0][0], rows[0][1], rows[0][2],
+                rows[1][0], rows[1][1], rows[1][2],
+                rows[2][0], rows[2][1], rows[2][2]);
+    if( fabs_(det) < qh NEARzero[2] )  /* not really correct, what should this
+                                         be? */
+      {
+      *nearzero = True;
+      }
+    }
+  else
+    {
+    qh_gausselim(rows, dim, dim, &sign, nearzero);  /* if nearzero, diagonal
+                                                      still ok*/
+    det = 1.0;
+    for( i = dim; i--; )
+      {
+      det *= (rows[i])[i];
+      }
+    if( sign )
+      {
+      det = -det;
+      }
+    }
+  return det;
+} /* determinant */
+
+/*---------------------------------
+
+  qh_detjoggle( points, numpoints, dimension )
+  determine default max joggle for point array
+  as qh_distround * qh_JOGGLEdefault
+
+  returns:
+  initial value for JOGGLEmax from points and REALepsilon
+
+  notes:
+  computes DISTround since qh_maxmin not called yet
+  if qh SCALElast, last dimension will be scaled later to MAXwidth
+
+  loop duplicated from qh_maxmin
+*/
+realT qh_detjoggle(pointT *points, int numpoints, int dimension)
+{
+  realT   abscoord, distround, joggle, maxcoord, mincoord;
+  pointT *point, *pointtemp;
+  realT   maxabs = -REALmax;
+  realT   sumabs = 0;
+  realT   maxwidth = 0;
+  int     k;
+  for( k = 0; k < dimension; k++ )
+    {
+    if( qh SCALElast && k == dimension - 1 )
+      {
+      abscoord = maxwidth;
+      }
+    else if( qh DELAUNAY && k == dimension - 1 ) /* will qh_setdelaunay() */
+      {
+      abscoord = 2 * maxabs * maxabs;  /* may be low by qh hull_dim/2 */
+      }
+    else
+      {
+      maxcoord = -REALmax;
+      mincoord = REALmax;
+      FORALLpoint_(points, numpoints) {
+        maximize_(maxcoord, point[k]);
+        minimize_(mincoord, point[k]);
+        }
+      maximize_(maxwidth, maxcoord - mincoord);
+      abscoord = fmax_(maxcoord, -mincoord);
+      }
+    sumabs += abscoord;
+    maximize_(maxabs, abscoord);
+    } /* for k */
+  distround = qh_distround(qh hull_dim, maxabs, sumabs);
+  joggle = distround * qh_JOGGLEdefault;
+  maximize_(joggle, REALepsilon * qh_JOGGLEdefault);
+  trace2( (qh ferr, "qh_detjoggle: joggle=%2.2g maxwidth=%2.2g\n", joggle, maxwidth) );
+  return joggle;
+} /* detjoggle */
+
+/*---------------------------------
+
+  qh_detroundoff()
+  determine maximum roundoff errors from
+  REALepsilon, REALmax, REALmin, qh.hull_dim, qh.MAXabs_coord,
+  qh.MAXsumcoord, qh.MAXwidth, qh.MINdenom_1
+
+  accounts for qh.SETroundoff, qh.RANDOMdist, qh MERGEexact
+  qh.premerge_cos, qh.postmerge_cos, qh.premerge_centrum,
+  qh.postmerge_centrum, qh.MINoutside,
+  qh_RATIOnearinside, qh_COPLANARratio, qh_WIDEcoplanar
+
+  returns:
+  sets qh.DISTround, etc. (see below)
+  appends precision constants to qh.qhull_options
+
+  see:
+  qh_maxmin() for qh.NEARzero
+
+  design:
+  determine qh.DISTround for distance computations
+  determine minimum denominators for qh_divzero
+  determine qh.ANGLEround for angle computations
+  adjust qh.premerge_cos,... for roundoff error
+  determine qh.ONEmerge for maximum error due to a single merge
+  determine qh.NEARinside, qh.MAXcoplanar, qh.MINvisible,
+  qh.MINoutside, qh.WIDEfacet
+  initialize qh.max_vertex and qh.minvertex
+*/
+void qh_detroundoff(void)
+{
+
+  qh_option("_max-width", NULL, &qh MAXwidth);
+  if( !qh SETroundoff )
+    {
+    qh DISTround = qh_distround(qh hull_dim, qh MAXabs_coord, qh MAXsumcoord);
+    if( qh RANDOMdist )
+      {
+      qh DISTround += qh RANDOMfactor * qh MAXabs_coord;
+      }
+    qh_option("Error-roundoff", NULL, &qh DISTround);
+    }
+  qh MINdenom = qh MINdenom_1 * qh MAXabs_coord;
+  qh MINdenom_1_2 = sqrt(qh MINdenom_1 * qh hull_dim);   /* if will be
+                                                           normalized */
+  qh MINdenom_2 = qh MINdenom_1_2 * qh MAXabs_coord;
+  /* for inner product */
+  qh ANGLEround = 1.01 * qh hull_dim * REALepsilon;
+  if( qh RANDOMdist )
+    {
+    qh ANGLEround += qh RANDOMfactor;
+    }
+  if( qh premerge_cos < REALmax / 2 )
+    {
+    qh premerge_cos -= qh ANGLEround;
+    if( qh RANDOMdist )
+      {
+      qh_option("Angle-premerge-with-random", NULL, &qh premerge_cos);
+      }
+    }
+  if( qh postmerge_cos < REALmax / 2 )
+    {
+    qh postmerge_cos -= qh ANGLEround;
+    if( qh RANDOMdist )
+      {
+      qh_option("Angle-postmerge-with-random", NULL, &qh postmerge_cos);
+      }
+    }
+  qh premerge_centrum += 2 * qh DISTround;    /*2 for centrum and distplane()*/
+  qh postmerge_centrum += 2 * qh DISTround;
+  if( qh RANDOMdist && (qh MERGEexact || qh PREmerge) )
+    {
+    qh_option("Centrum-premerge-with-random", NULL, &qh premerge_centrum);
+    }
+  if( qh RANDOMdist && qh POSTmerge )
+    {
+    qh_option("Centrum-postmerge-with-random", NULL, &qh postmerge_centrum);
+    }
+    { /* compute ONEmerge, max vertex offset for merging simplicial facets */
+    realT maxangle = 1.0, maxrho;
+
+    minimize_(maxangle, qh premerge_cos);
+    minimize_(maxangle, qh postmerge_cos);
+    /* max diameter * sin theta + DISTround for vertex to its hyperplane */
+    qh ONEmerge = sqrt( (double)qh hull_dim) * qh MAXwidth
+      * sqrt(1.0 - maxangle * maxangle) + qh DISTround;
+    maxrho = qh hull_dim * qh premerge_centrum + qh DISTround;
+    maximize_(qh ONEmerge, maxrho);
+    maxrho = qh hull_dim * qh postmerge_centrum + qh DISTround;
+    maximize_(qh ONEmerge, maxrho);
+    if( qh MERGING )
+      {
+      qh_option("_one-merge", NULL, &qh ONEmerge);
+      }
+    }
+  qh NEARinside = qh ONEmerge * qh_RATIOnearinside; /* only used if qh
+                                                      KEEPnearinside */
+  if( qh JOGGLEmax < REALmax / 2 && (qh KEEPcoplanar || qh KEEPinside) )
+    {
+    realT maxdist;         /* adjust qh.NEARinside for joggle */
+    qh    KEEPnearinside = True;
+    maxdist = sqrt( (double)qh hull_dim) * qh JOGGLEmax + qh DISTround;
+    maxdist = 2 * maxdist;             /* vertex and coplanar point can joggle
+                                         in opposite directions */
+    maximize_(qh NEARinside, maxdist); /* must agree with qh_nearcoplanar() */
+    }
+  if( qh KEEPnearinside )
+    {
+    qh_option("_near-inside", NULL, &qh NEARinside);
+    }
+  if( qh JOGGLEmax < qh DISTround )
+    {
+    fprintf(qh ferr, "qhull error: the joggle for 'QJn', %.2g, is below roundoff for distance computations, %.2g\n",
+            qh JOGGLEmax, qh DISTround);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh MINvisible > REALmax / 2 )
+    {
+    if( !qh MERGING )
+      {
+      qh MINvisible = qh DISTround;
+      }
+    else if( qh hull_dim <= 3 )
+      {
+      qh MINvisible = qh premerge_centrum;
+      }
+    else
+      {
+      qh MINvisible = qh_COPLANARratio * qh premerge_centrum;
+      }
+    if( qh APPROXhull && qh MINvisible > qh MINoutside )
+      {
+      qh MINvisible = qh MINoutside;
+      }
+    qh_option("Visible-distance", NULL, &qh MINvisible);
+    }
+  if( qh MAXcoplanar > REALmax / 2 )
+    {
+    qh MAXcoplanar = qh MINvisible;
+    qh_option("U-coplanar-distance", NULL, &qh MAXcoplanar);
+    }
+  if( !qh APPROXhull )               /* user may specify qh MINoutside */
+    {
+    qh MINoutside = 2 * qh MINvisible;
+    if( qh premerge_cos < REALmax / 2 )
+      {
+      maximize_(qh MINoutside, (1 - qh premerge_cos) * qh MAXabs_coord);
+      }
+    qh_option("Width-outside", NULL, &qh MINoutside);
+    }
+  qh WIDEfacet = qh MINoutside;
+  maximize_(qh WIDEfacet, qh_WIDEcoplanar * qh MAXcoplanar);
+  maximize_(qh WIDEfacet, qh_WIDEcoplanar * qh MINvisible);
+  qh_option("_wide-facet", NULL, &qh WIDEfacet);
+  if( qh MINvisible > qh MINoutside + 3 * REALepsilon
+      && !qh BESToutside && !qh FORCEoutput )
+    {
+    fprintf(
+      qh ferr,
+      "qhull input warning: minimum visibility V%.2g is greater than \nminimum outside W%.2g.  Flipped facets are likely.\n",
+      qh MINvisible, qh MINoutside);
+    }
+  qh max_vertex = qh DISTround;
+  qh min_vertex = -qh DISTround;
+  /* numeric constants reported in printsummary */
+} /* detroundoff */
+
+/*---------------------------------
+
+  qh_detsimplex( apex, points, dim, nearzero )
+  compute determinant of a simplex with point apex and base points
+
+  returns:
+  signed determinant and nearzero from qh_determinant
+
+  notes:
+  uses qh.gm_matrix/qh.gm_row (assumes they're big enough)
+
+  design:
+  construct qm_matrix by subtracting apex from points
+  compute determinate
+*/
+realT qh_detsimplex(pointT *apex, setT *points, int dim, boolT *nearzero)
+{
+  pointT *  coorda, *coordp, *gmcoord, *point, * *pointp;
+  coordT * *rows;
+  int       k,  i = 0;
+  realT     det;
+
+  zinc_(Zdetsimplex);
+  gmcoord = qh gm_matrix;
+  rows = qh gm_row;
+  FOREACHpoint_(points) {
+    if( i == dim )
+      {
+      break;
+      }
+    rows[i++] = gmcoord;
+    coordp = point;
+    coorda = apex;
+    for( k = dim; k--; )
+      {
+      *(gmcoord++) = *coordp++ - *coorda++;
+      }
+    }
+  if( i < dim )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_detsimplex): #points %d < dimension %d\n",
+            i, dim);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  det = qh_determinant(rows, dim, nearzero);
+  trace2( (qh ferr, "qh_detsimplex: det=%2.2g for point p%d, dim %d, nearzero? %d\n",
+           det, qh_pointid(apex), dim, *nearzero) );
+  return det;
+} /* detsimplex */
+
+/*---------------------------------
+
+  qh_distnorm( dim, point, normal, offset )
+  return distance from point to hyperplane at normal/offset
+
+  returns:
+  dist
+
+  notes:
+  dist > 0 if point is outside of hyperplane
+
+  see:
+  qh_distplane in geom.c
+*/
+realT qh_distnorm(int dim, pointT *point, pointT *normal, realT *offsetp)
+{
+  coordT *normalp = normal, *coordp = point;
+  realT   dist;
+  int     k;
+
+  dist = *offsetp;
+  for( k = dim; k--; )
+    {
+    dist += *(coordp++) * *(normalp++);
+    }
+  return dist;
+} /* distnorm */
+
+/*---------------------------------
+
+  qh_distround ( dimension, maxabs, maxsumabs )
+  compute maximum round-off error for a distance computation
+  to a normalized hyperplane
+  maxabs is the maximum absolute value of a coordinate
+  maxsumabs is the maximum possible sum of absolute coordinate values
+
+  returns:
+  max dist round for REALepsilon
+
+  notes:
+  calculate roundoff error according to
+  Lemma 3.2-1 of Golub and van Loan "Matrix Computation"
+  use sqrt(dim) since one vector is normalized
+  or use maxsumabs since one vector is < 1
+*/
+realT qh_distround(int dimension, realT maxabs, realT maxsumabs)
+{
+  realT maxdistsum, maxround;
+
+  maxdistsum = sqrt( (double)dimension) * maxabs;
+  minimize_( maxdistsum, maxsumabs);
+  maxround = REALepsilon * (dimension * maxdistsum * 1.01 + maxabs);
+  /* adds maxabs for offset */
+  trace4( (qh ferr, "qh_distround: %2.2g maxabs %2.2g maxsumabs %2.2g maxdistsum %2.2g\n",
+           maxround, maxabs, maxsumabs, maxdistsum) );
+  return maxround;
+} /* distround */
+
+/*---------------------------------
+
+  qh_divzero( numer, denom, mindenom1, zerodiv )
+  divide by a number that's nearly zero
+  mindenom1= minimum denominator for dividing into 1.0
+
+  returns:
+  quotient
+  sets zerodiv and returns 0.0 if it would overflow
+
+  design:
+  if numer is nearly zero and abs(numer) < abs(denom)
+  return numer/denom
+  else if numer is nearly zero
+  return 0 and zerodiv
+  else if denom/numer non-zero
+  return numer/denom
+  else
+  return 0 and zerodiv
+*/
+realT qh_divzero(realT numer, realT denom, realT mindenom1, boolT *zerodiv)
+{
+  realT temp, numerx, denomx;
+
+  if( numer < mindenom1 && numer > -mindenom1 )
+    {
+    numerx = fabs_(numer);
+    denomx = fabs_(denom);
+    if( numerx < denomx )
+      {
+      *zerodiv = False;
+      return numer / denom;
+      }
+    else
+      {
+      *zerodiv = True;
+      return 0.0;
+      }
+    }
+  temp = denom / numer;
+  if( temp > mindenom1 || temp < -mindenom1 )
+    {
+    *zerodiv = False;
+    return numer / denom;
+    }
+  else
+    {
+    *zerodiv = True;
+    return 0.0;
+    }
+} /* divzero */
+
+/*---------------------------------
+
+  qh_facetarea( facet )
+  return area for a facet
+
+  notes:
+  if non-simplicial,
+  uses centrum to triangulate facet and sums the projected areas.
+  if (qh DELAUNAY),
+  computes projected area instead for last coordinate
+  assumes facet->normal exists
+  projecting tricoplanar facets to the hyperplane does not appear to make a difference
+
+  design:
+  if simplicial
+  compute area
+  else
+  for each ridge
+  compute area from centrum to ridge
+  negate area if upper Delaunay facet
+*/
+realT qh_facetarea(facetT *facet)
+{
+  vertexT *apex;
+  pointT * centrum;
+  realT    area = 0.0;
+  ridgeT * ridge, * *ridgep;
+
+  if( facet->simplicial )
+    {
+    apex = SETfirstt_(facet->vertices, vertexT);
+    area = qh_facetarea_simplex(qh hull_dim, apex->point, facet->vertices,
+                                apex, facet->toporient, facet->normal, &facet->offset);
+    }
+  else
+    {
+    if( qh CENTERtype == qh_AScentrum )
+      {
+      centrum = facet->center;
+      }
+    else
+      {
+      centrum = qh_getcentrum(facet);
+      }
+    FOREACHridge_(facet->ridges)
+    area += qh_facetarea_simplex(qh hull_dim, centrum, ridge->vertices,
+                                 NULL, (boolT)(ridge->top == facet),  facet->normal, &facet->offset);
+    if( qh CENTERtype != qh_AScentrum )
+      {
+      qh_memfree(centrum, qh normal_size);
+      }
+    }
+  if( facet->upperdelaunay && qh DELAUNAY )
+    {
+    area = -area;  /* the normal should be [0,...,1] */
+    }
+  trace4( (qh ferr, "qh_facetarea: f%d area %2.2g\n", facet->id, area) );
+  return area;
+} /* facetarea */
+
+/*---------------------------------
+
+  qh_facetarea_simplex( dim, apex, vertices, notvertex, toporient, normal, offset )
+  return area for a simplex defined by
+  an apex, a base of vertices, an orientation, and a unit normal
+  if simplicial or tricoplanar facet,
+  notvertex is defined and it is skipped in vertices
+
+  returns:
+  computes area of simplex projected to plane [normal,offset]
+  returns 0 if vertex too far below plane (qh WIDEfacet)
+  vertex can't be apex of tricoplanar facet
+
+  notes:
+  if (qh DELAUNAY),
+  computes projected area instead for last coordinate
+  uses qh gm_matrix/gm_row and qh hull_dim
+  helper function for qh_facetarea
+
+  design:
+  if Notvertex
+  translate simplex to apex
+  else
+  project simplex to normal/offset
+  translate simplex to apex
+  if Delaunay
+  set last row/column to 0 with -1 on diagonal
+  else
+  set last row to Normal
+  compute determinate
+  scale and flip sign for area
+*/
+realT qh_facetarea_simplex(int dim, coordT *apex, setT *vertices,
+                           vertexT *notvertex,  boolT toporient, coordT *normal, realT *offset)
+{
+  pointT *  coorda, *coordp, *gmcoord;
+  coordT * *rows, *normalp;
+  int       k,  i = 0;
+  realT     area, dist;
+  vertexT * vertex, * *vertexp;
+  boolT     nearzero;
+
+  gmcoord = qh gm_matrix;
+  rows = qh gm_row;
+  FOREACHvertex_(vertices) {
+    if( vertex == notvertex )
+      {
+      continue;
+      }
+    rows[i++] = gmcoord;
+    coorda = apex;
+    coordp = vertex->point;
+    normalp = normal;
+    if( notvertex )
+      {
+      for( k = dim; k--; )
+        {
+        *(gmcoord++) = *coordp++ - *coorda++;
+        }
+      }
+    else
+      {
+      dist = *offset;
+      for( k = dim; k--; )
+        {
+        dist += *coordp++ **normalp++;
+        }
+      if( dist < -qh WIDEfacet )
+        {
+        zinc_(Znoarea);
+        return 0.0;
+        }
+      coordp = vertex->point;
+      normalp = normal;
+      for( k = dim; k--; )
+        {
+        *(gmcoord++) = (*coordp++ - dist * *normalp++) - *coorda++;
+        }
+      }
+    }
+  if( i != dim - 1 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_facetarea_simplex): #points %d != dim %d -1\n",
+            i, dim);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  rows[i] = gmcoord;
+  if( qh DELAUNAY )
+    {
+    for( i = 0; i < dim - 1; i++ )
+      {
+      rows[i][dim - 1] = 0.0;
+      }
+    for( k = dim; k--; )
+      {
+      *(gmcoord++) = 0.0;
+      }
+    rows[dim - 1][dim - 1] = -1.0;
+    }
+  else
+    {
+    normalp = normal;
+    for( k = dim; k--; )
+      {
+      *(gmcoord++) = *normalp++;
+      }
+    }
+  zinc_(Zdetsimplex);
+  area = qh_determinant(rows, dim, &nearzero);
+  if( toporient )
+    {
+    area = -area;
+    }
+  area *= qh AREAfactor;
+  trace4( (qh ferr, "qh_facetarea_simplex: area=%2.2g for point p%d, toporient %d, nearzero? %d\n",
+           area, qh_pointid(apex), toporient, nearzero) );
+  return area;
+} /* facetarea_simplex */
+
+/*---------------------------------
+
+  qh_facetcenter( vertices )
+  return Voronoi center (Voronoi vertex) for a facet's vertices
+
+  returns:
+  return temporary point equal to the center
+
+  see:
+  qh_voronoi_center()
+*/
+pointT * qh_facetcenter(setT *vertices)
+{
+  setT *   points = qh_settemp(qh_setsize(vertices) );
+  vertexT *vertex, * *vertexp;
+  pointT * center;
+
+  FOREACHvertex_(vertices)
+  qh_setappend(&points, vertex->point);
+  center = qh_voronoi_center(qh hull_dim - 1, points);
+  qh_settempfree(&points);
+  return center;
+} /* facetcenter */
+
+/*---------------------------------
+
+  qh_findgooddist( point, facetA, dist, facetlist )
+  find best good facet visible for point from facetA
+  assumes facetA is visible from point
+
+  returns:
+  best facet, i.e., good facet that is furthest from point
+  distance to best facet
+  NULL if none
+
+  moves good, visible facets (and some other visible facets)
+  to end of qh facet_list
+
+  notes:
+  uses qh visit_id
+
+  design:
+  initialize bestfacet if facetA is good
+  move facetA to end of facetlist
+  for each facet on facetlist
+  for each unvisited neighbor of facet
+  move visible neighbors to end of facetlist
+  update best good neighbor
+  if no good neighbors, update best facet
+*/
+facetT * qh_findgooddist(pointT *point, facetT *facetA, realT *distp,
+                         facetT * *facetlist)
+{
+  realT   bestdist = -REALmax, dist;
+  facetT *neighbor, * *neighborp, *bestfacet = NULL, *facet;
+  boolT   goodseen = False;
+
+  if( facetA->good )
+    {
+    zinc_(Zcheckpart);  /* calls from check_bestdist occur after print stats */
+    qh_distplane(point, facetA, &bestdist);
+    bestfacet = facetA;
+    goodseen = True;
+    }
+  qh_removefacet(facetA);
+  qh_appendfacet(facetA);
+  *facetlist = facetA;
+  facetA->visitid = ++qh visit_id;
+  FORALLfacet_(*facetlist) {
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid == qh visit_id )
+        {
+        continue;
+        }
+      neighbor->visitid = qh visit_id;
+      if( goodseen && !neighbor->good )
+        {
+        continue;
+        }
+      zinc_(Zcheckpart);
+      qh_distplane(point, neighbor, &dist);
+      if( dist > 0 )
+        {
+        qh_removefacet(neighbor);
+        qh_appendfacet(neighbor);
+        if( neighbor->good )
+          {
+          goodseen = True;
+          if( dist > bestdist )
+            {
+            bestdist = dist;
+            bestfacet = neighbor;
+            }
+          }
+        }
+      }
+    }
+  if( bestfacet )
+    {
+    *distp = bestdist;
+    trace2( (qh ferr, "qh_findgooddist: p%d is %2.2g above good facet f%d\n",
+             qh_pointid(point), bestdist, bestfacet->id) );
+    return bestfacet;
+    }
+  trace4( (qh ferr, "qh_findgooddist: no good facet for p%d above f%d\n",
+           qh_pointid(point), facetA->id) );
+  return NULL;
+}  /* findgooddist */
+
+/*---------------------------------
+
+  qh_getarea( facetlist )
+  set area of all facets in facetlist
+  collect statistics
+
+  returns:
+  sets qh totarea/totvol to total area and volume of convex hull
+  for Delaunay triangulation, computes projected area of the lower or upper hull
+  ignores upper hull if qh ATinfinity
+
+  notes:
+  could compute outer volume by expanding facet area by rays from interior
+  the following attempt at perpendicular projection underestimated badly:
+  qh.totoutvol += (-dist + facet->maxoutside + qh DISTround)
+  * area/ qh hull_dim;
+  design:
+  for each facet on facetlist
+  compute facet->area
+  update qh.totarea and qh.totvol
+*/
+void qh_getarea(facetT *facetlist)
+{
+  realT   area;
+  realT   dist;
+  facetT *facet;
+
+  if( qh REPORTfreq )
+    {
+    fprintf(qh ferr, "computing area of each facet and volume of the convex hull\n");
+    }
+  else
+    {
+    trace1( (qh ferr, "qh_getarea: computing volume and area for each facet\n") );
+    }
+  qh totarea = qh totvol = 0.0;
+  FORALLfacet_(facetlist) {
+    if( !facet->normal )
+      {
+      continue;
+      }
+    if( facet->upperdelaunay && qh ATinfinity )
+      {
+      continue;
+      }
+    facet->f.area = area = qh_facetarea(facet);
+    facet->isarea = True;
+    if( qh DELAUNAY )
+      {
+      if( facet->upperdelaunay == qh UPPERdelaunay )
+        {
+        qh totarea += area;
+        }
+      }
+    else
+      {
+      qh totarea += area;
+      qh_distplane(qh interior_point, facet, &dist);
+      qh totvol += -dist * area / qh hull_dim;
+      }
+    if( qh PRINTstatistics )
+      {
+      wadd_(Wareatot, area);
+      wmax_(Wareamax, area);
+      wmin_(Wareamin, area);
+      }
+    }
+} /* getarea */
+
+/*---------------------------------
+
+  qh_gram_schmidt( dim, row )
+  implements Gram-Schmidt orthogonalization by rows
+
+  returns:
+  false if zero norm
+  overwrites rows[dim][dim]
+
+  notes:
+  see Golub & van Loan Algorithm 6.2-2
+  overflow due to small divisors not handled
+
+  design:
+  for each row
+  compute norm for row
+  if non-zero, normalize row
+  for each remaining rowA
+  compute inner product of row and rowA
+  reduce rowA by row * inner product
+*/
+boolT qh_gram_schmidt(int dim, realT * *row)
+{
+  realT *rowi, *rowj, norm;
+  int    i, j, k;
+  for( i = 0; i < dim; i++ )
+    {
+    rowi = row[i];
+    for( norm = 0.0, k = dim; k--; rowi++ )
+      {
+      norm += *rowi * *rowi;
+      }
+    norm = sqrt(norm);
+    wmin_(Wmindenom, norm);
+    if( norm == 0.0 )  /* either 0 or overflow due to sqrt */
+      {
+      return False;
+      }
+    for( k = dim; k--; )
+      {
+      *(--rowi) /= norm;
+      }
+    for( j = i + 1; j < dim; j++ )
+      {
+      rowj = row[j];
+      for( norm = 0.0, k = dim; k--; )
+        {
+        norm += *rowi++ **rowj++;
+        }
+      for( k = dim; k--; )
+        {
+        *(--rowj) -= *(--rowi) * norm;
+        }
+      }
+    }
+  return True;
+} /* gram_schmidt */
+
+/*---------------------------------
+
+  qh_inthresholds( normal, angle )
+  return True if normal within qh.lower_/upper_threshold
+
+  returns:
+  estimate of angle by summing of threshold diffs
+  angle may be NULL
+  smaller "angle" is better
+
+  notes:
+  invalid if qh.SPLITthresholds
+
+  see:
+  qh.lower_threshold in qh_initbuild()
+  qh_initthresholds()
+
+  design:
+  for each dimension
+  test threshold
+*/
+boolT qh_inthresholds(coordT *normal, realT *angle)
+{
+  boolT within = True;
+  int   k;
+  realT threshold;
+
+  if( angle )
+    {
+    *angle = 0.0;
+    }
+  for( k = 0; k < qh hull_dim; k++ )
+    {
+    threshold = qh lower_threshold[k];
+    if( threshold > -REALmax / 2 )
+      {
+      if( normal[k] < threshold )
+        {
+        within = False;
+        }
+      if( angle )
+        {
+        threshold -= normal[k];
+        *angle += fabs_(threshold);
+        }
+      }
+    if( qh upper_threshold[k] < REALmax / 2 )
+      {
+      threshold = qh upper_threshold[k];
+      if( normal[k] > threshold )
+        {
+        within = False;
+        }
+      if( angle )
+        {
+        threshold -= normal[k];
+        *angle += fabs_(threshold);
+        }
+      }
+    }
+  return within;
+} /* inthresholds */
+
+/*---------------------------------
+
+  qh_joggleinput()
+  randomly joggle input to Qhull by qh.JOGGLEmax
+  initial input is qh.first_point/qh.num_points of qh.hull_dim
+  repeated calls use qh.input_points/qh.num_points
+
+  returns:
+  joggles points at qh.first_point/qh.num_points
+  copies data to qh.input_points/qh.input_malloc if first time
+  determines qh.JOGGLEmax if it was zero
+  if qh.DELAUNAY
+  computes the Delaunay projection of the joggled points
+
+  notes:
+  if qh.DELAUNAY, unnecessarily joggles the last coordinate
+  the initial 'QJn' may be set larger than qh_JOGGLEmaxincrease
+
+  design:
+  if qh.DELAUNAY
+  set qh.SCALElast for reduced precision errors
+  if first call
+  initialize qh.input_points to the original input points
+  if qh.JOGGLEmax == 0
+  determine default qh.JOGGLEmax
+  else
+  increase qh.JOGGLEmax according to qh.build_cnt
+  joggle the input by adding a random number in [-qh.JOGGLEmax,qh.JOGGLEmax]
+  if qh.DELAUNAY
+  sets the Delaunay projection
+*/
+void qh_joggleinput(void)
+{
+  size_t  size; int i, seed;
+  coordT *coordp, *inputp;
+  realT   randr, randa, randb;
+
+  if( !qh input_points )   /* first call */
+    {
+    qh input_points = qh first_point;
+    qh input_malloc = qh POINTSmalloc;
+    size = qh num_points * qh hull_dim * sizeof(coordT);
+    if( !(qh first_point = (coordT *)malloc(size) ) )
+      {
+      fprintf(qh ferr, "qhull error: insufficient memory to joggle %d points\n",
+              qh num_points);
+      qh_errexit(qh_ERRmem, NULL, NULL);
+      }
+    qh POINTSmalloc = True;
+    if( qh JOGGLEmax == 0.0 )
+      {
+      qh JOGGLEmax = qh_detjoggle(qh input_points, qh num_points, qh hull_dim);
+      qh_option("QJoggle", NULL, &qh JOGGLEmax);
+      }
+    }
+  else                    /* repeated call */
+    {
+    if( !qh RERUN && qh build_cnt > qh_JOGGLEretry )
+      {
+      if( ( (qh build_cnt - qh_JOGGLEretry - 1) % qh_JOGGLEagain) == 0 )
+        {
+        realT maxjoggle = qh MAXwidth * qh_JOGGLEmaxincrease;
+        if( qh JOGGLEmax < maxjoggle )
+          {
+          qh JOGGLEmax *= qh_JOGGLEincrease;
+          minimize_(qh JOGGLEmax, maxjoggle);
+          }
+        }
+      }
+    qh_option("QJoggle", NULL, &qh JOGGLEmax);
+    }
+  if( qh build_cnt > 1 && qh JOGGLEmax > fmax_(qh MAXwidth / 4, 0.1) )
+    {
+    fprintf(
+      qh ferr,
+      "qhull error: the current joggle for 'QJn', %.2g, is too large for the width\nof the input.  If possible, recompile Qhull with higher-precision reals.\n",
+      qh JOGGLEmax);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  /* for some reason, using qh ROTATErandom and qh_RANDOMseed does not repeat
+    the run. Use 'TRn' instead */
+  seed = qh_RANDOMint;
+  qh_option("_joggle-seed", &seed, NULL);
+  trace0( (qh ferr, "qh_joggleinput: joggle input by %2.2g with seed %d\n",
+           qh JOGGLEmax, seed) );
+  inputp = qh input_points;
+  coordp = qh first_point;
+  randa = 2.0 * qh JOGGLEmax / qh_RANDOMmax;
+  randb = -qh JOGGLEmax;
+  size = qh num_points * qh hull_dim;
+  for( i = size; i--; )
+    {
+    randr = qh_RANDOMint;
+    *(coordp++) = *(inputp++) + (randr * randa + randb);
+    }
+  if( qh DELAUNAY )
+    {
+    qh last_low = qh last_high = qh last_newhigh = REALmax;
+    qh_setdelaunay(qh hull_dim, qh num_points, qh first_point);
+    }
+} /* joggleinput */
+
+/*---------------------------------
+
+  qh_maxabsval( normal, dim )
+  return pointer to maximum absolute value of a dim vector
+  returns NULL if dim=0
+*/
+realT * qh_maxabsval(realT *normal, int dim)
+{
+  realT  maxval = -REALmax;
+  realT *maxp = NULL, *colp, absval;
+  int    k;
+  for( k = dim, colp = normal; k--; colp++ )
+    {
+    absval = fabs_(*colp);
+    if( absval > maxval )
+      {
+      maxval = absval;
+      maxp = colp;
+      }
+    }
+  return maxp;
+} /* maxabsval */
+
+/*---------------------------------
+
+  qh_maxmin( points, numpoints, dimension )
+  return max/min points for each dimension
+  determine max and min coordinates
+
+  returns:
+  returns a temporary set of max and min points
+  may include duplicate points. Does not include qh.GOODpoint
+  sets qh.NEARzero, qh.MAXabs_coord, qh.MAXsumcoord, qh.MAXwidth
+  qh.MAXlastcoord, qh.MINlastcoord
+  initializes qh.max_outside, qh.min_vertex, qh.WAScoplanar, qh.ZEROall_ok
+
+  notes:
+  loop duplicated in qh_detjoggle()
+
+  design:
+  initialize global precision variables
+  checks definition of REAL...
+  for each dimension
+  for each point
+  collect maximum and minimum point
+  collect maximum of maximums and minimum of minimums
+  determine qh.NEARzero for Gaussian Elimination
+*/
+setT * qh_maxmin(pointT *points, int numpoints, int dimension)
+{
+  int     k;
+  realT   maxcoord, temp;
+  pointT *minimum, *maximum, *point, *pointtemp;
+  setT *  set;
+
+  qh max_outside = 0.0;
+  qh MAXabs_coord = 0.0;
+  qh MAXwidth = -REALmax;
+  qh MAXsumcoord = 0.0;
+  qh min_vertex = 0.0;
+  qh WAScoplanar = False;
+
+  if( qh ZEROcentrum )
+    {
+    qh ZEROall_ok = True;
+    }
+  if( REALmin < REALepsilon && REALmin < REALmax && REALmin > -REALmax
+      && REALmax > 0.0 && -REALmax < 0.0 )
+    {
+    ; /* all ok */
+    }
+  else
+    {
+    fprintf(
+      qh ferr,
+      "qhull error: floating point constants in user.h are wrong\n\
+REALepsilon %g REALmin %g REALmax %g -REALmax %g\n"                                                                    ,
+      REALepsilon, REALmin, REALmax,
+      -REALmax);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  set = qh_settemp(2 * dimension);
+  for( k = 0; k < dimension; k++ )
+    {
+    if( points == qh GOODpointp )
+      {
+      minimum = maximum = points + dimension;
+      }
+    else
+      {
+      minimum = maximum = points;
+      }
+    FORALLpoint_(points, numpoints) {
+      if( point == qh GOODpointp )
+        {
+        continue;
+        }
+      if( maximum[k] < point[k] )
+        {
+        maximum = point;
+        }
+      else if( minimum[k] > point[k] )
+        {
+        minimum = point;
+        }
+      }
+    if( k == dimension - 1 )
+      {
+      qh MINlastcoord = minimum[k];
+      qh MAXlastcoord = maximum[k];
+      }
+    if( qh SCALElast && k == dimension - 1 )
+      {
+      maxcoord = qh MAXwidth;
+      }
+    else
+      {
+      maxcoord = fmax_(maximum[k], -minimum[k]);
+      if( qh GOODpointp )
+        {
+        temp = fmax_(qh GOODpointp[k], -qh GOODpointp[k]);
+        maximize_(maxcoord, temp);
+        }
+      temp = maximum[k] - minimum[k];
+      maximize_(qh MAXwidth, temp);
+      }
+    maximize_(qh MAXabs_coord, maxcoord);
+    qh MAXsumcoord += maxcoord;
+    qh_setappend(&set, maximum);
+    qh_setappend(&set, minimum);
+    /* calculation of qh NEARzero is based on error formula 4.4-13 of
+       Golub & van Loan, authors say n^3 can be ignored and 10 be used in
+       place of rho */
+    qh NEARzero[k] = 80 * qh MAXsumcoord * REALepsilon;
+    }
+  if( qh IStracing >= 1 )
+    {
+    qh_printpoints(qh ferr, "qh_maxmin: found the max and min points (by dim):", set);
+    }
+  return set;
+} /* maxmin */
+
+/*---------------------------------
+
+  qh_maxouter()
+  return maximum distance from facet to outer plane
+  normally this is qh.max_outside+qh.DISTround
+  does not include qh.JOGGLEmax
+
+  see:
+  qh_outerinner()
+
+  notes:
+  need to add another qh.DISTround if testing actual point with computation
+
+  for joggle:
+  qh_setfacetplane() updated qh.max_outer for Wnewvertexmax (max distance to vertex)
+  need to use Wnewvertexmax since could have a coplanar point for a high
+  facet that is replaced by a low facet
+  need to add qh.JOGGLEmax if testing input points
+*/
+realT qh_maxouter(void)
+{
+  realT dist;
+
+  dist = fmax_(qh max_outside, qh DISTround);
+  dist += qh DISTround;
+  trace4( (qh ferr, "qh_maxouter: max distance from facet to outer plane is %2.2g max_outside is %2.2g\n", dist,
+           qh max_outside) );
+  return dist;
+} /* maxouter */
+
+/*---------------------------------
+
+  qh_maxsimplex( dim, maxpoints, points, numpoints, simplex )
+  determines maximum simplex for a set of points
+  starts from points already in simplex
+  skips qh.GOODpointp (assumes that it isn't in maxpoints)
+
+  returns:
+  simplex with dim+1 points
+
+  notes:
+  assumes at least pointsneeded points in points
+  maximizes determinate for x,y,z,w, etc.
+  uses maxpoints as long as determinate is clearly non-zero
+
+  design:
+  initialize simplex with at least two points
+  (find points with max or min x coordinate)
+  for each remaining dimension
+  add point that maximizes the determinate
+  (use points from maxpoints first)
+*/
+void qh_maxsimplex(int dim, setT *maxpoints, pointT *points, int numpoints, setT * *simplex)
+{
+  pointT *point, * *pointp, *pointtemp, *maxpoint, *minx = NULL, *maxx = NULL;
+  boolT   nearzero, maxnearzero = False;
+  int     k, sizinit;
+  realT   maxdet = -REALmax, det, mincoord = REALmax, maxcoord = -REALmax;
+
+  sizinit = qh_setsize(*simplex);
+  if( sizinit < 2 )
+    {
+    if( qh_setsize(maxpoints) >= 2 )
+      {
+      FOREACHpoint_(maxpoints) {
+        if( maxcoord < point[0] )
+          {
+          maxcoord = point[0];
+          maxx = point;
+          }
+        if( mincoord > point[0] )
+          {
+          mincoord = point[0];
+          minx = point;
+          }
+        }
+      }
+    else
+      {
+      FORALLpoint_(points, numpoints) {
+        if( point == qh GOODpointp )
+          {
+          continue;
+          }
+        if( maxcoord < point[0] )
+          {
+          maxcoord = point[0];
+          maxx = point;
+          }
+        if( mincoord > point[0] )
+          {
+          mincoord = point[0];
+          minx = point;
+          }
+        }
+      }
+    qh_setunique(simplex, minx);
+    if( qh_setsize(*simplex) < 2 )
+      {
+      qh_setunique(simplex, maxx);
+      }
+    sizinit = qh_setsize(*simplex);
+    if( sizinit < 2 )
+      {
+      qh_precision("input has same x coordinate");
+      if( zzval_(Zsetplane) > qh hull_dim + 1 )
+        {
+        fprintf(qh ferr,
+                "qhull precision error (qh_maxsimplex for voronoi_center):\n%d points with the same x coordinate.\n",
+                qh_setsize(
+                  maxpoints) + numpoints);
+        qh_errexit(qh_ERRprec, NULL, NULL);
+        }
+      else
+        {
+        fprintf(qh ferr, "qhull input error: input is less than %d-dimensional since it has the same x coordinate\n",
+                qh hull_dim);
+        qh_errexit(qh_ERRinput, NULL, NULL);
+        }
+      }
+    }
+  for( k = sizinit; k < dim + 1; k++ )
+    {
+    maxpoint = NULL;
+    maxdet = -REALmax;
+    FOREACHpoint_(maxpoints) {
+      if( !qh_setin(*simplex, point) )
+        {
+        det = qh_detsimplex(point, *simplex, k, &nearzero);
+        if( (det = fabs_(det) ) > maxdet )
+          {
+          maxdet = det;
+          maxpoint = point;
+          maxnearzero = nearzero;
+          }
+        }
+      }
+    if( !maxpoint || maxnearzero )
+      {
+      zinc_(Zsearchpoints);
+      if( !maxpoint )
+        {
+        trace0( (qh ferr, "qh_maxsimplex: searching all points for %d-th initial vertex.\n", k + 1) );
+        }
+      else
+        {
+        trace0( (qh ferr, "qh_maxsimplex: searching all points for %d-th initial vertex, better than p%d det %2.2g\n",
+                 k + 1, qh_pointid(maxpoint), maxdet) );
+        }
+      FORALLpoint_(points, numpoints) {
+        if( point == qh GOODpointp )
+          {
+          continue;
+          }
+        if( !qh_setin(*simplex, point) )
+          {
+          det = qh_detsimplex(point, *simplex, k, &nearzero);
+          if( (det = fabs_(det) ) > maxdet )
+            {
+            maxdet = det;
+            maxpoint = point;
+            maxnearzero = nearzero;
+            }
+          }
+        }
+      } /* !maxpoint */
+    if( !maxpoint )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_maxsimplex): not enough points available\n");
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    qh_setappend(simplex, maxpoint);
+    trace1( (qh ferr, "qh_maxsimplex: selected point p%d for %d`th initial vertex, det=%2.2g\n",
+             qh_pointid(maxpoint), k + 1, maxdet) );
+    } /* k */
+}     /* maxsimplex */
+
+/*---------------------------------
+
+  qh_minabsval( normal, dim )
+  return minimum absolute value of a dim vector
+*/
+realT qh_minabsval(realT *normal, int dim)
+{
+  realT  minval = 0;
+  realT  maxval = 0;
+  realT *colp;
+  int    k;
+  for( k = dim, colp = normal; k--; colp++ )
+    {
+    maximize_(maxval, *colp);
+    minimize_(minval, *colp);
+    }
+  return fmax_(maxval, -minval);
+} /* minabsval */
+
+/*---------------------------------
+
+  qh_mindif( vecA, vecB, dim )
+  return index of min abs. difference of two vectors
+*/
+int qh_mindiff(realT *vecA, realT *vecB, int dim)
+{
+  realT  mindiff = REALmax, diff;
+  realT *vecAp = vecA, *vecBp = vecB;
+  int    k, mink = 0;
+  for( k = 0; k < dim; k++ )
+    {
+    diff = *vecAp++ - *vecBp++;
+    diff = fabs_(diff);
+    if( diff < mindiff )
+      {
+      mindiff = diff;
+      mink = k;
+      }
+    }
+  return mink;
+} /* mindiff */
+
+/*---------------------------------
+
+  qh_orientoutside( facet  )
+  make facet outside oriented via qh.interior_point
+
+  returns:
+  True if facet reversed orientation.
+*/
+boolT qh_orientoutside(facetT *facet)
+{
+  int   k;
+  realT dist;
+
+  qh_distplane(qh interior_point, facet, &dist);
+  if( dist > 0 )
+    {
+    for( k = qh hull_dim; k--; )
+      {
+      facet->normal[k] = -facet->normal[k];
+      }
+    facet->offset = -facet->offset;
+    return True;
+    }
+  return False;
+} /* orientoutside */
+
+/*---------------------------------
+
+  qh_outerinner( facet, outerplane, innerplane  )
+  if facet and qh.maxoutdone (i.e., qh_check_maxout)
+  returns outer and inner plane for facet
+  else
+  returns maximum outer and inner plane
+  accounts for qh.JOGGLEmax
+
+  see:
+  qh_maxouter(), qh_check_bestdist(), qh_check_points()
+
+  notes:
+  outerplaner or innerplane may be NULL
+
+  includes qh.DISTround for actual points
+  adds another qh.DISTround if testing with floating point arithmetic
+*/
+void qh_outerinner(facetT *facet, realT *outerplane, realT *innerplane)
+{
+  realT    dist, mindist;
+  vertexT *vertex, * *vertexp;
+
+  if( outerplane )
+    {
+    if( !qh_MAXoutside || !facet || !qh maxoutdone )
+      {
+      *outerplane = qh_maxouter();       /* includes qh.DISTround */
+      }
+    else    /* qh_MAXoutside ... */
+      {
+#if qh_MAXoutside
+      *outerplane = facet->maxoutside + qh DISTround;
+#endif
+
+      }
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      *outerplane += qh JOGGLEmax * sqrt( (double)qh hull_dim);
+      }
+    }
+  if( innerplane )
+    {
+    if( facet )
+      {
+      mindist = REALmax;
+      FOREACHvertex_(facet->vertices) {
+        zinc_(Zdistio);
+        qh_distplane(vertex->point, facet, &dist);
+        minimize_(mindist, dist);
+        }
+      *innerplane = mindist - qh DISTround;
+      }
+    else
+      {
+      *innerplane = qh min_vertex - qh DISTround;
+      }
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      *innerplane -= qh JOGGLEmax * sqrt( (double)qh hull_dim);
+      }
+    }
+} /* outerinner */
+
+/*---------------------------------
+
+  qh_pointdist( point1, point2, dim )
+  return distance between two points
+
+  notes:
+  returns distance squared if 'dim' is negative
+*/
+coordT qh_pointdist(pointT *point1, pointT *point2, int dim)
+{
+  coordT dist, diff;
+  int    k;
+
+  dist = 0.0;
+  for( k = (dim > 0 ? dim : -dim); k--; )
+    {
+    diff = *point1++ - *point2++;
+    dist += diff * diff;
+    }
+  if( dim > 0 )
+    {
+    return sqrt(dist);
+    }
+  return dist;
+} /* pointdist */
+
+/*---------------------------------
+
+  qh_printmatrix( fp, string, rows, numrow, numcol )
+  print matrix to fp given by row vectors
+  print string as header
+
+  notes:
+  print a vector by qh_printmatrix(fp, "", &vect, 1, len)
+*/
+void qh_printmatrix(FILE *fp, const char *string, realT * *rows, int numrow, int numcol)
+{
+  realT *rowp;
+  realT  r; /*bug fix*/
+  int    i, k;
+
+  fprintf(fp, "%s\n", string);
+  for( i = 0; i < numrow; i++ )
+    {
+    rowp = rows[i];
+    for( k = 0; k < numcol; k++ )
+      {
+      r = *rowp++;
+      fprintf(fp, "%6.3g ", r);
+      }
+    fprintf(fp, "\n");
+    }
+} /* printmatrix */
+
+/*---------------------------------
+
+  qh_printpoints( fp, string, points )
+  print pointids to fp for a set of points
+  if string, prints string and 'p' point ids
+*/
+void qh_printpoints(FILE *fp, const char *string, setT *points)
+{
+  pointT *point, * *pointp;
+
+  if( string )
+    {
+    fprintf(fp, "%s", string);
+    FOREACHpoint_(points)
+    fprintf(fp, " p%d", qh_pointid(point) );
+    fprintf(fp, "\n");
+    }
+  else
+    {
+    FOREACHpoint_(points)
+    fprintf(fp, " %d", qh_pointid(point) );
+    fprintf(fp, "\n");
+    }
+} /* printpoints */
+
+/*---------------------------------
+
+  qh_projectinput()
+  project input points using qh.lower_bound/upper_bound and qh DELAUNAY
+  if qh.lower_bound[k]=qh.upper_bound[k]= 0,
+  removes dimension k
+  if halfspace intersection
+  removes dimension k from qh.feasible_point
+  input points in qh first_point, num_points, input_dim
+
+  returns:
+  new point array in qh first_point of qh hull_dim coordinates
+  sets qh POINTSmalloc
+  if qh DELAUNAY
+  projects points to paraboloid
+  lowbound/highbound is also projected
+  if qh ATinfinity
+  adds point "at-infinity"
+  if qh POINTSmalloc
+  frees old point array
+
+  notes:
+  checks that qh.hull_dim agrees with qh.input_dim, PROJECTinput, and DELAUNAY
+
+
+  design:
+  sets project[k] to -1 (delete), 0 (keep), 1 (add for Delaunay)
+  determines newdim and newnum for qh hull_dim and qh num_points
+  projects points to newpoints
+  projects qh.lower_bound to itself
+  projects qh.upper_bound to itself
+  if qh DELAUNAY
+  if qh ATINFINITY
+  projects points to paraboloid
+  computes "infinity" point as vertex average and 10% above all points
+  else
+  uses qh_setdelaunay to project points to paraboloid
+*/
+void qh_projectinput(void)
+{
+  int          k, i;
+  int          newdim = qh input_dim, newnum = qh num_points;
+  signed char *project;
+  size_t       size = (qh input_dim + 1) * sizeof(*project);
+  pointT *     newpoints, *coord, *infinity;
+  realT        paraboloid, maxboloid = 0;
+
+  project = (signed char *)qh_memalloc(size);
+  memset( (char *)project, 0, size);
+  for( k = 0; k < qh input_dim; k++ )     /* skip Delaunay bound */
+    {
+    if( qh lower_bound[k] == 0 && qh upper_bound[k] == 0 )
+      {
+      project[k] = -1;
+      newdim--;
+      }
+    }
+  if( qh DELAUNAY )
+    {
+    project[k] = 1;
+    newdim++;
+    if( qh ATinfinity )
+      {
+      newnum++;
+      }
+    }
+  if( newdim != qh hull_dim )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_projectinput): dimension after projection %d != hull_dim %d\n", newdim,
+            qh hull_dim);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  if( !(newpoints = (coordT *)malloc(newnum * newdim * sizeof(coordT) ) ) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory to project %d points\n",
+            qh num_points);
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  qh_projectpoints(project, qh input_dim + 1, qh first_point,
+                   qh num_points, qh input_dim, newpoints, newdim);
+  trace1( (qh ferr, "qh_projectinput: updating lower and upper_bound\n") );
+  qh_projectpoints(project, qh input_dim + 1, qh lower_bound,
+                   1, qh input_dim + 1, qh lower_bound, newdim + 1);
+  qh_projectpoints(project, qh input_dim + 1, qh upper_bound,
+                   1, qh input_dim + 1, qh upper_bound, newdim + 1);
+  if( qh HALFspace )
+    {
+    if( !qh feasible_point )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_projectinput): HALFspace defined without qh.feasible_point\n");
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    qh_projectpoints(project, qh input_dim, qh feasible_point,
+                     1, qh input_dim, qh feasible_point, newdim);
+    }
+  qh_memfree(project, ( (qh input_dim + 1) * sizeof(*project) ) );
+  if( qh POINTSmalloc )
+    {
+    free(qh first_point);
+    }
+  qh first_point = newpoints;
+  qh POINTSmalloc = True;
+  if( qh DELAUNAY && qh ATinfinity )
+    {
+    coord = qh first_point;
+    infinity = qh first_point + qh hull_dim * qh num_points;
+    for( k = qh hull_dim - 1; k--; )
+      {
+      infinity[k] = 0.0;
+      }
+    for( i = qh num_points; i--; )
+      {
+      paraboloid = 0.0;
+      for( k = 0; k < qh hull_dim - 1; k++ )
+        {
+        paraboloid += *coord * *coord;
+        infinity[k] += *coord;
+        coord++;
+        }
+      *(coord++) = paraboloid;
+      maximize_(maxboloid, paraboloid);
+      }
+    /* coord == infinity */
+    for( k = qh hull_dim - 1; k--; )
+      {
+      *(coord++) /= qh num_points;
+      }
+    *(coord++) = maxboloid * 1.1;
+    qh num_points++;
+    trace0( (qh ferr, "qh_projectinput: projected points to paraboloid for Delaunay\n") );
+    }
+  else if( qh DELAUNAY )  /* !qh ATinfinity */
+    {
+    qh_setdelaunay( qh hull_dim, qh num_points, qh first_point);
+    }
+} /* projectinput */
+
+/*---------------------------------
+
+  qh_projectpoints( project, n, points, numpoints, dim, newpoints, newdim )
+  project points/numpoints/dim to newpoints/newdim
+  if project[k] == -1
+  delete dimension k
+  if project[k] == 1
+  add dimension k by duplicating previous column
+  n is size of project
+
+  notes:
+  newpoints may be points if only adding dimension at end
+
+  design:
+  check that 'project' and 'newdim' agree
+  for each dimension
+  if project == -1
+  skip dimension
+  else
+  determine start of column in newpoints
+  determine start of column in points
+  if project == +1, duplicate previous column
+  copy dimension (column) from points to newpoints
+*/
+void qh_projectpoints(signed char *project, int n, realT *points,
+                      int numpoints, int dim, realT *newpoints, int newdim)
+{
+  int    testdim = dim, oldk = 0, newk = 0, i, j = 0, k;
+  realT *newp, *oldp;
+  for( k = 0; k < n; k++ )
+    {
+    testdim += project[k];
+    }
+  if( testdim != newdim )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_projectpoints): newdim %d should be %d after projection\n",
+            newdim, testdim);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  for( j = 0; j < n; j++ )
+    {
+    if( project[j] == -1 )
+      {
+      oldk++;
+      }
+    else
+      {
+      newp = newpoints + newk++;
+      if( project[j] == +1 )
+        {
+        if( oldk >= dim )
+          {
+          continue;
+          }
+        oldp = points + oldk;
+        }
+      else
+        {
+        oldp = points + oldk++;
+        }
+      for( i = numpoints; i--; )
+        {
+        *newp = *oldp;
+        newp += newdim;
+        oldp += dim;
+        }
+      }
+    if( oldk >= dim )
+      {
+      break;
+      }
+    }
+  trace1( (qh ferr, "qh_projectpoints: projected %d points from dim %d to dim %d\n",
+           numpoints, dim, newdim) );
+} /* projectpoints */
+
+/*---------------------------------
+
+  qh_rand()
+  qh_srand( seed )
+  generate pseudo-random number between 1 and 2^31 -2
+
+  notes:
+  from Park & Miller's minimimal standard random number generator
+  Communications of the ACM, 31:1192-1201, 1988.
+  does not use 0 or 2^31 -1
+  this is silently enforced by qh_srand()
+  can make 'Rn' much faster by moving qh_rand to qh_distplane
+*/
+int qh_rand_seed = 1;  /* define as global variable instead of using qh */
+
+int qh_rand( void)
+{
+#define qh_rand_a 16807
+#define qh_rand_m 2147483647
+#define qh_rand_q 127773  /* m div a */
+#define qh_rand_r 2836    /* m mod a */
+  int lo, hi, test;
+  int seed = qh_rand_seed;
+
+  hi = seed / qh_rand_q;  /* seed div q */
+  lo = seed % qh_rand_q;  /* seed mod q */
+  test = qh_rand_a * lo - qh_rand_r * hi;
+  if( test > 0 )
+    {
+    seed = test;
+    }
+  else
+    {
+    seed = test + qh_rand_m;
+    }
+  qh_rand_seed = seed;
+  /* seed = seed < qh_RANDOMmax/2 ? 0 : qh_RANDOMmax;  for testing */
+  /* seed = qh_RANDOMmax;  for testing */
+  return seed;
+} /* rand */
+
+void qh_srand( int seed)
+{
+  if( seed < 1 )
+    {
+    qh_rand_seed = 1;
+    }
+  else if( seed >= qh_rand_m )
+    {
+    qh_rand_seed = qh_rand_m - 1;
+    }
+  else
+    {
+    qh_rand_seed = seed;
+    }
+} /* qh_srand */
+
+/*---------------------------------
+
+  qh_randomfactor()
+  return a random factor within qh.RANDOMmax of 1.0
+
+  notes:
+  qh.RANDOMa/b are defined in global.c
+*/
+realT qh_randomfactor(void)
+{
+  realT randr;
+
+  randr = qh_RANDOMint;
+  return randr * qh RANDOMa + qh RANDOMb;
+} /* randomfactor */
+
+/*---------------------------------
+
+  qh_randommatrix( buffer, dim, rows )
+  generate a random dim X dim matrix in range [-1,1]
+  assumes buffer is [dim+1, dim]
+
+  returns:
+  sets buffer to random numbers
+  sets rows to rows of buffer
+  sets row[dim] as scratch row
+*/
+void qh_randommatrix(realT *buffer, int dim, realT * *rows)
+{
+  int      i, k;
+  realT * *rowi, *coord, realr;
+
+  coord = buffer;
+  rowi = rows;
+  for( i = 0; i < dim; i++ )
+    {
+    *(rowi++) = coord;
+    for( k = 0; k < dim; k++ )
+      {
+      realr = qh_RANDOMint;
+      *(coord++) = 2.0 * realr / (qh_RANDOMmax + 1) - 1.0;
+      }
+    }
+  *rowi = coord;
+} /* randommatrix */
+
+/*---------------------------------
+
+  qh_rotateinput( rows )
+  rotate input using row matrix
+  input points given by qh first_point, num_points, hull_dim
+  assumes rows[dim] is a scratch buffer
+  if qh POINTSmalloc, overwrites input points, else mallocs a new array
+
+  returns:
+  rotated input
+  sets qh POINTSmalloc
+
+  design:
+  see qh_rotatepoints
+*/
+void qh_rotateinput(realT * *rows)
+{
+
+  if( !qh POINTSmalloc )
+    {
+    qh first_point = qh_copypoints(qh first_point, qh num_points, qh hull_dim);
+    qh POINTSmalloc = True;
+    }
+  qh_rotatepoints(qh first_point, qh num_points, qh hull_dim, rows);
+}  /* rotateinput */
+
+/*---------------------------------
+
+  qh_rotatepoints( points, numpoints, dim, row )
+  rotate numpoints points by a d-dim row matrix
+  assumes rows[dim] is a scratch buffer
+
+  returns:
+  rotated points in place
+
+  design:
+  for each point
+  for each coordinate
+  use row[dim] to compute partial inner product
+  for each coordinate
+  rotate by partial inner product
+*/
+void qh_rotatepoints(realT *points, int numpoints, int dim, realT * *row)
+{
+  realT *point, *rowi, *coord = NULL, sum, *newval;
+  int    i, j, k;
+
+  if( qh IStracing >= 1 )
+    {
+    qh_printmatrix(qh ferr, "qh_rotatepoints: rotate points by", row, dim, dim);
+    }
+  for( point = points, j = numpoints; j--; point += dim )
+    {
+    newval = row[dim];
+    for( i = 0; i < dim; i++ )
+      {
+      rowi = row[i];
+      coord = point;
+      for( sum = 0.0, k = dim; k--; )
+        {
+        sum += *rowi++ **coord++;
+        }
+      *(newval++) = sum;
+      }
+    for( k = dim; k--; )
+      {
+      *(--coord) = *(--newval);
+      }
+    }
+} /* rotatepoints */
+
+/*---------------------------------
+
+  qh_scaleinput()
+  scale input points using qh low_bound/high_bound
+  input points given by qh first_point, num_points, hull_dim
+  if qh POINTSmalloc, overwrites input points, else mallocs a new array
+
+  returns:
+  scales coordinates of points to low_bound[k], high_bound[k]
+  sets qh POINTSmalloc
+
+  design:
+  see qh_scalepoints
+*/
+void qh_scaleinput(void)
+{
+
+  if( !qh POINTSmalloc )
+    {
+    qh first_point = qh_copypoints(qh first_point, qh num_points, qh hull_dim);
+    qh POINTSmalloc = True;
+    }
+  qh_scalepoints(qh first_point, qh num_points, qh hull_dim,
+                 qh lower_bound, qh upper_bound);
+}  /* scaleinput */
+
+/*---------------------------------
+
+  qh_scalelast( points, numpoints, dim, low, high, newhigh )
+  scale last coordinate to [0,m] for Delaunay triangulations
+  input points given by points, numpoints, dim
+
+  returns:
+  changes scale of last coordinate from [low, high] to [0, newhigh]
+  overwrites last coordinate of each point
+  saves low/high/newhigh in qh.last_low, etc. for qh_setdelaunay()
+
+  notes:
+  when called by qh_setdelaunay, low/high may not match actual data
+
+  design:
+  compute scale and shift factors
+  apply to last coordinate of each point
+*/
+void qh_scalelast(coordT *points, int numpoints, int dim, coordT low,
+                  coordT high, coordT newhigh)
+{
+  realT   scale, shift;
+  coordT *coord;
+  int     i;
+  boolT   nearzero = False;
+
+  trace4( (qh ferr, "qh_scalelast: scale last coordinate from [%2.2g, %2.2g] to [0,%2.2g]\n",
+           low, high, newhigh) );
+  qh last_low = low;
+  qh last_high = high;
+  qh last_newhigh = newhigh;
+  scale = qh_divzero(newhigh, high - low,
+                     qh MINdenom_1, &nearzero);
+  if( nearzero )
+    {
+    if( qh DELAUNAY )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input error: can not scale last coordinate.  Input is cocircular\n   or cospherical.   Use option 'Qz' to add a point at infinity.\n");
+      }
+    else
+      {
+      fprintf(
+        qh ferr,
+        "qhull input error: can not scale last coordinate.  New bounds [0, %2.2g] are too wide for\nexisting bounds [%2.2g, %2.2g] (width %2.2g)\n",
+        newhigh, low, high, high - low);
+      }
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  shift = -low * newhigh / (high - low);
+  coord = points + dim - 1;
+  for( i = numpoints; i--; coord += dim )
+    {
+    *coord = *coord * scale + shift;
+    }
+} /* scalelast */
+
+/*---------------------------------
+
+  qh_scalepoints( points, numpoints, dim, newlows, newhighs )
+  scale points to new lowbound and highbound
+  retains old bound when newlow= -REALmax or newhigh= +REALmax
+
+  returns:
+  scaled points
+  overwrites old points
+
+  design:
+  for each coordinate
+  compute current low and high bound
+  compute scale and shift factors
+  scale all points
+  enforce new low and high bound for all points
+*/
+void qh_scalepoints(pointT *points, int numpoints, int dim,
+                    realT *newlows, realT *newhighs)
+{
+  int   i, k;
+  realT shift, scale, *coord, low, high, newlow, newhigh, mincoord, maxcoord;
+  boolT nearzero = False;
+  for( k = 0; k < dim; k++ )
+    {
+    newhigh = newhighs[k];
+    newlow = newlows[k];
+    if( newhigh > REALmax / 2 && newlow < -REALmax / 2 )
+      {
+      continue;
+      }
+    low = REALmax;
+    high = -REALmax;
+    for( i = numpoints, coord = points + k; i--; coord += dim )
+      {
+      minimize_(low, *coord);
+      maximize_(high, *coord);
+      }
+    if( newhigh > REALmax / 2 )
+      {
+      newhigh = high;
+      }
+    if( newlow < -REALmax / 2 )
+      {
+      newlow = low;
+      }
+    if( qh DELAUNAY && k == dim - 1 && newhigh < newlow )
+      {
+      fprintf(qh ferr,
+              "qhull input error: 'Qb%d' or 'QB%d' inverts paraboloid since high bound %.2g < low bound %.2g\n",
+              k, k, newhigh,
+              newlow);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    scale = qh_divzero(newhigh - newlow, high - low,
+                       qh MINdenom_1, &nearzero);
+    if( nearzero )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input error: %d'th dimension's new bounds [%2.2g, %2.2g] too wide for\nexisting bounds [%2.2g, %2.2g]\n",
+        k, newlow, newhigh, low, high);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    shift = (newlow * high - low * newhigh) / (high - low);
+    coord = points + k;
+    for( i = numpoints; i--; coord += dim )
+      {
+      *coord = *coord * scale + shift;
+      }
+    coord = points + k;
+    if( newlow < newhigh )
+      {
+      mincoord = newlow;
+      maxcoord = newhigh;
+      }
+    else
+      {
+      mincoord = newhigh;
+      maxcoord = newlow;
+      }
+    for( i = numpoints; i--; coord += dim )
+      {
+      minimize_(*coord, maxcoord);  /* because of roundoff error */
+      maximize_(*coord, mincoord);
+      }
+    trace0( (qh ferr,
+             "qh_scalepoints: scaled %d'th coordinate [%2.2g, %2.2g] to [%.2g, %.2g] for %d points by %2.2g and shifted %2.2g\n",
+             k, low, high, newlow, newhigh, numpoints, scale, shift) );
+    }
+} /* scalepoints */
+
+/*---------------------------------
+
+  qh_setdelaunay( dim, count, points )
+  project count points to dim-d paraboloid for Delaunay triangulation
+
+  dim is one more than the dimension of the input set
+  assumes dim is at least 3 (i.e., at least a 2-d Delaunay triangulation)
+
+  points is a dim*count realT array.  The first dim-1 coordinates
+  are the coordinates of the first input point.  array[dim] is
+  the first coordinate of the second input point.  array[2*dim] is
+  the first coordinate of the third input point.
+
+  if qh.last_low defined (i.e., 'Qbb' called qh_scalelast)
+  calls qh_scalelast to scale the last coordinate the same as the other points
+
+  returns:
+  for each point
+  sets point[dim-1] to sum of squares of coordinates
+  scale points to 'Qbb' if needed
+
+  notes:
+  to project one point, use
+  qh_setdelaunay (qh hull_dim, 1, point)
+
+  Do not use options 'Qbk', 'QBk', or 'QbB' since they scale
+  the coordinates after the original projection.
+
+*/
+void qh_setdelaunay(int dim, int count, pointT *points)
+{
+  int     i, k;
+  coordT *coordp, coord;
+  realT   paraboloid;
+
+  trace0( (qh ferr, "qh_setdelaunay: project %d points to paraboloid for Delaunay triangulation\n", count) );
+  coordp = points;
+  for( i = 0; i < count; i++ )
+    {
+    coord = *coordp++;
+    paraboloid = coord * coord;
+    for( k = dim - 2; k--; )
+      {
+      coord = *coordp++;
+      paraboloid += coord * coord;
+      }
+    *coordp++ = paraboloid;
+    }
+  if( qh last_low < REALmax / 2 )
+    {
+    qh_scalelast(points, count, dim, qh last_low, qh last_high, qh last_newhigh);
+    }
+} /* setdelaunay */
+
+/*---------------------------------
+
+  qh_sethalfspace( dim, coords, nextp, normal, offset, feasible )
+  set point to dual of halfspace relative to feasible point
+  halfspace is normal coefficients and offset.
+
+  returns:
+  false if feasible point is outside of hull (error message already reported)
+  overwrites coordinates for point at dim coords
+  nextp= next point (coords)
+
+  design:
+  compute distance from feasible point to halfspace
+  divide each normal coefficient by -dist
+*/
+boolT qh_sethalfspace(int dim, coordT *coords, coordT * *nextp,
+                      coordT *normal, coordT *offset, coordT *feasible)
+{
+  coordT *normp = normal, *feasiblep = feasible, *coordp = coords;
+  realT   dist;
+  realT   r; /*bug fix*/
+  int     k;
+  boolT   zerodiv;
+
+  dist = *offset;
+  for( k = dim; k--; )
+    {
+    dist += *(normp++) * *(feasiblep++);
+    }
+  if( dist > 0 )
+    {
+    goto LABELerroroutside;
+    }
+  normp = normal;
+  if( dist < -qh MINdenom )
+    {
+    for( k = dim; k--; )
+      {
+      *(coordp++) = *(normp++) / -dist;
+      }
+    }
+  else
+    {
+    for( k = dim; k--; )
+      {
+      *(coordp++) = qh_divzero(*(normp++), -dist, qh MINdenom_1, &zerodiv);
+      if( zerodiv )
+        {
+        goto LABELerroroutside;
+        }
+      }
+    }
+  *nextp = coordp;
+  if( qh IStracing >= 4 )
+    {
+    fprintf(qh ferr, "qh_sethalfspace: halfspace at offset %6.2g to point: ", *offset);
+    for( k = dim, coordp = coords; k--; )
+      {
+      r = *coordp++;
+      fprintf(qh ferr, " %6.2g", r);
+      }
+    fprintf(qh ferr, "\n");
+    }
+  return True;
+LABELerroroutside:
+  feasiblep = feasible;
+  normp = normal;
+  fprintf(qh ferr, "qhull input error: feasible point is not clearly inside halfspace\nfeasible point: ");
+  for( k = dim; k--; )
+    {
+    fprintf(qh ferr, qh_REAL_1, r = *(feasiblep++) );
+    }
+  fprintf(qh ferr, "\n     halfspace: ");
+  for( k = dim; k--; )
+    {
+    fprintf(qh ferr, qh_REAL_1, r = *(normp++) );
+    }
+  fprintf(qh ferr, "\n     at offset: ");
+  fprintf(qh ferr, qh_REAL_1, *offset);
+  fprintf(qh ferr, " and distance: ");
+  fprintf(qh ferr, qh_REAL_1, dist);
+  fprintf(qh ferr, "\n");
+  return False;
+} /* sethalfspace */
+
+/*---------------------------------
+
+  qh_sethalfspace_all( dim, count, halfspaces, feasible )
+  generate dual for halfspace intersection with feasible point
+  array of count halfspaces
+  each halfspace is normal coefficients followed by offset
+  the origin is inside the halfspace if the offset is negative
+
+  returns:
+  malloc'd array of count X dim-1 points
+
+  notes:
+  call before qh_init_B or qh_initqhull_globals
+  unused/untested code: please email bradb@shore.net if this works ok for you
+  If using option 'Fp', also set qh feasible_point. It is a malloc'd array
+  that is freed by qh_freebuffers.
+
+  design:
+  see qh_sethalfspace
+*/
+coordT * qh_sethalfspace_all(int dim, int count, coordT *halfspaces, pointT *feasible)
+{
+  int     i, newdim;
+  pointT *newpoints;
+  coordT *coordp, *normalp, *offsetp;
+
+  trace0( (qh ferr, "qh_sethalfspace_all: compute dual for halfspace intersection\n") );
+  newdim = dim - 1;
+  if( !(newpoints = (coordT *)malloc(count * newdim * sizeof(coordT) ) ) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory to compute dual of %d halfspaces\n",
+            count);
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  coordp = newpoints;
+  normalp = halfspaces;
+  for( i = 0; i < count; i++ )
+    {
+    offsetp = normalp + newdim;
+    if( !qh_sethalfspace(newdim, coordp, &coordp, normalp, offsetp, feasible) )
+      {
+      fprintf(qh ferr, "The halfspace was at index %d\n", i);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    normalp = offsetp + 1;
+    }
+  return newpoints;
+} /* sethalfspace_all */
+
+/*---------------------------------
+
+  qh_sharpnewfacets()
+
+  returns:
+  true if could be an acute angle (facets in different quadrants)
+
+  notes:
+  for qh_findbest
+
+  design:
+  for all facets on qh.newfacet_list
+  if two facets are in different quadrants
+  set issharp
+*/
+boolT qh_sharpnewfacets()
+{
+  facetT *facet;
+  boolT   issharp = False;
+  int *   quadrant, k;
+
+  quadrant = (int *)qh_memalloc(qh hull_dim * sizeof(int) );
+  FORALLfacet_(qh newfacet_list) {
+    if( facet == qh newfacet_list )
+      {
+      for( k = qh hull_dim; k--; )
+        {
+        quadrant[k] = (facet->normal[k] > 0);
+        }
+      }
+    else
+      {
+      for( k = qh hull_dim; k--; )
+        {
+        if( quadrant[k] != (facet->normal[k] > 0) )
+          {
+          issharp = True;
+          break;
+          }
+        }
+      }
+    if( issharp )
+      {
+      break;
+      }
+    }
+  qh_memfree( quadrant, qh hull_dim * sizeof(int) );
+  trace3( (qh ferr, "qh_sharpnewfacets: %d\n", issharp) );
+  return issharp;
+} /* sharpnewfacets */
+
+/*---------------------------------
+
+  qh_voronoi_center( dim, points )
+  return Voronoi center for a set of points
+  dim is the orginal dimension of the points
+  gh.gm_matrix/qh.gm_row are scratch buffers
+
+  returns:
+  center as a temporary point
+  if non-simplicial,
+  returns center for max simplex of points
+
+  notes:
+  from Bowyer & Woodwark, A Programmer's Geometry, 1983, p. 65
+
+  design:
+  if non-simplicial
+  determine max simplex for points
+  translate point0 of simplex to origin
+  compute sum of squares of diagonal
+  compute determinate
+  compute Voronoi center (see Bowyer & Woodwark)
+*/
+pointT * qh_voronoi_center(int dim, setT *points)
+{
+  pointT *point, * *pointp, *point0;
+  pointT *center = (pointT *)qh_memalloc(qh center_size);
+  setT *  simplex;
+  int     i, j, k, size = qh_setsize(points);
+  coordT *gmcoord;
+  realT * diffp, sum2, *sum2row, *sum2p, det, factor;
+  boolT   nearzero, infinite;
+
+  if( size == dim + 1 )
+    {
+    simplex = points;
+    }
+  else if( size < dim + 1 )
+    {
+    fprintf(qh ferr,
+            "qhull internal error (qh_voronoi_center):\n  need at least %d points to construct a Voronoi center\n",
+            dim + 1);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  else
+    {
+    simplex = qh_settemp(dim + 1);
+    qh_maxsimplex(dim, points, NULL, 0, &simplex);
+    }
+  point0 = SETfirstt_(simplex, pointT);
+  gmcoord = qh gm_matrix;
+  for( k = 0; k < dim; k++ )
+    {
+    qh gm_row[k] = gmcoord;
+    FOREACHpoint_(simplex) {
+      if( point != point0 )
+        {
+        *(gmcoord++) = point[k] - point0[k];
+        }
+      }
+    }
+  sum2row = gmcoord;
+  for( i = 0; i < dim; i++ )
+    {
+    sum2 = 0.0;
+    for( k = 0; k < dim; k++ )
+      {
+      diffp = qh gm_row[k] + i;
+      sum2 += *diffp * *diffp;
+      }
+    *(gmcoord++) = sum2;
+    }
+  det = qh_determinant(qh gm_row, dim, &nearzero);
+  factor = qh_divzero(0.5, det, qh MINdenom, &infinite);
+  if( infinite )
+    {
+    for( k = dim; k--; )
+      {
+      center[k] = qh_INFINITE;
+      }
+    if( qh IStracing )
+      {
+      qh_printpoints(qh ferr, "qh_voronoi_center: at infinity for ", simplex);
+      }
+    }
+  else
+    {
+    for( i = 0; i < dim; i++ )
+      {
+      gmcoord = qh gm_matrix;
+      sum2p = sum2row;
+      for( k = 0; k < dim; k++ )
+        {
+        qh gm_row[k] = gmcoord;
+        if( k == i )
+          {
+          for( j = dim; j--; )
+            {
+            *(gmcoord++) = *sum2p++;
+            }
+          }
+        else
+          {
+          FOREACHpoint_(simplex) {
+            if( point != point0 )
+              {
+              *(gmcoord++) = point[k] - point0[k];
+              }
+            }
+          }
+        }
+      center[i] = qh_determinant(qh gm_row, dim, &nearzero) * factor + point0[i];
+      }
+#ifndef qh_NOtrace
+    if( qh IStracing >= 3 )
+      {
+      fprintf(qh ferr, "qh_voronoi_center: det %2.2g factor %2.2g ", det, factor);
+      qh_printmatrix(qh ferr, "center:", ¢er, 1, dim);
+      if( qh IStracing >= 5 )
+        {
+        qh_printpoints(qh ferr, "points", simplex);
+        FOREACHpoint_(simplex)
+        fprintf(qh ferr, "p%d dist %.2g, ", qh_pointid(point),
+                qh_pointdist(point, center, dim) );
+        fprintf(qh ferr, "\n");
+        }
+      }
+#endif
+    }
+  if( simplex != points )
+    {
+    qh_settempfree(&simplex);
+    }
+  return center;
+} /* voronoi_center */
+
diff --git a/BRAINSABC/qhull/global.c b/BRAINSABC/qhull/global.c
new file mode 100644
index 00000000..7db408c9
--- /dev/null
+++ b/BRAINSABC/qhull/global.c
@@ -0,0 +1,2591 @@
+/*
  ---------------------------------
+
+  global.c
+  initializes all the globals of the qhull application
+
+  see README
+
+  see qhull.h for qh.globals and function prototypes
+
+  see qhull_a.h for internal functions
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*========= qh definition (see qhull.h) =======================*/
+
+#if qh_QHpointer
+qhT *qh_qh = NULL; /* pointer to all global variables */
+#else
+qhT qh_qh;        /* all global variables.
+         Add "= {0}" if this causes a compiler error.
+         Also qh_qhstat in stat.c and qhmem in mem.c.  */
+#endif
+
+/*----------------------------------
+
+  qh_version
+  version string by year and date
+
+  the revision increases on code changes only
+
+  notes:
+  change date:    Changes.txt, Announce.txt, README.txt,
+  qhull.man, qhull.txt, qhull-news.html, Eudora signatures,
+  change version: README.txt, qh-get.htm, File_id.diz, Makefile.txt
+  change year:    Copying.txt
+  check download size
+  recompile user_eg.c, rbox.c, qhull.c, qconvex.c, qdelaun.c qvoronoi.c, qhalf.c
+*/
+
+const char *qh_version = "2009.1 2009/06/11";
+
+/*---------------------------------
+
+  qh_appendprint( printFormat )
+  append printFormat to qh.PRINTout unless already defined
+*/
+void qh_appendprint(qh_PRINT format)
+{
+  int i;
+  for( i = 0; i < qh_PRINTEND; i++ )
+    {
+    if( qh PRINTout[i] == format && format != qh_PRINTqhull )
+      {
+      break;
+      }
+    if( !qh PRINTout[i] )
+      {
+      qh PRINTout[i] = format;
+      break;
+      }
+    }
+} /* appendprint */
+
+/*---------------------------------
+
+  qh_checkflags( commandStr, hiddenFlags )
+  errors if commandStr contains hiddenFlags
+  hiddenFlags starts and ends with a space and is space deliminated (checked)
+
+  notes:
+  ignores first word (e.g., "qconvex i")
+  use qh_strtol/strtod since strtol/strtod may or may not skip trailing spaces
+
+  see:
+  qh_initflags() initializes Qhull according to commandStr
+*/
+void qh_checkflags(char *command, char *hiddenflags)
+{
+  char *s = command, *t, *chkerr, key, opt, prevopt;
+  char  chkkey[] = "   ";
+  char  chkopt[] =  "    ";
+  char  chkopt2[] = "     ";
+
+  if( *hiddenflags != ' ' || hiddenflags[strlen(hiddenflags) - 1] != ' ' )
+    {
+    fprintf(qh ferr, "qhull error (qh_checkflags): hiddenflags must start and end with a space: \"%s\"", hiddenflags);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( strpbrk(hiddenflags, ",\n\r\t") )
+    {
+    fprintf(qh ferr, "qhull error (qh_checkflags): hiddenflags contains commas, newlines, or tabs: \"%s\"", hiddenflags);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  while( *s && !isspace(*s) )  /* skip program name */
+    {
+    s++;
+    }
+
+  while( *s )
+    {
+    while( *s && isspace(*s) )
+      {
+      s++;
+      }
+
+    if( *s == '-' )
+      {
+      s++;
+      }
+    if( !*s )
+      {
+      break;
+      }
+    key = *s++;
+    chkerr = NULL;
+    if( key == '\'' )           /* TO 'file name' */
+      {
+      t = strchr(s, '\'');
+      if( !t )
+        {
+        fprintf(qh ferr, "qhull error (qh_checkflags): missing the 2nd single-quote for:\n%s\n", s - 1);
+        qh_errexit(qh_ERRinput, NULL, NULL);
+        }
+      s = t + 1;
+      continue;
+      }
+    chkkey[1] = key;
+    if( strstr(hiddenflags, chkkey) )
+      {
+      chkerr = chkkey;
+      }
+    else if( isupper(key) )
+      {
+      opt = ' ';
+      prevopt = ' ';
+      chkopt[1] = key;
+      chkopt2[1] = key;
+      while( !chkerr && *s && !isspace(*s) )
+        {
+        opt = *s++;
+        if( isalpha(opt) )
+          {
+          chkopt[2] = opt;
+          if( strstr(hiddenflags, chkopt) )
+            {
+            chkerr = chkopt;
+            }
+          if( prevopt != ' ' )
+            {
+            chkopt2[2] = prevopt;
+            chkopt2[3] = opt;
+            if( strstr(hiddenflags, chkopt2) )
+              {
+              chkerr = chkopt2;
+              }
+            }
+          }
+        else if( key == 'Q' && isdigit(opt) && prevopt != 'b'
+                 && (prevopt == ' ' || islower(prevopt) ) )
+          {
+          chkopt[2] = opt;
+          if( strstr(hiddenflags, chkopt) )
+            {
+            chkerr = chkopt;
+            }
+          }
+        else
+          {
+          qh_strtod(s - 1, &t);
+          if( s < t )
+            {
+            s = t;
+            }
+          }
+        prevopt = opt;
+        }
+      }
+    if( chkerr )
+      {
+      *chkerr = '\'';
+      chkerr[strlen(chkerr) - 1] =  '\'';
+      fprintf(qh ferr,
+              "qhull error: option %s is not used with this program.\n             It may be used with qhull.\n",
+              chkerr);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    }
+} /* checkflags */
+
+/*---------------------------------
+
+  qh_clock()
+  return user CPU time in 100ths (qh_SECtick)
+  only defined for qh_CLOCKtype == 2
+
+  notes:
+  use first value to determine time 0
+  from Stevens '92 8.15
+*/
+unsigned long qh_clock(void)
+{
+
+#if (qh_CLOCKtype == 2)
+  struct tms    time;
+  static long   clktck; /* initialized first call */
+  double        ratio, cpu;
+  unsigned long ticks;
+
+  if( !clktck )
+    {
+    if( (clktck = sysconf(_SC_CLK_TCK) ) < 0 )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_clock): sysconf() failed.  Use qh_CLOCKtype 1 in user.h\n");
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    }
+  if( times(&time) == -1 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_clock): times() failed.  Use qh_CLOCKtype 1 in user.h\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  ratio = qh_SECticks / (double)clktck;
+  ticks = time.tms_utime * ratio;
+  return ticks;
+#else
+  fprintf(qh ferr, "qhull internal error (qh_clock): use qh_CLOCKtype 2 in user.h\n");
+  qh_errexit(qh_ERRqhull, NULL, NULL);  /* never returns */
+  return 0;
+#endif
+} /* clock */
+
+/*---------------------------------
+
+  qh_freebuffers()
+  free up global memory buffers
+
+  notes:
+  must match qh_initbuffers()
+*/
+void qh_freebuffers(void)
+{
+
+  trace5( (qh ferr, "qh_freebuffers: freeing up global memory buffers\n") );
+  /* allocated by qh_initqhull_buffers */
+  qh_memfree(qh NEARzero, qh hull_dim * sizeof(realT) );
+  qh_memfree(qh lower_threshold, (qh input_dim + 1) * sizeof(realT) );
+  qh_memfree(qh upper_threshold, (qh input_dim + 1) * sizeof(realT) );
+  qh_memfree(qh lower_bound, (qh input_dim + 1) * sizeof(realT) );
+  qh_memfree(qh upper_bound, (qh input_dim + 1) * sizeof(realT) );
+  qh_memfree(qh gm_matrix, (qh hull_dim + 1) * qh hull_dim * sizeof(coordT) );
+  qh_memfree(qh gm_row, (qh hull_dim + 1) * sizeof(coordT *) );
+  qh NEARzero = qh lower_threshold = qh upper_threshold = NULL;
+  qh lower_bound = qh upper_bound = NULL;
+  qh gm_matrix = NULL;
+  qh gm_row = NULL;
+  qh_setfree(&qh other_points);
+  qh_setfree(&qh del_vertices);
+  qh_setfree(&qh coplanarset);
+  if( qh line )                /* allocated by qh_readinput, freed if no error
+                                 */
+    {
+    free(qh line);
+    }
+  if( qh half_space )
+    {
+    free(qh half_space);
+    }
+  if( qh temp_malloc )
+    {
+    free(qh temp_malloc);
+    }
+  if( qh feasible_point )      /* allocated by qh_readfeasible */
+    {
+    free(qh feasible_point);
+    }
+  if( qh feasible_string )     /* allocated by qh_initflags */
+    {
+    free(qh feasible_string);
+    }
+  qh line = qh feasible_string = NULL;
+  qh half_space = qh feasible_point = qh temp_malloc = NULL;
+  /* usually allocated by qh_readinput */
+  if( qh first_point && qh POINTSmalloc )
+    {
+    free(qh first_point);
+    qh first_point = NULL;
+    }
+  if( qh input_points && qh input_malloc )   /* set by qh_joggleinput */
+    {
+    free(qh input_points);
+    qh input_points = NULL;
+    }
+  trace5( (qh ferr, "qh_freebuffers: finished\n") );
+} /* freebuffers */
+
+/*---------------------------------
+
+  qh_freebuild( allmem )
+  free global memory used by qh_initbuild and qh_buildhull
+  if !allmem,
+  does not free short memory (freed by qh_memfreeshort)
+
+  design:
+  free centrums
+  free each vertex
+  mark unattached ridges
+  for each facet
+  free ridges
+  free outside set, coplanar set, neighbor set, ridge set, vertex set
+  free facet
+  free hash table
+  free interior point
+  free merge set
+  free temporary sets
+*/
+void qh_freebuild(boolT allmem)
+{
+  facetT * facet;
+  vertexT *vertex;
+  ridgeT * ridge, * *ridgep;
+  mergeT * merge, * *mergep;
+
+  trace1( (qh ferr, "qh_freebuild: free memory from qh_inithull and qh_buildhull\n") );
+  if( qh del_vertices )
+    {
+    qh_settruncate(qh del_vertices, (size_t)0);
+    }
+  if( allmem )
+    {
+    qh_clearcenters(qh_ASnone);
+    while( (vertex = qh vertex_list) )
+      {
+      if( vertex->next )
+        {
+        qh_delvertex(vertex);
+        }
+      else
+        {
+        qh_memfree(vertex, sizeof(vertexT) );
+        qh newvertex_list = qh vertex_list = NULL;
+        }
+      }
+    }
+  else if( qh VERTEXneighbors )
+    {
+    FORALLvertices
+    qh_setfreelong(&(vertex->neighbors) );
+    }
+  qh VERTEXneighbors = False;
+  qh GOODclosest = NULL;
+  if( allmem )
+    {
+    FORALLfacets {
+      FOREACHridge_(facet->ridges)
+      ridge->seen = False;
+      }
+    FORALLfacets {
+      if( facet->visible )
+        {
+        FOREACHridge_(facet->ridges) {
+          if( !otherfacet_(ridge, facet)->visible )
+            {
+            ridge->seen = True; /* an unattached ridge */
+            }
+          }
+        }
+      }
+    while( (facet = qh facet_list) )
+      {
+      FOREACHridge_(facet->ridges) {
+        if( ridge->seen )
+          {
+          qh_setfree(&(ridge->vertices) );
+          qh_memfree(ridge, sizeof(ridgeT) );
+          }
+        else
+          {
+          ridge->seen = True;
+          }
+        }
+      qh_setfree(&(facet->outsideset) );
+      qh_setfree(&(facet->coplanarset) );
+      qh_setfree(&(facet->neighbors) );
+      qh_setfree(&(facet->ridges) );
+      qh_setfree(&(facet->vertices) );
+      if( facet->next )
+        {
+        qh_delfacet(facet);
+        }
+      else
+        {
+        qh_memfree(facet, sizeof(facetT) );
+        qh visible_list = qh newfacet_list = qh facet_list = NULL;
+        }
+      }
+    }
+  else
+    {
+    FORALLfacets {
+      qh_setfreelong(&(facet->outsideset) );
+      qh_setfreelong(&(facet->coplanarset) );
+      if( !facet->simplicial )
+        {
+        qh_setfreelong(&(facet->neighbors) );
+        qh_setfreelong(&(facet->ridges) );
+        qh_setfreelong(&(facet->vertices) );
+        }
+      }
+    }
+  qh_setfree(&(qh hash_table) );
+  qh_memfree(qh interior_point, qh normal_size);
+  qh interior_point = NULL;
+  FOREACHmerge_(qh facet_mergeset)  /* usually empty */
+  qh_memfree(merge, sizeof(mergeT) );
+  qh facet_mergeset = NULL;  /* temp set */
+  qh degen_mergeset = NULL;  /* temp set */
+  qh_settempfree_all();
+} /* freebuild */
+
+/*---------------------------------
+
+  qh_freeqhull( allmem )
+  free global memory
+  if !allmem,
+  does not free short memory (freed by qh_memfreeshort)
+
+  notes:
+  sets qh.NOerrexit in case caller forgets to
+
+  design:
+  free global and temporary memory from qh_initbuild and qh_buildhull
+  free buffers
+  free statistics
+*/
+void qh_freeqhull(boolT allmem)
+{
+
+  trace1( (qh ferr, "qh_freeqhull: free global memory\n") );
+  qh NOerrexit = True;  /* no more setjmp since called at exit */
+  qh_freebuild(allmem);
+  qh_freebuffers();
+  qh_freestatistics();
+#if qh_QHpointer
+  free(qh_qh);
+  qh_qh = NULL;
+#else
+  memset( (char *)&qh_qh, 0, sizeof(qhT) );
+  qh NOerrexit = True;
+#endif
+} /* freeqhull */
+
+/*---------------------------------
+
+  qh_init_A( infile, outfile, errfile, argc, argv )
+  initialize memory and stdio files
+  convert input options to option string (qh.qhull_command)
+
+  notes:
+  infile may be NULL if qh_readpoints() is not called
+
+  errfile should always be defined.  It is used for reporting
+  errors.  outfile is used for output and format options.
+
+  argc/argv may be 0/NULL
+
+  called before error handling initialized
+  qh_errexit() may not be used
+*/
+void qh_init_A(FILE *infile, FILE *outfile, FILE *errfile, int argc, char *argv[])
+{
+  qh_meminit(errfile);
+  qh_initqhull_start(infile, outfile, errfile);
+  qh_init_qhull_command(argc, argv);
+} /* init_A */
+
+/*---------------------------------
+
+  qh_init_B( points, numpoints, dim, ismalloc )
+  initialize globals for points array
+
+  points has numpoints dim-dimensional points
+  points[0] is the first coordinate of the first point
+  points[1] is the second coordinate of the first point
+  points[dim] is the first coordinate of the second point
+
+  ismalloc=True
+  Qhull will call free(points) on exit or input transformation
+  ismalloc=False
+  Qhull will allocate a new point array if needed for input transformation
+
+  qh.qhull_command
+  is the option string.
+  It is defined by qh_init_B(), qh_qhull_command(), or qh_initflags
+
+  returns:
+  if qh.PROJECTinput or (qh.DELAUNAY and qh.PROJECTdelaunay)
+  projects the input to a new point array
+
+  if qh.DELAUNAY,
+  qh.hull_dim is increased by one
+  if qh.ATinfinity,
+  qh_projectinput adds point-at-infinity for Delaunay tri.
+
+  if qh.SCALEinput
+  changes the upper and lower bounds of the input, see qh_scaleinput()
+
+  if qh.ROTATEinput
+  rotates the input by a random rotation, see qh_rotateinput()
+  if qh.DELAUNAY
+  rotates about the last coordinate
+
+  notes:
+  called after points are defined
+  qh_errexit() may be used
+*/
+void qh_init_B(coordT *points, int numpoints, int dim, boolT ismalloc)
+{
+  qh_initqhull_globals(points, numpoints, dim, ismalloc);
+  if( qhmem.LASTsize == 0 )
+    {
+    qh_initqhull_mem();
+    }
+  /* mem.c and qset.c are initialized */
+  qh_initqhull_buffers();
+  qh_initthresholds(qh qhull_command);
+  if( qh PROJECTinput || (qh DELAUNAY && qh PROJECTdelaunay) )
+    {
+    qh_projectinput();
+    }
+  if( qh SCALEinput )
+    {
+    qh_scaleinput();
+    }
+  if( qh ROTATErandom >= 0 )
+    {
+    qh_randommatrix(qh gm_matrix, qh hull_dim, qh gm_row);
+    if( qh DELAUNAY )
+      {
+      int k, lastk = qh hull_dim - 1;
+      for( k = 0; k < lastk; k++ )
+        {
+        qh gm_row[k][lastk] = 0.0;
+        qh gm_row[lastk][k] = 0.0;
+        }
+      qh gm_row[lastk][lastk] = 1.0;
+      }
+    qh_gram_schmidt(qh hull_dim, qh gm_row);
+    qh_rotateinput(qh gm_row);
+    }
+} /* init_B */
+
+/*---------------------------------
+
+  qh_init_qhull_command( argc, argv )
+  build qh.qhull_command from argc/argv
+
+  returns:
+  a space-deliminated string of options (just as typed)
+
+  notes:
+  makes option string easy to input and output
+
+  argc/argv may be 0/NULL
+*/
+void qh_init_qhull_command(int argc, char *argv[])
+{
+  int   i;
+  char *s;
+
+  if( argc )
+    {
+    if( (s = strrchr( argv[0], '\\') ) ) /* Borland gives full path */
+      {
+      strcpy(qh qhull_command, s + 1);
+      }
+    else
+      {
+      strcpy(qh qhull_command, argv[0]);
+      }
+    if( (s = strstr(qh qhull_command, ".EXE") )
+        ||  (s = strstr(qh qhull_command, ".exe") ) )
+      {
+      *s = '\0';
+      }
+    }
+  for( i = 1; i < argc; i++ )
+    {
+    if( strlen(qh qhull_command) + strlen(argv[i]) + 1 < sizeof(qh qhull_command) )
+      {
+      strcat(qh qhull_command, " ");
+      strcat(qh qhull_command, argv[i]);
+      }
+    else
+      {
+      fprintf(qh ferr, "qhull input error: more than %d characters in command line\n",
+              (int)sizeof(qh qhull_command) );
+      exit(1);   /* can not use qh_errexit */
+      }
+    }
+} /* init_qhull_command */
+
+/*---------------------------------
+
+  qh_initflags( commandStr )
+  set flags and initialized constants from commandStr
+
+  returns:
+  sets qh.qhull_command to command if needed
+
+  notes:
+  ignores first word (e.g., "qhull d")
+  use qh_strtol/strtod since strtol/strtod may or may not skip trailing spaces
+
+  see:
+  qh_initthresholds() continues processing of 'Pdn' and 'PDn'
+  'prompt' in unix.c for documentation
+
+  design:
+  for each space-deliminated option group
+  if top-level option
+  check syntax
+  append approriate option to option string
+  set appropriate global variable or append printFormat to print options
+  else
+  for each sub-option
+  check syntax
+  append approriate option to option string
+  set appropriate global variable or append printFormat to print options
+
+
+*/
+void qh_initflags(char *command)
+{
+  int   k, i, lastproject;
+  char *s = command, *t, *prev_s, *start, key;
+  boolT isgeom = False, wasproject;
+  realT r;
+
+  if( command != &qh qhull_command[0] )
+    {
+    *qh qhull_command = '\0';
+    strncat( qh qhull_command, command, sizeof( qh qhull_command) );
+    }
+  while( *s && !isspace(*s) )  /* skip program name */
+    {
+    s++;
+    }
+
+  while( *s )
+    {
+    while( *s && isspace(*s) )
+      {
+      s++;
+      }
+
+    if( *s == '-' )
+      {
+      s++;
+      }
+    if( !*s )
+      {
+      break;
+      }
+    prev_s = s;
+
+    switch( *s++ )
+      {
+      case 'd':
+        qh_option("delaunay", NULL, NULL);
+        qh DELAUNAY = True;
+        break;
+      case 'f':
+        qh_option("facets", NULL, NULL);
+        qh_appendprint(qh_PRINTfacets);
+        break;
+      case 'i':
+        qh_option("incidence", NULL, NULL);
+        qh_appendprint(qh_PRINTincidences);
+        break;
+      case 'm':
+        qh_option("mathematica", NULL, NULL);
+        qh_appendprint(qh_PRINTmathematica);
+        break;
+      case 'n':
+        qh_option("normals", NULL, NULL);
+        qh_appendprint(qh_PRINTnormals);
+        break;
+      case 'o':
+        qh_option("offFile", NULL, NULL);
+        qh_appendprint(qh_PRINToff);
+        break;
+      case 'p':
+        qh_option("points", NULL, NULL);
+        qh_appendprint(qh_PRINTpoints);
+        break;
+      case 's':
+        qh_option("summary", NULL, NULL);
+        qh PRINTsummary = True;
+        break;
+      case 'v':
+        qh_option("voronoi", NULL, NULL);
+        qh VORONOI = True;
+        qh DELAUNAY = True;
+        break;
+      case 'A':
+        if( !isdigit(*s) && *s != '.' && *s != '-' )
+          {
+          fprintf(qh ferr, "qhull warning: no maximum cosine angle given for option 'An'.  Ignored.\n");
+          }
+        else
+          {
+          if( *s == '-' )
+            {
+            qh premerge_cos = -qh_strtod(s, &s);
+            qh_option("Angle-premerge-", NULL, &qh premerge_cos);
+            qh PREmerge = True;
+            }
+          else
+            {
+            qh postmerge_cos = qh_strtod(s, &s);
+            qh_option("Angle-postmerge", NULL, &qh postmerge_cos);
+            qh POSTmerge = True;
+            }
+          qh MERGING = True;
+          }
+        break;
+      case 'C':
+        if( !isdigit(*s) && *s != '.' && *s != '-' )
+          {
+          fprintf(qh ferr, "qhull warning: no centrum radius given for option 'Cn'.  Ignored.\n");
+          }
+        else
+          {
+          if( *s == '-' )
+            {
+            qh premerge_centrum = -qh_strtod(s, &s);
+            qh_option("Centrum-premerge-", NULL, &qh premerge_centrum);
+            qh PREmerge = True;
+            }
+          else
+            {
+            qh postmerge_centrum = qh_strtod(s, &s);
+            qh_option("Centrum-postmerge", NULL, &qh postmerge_centrum);
+            qh POSTmerge = True;
+            }
+          qh MERGING = True;
+          }
+        break;
+      case 'E':
+        if( *s == '-' )
+          {
+          fprintf(qh ferr, "qhull warning: negative maximum roundoff given for option 'An'.  Ignored.\n");
+          }
+        else if( !isdigit(*s) )
+          {
+          fprintf(qh ferr, "qhull warning: no maximum roundoff given for option 'En'.  Ignored.\n");
+          }
+        else
+          {
+          qh DISTround = qh_strtod(s, &s);
+          qh_option("Distance-roundoff", NULL, &qh DISTround);
+          qh SETroundoff = True;
+          }
+        break;
+      case 'H':
+        start = s;
+        qh HALFspace = True;
+        qh_strtod(s, &t);
+        while( t > s )
+          {
+          if( *t && !isspace(*t) )
+            {
+            if( *t == ',' )
+              {
+              t++;
+              }
+            else
+              {
+              fprintf(qh ferr, "qhull warning: origin for Halfspace intersection should be 'Hn,n,n,...'\n");
+              }
+            }
+          s = t;
+          qh_strtod(s, &t);
+          }
+
+        if( start < t )
+          {
+          if( !(qh feasible_string = (char *)calloc( (size_t)(t - start + 1), (size_t)1) ) )
+            {
+            fprintf(qh ferr, "qhull error: insufficient memory for 'Hn,n,n'\n");
+            qh_errexit(qh_ERRmem, NULL, NULL);
+            }
+          strncpy(qh feasible_string, start, (size_t)(t - start) );
+          qh_option("Halfspace-about", NULL, NULL);
+          qh_option(qh feasible_string, NULL, NULL);
+          }
+        else
+          {
+          qh_option("Halfspace", NULL, NULL);
+          }
+        break;
+      case 'R':
+        if( !isdigit(*s) )
+          {
+          fprintf(qh ferr, "qhull warning: missing random perturbation for option 'Rn'.  Ignored\n");
+          }
+        else
+          {
+          qh RANDOMfactor = qh_strtod(s, &s);
+          qh_option("Random_perturb", NULL, &qh RANDOMfactor);
+          qh RANDOMdist = True;
+          }
+        break;
+      case 'V':
+        if( !isdigit(*s) && *s != '-' )
+          {
+          fprintf(qh ferr, "qhull warning: missing visible distance for option 'Vn'.  Ignored\n");
+          }
+        else
+          {
+          qh MINvisible = qh_strtod(s, &s);
+          qh_option("Visible", NULL, &qh MINvisible);
+          }
+        break;
+      case 'U':
+        if( !isdigit(*s) && *s != '-' )
+          {
+          fprintf(qh ferr, "qhull warning: missing coplanar distance for option 'Un'.  Ignored\n");
+          }
+        else
+          {
+          qh MAXcoplanar = qh_strtod(s, &s);
+          qh_option("U-coplanar", NULL, &qh MAXcoplanar);
+          }
+        break;
+      case 'W':
+        if( *s == '-' )
+          {
+          fprintf(qh ferr, "qhull warning: negative outside width for option 'Wn'.  Ignored.\n");
+          }
+        else if( !isdigit(*s) )
+          {
+          fprintf(qh ferr, "qhull warning: missing outside width for option 'Wn'.  Ignored\n");
+          }
+        else
+          {
+          qh MINoutside = qh_strtod(s, &s);
+          qh_option("W-outside", NULL, &qh MINoutside);
+          qh APPROXhull = True;
+          }
+        break;
+      /************  sub menus ***************/
+      case 'F':
+        while( *s && !isspace(*s) )
+          {
+          switch( *s++ )
+            {
+            case 'a':
+              qh_option("Farea", NULL, NULL);
+              qh_appendprint(qh_PRINTarea);
+              qh GETarea = True;
+              break;
+            case 'A':
+              qh_option("FArea-total", NULL, NULL);
+              qh GETarea = True;
+              break;
+            case 'c':
+              qh_option("Fcoplanars", NULL, NULL);
+              qh_appendprint(qh_PRINTcoplanars);
+              break;
+            case 'C':
+              qh_option("FCentrums", NULL, NULL);
+              qh_appendprint(qh_PRINTcentrums);
+              break;
+            case 'd':
+              qh_option("Fd-cdd-in", NULL, NULL);
+              qh CDDinput = True;
+              break;
+            case 'D':
+              qh_option("FD-cdd-out", NULL, NULL);
+              qh CDDoutput = True;
+              break;
+            case 'F':
+              qh_option("FFacets-xridge", NULL, NULL);
+              qh_appendprint(qh_PRINTfacets_xridge);
+              break;
+            case 'i':
+              qh_option("Finner", NULL, NULL);
+              qh_appendprint(qh_PRINTinner);
+              break;
+            case 'I':
+              qh_option("FIDs", NULL, NULL);
+              qh_appendprint(qh_PRINTids);
+              break;
+            case 'm':
+              qh_option("Fmerges", NULL, NULL);
+              qh_appendprint(qh_PRINTmerges);
+              break;
+            case 'M':
+              qh_option("FMaple", NULL, NULL);
+              qh_appendprint(qh_PRINTmaple);
+              break;
+            case 'n':
+              qh_option("Fneighbors", NULL, NULL);
+              qh_appendprint(qh_PRINTneighbors);
+              break;
+            case 'N':
+              qh_option("FNeighbors-vertex", NULL, NULL);
+              qh_appendprint(qh_PRINTvneighbors);
+              break;
+            case 'o':
+              qh_option("Fouter", NULL, NULL);
+              qh_appendprint(qh_PRINTouter);
+              break;
+            case 'O':
+              if( qh PRINToptions1st )
+                {
+                qh_option("FOptions", NULL, NULL);
+                qh_appendprint(qh_PRINToptions);
+                }
+              else
+                {
+                qh PRINToptions1st = True;
+                }
+              break;
+            case 'p':
+              qh_option("Fpoint-intersect", NULL, NULL);
+              qh_appendprint(qh_PRINTpointintersect);
+              break;
+            case 'P':
+              qh_option("FPoint-nearest", NULL, NULL);
+              qh_appendprint(qh_PRINTpointnearest);
+              break;
+            case 'Q':
+              qh_option("FQhull", NULL, NULL);
+              qh_appendprint(qh_PRINTqhull);
+              break;
+            case 's':
+              qh_option("Fsummary", NULL, NULL);
+              qh_appendprint(qh_PRINTsummary);
+              break;
+            case 'S':
+              qh_option("FSize", NULL, NULL);
+              qh_appendprint(qh_PRINTsize);
+              qh GETarea = True;
+              break;
+            case 't':
+              qh_option("Ftriangles", NULL, NULL);
+              qh_appendprint(qh_PRINTtriangles);
+              break;
+            case 'v':
+              /* option set in qh_initqhull_globals */
+              qh_appendprint(qh_PRINTvertices);
+              break;
+            case 'V':
+              qh_option("FVertex-average", NULL, NULL);
+              qh_appendprint(qh_PRINTaverage);
+              break;
+            case 'x':
+              qh_option("Fxtremes", NULL, NULL);
+              qh_appendprint(qh_PRINTextremes);
+              break;
+            default:
+              s--;
+              fprintf(qh ferr, "qhull warning: unknown 'F' output option %c, rest ignored\n", (int)s[0]);
+              while( *++s && !isspace(*s) )
+                {
+                ;
+                }
+
+              break;
+            }
+          }
+
+        break;
+      case 'G':
+        isgeom = True;
+        qh_appendprint(qh_PRINTgeom);
+        while( *s && !isspace(*s) )
+          {
+          switch( *s++ )
+            {
+            case 'a':
+              qh_option("Gall-points", NULL, NULL);
+              qh PRINTdots = True;
+              break;
+            case 'c':
+              qh_option("Gcentrums", NULL, NULL);
+              qh PRINTcentrums = True;
+              break;
+            case 'h':
+              qh_option("Gintersections", NULL, NULL);
+              qh DOintersections = True;
+              break;
+            case 'i':
+              qh_option("Ginner", NULL, NULL);
+              qh PRINTinner = True;
+              break;
+            case 'n':
+              qh_option("Gno-planes", NULL, NULL);
+              qh PRINTnoplanes = True;
+              break;
+            case 'o':
+              qh_option("Gouter", NULL, NULL);
+              qh PRINTouter = True;
+              break;
+            case 'p':
+              qh_option("Gpoints", NULL, NULL);
+              qh PRINTcoplanar = True;
+              break;
+            case 'r':
+              qh_option("Gridges", NULL, NULL);
+              qh PRINTridges = True;
+              break;
+            case 't':
+              qh_option("Gtransparent", NULL, NULL);
+              qh PRINTtransparent = True;
+              break;
+            case 'v':
+              qh_option("Gvertices", NULL, NULL);
+              qh PRINTspheres = True;
+              break;
+            case 'D':
+              if( !isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull input error: missing dimension for option 'GDn'\n");
+                }
+              else
+                {
+                if( qh DROPdim >= 0 )
+                  {
+                  fprintf(qh ferr, "qhull warning: can only drop one dimension.  Previous 'GD%d' ignored\n",
+                          qh DROPdim);
+                  }
+                qh DROPdim = qh_strtol(s, &s);
+                qh_option("GDrop-dim", &qh DROPdim, NULL);
+                }
+              break;
+            default:
+              s--;
+              fprintf(qh ferr, "qhull warning: unknown 'G' print option %c, rest ignored\n", (int)s[0]);
+              while( *++s && !isspace(*s) )
+                {
+                ;
+                }
+
+              break;
+            }
+          }
+
+        break;
+      case 'P':
+        while( *s && !isspace(*s) )
+          {
+          switch( *s++ )
+            {
+            case 'd': case 'D': /* see qh_initthresholds() */
+              key = s[-1];
+              i = qh_strtol(s, &s);
+              r = 0;
+              if( *s == ':' )
+                {
+                s++;
+                r = qh_strtod(s, &s);
+                }
+              if( key == 'd' )
+                {
+                qh_option("Pdrop-facets-dim-less", &i, &r);
+                }
+              else
+                {
+                qh_option("PDrop-facets-dim-more", &i, &r);
+                }
+              break;
+            case 'g':
+              qh_option("Pgood-facets", NULL, NULL);
+              qh PRINTgood = True;
+              break;
+            case 'G':
+              qh_option("PGood-facet-neighbors", NULL, NULL);
+              qh PRINTneighbors = True;
+              break;
+            case 'o':
+              qh_option("Poutput-forced", NULL, NULL);
+              qh FORCEoutput = True;
+              break;
+            case 'p':
+              qh_option("Pprecision-ignore", NULL, NULL);
+              qh PRINTprecision = False;
+              break;
+            case 'A':
+              if( !isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull input error: missing facet count for keep area option 'PAn'\n");
+                }
+              else
+                {
+                qh KEEParea = qh_strtol(s, &s);
+                qh_option("PArea-keep", &qh KEEParea, NULL);
+                qh GETarea = True;
+                }
+              break;
+            case 'F':
+              if( !isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull input error: missing facet area for option 'PFn'\n");
+                }
+              else
+                {
+                qh KEEPminArea = qh_strtod(s, &s);
+                qh_option("PFacet-area-keep", NULL, &qh KEEPminArea);
+                qh GETarea = True;
+                }
+              break;
+            case 'M':
+              if( !isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull input error: missing merge count for option 'PMn'\n");
+                }
+              else
+                {
+                qh KEEPmerge = qh_strtol(s, &s);
+                qh_option("PMerge-keep", &qh KEEPmerge, NULL);
+                }
+              break;
+            default:
+              s--;
+              fprintf(qh ferr, "qhull warning: unknown 'P' print option %c, rest ignored\n", (int)s[0]);
+              while( *++s && !isspace(*s) )
+                {
+                ;
+                }
+
+              break;
+            }
+          }
+
+        break;
+      case 'Q':
+        lastproject = -1;
+        while( *s && !isspace(*s) )
+          {
+          switch( *s++ )
+            {
+            case 'b': case 'B': /* handled by qh_initthresholds */
+              key = s[-1];
+              if( key == 'b' && *s == 'B' )
+                {
+                s++;
+                r = qh_DEFAULTbox;
+                qh SCALEinput = True;
+                qh_option("QbBound-unit-box", NULL, &r);
+                break;
+                }
+              if( key == 'b' && *s == 'b' )
+                {
+                s++;
+                qh SCALElast = True;
+                qh_option("Qbbound-last", NULL, NULL);
+                break;
+                }
+              k = qh_strtol(s, &s);
+              r = 0.0;
+              wasproject = False;
+              if( *s == ':' )
+                {
+                s++;
+                if( (r = qh_strtod(s, &s) ) == 0.0 )
+                  {
+                  t = s; /* need true dimension for memory allocation */
+                  while( *t && !isspace(*t) )
+                    {
+                    if( toupper(*t++) == 'B'
+                        && k == qh_strtol(t, &t)
+                        && *t++ == ':'
+                        && qh_strtod(t, &t) == 0.0 )
+                      {
+                      qh PROJECTinput++;
+                      trace2( (qh ferr, "qh_initflags: project dimension %d\n", k) );
+                      qh_option("Qb-project-dim", &k, NULL);
+                      wasproject = True;
+                      lastproject = k;
+                      break;
+                      }
+                    }
+                  }
+                }
+              if( !wasproject )
+                {
+                if( lastproject == k && r == 0.0 )
+                  {
+                  lastproject = -1; /* doesn't catch all possible sequences */
+                  }
+                else if( key == 'b' )
+                  {
+                  qh SCALEinput = True;
+                  if( r == 0.0 )
+                    {
+                    r = -qh_DEFAULTbox;
+                    }
+                  qh_option("Qbound-dim-low", &k, &r);
+                  }
+                else
+                  {
+                  qh SCALEinput = True;
+                  if( r == 0.0 )
+                    {
+                    r = qh_DEFAULTbox;
+                    }
+                  qh_option("QBound-dim-high", &k, &r);
+                  }
+                }
+              break;
+            case 'c':
+              qh_option("Qcoplanar-keep", NULL, NULL);
+              qh KEEPcoplanar = True;
+              break;
+            case 'f':
+              qh_option("Qfurthest-outside", NULL, NULL);
+              qh BESToutside = True;
+              break;
+            case 'g':
+              qh_option("Qgood-facets-only", NULL, NULL);
+              qh ONLYgood = True;
+              break;
+            case 'i':
+              qh_option("Qinterior-keep", NULL, NULL);
+              qh KEEPinside = True;
+              break;
+            case 'm':
+              qh_option("Qmax-outside-only", NULL, NULL);
+              qh ONLYmax = True;
+              break;
+            case 'r':
+              qh_option("Qrandom-outside", NULL, NULL);
+              qh RANDOMoutside = True;
+              break;
+            case 's':
+              qh_option("Qsearch-initial-simplex", NULL, NULL);
+              qh ALLpoints = True;
+              break;
+            case 't':
+              qh_option("Qtriangulate", NULL, NULL);
+              qh TRIangulate = True;
+              break;
+            case 'T':
+              qh_option("QTestPoints", NULL, NULL);
+              if( !isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull input error: missing number of test points for option 'QTn'\n");
+                }
+              else
+                {
+                qh TESTpoints = qh_strtol(s, &s);
+                qh_option("QTestPoints", &qh TESTpoints, NULL);
+                }
+              break;
+            case 'u':
+              qh_option("QupperDelaunay", NULL, NULL);
+              qh UPPERdelaunay = True;
+              break;
+            case 'v':
+              qh_option("Qvertex-neighbors-convex", NULL, NULL);
+              qh TESTvneighbors = True;
+              break;
+            case 'x':
+              qh_option("Qxact-merge", NULL, NULL);
+              qh MERGEexact = True;
+              break;
+            case 'z':
+              qh_option("Qz-infinity-point", NULL, NULL);
+              qh ATinfinity = True;
+              break;
+            case '0':
+              qh_option("Q0-no-premerge", NULL, NULL);
+              qh NOpremerge = True;
+              break;
+            case '1':
+              if( !isdigit(*s) )
+                {
+                qh_option("Q1-no-angle-sort", NULL, NULL);
+                qh ANGLEmerge = False;
+                break;
+                }
+
+              switch( *s++ )
+                {
+                case '0':
+                  qh_option("Q10-no-narrow", NULL, NULL);
+                  qh NOnarrow = True;
+                  break;
+                case '1':
+                  qh_option("Q11-trinormals Qtriangulate", NULL, NULL);
+                  qh TRInormals = True;
+                  qh TRIangulate = True;
+                  break;
+                default:
+                  s--;
+                  fprintf(qh ferr, "qhull warning: unknown 'Q' qhull option 1%c, rest ignored\n", (int)s[0]);
+                  while( *++s && !isspace(*s) )
+                    {
+                    ;
+                    }
+
+                  break;
+                }
+              break;
+            case '2':
+              qh_option("Q2-no-merge-independent", NULL, NULL);
+              qh MERGEindependent = False;
+              goto LABELcheckdigit;
+              break; /* no warnings */
+            case '3':
+              qh_option("Q3-no-merge-vertices", NULL, NULL);
+              qh MERGEvertices = False;
+LABELcheckdigit:
+              if( isdigit(*s) )
+                {
+                fprintf(qh ferr, "qhull warning: can not follow '1', '2', or '3' with a digit.  '%c' skipped.\n",
+                        *s++);
+                }
+              break;
+            case '4':
+              qh_option("Q4-avoid-old-into-new", NULL, NULL);
+              qh AVOIDold = True;
+              break;
+            case '5':
+              qh_option("Q5-no-check-outer", NULL, NULL);
+              qh SKIPcheckmax = True;
+              break;
+            case '6':
+              qh_option("Q6-no-concave-merge", NULL, NULL);
+              qh SKIPconvex = True;
+              break;
+            case '7':
+              qh_option("Q7-no-breadth-first", NULL, NULL);
+              qh VIRTUALmemory = True;
+              break;
+            case '8':
+              qh_option("Q8-no-near-inside", NULL, NULL);
+              qh NOnearinside = True;
+              break;
+            case '9':
+              qh_option("Q9-pick-furthest", NULL, NULL);
+              qh PICKfurthest = True;
+              break;
+            case 'G':
+              i = qh_strtol(s, &t);
+              if( qh GOODpoint )
+                {
+                fprintf(qh ferr, "qhull warning: good point already defined for option 'QGn'.  Ignored\n");
+                }
+              else if( s == t )
+                {
+                fprintf(qh ferr, "qhull warning: missing good point id for option 'QGn'.  Ignored\n");
+                }
+              else if( i < 0 || *s == '-' )
+                {
+                qh GOODpoint = i - 1;
+                qh_option("QGood-if-dont-see-point", &i, NULL);
+                }
+              else
+                {
+                qh GOODpoint = i + 1;
+                qh_option("QGood-if-see-point", &i, NULL);
+                }
+              s = t;
+              break;
+            case 'J':
+              if( !isdigit(*s) && *s != '-' )
+                {
+                qh JOGGLEmax = 0.0;
+                }
+              else
+                {
+                qh JOGGLEmax = (realT) qh_strtod(s, &s);
+                qh_option("QJoggle", NULL, &qh JOGGLEmax);
+                }
+              break;
+            case 'R':
+              if( !isdigit(*s) && *s != '-' )
+                {
+                fprintf(qh ferr, "qhull warning: missing random seed for option 'QRn'.  Ignored\n");
+                }
+              else
+                {
+                qh ROTATErandom = i = qh_strtol(s, &s);
+                if( i > 0 )
+                  {
+                  qh_option("QRotate-id", &i, NULL );
+                  }
+                else if( i < -1 )
+                  {
+                  qh_option("QRandom-seed", &i, NULL );
+                  }
+                }
+              break;
+            case 'V':
+              i = qh_strtol(s, &t);
+              if( qh GOODvertex )
+                {
+                fprintf(qh ferr, "qhull warning: good vertex already defined for option 'QVn'.  Ignored\n");
+                }
+              else if( s == t )
+                {
+                fprintf(qh ferr, "qhull warning: no good point id given for option 'QVn'.  Ignored\n");
+                }
+              else if( i < 0 )
+                {
+                qh GOODvertex = i - 1;
+                qh_option("QV-good-facets-not-point", &i, NULL);
+                }
+              else
+                {
+                qh_option("QV-good-facets-point", &i, NULL);
+                qh GOODvertex = i + 1;
+                }
+              s = t;
+              break;
+            default:
+              s--;
+              fprintf(qh ferr, "qhull warning: unknown 'Q' qhull option %c, rest ignored\n", (int)s[0]);
+              while( *++s && !isspace(*s) )
+                {
+                ;
+                }
+
+              break;
+            }
+          }
+
+        break;
+      case 'T':
+        while( *s && !isspace(*s) )
+          {
+          if( isdigit(*s) || *s == '-' )
+            {
+            qh IStracing = qh_strtol(s, &s);
+            }
+          else
+            {
+            switch( *s++ )
+              {
+              case 'c':
+                qh_option("Tcheck-frequently", NULL, NULL);
+                qh CHECKfrequently = True;
+                break;
+              case 's':
+                qh_option("Tstatistics", NULL, NULL);
+                qh PRINTstatistics = True;
+                break;
+              case 'v':
+                qh_option("Tverify", NULL, NULL);
+                qh VERIFYoutput = True;
+                break;
+              case 'z':
+                if( !qh fout )
+                  {
+                  fprintf(qh ferr, "qhull warning: output file undefined (stdout).  Option 'Tz' ignored.\n");
+                  }
+                else
+                  {
+                  qh_option("Tz-stdout", NULL, NULL);
+                  qh ferr = qh fout;
+                  qhmem.ferr = qh fout;
+                  }
+                break;
+              case 'C':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing point id for cone for trace option 'TCn'.  Ignored\n");
+                  }
+                else
+                  {
+                  i = qh_strtol(s, &s);
+                  qh_option("TCone-stop", &i, NULL);
+                  qh STOPcone = i + 1;
+                  }
+                break;
+              case 'F':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing frequency count for trace option 'TFn'.  Ignored\n");
+                  }
+                else
+                  {
+                  qh REPORTfreq = qh_strtol(s, &s);
+                  qh_option("TFacet-log", &qh REPORTfreq, NULL);
+                  qh REPORTfreq2 = qh REPORTfreq / 2; /* for tracemerging() */
+                  }
+                break;
+              case 'I':
+                if( s[0] != ' ' || s[1] == '\"' || s[1] == '\'' || isspace(s[1]) )
+                  {
+                  s++;
+                  fprintf(
+                    qh ferr,
+                    "qhull warning: option 'TI' mistyped.\nUse 'TI', one space, file name, and space or end-of-line.\nDo not use quotes.  Option 'FI' ignored.\n");
+                  }
+                else /* not a procedure because of qh_option (filename, NULL,
+                       NULL); */
+                  {
+                  char filename[500], *T = filename;
+
+                  s++;
+                  while( *s )
+                    {
+                    if( T - filename >= (int)sizeof (filename) - 2 )
+                      {
+                      fprintf(qh ferr, "qhull error: filename for 'TI' too long.\n");
+                      qh_errexit(qh_ERRinput, NULL, NULL);
+                      }
+                    if( isspace(*s) )
+                      {
+                      break;
+                      }
+                    *(T++) = *s++;
+                    }
+
+                  *T = '\0';
+                  if( !freopen(filename, "r", stdin) )
+                    {
+                    fprintf(qh ferr, "qhull error: could not open file \"%s\".", filename);
+                    qh_errexit(qh_ERRinput, NULL, NULL);
+                    }
+                  else
+                    {
+                    qh_option("TInput-file", NULL, NULL);
+                    qh_option(filename, NULL, NULL);
+                    }
+                  }
+                break;
+              case 'O':
+                if( s[0] != ' ' || s[1] == '\"' || isspace(s[1]) )
+                  {
+                  s++;
+                  fprintf(
+                    qh ferr,
+                    "qhull warning: option 'TO' mistyped.\nUse 'TO', one space, file name, and space or end-of-line.\nThe file name may be enclosed in single quotes.\nDo not use double quotes.  Option 'FO' ignored.\n");
+                  }
+                else /* not a procedure because of qh_option (filename, NULL,
+                       NULL); */
+                  {
+                  char  filename[500], *T = filename;
+                  boolT isquote = False;
+
+                  s++;
+                  if( *s == '\'' )
+                    {
+                    isquote = True;
+                    s++;
+                    }
+                  while( *s )
+                    {
+                    if( T - filename >= (int)sizeof (filename) - 2 )
+                      {
+                      fprintf(qh ferr, "qhull error: filename for 'TO' too long.\n");
+                      qh_errexit(qh_ERRinput, NULL, NULL);
+                      }
+                    if( isquote )
+                      {
+                      if( *s == '\'' )
+                        {
+                        s++;
+                        isquote = False;
+                        break;
+                        }
+                      }
+                    else if( isspace(*s) )
+                      {
+                      break;
+                      }
+                    *(T++) = *s++;
+                    }
+
+                  *T = '\0';
+                  if( isquote )
+                    {
+                    fprintf(qh ferr, "qhull error: missing end quote for option 'TO'.  Rest of line ignored.\n");
+                    }
+                  else if( !freopen(filename, "w", stdout) )
+                    {
+                    fprintf(qh ferr, "qhull error: could not open file \"%s\".", filename);
+                    qh_errexit(qh_ERRinput, NULL, NULL);
+                    }
+                  else
+                    {
+                    qh_option("TOutput-file", NULL, NULL);
+                    qh_option(filename, NULL, NULL);
+                    }
+                  }
+                break;
+              case 'P':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing point id for trace option 'TPn'.  Ignored\n");
+                  }
+                else
+                  {
+                  qh TRACEpoint = qh_strtol(s, &s);
+                  qh_option("Trace-point", &qh TRACEpoint, NULL);
+                  }
+                break;
+              case 'M':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing merge id for trace option 'TMn'.  Ignored\n");
+                  }
+                else
+                  {
+                  qh TRACEmerge = qh_strtol(s, &s);
+                  qh_option("Trace-merge", &qh TRACEmerge, NULL);
+                  }
+                break;
+              case 'R':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing rerun count for trace option 'TRn'.  Ignored\n");
+                  }
+                else
+                  {
+                  qh RERUN = qh_strtol(s, &s);
+                  qh_option("TRerun", &qh RERUN, NULL);
+                  }
+                break;
+              case 'V':
+                i = qh_strtol(s, &t);
+                if( s == t )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing furthest point id for trace option 'TVn'.  Ignored\n");
+                  }
+                else if( i < 0 )
+                  {
+                  qh STOPpoint = i - 1;
+                  qh_option("TV-stop-before-point", &i, NULL);
+                  }
+                else
+                  {
+                  qh STOPpoint = i + 1;
+                  qh_option("TV-stop-after-point", &i, NULL);
+                  }
+                s = t;
+                break;
+              case 'W':
+                if( !isdigit(*s) )
+                  {
+                  fprintf(qh ferr, "qhull warning: missing max width for trace option 'TWn'.  Ignored\n");
+                  }
+                else
+                  {
+                  qh TRACEdist = (realT) qh_strtod(s, &s);
+                  qh_option("TWide-trace", NULL, &qh TRACEdist);
+                  }
+                break;
+              default:
+                s--;
+                fprintf(qh ferr, "qhull warning: unknown 'T' trace option %c, rest ignored\n", (int)s[0]);
+                while( *++s && !isspace(*s) )
+                  {
+                  ;
+                  }
+
+                break;
+              }
+            }
+          }
+
+        break;
+      default:
+        fprintf(qh ferr, "qhull warning: unknown flag %c (%x)\n", (int)s[-1],
+                (int)s[-1]);
+        break;
+      }
+    if( s - 1 == prev_s && *s && !isspace(*s) )
+      {
+      fprintf(qh ferr, "qhull warning: missing space after flag %c (%x); reserved for menu. Skipped.\n",
+              (int)*prev_s, (int)*prev_s);
+      while( *s && !isspace(*s) )
+        {
+        s++;
+        }
+      }
+    }
+
+  if( isgeom && !qh FORCEoutput && qh PRINTout[1] )
+    {
+    fprintf(qh ferr, "qhull warning: additional output formats are not compatible with Geomview\n");
+    }
+  /* set derived values in qh_initqhull_globals */
+} /* initflags */
+
+/*---------------------------------
+
+  qh_initqhull_buffers()
+  initialize global memory buffers
+
+  notes:
+  must match qh_freebuffers()
+*/
+void qh_initqhull_buffers(void)
+{
+  int k;
+
+  qh TEMPsize = (qhmem.LASTsize - sizeof (setT) ) / SETelemsize;
+
+  if( qh TEMPsize <= 0 || qh TEMPsize > qhmem.LASTsize )
+    {
+    qh TEMPsize = 8;  /* e.g., if qh_NOmem */
+    }
+  qh other_points = qh_setnew(qh TEMPsize);
+  qh del_vertices = qh_setnew(qh TEMPsize);
+  qh coplanarset = qh_setnew(qh TEMPsize);
+  qh NEARzero = (realT *)qh_memalloc(qh hull_dim * sizeof(realT) );
+  qh lower_threshold = (realT *)qh_memalloc( (qh input_dim + 1) * sizeof(realT) );
+  qh upper_threshold = (realT *)qh_memalloc( (qh input_dim + 1) * sizeof(realT) );
+  qh lower_bound = (realT *)qh_memalloc( (qh input_dim + 1) * sizeof(realT) );
+  qh upper_bound = (realT *)qh_memalloc( (qh input_dim + 1) * sizeof(realT) );
+  for( k = qh input_dim + 1; k--; )
+    {
+    qh lower_threshold[k] = -REALmax;
+    qh upper_threshold[k] = REALmax;
+    qh lower_bound[k] = -REALmax;
+    qh upper_bound[k] = REALmax;
+    }
+  qh gm_matrix = (coordT *)qh_memalloc( (qh hull_dim + 1) * qh hull_dim * sizeof(coordT) );
+  qh gm_row = (coordT * *)qh_memalloc( (qh hull_dim + 1) * sizeof(coordT *) );
+} /* initqhull_buffers */
+
+/*---------------------------------
+
+  qh_initqhull_globals( points, numpoints, dim, ismalloc )
+  initialize globals
+  if ismalloc
+  points were malloc'd and qhull should free at end
+
+  returns:
+  sets qh.first_point, num_points, input_dim, hull_dim and others
+  seeds random number generator (seed=1 if tracing)
+  modifies qh.hull_dim if ((qh.DELAUNAY and qh.PROJECTdelaunay) or qh.PROJECTinput)
+  adjust user flags as needed
+  also checks DIM3 dependencies and constants
+
+  notes:
+  do not use qh_point() since an input transformation may move them elsewhere
+
+  see:
+  qh_initqhull_start() sets default values for non-zero globals
+
+  design:
+  initialize points array from input arguments
+  test for qh.ZEROcentrum
+  (i.e., use opposite vertex instead of cetrum for convexity testing)
+  test for qh.PRINTgood (i.e., only print 'good' facets)
+  initialize qh.CENTERtype, qh.normal_size,
+  qh.center_size, qh.TRACEpoint/level,
+  initialize and test random numbers
+  check for conflicting print output options
+*/
+void qh_initqhull_globals(coordT *points, int numpoints, int dim, boolT ismalloc)
+{
+  int   seed, pointsneeded, extra = 0, i, randi, k;
+  boolT printgeom = False, printmath = False, printcoplanar = False;
+  realT randr;
+  realT factorial;
+
+  time_t timedata;
+
+  trace0( (qh ferr, "qh_initqhull_globals: for %s | %s\n", qh rbox_command,
+           qh qhull_command) );
+  qh POINTSmalloc = ismalloc;
+  qh first_point = points;
+  qh num_points = numpoints;
+  qh hull_dim = qh input_dim = dim;
+  if( !qh NOpremerge && !qh MERGEexact && !qh PREmerge && qh JOGGLEmax > REALmax / 2 )
+    {
+    qh MERGING = True;
+    if( qh hull_dim <= 4 )
+      {
+      qh PREmerge = True;
+      qh_option("_pre-merge", NULL, NULL);
+      }
+    else
+      {
+      qh MERGEexact = True;
+      qh_option("Qxact_merge", NULL, NULL);
+      }
+    }
+  else if( qh MERGEexact )
+    {
+    qh MERGING = True;
+    }
+  if( !qh NOpremerge && qh JOGGLEmax > REALmax / 2 )
+    {
+#ifdef qh_NOmerge
+    qh JOGGLEmax = 0.0;
+#endif
+    }
+  if( qh TRIangulate && qh JOGGLEmax < REALmax / 2 && qh PRINTprecision )
+    {
+    fprintf(
+      qh ferr,
+      "qhull warning: joggle ('QJ') always produces simplicial output.  Triangulated output ('Qt') does nothing.\n");
+    }
+  if( qh JOGGLEmax < REALmax / 2 && qh DELAUNAY && !qh SCALEinput && !qh SCALElast )
+    {
+    qh SCALElast = True;
+    qh_option("Qbbound-last-qj", NULL, NULL);
+    }
+  if( qh MERGING && !qh POSTmerge && qh premerge_cos > REALmax / 2
+      && qh premerge_centrum == 0 )
+    {
+    qh ZEROcentrum = True;
+    qh ZEROall_ok = True;
+    qh_option("_zero-centrum", NULL, NULL);
+    }
+  if( qh JOGGLEmax < REALmax / 2 && REALepsilon > 2e-8 && qh PRINTprecision )
+    {
+    fprintf(
+      qh ferr,
+      "qhull warning: real epsilon, %2.2g, is probably too large for joggle ('QJn')\nRecompile with double precision reals (see user.h).\n",
+      REALepsilon);
+    }
+#ifdef qh_NOmerge
+  if( qh MERGING )
+    {
+    fprintf(qh ferr, "qhull input error: merging not installed (qh_NOmerge + 'Qx', 'Cn' or 'An')\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+#endif
+  if( !(qh PRINTgood || qh PRINTneighbors) )
+    {
+    if( qh KEEParea || qh KEEPminArea < REALmax / 2 || qh KEEPmerge || qh DELAUNAY
+        || (!qh ONLYgood && (qh GOODvertex || qh GOODpoint) ) )
+      {
+      qh PRINTgood = True;
+      qh_option("Pgood", NULL, NULL);
+      }
+    }
+  if( qh DELAUNAY && qh KEEPcoplanar && !qh KEEPinside )
+    {
+    qh KEEPinside = True;
+    qh_option("Qinterior-keep", NULL, NULL);
+    }
+  if( qh DELAUNAY && qh HALFspace )
+    {
+    fprintf(qh ferr,
+            "qhull input error: can not use Delaunay ('d') or Voronoi ('v') with halfspace intersection ('H')\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( !qh DELAUNAY && (qh UPPERdelaunay || qh ATinfinity) )
+    {
+    fprintf(
+      qh ferr,
+      "qhull input error: use upper-Delaunay ('Qu') or infinity-point ('Qz') with Delaunay ('d') or Voronoi ('v')\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh UPPERdelaunay && qh ATinfinity )
+    {
+    fprintf(qh ferr, "qhull input error: can not use infinity-point ('Qz') with upper-Delaunay ('Qu')\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh SCALElast && !qh DELAUNAY && qh PRINTprecision )
+    {
+    fprintf(qh ferr, "qhull input warning: option 'Qbb' (scale-last-coordinate) is normally used with 'd' or 'v'\n");
+    }
+  qh DOcheckmax = (!qh SKIPcheckmax && qh MERGING );
+  qh KEEPnearinside = (qh DOcheckmax && !(qh KEEPinside && qh KEEPcoplanar)
+                       && !qh NOnearinside);
+  if( qh MERGING )
+    {
+    qh CENTERtype = qh_AScentrum;
+    }
+  else if( qh VORONOI )
+    {
+    qh CENTERtype = qh_ASvoronoi;
+    }
+  if( qh TESTvneighbors && !qh MERGING )
+    {
+    fprintf(qh ferr, "qhull input error: test vertex neighbors ('Qv') needs a merge option\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh PROJECTinput || (qh DELAUNAY && qh PROJECTdelaunay) )
+    {
+    qh hull_dim -= qh PROJECTinput;
+    if( qh DELAUNAY )
+      {
+      qh hull_dim++;
+      extra = 1;
+      }
+    }
+  if( qh hull_dim <= 1 )
+    {
+    fprintf(qh ferr, "qhull error: dimension %d must be > 1\n", qh hull_dim);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  for( k = 2, factorial = 1.0; k < qh hull_dim; k++ )
+    {
+    factorial *= k;
+    }
+  qh AREAfactor = 1.0 / factorial;
+  trace2( (qh ferr,
+           "qh_initqhull_globals: initialize globals.  dim %d numpoints %d malloc? %d projected %d to hull_dim %d\n",
+           dim, numpoints, ismalloc, qh PROJECTinput, qh hull_dim) );
+  qh normal_size = qh hull_dim * sizeof(coordT);
+  qh center_size = qh normal_size - sizeof(coordT);
+  pointsneeded = qh hull_dim + 1;
+  if( qh hull_dim > qh_DIMmergeVertex )
+    {
+    qh MERGEvertices = False;
+    qh_option("Q3-no-merge-vertices-dim-high", NULL, NULL);
+    }
+  if( qh GOODpoint )
+    {
+    pointsneeded++;
+    }
+#ifdef qh_NOtrace
+  if( qh IStracing )
+    {
+    fprintf(qh ferr, "qhull input error: tracing is not installed (qh_NOtrace in user.h)");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+#endif
+  if( qh RERUN > 1 )
+    {
+    qh TRACElastrun = qh IStracing; /* qh_build_withrestart duplicates next
+                                      conditional */
+    if( qh IStracing != -1 )
+      {
+      qh IStracing = 0;
+      }
+    }
+  else if( qh TRACEpoint != -1 || qh TRACEdist < REALmax / 2 || qh TRACEmerge )
+    {
+    qh TRACElevel = (qh IStracing ? qh IStracing : 3);
+    qh IStracing = 0;
+    }
+  if( qh ROTATErandom == 0 || qh ROTATErandom == -1 )
+    {
+    seed = time(&timedata);
+    if( qh ROTATErandom  == -1 )
+      {
+      seed = -seed;
+      qh_option("QRandom-seed", &seed, NULL );
+      }
+    else
+      {
+      qh_option("QRotate-random", &seed, NULL);
+      }
+    qh ROTATErandom = seed;
+    }
+  seed = qh ROTATErandom;
+  if( seed == INT_MIN )    /* default value */
+    {
+    seed = 1;
+    }
+  else if( seed < 0 )
+    {
+    seed = -seed;
+    }
+  qh_RANDOMseed_(seed);
+  randr = 0.0;
+  for( i = 1000; i--; )
+    {
+    randi = qh_RANDOMint;
+    randr += randi;
+    if( randi > qh_RANDOMmax )
+      {
+      fprintf(qh ferr,
+              "\
+qhull configuration error (qh_RANDOMmax in user.h):\n\
+   random integer %d > qh_RANDOMmax (%.8g)\n"                                                                        ,
+              randi,
+              qh_RANDOMmax);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    }
+  qh_RANDOMseed_(seed);
+  randr = randr / 1000;
+  if( randr < qh_RANDOMmax / 10
+      || randr > qh_RANDOMmax * 5 )
+    {
+    fprintf(
+      qh ferr,
+      "\
+qhull configuration warning (qh_RANDOMmax in user.h):\n\
+   average of 1000 random integers (%.2g) is much different than expected (%.2g).\n\
+   Is qh_RANDOMmax (%.2g) wrong?\n"                                                                                                                                                       ,
+      randr, qh_RANDOMmax / 2.0,
+      qh_RANDOMmax);
+    }
+  qh RANDOMa = 2.0 * qh RANDOMfactor / qh_RANDOMmax;
+  qh RANDOMb = 1.0 - qh RANDOMfactor;
+  if( qh_HASHfactor < 1.1 )
+    {
+    fprintf(
+      qh ferr,
+      "qhull internal error (qh_initqhull_globals): qh_HASHfactor %d must be at least 1.1.  Qhull uses linear hash probing\n",
+      qh_HASHfactor);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  if( numpoints + extra < pointsneeded )
+    {
+    fprintf(qh ferr, "qhull input error: not enough points (%d) to construct initial simplex (need %d)\n",
+            numpoints, pointsneeded);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh PRINTtransparent )
+    {
+    if( qh hull_dim != 4 || !qh DELAUNAY || qh VORONOI || qh DROPdim >= 0 )
+      {
+      fprintf(qh ferr, "qhull input error: transparent Delaunay ('Gt') needs 3-d Delaunay ('d') w/o 'GDn'\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    qh DROPdim = 3;
+    qh PRINTridges = True;
+    }
+  for( i = qh_PRINTEND; i--; )
+    {
+    if( qh PRINTout[i] == qh_PRINTgeom )
+      {
+      printgeom = True;
+      }
+    else if( qh PRINTout[i] == qh_PRINTmathematica || qh PRINTout[i] == qh_PRINTmaple )
+      {
+      printmath = True;
+      }
+    else if( qh PRINTout[i] == qh_PRINTcoplanars )
+      {
+      printcoplanar = True;
+      }
+    else if( qh PRINTout[i] == qh_PRINTpointnearest )
+      {
+      printcoplanar = True;
+      }
+    else if( qh PRINTout[i] == qh_PRINTpointintersect && !qh HALFspace )
+      {
+      fprintf(qh ferr, "qhull input error: option 'Fp' is only used for \nhalfspace intersection ('Hn,n,n').\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    else if( qh PRINTout[i] == qh_PRINTtriangles && (qh HALFspace || qh VORONOI) )
+      {
+      fprintf(qh ferr,
+              "qhull input error: option 'Ft' is not available for Voronoi vertices or halfspace intersection\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    else if( qh PRINTout[i] == qh_PRINTcentrums && qh VORONOI )
+      {
+      fprintf(qh ferr, "qhull input error: option 'FC' is not available for Voronoi vertices ('v')\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    else if( qh PRINTout[i] == qh_PRINTvertices )
+      {
+      if( qh VORONOI )
+        {
+        qh_option("Fvoronoi", NULL, NULL);
+        }
+      else
+        {
+        qh_option("Fvertices", NULL, NULL);
+        }
+      }
+    }
+  if( printcoplanar && qh DELAUNAY && qh JOGGLEmax < REALmax / 2 )
+    {
+    if( qh PRINTprecision )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input warning: 'QJ' (joggle) will usually prevent coincident input sites for options 'Fc' and 'FP'\n");
+      }
+    }
+  if( !qh KEEPcoplanar && !qh KEEPinside && !qh ONLYgood )
+    {
+    if( (qh PRINTcoplanar && qh PRINTspheres) || printcoplanar )
+      {
+      qh KEEPcoplanar = True;
+      qh_option("Qcoplanar", NULL, NULL);
+      }
+    }
+  if( printmath && (qh hull_dim > 3 || qh VORONOI) )
+    {
+    fprintf(
+      qh ferr,
+      "qhull input error: Mathematica and Maple output is only available for 2-d and 3-d convex hulls and 2-d Delaunay triangulations\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( printgeom )
+    {
+    if( qh hull_dim > 4 )
+      {
+      fprintf(qh ferr, "qhull input error: Geomview output is only available for 2-d, 3-d and 4-d\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    if( qh PRINTnoplanes && !(qh PRINTcoplanar + qh PRINTcentrums
+                              + qh PRINTdots + qh PRINTspheres + qh DOintersections + qh PRINTridges) )
+      {
+      fprintf(qh ferr, "qhull input error: no output specified for Geomview\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    if( qh VORONOI && (qh hull_dim > 3 || qh DROPdim >= 0) )
+      {
+      fprintf(qh ferr, "qhull input error: Geomview output for Voronoi diagrams only for 2-d\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    /* can not warn about furthest-site Geomview output: no lower_threshold */
+    if( qh hull_dim == 4 && qh DROPdim == -1 &&
+        (qh PRINTcoplanar || qh PRINTspheres || qh PRINTcentrums) )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input warning: coplanars, vertices, and centrums output not\n\
+available for 4-d output (ignored).  Could use 'GDn' instead.\n"                                                                              );
+      qh PRINTcoplanar = qh PRINTspheres = qh PRINTcentrums = False;
+      }
+    }
+  qh PRINTdim = qh hull_dim;
+  if( qh DROPdim >= 0 )      /* after Geomview checks */
+    {
+    if( qh DROPdim < qh hull_dim )
+      {
+      qh PRINTdim--;
+      if( !printgeom || qh hull_dim < 3 )
+        {
+        fprintf(qh ferr, "qhull input warning: drop dimension 'GD%d' is only available for 3-d/4-d Geomview\n",
+                qh DROPdim);
+        }
+      }
+    else
+      {
+      qh DROPdim = -1;
+      }
+    }
+  else if( qh VORONOI )
+    {
+    qh DROPdim = qh hull_dim - 1;
+    qh PRINTdim = qh hull_dim - 1;
+    }
+} /* initqhull_globals */
+
+/*---------------------------------
+
+  qh_initqhull_mem(  )
+  initialize mem.c for qhull
+  qh.hull_dim and qh.normal_size determine some of the allocation sizes
+  if qh.MERGING,
+  includes ridgeT
+  calls qh_user_memsizes() to add up to 10 additional sizes for quick allocation
+  (see numsizes below)
+
+  returns:
+  mem.c already for qh_memalloc/qh_memfree (errors if called beforehand)
+
+  notes:
+  qh_produceoutput() prints memsizes
+
+*/
+void qh_initqhull_mem(void)
+{
+  int numsizes;
+  int i;
+
+  numsizes = 8 + 10;
+  qh_meminitbuffers(qh IStracing, qh_MEMalign, numsizes,
+                    qh_MEMbufsize, qh_MEMinitbuf);
+  qh_memsize(sizeof(vertexT) );
+  if( qh MERGING )
+    {
+    qh_memsize(sizeof(ridgeT) );
+    qh_memsize(sizeof(mergeT) );
+    }
+  qh_memsize(sizeof(facetT) );
+  i = sizeof(setT) + (qh hull_dim - 1) * SETelemsize;  /* ridge.vertices */
+  qh_memsize( (size_t)i);
+  qh_memsize(qh normal_size);       /* normal */
+  i += SETelemsize;                 /* facet.vertices, .ridges, .neighbors */
+  qh_memsize( (size_t)i);
+  qh_user_memsizes();
+  qh_memsetup();
+} /* initqhull_mem */
+
+/*---------------------------------
+
+  qh_initqhull_start( infile, outfile, errfile )
+  start initialization of qhull
+  initialize statistics, stdio, default values for global variables
+
+  see:
+  qh_maxmin() determines the precision constants
+*/
+void qh_initqhull_start(FILE *infile, FILE *outfile, FILE *errfile)
+{
+
+  (void)qh_CPUclock; /* start the clock */
+#if qh_QHpointer
+  if( !(qh_qh = (qhT *)malloc(sizeof(qhT) ) ) )
+    {
+    fprintf(errfile, "qhull error (qh_initqhull_globals): insufficient memory\n");
+    exit(qh_ERRmem);   /* no error handler */
+    }
+  memset( (char *)qh_qh, 0, sizeof(qhT) );   /* every field is 0, FALSE, NULL */
+#else
+  memset( (char *)&qh_qh, 0, sizeof(qhT) );
+#endif
+  strcat(qh qhull, "qhull");
+  qh_initstatistics();
+  qh ANGLEmerge = True;
+  qh DROPdim = -1;
+  qh ferr = errfile;
+  qh fin = infile;
+  qh fout = outfile;
+  qh furthest_id = -1;
+  qh JOGGLEmax = REALmax;
+  qh KEEPminArea = REALmax;
+  qh last_low = REALmax;
+  qh last_high = REALmax;
+  qh last_newhigh = REALmax;
+  qh max_outside = 0.0;
+  qh max_vertex = 0.0;
+  qh MAXabs_coord = 0.0;
+  qh MAXsumcoord = 0.0;
+  qh MAXwidth = -REALmax;
+  qh MERGEindependent = True;
+  qh MINdenom_1 = fmax_(1.0 / REALmax, REALmin); /* used by qh_scalepoints */
+  qh MINoutside = 0.0;
+  qh MINvisible = REALmax;
+  qh MAXcoplanar = REALmax;
+  qh outside_err = REALmax;
+  qh premerge_centrum = 0.0;
+  qh premerge_cos = REALmax;
+  qh PRINTprecision = True;
+  qh PRINTradius = 0.0;
+  qh postmerge_cos = REALmax;
+  qh postmerge_centrum = 0.0;
+  qh ROTATErandom = INT_MIN;
+  qh MERGEvertices = True;
+  qh totarea = 0.0;
+  qh totvol = 0.0;
+  qh TRACEdist = REALmax;
+  qh TRACEpoint = -1;           /* recompile or use 'TPn' */
+  qh tracefacet_id = UINT_MAX;  /* recompile to trace a facet */
+  qh tracevertex_id = UINT_MAX; /* recompile to trace a vertex */
+  qh_RANDOMseed_(1);
+} /* initqhull_start */
+
+/*---------------------------------
+
+  qh_initthresholds( commandString )
+  set thresholds for printing and scaling from commandString
+
+  returns:
+  sets qh.GOODthreshold or qh.SPLITthreshold if 'Pd0D1' used
+
+  see:
+  qh_initflags(), 'Qbk' 'QBk' 'Pdk' and 'PDk'
+  qh_inthresholds()
+
+  design:
+  for each 'Pdn' or 'PDn' option
+  check syntax
+  set qh.lower_threshold or qh.upper_threshold
+  set qh.GOODthreshold if an unbounded threshold is used
+  set qh.SPLITthreshold if a bounded threshold is used
+*/
+void qh_initthresholds(char *command)
+{
+  realT value;
+  int   idx, maxdim, k;
+  char *s = command;
+  char  key;
+
+  maxdim = qh input_dim;
+  if( qh DELAUNAY && (qh PROJECTdelaunay || qh PROJECTinput) )
+    {
+    maxdim++;
+    }
+  while( *s )
+    {
+    if( *s == '-' )
+      {
+      s++;
+      }
+    if( *s == 'P' )
+      {
+      s++;
+      while( *s && !isspace(key = *s++) )
+        {
+        if( key == 'd' || key == 'D' )
+          {
+          if( !isdigit(*s) )
+            {
+            fprintf(qh ferr, "qhull warning: no dimension given for Print option '%c' at: %s.  Ignored\n",
+                    key, s - 1);
+            continue;
+            }
+          idx = qh_strtol(s, &s);
+          if( idx >= qh hull_dim )
+            {
+            fprintf(qh ferr, "qhull warning: dimension %d for Print option '%c' is >= %d.  Ignored\n",
+                    idx, key, qh hull_dim);
+            continue;
+            }
+          if( *s == ':' )
+            {
+            s++;
+            value = qh_strtod(s, &s);
+            if( fabs( (double)value) > 1.0 )
+              {
+              fprintf(qh ferr, "qhull warning: value %2.4g for Print option %c is > +1 or < -1.  Ignored\n",
+                      value, key);
+              continue;
+              }
+            }
+          else
+            {
+            value = 0.0;
+            }
+          if( key == 'd' )
+            {
+            qh lower_threshold[idx] = value;
+            }
+          else
+            {
+            qh upper_threshold[idx] = value;
+            }
+          }
+        }
+      }
+    else if( *s == 'Q' )
+      {
+      s++;
+      while( *s && !isspace(key = *s++) )
+        {
+        if( key == 'b' && *s == 'B' )
+          {
+          s++;
+          for( k = maxdim; k--; )
+            {
+            qh lower_bound[k] = -qh_DEFAULTbox;
+            qh upper_bound[k] = qh_DEFAULTbox;
+            }
+          }
+        else if( key == 'b' && *s == 'b' )
+          {
+          s++;
+          }
+        else if( key == 'b' || key == 'B' )
+          {
+          if( !isdigit(*s) )
+            {
+            fprintf(qh ferr, "qhull warning: no dimension given for Qhull option %c.  Ignored\n",
+                    key);
+            continue;
+            }
+          idx = qh_strtol(s, &s);
+          if( idx >= maxdim )
+            {
+            fprintf(qh ferr, "qhull warning: dimension %d for Qhull option %c is >= %d.  Ignored\n",
+                    idx, key, maxdim);
+            continue;
+            }
+          if( *s == ':' )
+            {
+            s++;
+            value = qh_strtod(s, &s);
+            }
+          else if( key == 'b' )
+            {
+            value = -qh_DEFAULTbox;
+            }
+          else
+            {
+            value = qh_DEFAULTbox;
+            }
+          if( key == 'b' )
+            {
+            qh lower_bound[idx] = value;
+            }
+          else
+            {
+            qh upper_bound[idx] = value;
+            }
+          }
+        }
+      }
+    else
+      {
+      while( *s && !isspace(*s) )
+        {
+        s++;
+        }
+      }
+    while( isspace(*s) )
+      {
+      s++;
+      }
+    }
+  for( k = qh hull_dim; k--; )
+    {
+    if( qh lower_threshold[k] > -REALmax / 2 )
+      {
+      qh GOODthreshold = True;
+      if( qh upper_threshold[k] < REALmax / 2 )
+        {
+        qh SPLITthresholds = True;
+        qh GOODthreshold = False;
+        break;
+        }
+      }
+    else if( qh upper_threshold[k] < REALmax / 2 )
+      {
+      qh GOODthreshold = True;
+      }
+    }
+} /* initthresholds */
+
+/*---------------------------------
+
+  qh_option( option, intVal, realVal )
+  add an option description to qh.qhull_options
+
+  notes:
+  will be printed with statistics ('Ts') and errors
+  strlen(option) < 40
+*/
+void qh_option(const char *option, int *i, realT *r)
+{
+  char buf[200];
+  int  len, maxlen;
+
+  sprintf(buf, "  %s", option);
+  if( i )
+    {
+    sprintf(buf + strlen(buf), " %d", *i);
+    }
+  if( r )
+    {
+    sprintf(buf + strlen(buf), " %2.2g", *r);
+    }
+  len = strlen(buf);
+  qh qhull_optionlen += len;
+  maxlen = sizeof (qh qhull_options) - len - 1;
+  maximize_(maxlen, 0);
+  if( qh qhull_optionlen >= 80 && maxlen > 0 )
+    {
+    qh qhull_optionlen = len;
+    strncat(qh qhull_options, "\n", (size_t)(maxlen--) );
+    }
+  strncat(qh qhull_options, buf, (size_t)maxlen);
+} /* option */
+
+#if qh_QHpointer
+/*---------------------------------
+
+  qh_restore_qhull( oldqh )
+  restores a previously saved qhull
+  also restores qh_qhstat and qhmem.tempstack
+
+  notes:
+  errors if current qhull hasn't been saved or freed
+  uses qhmem for error reporting
+
+  NOTE 1998/5/11:
+  Freeing memory after qh_save_qhull and qh_restore_qhull
+  is complicated.  The procedures will be redesigned.
+
+  see:
+  qh_save_qhull()
+*/
+void qh_restore_qhull(qhT * *oldqh)
+{
+
+  if( *oldqh && strcmp( (*oldqh)->qhull, "qhull") )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_restore_qhull): %p is not a qhull data structure\n",
+            *oldqh);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  if( qh_qh )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_restore_qhull): did not save or free existing qhull\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  if( !*oldqh || !(*oldqh)->old_qhstat )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_restore_qhull): did not previously save qhull %p\n",
+            *oldqh);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  qh_qh = *oldqh;
+  *oldqh = NULL;
+  qh_qhstat = qh old_qhstat;
+  qhmem.tempstack = qh old_tempstack;
+  trace1( (qh ferr, "qh_restore_qhull: restored qhull from %p\n", *oldqh) );
+} /* restore_qhull */
+
+/*---------------------------------
+
+  qh_save_qhull(  )
+  saves qhull for a later qh_restore_qhull
+  also saves qh_qhstat and qhmem.tempstack
+
+  returns:
+  qh_qh=NULL
+
+  notes:
+  need to initialize qhull or call qh_restore_qhull before continuing
+
+  NOTE 1998/5/11:
+  Freeing memory after qh_save_qhull and qh_restore_qhull
+  is complicated.  The procedures will be redesigned.
+
+  see:
+  qh_restore_qhull()
+*/
+qhT * qh_save_qhull(void)
+{
+  qhT *oldqh;
+
+  trace1( (qhmem.ferr, "qh_save_qhull: save qhull %p\n", qh_qh) );
+  if( !qh_qh )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_save_qhull): qhull not initialized\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  qh old_qhstat = qh_qhstat;
+  qh_qhstat = NULL;
+  qh old_tempstack = qhmem.tempstack;
+  qhmem.tempstack = NULL;
+  oldqh = qh_qh;
+  qh_qh = NULL;
+  return oldqh;
+} /* save_qhull */
+
+#endif
+
+/*---------------------------------
+
+  qh_strtol( s, endp) qh_strtod( s, endp)
+  internal versions of strtol() and strtod()
+  does not skip trailing spaces
+  notes:
+  some implementations of strtol()/strtod() skip trailing spaces
+*/
+double qh_strtod(const char *s, char * *endp)
+{
+  double result;
+
+  result = strtod(s, endp);
+  if( s < (*endp) && (*endp)[-1] == ' ' )
+    {
+    (*endp)--;
+    }
+  return result;
+} /* strtod */
+
+int qh_strtol(const char *s, char * *endp)
+{
+  int result;
+
+  result = (int) strtol(s, endp, 10);
+  if( s < (*endp) && (*endp)[-1] == ' ' )
+    {
+    (*endp)--;
+    }
+  return result;
+} /* strtol */
+
diff --git a/BRAINSABC/qhull/io.c b/BRAINSABC/qhull/io.c
new file mode 100644
index 00000000..78bf26e7
--- /dev/null
+++ b/BRAINSABC/qhull/io.c
@@ -0,0 +1,5346 @@
+/*
  ---------------------------------
+
+  io.c
+  Input/Output routines of qhull application
+
+  see qh-io.htm and io.h
+
+  see user.c for qh_errprint and qh_printfacetlist
+
+  unix.c calls qh_readpoints and qh_produce_output
+
+  unix.c and user.c are the only callers of io.c functions
+  This allows the user to avoid loading io.o from qhull.a
+
+  copyright (c) 1993-2003 The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*========= -functions in alphabetical order after qh_produce_output()  =====*/
+
+/*---------------------------------
+
+  qh_produce_output()
+  prints out the result of qhull in desired format
+  if qh.GETarea
+  computes and prints area and volume
+  qh.PRINTout[] is an array of output formats
+
+  notes:
+  prints output in qh.PRINTout order
+*/
+void qh_produce_output(void)
+{
+  int i, tempsize = qh_setsize( (setT *)qhmem.tempstack), d_1;
+
+  if( qh VORONOI )
+    {
+    qh_clearcenters(qh_ASvoronoi);
+    qh_vertexneighbors();
+    }
+  if( qh TRIangulate )
+    {
+    qh_triangulate();
+    if( qh VERIFYoutput && !qh CHECKfrequently )
+      {
+      qh_checkpolygon(qh facet_list);
+      }
+    }
+  qh_findgood_all(qh facet_list);
+  if( qh GETarea )
+    {
+    qh_getarea(qh facet_list);
+    }
+  if( qh KEEParea || qh KEEPmerge || qh KEEPminArea < REALmax / 2 )
+    {
+    qh_markkeep(qh facet_list);
+    }
+  if( qh PRINTsummary )
+    {
+    qh_printsummary(qh ferr);
+    }
+  else if( qh PRINTout[0] == qh_PRINTnone )
+    {
+    qh_printsummary(qh fout);
+    }
+  for( i = 0; i < qh_PRINTEND; i++ )
+    {
+    qh_printfacets(qh fout, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
+    }
+  qh_allstatistics();
+  if( qh PRINTprecision && !qh MERGING && (qh JOGGLEmax > REALmax / 2 || qh RERUN) )
+    {
+    qh_printstats(qh ferr, qhstat precision, NULL);
+    }
+  if( qh VERIFYoutput && (zzval_(Zridge) > 0 || zzval_(Zridgemid) > 0) )
+    {
+    qh_printstats(qh ferr, qhstat vridges, NULL);
+    }
+  if( qh PRINTstatistics )
+    {
+    qh_collectstatistics();
+    qh_printstatistics(qh ferr, "");
+    qh_memstatistics(qh ferr);
+    d_1 = sizeof(setT) + (qh hull_dim - 1) * SETelemsize;
+    fprintf(
+      qh ferr,
+      "\
+    size in bytes: merge %lu ridge %lu vertex %lu facet %lu\n\
+         normal %lu ridge vertices %d facet vertices or neighbors %lu\n"                                                                        ,
+      sizeof(mergeT), sizeof(ridgeT),
+      sizeof(vertexT), sizeof(facetT),
+      (unsigned long)qh normal_size, d_1,
+      (unsigned long)d_1 + SETelemsize);
+    }
+  if( qh_setsize( (setT *)qhmem.tempstack) != tempsize )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_produce_output): temporary sets not empty (%d)\n",
+            qh_setsize( (setT *)qhmem.tempstack) );
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+} /* produce_output */
+
+/*---------------------------------
+
+  dfacet( id )
+  print facet by id, for debugging
+
+*/
+void dfacet(unsigned id)
+{
+  facetT *facet;
+
+  FORALLfacets {
+    if( facet->id == id )
+      {
+      qh_printfacet(qh fout, facet);
+      break;
+      }
+    }
+} /* dfacet */
+
+/*---------------------------------
+
+  dvertex( id )
+  print vertex by id, for debugging
+*/
+void dvertex(unsigned id)
+{
+  vertexT *vertex;
+
+  FORALLvertices {
+    if( vertex->id == id )
+      {
+      qh_printvertex(qh fout, vertex);
+      break;
+      }
+    }
+} /* dvertex */
+
+/*---------------------------------
+
+  qh_compare_vertexpoint( p1, p2 )
+  used by qsort() to order vertices by point id
+*/
+int qh_compare_vertexpoint(const void *p1, const void *p2)
+{
+  const vertexT *a = *( (vertexT *const *)p1), *b = *( (vertexT *const *)p2);
+
+  return (qh_pointid(a->point) > qh_pointid(b->point) ? 1 : -1);
+} /* compare_vertexpoint */
+
+/*---------------------------------
+
+  qh_compare_facetarea( p1, p2 )
+  used by qsort() to order facets by area
+*/
+int qh_compare_facetarea(const void *p1, const void *p2)
+{
+  const facetT *a = *( (facetT *const *)p1), *b = *( (facetT *const *)p2);
+
+  if( !a->isarea )
+    {
+    return -1;
+    }
+  if( !b->isarea )
+    {
+    return 1;
+    }
+  if( a->f.area > b->f.area )
+    {
+    return 1;
+    }
+  else if( a->f.area == b->f.area )
+    {
+    return 0;
+    }
+  return -1;
+} /* compare_facetarea */
+
+/*---------------------------------
+
+  qh_compare_facetmerge( p1, p2 )
+  used by qsort() to order facets by number of merges
+*/
+int qh_compare_facetmerge(const void *p1, const void *p2)
+{
+  const facetT *a = *( (facetT *const *)p1), *b = *( (facetT *const *)p2);
+
+  return a->nummerge - b->nummerge;
+} /* compare_facetvisit */
+
+/*---------------------------------
+
+  qh_compare_facetvisit( p1, p2 )
+  used by qsort() to order facets by visit id or id
+*/
+int qh_compare_facetvisit(const void *p1, const void *p2)
+{
+  const facetT *a = *( (facetT *const *)p1), *b = *( (facetT *const *)p2);
+  int           i, j;
+
+  if( !(i = a->visitid) )
+    {
+    i = -a->id; /* do not convert to int */
+    }
+  if( !(j = b->visitid) )
+    {
+    j = -b->id;
+    }
+  return i - j;
+} /* compare_facetvisit */
+
+/*---------------------------------
+
+  qh_countfacets( facetlist, facets, printall,
+  numfacets, numsimplicial, totneighbors, numridges, numcoplanar, numtricoplanars  )
+  count good facets for printing and set visitid
+  if allfacets, ignores qh_skipfacet()
+
+  notes:
+  qh_printsummary and qh_countfacets must match counts
+
+  returns:
+  numfacets, numsimplicial, total neighbors, numridges, coplanars
+  each facet with ->visitid indicating 1-relative position
+  ->visitid==0 indicates not good
+
+  notes
+  numfacets >= numsimplicial
+  if qh.NEWfacets,
+  does not count visible facets (matches qh_printafacet)
+
+  design:
+  for all facets on facetlist and in facets set
+  unless facet is skipped or visible (i.e., will be deleted)
+  mark facet->visitid
+  update counts
+*/
+void qh_countfacets(facetT *facetlist, setT *facets, boolT printall,
+                    int *numfacetsp, int *numsimplicialp, int *totneighborsp, int *numridgesp, int *numcoplanarsp,
+                    int *numtricoplanarsp)
+{
+  facetT *facet, * *facetp;
+  int     numfacets = 0, numsimplicial = 0, numridges = 0, totneighbors = 0, numcoplanars = 0, numtricoplanars = 0;
+
+  FORALLfacet_(facetlist) {
+    if( (facet->visible && qh NEWfacets)
+        || (!printall && qh_skipfacet(facet) ) )
+      {
+      facet->visitid = 0;
+      }
+    else
+      {
+      facet->visitid = ++numfacets;
+      totneighbors += qh_setsize(facet->neighbors);
+      if( facet->simplicial )
+        {
+        numsimplicial++;
+        if( facet->keepcentrum && facet->tricoplanar )
+          {
+          numtricoplanars++;
+          }
+        }
+      else
+        {
+        numridges += qh_setsize(facet->ridges);
+        }
+      if( facet->coplanarset )
+        {
+        numcoplanars += qh_setsize(facet->coplanarset);
+        }
+      }
+    }
+  FOREACHfacet_(facets) {
+    if( (facet->visible && qh NEWfacets)
+        || (!printall && qh_skipfacet(facet) ) )
+      {
+      facet->visitid = 0;
+      }
+    else
+      {
+      facet->visitid = ++numfacets;
+      totneighbors += qh_setsize(facet->neighbors);
+      if( facet->simplicial )
+        {
+        numsimplicial++;
+        if( facet->keepcentrum && facet->tricoplanar )
+          {
+          numtricoplanars++;
+          }
+        }
+      else
+        {
+        numridges += qh_setsize(facet->ridges);
+        }
+      if( facet->coplanarset )
+        {
+        numcoplanars += qh_setsize(facet->coplanarset);
+        }
+      }
+    }
+  qh visit_id += numfacets + 1;
+  *numfacetsp = numfacets;
+  *numsimplicialp = numsimplicial;
+  *totneighborsp = totneighbors;
+  *numridgesp = numridges;
+  *numcoplanarsp = numcoplanars;
+  *numtricoplanarsp = numtricoplanars;
+} /* countfacets */
+
+/*---------------------------------
+
+  qh_detvnorm( vertex, vertexA, centers, offset )
+  compute separating plane of the Voronoi diagram for a pair of input sites
+  centers= set of facets (i.e., Voronoi vertices)
+  facet->visitid= 0 iff vertex-at-infinity (i.e., unbounded)
+
+  assumes:
+  qh_ASvoronoi and qh_vertexneighbors() already set
+
+  returns:
+  norm
+  a pointer into qh.gm_matrix to qh.hull_dim-1 reals
+  copy the data before reusing qh.gm_matrix
+  offset
+  if 'QVn'
+  sign adjusted so that qh.GOODvertexp is inside
+  else
+  sign adjusted so that vertex is inside
+
+  qh.gm_matrix= simplex of points from centers relative to first center
+
+  notes:
+  in io.c so that code for 'v Tv' can be removed by removing io.c
+  returns pointer into qh.gm_matrix to avoid tracking of temporary memory
+
+  design:
+  determine midpoint of input sites
+  build points as the set of Voronoi vertices
+  select a simplex from points (if necessary)
+  include midpoint if the Voronoi region is unbounded
+  relocate the first vertex of the simplex to the origin
+  compute the normalized hyperplane through the simplex
+  orient the hyperplane toward 'QVn' or 'vertex'
+  if 'Tv' or 'Ts'
+  if bounded
+  test that hyperplane is the perpendicular bisector of the input sites
+  test that Voronoi vertices not in the simplex are still on the hyperplane
+  free up temporary memory
+*/
+pointT * qh_detvnorm(vertexT *vertex, vertexT *vertexA, setT *centers, realT *offsetp)
+{
+  facetT *facet, * *facetp;
+  int     i, k, pointid, pointidA, point_i, point_n;
+  setT *  simplex = NULL;
+  pointT *point, * *pointp, *point0, *midpoint, *normal, *inpoint;
+  coordT *coord, *gmcoord, *normalp;
+  setT *  points = qh_settemp(qh TEMPsize);
+  boolT   nearzero = False;
+  boolT   unbounded = False;
+  int     numcenters = 0;
+  int     dim = qh hull_dim - 1;
+  realT   dist, offset, angle, zero = 0.0;
+
+  midpoint = qh gm_matrix + qh hull_dim * qh hull_dim;  /* last row */
+  for( k = 0; k < dim; k++ )
+    {
+    midpoint[k] = (vertex->point[k] + vertexA->point[k]) / 2;
+    }
+  FOREACHfacet_(centers) {
+    numcenters++;
+    if( !facet->visitid )
+      {
+      unbounded = True;
+      }
+    else
+      {
+      if( !facet->center )
+        {
+        facet->center = qh_facetcenter(facet->vertices);
+        }
+      qh_setappend(&points, facet->center);
+      }
+    }
+  if( numcenters > dim )
+    {
+    simplex = qh_settemp(qh TEMPsize);
+    qh_setappend(&simplex, vertex->point);
+    if( unbounded )
+      {
+      qh_setappend(&simplex, midpoint);
+      }
+    qh_maxsimplex(dim, points, NULL, 0, &simplex);
+    qh_setdelnth(simplex, (size_t)0);
+    }
+  else if( numcenters == dim )
+    {
+    if( unbounded )
+      {
+      qh_setappend(&points, midpoint);
+      }
+    simplex = points;
+    }
+  else
+    {
+    fprintf(qh ferr, "qh_detvnorm: too few points (%d) to compute separating plane\n", numcenters);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  i = 0;
+  gmcoord = qh gm_matrix;
+  point0 = SETfirstt_(simplex, pointT);
+  FOREACHpoint_(simplex) {
+    if( qh IStracing >= 4 )
+      {
+      qh_printmatrix(qh ferr, "qh_detvnorm: Voronoi vertex or midpoint",
+                     &point, 1, dim);
+      }
+    if( point != point0 )
+      {
+      qh gm_row[i++] = gmcoord;
+      coord = point0;
+      for( k = dim; k--; )
+        {
+        *(gmcoord++) = *point++ - *coord++;
+        }
+      }
+    }
+  qh gm_row[i] = gmcoord;  /* does not overlap midpoint, may be used later for
+                             qh_areasimplex */
+  normal = gmcoord;
+  qh_sethyperplane_gauss(dim, qh gm_row, point0, True,
+                         normal, &offset, &nearzero);
+  if( qh GOODvertexp == vertexA->point )
+    {
+    inpoint = vertexA->point;
+    }
+  else
+    {
+    inpoint = vertex->point;
+    }
+  zinc_(Zdistio);
+  dist = qh_distnorm(dim, inpoint, normal, &offset);
+  if( dist > 0 )
+    {
+    offset = -offset;
+    normalp = normal;
+    for( k = dim; k--; )
+      {
+      *normalp = -(*normalp);
+      normalp++;
+      }
+    }
+  if( qh VERIFYoutput || qh PRINTstatistics )
+    {
+    pointid = qh_pointid(vertex->point);
+    pointidA = qh_pointid(vertexA->point);
+    if( !unbounded )
+      {
+      zinc_(Zdiststat);
+      dist = qh_distnorm(dim, midpoint, normal, &offset);
+      if( dist < 0 )
+        {
+        dist = -dist;
+        }
+      zzinc_(Zridgemid);
+      wwmax_(Wridgemidmax, dist);
+      wwadd_(Wridgemid, dist);
+      trace4( (qh ferr, "qh_detvnorm: points %d %d midpoint dist %2.2g\n",
+               pointid, pointidA, dist) );
+      for( k = 0; k < dim; k++ )
+        {
+        midpoint[k] = vertexA->point[k] - vertex->point[k];  /* overwrites
+                                                               midpoint! */
+        }
+      qh_normalize(midpoint, dim, False);
+      angle = qh_distnorm(dim, midpoint, normal, &zero); /* qh_detangle uses
+                                                           dim+1 */
+      if( angle < 0.0 )
+        {
+        angle = angle + 1.0;
+        }
+      else
+        {
+        angle = angle - 1.0;
+        }
+      if( angle < 0.0 )
+        {
+        angle -= angle;
+        }
+      trace4( (qh ferr, "qh_detvnorm: points %d %d angle %2.2g nearzero %d\n",
+               pointid, pointidA, angle, nearzero) );
+      if( nearzero )
+        {
+        zzinc_(Zridge0);
+        wwmax_(Wridge0max, angle);
+        wwadd_(Wridge0, angle);
+        }
+      else
+        {
+        zzinc_(Zridgeok)
+        wwmax_(Wridgeokmax, angle);
+        wwadd_(Wridgeok, angle);
+        }
+      }
+    if( simplex != points )
+      {
+      FOREACHpoint_i_(points) {
+        if( !qh_setin(simplex, point) )
+          {
+          facet = SETelemt_(centers, point_i, facetT);
+          zinc_(Zdiststat);
+          dist = qh_distnorm(dim, point, normal, &offset);
+          if( dist < 0 )
+            {
+            dist = -dist;
+            }
+          zzinc_(Zridge);
+          wwmax_(Wridgemax, dist);
+          wwadd_(Wridge, dist);
+          trace4( (qh ferr, "qh_detvnorm: points %d %d Voronoi vertex %d dist %2.2g\n",
+                   pointid, pointidA, facet->visitid, dist) );
+          }
+        }
+      }
+    }
+  *offsetp = offset;
+  if( simplex != points )
+    {
+    qh_settempfree(&simplex);
+    }
+  qh_settempfree(&points);
+  return normal;
+} /* detvnorm */
+
+/*---------------------------------
+
+  qh_detvridge( vertexA )
+  determine Voronoi ridge from 'seen' neighbors of vertexA
+  include one vertex-at-infinite if an !neighbor->visitid
+
+  returns:
+  temporary set of centers (facets, i.e., Voronoi vertices)
+  sorted by center id
+*/
+setT * qh_detvridge(vertexT *vertex)
+{
+  setT *  centers = qh_settemp(qh TEMPsize);
+  setT *  tricenters = qh_settemp(qh TEMPsize);
+  facetT *neighbor, * *neighborp;
+  boolT   firstinf = True;
+
+  FOREACHneighbor_(vertex) {
+    if( neighbor->seen )
+      {
+      if( neighbor->visitid )
+        {
+        if( !neighbor->tricoplanar || qh_setunique(&tricenters, neighbor->center) )
+          {
+          qh_setappend(¢ers, neighbor);
+          }
+        }
+      else if( firstinf )
+        {
+        firstinf = False;
+        qh_setappend(¢ers, neighbor);
+        }
+      }
+    }
+  qsort(SETaddr_(centers, facetT), (size_t)qh_setsize(centers),
+        sizeof (facetT *), qh_compare_facetvisit);
+  qh_settempfree(&tricenters);
+  return centers;
+} /* detvridge */
+
+/*---------------------------------
+
+  qh_detvridge3( atvertex, vertex )
+  determine 3-d Voronoi ridge from 'seen' neighbors of atvertex and vertex
+  include one vertex-at-infinite for !neighbor->visitid
+  assumes all facet->seen2= True
+
+  returns:
+  temporary set of centers (facets, i.e., Voronoi vertices)
+  listed in adjacency order (not oriented)
+  all facet->seen2= True
+
+  design:
+  mark all neighbors of atvertex
+  for each adjacent neighbor of both atvertex and vertex
+  if neighbor selected
+  add neighbor to set of Voronoi vertices
+*/
+setT * qh_detvridge3(vertexT *atvertex, vertexT *vertex)
+{
+  setT *  centers = qh_settemp(qh TEMPsize);
+  setT *  tricenters = qh_settemp(qh TEMPsize);
+  facetT *neighbor, * *neighborp, *facet = NULL;
+  boolT   firstinf = True;
+
+  FOREACHneighbor_(atvertex)
+  neighbor->seen2 = False;
+  FOREACHneighbor_(vertex) {
+    if( !neighbor->seen2 )
+      {
+      facet = neighbor;
+      break;
+      }
+    }
+  while( facet )
+    {
+    facet->seen2 = True;
+    if( neighbor->seen )
+      {
+      if( facet->visitid )
+        {
+        if( !facet->tricoplanar || qh_setunique(&tricenters, facet->center) )
+          {
+          qh_setappend(¢ers, facet);
+          }
+        }
+      else if( firstinf )
+        {
+        firstinf = False;
+        qh_setappend(¢ers, facet);
+        }
+      }
+    FOREACHneighbor_(facet) {
+      if( !neighbor->seen2 )
+        {
+        if( qh_setin(vertex->neighbors, neighbor) )
+          {
+          break;
+          }
+        else
+          {
+          neighbor->seen2 = True;
+          }
+        }
+      }
+    facet = neighbor;
+    }
+
+  if( qh CHECKfrequently )
+    {
+    FOREACHneighbor_(vertex) {
+      if( !neighbor->seen2 )
+        {
+        fprintf(stderr, "qh_detvridge3: neigbors of vertex p%d are not connected at facet %d\n",
+                qh_pointid(vertex->point), neighbor->id);
+        qh_errexit(qh_ERRqhull, neighbor, NULL);
+        }
+      }
+    }
+  FOREACHneighbor_(atvertex)
+  neighbor->seen2 = True;
+  qh_settempfree(&tricenters);
+  return centers;
+} /* detvridge3 */
+
+/*---------------------------------
+
+  qh_eachvoronoi( fp, printvridge, vertex, visitall, innerouter, inorder )
+  if visitall,
+  visit all Voronoi ridges for vertex (i.e., an input site)
+  else
+  visit all unvisited Voronoi ridges for vertex
+  all vertex->seen= False if unvisited
+  assumes
+  all facet->seen= False
+  all facet->seen2= True (for qh_detvridge3)
+  all facet->visitid == 0 if vertex_at_infinity
+  == index of Voronoi vertex
+  >= qh.num_facets if ignored
+  innerouter:
+  qh_RIDGEall--  both inner (bounded) and outer (unbounded) ridges
+  qh_RIDGEinner- only inner
+  qh_RIDGEouter- only outer
+
+  if inorder
+  orders vertices for 3-d Voronoi diagrams
+
+  returns:
+  number of visited ridges (does not include previously visited ridges)
+
+  if printvridge,
+  calls printvridge( fp, vertex, vertexA, centers)
+  fp== any pointer (assumes FILE*)
+  vertex,vertexA= pair of input sites that define a Voronoi ridge
+  centers= set of facets (i.e., Voronoi vertices)
+  ->visitid == index or 0 if vertex_at_infinity
+  ordered for 3-d Voronoi diagram
+  notes:
+  uses qh.vertex_visit
+
+  see:
+  qh_eachvoronoi_all()
+
+  design:
+  mark selected neighbors of atvertex
+  for each selected neighbor (either Voronoi vertex or vertex-at-infinity)
+  for each unvisited vertex
+  if atvertex and vertex share more than d-1 neighbors
+  bump totalcount
+  if printvridge defined
+  build the set of shared neighbors (i.e., Voronoi vertices)
+  call printvridge
+*/
+int qh_eachvoronoi(FILE *fp, printvridgeT printvridge, vertexT *atvertex, boolT visitall, qh_RIDGE innerouter,
+                   boolT inorder)
+{
+  boolT   unbounded;
+  int     count;
+  facetT *neighbor, * *neighborp, *neighborA, * *neighborAp;
+  setT *  centers;
+  setT *  tricenters = qh_settemp(qh TEMPsize);
+
+  vertexT *    vertex, * *vertexp;
+  boolT        firstinf;
+  unsigned int numfacets = (unsigned int)qh num_facets;
+  int          totridges = 0;
+
+  qh vertex_visit++;
+
+  atvertex->seen = True;
+  if( visitall )
+    {
+    FORALLvertices
+    vertex-> seen = False;
+    }
+  FOREACHneighbor_(atvertex) {
+    if( neighbor->visitid < numfacets )
+      {
+      neighbor->seen = True;
+      }
+    }
+  FOREACHneighbor_(atvertex) {
+    if( neighbor->seen )
+      {
+      FOREACHvertex_(neighbor->vertices) {
+        if( vertex->visitid != qh vertex_visit && !vertex->seen )
+          {
+          vertex->visitid = qh vertex_visit;
+          count = 0;
+          firstinf = True;
+          qh_settruncate(tricenters, (size_t)0);
+          FOREACHneighborA_(vertex) {
+            if( neighborA->seen )
+              {
+              if( neighborA->visitid )
+                {
+                if( !neighborA->tricoplanar || qh_setunique(&tricenters, neighborA->center) )
+                  {
+                  count++;
+                  }
+                }
+              else if( firstinf )
+                {
+                count++;
+                firstinf = False;
+                }
+              }
+            }
+          if( count >= qh hull_dim - 1 )    /* e.g., 3 for 3-d Voronoi */
+            {
+            if( firstinf )
+              {
+              if( innerouter == qh_RIDGEouter )
+                {
+                continue;
+                }
+              unbounded = False;
+              }
+            else
+              {
+              if( innerouter == qh_RIDGEinner )
+                {
+                continue;
+                }
+              unbounded = True;
+              }
+            totridges++;
+            trace4( (qh ferr, "qh_eachvoronoi: Voronoi ridge of %d vertices between sites %d and %d\n",
+                     count, qh_pointid(atvertex->point), qh_pointid(vertex->point) ) );
+            if( printvridge )
+              {
+              if( inorder && qh hull_dim == 3 + 1 ) /* 3-d Voronoi diagram */
+                {
+                centers = qh_detvridge3(atvertex, vertex);
+                }
+              else
+                {
+                centers = qh_detvridge(vertex);
+                }
+              (*printvridge)(fp, atvertex, vertex, centers, unbounded);
+              qh_settempfree(¢ers);
+              }
+            }
+          }
+        }
+      }
+    }
+  FOREACHneighbor_(atvertex)
+  neighbor->seen = False;
+  qh_settempfree(&tricenters);
+  return totridges;
+} /* eachvoronoi */
+
+/*---------------------------------
+
+  qh_eachvoronoi_all( fp, printvridge, isUpper, innerouter, inorder )
+  visit all Voronoi ridges
+
+  innerouter:
+  see qh_eachvoronoi()
+
+  if inorder
+  orders vertices for 3-d Voronoi diagrams
+
+  returns
+  total number of ridges
+
+  if isUpper == facet->upperdelaunay  (i.e., a Vornoi vertex)
+  facet->visitid= Voronoi vertex index (same as 'o' format)
+  else
+  facet->visitid= 0
+
+  if printvridge,
+  calls printvridge( fp, vertex, vertexA, centers)
+  [see qh_eachvoronoi]
+
+  notes:
+  Not used for qhull.exe
+  same effect as qh_printvdiagram but ridges not sorted by point id
+*/
+int qh_eachvoronoi_all(FILE *fp, printvridgeT printvridge, boolT isUpper, qh_RIDGE innerouter, boolT inorder)
+{
+  facetT * facet;
+  vertexT *vertex;
+  int      numcenters = 1; /* vertex 0 is vertex-at-infinity */
+  int      totridges = 0;
+
+  qh_clearcenters(qh_ASvoronoi);
+  qh_vertexneighbors();
+  maximize_(qh visit_id, (unsigned) qh num_facets);
+  FORALLfacets {
+    facet->visitid = 0;
+    facet->seen = False;
+    facet->seen2 = True;
+    }
+  FORALLfacets {
+    if( facet->upperdelaunay == isUpper )
+      {
+      facet->visitid = numcenters++;
+      }
+    }
+  FORALLvertices
+  vertex-> seen = False;
+  FORALLvertices {
+    if( qh GOODvertex > 0 && qh_pointid(vertex->point) + 1 != qh GOODvertex )
+      {
+      continue;
+      }
+    totridges += qh_eachvoronoi(fp, printvridge, vertex,
+                                !qh_ALL, innerouter, inorder);
+    }
+  return totridges;
+} /* eachvoronoi_all */
+
+/*---------------------------------
+
+  qh_facet2point( facet, point0, point1, mindist )
+  return two projected temporary vertices for a 2-d facet
+  may be non-simplicial
+
+  returns:
+  point0 and point1 oriented and projected to the facet
+  returns mindist (maximum distance below plane)
+*/
+void qh_facet2point(facetT *facet, pointT * *point0, pointT * *point1, realT *mindist)
+{
+  vertexT *vertex0, *vertex1;
+  realT    dist;
+
+  if( facet->toporient ^ qh_ORIENTclock )
+    {
+    vertex0 = SETfirstt_(facet->vertices, vertexT);
+    vertex1 = SETsecondt_(facet->vertices, vertexT);
+    }
+  else
+    {
+    vertex1 = SETfirstt_(facet->vertices, vertexT);
+    vertex0 = SETsecondt_(facet->vertices, vertexT);
+    }
+  zadd_(Zdistio, 2);
+  qh_distplane(vertex0->point, facet, &dist);
+  *mindist = dist;
+  *point0 = qh_projectpoint(vertex0->point, facet, dist);
+  qh_distplane(vertex1->point, facet, &dist);
+  minimize_(*mindist, dist);
+  *point1 = qh_projectpoint(vertex1->point, facet, dist);
+} /* facet2point */
+
+/*---------------------------------
+
+  qh_facetvertices( facetlist, facets, allfacets )
+  returns temporary set of vertices in a set and/or list of facets
+  if allfacets, ignores qh_skipfacet()
+
+  returns:
+  vertices with qh.vertex_visit
+
+  notes:
+  optimized for allfacets of facet_list
+
+  design:
+  if allfacets of facet_list
+  create vertex set from vertex_list
+  else
+  for each selected facet in facets or facetlist
+  append unvisited vertices to vertex set
+*/
+setT * qh_facetvertices(facetT *facetlist, setT *facets, boolT allfacets)
+{
+  setT *   vertices;
+  facetT * facet, * *facetp;
+  vertexT *vertex, * *vertexp;
+
+  qh vertex_visit++;
+
+  if( facetlist == qh facet_list && allfacets && !facets )
+    {
+    vertices = qh_settemp(qh num_vertices);
+    FORALLvertices {
+      vertex->visitid = qh vertex_visit;
+      qh_setappend(&vertices, vertex);
+      }
+    }
+  else
+    {
+    vertices = qh_settemp(qh TEMPsize);
+    FORALLfacet_(facetlist) {
+      if( !allfacets && qh_skipfacet(facet) )
+        {
+        continue;
+        }
+      FOREACHvertex_(facet->vertices) {
+        if( vertex->visitid != qh vertex_visit )
+          {
+          vertex->visitid = qh vertex_visit;
+          qh_setappend(&vertices, vertex);
+          }
+        }
+      }
+    }
+  FOREACHfacet_(facets) {
+    if( !allfacets && qh_skipfacet(facet) )
+      {
+      continue;
+      }
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        vertex->visitid = qh vertex_visit;
+        qh_setappend(&vertices, vertex);
+        }
+      }
+    }
+  return vertices;
+} /* facetvertices */
+
+/*---------------------------------
+
+  qh_geomplanes( facet, outerplane, innerplane )
+  return outer and inner planes for Geomview
+  qh.PRINTradius is size of vertices and points (includes qh.JOGGLEmax)
+
+  notes:
+  assume precise calculations in io.c with roundoff covered by qh_GEOMepsilon
+*/
+void qh_geomplanes(facetT *facet, realT *outerplane, realT *innerplane)
+{
+  realT radius;
+
+  if( qh MERGING || qh JOGGLEmax < REALmax / 2 )
+    {
+    qh_outerinner(facet, outerplane, innerplane);
+    radius = qh PRINTradius;
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      radius -= qh JOGGLEmax * sqrt( (double)qh hull_dim);  /* already accounted
+                                                              for in
+                                                              qh_outerinner() */
+      }
+    *outerplane += radius;
+    *innerplane -= radius;
+    if( qh PRINTcoplanar || qh PRINTspheres )
+      {
+      *outerplane += qh MAXabs_coord * qh_GEOMepsilon;
+      *innerplane -= qh MAXabs_coord * qh_GEOMepsilon;
+      }
+    }
+  else
+    {
+    *innerplane = *outerplane = 0;
+    }
+} /* geomplanes */
+
+/*---------------------------------
+
+  qh_markkeep( facetlist )
+  mark good facets that meet qh.KEEParea, qh.KEEPmerge, and qh.KEEPminArea
+  ignores visible facets (not part of convex hull)
+
+  returns:
+  may clear facet->good
+  recomputes qh.num_good
+
+  design:
+  get set of good facets
+  if qh.KEEParea
+  sort facets by area
+  clear facet->good for all but n largest facets
+  if qh.KEEPmerge
+  sort facets by merge count
+  clear facet->good for all but n most merged facets
+  if qh.KEEPminarea
+  clear facet->good if area too small
+  update qh.num_good
+*/
+void qh_markkeep(facetT *facetlist)
+{
+  facetT *facet, * *facetp;
+  setT *  facets = qh_settemp(qh num_facets);
+  int     size, count;
+
+  trace2( (qh ferr, "qh_markkeep: only keep %d largest and/or %d most merged facets and/or min area %.2g\n",
+           qh KEEParea, qh KEEPmerge, qh KEEPminArea) );
+  FORALLfacet_(facetlist) {
+    if( !facet->visible && facet->good )
+      {
+      qh_setappend(&facets, facet);
+      }
+    }
+  size = qh_setsize(facets);
+  if( qh KEEParea )
+    {
+    qsort(SETaddr_(facets, facetT), (size_t) size,
+          sizeof (facetT *), qh_compare_facetarea);
+    if( (count = size - qh KEEParea) > 0 )
+      {
+      FOREACHfacet_(facets) {
+        facet->good = False;
+        if( --count == 0 )
+          {
+          break;
+          }
+        }
+      }
+    }
+  if( qh KEEPmerge )
+    {
+    qsort(SETaddr_(facets, facetT), (size_t)size,
+          sizeof (facetT *), qh_compare_facetmerge);
+    if( (count = size - qh KEEPmerge) > 0 )
+      {
+      FOREACHfacet_(facets) {
+        facet->good = False;
+        if( --count == 0 )
+          {
+          break;
+          }
+        }
+      }
+    }
+  if( qh KEEPminArea < REALmax / 2 )
+    {
+    FOREACHfacet_(facets) {
+      if( !facet->isarea || facet->f.area < qh KEEPminArea )
+        {
+        facet->good = False;
+        }
+      }
+    }
+  qh_settempfree(&facets);
+  count = 0;
+  FORALLfacet_(facetlist) {
+    if( facet->good )
+      {
+      count++;
+      }
+    }
+  qh num_good = count;
+} /* markkeep */
+
+/*---------------------------------
+
+  qh_markvoronoi( facetlist, facets, printall, islower, numcenters )
+  mark voronoi vertices for printing by site pairs
+
+  returns:
+  temporary set of vertices indexed by pointid
+  islower set if printing lower hull (i.e., at least one facet is lower hull)
+  numcenters= total number of Voronoi vertices
+  bumps qh.printoutnum for vertex-at-infinity
+  clears all facet->seen and sets facet->seen2
+
+  if selected
+  facet->visitid= Voronoi vertex id
+  else if upper hull (or 'Qu' and lower hull)
+  facet->visitid= 0
+  else
+  facet->visitid >= qh num_facets
+
+  notes:
+  ignores qh.ATinfinity, if defined
+*/
+setT * qh_markvoronoi(facetT *facetlist, setT *facets, boolT printall, boolT *islowerp, int *numcentersp)
+{
+  int     numcenters = 0;
+  facetT *facet, * *facetp;
+  setT *  vertices;
+  boolT   isLower = False;
+
+  qh printoutnum++;
+
+  qh_clearcenters(qh_ASvoronoi);   /* in case, qh_printvdiagram2 called by user
+                                     */
+  qh_vertexneighbors();
+  vertices = qh_pointvertex();
+  if( qh ATinfinity )
+    {
+    SETelem_(vertices, qh num_points - 1) = NULL;
+    }
+  qh visit_id++;
+  maximize_(qh visit_id, (unsigned) qh num_facets);
+  FORALLfacet_(facetlist) {
+    if( printall || !qh_skipfacet(facet) )
+      {
+      if( !facet->upperdelaunay )
+        {
+        isLower = True;
+        break;
+        }
+      }
+    }
+  FOREACHfacet_(facets) {
+    if( printall || !qh_skipfacet(facet) )
+      {
+      if( !facet->upperdelaunay )
+        {
+        isLower = True;
+        break;
+        }
+      }
+    }
+  FORALLfacets {
+    if( facet->normal && (facet->upperdelaunay == isLower) )
+      {
+      facet->visitid = 0;  /* facetlist or facets may overwrite */
+      }
+    else
+      {
+      facet->visitid = qh visit_id;
+      }
+    facet->seen = False;
+    facet->seen2 = True;
+    }
+  numcenters++;  /* qh_INFINITE */
+  FORALLfacet_(facetlist) {
+    if( printall || !qh_skipfacet(facet) )
+      {
+      facet->visitid = numcenters++;
+      }
+    }
+  FOREACHfacet_(facets) {
+    if( printall || !qh_skipfacet(facet) )
+      {
+      facet->visitid = numcenters++;
+      }
+    }
+  *islowerp = isLower;
+  *numcentersp = numcenters;
+  trace2( (qh ferr, "qh_markvoronoi: islower %d numcenters %d\n", isLower, numcenters) );
+  return vertices;
+} /* markvoronoi */
+
+/*---------------------------------
+
+  qh_order_vertexneighbors( vertex )
+  order facet neighbors of a 2-d or 3-d vertex by adjacency
+
+  notes:
+  does not orient the neighbors
+
+  design:
+  initialize a new neighbor set with the first facet in vertex->neighbors
+  while vertex->neighbors non-empty
+  select next neighbor in the previous facet's neighbor set
+  set vertex->neighbors to the new neighbor set
+*/
+void qh_order_vertexneighbors(vertexT *vertex)
+{
+  setT *  newset;
+  facetT *facet, *neighbor, * *neighborp;
+
+  trace4( (qh ferr, "qh_order_vertexneighbors: order neighbors of v%d for 3-d\n", vertex->id) );
+  newset = qh_settemp(qh_setsize(vertex->neighbors) );
+  facet = (facetT *)qh_setdellast(vertex->neighbors);
+  qh_setappend(&newset, facet);
+  while( qh_setsize(vertex->neighbors) )
+    {
+    FOREACHneighbor_(vertex) {
+      if( qh_setin(facet->neighbors, neighbor) )
+        {
+        qh_setdel(vertex->neighbors, neighbor);
+        qh_setappend(&newset, neighbor);
+        facet = neighbor;
+        break;
+        }
+      }
+    if( !neighbor )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_order_vertexneighbors): no neighbor of v%d for f%d\n",
+              vertex->id, facet->id);
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    }
+
+  qh_setfree(&vertex->neighbors);
+  qh_settemppop();
+  vertex->neighbors = newset;
+} /* order_vertexneighbors */
+
+/*---------------------------------
+
+  qh_printafacet( fp, format, facet, printall )
+  print facet to fp in given output format (see qh.PRINTout)
+
+  returns:
+  nop if !printall and qh_skipfacet()
+  nop if visible facet and NEWfacets and format != PRINTfacets
+  must match qh_countfacets
+
+  notes
+  preserves qh.visit_id
+  facet->normal may be null if PREmerge/MERGEexact and STOPcone before merge
+
+  see
+  qh_printbegin() and qh_printend()
+
+  design:
+  test for printing facet
+  call appropriate routine for format
+  or output results directly
+*/
+void qh_printafacet(FILE *fp, qh_PRINT format, facetT *facet, boolT printall)
+{
+  realT    color[4], offset, dist, outerplane, innerplane;
+  boolT    zerodiv;
+  coordT * point, *normp, *coordp, * *pointp, *feasiblep;
+  int      k;
+  vertexT *vertex, * *vertexp;
+  facetT * neighbor, * *neighborp;
+
+  if( !printall && qh_skipfacet(facet) )
+    {
+    return;
+    }
+  if( facet->visible && qh NEWfacets && format != qh_PRINTfacets )
+    {
+    return;
+    }
+  qh printoutnum++;
+
+  switch( format )
+    {
+    case qh_PRINTarea:
+      if( facet->isarea )
+        {
+        fprintf(fp, qh_REAL_1, facet->f.area);
+        fprintf(fp, "\n");
+        }
+      else
+        {
+        fprintf(fp, "0\n");
+        }
+      break;
+    case qh_PRINTcoplanars:
+      fprintf(fp, "%d", qh_setsize(facet->coplanarset) );
+      FOREACHpoint_(facet->coplanarset)
+      fprintf(fp, " %d", qh_pointid(point) );
+      fprintf(fp, "\n");
+      break;
+    case qh_PRINTcentrums:
+      qh_printcenter(fp, format, NULL, facet);
+      break;
+    case qh_PRINTfacets:
+      qh_printfacet(fp, facet);
+      break;
+    case qh_PRINTfacets_xridge:
+      qh_printfacetheader(fp, facet);
+      break;
+    case qh_PRINTgeom: /* either 2 , 3, or 4-d by qh_printbegin */
+      if( !facet->normal )
+        {
+        break;
+        }
+      for( k = qh hull_dim; k--; )
+        {
+        color[k] = (facet->normal[k] + 1.0) / 2.0;
+        maximize_(color[k], -1.0);
+        minimize_(color[k], +1.0);
+        }
+      qh_projectdim3(color, color);
+      if( qh PRINTdim != qh hull_dim )
+        {
+        qh_normalize2(color, 3, True, NULL, NULL);
+        }
+      if( qh hull_dim <= 2 )
+        {
+        qh_printfacet2geom(fp, facet, color);
+        }
+      else if( qh hull_dim == 3 )
+        {
+        if( facet->simplicial )
+          {
+          qh_printfacet3geom_simplicial(fp, facet, color);
+          }
+        else
+          {
+          qh_printfacet3geom_nonsimplicial(fp, facet, color);
+          }
+        }
+      else
+        {
+        if( facet->simplicial )
+          {
+          qh_printfacet4geom_simplicial(fp, facet, color);
+          }
+        else
+          {
+          qh_printfacet4geom_nonsimplicial(fp, facet, color);
+          }
+        }
+      break;
+    case qh_PRINTids:
+      fprintf(fp, "%d\n", facet->id);
+      break;
+    case qh_PRINTincidences:
+    case qh_PRINToff:
+    case qh_PRINTtriangles:
+      if( qh hull_dim == 3 && format != qh_PRINTtriangles )
+        {
+        qh_printfacet3vertex(fp, facet, format);
+        }
+      else if( facet->simplicial || qh hull_dim == 2 || format == qh_PRINToff )
+        {
+        qh_printfacetNvertex_simplicial(fp, facet, format);
+        }
+      else
+        {
+        qh_printfacetNvertex_nonsimplicial(fp, facet, qh printoutvar++, format);
+        }
+      break;
+    case qh_PRINTinner:
+      qh_outerinner(facet, NULL, &innerplane);
+      offset = facet->offset - innerplane;
+      goto LABELprintnorm;
+      break; /* prevent warning */
+    case qh_PRINTmerges:
+      fprintf(fp, "%d\n", facet->nummerge);
+      break;
+    case qh_PRINTnormals:
+      offset = facet->offset;
+      goto LABELprintnorm;
+      break; /* prevent warning */
+    case qh_PRINTouter:
+      qh_outerinner(facet, &outerplane, NULL);
+      offset = facet->offset - outerplane;
+LABELprintnorm:
+      if( !facet->normal )
+        {
+        fprintf(fp, "no normal for facet f%d\n", facet->id);
+        break;
+        }
+      if( qh CDDoutput )
+        {
+        fprintf(fp, qh_REAL_1, -offset);
+        for( k = 0; k < qh hull_dim; k++ )
+          {
+          fprintf(fp, qh_REAL_1, -facet->normal[k]);
+          }
+        }
+      else
+        {
+        for( k = 0; k < qh hull_dim; k++ )
+          {
+          fprintf(fp, qh_REAL_1, facet->normal[k]);
+          }
+        fprintf(fp, qh_REAL_1, offset);
+        }
+      fprintf(fp, "\n");
+      break;
+    case qh_PRINTmathematica: /* either 2 or 3-d by qh_printbegin */
+    case qh_PRINTmaple:
+      if( qh hull_dim == 2 )
+        {
+        qh_printfacet2math(fp, facet, format, qh printoutvar++);
+        }
+      else
+        {
+        qh_printfacet3math(fp, facet, format, qh printoutvar++);
+        }
+      break;
+    case qh_PRINTneighbors:
+      fprintf(fp, "%d", qh_setsize(facet->neighbors) );
+      FOREACHneighbor_(facet)
+      fprintf(fp, " %d",
+              neighbor->visitid ? neighbor->visitid - 1 : -neighbor->id);
+      fprintf(fp, "\n");
+      break;
+    case qh_PRINTpointintersect:
+      if( !qh feasible_point )
+        {
+        fprintf(fp, "qhull input error (qh_printafacet): option 'Fp' needs qh feasible_point\n");
+        qh_errexit( qh_ERRinput, NULL, NULL);
+        }
+      if( facet->offset > 0 )
+        {
+        goto LABELprintinfinite;
+        }
+      point = coordp = (coordT *)qh_memalloc(qh normal_size);
+      normp = facet->normal;
+      feasiblep = qh feasible_point;
+      if( facet->offset < -qh MINdenom )
+        {
+        for( k = qh hull_dim; k--; )
+          {
+          *(coordp++) = (*(normp++) / -facet->offset) + *(feasiblep++);
+          }
+        }
+      else
+        {
+        for( k = qh hull_dim; k--; )
+          {
+          *(coordp++) = qh_divzero(*(normp++), facet->offset, qh MINdenom_1,
+                                   &zerodiv) + *(feasiblep++);
+          if( zerodiv )
+            {
+            qh_memfree(point, qh normal_size);
+            goto LABELprintinfinite;
+            }
+          }
+        }
+      qh_printpoint(fp, NULL, point);
+      qh_memfree(point, qh normal_size);
+      break;
+LABELprintinfinite:
+      for( k = qh hull_dim; k--; )
+        {
+        fprintf(fp, qh_REAL_1, qh_INFINITE);
+        }
+      fprintf(fp, "\n");
+      break;
+    case qh_PRINTpointnearest:
+      FOREACHpoint_(facet->coplanarset) {
+        int id, id2;
+
+        vertex = qh_nearvertex(facet, point, &dist);
+        id = qh_pointid(vertex->point);
+        id2 = qh_pointid(point);
+        fprintf(fp, "%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
+        }
+      break;
+    case qh_PRINTpoints: /* VORONOI only by qh_printbegin */
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "1 ");
+        }
+      qh_printcenter(fp, format, NULL, facet);
+      break;
+    case qh_PRINTvertices:
+      fprintf(fp, "%d", qh_setsize(facet->vertices) );
+      FOREACHvertex_(facet->vertices)
+      fprintf(fp, " %d", qh_pointid(vertex->point) );
+      fprintf(fp, "\n");
+    default:
+      break;
+    }
+} /* printafacet */
+
+/*---------------------------------
+
+  qh_printbegin(  )
+  prints header for all output formats
+
+  returns:
+  checks for valid format
+
+  notes:
+  uses qh.visit_id for 3/4off
+  changes qh.interior_point if printing centrums
+  qh_countfacets clears facet->visitid for non-good facets
+
+  see
+  qh_printend() and qh_printafacet()
+
+  design:
+  count facets and related statistics
+  print header for format
+*/
+void qh_printbegin(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall)
+{
+  int      numfacets, numsimplicial, numridges, totneighbors, numcoplanars, numtricoplanars;
+  int      i, num;
+  facetT * facet, * *facetp;
+  vertexT *vertex, * *vertexp;
+  setT *   vertices;
+  pointT * point, * *pointp, *pointtemp;
+
+  qh printoutnum = 0;
+
+  qh_countfacets(facetlist, facets, printall, &numfacets, &numsimplicial,
+                 &totneighbors, &numridges, &numcoplanars, &numtricoplanars);
+
+  switch( format )
+    {
+    case qh_PRINTnone:
+      break;
+    case qh_PRINTarea:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINTcoplanars:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINTcentrums:
+      if( qh CENTERtype == qh_ASnone )
+        {
+        qh_clearcenters(qh_AScentrum);
+        }
+      fprintf(fp, "%d\n%d\n", qh hull_dim, numfacets);
+      break;
+    case qh_PRINTfacets:
+    case qh_PRINTfacets_xridge:
+      if( facetlist )
+        {
+        qh_printvertexlist(fp, "Vertices and facets:\n", facetlist, facets, printall);
+        }
+      break;
+    case qh_PRINTgeom:
+      if( qh hull_dim > 4 ) /* qh_initqhull_globals also checks */
+        {
+        goto LABELnoformat;
+        }
+      if( qh VORONOI && qh hull_dim > 3 ) /* PRINTdim == DROPdim == hull_dim-1
+                                            */
+        {
+        goto LABELnoformat;
+        }
+      if( qh hull_dim == 2 && (qh PRINTridges || qh DOintersections) )
+        {
+        fprintf(qh ferr, "qhull warning: output for ridges and intersections not implemented in 2-d\n");
+        }
+      if( qh hull_dim == 4 && (qh PRINTinner || qh PRINTouter ||
+                               (qh PRINTdim == 4 && qh PRINTcentrums) ) )
+        {
+        fprintf(qh ferr, "qhull warning: output for outer/inner planes and centrums not implemented in 4-d\n");
+        }
+      if( qh PRINTdim == 4 && (qh PRINTspheres) )
+        {
+        fprintf(qh ferr, "qhull warning: output for vertices not implemented in 4-d\n");
+        }
+      if( qh PRINTdim == 4 && qh DOintersections && qh PRINTnoplanes )
+        {
+        fprintf(qh ferr, "qhull warning: 'Gnh' generates no output in 4-d\n");
+        }
+      if( qh PRINTdim == 2 )
+        {
+        fprintf(fp, "{appearance {linewidth 3} LIST #%s | %s\n",
+                qh rbox_command, qh qhull_command);
+        }
+      else if( qh PRINTdim == 3 )
+        {
+        fprintf(fp, "{appearance {+edge -evert linewidth 2} LIST #%s | %s\n",
+                qh rbox_command, qh qhull_command);
+        }
+      else if( qh PRINTdim == 4 )
+        {
+        qh visit_id++;
+        num = 0;
+        FORALLfacet_(facetlist)  /* get number of ridges to be printed */
+        qh_printend4geom(NULL, facet, &num, printall);
+        FOREACHfacet_(facets)
+        qh_printend4geom(NULL, facet, &num, printall);
+        qh ridgeoutnum = num;
+        qh printoutvar = 0; /* counts number of ridges in output */
+        fprintf(fp, "LIST #%s | %s\n", qh rbox_command, qh qhull_command);
+        }
+      if( qh PRINTdots )
+        {
+        qh printoutnum++;
+        num = qh num_points + qh_setsize(qh other_points);
+        if( qh DELAUNAY && qh ATinfinity )
+          {
+          num--;
+          }
+        if( qh PRINTdim == 4 )
+          {
+          fprintf(fp, "4VECT %d %d 1\n", num, num);
+          }
+        else
+          {
+          fprintf(fp, "VECT %d %d 1\n", num, num);
+          }
+        for( i = num; i--; )
+          {
+          if( i % 20 == 0 )
+            {
+            fprintf(fp, "\n");
+            }
+          fprintf(fp, "1 ");
+          }
+        fprintf(fp, "#1 point per line\n1 ");
+        for( i = num - 1; i--; )
+          {
+          if( i % 20 == 0 )
+            {
+            fprintf(fp, "\n");
+            }
+          fprintf(fp, "0 ");
+          }
+        fprintf(fp, "#1 color for all\n");
+        FORALLpoints {
+          if( !qh DELAUNAY || !qh ATinfinity || qh_pointid(point) != qh num_points - 1 )
+            {
+            if( qh PRINTdim == 4 )
+              {
+              qh_printpoint(fp, NULL, point);
+              }
+            else
+              {
+              qh_printpoint3(fp, point);
+              }
+            }
+          }
+        FOREACHpoint_(qh other_points) {
+          if( qh PRINTdim == 4 )
+            {
+            qh_printpoint(fp, NULL, point);
+            }
+          else
+            {
+            qh_printpoint3(fp, point);
+            }
+          }
+        fprintf(fp, "0 1 1 1  #color of points\n");
+        }
+      if( qh PRINTdim == 4  && !qh PRINTnoplanes )
+        {
+        /* 4dview loads up multiple 4OFF objects slowly */
+        fprintf(fp, "4OFF %d %d 1\n", 3 * qh ridgeoutnum, qh ridgeoutnum);
+        }
+      qh PRINTcradius = 2 * qh DISTround; /* include test DISTround */
+      if( qh PREmerge )
+        {
+        maximize_(qh PRINTcradius, qh premerge_centrum + qh DISTround);
+        }
+      else if( qh POSTmerge )
+        {
+        maximize_(qh PRINTcradius, qh postmerge_centrum + qh DISTround);
+        }
+      qh PRINTradius = qh PRINTcradius;
+      if( qh PRINTspheres + qh PRINTcoplanar )
+        {
+        maximize_(qh PRINTradius, qh MAXabs_coord * qh_MINradius);
+        }
+      if( qh premerge_cos < REALmax / 2 )
+        {
+        maximize_(qh PRINTradius, (1 - qh premerge_cos) * qh MAXabs_coord);
+        }
+      else if( !qh PREmerge && qh POSTmerge && qh postmerge_cos < REALmax / 2 )
+        {
+        maximize_(qh PRINTradius, (1 - qh postmerge_cos) * qh MAXabs_coord);
+        }
+      maximize_(qh PRINTradius, qh MINvisible);
+      if( qh JOGGLEmax < REALmax / 2 )
+        {
+        qh PRINTradius += qh JOGGLEmax * sqrt( (double)qh hull_dim);
+        }
+      if( qh PRINTdim != 4 &&
+          (qh PRINTcoplanar || qh PRINTspheres || qh PRINTcentrums) )
+        {
+        vertices = qh_facetvertices(facetlist, facets, printall);
+        if( qh PRINTspheres && qh PRINTdim <= 3 )
+          {
+          qh_printspheres(fp, vertices, qh PRINTradius);
+          }
+        if( qh PRINTcoplanar || qh PRINTcentrums )
+          {
+          qh firstcentrum = True;
+          if( qh PRINTcoplanar && !qh PRINTspheres )
+            {
+            FOREACHvertex_(vertices)
+            qh_printpointvect2(fp, vertex->point, NULL,
+                               qh interior_point, qh PRINTradius);
+            }
+          FORALLfacet_(facetlist) {
+            if( !printall && qh_skipfacet(facet) )
+              {
+              continue;
+              }
+            if( !facet->normal )
+              {
+              continue;
+              }
+            if( qh PRINTcentrums && qh PRINTdim <= 3 )
+              {
+              qh_printcentrum(fp, facet, qh PRINTcradius);
+              }
+            if( !qh PRINTcoplanar )
+              {
+              continue;
+              }
+            FOREACHpoint_(facet->coplanarset)
+            qh_printpointvect2(fp, point, facet->normal, NULL, qh PRINTradius);
+            FOREACHpoint_(facet->outsideset)
+            qh_printpointvect2(fp, point, facet->normal, NULL, qh PRINTradius);
+            }
+          FOREACHfacet_(facets) {
+            if( !printall && qh_skipfacet(facet) )
+              {
+              continue;
+              }
+            if( !facet->normal )
+              {
+              continue;
+              }
+            if( qh PRINTcentrums && qh PRINTdim <= 3 )
+              {
+              qh_printcentrum(fp, facet, qh PRINTcradius);
+              }
+            if( !qh PRINTcoplanar )
+              {
+              continue;
+              }
+            FOREACHpoint_(facet->coplanarset)
+            qh_printpointvect2(fp, point, facet->normal, NULL, qh PRINTradius);
+            FOREACHpoint_(facet->outsideset)
+            qh_printpointvect2(fp, point, facet->normal, NULL, qh PRINTradius);
+            }
+          }
+        qh_settempfree(&vertices);
+        }
+      qh visit_id++; /* for printing hyperplane intersections */
+      break;
+    case qh_PRINTids:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINTincidences:
+      if( qh VORONOI && qh PRINTprecision )
+        {
+        fprintf(qh ferr, "qhull warning: writing Delaunay.  Use 'p' or 'o' for Voronoi centers\n");
+        }
+      qh printoutvar = qh vertex_id; /* centrum id for non-simplicial facets */
+      if( qh hull_dim <= 3 )
+        {
+        fprintf(fp, "%d\n", numfacets);
+        }
+      else
+        {
+        fprintf(fp, "%d\n", numsimplicial + numridges);
+        }
+      break;
+    case qh_PRINTinner:
+    case qh_PRINTnormals:
+    case qh_PRINTouter:
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "%s | %s\nbegin\n    %d %d real\n", qh rbox_command,
+                qh qhull_command, numfacets, qh hull_dim + 1);
+        }
+      else
+        {
+        fprintf(fp, "%d\n%d\n", qh hull_dim + 1, numfacets);
+        }
+      break;
+    case qh_PRINTmathematica:
+    case qh_PRINTmaple:
+      if( qh hull_dim > 3 ) /* qh_initbuffers also checks */
+        {
+        goto LABELnoformat;
+        }
+      if( qh VORONOI )
+        {
+        fprintf(qh ferr, "qhull warning: output is the Delaunay triangulation\n");
+        }
+      if( format == qh_PRINTmaple )
+        {
+        if( qh hull_dim == 2 )
+          {
+          fprintf(fp, "PLOT(CURVES(\n");
+          }
+        else
+          {
+          fprintf(fp, "PLOT3D(POLYGONS(\n");
+          }
+        }
+      else
+        {
+        fprintf(fp, "{\n");
+        }
+      qh printoutvar = 0; /* counts number of facets for notfirst */
+      break;
+    case qh_PRINTmerges:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINTpointintersect:
+      fprintf(fp, "%d\n%d\n", qh hull_dim, numfacets);
+      break;
+    case qh_PRINTneighbors:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINToff:
+    case qh_PRINTtriangles:
+      if( qh VORONOI )
+        {
+        goto LABELnoformat;
+        }
+      num = qh hull_dim;
+      if( format == qh_PRINToff || qh hull_dim == 2 )
+        {
+        fprintf(fp, "%d\n%d %d %d\n", num,
+                qh num_points + qh_setsize(qh other_points), numfacets, totneighbors / 2);
+        }
+      else /* qh_PRINTtriangles */
+        {
+        qh printoutvar = qh num_points + qh_setsize(qh other_points); /* first
+                                                                        centrum
+                                                                        */
+        if( qh DELAUNAY )
+          {
+          num--; /* drop last dimension */
+          }
+        fprintf(fp, "%d\n%d %d %d\n", num, qh printoutvar
+                + numfacets - numsimplicial, numsimplicial + numridges, totneighbors / 2);
+        }
+      FORALLpoints
+      qh_printpointid(qh fout, NULL, num, point, -1);
+      FOREACHpoint_(qh other_points)
+      qh_printpointid(qh fout, NULL, num, point, -1);
+      if( format == qh_PRINTtriangles && qh hull_dim > 2 )
+        {
+        FORALLfacets {
+          if( !facet->simplicial && facet->visitid )
+            {
+            qh_printcenter(qh fout, format, NULL, facet);
+            }
+          }
+        }
+      break;
+    case qh_PRINTpointnearest:
+      fprintf(fp, "%d\n", numcoplanars);
+      break;
+    case qh_PRINTpoints:
+      if( !qh VORONOI )
+        {
+        goto LABELnoformat;
+        }
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "%s | %s\nbegin\n%d %d real\n", qh rbox_command,
+                qh qhull_command, numfacets, qh hull_dim);
+        }
+      else
+        {
+        fprintf(fp, "%d\n%d\n", qh hull_dim - 1, numfacets);
+        }
+      break;
+    case qh_PRINTvertices:
+      fprintf(fp, "%d\n", numfacets);
+      break;
+    case qh_PRINTsummary:
+    default:
+LABELnoformat:
+      fprintf(qh ferr, "qhull internal error (qh_printbegin): can not use this format for dimension %d\n",
+              qh hull_dim);
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+} /* printbegin */
+
+/*---------------------------------
+
+  qh_printcenter( fp, string, facet )
+  print facet->center as centrum or Voronoi center
+  string may be NULL.  Don't include '%' codes.
+  nop if qh CENTERtype neither CENTERvoronoi nor CENTERcentrum
+  if upper envelope of Delaunay triangulation and point at-infinity
+  prints qh_INFINITE instead;
+
+  notes:
+  defines facet->center if needed
+  if format=PRINTgeom, adds a 0 if would otherwise be 2-d
+*/
+void qh_printcenter(FILE *fp, qh_PRINT format, const char *string, facetT *facet)
+{
+  int k, num;
+
+  if( qh CENTERtype != qh_ASvoronoi && qh CENTERtype != qh_AScentrum )
+    {
+    return;
+    }
+  if( string )
+    {
+    fprintf(fp, string, facet->id);
+    }
+  if( qh CENTERtype == qh_ASvoronoi )
+    {
+    num = qh hull_dim - 1;
+    if( !facet->normal || !facet->upperdelaunay || !qh ATinfinity )
+      {
+      if( !facet->center )
+        {
+        facet->center = qh_facetcenter(facet->vertices);
+        }
+      for( k = 0; k < num; k++ )
+        {
+        fprintf(fp, qh_REAL_1, facet->center[k]);
+        }
+      }
+    else
+      {
+      for( k = 0; k < num; k++ )
+        {
+        fprintf(fp, qh_REAL_1, qh_INFINITE);
+        }
+      }
+    }
+  else  /* qh CENTERtype == qh_AScentrum */
+    {
+    num = qh hull_dim;
+    if( format == qh_PRINTtriangles && qh DELAUNAY )
+      {
+      num--;
+      }
+    if( !facet->center )
+      {
+      facet->center = qh_getcentrum(facet);
+      }
+    for( k = 0; k < num; k++ )
+      {
+      fprintf(fp, qh_REAL_1, facet->center[k]);
+      }
+    }
+  if( format == qh_PRINTgeom && num == 2 )
+    {
+    fprintf(fp, " 0\n");
+    }
+  else
+    {
+    fprintf(fp, "\n");
+    }
+} /* printcenter */
+
+/*---------------------------------
+
+  qh_printcentrum( fp, facet, radius )
+  print centrum for a facet in OOGL format
+  radius defines size of centrum
+  2-d or 3-d only
+
+  returns:
+  defines facet->center if needed
+*/
+void qh_printcentrum(FILE *fp, facetT *facet, realT radius)
+{
+  pointT * centrum, *projpt;
+  boolT    tempcentrum = False;
+  realT    xaxis[4], yaxis[4], normal[4], dist;
+  realT    green[3] = {0, 1, 0};
+  vertexT *apex;
+  int      k;
+
+  if( qh CENTERtype == qh_AScentrum )
+    {
+    if( !facet->center )
+      {
+      facet->center = qh_getcentrum(facet);
+      }
+    centrum = facet->center;
+    }
+  else
+    {
+    centrum = qh_getcentrum(facet);
+    tempcentrum = True;
+    }
+  fprintf(fp, "{appearance {-normal -edge normscale 0} ");
+  if( qh firstcentrum )
+    {
+    qh firstcentrum = False;
+    fprintf(
+      fp,
+      "{INST geom { define centrum CQUAD  #f%d\n\
+-0.3 -0.3 0.0001     0 0 1 1\n\
+ 0.3 -0.3 0.0001     0 0 1 1\n\
+ 0.3  0.3 0.0001     0 0 1 1\n\
+-0.3  0.3 0.0001     0 0 1 1 } transform { \n"                                                                                                                                                   ,
+      facet->id);
+    }
+  else
+    {
+    fprintf(fp, "{INST geom { : centrum } transform { #f%d\n", facet->id);
+    }
+  apex = SETfirstt_(facet->vertices, vertexT);
+  qh_distplane(apex->point, facet, &dist);
+  projpt = qh_projectpoint(apex->point, facet, dist);
+  for( k = qh hull_dim; k--; )
+    {
+    xaxis[k] = projpt[k] - centrum[k];
+    normal[k] = facet->normal[k];
+    }
+  if( qh hull_dim == 2 )
+    {
+    xaxis[2] = 0;
+    normal[2] = 0;
+    }
+  else if( qh hull_dim == 4 )
+    {
+    qh_projectdim3(xaxis, xaxis);
+    qh_projectdim3(normal, normal);
+    qh_normalize2(normal, qh PRINTdim, True, NULL, NULL);
+    }
+  qh_crossproduct(3, xaxis, normal, yaxis);
+  fprintf(fp, "%8.4g %8.4g %8.4g 0\n", xaxis[0], xaxis[1], xaxis[2]);
+  fprintf(fp, "%8.4g %8.4g %8.4g 0\n", yaxis[0], yaxis[1], yaxis[2]);
+  fprintf(fp, "%8.4g %8.4g %8.4g 0\n", normal[0], normal[1], normal[2]);
+  qh_printpoint3(fp, centrum);
+  fprintf(fp, "1 }}}\n");
+  qh_memfree(projpt, qh normal_size);
+  qh_printpointvect(fp, centrum, facet->normal, NULL, radius, green);
+  if( tempcentrum )
+    {
+    qh_memfree(centrum, qh normal_size);
+    }
+} /* printcentrum */
+
+/*---------------------------------
+
+  qh_printend( fp, format )
+  prints trailer for all output formats
+
+  see:
+  qh_printbegin() and qh_printafacet()
+
+*/
+void qh_printend(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall)
+{
+  int     num;
+  facetT *facet, * *facetp;
+
+  if( !qh printoutnum )
+    {
+    fprintf(qh ferr, "qhull warning: no facets printed\n");
+    }
+
+  switch( format )
+    {
+    case qh_PRINTgeom:
+      if( qh hull_dim == 4 && qh DROPdim < 0  && !qh PRINTnoplanes )
+        {
+        qh visit_id++;
+        num = 0;
+        FORALLfacet_(facetlist)
+        qh_printend4geom(fp, facet, &num, printall);
+        FOREACHfacet_(facets)
+        qh_printend4geom(fp, facet, &num, printall);
+        if( num != qh ridgeoutnum || qh printoutvar != qh ridgeoutnum )
+          {
+          fprintf(qh ferr,
+                  "qhull internal error (qh_printend): number of ridges %d != number printed %d and at end %d\n",
+                  qh ridgeoutnum,
+                  qh printoutvar,
+                  num);
+          qh_errexit(qh_ERRqhull, NULL, NULL);
+          }
+        }
+      else
+        {
+        fprintf(fp, "}\n");
+        }
+      break;
+    case qh_PRINTinner:
+    case qh_PRINTnormals:
+    case qh_PRINTouter:
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "end\n");
+        }
+      break;
+    case qh_PRINTmaple:
+      fprintf(fp, "));\n");
+      break;
+    case qh_PRINTmathematica:
+      fprintf(fp, "}\n");
+      break;
+    case qh_PRINTpoints:
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "end\n");
+        }
+    default:
+      break;
+    }
+} /* printend */
+
+/*---------------------------------
+
+  qh_printend4geom( fp, facet, numridges, printall )
+  helper function for qh_printbegin/printend
+
+  returns:
+  number of printed ridges
+
+  notes:
+  just counts printed ridges if fp=NULL
+  uses facet->visitid
+  must agree with qh_printfacet4geom...
+
+  design:
+  computes color for facet from its normal
+  prints each ridge of facet
+*/
+void qh_printend4geom(FILE *fp, facetT *facet, int *nump, boolT printall)
+{
+  realT   color[3];
+  int     i, num = *nump;
+  facetT *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+
+  if( !printall && qh_skipfacet(facet) )
+    {
+    return;
+    }
+  if( qh PRINTnoplanes || (facet->visible && qh NEWfacets) )
+    {
+    return;
+    }
+  if( !facet->normal )
+    {
+    return;
+    }
+  if( fp )
+    {
+    for( i = 0; i < 3; i++ )
+      {
+      color[i] = (facet->normal[i] + 1.0) / 2.0;
+      maximize_(color[i], -1.0);
+      minimize_(color[i], +1.0);
+      }
+    }
+  facet->visitid = qh visit_id;
+  if( facet->simplicial )
+    {
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid != qh visit_id )
+        {
+        if( fp )
+          {
+          fprintf(fp, "3 %d %d %d %8.4g %8.4g %8.4g 1 #f%d f%d\n",
+                  3 * num, 3 * num + 1, 3 * num + 2, color[0], color[1], color[2],
+                  facet->id, neighbor->id);
+          }
+        num++;
+        }
+      }
+    }
+  else
+    {
+    FOREACHridge_(facet->ridges) {
+      neighbor = otherfacet_(ridge, facet);
+      if( neighbor->visitid != qh visit_id )
+        {
+        if( fp )
+          {
+          fprintf(fp, "3 %d %d %d %8.4g %8.4g %8.4g 1 #r%d f%d f%d\n",
+                  3 * num, 3 * num + 1, 3 * num + 2, color[0], color[1], color[2],
+                  ridge->id, facet->id, neighbor->id);
+          }
+        num++;
+        }
+      }
+    }
+  *nump = num;
+} /* printend4geom */
+
+/*---------------------------------
+
+  qh_printextremes( fp, facetlist, facets, printall )
+  print extreme points for convex hulls or halfspace intersections
+
+  notes:
+  #points, followed by ids, one per line
+
+  sorted by id
+  same order as qh_printpoints_out if no coplanar/interior points
+*/
+void qh_printextremes(FILE *fp, facetT *facetlist, setT *facets, boolT printall)
+{
+  setT *   vertices, *points;
+  pointT * point;
+  vertexT *vertex, * *vertexp;
+  int      id;
+  int      numpoints = 0, point_i, point_n;
+  int      allpoints = qh num_points + qh_setsize(qh other_points);
+
+  points = qh_settemp(allpoints);
+  qh_setzero(points, 0, allpoints);
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  FOREACHvertex_(vertices) {
+    id = qh_pointid(vertex->point);
+    if( id >= 0 )
+      {
+      SETelem_(points, id) = vertex->point;
+      numpoints++;
+      }
+    }
+  qh_settempfree(&vertices);
+  fprintf(fp, "%d\n", numpoints);
+  FOREACHpoint_i_(points) {
+    if( point )
+      {
+      fprintf(fp, "%d\n", point_i);
+      }
+    }
+  qh_settempfree(&points);
+} /* printextremes */
+
+/*---------------------------------
+
+  qh_printextremes_2d( fp, facetlist, facets, printall )
+  prints point ids for facets in qh_ORIENTclock order
+
+  notes:
+  #points, followed by ids, one per line
+  if facetlist/facets are disjoint than the output includes skips
+  errors if facets form a loop
+  does not print coplanar points
+*/
+void qh_printextremes_2d(FILE *fp, facetT *facetlist, setT *facets, boolT printall)
+{
+  int      numfacets, numridges, totneighbors, numcoplanars, numsimplicial, numtricoplanars;
+  setT *   vertices;
+  facetT * facet, *startfacet, *nextfacet;
+  vertexT *vertexA, *vertexB;
+
+  qh_countfacets(facetlist, facets, printall, &numfacets, &numsimplicial,
+                 &totneighbors, &numridges, &numcoplanars, &numtricoplanars); /*
+                                                                                marks
+                                                                                qh
+                                                                                visit_id
+                                                                                */
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  fprintf(fp, "%d\n", qh_setsize(vertices) );
+  qh_settempfree(&vertices);
+  if( !numfacets )
+    {
+    return;
+    }
+  facet = startfacet = facetlist ? facetlist : SETfirstt_(facets, facetT);
+  qh vertex_visit++;
+  qh visit_id++;
+
+  do
+    {
+    if( facet->toporient ^ qh_ORIENTclock )
+      {
+      vertexA = SETfirstt_(facet->vertices, vertexT);
+      vertexB = SETsecondt_(facet->vertices, vertexT);
+      nextfacet = SETfirstt_(facet->neighbors, facetT);
+      }
+    else
+      {
+      vertexA = SETsecondt_(facet->vertices, vertexT);
+      vertexB = SETfirstt_(facet->vertices, vertexT);
+      nextfacet = SETsecondt_(facet->neighbors, facetT);
+      }
+    if( facet->visitid == qh visit_id )
+      {
+      fprintf(qh ferr, "qh_printextremes_2d: loop in facet list.  facet %d nextfacet %d\n",
+              facet->id, nextfacet->id);
+      qh_errexit2(qh_ERRqhull, facet, nextfacet);
+      }
+    if( facet->visitid )
+      {
+      if( vertexA->visitid != qh vertex_visit )
+        {
+        vertexA->visitid = qh vertex_visit;
+        fprintf(fp, "%d\n", qh_pointid(vertexA->point) );
+        }
+      if( vertexB->visitid != qh vertex_visit )
+        {
+        vertexB->visitid = qh vertex_visit;
+        fprintf(fp, "%d\n", qh_pointid(vertexB->point) );
+        }
+      }
+    facet->visitid = qh visit_id;
+    facet = nextfacet;
+    }
+  while( facet && facet != startfacet );
+} /* printextremes_2d */
+
+/*---------------------------------
+
+  qh_printextremes_d( fp, facetlist, facets, printall )
+  print extreme points of input sites for Delaunay triangulations
+
+  notes:
+  #points, followed by ids, one per line
+
+  unordered
+*/
+void qh_printextremes_d(FILE *fp, facetT *facetlist, setT *facets, boolT printall)
+{
+  setT *   vertices;
+  vertexT *vertex, * *vertexp;
+  boolT    upperseen, lowerseen;
+  facetT * neighbor, * *neighborp;
+  int      numpoints = 0;
+
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  qh_vertexneighbors();
+  FOREACHvertex_(vertices) {
+    upperseen = lowerseen = False;
+    FOREACHneighbor_(vertex) {
+      if( neighbor->upperdelaunay )
+        {
+        upperseen = True;
+        }
+      else
+        {
+        lowerseen = True;
+        }
+      }
+    if( upperseen && lowerseen )
+      {
+      vertex->seen = True;
+      numpoints++;
+      }
+    else
+      {
+      vertex->seen = False;
+      }
+    }
+  fprintf(fp, "%d\n", numpoints);
+  FOREACHvertex_(vertices) {
+    if( vertex->seen )
+      {
+      fprintf(fp, "%d\n", qh_pointid(vertex->point) );
+      }
+    }
+  qh_settempfree(&vertices);
+} /* printextremes_d */
+
+/*---------------------------------
+
+  qh_printfacet( fp, facet )
+  prints all fields of a facet to fp
+
+  notes:
+  ridges printed in neighbor order
+*/
+void qh_printfacet(FILE *fp, facetT *facet)
+{
+
+  qh_printfacetheader(fp, facet);
+  if( facet->ridges )
+    {
+    qh_printfacetridges(fp, facet);
+    }
+} /* printfacet */
+
+/*---------------------------------
+
+  qh_printfacet2geom( fp, facet, color )
+  print facet as part of a 2-d VECT for Geomview
+
+  notes:
+  assume precise calculations in io.c with roundoff covered by qh_GEOMepsilon
+  mindist is calculated within io.c.  maxoutside is calculated elsewhere
+  so a DISTround error may have occured.
+*/
+void qh_printfacet2geom(FILE *fp, facetT *facet, realT color[3])
+{
+  pointT *point0, *point1;
+  realT   mindist, innerplane, outerplane;
+  int     k;
+
+  qh_facet2point(facet, &point0, &point1, &mindist);
+  qh_geomplanes(facet, &outerplane, &innerplane);
+  if( qh PRINTouter || (!qh PRINTnoplanes && !qh PRINTinner) )
+    {
+    qh_printfacet2geom_points(fp, point0, point1, facet, outerplane, color);
+    }
+  if( qh PRINTinner || (!qh PRINTnoplanes && !qh PRINTouter &&
+                        outerplane - innerplane > 2 * qh MAXabs_coord * qh_GEOMepsilon) )
+    {
+    for( k = 3; k--; )
+      {
+      color[k] = 1.0 - color[k];
+      }
+    qh_printfacet2geom_points(fp, point0, point1, facet, innerplane, color);
+    }
+  qh_memfree(point1, qh normal_size);
+  qh_memfree(point0, qh normal_size);
+} /* printfacet2geom */
+
+/*---------------------------------
+
+  qh_printfacet2geom_points( fp, point1, point2, facet, offset, color )
+  prints a 2-d facet as a VECT with 2 points at some offset.
+  The points are on the facet's plane.
+*/
+void qh_printfacet2geom_points(FILE *fp, pointT *point1, pointT *point2,
+                               facetT *facet, realT offset, realT color[3])
+{
+  pointT *p1 = point1, *p2 = point2;
+
+  fprintf(fp, "VECT 1 2 1 2 1 #f%d\n", facet->id);
+  if( offset != 0.0 )
+    {
+    p1 = qh_projectpoint(p1, facet, -offset);
+    p2 = qh_projectpoint(p2, facet, -offset);
+    }
+  fprintf(fp, "%8.4g %8.4g %8.4g\n%8.4g %8.4g %8.4g\n",
+          p1[0], p1[1], 0.0, p2[0], p2[1], 0.0);
+  if( offset != 0.0 )
+    {
+    qh_memfree(p1, qh normal_size);
+    qh_memfree(p2, qh normal_size);
+    }
+  fprintf(fp, "%8.4g %8.4g %8.4g 1.0\n", color[0], color[1], color[2]);
+} /* printfacet2geom_points */
+
+/*---------------------------------
+
+  qh_printfacet2math( fp, facet, format, notfirst )
+  print 2-d Maple or Mathematica output for a facet
+  may be non-simplicial
+
+  notes:
+  use %16.8f since Mathematica 2.2 does not handle exponential format
+  see qh_printfacet3math
+*/
+void qh_printfacet2math(FILE *fp, facetT *facet, qh_PRINT format, int notfirst)
+{
+  pointT *    point0, *point1;
+  realT       mindist;
+  const char *pointfmt;
+
+  qh_facet2point(facet, &point0, &point1, &mindist);
+  if( notfirst )
+    {
+    fprintf(fp, ",");
+    }
+  if( format == qh_PRINTmaple )
+    {
+    pointfmt = "[[%16.8f, %16.8f], [%16.8f, %16.8f]]\n";
+    }
+  else
+    {
+    pointfmt = "Line[{{%16.8f, %16.8f}, {%16.8f, %16.8f}}]\n";
+    }
+  fprintf(fp, pointfmt, point0[0], point0[1], point1[0], point1[1]);
+  qh_memfree(point1, qh normal_size);
+  qh_memfree(point0, qh normal_size);
+} /* printfacet2math */
+
+/*---------------------------------
+
+  qh_printfacet3geom_nonsimplicial( fp, facet, color )
+  print Geomview OFF for a 3-d nonsimplicial facet.
+  if DOintersections, prints ridges to unvisited neighbors (qh visit_id)
+
+  notes
+  uses facet->visitid for intersections and ridges
+*/
+void qh_printfacet3geom_nonsimplicial(FILE *fp, facetT *facet, realT color[3])
+{
+  ridgeT * ridge, * *ridgep;
+  setT *   projectedpoints, *vertices;
+  vertexT *vertex, * *vertexp, *vertexA, *vertexB;
+  pointT * projpt, *point, * *pointp;
+  facetT * neighbor;
+  realT    dist, outerplane, innerplane;
+  int      cntvertices, k;
+  realT    black[3] = {0, 0, 0}, green[3] = {0, 1, 0};
+
+  qh_geomplanes(facet, &outerplane, &innerplane);
+  vertices = qh_facet3vertex(facet); /* oriented */
+  cntvertices = qh_setsize(vertices);
+  projectedpoints = qh_settemp(cntvertices);
+  FOREACHvertex_(vertices) {
+    zinc_(Zdistio);
+    qh_distplane(vertex->point, facet, &dist);
+    projpt = qh_projectpoint(vertex->point, facet, dist);
+    qh_setappend(&projectedpoints, projpt);
+    }
+  if( qh PRINTouter || (!qh PRINTnoplanes && !qh PRINTinner) )
+    {
+    qh_printfacet3geom_points(fp, projectedpoints, facet, outerplane, color);
+    }
+  if( qh PRINTinner || (!qh PRINTnoplanes && !qh PRINTouter &&
+                        outerplane - innerplane > 2 * qh MAXabs_coord * qh_GEOMepsilon) )
+    {
+    for( k = 3; k--; )
+      {
+      color[k] = 1.0 - color[k];
+      }
+    qh_printfacet3geom_points(fp, projectedpoints, facet, innerplane, color);
+    }
+  FOREACHpoint_(projectedpoints)
+  qh_memfree(point, qh normal_size);
+  qh_settempfree(&projectedpoints);
+  qh_settempfree(&vertices);
+  if( (qh DOintersections || qh PRINTridges)
+      && (!facet->visible || !qh NEWfacets) )
+    {
+    facet->visitid = qh visit_id;
+    FOREACHridge_(facet->ridges) {
+      neighbor = otherfacet_(ridge, facet);
+      if( neighbor->visitid != qh visit_id )
+        {
+        if( qh DOintersections )
+          {
+          qh_printhyperplaneintersection(fp, facet, neighbor, ridge->vertices, black);
+          }
+        if( qh PRINTridges )
+          {
+          vertexA = SETfirstt_(ridge->vertices, vertexT);
+          vertexB = SETsecondt_(ridge->vertices, vertexT);
+          qh_printline3geom(fp, vertexA->point, vertexB->point, green);
+          }
+        }
+      }
+    }
+} /* printfacet3geom_nonsimplicial */
+
+/*---------------------------------
+
+  qh_printfacet3geom_points( fp, points, facet, offset )
+  prints a 3-d facet as OFF Geomview object.
+  offset is relative to the facet's hyperplane
+  Facet is determined as a list of points
+*/
+void qh_printfacet3geom_points(FILE *fp, setT *points, facetT *facet, realT offset, realT color[3])
+{
+  int     k, n = qh_setsize(points), i;
+  pointT *point, * *pointp;
+  setT *  printpoints;
+
+  fprintf(fp, "{ OFF %d 1 1 #f%d\n", n, facet->id);
+  if( offset != 0.0 )
+    {
+    printpoints = qh_settemp(n);
+    FOREACHpoint_(points)
+    qh_setappend(&printpoints, qh_projectpoint(point, facet, -offset) );
+    }
+  else
+    {
+    printpoints = points;
+    }
+  FOREACHpoint_(printpoints) {
+    for( k = 0; k < qh hull_dim; k++ )
+      {
+      if( k == qh DROPdim )
+        {
+        fprintf(fp, "0 ");
+        }
+      else
+        {
+        fprintf(fp, "%8.4g ", point[k]);
+        }
+      }
+    if( printpoints != points )
+      {
+      qh_memfree(point, qh normal_size);
+      }
+    fprintf(fp, "\n");
+    }
+  if( printpoints != points )
+    {
+    qh_settempfree(&printpoints);
+    }
+  fprintf(fp, "%d ", n);
+  for( i = 0; i < n; i++ )
+    {
+    fprintf(fp, "%d ", i);
+    }
+  fprintf(fp, "%8.4g %8.4g %8.4g 1.0 }\n", color[0], color[1], color[2]);
+} /* printfacet3geom_points */
+
+/*---------------------------------
+
+  qh_printfacet3geom_simplicial(  )
+  print Geomview OFF for a 3-d simplicial facet.
+
+  notes:
+  may flip color
+  uses facet->visitid for intersections and ridges
+
+  assume precise calculations in io.c with roundoff covered by qh_GEOMepsilon
+  innerplane may be off by qh DISTround.  Maxoutside is calculated elsewhere
+  so a DISTround error may have occured.
+*/
+void qh_printfacet3geom_simplicial(FILE *fp, facetT *facet, realT color[3])
+{
+  setT *   points, *vertices;
+  vertexT *vertex, * *vertexp, *vertexA, *vertexB;
+  facetT * neighbor, * *neighborp;
+  realT    outerplane, innerplane;
+  realT    black[3] = {0, 0, 0}, green[3] = {0, 1, 0};
+  int      k;
+
+  qh_geomplanes(facet, &outerplane, &innerplane);
+  vertices = qh_facet3vertex(facet);
+  points = qh_settemp(qh TEMPsize);
+  FOREACHvertex_(vertices)
+  qh_setappend(&points, vertex->point);
+  if( qh PRINTouter || (!qh PRINTnoplanes && !qh PRINTinner) )
+    {
+    qh_printfacet3geom_points(fp, points, facet, outerplane, color);
+    }
+  if( qh PRINTinner || (!qh PRINTnoplanes && !qh PRINTouter &&
+                        outerplane - innerplane > 2 * qh MAXabs_coord * qh_GEOMepsilon) )
+    {
+    for( k = 3; k--; )
+      {
+      color[k] = 1.0 - color[k];
+      }
+    qh_printfacet3geom_points(fp, points, facet, innerplane, color);
+    }
+  qh_settempfree(&points);
+  qh_settempfree(&vertices);
+  if( (qh DOintersections || qh PRINTridges)
+      && (!facet->visible || !qh NEWfacets) )
+    {
+    facet->visitid = qh visit_id;
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid != qh visit_id )
+        {
+        vertices = qh_setnew_delnthsorted(facet->vertices, qh hull_dim,
+                                          (size_t)SETindex_(facet->neighbors, neighbor), (size_t)0);
+        if( qh DOintersections )
+          {
+          qh_printhyperplaneintersection(fp, facet, neighbor, vertices, black);
+          }
+        if( qh PRINTridges )
+          {
+          vertexA = SETfirstt_(vertices, vertexT);
+          vertexB = SETsecondt_(vertices, vertexT);
+          qh_printline3geom(fp, vertexA->point, vertexB->point, green);
+          }
+        qh_setfree(&vertices);
+        }
+      }
+    }
+} /* printfacet3geom_simplicial */
+
+/*---------------------------------
+
+  qh_printfacet3math( fp, facet, notfirst )
+  print 3-d Maple or Mathematica output for a facet
+
+  notes:
+  may be non-simplicial
+  use %16.8f since Mathematica 2.2 does not handle exponential format
+  see qh_printfacet2math
+*/
+void qh_printfacet3math(FILE *fp, facetT *facet, qh_PRINT format, int notfirst)
+{
+  vertexT *   vertex, * *vertexp;
+  setT *      points, *vertices;
+  pointT *    point, * *pointp;
+  boolT       firstpoint = True;
+  realT       dist;
+  const char *pointfmt, *endfmt;
+
+  if( notfirst )
+    {
+    fprintf(fp, ",\n");
+    }
+  vertices = qh_facet3vertex(facet);
+  points = qh_settemp(qh_setsize(vertices) );
+  FOREACHvertex_(vertices) {
+    zinc_(Zdistio);
+    qh_distplane(vertex->point, facet, &dist);
+    point = qh_projectpoint(vertex->point, facet, dist);
+    qh_setappend(&points, point);
+    }
+  if( format == qh_PRINTmaple )
+    {
+    fprintf(fp, "[");
+    pointfmt = "[%16.8f, %16.8f, %16.8f]";
+    endfmt = "]";
+    }
+  else
+    {
+    fprintf(fp, "Polygon[{");
+    pointfmt = "{%16.8f, %16.8f, %16.8f}";
+    endfmt = "}]";
+    }
+  FOREACHpoint_(points) {
+    if( firstpoint )
+      {
+      firstpoint = False;
+      }
+    else
+      {
+      fprintf(fp, ",\n");
+      }
+    fprintf(fp, pointfmt, point[0], point[1], point[2]);
+    }
+  FOREACHpoint_(points)
+  qh_memfree(point, qh normal_size);
+  qh_settempfree(&points);
+  qh_settempfree(&vertices);
+  fputs(endfmt, fp);
+} /* printfacet3math */
+
+/*---------------------------------
+
+  qh_printfacet3vertex( fp, facet, format )
+  print vertices in a 3-d facet as point ids
+
+  notes:
+  prints number of vertices first if format == qh_PRINToff
+  the facet may be non-simplicial
+*/
+void qh_printfacet3vertex(FILE *fp, facetT *facet, qh_PRINT format)
+{
+  vertexT *vertex, * *vertexp;
+  setT *   vertices;
+
+  vertices = qh_facet3vertex(facet);
+  if( format == qh_PRINToff )
+    {
+    fprintf(fp, "%d ", qh_setsize(vertices) );
+    }
+  FOREACHvertex_(vertices)
+  fprintf(fp, "%d ", qh_pointid(vertex->point) );
+  fprintf(fp, "\n");
+  qh_settempfree(&vertices);
+} /* printfacet3vertex */
+
+/*---------------------------------
+
+  qh_printfacet4geom_nonsimplicial(  )
+  print Geomview 4OFF file for a 4d nonsimplicial facet
+  prints all ridges to unvisited neighbors (qh.visit_id)
+  if qh.DROPdim
+  prints in OFF format
+
+  notes:
+  must agree with printend4geom()
+*/
+void qh_printfacet4geom_nonsimplicial(FILE *fp, facetT *facet, realT color[3])
+{
+  facetT * neighbor;
+  ridgeT * ridge, * *ridgep;
+  vertexT *vertex, * *vertexp;
+  pointT * point;
+  int      k;
+  realT    dist;
+
+  facet->visitid = qh visit_id;
+  if( qh PRINTnoplanes || (facet->visible && qh NEWfacets) )
+    {
+    return;
+    }
+  FOREACHridge_(facet->ridges) {
+    neighbor = otherfacet_(ridge, facet);
+    if( neighbor->visitid == qh visit_id )
+      {
+      continue;
+      }
+    if( qh PRINTtransparent && !neighbor->good )
+      {
+      continue;
+      }
+    if( qh DOintersections )
+      {
+      qh_printhyperplaneintersection(fp, facet, neighbor, ridge->vertices, color);
+      }
+    else
+      {
+      if( qh DROPdim >= 0 )
+        {
+        fprintf(fp, "OFF 3 1 1 #f%d\n", facet->id);
+        }
+      else
+        {
+        qh printoutvar++;
+        fprintf(fp, "#r%d between f%d f%d\n", ridge->id, facet->id, neighbor->id);
+        }
+      FOREACHvertex_(ridge->vertices) {
+        zinc_(Zdistio);
+        qh_distplane(vertex->point, facet, &dist);
+        point = qh_projectpoint(vertex->point, facet, dist);
+        for( k = 0; k < qh hull_dim; k++ )
+          {
+          if( k != qh DROPdim )
+            {
+            fprintf(fp, "%8.4g ", point[k]);
+            }
+          }
+        fprintf(fp, "\n");
+        qh_memfree(point, qh normal_size);
+        }
+      if( qh DROPdim >= 0 )
+        {
+        fprintf(fp, "3 0 1 2 %8.4g %8.4g %8.4g\n", color[0], color[1], color[2]);
+        }
+      }
+    }
+} /* printfacet4geom_nonsimplicial */
+
+/*---------------------------------
+
+  qh_printfacet4geom_simplicial( fp, facet, color )
+  print Geomview 4OFF file for a 4d simplicial facet
+  prints triangles for unvisited neighbors (qh.visit_id)
+
+  notes:
+  must agree with printend4geom()
+*/
+void qh_printfacet4geom_simplicial(FILE *fp, facetT *facet, realT color[3])
+{
+  setT *   vertices;
+  facetT * neighbor, * *neighborp;
+  vertexT *vertex, * *vertexp;
+  int      k;
+
+  facet->visitid = qh visit_id;
+  if( qh PRINTnoplanes || (facet->visible && qh NEWfacets) )
+    {
+    return;
+    }
+  FOREACHneighbor_(facet) {
+    if( neighbor->visitid == qh visit_id )
+      {
+      continue;
+      }
+    if( qh PRINTtransparent && !neighbor->good )
+      {
+      continue;
+      }
+    vertices = qh_setnew_delnthsorted(facet->vertices, qh hull_dim,
+                                      (size_t)SETindex_(facet->neighbors, neighbor), (size_t)0);
+    if( qh DOintersections )
+      {
+      qh_printhyperplaneintersection(fp, facet, neighbor, vertices, color);
+      }
+    else
+      {
+      if( qh DROPdim >= 0 )
+        {
+        fprintf(fp, "OFF 3 1 1 #ridge between f%d f%d\n",
+                facet->id, neighbor->id);
+        }
+      else
+        {
+        qh printoutvar++;
+        fprintf(fp, "#ridge between f%d f%d\n", facet->id, neighbor->id);
+        }
+      FOREACHvertex_(vertices) {
+        for( k = 0; k < qh hull_dim; k++ )
+          {
+          if( k != qh DROPdim )
+            {
+            fprintf(fp, "%8.4g ", vertex->point[k]);
+            }
+          }
+        fprintf(fp, "\n");
+        }
+      if( qh DROPdim >= 0 )
+        {
+        fprintf(fp, "3 0 1 2 %8.4g %8.4g %8.4g\n", color[0], color[1], color[2]);
+        }
+      }
+    qh_setfree(&vertices);
+    }
+} /* printfacet4geom_simplicial */
+
+/*---------------------------------
+
+  qh_printfacetNvertex_nonsimplicial( fp, facet, id, format )
+  print vertices for an N-d non-simplicial facet
+  triangulates each ridge to the id
+*/
+void qh_printfacetNvertex_nonsimplicial(FILE *fp, facetT *facet, int id, qh_PRINT format)
+{
+  vertexT *vertex, * *vertexp;
+  ridgeT * ridge, * *ridgep;
+
+  if( facet->visible && qh NEWfacets )
+    {
+    return;
+    }
+  FOREACHridge_(facet->ridges) {
+    if( format == qh_PRINTtriangles )
+      {
+      fprintf(fp, "%d ", qh hull_dim);
+      }
+    fprintf(fp, "%d ", id);
+    if( (ridge->top == facet) ^ qh_ORIENTclock )
+      {
+      FOREACHvertex_(ridge->vertices)
+      fprintf(fp, "%d ", qh_pointid(vertex->point) );
+      }
+    else
+      {
+      FOREACHvertexreverse12_(ridge->vertices)
+      fprintf(fp, "%d ", qh_pointid(vertex->point) );
+      }
+    fprintf(fp, "\n");
+    }
+} /* printfacetNvertex_nonsimplicial */
+
+/*---------------------------------
+
+  qh_printfacetNvertex_simplicial( fp, facet, format )
+  print vertices for an N-d simplicial facet
+  prints vertices for non-simplicial facets
+  2-d facets (orientation preserved by qh_mergefacet2d)
+  PRINToff ('o') for 4-d and higher
+*/
+void qh_printfacetNvertex_simplicial(FILE *fp, facetT *facet, qh_PRINT format)
+{
+  vertexT *vertex, * *vertexp;
+
+  if( format == qh_PRINToff || format == qh_PRINTtriangles )
+    {
+    fprintf(fp, "%d ", qh_setsize(facet->vertices) );
+    }
+  if( (facet->toporient ^ qh_ORIENTclock)
+      || (qh hull_dim > 2 && !facet->simplicial) )
+    {
+    FOREACHvertex_(facet->vertices)
+    fprintf(fp, "%d ", qh_pointid(vertex->point) );
+    }
+  else
+    {
+    FOREACHvertexreverse12_(facet->vertices)
+    fprintf(fp, "%d ", qh_pointid(vertex->point) );
+    }
+  fprintf(fp, "\n");
+} /* printfacetNvertex_simplicial */
+
+/*---------------------------------
+
+  qh_printfacetheader( fp, facet )
+  prints header fields of a facet to fp
+
+  notes:
+  for 'f' output and debugging
+*/
+void qh_printfacetheader(FILE *fp, facetT *facet)
+{
+  pointT *point, * *pointp, *furthest;
+  facetT *neighbor, * *neighborp;
+  realT   dist;
+
+  if( facet == qh_MERGEridge )
+    {
+    fprintf(fp, " MERGEridge\n");
+    return;
+    }
+  else if( facet == qh_DUPLICATEridge )
+    {
+    fprintf(fp, " DUPLICATEridge\n");
+    return;
+    }
+  else if( !facet )
+    {
+    fprintf(fp, " NULLfacet\n");
+    return;
+    }
+  qh old_randomdist = qh RANDOMdist;
+  qh RANDOMdist = False;
+  fprintf(fp, "- f%d\n", facet->id);
+  fprintf(fp, "    - flags:");
+  if( facet->toporient )
+    {
+    fprintf(fp, " top");
+    }
+  else
+    {
+    fprintf(fp, " bottom");
+    }
+  if( facet->simplicial )
+    {
+    fprintf(fp, " simplicial");
+    }
+  if( facet->tricoplanar )
+    {
+    fprintf(fp, " tricoplanar");
+    }
+  if( facet->upperdelaunay )
+    {
+    fprintf(fp, " upperDelaunay");
+    }
+  if( facet->visible )
+    {
+    fprintf(fp, " visible");
+    }
+  if( facet->newfacet )
+    {
+    fprintf(fp, " new");
+    }
+  if( facet->tested )
+    {
+    fprintf(fp, " tested");
+    }
+  if( !facet->good )
+    {
+    fprintf(fp, " notG");
+    }
+  if( facet->seen )
+    {
+    fprintf(fp, " seen");
+    }
+  if( facet->coplanar )
+    {
+    fprintf(fp, " coplanar");
+    }
+  if( facet->mergehorizon )
+    {
+    fprintf(fp, " mergehorizon");
+    }
+  if( facet->keepcentrum )
+    {
+    fprintf(fp, " keepcentrum");
+    }
+  if( facet->dupridge )
+    {
+    fprintf(fp, " dupridge");
+    }
+  if( facet->mergeridge && !facet->mergeridge2 )
+    {
+    fprintf(fp, " mergeridge1");
+    }
+  if( facet->mergeridge2 )
+    {
+    fprintf(fp, " mergeridge2");
+    }
+  if( facet->newmerge )
+    {
+    fprintf(fp, " newmerge");
+    }
+  if( facet->flipped )
+    {
+    fprintf(fp, " flipped");
+    }
+  if( facet->notfurthest )
+    {
+    fprintf(fp, " notfurthest");
+    }
+  if( facet->degenerate )
+    {
+    fprintf(fp, " degenerate");
+    }
+  if( facet->redundant )
+    {
+    fprintf(fp, " redundant");
+    }
+  fprintf(fp, "\n");
+  if( facet->isarea )
+    {
+    fprintf(fp, "    - area: %2.2g\n", facet->f.area);
+    }
+  else if( qh NEWfacets && facet->visible && facet->f.replace )
+    {
+    fprintf(fp, "    - replacement: f%d\n", facet->f.replace->id);
+    }
+  else if( facet->newfacet )
+    {
+    if( facet->f.samecycle && facet->f.samecycle != facet )
+      {
+      fprintf(fp, "    - shares same visible/horizon as f%d\n", facet->f.samecycle->id);
+      }
+    }
+  else if( facet->tricoplanar /* !isarea */ )
+    {
+    if( facet->f.triowner )
+      {
+      fprintf(fp, "    - owner of normal & centrum is facet f%d\n", facet->f.triowner->id);
+      }
+    }
+  else if( facet->f.newcycle )
+    {
+    fprintf(fp, "    - was horizon to f%d\n", facet->f.newcycle->id);
+    }
+  if( facet->nummerge )
+    {
+    fprintf(fp, "    - merges: %d\n", facet->nummerge);
+    }
+  qh_printpointid(fp, "    - normal: ", qh hull_dim, facet->normal, -1);
+  fprintf(fp, "    - offset: %10.7g\n", facet->offset);
+  if( qh CENTERtype == qh_ASvoronoi || facet->center )
+    {
+    qh_printcenter(fp, qh_PRINTfacets, "    - center: ", facet);
+    }
+#if qh_MAXoutside
+  if( facet->maxoutside > qh DISTround )
+    {
+    fprintf(fp, "    - maxoutside: %10.7g\n", facet->maxoutside);
+    }
+#endif
+  if( !SETempty_(facet->outsideset) )
+    {
+    furthest = (pointT *)qh_setlast(facet->outsideset);
+    if( qh_setsize(facet->outsideset) < 6 )
+      {
+      fprintf(fp, "    - outside set (furthest p%d):\n", qh_pointid(furthest) );
+      FOREACHpoint_(facet->outsideset)
+      qh_printpoint(fp, "     ", point);
+      }
+    else if( qh_setsize(facet->outsideset) < 21 )
+      {
+      qh_printpoints(fp, "    - outside set:", facet->outsideset);
+      }
+    else
+      {
+      fprintf(fp, "    - outside set:  %d points.", qh_setsize(facet->outsideset) );
+      qh_printpoint(fp, "  Furthest", furthest);
+      }
+#if !qh_COMPUTEfurthest
+    fprintf(fp, "    - furthest distance= %2.2g\n", facet->furthestdist);
+#endif
+    }
+  if( !SETempty_(facet->coplanarset) )
+    {
+    furthest = (pointT *)qh_setlast(facet->coplanarset);
+    if( qh_setsize(facet->coplanarset) < 6 )
+      {
+      fprintf(fp, "    - coplanar set (furthest p%d):\n", qh_pointid(furthest) );
+      FOREACHpoint_(facet->coplanarset)
+      qh_printpoint(fp, "     ", point);
+      }
+    else if( qh_setsize(facet->coplanarset) < 21 )
+      {
+      qh_printpoints(fp, "    - coplanar set:", facet->coplanarset);
+      }
+    else
+      {
+      fprintf(fp, "    - coplanar set:  %d points.", qh_setsize(facet->coplanarset) );
+      qh_printpoint(fp, "  Furthest", furthest);
+      }
+    zinc_(Zdistio);
+    qh_distplane(furthest, facet, &dist);
+    fprintf(fp, "      furthest distance= %2.2g\n", dist);
+    }
+  qh_printvertices(fp, "    - vertices:", facet->vertices);
+  fprintf(fp, "    - neighboring facets: ");
+  FOREACHneighbor_(facet) {
+    if( neighbor == qh_MERGEridge )
+      {
+      fprintf(fp, " MERGE");
+      }
+    else if( neighbor == qh_DUPLICATEridge )
+      {
+      fprintf(fp, " DUP");
+      }
+    else
+      {
+      fprintf(fp, " f%d", neighbor->id);
+      }
+    }
+  fprintf(fp, "\n");
+  qh RANDOMdist = qh old_randomdist;
+} /* printfacetheader */
+
+/*---------------------------------
+
+  qh_printfacetridges( fp, facet )
+  prints ridges of a facet to fp
+
+  notes:
+  ridges printed in neighbor order
+  assumes the ridges exist
+  for 'f' output
+*/
+void qh_printfacetridges(FILE *fp, facetT *facet)
+{
+  facetT *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+  int     numridges = 0;
+
+  if( facet->visible && qh NEWfacets )
+    {
+    fprintf(fp, "    - ridges (ids may be garbage):");
+    FOREACHridge_(facet->ridges)
+    fprintf(fp, " r%d", ridge->id);
+    fprintf(fp, "\n");
+    }
+  else
+    {
+    fprintf(fp, "    - ridges:\n");
+    FOREACHridge_(facet->ridges)
+    ridge->seen = False;
+    if( qh hull_dim == 3 )
+      {
+      ridge = SETfirstt_(facet->ridges, ridgeT);
+      while( ridge && !ridge->seen )
+        {
+        ridge->seen = True;
+        qh_printridge(fp, ridge);
+        numridges++;
+        ridge = qh_nextridge3d(ridge, facet, NULL);
+        }
+      }
+    else
+      {
+      FOREACHneighbor_(facet) {
+        FOREACHridge_(facet->ridges) {
+          if( otherfacet_(ridge, facet) == neighbor )
+            {
+            ridge->seen = True;
+            qh_printridge(fp, ridge);
+            numridges++;
+            }
+          }
+        }
+      }
+    if( numridges != qh_setsize(facet->ridges) )
+      {
+      fprintf(fp, "     - all ridges:");
+      FOREACHridge_(facet->ridges)
+      fprintf(fp, " r%d", ridge->id);
+      fprintf(fp, "\n");
+      }
+    FOREACHridge_(facet->ridges) {
+      if( !ridge->seen )
+        {
+        qh_printridge(fp, ridge);
+        }
+      }
+    }
+} /* printfacetridges */
+
+/*---------------------------------
+
+  qh_printfacets( fp, format, facetlist, facets, printall )
+  prints facetlist and/or facet set in output format
+
+  notes:
+  also used for specialized formats ('FO' and summary)
+  turns off 'Rn' option since want actual numbers
+*/
+void qh_printfacets(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall)
+{
+  int     numfacets, numsimplicial, numridges, totneighbors, numcoplanars, numtricoplanars;
+  facetT *facet, * *facetp;
+  setT *  vertices;
+  coordT *center;
+  realT   outerplane, innerplane;
+
+  qh old_randomdist = qh RANDOMdist;
+  qh RANDOMdist = False;
+
+  if( qh CDDoutput && (format == qh_PRINTcentrums || format == qh_PRINTpointintersect || format == qh_PRINToff) )
+    {
+    fprintf(qh ferr,
+            "qhull warning: CDD format is not available for centrums, halfspace\nintersections, and OFF file format.\n");
+    }
+  if( format == qh_PRINTnone )
+    {
+    ; /* print nothing */
+    }
+  else if( format == qh_PRINTaverage )
+    {
+    vertices = qh_facetvertices(facetlist, facets, printall);
+    center = qh_getcenter(vertices);
+    fprintf(fp, "%d 1\n", qh hull_dim);
+    qh_printpointid(fp, NULL, qh hull_dim, center, -1);
+    qh_memfree(center, qh normal_size);
+    qh_settempfree(&vertices);
+    }
+  else if( format == qh_PRINTextremes )
+    {
+    if( qh DELAUNAY )
+      {
+      qh_printextremes_d(fp, facetlist, facets, printall);
+      }
+    else if( qh hull_dim == 2 )
+      {
+      qh_printextremes_2d(fp, facetlist, facets, printall);
+      }
+    else
+      {
+      qh_printextremes(fp, facetlist, facets, printall);
+      }
+    }
+  else if( format == qh_PRINToptions )
+    {
+    fprintf(fp, "Options selected for Qhull %s:\n%s\n", qh_version, qh qhull_options);
+    }
+  else if( format == qh_PRINTpoints && !qh VORONOI )
+    {
+    qh_printpoints_out(fp, facetlist, facets, printall);
+    }
+  else if( format == qh_PRINTqhull )
+    {
+    fprintf(fp, "%s | %s\n", qh rbox_command, qh qhull_command);
+    }
+  else if( format == qh_PRINTsize )
+    {
+    fprintf(fp, "0\n2 ");
+    fprintf(fp, qh_REAL_1, qh totarea);
+    fprintf(fp, qh_REAL_1, qh totvol);
+    fprintf(fp, "\n");
+    }
+  else if( format == qh_PRINTsummary )
+    {
+    qh_countfacets(facetlist, facets, printall, &numfacets, &numsimplicial,
+                   &totneighbors, &numridges, &numcoplanars, &numtricoplanars);
+    vertices = qh_facetvertices(facetlist, facets, printall);
+    fprintf(fp, "10 %d %d %d %d %d %d %d %d %d %d\n2 ", qh hull_dim,
+            qh num_points + qh_setsize(qh other_points),
+            qh num_vertices, qh num_facets - qh num_visible,
+            qh_setsize(vertices), numfacets, numcoplanars,
+            numfacets - numsimplicial, zzval_(Zdelvertextot),
+            numtricoplanars);
+    qh_settempfree(&vertices);
+    qh_outerinner(NULL, &outerplane, &innerplane);
+    fprintf(fp, qh_REAL_2n, outerplane, innerplane);
+    }
+  else if( format == qh_PRINTvneighbors )
+    {
+    qh_printvneighbors(fp, facetlist, facets, printall);
+    }
+  else if( qh VORONOI && format == qh_PRINToff )
+    {
+    qh_printvoronoi(fp, format, facetlist, facets, printall);
+    }
+  else if( qh VORONOI && format == qh_PRINTgeom )
+    {
+    qh_printbegin(fp, format, facetlist, facets, printall);
+    qh_printvoronoi(fp, format, facetlist, facets, printall);
+    qh_printend(fp, format, facetlist, facets, printall);
+    }
+  else if( qh VORONOI
+           && (format == qh_PRINTvertices || format == qh_PRINTinner || format == qh_PRINTouter) )
+    {
+    qh_printvdiagram(fp, format, facetlist, facets, printall);
+    }
+  else
+    {
+    qh_printbegin(fp, format, facetlist, facets, printall);
+    FORALLfacet_(facetlist)
+    qh_printafacet(fp, format, facet, printall);
+    FOREACHfacet_(facets)
+    qh_printafacet(fp, format, facet, printall);
+    qh_printend(fp, format, facetlist, facets, printall);
+    }
+  qh RANDOMdist = qh old_randomdist;
+} /* printfacets */
+
+/*---------------------------------
+
+  qh_printhelp_degenerate( fp )
+  prints descriptive message for precision error
+
+  notes:
+  no message if qh_QUICKhelp
+*/
+void qh_printhelp_degenerate(FILE *fp)
+{
+
+  if( qh MERGEexact || qh PREmerge || qh JOGGLEmax < REALmax / 2 )
+    {
+    fprintf(
+      fp,
+      "\n\
+A Qhull error has occurred.  Qhull should have corrected the above\n\
+precision error.  Please send the input and all of the output to\n\
+qhull_bug@qhull.org\n"                                                                                                                                                     );
+    }
+  else if( !qh_QUICKhelp )
+    {
+    fprintf(
+      fp,
+      "\n\
+Precision problems were detected during construction of the convex hull.\n\
+This occurs because convex hull algorithms assume that calculations are\n\
+exact, but floating-point arithmetic has roundoff errors.\n\
+\n\
+To correct for precision problems, do not use 'Q0'.  By default, Qhull\n\
+selects 'C-0' or 'Qx' and merges non-convex facets.  With option 'QJ',\n\
+Qhull joggles the input to prevent precision problems.  See \"Imprecision\n\
+in Qhull\" (qh-impre.htm).\n\
+\n\
+If you use 'Q0', the output may include\n\
+coplanar ridges, concave ridges, and flipped facets.  In 4-d and higher,\n\
+Qhull may produce a ridge with four neighbors or two facets with the same \n\
+vertices.  Qhull reports these events when they occur.  It stops when a\n\
+concave ridge, flipped facet, or duplicate facet occurs.\n"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      );
+#if REALfloat
+    fprintf(
+      fp,
+      "\
+\n\
+Qhull is currently using single precision arithmetic.  The following\n\
+will probably remove the precision problems:\n\
+  - recompile qhull for double precision (#define REALfloat 0 in user.h).\n"                                                                                                                                     );
+#endif
+    if( qh DELAUNAY && !qh SCALElast && qh MAXabs_coord > 1e4 )
+      {
+      fprintf(
+        fp,
+        "\
+\n\
+When computing the Delaunay triangulation of coordinates > 1.0,\n\
+  - use 'Qbb' to scale the last coordinate to [0,m] (max previous coordinate)\n"                                                                                  );
+      }
+    if( qh DELAUNAY && !qh ATinfinity )
+      {
+      fprintf(
+        fp,
+        "\
+When computing the Delaunay triangulation:\n\
+  - use 'Qz' to add a point at-infinity.  This reduces precision problems.\n"                                                         );
+      }
+
+    fprintf(
+      fp,
+      "\
+\n\
+If you need triangular output:\n\
+  - use option 'Qt' to triangulate the output\n\
+  - use option 'QJ' to joggle the input points and remove precision errors\n\
+  - use option 'Ft'.  It triangulates non-simplicial facets with added points.\n\
+\n\
+If you must use 'Q0',\n\
+try one or more of the following options.  They can not guarantee an output.\n\
+  - use 'QbB' to scale the input to a cube.\n\
+  - use 'Po' to produce output and prevent partitioning for flipped facets\n\
+  - use 'V0' to set min. distance to visible facet as 0 instead of roundoff\n\
+  - use 'En' to specify a maximum roundoff error less than %2.2g.\n\
+  - options 'Qf', 'Qbb', and 'QR0' may also help\n"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ,
+      qh DISTround);
+    fprintf(
+      fp,
+      "\
+\n\
+To guarantee simplicial output:\n\
+  - use option 'Qt' to triangulate the output\n\
+  - use option 'QJ' to joggle the input points and remove precision errors\n\
+  - use option 'Ft' to triangulate the output by adding points\n\
+  - use exact arithmetic (see \"Imprecision in Qhull\", qh-impre.htm)\n\
+"                                                                                                                                                                                                                                                                                                                          );
+    }
+} /* printhelp_degenerate */
+
+/*---------------------------------
+
+  qh_printhelp_singular( fp )
+  prints descriptive message for singular input
+*/
+void qh_printhelp_singular(FILE *fp)
+{
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+  realT    min, max, *coord, dist;
+  int      i, k;
+
+  fprintf(
+    fp,
+    "\n\
+The input to qhull appears to be less than %d dimensional, or a\n\
+computation has overflowed.\n\n\
+Qhull could not construct a clearly convex simplex from points:\n"                                                                                                             ,
+    qh hull_dim);
+  qh_printvertexlist(fp, "", qh facet_list, NULL, qh_ALL);
+  if( !qh_QUICKhelp )
+    {
+    fprintf(
+      fp,
+      "\n\
+The center point is coplanar with a facet, or a vertex is coplanar\n\
+with a neighboring facet.  The maximum round off error for\n\
+computing distances is %2.2g.  The center point, facets and distances\n\
+to the center point are as follows:\n\n"                                                                                                                                                                                                                        ,
+      qh DISTround);
+    }
+  qh_printpointid(fp, "center point", qh hull_dim, qh interior_point, -1);
+  fprintf(fp, "\n");
+  FORALLfacets {
+    fprintf(fp, "facet");
+    FOREACHvertex_(facet->vertices)
+    fprintf(fp, " p%d", qh_pointid(vertex->point) );
+    zinc_(Zdistio);
+    qh_distplane(qh interior_point, facet, &dist);
+    fprintf(fp, " distance= %4.2g\n", dist);
+    }
+  if( !qh_QUICKhelp )
+    {
+    if( qh HALFspace )
+      {
+      fprintf(
+        fp,
+        "\n\
+These points are the dual of the given halfspaces.  They indicate that\n\
+the intersection is degenerate.\n"                                                                                       );
+      }
+    fprintf(
+      fp,
+      "\n\
+These points either have a maximum or minimum x-coordinate, or\n\
+they maximize the determinant for k coordinates.  Trial points\n\
+are first selected from points that maximize a coordinate.\n"                                                                                                                                               );
+    if( qh hull_dim >= qh_INITIALmax )
+      {
+      fprintf(
+        fp,
+        "\n\
+Because of the high dimension, the min x-coordinate and max-coordinate\n\
+points are used if the determinant is non-zero.  Option 'Qs' will\n\
+do a better, though much slower, job.  Instead of 'Qs', you can change\n\
+the points by randomly rotating the input with 'QR0'.\n"                                                                                                                                                                                                                                      );
+      }
+    }
+  fprintf(fp, "\nThe min and max coordinates for each dimension are:\n");
+  for( k = 0; k < qh hull_dim; k++ )
+    {
+    min = REALmax;
+    max = -REALmin;
+    for( i = qh num_points, coord = qh first_point + k; i--; coord += qh hull_dim )
+      {
+      maximize_(max, *coord);
+      minimize_(min, *coord);
+      }
+    fprintf(fp, "  %d:  %8.4g  %8.4g  difference= %4.4g\n", k, min, max, max - min);
+    }
+  if( !qh_QUICKhelp )
+    {
+    fprintf(
+      fp,
+      "\n\
+If the input should be full dimensional, you have several options that\n\
+may determine an initial simplex:\n\
+  - use 'QJ'  to joggle the input and make it full dimensional\n\
+  - use 'QbB' to scale the points to the unit cube\n\
+  - use 'QR0' to randomly rotate the input for different maximum points\n\
+  - use 'Qs'  to search all points for the initial simplex\n\
+  - use 'En'  to specify a maximum roundoff error less than %2.2g.\n\
+  - trace execution with 'T3' to see the determinant for each point.\n"                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ,
+      qh DISTround);
+#if REALfloat
+    fprintf(fp, "\
+  - recompile qhull for double precision (#define REALfloat 0 in qhull.h).\n");
+#endif
+    fprintf(
+      fp,
+      "\n\
+If the input is lower dimensional:\n\
+  - use 'QJ' to joggle the input and make it full dimensional\n\
+  - use 'Qbk:0Bk:0' to delete coordinate k from the input.  You should\n\
+    pick the coordinate with the least range.  The hull will have the\n\
+    correct topology.\n\
+  - determine the flat containing the points, rotate the points\n\
+    into a coordinate plane, and delete the other coordinates.\n\
+  - add one or more points to make the input full dimensional.\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     );
+    if( qh DELAUNAY && !qh ATinfinity )
+      {
+      fprintf(
+        fp,
+        "\n\n\
+This is a Delaunay triangulation and the input is co-circular or co-spherical:\n\
+  - use 'Qz' to add a point \"at infinity\" (i.e., above the paraboloid)\n\
+  - or use 'QJ' to joggle the input and avoid co-circular data\n"                                                                                                                                                                             );
+      }
+    }
+} /* printhelp_singular */
+
+/*---------------------------------
+
+  qh_printhyperplaneintersection( fp, facet1, facet2, vertices, color )
+  print Geomview OFF or 4OFF for the intersection of two hyperplanes in 3-d or 4-d
+*/
+void qh_printhyperplaneintersection(FILE *fp, facetT *facet1, facetT *facet2,
+                                    setT *vertices, realT color[3])
+{
+  realT    costheta, denominator, dist1, dist2, s, t, mindenom, p[4];
+  vertexT *vertex, * *vertexp;
+  int      i, k;
+  boolT    nearzero1, nearzero2;
+
+  costheta = qh_getangle(facet1->normal, facet2->normal);
+  denominator = 1 - costheta * costheta;
+  i = qh_setsize(vertices);
+  if( qh hull_dim == 3 )
+    {
+    fprintf(fp, "VECT 1 %d 1 %d 1 ", i, i);
+    }
+  else if( qh hull_dim == 4 && qh DROPdim >= 0 )
+    {
+    fprintf(fp, "OFF 3 1 1 ");
+    }
+  else
+    {
+    qh printoutvar++;
+    }
+  fprintf(fp, "#intersect f%d f%d\n", facet1->id, facet2->id);
+  mindenom = 1 / (10.0 * qh MAXabs_coord);
+  FOREACHvertex_(vertices) {
+    zadd_(Zdistio, 2);
+    qh_distplane(vertex->point, facet1, &dist1);
+    qh_distplane(vertex->point, facet2, &dist2);
+    s = qh_divzero(-dist1 + costheta * dist2, denominator, mindenom, &nearzero1);
+    t = qh_divzero(-dist2 + costheta * dist1, denominator, mindenom, &nearzero2);
+    if( nearzero1 || nearzero2 )
+      {
+      s = t = 0.0;
+      }
+    for( k = qh hull_dim; k--; )
+      {
+      p[k] = vertex->point[k] + facet1->normal[k] * s + facet2->normal[k] * t;
+      }
+    if( qh PRINTdim <= 3 )
+      {
+      qh_projectdim3(p, p);
+      fprintf(fp, "%8.4g %8.4g %8.4g #", p[0], p[1], p[2]);
+      }
+    else
+      {
+      fprintf(fp, "%8.4g %8.4g %8.4g %8.4g #", p[0], p[1], p[2], p[3]);
+      }
+    if( nearzero1 + nearzero2 )
+      {
+      fprintf(fp, "p%d (coplanar facets)\n", qh_pointid(vertex->point) );
+      }
+    else
+      {
+      fprintf(fp, "projected p%d\n", qh_pointid(vertex->point) );
+      }
+    }
+  if( qh hull_dim == 3 )
+    {
+    fprintf(fp, "%8.4g %8.4g %8.4g 1.0\n", color[0], color[1], color[2]);
+    }
+  else if( qh hull_dim == 4 && qh DROPdim >= 0 )
+    {
+    fprintf(fp, "3 0 1 2 %8.4g %8.4g %8.4g 1.0\n", color[0], color[1], color[2]);
+    }
+} /* printhyperplaneintersection */
+
+/*---------------------------------
+
+  qh_printline3geom( fp, pointA, pointB, color )
+  prints a line as a VECT
+  prints 0's for qh.DROPdim
+
+  notes:
+  if pointA == pointB,
+  it's a 1 point VECT
+*/
+void qh_printline3geom(FILE *fp, pointT *pointA, pointT *pointB, realT color[3])
+{
+  int   k;
+  realT pA[4], pB[4];
+
+  qh_projectdim3(pointA, pA);
+  qh_projectdim3(pointB, pB);
+  if( (fabs(pA[0] - pB[0]) > 1e-3) ||
+      (fabs(pA[1] - pB[1]) > 1e-3) ||
+      (fabs(pA[2] - pB[2]) > 1e-3) )
+    {
+    fprintf(fp, "VECT 1 2 1 2 1\n");
+    for( k = 0; k < 3; k++ )
+      {
+      fprintf(fp, "%8.4g ", pB[k]);
+      }
+    fprintf(fp, " #p%d\n", qh_pointid(pointB) );
+    }
+  else
+    {
+    fprintf(fp, "VECT 1 1 1 1 1\n");
+    }
+  for( k = 0; k < 3; k++ )
+    {
+    fprintf(fp, "%8.4g ", pA[k]);
+    }
+  fprintf(fp, " #p%d\n", qh_pointid(pointA) );
+  fprintf(fp, "%8.4g %8.4g %8.4g 1\n", color[0], color[1], color[2]);
+}
+
+/*---------------------------------
+
+  qh_printneighborhood( fp, format, facetA, facetB, printall )
+  print neighborhood of one or two facets
+
+  notes:
+  calls qh_findgood_all()
+  bumps qh.visit_id
+*/
+void qh_printneighborhood(FILE *fp, qh_PRINT format, facetT *facetA, facetT *facetB, boolT printall)
+{
+  facetT *neighbor, * *neighborp, *facet;
+  setT *  facets;
+
+  if( format == qh_PRINTnone )
+    {
+    return;
+    }
+  qh_findgood_all(qh facet_list);
+  if( facetA == facetB )
+    {
+    facetB = NULL;
+    }
+  facets = qh_settemp(2 * (qh_setsize(facetA->neighbors) + 1) );
+  qh visit_id++;
+  for( facet = facetA; facet; facet = ( (facet == facetA) ? facetB : NULL) )
+    {
+    if( facet->visitid != qh visit_id )
+      {
+      facet->visitid = qh visit_id;
+      qh_setappend(&facets, facet);
+      }
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid == qh visit_id )
+        {
+        continue;
+        }
+      neighbor->visitid = qh visit_id;
+      if( printall || !qh_skipfacet(neighbor) )
+        {
+        qh_setappend(&facets, neighbor);
+        }
+      }
+    }
+  qh_printfacets(fp, format, NULL, facets, printall);
+  qh_settempfree(&facets);
+} /* printneighborhood */
+
+/*---------------------------------
+
+  qh_printpoint( fp, string, point )
+  qh_printpointid( fp, string, dim, point, id )
+  prints the coordinates of a point
+
+  returns:
+  if string is defined
+  prints 'string p%d' (skips p%d if id=-1)
+
+  notes:
+  nop if point is NULL
+  prints id unless it is undefined (-1)
+*/
+void qh_printpoint(FILE *fp, const char *string, pointT *point)
+{
+  int id = qh_pointid( point);
+
+  qh_printpointid( fp, string, qh hull_dim, point, id);
+} /* printpoint */
+
+void qh_printpointid(FILE *fp, const char *string, int dim, pointT *point, int id)
+{
+  int   k;
+  realT r; /*bug fix*/
+
+  if( !point )
+    {
+    return;
+    }
+  if( string )
+    {
+    fputs(string, fp);
+    if( id != -1 )
+      {
+      fprintf(fp, " p%d: ", id);
+      }
+    }
+  for( k = dim; k--; )
+    {
+    r = *point++;
+    if( string )
+      {
+      fprintf(fp, " %8.4g", r);
+      }
+    else
+      {
+      fprintf(fp, qh_REAL_1, r);
+      }
+    }
+  fprintf(fp, "\n");
+} /* printpointid */
+
+/*---------------------------------
+
+  qh_printpoint3( fp, point )
+  prints 2-d, 3-d, or 4-d point as Geomview 3-d coordinates
+*/
+void qh_printpoint3(FILE *fp, pointT *point)
+{
+  int   k;
+  realT p[4];
+
+  qh_projectdim3(point, p);
+  for( k = 0; k < 3; k++ )
+    {
+    fprintf(fp, "%8.4g ", p[k]);
+    }
+  fprintf(fp, " #p%d\n", qh_pointid(point) );
+} /* printpoint3 */
+
+/*----------------------------------------
+  -printpoints- print pointids for a set of points starting at index
+  see geom.c
+*/
+
+/*---------------------------------
+
+  qh_printpoints_out( fp, facetlist, facets, printall )
+  prints vertices, coplanar/inside points, for facets by their point coordinates
+  allows qh.CDDoutput
+
+  notes:
+  same format as qhull input
+  if no coplanar/interior points,
+  same order as qh_printextremes
+*/
+void qh_printpoints_out(FILE *fp, facetT *facetlist, setT *facets, boolT printall)
+{
+  int      allpoints = qh num_points + qh_setsize(qh other_points);
+  int      numpoints = 0, point_i, point_n;
+  setT *   vertices, *points;
+  facetT * facet, * *facetp;
+  pointT * point, * *pointp;
+  vertexT *vertex, * *vertexp;
+  int      id;
+
+  points = qh_settemp(allpoints);
+  qh_setzero(points, 0, allpoints);
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  FOREACHvertex_(vertices) {
+    id = qh_pointid(vertex->point);
+    if( id >= 0 )
+      {
+      SETelem_(points, id) = vertex->point;
+      }
+    }
+  if( qh KEEPinside || qh KEEPcoplanar || qh KEEPnearinside )
+    {
+    FORALLfacet_(facetlist) {
+      if( !printall && qh_skipfacet(facet) )
+        {
+        continue;
+        }
+      FOREACHpoint_(facet->coplanarset) {
+        id = qh_pointid(point);
+        if( id >= 0 )
+          {
+          SETelem_(points, id) = point;
+          }
+        }
+      }
+    FOREACHfacet_(facets) {
+      if( !printall && qh_skipfacet(facet) )
+        {
+        continue;
+        }
+      FOREACHpoint_(facet->coplanarset) {
+        id = qh_pointid(point);
+        if( id >= 0 )
+          {
+          SETelem_(points, id) = point;
+          }
+        }
+      }
+    }
+  qh_settempfree(&vertices);
+  FOREACHpoint_i_(points) {
+    if( point )
+      {
+      numpoints++;
+      }
+    }
+  if( qh CDDoutput )
+    {
+    fprintf(fp, "%s | %s\nbegin\n%d %d real\n", qh rbox_command,
+            qh qhull_command, numpoints, qh hull_dim + 1);
+    }
+  else
+    {
+    fprintf(fp, "%d\n%d\n", qh hull_dim, numpoints);
+    }
+  FOREACHpoint_i_(points) {
+    if( point )
+      {
+      if( qh CDDoutput )
+        {
+        fprintf(fp, "1 ");
+        }
+      qh_printpoint(fp, NULL, point);
+      }
+    }
+  if( qh CDDoutput )
+    {
+    fprintf(fp, "end\n");
+    }
+  qh_settempfree(&points);
+} /* printpoints_out */
+
+/*---------------------------------
+
+  qh_printpointvect( fp, point, normal, center, radius, color )
+  prints a 2-d, 3-d, or 4-d point as 3-d VECT's relative to normal or to center point
+*/
+void qh_printpointvect(FILE *fp, pointT *point, coordT *normal, pointT *center, realT radius, realT color[3])
+{
+  realT diff[4], pointA[4];
+  int   k;
+  for( k = qh hull_dim; k--; )
+    {
+    if( center )
+      {
+      diff[k] = point[k] - center[k];
+      }
+    else if( normal )
+      {
+      diff[k] = normal[k];
+      }
+    else
+      {
+      diff[k] = 0;
+      }
+    }
+  if( center )
+    {
+    qh_normalize2(diff, qh hull_dim, True, NULL, NULL);
+    }
+  for( k = qh hull_dim; k--; )
+    {
+    pointA[k] = point[k] + diff[k] * radius;
+    }
+  qh_printline3geom(fp, point, pointA, color);
+} /* printpointvect */
+
+/*---------------------------------
+
+  qh_printpointvect2( fp, point, normal, center, radius )
+  prints a 2-d, 3-d, or 4-d point as 2 3-d VECT's for an imprecise point
+*/
+void qh_printpointvect2(FILE *fp, pointT *point, coordT *normal, pointT *center, realT radius)
+{
+  realT red[3] = {1, 0, 0}, yellow[3] = {1, 1, 0};
+
+  qh_printpointvect(fp, point, normal, center, radius, red);
+  qh_printpointvect(fp, point, normal, center, -radius, yellow);
+} /* printpointvect2 */
+
+/*---------------------------------
+
+  qh_printridge( fp, ridge )
+  prints the information in a ridge
+
+  notes:
+  for qh_printfacetridges()
+*/
+void qh_printridge(FILE *fp, ridgeT *ridge)
+{
+
+  fprintf(fp, "     - r%d", ridge->id);
+  if( ridge->tested )
+    {
+    fprintf(fp, " tested");
+    }
+  if( ridge->nonconvex )
+    {
+    fprintf(fp, " nonconvex");
+    }
+  fprintf(fp, "\n");
+  qh_printvertices(fp, "           vertices:", ridge->vertices);
+  if( ridge->top && ridge->bottom )
+    {
+    fprintf(fp, "           between f%d and f%d\n",
+            ridge->top->id, ridge->bottom->id);
+    }
+} /* printridge */
+
+/*---------------------------------
+
+  qh_printspheres( fp, vertices, radius )
+  prints 3-d vertices as OFF spheres
+
+  notes:
+  inflated octahedron from Stuart Levy earth/mksphere2
+*/
+void qh_printspheres(FILE *fp, setT *vertices, realT radius)
+{
+  vertexT *vertex, * *vertexp;
+
+  qh printoutnum++;
+
+  fprintf(
+    fp,
+    "{appearance {-edge -normal normscale 0} {\n\
+INST geom {define vsphere OFF\n\
+18 32 48\n\
+\n\
+0 0 1\n\
+1 0 0\n\
+0 1 0\n\
+-1 0 0\n\
+0 -1 0\n\
+0 0 -1\n\
+0.707107 0 0.707107\n\
+0 -0.707107 0.707107\n\
+0.707107 -0.707107 0\n\
+-0.707107 0 0.707107\n\
+-0.707107 -0.707107 0\n\
+0 0.707107 0.707107\n\
+-0.707107 0.707107 0\n\
+0.707107 0.707107 0\n\
+0.707107 0 -0.707107\n\
+0 0.707107 -0.707107\n\
+-0.707107 0 -0.707107\n\
+0 -0.707107 -0.707107\n\
+\n\
+3 0 6 11\n\
+3 0 7 6	\n\
+3 0 9 7	\n\
+3 0 11 9\n\
+3 1 6 8	\n\
+3 1 8 14\n\
+3 1 13 6\n\
+3 1 14 13\n\
+3 2 11 13\n\
+3 2 12 11\n\
+3 2 13 15\n\
+3 2 15 12\n\
+3 3 9 12\n\
+3 3 10 9\n\
+3 3 12 16\n\
+3 3 16 10\n\
+3 4 7 10\n\
+3 4 8 7\n\
+3 4 10 17\n\
+3 4 17 8\n\
+3 5 14 17\n\
+3 5 15 14\n\
+3 5 16 15\n\
+3 5 17 16\n\
+3 6 13 11\n\
+3 7 8 6\n\
+3 9 10 7\n\
+3 11 12 9\n\
+3 14 8 17\n\
+3 15 13 14\n\
+3 16 12 15\n\
+3 17 10 16\n} transforms { TLIST\n"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     );
+  FOREACHvertex_(vertices) {
+    fprintf(fp, "%8.4g 0 0 0 #v%d\n 0 %8.4g 0 0\n0 0 %8.4g 0\n",
+            radius, vertex->id, radius, radius);
+    qh_printpoint3(fp, vertex->point);
+    fprintf(fp, "1\n");
+    }
+  fprintf(fp, "}}}\n");
+} /* printspheres */
+
+/*----------------------------------------------
+  -printsummary-
+  see qhull.c
+*/
+
+/*---------------------------------
+
+  qh_printvdiagram( fp, format, facetlist, facets, printall )
+  print voronoi diagram
+  #of pairs of input sites
+  #indices site1 site2 vertex1 ...
+
+  sites indexed by input point id
+  point 0 is the first input point
+  vertices indexed by 'o' and 'p' order
+  vertex 0 is the 'vertex-at-infinity'
+  vertex 1 is the first Voronoi vertex
+
+  see:
+  qh_printvoronoi()
+  qh_eachvoronoi_all()
+
+  notes:
+  if all facets are upperdelaunay,
+  prints upper hull (furthest-site Voronoi diagram)
+*/
+void qh_printvdiagram(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall)
+{
+  setT *       vertices;
+  int          totcount, numcenters;
+  boolT        isLower;
+  qh_RIDGE     innerouter = qh_RIDGEall;
+  printvridgeT printvridge = NULL;
+
+  if( format == qh_PRINTvertices )
+    {
+    innerouter = qh_RIDGEall;
+    printvridge = qh_printvridge;
+    }
+  else if( format == qh_PRINTinner )
+    {
+    innerouter = qh_RIDGEinner;
+    printvridge = qh_printvnorm;
+    }
+  else if( format == qh_PRINTouter )
+    {
+    innerouter = qh_RIDGEouter;
+    printvridge = qh_printvnorm;
+    }
+  else
+    {
+    fprintf(qh ferr, "qh_printvdiagram: unknown print format %d.\n", format);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  vertices = qh_markvoronoi(facetlist, facets, printall, &isLower, &numcenters);
+  totcount = qh_printvdiagram2(NULL, NULL, vertices, innerouter, False);
+  fprintf(fp, "%d\n", totcount);
+  totcount = qh_printvdiagram2(fp, printvridge, vertices, innerouter, True /*
+                                                                             inorder*/ );
+  qh_settempfree(&vertices);
+#if 0  /* for testing qh_eachvoronoi_all */
+  fprintf(fp, "\n");
+  totcount = qh_eachvoronoi_all(fp, printvridge, qh UPPERdelaunay, innerouter, True /*
+                                                                                      inorder*/ );
+  fprintf(fp, "%d\n", totcount);
+#endif
+} /* printvdiagram */
+
+/*---------------------------------
+
+  qh_printvdiagram2( fp, printvridge, vertices, innerouter, inorder )
+  visit all pairs of input sites (vertices) for selected Voronoi vertices
+  vertices may include NULLs
+
+  innerouter:
+  qh_RIDGEall   print inner ridges (bounded) and outer ridges (unbounded)
+  qh_RIDGEinner print only inner ridges
+  qh_RIDGEouter print only outer ridges
+
+  inorder:
+  print 3-d Voronoi vertices in order
+
+  assumes:
+  qh_markvoronoi marked facet->visitid for Voronoi vertices
+  all facet->seen= False
+  all facet->seen2= True
+
+  returns:
+  total number of Voronoi ridges
+  if printvridge,
+  calls printvridge( fp, vertex, vertexA, centers) for each ridge
+  [see qh_eachvoronoi()]
+
+  see:
+  qh_eachvoronoi_all()
+*/
+int qh_printvdiagram2(FILE *fp, printvridgeT printvridge, setT *vertices, qh_RIDGE innerouter, boolT inorder)
+{
+  int      totcount = 0;
+  int      vertex_i, vertex_n;
+  vertexT *vertex;
+
+  FORALLvertices
+  vertex-> seen = False;
+  FOREACHvertex_i_(vertices) {
+    if( vertex )
+      {
+      if( qh GOODvertex > 0 && qh_pointid(vertex->point) + 1 != qh GOODvertex )
+        {
+        continue;
+        }
+      totcount += qh_eachvoronoi(fp, printvridge, vertex, !qh_ALL, innerouter, inorder);
+      }
+    }
+  return totcount;
+} /* printvdiagram2 */
+
+/*---------------------------------
+
+  qh_printvertex( fp, vertex )
+  prints the information in a vertex
+*/
+void qh_printvertex(FILE *fp, vertexT *vertex)
+{
+  pointT *point;
+  int     k, count = 0;
+  facetT *neighbor, * *neighborp;
+  realT   r; /*bug fix*/
+
+  if( !vertex )
+    {
+    fprintf(fp, "  NULLvertex\n");
+    return;
+    }
+  fprintf(fp, "- p%d (v%d):", qh_pointid(vertex->point), vertex->id);
+  point = vertex->point;
+  if( point )
+    {
+    for( k = qh hull_dim; k--; )
+      {
+      r = *point++;
+      fprintf(fp, " %5.2g", r);
+      }
+    }
+  if( vertex->deleted )
+    {
+    fprintf(fp, " deleted");
+    }
+  if( vertex->delridge )
+    {
+    fprintf(fp, " ridgedeleted");
+    }
+  fprintf(fp, "\n");
+  if( vertex->neighbors )
+    {
+    fprintf(fp, "  neighbors:");
+    FOREACHneighbor_(vertex) {
+      if( ++count % 100 == 0 )
+        {
+        fprintf(fp, "\n     ");
+        }
+      fprintf(fp, " f%d", neighbor->id);
+      }
+    fprintf(fp, "\n");
+    }
+} /* printvertex */
+
+/*---------------------------------
+
+  qh_printvertexlist( fp, string, facetlist, facets, printall )
+  prints vertices used by a facetlist or facet set
+  tests qh_skipfacet() if !printall
+*/
+void qh_printvertexlist(FILE *fp, const char* string, facetT *facetlist,
+                        setT *facets, boolT printall)
+{
+  vertexT *vertex, * *vertexp;
+  setT *   vertices;
+
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  fputs(string, fp);
+  FOREACHvertex_(vertices)
+  qh_printvertex(fp, vertex);
+  qh_settempfree(&vertices);
+} /* printvertexlist */
+
+/*---------------------------------
+
+  qh_printvertices( fp, string, vertices )
+  prints vertices in a set
+*/
+void qh_printvertices(FILE *fp, const char* string, setT *vertices)
+{
+  vertexT *vertex, * *vertexp;
+
+  fputs(string, fp);
+  FOREACHvertex_(vertices)
+  fprintf(fp, " p%d (v%d)", qh_pointid(vertex->point), vertex->id);
+  fprintf(fp, "\n");
+} /* printvertices */
+
+/*---------------------------------
+
+  qh_printvneighbors( fp, facetlist, facets, printall )
+  print vertex neighbors of vertices in facetlist and facets ('FN')
+
+  notes:
+  qh_countfacets clears facet->visitid for non-printed facets
+
+  design:
+  collect facet count and related statistics
+  if necessary, build neighbor sets for each vertex
+  collect vertices in facetlist and facets
+  build a point array for point->vertex and point->coplanar facet
+  for each point
+  list vertex neighbors or coplanar facet
+*/
+void qh_printvneighbors(FILE *fp, facetT* facetlist, setT *facets, boolT printall)
+{
+  int      numfacets, numsimplicial, numridges, totneighbors, numneighbors, numcoplanars, numtricoplanars;
+  setT *   vertices, *vertex_points, *coplanar_points;
+  int      numpoints = qh num_points + qh_setsize(qh other_points);
+  vertexT *vertex, * *vertexp;
+  int      vertex_i, vertex_n;
+  facetT * facet, * *facetp, *neighbor, * *neighborp;
+  pointT * point, * *pointp;
+
+  qh_countfacets(facetlist, facets, printall, &numfacets, &numsimplicial,
+                 &totneighbors, &numridges, &numcoplanars, &numtricoplanars); /*
+                                                                                sets
+                                                                                facet->visitid
+                                                                                */
+  fprintf(fp, "%d\n", numpoints);
+  qh_vertexneighbors();
+  vertices = qh_facetvertices(facetlist, facets, printall);
+  vertex_points = qh_settemp(numpoints);
+  coplanar_points = qh_settemp(numpoints);
+  qh_setzero(vertex_points, 0, numpoints);
+  qh_setzero(coplanar_points, 0, numpoints);
+  FOREACHvertex_(vertices)
+  qh_point_add(vertex_points, vertex->point, vertex);
+  FORALLfacet_(facetlist) {
+    FOREACHpoint_(facet->coplanarset)
+    qh_point_add(coplanar_points, point, facet);
+    }
+  FOREACHfacet_(facets) {
+    FOREACHpoint_(facet->coplanarset)
+    qh_point_add(coplanar_points, point, facet);
+    }
+  FOREACHvertex_i_(vertex_points) {
+    if( vertex )
+      {
+      numneighbors = qh_setsize(vertex->neighbors);
+      fprintf(fp, "%d", numneighbors);
+      if( qh hull_dim == 3 )
+        {
+        qh_order_vertexneighbors(vertex);
+        }
+      else if( qh hull_dim >= 4 )
+        {
+        qsort(SETaddr_(vertex->neighbors, facetT), (size_t)numneighbors,
+              sizeof (facetT *), qh_compare_facetvisit);
+        }
+      FOREACHneighbor_(vertex)
+      fprintf(fp, " %d",
+              neighbor->visitid ? neighbor->visitid - 1 : -neighbor->id);
+      fprintf(fp, "\n");
+      }
+    else if( (facet = SETelemt_(coplanar_points, vertex_i, facetT) ) )
+      {
+      fprintf(fp, "1 %d\n",
+              facet->visitid ? facet->visitid - 1 : -facet->id);
+      }
+    else
+      {
+      fprintf(fp, "0\n");
+      }
+    }
+  qh_settempfree(&coplanar_points);
+  qh_settempfree(&vertex_points);
+  qh_settempfree(&vertices);
+} /* printvneighbors */
+
+/*---------------------------------
+
+  qh_printvoronoi( fp, format, facetlist, facets, printall )
+  print voronoi diagram in 'o' or 'G' format
+  for 'o' format
+  prints voronoi centers for each facet and for infinity
+  for each vertex, lists ids of printed facets or infinity
+  assumes facetlist and facets are disjoint
+  for 'G' format
+  prints an OFF object
+  adds a 0 coordinate to center
+  prints infinity but does not list in vertices
+
+  see:
+  qh_printvdiagram()
+
+  notes:
+  if 'o',
+  prints a line for each point except "at-infinity"
+  if all facets are upperdelaunay,
+  reverses lower and upper hull
+*/
+void qh_printvoronoi(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall)
+{
+  int          k, numcenters, numvertices = 0, numneighbors, numinf, vid = 1, vertex_i, vertex_n;
+  facetT *     facet, * *facetp, *neighbor, * *neighborp;
+  setT *       vertices;
+  vertexT *    vertex;
+  boolT        isLower;
+  unsigned int numfacets = (unsigned int) qh num_facets;
+
+  vertices = qh_markvoronoi(facetlist, facets, printall, &isLower, &numcenters);
+  FOREACHvertex_i_(vertices) {
+    if( vertex )
+      {
+      numvertices++;
+      numneighbors = numinf = 0;
+      FOREACHneighbor_(vertex) {
+        if( neighbor->visitid == 0 )
+          {
+          numinf = 1;
+          }
+        else if( neighbor->visitid < numfacets )
+          {
+          numneighbors++;
+          }
+        }
+      if( numinf && !numneighbors )
+        {
+        SETelem_(vertices, vertex_i) = NULL;
+        numvertices--;
+        }
+      }
+    }
+  if( format == qh_PRINTgeom )
+    {
+    fprintf(fp, "{appearance {+edge -face} OFF %d %d 1 #Voronoi centers and cells\n",
+            numcenters, numvertices);
+    }
+  else
+    {
+    fprintf(fp, "%d\n%d %d 1\n", qh hull_dim - 1, numcenters, qh_setsize(vertices) );
+    }
+  if( format == qh_PRINTgeom )
+    {
+    for( k = qh hull_dim - 1; k--; )
+      {
+      fprintf(fp, qh_REAL_1, 0.0);
+      }
+    fprintf(fp, " 0 #infinity not used\n");
+    }
+  else
+    {
+    for( k = qh hull_dim - 1; k--; )
+      {
+      fprintf(fp, qh_REAL_1, qh_INFINITE);
+      }
+    fprintf(fp, "\n");
+    }
+  FORALLfacet_(facetlist) {
+    if( facet->visitid && facet->visitid < numfacets )
+      {
+      if( format == qh_PRINTgeom )
+        {
+        fprintf(fp, "#%d f%d\n", vid++, facet->id);
+        }
+      qh_printcenter(fp, format, NULL, facet);
+      }
+    }
+  FOREACHfacet_(facets) {
+    if( facet->visitid && facet->visitid < numfacets )
+      {
+      if( format == qh_PRINTgeom )
+        {
+        fprintf(fp, "#%d f%d\n", vid++, facet->id);
+        }
+      qh_printcenter(fp, format, NULL, facet);
+      }
+    }
+  FOREACHvertex_i_(vertices) {
+    numneighbors = 0;
+    numinf = 0;
+    if( vertex )
+      {
+      if( qh hull_dim == 3 )
+        {
+        qh_order_vertexneighbors(vertex);
+        }
+      else if( qh hull_dim >= 4 )
+        {
+        qsort(SETaddr_(vertex->neighbors, vertexT),
+              (size_t)qh_setsize(vertex->neighbors),
+              sizeof (facetT *), qh_compare_facetvisit);
+        }
+      FOREACHneighbor_(vertex) {
+        if( neighbor->visitid == 0 )
+          {
+          numinf = 1;
+          }
+        else if( neighbor->visitid < numfacets )
+          {
+          numneighbors++;
+          }
+        }
+      }
+    if( format == qh_PRINTgeom )
+      {
+      if( vertex )
+        {
+        fprintf(fp, "%d", numneighbors);
+        if( vertex )
+          {
+          FOREACHneighbor_(vertex) {
+            if( neighbor->visitid && neighbor->visitid < numfacets )
+              {
+              fprintf(fp, " %d", neighbor->visitid);
+              }
+            }
+          }
+        fprintf(fp, " #p%d (v%d)\n", vertex_i, vertex->id);
+        }
+      else
+        {
+        fprintf(fp, " #p%d is coplanar or isolated\n", vertex_i);
+        }
+      }
+    else
+      {
+      if( numinf )
+        {
+        numneighbors++;
+        }
+      fprintf(fp, "%d", numneighbors);
+      if( vertex )
+        {
+        FOREACHneighbor_(vertex) {
+          if( neighbor->visitid == 0 )
+            {
+            if( numinf )
+              {
+              numinf = 0;
+              fprintf(fp, " %d", neighbor->visitid);
+              }
+            }
+          else if( neighbor->visitid < numfacets )
+            {
+            fprintf(fp, " %d", neighbor->visitid);
+            }
+          }
+        }
+      fprintf(fp, "\n");
+      }
+    }
+  if( format == qh_PRINTgeom )
+    {
+    fprintf(fp, "}\n");
+    }
+  qh_settempfree(&vertices);
+} /* printvoronoi */
+
+/*---------------------------------
+
+  qh_printvnorm( fp, vertex, vertexA, centers, unbounded )
+  print one separating plane of the Voronoi diagram for a pair of input sites
+  unbounded==True if centers includes vertex-at-infinity
+
+  assumes:
+  qh_ASvoronoi and qh_vertexneighbors() already set
+
+  see:
+  qh_printvdiagram()
+  qh_eachvoronoi()
+*/
+void qh_printvnorm(FILE *fp, vertexT *vertex, vertexT *vertexA, setT *centers, boolT unbounded)
+{
+  pointT *normal;
+  realT   offset;
+  int     k;
+
+  normal = qh_detvnorm(vertex, vertexA, centers, &offset);
+  fprintf(fp, "%d %d %d ",
+          2 + qh hull_dim, qh_pointid(vertex->point), qh_pointid(vertexA->point) );
+  for( k = 0; k < qh hull_dim - 1; k++ )
+    {
+    fprintf(fp, qh_REAL_1, normal[k]);
+    }
+  fprintf(fp, qh_REAL_1, offset);
+  fprintf(fp, "\n");
+} /* printvnorm */
+
+/*---------------------------------
+
+  qh_printvridge( fp, vertex, vertexA, centers, unbounded )
+  print one ridge of the Voronoi diagram for a pair of input sites
+  unbounded==True if centers includes vertex-at-infinity
+
+  see:
+  qh_printvdiagram()
+
+  notes:
+  the user may use a different function
+*/
+void qh_printvridge(FILE *fp, vertexT *vertex, vertexT *vertexA, setT *centers, boolT unbounded)
+{
+  facetT *facet, * *facetp;
+
+  fprintf(fp, "%d %d %d", qh_setsize(centers) + 2,
+          qh_pointid(vertex->point), qh_pointid(vertexA->point) );
+  FOREACHfacet_(centers)
+  fprintf(fp, " %d", facet->visitid);
+  fprintf(fp, "\n");
+} /* printvridge */
+
+/*---------------------------------
+
+  qh_projectdim3( source, destination )
+  project 2-d 3-d or 4-d point to a 3-d point
+  uses qh.DROPdim and qh.hull_dim
+  source and destination may be the same
+
+  notes:
+  allocate 4 elements to destination just in case
+*/
+void qh_projectdim3(pointT *source, pointT *destination)
+{
+  int i, k;
+  for( k = 0, i = 0; k < qh hull_dim; k++ )
+    {
+    if( qh hull_dim == 4 )
+      {
+      if( k != qh DROPdim )
+        {
+        destination[i++] = source[k];
+        }
+      }
+    else if( k == qh DROPdim )
+      {
+      destination[i++] = 0;
+      }
+    else
+      {
+      destination[i++] = source[k];
+      }
+    }
+  while( i < 3 )
+    {
+    destination[i++] = 0.0;
+    }
+} /* projectdim3 */
+
+/*---------------------------------
+
+  qh_readfeasible( dim, remainder )
+  read feasible point from remainder string and qh.fin
+
+  returns:
+  number of lines read from qh.fin
+  sets qh.FEASIBLEpoint with malloc'd coordinates
+
+  notes:
+  checks for qh.HALFspace
+  assumes dim > 1
+
+  see:
+  qh_setfeasible
+*/
+int qh_readfeasible(int dim, char *Remainder)
+{
+  boolT   isfirst = True;
+  int     linecount = 0, tokcount = 0;
+  char *  s, *t, firstline[qh_MAXfirst + 1];
+  coordT *coords, value;
+
+  if( !qh HALFspace )
+    {
+    fprintf(qh ferr, "qhull input error: feasible point (dim 1 coords) is only valid for halfspace intersection\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh feasible_string )
+    {
+    fprintf(
+      qh ferr,
+      "qhull input warning: feasible point (dim 1 coords) overrides 'Hn,n,n' feasible point for halfspace intersection\n");
+    }
+  if( !(qh feasible_point = (coordT *)malloc(dim * sizeof(coordT) ) ) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory for feasible point\n");
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  coords = qh feasible_point;
+  while( (s = (isfirst ?  Remainder : fgets(firstline, qh_MAXfirst, qh fin) ) ) )
+    {
+    if( isfirst )
+      {
+      isfirst = False;
+      }
+    else
+      {
+      linecount++;
+      }
+    while( *s )
+      {
+      while( isspace(*s) )
+        {
+        s++;
+        }
+
+      value = qh_strtod(s, &t);
+      if( s == t )
+        {
+        break;
+        }
+      s = t;
+      *(coords++) = value;
+      if( ++tokcount == dim )
+        {
+        while( isspace(*s) )
+          {
+          s++;
+          }
+
+        qh_strtod(s, &t);
+        if( s != t )
+          {
+          fprintf(qh ferr, "qhull input error: coordinates for feasible point do not finish out the line: %s\n",
+                  s);
+          qh_errexit(qh_ERRinput, NULL, NULL);
+          }
+        return linecount;
+        }
+      }
+    }
+
+  fprintf(qh ferr, "qhull input error: only %d coordinates.  Could not read %d-d feasible point.\n",
+          tokcount, dim);
+  qh_errexit(qh_ERRinput, NULL, NULL);
+  return 0;
+} /* readfeasible */
+
+/*---------------------------------
+
+  qh_readpoints( numpoints, dimension, ismalloc )
+  read points from qh.fin into qh.first_point, qh.num_points
+  qh.fin is lines of coordinates, one per vertex, first line number of points
+  if 'rbox D4',
+  gives message
+  if qh.ATinfinity,
+  adds point-at-infinity for Delaunay triangulations
+
+  returns:
+  number of points, array of point coordinates, dimension, ismalloc True
+  if qh.DELAUNAY & !qh.PROJECTinput, projects points to paraboloid
+  and clears qh.PROJECTdelaunay
+  if qh.HALFspace, reads optional feasible point, reads halfspaces,
+  converts to dual.
+
+  for feasible point in "cdd format" in 3-d:
+  3 1
+  coordinates
+  comments
+  begin
+  n 4 real/integer
+  ...
+  end
+
+  notes:
+  dimension will change in qh_initqhull_globals if qh.PROJECTinput
+  uses malloc() since qh_mem not initialized
+  FIXUP: this routine needs rewriting
+*/
+coordT * qh_readpoints(int *numpoints, int *dimension, boolT *ismalloc)
+{
+  coordT *points, *coords, *infinity = NULL;
+  realT   paraboloid, maxboloid = -REALmax, value;
+  realT * coordp = NULL, *offsetp = NULL, *normalp = NULL;
+  char *  s, *t, firstline[qh_MAXfirst + 1];
+  int     diminput = 0, numinput = 0, dimfeasible = 0, newnum, k, tempi;
+  int     firsttext = 0, firstshort = 0, firstlong = 0, firstpoint = 0;
+  int     tokcount = 0, linecount = 0, maxcount, coordcount = 0;
+  boolT   islong, isfirst = True, wasbegin = False;
+  boolT   isdelaunay = qh DELAUNAY && !qh PROJECTinput;
+
+  if( qh CDDinput )
+    {
+    while( (s = fgets(firstline, qh_MAXfirst, qh fin) ) )
+      {
+      linecount++;
+      if( qh HALFspace && linecount == 1 && isdigit(*s) )
+        {
+        dimfeasible = qh_strtol(s, &s);
+        while( isspace(*s) )
+          {
+          s++;
+          }
+
+        if( qh_strtol(s, &s) == 1 )
+          {
+          linecount += qh_readfeasible(dimfeasible, s);
+          }
+        else
+          {
+          dimfeasible = 0;
+          }
+        }
+      else if( !memcmp(firstline, "begin", (size_t)5) || !memcmp(firstline, "BEGIN", (size_t)5) )
+        {
+        break;
+        }
+      else if( !*qh rbox_command )
+        {
+        strncat(qh rbox_command, s, sizeof (qh rbox_command) - 1);
+        }
+      }
+
+    if( !s )
+      {
+      fprintf(qh ferr, "qhull input error: missing \"begin\" for cdd-formated input\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    }
+  while( !numinput && (s = fgets(firstline, qh_MAXfirst, qh fin) ) )
+    {
+    linecount++;
+    if( !memcmp(s, "begin", (size_t)5) || !memcmp(s, "BEGIN", (size_t)5) )
+      {
+      wasbegin = True;
+      }
+    while( *s )
+      {
+      while( isspace(*s) )
+        {
+        s++;
+        }
+
+      if( !*s )
+        {
+        break;
+        }
+      if( !isdigit(*s) )
+        {
+        if( !*qh rbox_command )
+          {
+          strncat(qh rbox_command, s, sizeof (qh rbox_command) - 1);
+          firsttext = linecount;
+          }
+        break;
+        }
+      if( !diminput )
+        {
+        diminput = qh_strtol(s, &s);
+        }
+      else
+        {
+        numinput = qh_strtol(s, &s);
+        if( numinput == 1 && diminput >= 2 && qh HALFspace && !qh CDDinput )
+          {
+          linecount += qh_readfeasible(diminput, s);  /* checks if ok */
+          dimfeasible = diminput;
+          diminput = numinput = 0;
+          }
+        else
+          {
+          break;
+          }
+        }
+      }
+    }
+
+  if( !s )
+    {
+    fprintf(qh ferr, "qhull input error: short input file.  Did not find dimension and number of points\n");
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( diminput > numinput )
+    {
+    tempi = diminput;  /* exchange dim and n, e.g., for cdd input format */
+    diminput = numinput;
+    numinput = tempi;
+    }
+  if( diminput < 2 )
+    {
+    fprintf(qh ferr, "qhull input error: dimension %d (first number) should be at least 2\n",
+            diminput);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( isdelaunay )
+    {
+    qh PROJECTdelaunay = False;
+    if( qh CDDinput )
+      {
+      *dimension = diminput;
+      }
+    else
+      {
+      *dimension = diminput + 1;
+      }
+    *numpoints = numinput;
+    if( qh ATinfinity )
+      {
+      (*numpoints)++;
+      }
+    }
+  else if( qh HALFspace )
+    {
+    *dimension = diminput - 1;
+    *numpoints = numinput;
+    if( diminput < 3 )
+      {
+      fprintf(qh ferr,
+              "qhull input error: dimension %d (first number, includes offset) should be at least 3 for halfspaces\n",
+              diminput);
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    if( dimfeasible )
+      {
+      if( dimfeasible != *dimension )
+        {
+        fprintf(qh ferr,
+                "qhull input error: dimension %d of feasible point is not one less than dimension %d for halfspaces\n",
+                dimfeasible,
+                diminput);
+        qh_errexit(qh_ERRinput, NULL, NULL);
+        }
+      }
+    else
+      {
+      qh_setfeasible(*dimension);
+      }
+    }
+  else
+    {
+    if( qh CDDinput )
+      {
+      *dimension = diminput - 1;
+      }
+    else
+      {
+      *dimension = diminput;
+      }
+    *numpoints = numinput;
+    }
+  qh normal_size = *dimension * sizeof(coordT); /* for tracing with
+                                                  qh_printpoint */
+  if( qh HALFspace )
+    {
+    qh half_space = coordp = (coordT *) malloc(qh normal_size + sizeof(coordT) );
+    if( qh CDDinput )
+      {
+      offsetp = qh half_space;
+      normalp = offsetp + 1;
+      }
+    else
+      {
+      normalp = qh half_space;
+      offsetp = normalp + *dimension;
+      }
+    }
+  qh maxline = diminput * (qh_REALdigits + 5);
+  maximize_(qh maxline, 500);
+  qh line = (char *)malloc( (qh maxline + 1) * sizeof (char) );
+  *ismalloc = True;  /* use malloc since memory not setup */
+  coords = points = qh temp_malloc =
+        (coordT *)malloc( (*numpoints) * (*dimension) * sizeof(coordT) );
+  if( !coords || !qh line || (qh HALFspace && !qh half_space) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory to read %d points\n",
+            numinput);
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  if( isdelaunay && qh ATinfinity )
+    {
+    infinity = points + numinput * (*dimension);
+    for( k = (*dimension) - 1; k--; )
+      {
+      infinity[k] = 0.0;
+      }
+    }
+  maxcount = numinput * diminput;
+  paraboloid = 0.0;
+  while( (s = (isfirst ?  s : fgets(qh line, qh maxline, qh fin) ) ) )
+    {
+    if( !isfirst )
+      {
+      linecount++;
+      if( *s == 'e' || *s == 'E' )
+        {
+        if( !memcmp(s, "end", (size_t)3) || !memcmp(s, "END", (size_t)3) )
+          {
+          if( qh CDDinput )
+            {
+            break;
+            }
+          else if( wasbegin )
+            {
+            fprintf(qh ferr, "qhull input warning: the input appears to be in cdd format.  If so, use 'Fd'\n");
+            }
+          }
+        }
+      }
+    islong = False;
+    while( *s )
+      {
+      while( isspace(*s) )
+        {
+        s++;
+        }
+
+      value = qh_strtod(s, &t);
+      if( s == t )
+        {
+        if( !*qh rbox_command )
+          {
+          strncat(qh rbox_command, s, sizeof (qh rbox_command) - 1);
+          }
+        if( *s && !firsttext )
+          {
+          firsttext = linecount;
+          }
+        if( !islong && !firstshort && coordcount )
+          {
+          firstshort = linecount;
+          }
+        break;
+        }
+      if( !firstpoint )
+        {
+        firstpoint = linecount;
+        }
+      s = t;
+      if( ++tokcount > maxcount )
+        {
+        continue;
+        }
+      if( qh HALFspace )
+        {
+        if( qh CDDinput )
+          {
+          *(coordp++) = -value; /* both coefficients and offset */
+          }
+        else
+          {
+          *(coordp++) = value;
+          }
+        }
+      else
+        {
+        *(coords++) = value;
+        if( qh CDDinput && !coordcount )
+          {
+          if( value != 1.0 )
+            {
+            fprintf(qh ferr, "qhull input error: for cdd format, point at line %d does not start with '1'\n",
+                    linecount);
+            qh_errexit(qh_ERRinput, NULL, NULL);
+            }
+          coords--;
+          }
+        else if( isdelaunay )
+          {
+          paraboloid += value * value;
+          if( qh ATinfinity )
+            {
+            if( qh CDDinput )
+              {
+              infinity[coordcount - 1] += value;
+              }
+            else
+              {
+              infinity[coordcount] += value;
+              }
+            }
+          }
+        }
+      if( ++coordcount == diminput )
+        {
+        coordcount = 0;
+        if( isdelaunay )
+          {
+          *(coords++) = paraboloid;
+          maximize_(maxboloid, paraboloid);
+          paraboloid = 0.0;
+          }
+        else if( qh HALFspace )
+          {
+          if( !qh_sethalfspace(*dimension, coords, &coords, normalp, offsetp, qh feasible_point) )
+            {
+            fprintf(qh ferr, "The halfspace was on line %d\n", linecount);
+            if( wasbegin )
+              {
+              fprintf(qh ferr, "The input appears to be in cdd format.  If so, you should use option 'Fd'\n");
+              }
+            qh_errexit(qh_ERRinput, NULL, NULL);
+            }
+          coordp = qh half_space;
+          }
+        while( isspace(*s) )
+          {
+          s++;
+          }
+
+        if( *s )
+          {
+          islong = True;
+          if( !firstlong )
+            {
+            firstlong = linecount;
+            }
+          }
+        }
+      }
+
+    if( !islong && !firstshort && coordcount )
+      {
+      firstshort = linecount;
+      }
+    if( !isfirst && s - qh line >= qh maxline )
+      {
+      fprintf(qh ferr, "qhull input error: line %d contained more than %d characters\n",
+              linecount, (int) (s - qh line) );
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    isfirst = False;
+    }
+
+  if( tokcount != maxcount )
+    {
+    newnum = fmin_(numinput, tokcount / diminput);
+    fprintf(
+      qh ferr,
+      "\
+qhull warning: instead of %d %d-dimensional points, input contains\n\
+%d points and %d extra coordinates.  Line %d is the first\npoint"                                                                               ,
+      numinput, diminput, tokcount / diminput, tokcount % diminput,
+      firstpoint);
+    if( firsttext )
+      {
+      fprintf(qh ferr, ", line %d is the first comment", firsttext);
+      }
+    if( firstshort )
+      {
+      fprintf(qh ferr, ", line %d is the first short\nline", firstshort);
+      }
+    if( firstlong )
+      {
+      fprintf(qh ferr, ", line %d is the first long line", firstlong);
+      }
+    fprintf(qh ferr, ".  Continue with %d points.\n", newnum);
+    numinput = newnum;
+    if( isdelaunay && qh ATinfinity )
+      {
+      for( k = tokcount % diminput; k--; )
+        {
+        infinity[k] -= *(--coords);
+        }
+      *numpoints = newnum + 1;
+      }
+    else
+      {
+      coords -= tokcount % diminput;
+      *numpoints = newnum;
+      }
+    }
+  if( isdelaunay && qh ATinfinity )
+    {
+    for( k = (*dimension) - 1; k--; )
+      {
+      infinity[k] /= numinput;
+      }
+    if( coords == infinity )
+      {
+      coords += (*dimension) - 1;
+      }
+    else
+      {
+      for( k = 0; k < (*dimension) - 1; k++ )
+        {
+        *(coords++) = infinity[k];
+        }
+      }
+    *(coords++) = maxboloid * 1.1;
+    }
+  if( qh rbox_command[0] )
+    {
+    qh rbox_command[strlen(qh rbox_command) - 1] = '\0';
+    if( !strcmp(qh rbox_command, "./rbox D4") )
+      {
+      fprintf(
+        qh ferr,
+        "\n\
+This is the qhull test case.  If any errors or core dumps occur,\n\
+recompile qhull with 'make new'.  If errors still occur, there is\n\
+an incompatibility.  You should try a different compiler.  You can also\n\
+change the choices in user.h.  If you discover the source of the problem,\n\
+please send mail to qhull_bug@qhull.org.\n\
+\n\
+Type 'qhull' for a short list of options.\n"                                                                                                                                                                                                                                                                                                                                                              );
+      }
+    }
+  free(qh line);
+  qh line = NULL;
+  if( qh half_space )
+    {
+    free(qh half_space);
+    qh half_space = NULL;
+    }
+  qh temp_malloc = NULL;
+  trace1( (qh ferr, "qh_readpoints: read in %d %d-dimensional points\n",
+           numinput, diminput) );
+  return points;
+} /* readpoints */
+
+/*---------------------------------
+
+  qh_setfeasible( dim )
+  set qh.FEASIBLEpoint from qh.feasible_string in "n,n,n" or "n n n" format
+
+  notes:
+  "n,n,n" already checked by qh_initflags()
+  see qh_readfeasible()
+*/
+void qh_setfeasible(int dim)
+{
+  int     tokcount = 0;
+  char *  s;
+  coordT *coords, value;
+
+  if( !(s = qh feasible_string) )
+    {
+    fprintf(
+      qh ferr,
+      "\
+qhull input error: halfspace intersection needs a feasible point.\n\
+Either prepend the input with 1 point or use 'Hn,n,n'.  See manual.\n"                                                                              );
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( !(qh feasible_point = (pointT *)malloc(dim * sizeof(coordT) ) ) )
+    {
+    fprintf(qh ferr, "qhull error: insufficient memory for 'Hn,n,n'\n");
+    qh_errexit(qh_ERRmem, NULL, NULL);
+    }
+  coords = qh feasible_point;
+  while( *s )
+    {
+    value = qh_strtod(s, &s);
+    if( ++tokcount > dim )
+      {
+      fprintf(qh ferr, "qhull input warning: more coordinates for 'H%s' than dimension %d\n",
+              qh feasible_string, dim);
+      break;
+      }
+    *(coords++) = value;
+    if( *s )
+      {
+      s++;
+      }
+    }
+
+  while( ++tokcount <= dim )
+    {
+    *(coords++) = 0.0;
+    }
+} /* setfeasible */
+
+/*---------------------------------
+
+  qh_skipfacet( facet )
+  returns 'True' if this facet is not to be printed
+
+  notes:
+  based on the user provided slice thresholds and 'good' specifications
+*/
+boolT qh_skipfacet(facetT *facet)
+{
+  facetT *neighbor, * *neighborp;
+
+  if( qh PRINTneighbors )
+    {
+    if( facet->good )
+      {
+      return !qh PRINTgood;
+      }
+    FOREACHneighbor_(facet) {
+      if( neighbor->good )
+        {
+        return False;
+        }
+      }
+    return True;
+    }
+  else if( qh PRINTgood )
+    {
+    return !facet->good;
+    }
+  else if( !facet->normal )
+    {
+    return True;
+    }
+  return !qh_inthresholds(facet->normal, NULL);
+} /* skipfacet */
+
diff --git a/BRAINSABC/qhull/io.h b/BRAINSABC/qhull/io.h
new file mode 100644
index 00000000..2573c6c6
--- /dev/null
+++ b/BRAINSABC/qhull/io.h
@@ -0,0 +1,212 @@
+/*
  ---------------------------------
+
+   io.h
+   declarations of Input/Output functions
+
+   see README, qhull.h and io.c
+
+   copyright (c) 1993-2003, The Geometry Center
+*/
+
+#ifndef qhDEFio
+#define qhDEFio 1
+
+/*============ constants and flags ==================*/
+
+/*----------------------------------
+
+  qh_MAXfirst
+    maximum length of first two lines of stdin
+*/
+#define qh_MAXfirst  200
+
+/*----------------------------------
+
+  qh_MINradius
+    min radius for Gp and Gv, fraction of maxcoord
+*/
+#define qh_MINradius 0.02
+
+/*----------------------------------
+
+  qh_GEOMepsilon
+    adjust outer planes for 'lines closer' and geomview roundoff.
+    This prevents bleed through.
+*/
+#define qh_GEOMepsilon 2e-3
+
+/*----------------------------------
+
+  qh_WHITESPACE
+    possible values of white space
+*/
+#define qh_WHITESPACE " \n\t\v\r\f"
+
+/*----------------------------------
+
+  qh_RIDGE
+    to select which ridges to print in qh_eachvoronoi
+*/
+typedef enum
+  {
+  qh_RIDGEall = 0, qh_RIDGEinner, qh_RIDGEouter
+  }
+qh_RIDGE;
+
+/*----------------------------------
+
+  printvridgeT
+    prints results of qh_printvdiagram
+
+  see:
+    qh_printvridge for an example
+*/
+typedef void ( *printvridgeT )(FILE *fp, vertexT *vertex, vertexT *vertexA, setT *centers, boolT unbounded);
+
+/*============== -prototypes in alphabetical order =========*/
+
+void    dfacet( unsigned id);
+
+void    dvertex( unsigned id);
+
+int qh_compare_facetarea(const void *p1, const void *p2);
+
+int qh_compare_facetmerge(const void *p1, const void *p2);
+
+int qh_compare_facetvisit(const void *p1, const void *p2);
+
+int qh_compare_vertexpoint(const void *p1, const void *p2); /* not used */
+
+void    qh_countfacets(facetT *facetlist, setT *facets, boolT printall, int *numfacetsp, int *numsimplicialp,
+                       int *totneighborsp, int *numridgesp, int *numcoplanarsp,
+                       int *numnumtricoplanarsp);
+
+pointT * qh_detvnorm(vertexT *vertex, vertexT *vertexA, setT *centers, realT *offsetp);
+
+setT   * qh_detvridge(vertexT *vertex);
+
+setT   * qh_detvridge3(vertexT *atvertex, vertexT *vertex);
+
+int     qh_eachvoronoi(FILE *fp, printvridgeT printvridge, vertexT *atvertex, boolT visitall, qh_RIDGE innerouter,
+                       boolT inorder);
+
+int     qh_eachvoronoi_all(FILE *fp, printvridgeT printvridge, boolT isUpper, qh_RIDGE innerouter, boolT inorder);
+
+void  qh_facet2point(facetT *facet, pointT * *point0, pointT * *point1, realT *mindist);
+
+setT   * qh_facetvertices(facetT *facetlist, setT *facets, boolT allfacets);
+
+void    qh_geomplanes(facetT *facet, realT *outerplane, realT *innerplane);
+
+void    qh_markkeep(facetT *facetlist);
+
+setT   * qh_markvoronoi(facetT *facetlist, setT *facets, boolT printall, boolT *islowerp, int *numcentersp);
+
+void    qh_order_vertexneighbors(vertexT *vertex);
+
+void  qh_printafacet(FILE *fp, qh_PRINT format, facetT *facet, boolT printall);
+
+void    qh_printbegin(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall);
+
+void  qh_printcenter(FILE *fp, qh_PRINT format, const char *string, facetT *facet);
+
+void    qh_printcentrum(FILE *fp, facetT *facet, realT radius);
+
+void    qh_printend(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall);
+
+void    qh_printend4geom(FILE *fp, facetT *facet, int *num, boolT printall);
+
+void    qh_printextremes(FILE *fp, facetT *facetlist, setT *facets, boolT printall);
+
+void    qh_printextremes_2d(FILE *fp, facetT *facetlist, setT *facets, boolT printall);
+
+void    qh_printextremes_d(FILE *fp, facetT *facetlist, setT *facets, boolT printall);
+
+void  qh_printfacet(FILE *fp, facetT *facet);
+
+void  qh_printfacet2math(FILE *fp, facetT *facet, qh_PRINT format, int notfirst);
+
+void qh_printfacet2geom(FILE * fp, facetT * facet, realT color[3]);
+void qh_printfacet2geom_points(FILE * fp, pointT * point1, pointT * point2,
+                               facetT * facet, realT offset, realT color[3]);
+void  qh_printfacet3math(FILE *fp, facetT *facet, qh_PRINT format, int notfirst);
+
+void qh_printfacet3geom_nonsimplicial(FILE * fp, facetT * facet, realT color[3]);
+void qh_printfacet3geom_points(FILE * fp, setT * points, facetT * facet, realT offset, realT color[3]);
+void qh_printfacet3geom_simplicial(FILE * fp, facetT * facet, realT color[3]);
+void  qh_printfacet3vertex(FILE *fp, facetT *facet, qh_PRINT format);
+
+void qh_printfacet4geom_nonsimplicial(FILE * fp, facetT * facet, realT color[3]);
+void qh_printfacet4geom_simplicial(FILE * fp, facetT * facet, realT color[3]);
+void  qh_printfacetNvertex_nonsimplicial(FILE *fp, facetT *facet, int id, qh_PRINT format);
+
+void  qh_printfacetNvertex_simplicial(FILE *fp, facetT *facet, qh_PRINT format);
+
+void    qh_printfacetheader(FILE *fp, facetT *facet);
+
+void    qh_printfacetridges(FILE *fp, facetT *facet);
+
+void  qh_printfacets(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall);
+
+void  qh_printhelp_degenerate(FILE *fp);
+
+void  qh_printhelp_singular(FILE *fp);
+
+void qh_printhyperplaneintersection(FILE * fp, facetT * facet1, facetT * facet2,
+                                    setT * vertices, realT color[3]);
+void  qh_printneighborhood(FILE *fp, qh_PRINT format, facetT *facetA, facetT *facetB, boolT printall);
+
+void qh_printline3geom(FILE * fp, pointT * pointA, pointT * pointB, realT color[3]);
+void  qh_printpoint(FILE *fp, const char *string, pointT *point);
+
+void  qh_printpointid(FILE *fp, const char *string, int dim, pointT *point, int id);
+
+void    qh_printpoint3(FILE *fp, pointT *point);
+
+void    qh_printpoints_out(FILE *fp, facetT *facetlist, setT *facets, boolT printall);
+
+void qh_printpointvect(FILE * fp, pointT * point, coordT * normal, pointT * center, realT radius, realT color[3]);
+void    qh_printpointvect2(FILE *fp, pointT *point, coordT *normal, pointT *center, realT radius);
+
+void  qh_printridge(FILE *fp, ridgeT *ridge);
+
+void    qh_printspheres(FILE *fp, setT *vertices, realT radius);
+
+void    qh_printvdiagram(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall);
+
+int     qh_printvdiagram2(FILE *fp, printvridgeT printvridge, setT *vertices, qh_RIDGE innerouter, boolT inorder);
+
+void  qh_printvertex(FILE *fp, vertexT *vertex);
+
+void  qh_printvertexlist(FILE *fp, const char *string, facetT *facetlist, setT *facets, boolT printall);
+
+void  qh_printvertices(FILE *fp, const char *string, setT *vertices);
+
+void    qh_printvneighbors(FILE *fp, facetT *facetlist, setT *facets, boolT printall);
+
+void    qh_printvoronoi(FILE *fp, qh_PRINT format, facetT *facetlist, setT *facets, boolT printall);
+
+void    qh_printvnorm(FILE *fp, vertexT *vertex, vertexT *vertexA, setT *centers, boolT unbounded);
+
+void    qh_printvridge(FILE *fp, vertexT *vertex, vertexT *vertexA, setT *centers, boolT unbounded);
+
+void  qh_produce_output(void);
+
+void    qh_projectdim3(pointT *source, pointT *destination);
+
+int     qh_readfeasible(int dim, char *Remainder);
+
+coordT * qh_readpoints(int *numpoints, int *dimension, boolT *ismalloc);
+
+void    qh_setfeasible(int dim);
+
+boolT qh_skipfacet(facetT *facet);
+
+#endif /* qhDEFio */
diff --git a/BRAINSABC/qhull/mem.c b/BRAINSABC/qhull/mem.c
new file mode 100644
index 00000000..a5d3a9c1
--- /dev/null
+++ b/BRAINSABC/qhull/mem.c
@@ -0,0 +1,535 @@
+/*
  ---------------------------------
+
+  mem.c
+  memory management routines for qhull
+
+  This is a standalone program.
+
+  To initialize memory:
+
+  qh_meminit (stderr);
+  qh_meminitbuffers (qh IStracing, qh_MEMalign, 7, qh_MEMbufsize,qh_MEMinitbuf);
+  qh_memsize(sizeof(facetT));
+  qh_memsize(sizeof(facetT));
+  ...
+  qh_memsetup();
+
+  To free up all memory buffers:
+  qh_memfreeshort (&curlong, &totlong);
+
+  if qh_NOmem,
+  malloc/free is used instead of mem.c
+
+  notes:
+  uses Quickfit algorithm (freelists for commonly allocated sizes)
+  assumes small sizes for freelists (it discards the tail of memory buffers)
+
+  see:
+  qh-mem.htm and mem.h
+  global.c (qh_initbuffers) for an example of using mem.c
+
+  copyright (c) 1993-2003 The Geometry Center
+*/
+
+#include 
+#include 
+#include 
+#include "mem.h"
+
+#ifndef qhDEFqhull
+typedef struct ridgeT ridgeT;
+typedef struct facetT facetT;
+void    qh_errexit(int exitcode, facetT *, ridgeT *);
+
+#endif
+
+/*============ -global data structure ==============
+  see mem.h for definition
+*/
+
+qhmemT qhmem = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+                0, 0, 0, 0}; /* remove "= {0}" if this causes a compiler error
+                               */
+
+#ifndef qh_NOmem
+
+/*============= internal functions ==============*/
+
+static int qh_intcompare(const void *i, const void *j);
+
+/*========== functions in alphabetical order ======== */
+
+/*---------------------------------
+
+  qh_intcompare( i, j )
+  used by qsort and bsearch to compare two integers
+*/
+static int qh_intcompare(const void *i, const void *j)
+{
+  return *( (const int *)i) - *( (const int *)j);
+} /* intcompare */
+
+/*----------------------------------
+
+  qh_memalloc( insize )
+  returns object of insize bytes
+  qhmem is the global memory structure
+
+  returns:
+  pointer to allocated memory
+  errors if insufficient memory
+
+  notes:
+  use explicit type conversion to avoid type warnings on some compilers
+  actual object may be larger than insize
+  use qh_memalloc_() for inline code for quick allocations
+  logs allocations if 'T5'
+
+  design:
+  if size < qhmem.LASTsize
+  if qhmem.freelists[size] non-empty
+  return first object on freelist
+  else
+  round up request to size of qhmem.freelists[size]
+  allocate new allocation buffer if necessary
+  allocate object from allocation buffer
+  else
+  allocate object with malloc()
+*/
+void * qh_memalloc(size_t insize)
+{
+  void * *freelistp, *newbuffer;
+  void *  object;
+
+  if( (unsigned) insize <= (unsigned) qhmem.LASTsize )
+    {
+    int idx = qhmem.indextable[insize];
+    freelistp = qhmem.freelists + idx;
+    if( (object = *freelistp) )
+      {
+      qhmem.cntquick++;
+      *freelistp = *( (void * *)*freelistp);  /* replace freelist with next
+                                                object */
+      return object;
+      }
+    else
+      {
+      outsize = qhmem.sizetable[idx];
+      qhmem.cntshort++;
+      if( outsize > qhmem.freesize )
+        {
+        int bufsize;
+        if( !qhmem.curbuffer )
+          {
+          bufsize = qhmem.BUFinit;
+          }
+        else
+          {
+          bufsize = qhmem.BUFsize;
+          }
+        qhmem.totshort += bufsize;
+        if( !(newbuffer = malloc( (size_t)bufsize) ) )
+          {
+          fprintf(qhmem.ferr, "qhull error (qh_memalloc): insufficient memory\n");
+          qh_errexit(qhmem_ERRmem, NULL, NULL);
+          }
+        *( (void * *)newbuffer) = qhmem.curbuffer; /* prepend newbuffer to curbuffer
+                list */
+        qhmem.curbuffer = newbuffer;
+        const int size = (sizeof(void * *) + qhmem.ALIGNmask) & ~ qhmem.ALIGNmask;
+        qhmem.freemem = (void *)( (char *)newbuffer + size);
+        qhmem.freesize = bufsize - size;
+        }
+      object = qhmem.freemem;
+      qhmem.freemem = (void *)( (char *)qhmem.freemem + outsize);
+      qhmem.freesize -= outsize;
+      return object;
+      }
+    }
+  else                        /* long allocation */
+    {
+    if( !qhmem.indextable )
+      {
+      fprintf(qhmem.ferr, "qhull internal error (qh_memalloc): qhmem has not been initialized.\n");
+      qh_errexit(qhmem_ERRqhull, NULL, NULL);
+      }
+    outsize = insize;
+    qhmem.cntlong++;
+    qhmem.curlong++;
+    qhmem.totlong += outsize;
+    if( qhmem.maxlong < qhmem.totlong )
+      {
+      qhmem.maxlong = qhmem.totlong;
+      }
+    if( !(object = malloc( (size_t)outsize) ) )
+      {
+      fprintf(qhmem.ferr, "qhull error (qh_memalloc): insufficient memory\n");
+      qh_errexit(qhmem_ERRmem, NULL, NULL);
+      }
+    if( qhmem.IStracing >= 5 )
+      {
+      fprintf(qhmem.ferr, "qh_memalloc long: %d bytes at %p\n", outsize, object);
+      }
+    }
+  return object;
+} /* memalloc */
+
+/*----------------------------------
+
+  qh_memfree( object, size )
+  free up an object of size bytes
+  size is insize from qh_memalloc
+
+  notes:
+  object may be NULL
+  type checking warns if using (void **)object
+  use qh_memfree_() for quick free's of small objects
+
+  design:
+  if size <= qhmem.LASTsize
+  append object to corresponding freelist
+  else
+  call free(object)
+*/
+void qh_memfree(void *object, size_t size)
+{
+  void * *freelistp;
+
+  if( !object )
+    {
+    return;
+    }
+  if( size <= (size_t)qhmem.LASTsize )
+    {
+    qhmem.freeshort++;
+    freelistp = qhmem.freelists + qhmem.indextable[size];
+    *( (void * *)object) = *freelistp;
+    *freelistp = object;
+    }
+  else
+    {
+    qhmem.freelong++;
+    qhmem.totlong -= size;
+    free(object);
+    if( qhmem.IStracing >= 5 )
+      {
+      fprintf(qhmem.ferr, "qh_memfree long: %lu bytes at %p\n",
+              (unsigned long)size, object);
+      }
+    }
+} /* memfree */
+
+/*---------------------------------
+
+  qh_memfreeshort( curlong, totlong )
+  frees up all short and qhmem memory allocations
+
+  returns:
+  number and size of current long allocations
+*/
+void qh_memfreeshort(int *curlong, int *totlong)
+{
+  void *buffer, *nextbuffer;
+  FILE *ferr;
+
+  *curlong = qhmem.cntlong - qhmem.freelong;
+  *totlong = qhmem.totlong;
+  for( buffer = qhmem.curbuffer; buffer; buffer = nextbuffer )
+    {
+    nextbuffer = *( (void * *) buffer);
+    free(buffer);
+    }
+  qhmem.curbuffer = NULL;
+  if( qhmem.LASTsize )
+    {
+    free(qhmem.indextable);
+    free(qhmem.freelists);
+    free(qhmem.sizetable);
+    }
+  ferr = qhmem.ferr;
+  memset( (char *)&qhmem, 0, sizeof qhmem);  /* every field is 0, FALSE, NULL */
+  qhmem.ferr = ferr;
+} /* memfreeshort */
+
+/*----------------------------------
+
+  qh_meminit( ferr )
+  initialize qhmem and test sizeof( void*)
+*/
+void qh_meminit(FILE *ferr)
+{
+
+  memset( (char *)&qhmem, 0, sizeof qhmem);  /* every field is 0, FALSE, NULL */
+  qhmem.ferr = ferr;
+  if( sizeof(void *) < sizeof(int) )
+    {
+    fprintf(ferr, "qhull internal error (qh_meminit): sizeof(void*) < sizeof(int).  qset.c will not work\n");
+    exit(1);   /* can not use qh_errexit() */
+    }
+} /* meminit */
+
+/*---------------------------------
+
+  qh_meminitbuffers( tracelevel, alignment, numsizes, bufsize, bufinit )
+  initialize qhmem
+  if tracelevel >= 5, trace memory allocations
+  alignment= desired address alignment for memory allocations
+  numsizes= number of freelists
+  bufsize=  size of additional memory buffers for short allocations
+  bufinit=  size of initial memory buffer for short allocations
+*/
+void qh_meminitbuffers(int tracelevel, size_t alignment, int numsizes, int bufsize, int bufinit)
+{
+
+  qhmem.IStracing = tracelevel;
+  qhmem.NUMsizes = numsizes;
+  qhmem.BUFsize = bufsize;
+  qhmem.BUFinit = bufinit;
+  qhmem.ALIGNmask = alignment - 1;
+  if( qhmem.ALIGNmask & ~ qhmem.ALIGNmask )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_meminit): memory alignment %lu is not a power of 2\n",
+            (unsigned long)alignment);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  qhmem.sizetable = (int *) calloc( (size_t)numsizes, sizeof(int) );
+  qhmem.freelists = (void * *) calloc( (size_t)numsizes, sizeof(void *) );
+  if( !qhmem.sizetable || !qhmem.freelists )
+    {
+    fprintf(qhmem.ferr, "qhull error (qh_meminit): insufficient memory\n");
+    qh_errexit(qhmem_ERRmem, NULL, NULL);
+    }
+  if( qhmem.IStracing >= 1 )
+    {
+    fprintf(qhmem.ferr, "qh_meminitbuffers: memory initialized with alignment %lu\n", (unsigned long)alignment);
+    }
+} /* meminitbuffers */
+
+/*---------------------------------
+
+  qh_memsetup()
+  set up memory after running memsize()
+*/
+void qh_memsetup(void)
+{
+  int k, i;
+
+  qsort(qhmem.sizetable, (size_t)qhmem.TABLEsize, sizeof(int), qh_intcompare);
+  qhmem.LASTsize = qhmem.sizetable[qhmem.TABLEsize - 1];
+  if( qhmem.LASTsize >= qhmem.BUFsize || qhmem.LASTsize >= qhmem.BUFinit )
+    {
+    fprintf(qhmem.ferr,
+            "qhull error (qh_memsetup): largest mem size %d is >= buffer size %d or initial buffer size %d\n",
+            qhmem.LASTsize, qhmem.BUFsize,
+            qhmem.BUFinit);
+    qh_errexit(qhmem_ERRmem, NULL, NULL);
+    }
+  if( !(qhmem.indextable = (int *)malloc( (qhmem.LASTsize + 1) * sizeof(int) ) ) )
+    {
+    fprintf(qhmem.ferr, "qhull error (qh_memsetup): insufficient memory\n");
+    qh_errexit(qhmem_ERRmem, NULL, NULL);
+    }
+  for( k = qhmem.LASTsize + 1; k--; )
+    {
+    qhmem.indextable[k] = k;
+    }
+  i = 0;
+  for( k = 0; k <= qhmem.LASTsize; k++ )
+    {
+    if( qhmem.indextable[k] <= qhmem.sizetable[i] )
+      {
+      qhmem.indextable[k] = i;
+      }
+    else
+      {
+      qhmem.indextable[k] = ++i;
+      }
+    }
+} /* memsetup */
+
+/*---------------------------------
+
+  qh_memsize( size )
+  define a free list for this size
+*/
+void qh_memsize(size_t size)
+{
+  int k;
+
+  if( qhmem.LASTsize )
+    {
+    fprintf(qhmem.ferr, "qhull error (qh_memsize): called after qhmem_setup\n");
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  size = (size + qhmem.ALIGNmask) & ~ qhmem.ALIGNmask;
+  for( k = qhmem.TABLEsize; k--; )
+    {
+    if( (size_t)qhmem.sizetable[k] == size )
+      {
+      return;
+      }
+    }
+  if( qhmem.TABLEsize < qhmem.NUMsizes )
+    {
+    qhmem.sizetable[qhmem.TABLEsize++] = size;
+    }
+  else
+    {
+    fprintf(qhmem.ferr, "qhull warning (memsize): free list table has room for only %d sizes\n", qhmem.NUMsizes);
+    }
+} /* memsize */
+
+/*---------------------------------
+
+  qh_memstatistics( fp )
+  print out memory statistics
+
+  notes:
+  does not account for wasted memory at the end of each block
+*/
+void qh_memstatistics(FILE *fp)
+{
+  int   i, count, totfree = 0;
+  void *object;
+  for( i = 0; i < qhmem.TABLEsize; i++ )
+    {
+    count = 0;
+    for( object = qhmem.freelists[i]; object; object = *( (void * *)object) )
+      {
+      count++;
+      }
+    totfree += qhmem.sizetable[i] * count;
+    }
+  fprintf(
+    fp,
+    "\nmemory statistics:\n\
+%7d quick allocations\n\
+%7d short allocations\n\
+%7d long allocations\n\
+%7d short frees\n\
+%7d long frees\n\
+%7d bytes of short memory in use\n\
+%7d bytes of short memory in freelists\n\
+%7d bytes of long memory allocated (except for input)\n\
+%7d bytes of long memory in use (in %d pieces)\n\
+%7d bytes per memory buffer (initially %d bytes)\n"                                                                                                                                                                                                                                                                                                                                     ,
+    qhmem.cntquick, qhmem.cntshort, qhmem.cntlong,
+    qhmem.freeshort, qhmem.freelong,
+    qhmem.totshort - qhmem.freesize - totfree,
+    totfree,
+    qhmem.maxlong, qhmem.totlong, qhmem.cntlong - qhmem.freelong,
+    qhmem.BUFsize,
+    qhmem.BUFinit);
+  if( qhmem.cntlarger )
+    {
+    fprintf(fp, "%7d calls to qh_setlarger\n%7.2g     average copy size\n",
+            qhmem.cntlarger, ( (float) qhmem.totlarger) / qhmem.cntlarger);
+    fprintf(fp, "  freelists (bytes->count):");
+    }
+  for( i = 0; i < qhmem.TABLEsize; i++ )
+    {
+    count = 0;
+    for( object = qhmem.freelists[i]; object; object = *( (void * *)object) )
+      {
+      count++;
+      }
+    fprintf(fp, " %d->%d", qhmem.sizetable[i], count);
+    }
+  fprintf(fp, "\n\n");
+} /* memstatistics */
+
+/*---------------------------------
+
+  qh_NOmem
+  turn off quick-fit memory allocation
+
+  notes:
+  uses malloc() and free() instead
+*/
+#else /* qh_NOmem */
+
+void * qh_memalloc(size_t insize)
+{
+  void *object;
+
+  if( !(object = malloc(insize) ) )
+    {
+    fprintf(qhmem.ferr, "qhull error (qh_memalloc): insufficient memory\n");
+    qh_errexit(qhmem_ERRmem, NULL, NULL);
+    }
+  if( qhmem.IStracing >= 5 )
+    {
+    fprintf(qhmem.ferr, "qh_memalloc long: %d bytes at %p\n", insize, object);
+    }
+  return object;
+}
+
+void qh_memfree(void *object, int size)
+{
+
+  if( !object )
+    {
+    return;
+    }
+  free(object);
+  if( qhmem.IStracing >= 5 )
+    {
+    fprintf(qhmem.ferr, "qh_memfree long: %d bytes at %p\n", size, object);
+    }
+}
+
+void qh_memfreeshort(int *curlong, int *totlong)
+{
+
+  memset( (char *)&qhmem, 0, sizeof qhmem);  /* every field is 0, FALSE, NULL */
+  *curlong = 0;
+  *totlong = 0;
+}
+
+void qh_meminit(FILE *ferr)
+{
+
+  memset( (char *)&qhmem, 0, sizeof qhmem);  /* every field is 0, FALSE, NULL */
+  qhmem.ferr = ferr;
+  if( sizeof(void *) < sizeof(int) )
+    {
+    fprintf(ferr, "qhull internal error (qh_meminit): sizeof(void*) < sizeof(int).  qset.c will not work\n");
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+}
+
+void qh_meminitbuffers(int tracelevel, int alignment, int numsizes, int bufsize, int bufinit)
+{
+
+  qhmem.IStracing = tracelevel;
+
+}
+
+void qh_memsetup(void)
+{
+
+}
+
+void qh_memsize(int size)
+{
+
+}
+
+void qh_memstatistics(FILE *fp)
+{
+
+}
+
+#endif /* qh_NOmem */
diff --git a/BRAINSABC/qhull/mem.h b/BRAINSABC/qhull/mem.h
new file mode 100644
index 00000000..75e7e438
--- /dev/null
+++ b/BRAINSABC/qhull/mem.h
@@ -0,0 +1,352 @@
+/*
  ---------------------------------
+
+   mem.h
+     prototypes for memory management functions
+
+   see qh-mem.htm, mem.c and qset.h
+
+   for error handling, writes message and calls
+     qh_errexit (qhmem_ERRmem, NULL, NULL) if insufficient memory
+       and
+     qh_errexit (qhmem_ERRqhull, NULL, NULL) otherwise
+
+   copyright (c) 1993-2003, The Geometry Center
+*/
+
+#ifndef qhDEFmem
+#define qhDEFmem
+
+/*---------------------------------
+
+  qh_NOmem
+    turn off quick-fit memory allocation
+
+  notes:
+    mem.c implements Quickfit memory allocation for about 20% time
+    savings.  If it fails on your machine, try to locate the
+    problem, and send the answer to qhull@qhull.org.  If this can
+    not be done, define qh_NOmem to use malloc/free instead.
+
+   #define qh_NOmem
+*/
+
+/*-------------------------------------------
+    to avoid bus errors, memory allocation must consider alignment requirements.
+    malloc() automatically takes care of alignment.   Since mem.c manages
+    its own memory, we need to explicitly specify alignment in
+    qh_meminitbuffers().
+
+    A safe choice is sizeof(double).  sizeof(float) may be used if doubles
+    do not occur in data structures and pointers are the same size.  Be careful
+    of machines (e.g., DEC Alpha) with large pointers.  If gcc is available,
+    use __alignof__(double) or fmax_(__alignof__(float), __alignof__(void *)).
+
+   see qh_MEMalign in user.h for qhull's alignment
+*/
+
+#define qhmem_ERRmem 4    /* matches qh_ERRmem in qhull.h */
+#define qhmem_ERRqhull 5  /* matches qh_ERRqhull in qhull.h */
+
+/*----------------------------------
+
+  ptr_intT
+    for casting a void* to an integer-type
+
+  notes:
+    On 64-bit machines, a pointer may be larger than an 'int'.
+    qh_meminit() checks that 'long' holds a 'void*'
+*/
+typedef unsigned long ptr_intT;
+
+/*----------------------------------
+
+  qhmemT
+    global memory structure for mem.c
+
+ notes:
+   users should ignore qhmem except for writing extensions
+   qhmem is allocated in mem.c
+
+   qhmem could be swapable like qh and qhstat, but then
+   multiple qh's and qhmem's would need to keep in synch.
+   A swapable qhmem would also waste memory buffers.  As long
+   as memory operations are atomic, there is no problem with
+   multiple qh structures being active at the same time.
+   If you need separate address spaces, you can swap the
+   contents of qhmem.
+*/
+typedef struct qhmemT qhmemT;
+extern qhmemT qhmem;
+
+struct qhmemT                                                                             /*
+                                                                                            global
+                                                                                            memory
+                                                                                            management
+                                                                                            variables
+                                                                                            */
+                                                                       { int BUFsize;     /*
+                                                                                            size
+                                                                                            of
+                                                                                            memory
+                                                                                            allocation
+                                                                                            buffer
+                                                                                            */
+                                                                       int BUFinit;       /*
+                                                                                            initial
+                                                                                            size
+                                                                                            of
+                                                                                            memory
+                                                                                            allocation
+                                                                                            buffer
+                                                                                            */
+                                                                       int TABLEsize;     /*
+                                                                                            actual
+                                                                                            number
+                                                                                            of
+                                                                                            sizes
+                                                                                            in
+                                                                                            free
+                                                                                            list
+                                                                                            table
+                                                                                            */
+                                                                       int NUMsizes;      /*
+                                                                                            maximum
+                                                                                            number
+                                                                                            of
+                                                                                            sizes
+                                                                                            in
+                                                                                            free
+                                                                                            list
+                                                                                            table
+                                                                                            */
+                                                                       int LASTsize;      /*
+                                                                                            last
+                                                                                            size
+                                                                                            in
+                                                                                            free
+                                                                                            list
+                                                                                            table
+                                                                                            */
+                                                                       int ALIGNmask;     /*
+                                                                                            worst-case
+                                                                                            alignment,
+                                                                                            must
+                                                                                            be
+                                                                                            2^n-1
+                                                                                            */
+                                                                       void * *freelists; /*
+                                                                                            free
+                                                                                            list
+                                                                                            table,
+                                                                                            linked
+                                                                                            by
+                                                                                            offset
+                                                                                            0
+                                                                                            */
+                                                                       int *sizetable;    /*
+                                                                                            size
+                                                                                            of
+                                                                                            each
+                                                                                            freelist
+                                                                                            */
+                                                                       int *indextable;   /*
+                                                                                            size->index
+                                                                                            table
+                                                                                            */
+                                                                       void *curbuffer;   /*
+                                                                                            current
+                                                                                            buffer,
+                                                                                            linked
+                                                                                            by
+                                                                                            offset
+                                                                                            0
+                                                                                            */
+                                                                       void *freemem;     /*
+
+
+                                                                                            free
+                                                                                            memory
+                                                                                            in
+                                                                                            curbuffer
+                                                                                            */
+                                                                       int freesize;      /*
+
+
+                                                                                            size
+                                                                                            of
+                                                                                            free
+                                                                                            memory
+                                                                                            in
+                                                                                            bytes
+                                                                                            */
+                                                                       void *tempstack;   /*
+                                                                                            stack
+                                                                                            of
+                                                                                            temporary
+                                                                                            memory,
+                                                                                            managed
+                                                                                            by
+                                                                                            users
+                                                                                            */
+                                                                       FILE *ferr;        /*
+                                                                                            file
+                                                                                            for
+                                                                                            reporting
+                                                                                            errors
+                                                                                            */
+                                                                       int IStracing;     /*
+                                                                                            =5
+                                                                                            if
+                                                                                            tracing
+                                                                                            memory
+                                                                                            allocations
+                                                                                            */
+                                                                       int cntquick;      /*
+                                                                                            count
+                                                                                            of
+                                                                                            quick
+                                                                                            allocations
+                                                                                            */
+                                                                                          /*
+                                                                                            remove
+                                                                                            statistics
+                                                                                            doesn't
+                                                                                            effect
+                                                                                            speed
+                                                                                            */
+                                                                       int cntshort;      /*
+                                                                                            count
+                                                                                            of
+                                                                                            short
+                                                                                            allocations
+                                                                                            */
+                                                                       int cntlong;       /*
+                                                                                            count
+                                                                                            of
+                                                                                            long
+                                                                                            allocations
+                                                                                            */
+                                                                       int curlong;       /*
+                                                                                            current
+                                                                                            count
+                                                                                            of
+                                                                                            inuse,
+                                                                                            long
+                                                                                            allocations
+                                                                                            */
+                                                                       int freeshort;     /*
+                                                                                            count
+                                                                                            of
+                                                                                            short
+                                                                                            memfrees
+                                                                                            */
+                                                                       int freelong;      /*
+                                                                                            count
+                                                                                            of
+                                                                                            long
+                                                                                            memfrees
+                                                                                            */
+                                                                       int totshort;      /*
+                                                                                            total
+                                                                                            size
+                                                                                            of
+                                                                                            short
+                                                                                            allocations
+                                                                                            */
+                                                                       int totlong;       /*
+                                                                                            total
+                                                                                            size
+                                                                                            of
+                                                                                            long
+                                                                                            allocations
+                                                                                            */
+                                                                       int maxlong;       /*
+                                                                                            maximum
+                                                                                            totlong
+                                                                                            */
+                                                                       int cntlarger;     /*
+                                                                                            count
+                                                                                            of
+                                                                                            setlarger's
+                                                                                            */
+                                                                       int totlarger;     /*
+                                                                                            total
+                                                                                            copied
+                                                                                            by
+                                                                                            setlarger
+                                                                                            */
+                                                                       };
+
+/*==================== -macros ====================*/
+
+/*----------------------------------
+
+  qh_memalloc_(size, object, type)
+    returns object of size bytes
+  assumes size<=qhmem.LASTsize and void **freelistp is a temp
+*/
+
+#ifdef qh_NOmem
+#define qh_memalloc_(size, freelistp, object, type)     \
+    {                                                     \
+    object = (type *)qh_memalloc(size); }
+#else /* !qh_NOmem */
+
+#define qh_memalloc_(size, freelistp, object, type)             \
+    {                                                             \
+    freelistp = qhmem.freelists + qhmem.indextable[size];       \
+    if( ( object = (type *) *freelistp ) ) {                    \
+      qhmem.cntquick ++;                                          \
+      *freelistp = *( (void * *) *freelistp );                      \
+      } else { object = (type *)qh_memalloc(size); } }
+#endif
+
+/*----------------------------------
+
+  qh_memfree_(object, size)
+    free up an object
+
+  notes:
+    object may be NULL
+    assumes size<=qhmem.LASTsize and void **freelistp is a temp
+*/
+#ifdef qh_NOmem
+#define qh_memfree_(object, size, freelistp)    \
+    {                                             \
+    qh_memfree(object, size); }
+#else /* !qh_NOmem */
+
+#define qh_memfree_(object, size, freelistp)                    \
+    {                                                             \
+    if( object ) {                                             \
+      qhmem.freeshort ++;                                         \
+      freelistp = qhmem.freelists + qhmem.indextable[size];       \
+      *( (void * *)object ) = *freelistp;                          \
+      *freelistp = object; }}
+#endif
+
+/*=============== prototypes in alphabetical order ============*/
+
+void * qh_memalloc(size_t insize);
+
+void qh_memfree(void *object, size_t size);
+
+void qh_memfreeshort(int *curlong, int *totlong);
+
+void qh_meminit(FILE *ferr);
+
+void qh_meminitbuffers(int tracelevel, size_t alignment, int numsizes, int bufsize, int bufinit);
+
+void qh_memsetup(void);
+
+void qh_memsize(size_t size);
+
+void qh_memstatistics(FILE *fp);
+
+#endif /* qhDEFmem */
diff --git a/BRAINSABC/qhull/merge.c b/BRAINSABC/qhull/merge.c
new file mode 100644
index 00000000..e70f8147
--- /dev/null
+++ b/BRAINSABC/qhull/merge.c
@@ -0,0 +1,4330 @@
+/*
  ---------------------------------
+
+  merge.c
+  merges non-convex facets
+
+  see qh-merge.htm and merge.h
+
+  other modules call qh_premerge() and qh_postmerge()
+
+  the user may call qh_postmerge() to perform additional merges.
+
+  To remove deleted facets and vertices (qhull() in qhull.c):
+  qh_partitionvisible (!qh_ALL, &numoutside);  // visible_list, newfacet_list
+  qh_deletevisible ();         // qh.visible_list
+  qh_resetlists (False, qh_RESETvisible);       // qh.visible_list newvertex_list newfacet_list
+
+  assumes qh.CENTERtype= centrum
+
+  merges occur in qh_mergefacet and in qh_mergecycle
+  vertex->neighbors not set until the first merge occurs
+
+  copyright (c) 1993-2003 The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+#ifndef qh_NOmerge
+
+/*===== functions (alphabetical after premerge and postmerge) ======*/
+
+/*---------------------------------
+
+  qh_premerge( apex, maxcentrum )
+  pre-merge nonconvex facets in qh.newfacet_list for apex
+  maxcentrum defines coplanar and concave (qh_test_appendmerge)
+
+  returns:
+  deleted facets added to qh.visible_list with facet->visible set
+
+  notes:
+  uses globals, qh.MERGEexact, qh.PREmerge
+
+  design:
+  mark duplicate ridges in qh.newfacet_list
+  merge facet cycles in qh.newfacet_list
+  merge duplicate ridges and concave facets in qh.newfacet_list
+  check merged facet cycles for degenerate and redundant facets
+  merge degenerate and redundant facets
+  collect coplanar and concave facets
+  merge concave, coplanar, degenerate, and redundant facets
+*/
+void qh_premerge(vertexT *apex, realT maxcentrum, realT maxangle)
+{
+  boolT   othermerge = False;
+  facetT *newfacet;
+
+  if( qh ZEROcentrum && qh_checkzero(!qh_ALL) )
+    {
+    return;
+    }
+  trace2( (qh ferr, "qh_premerge: premerge centrum %2.2g angle %2.2g for apex v%d facetlist f%d\n",
+           maxcentrum, maxangle, apex->id, getid_(qh newfacet_list) ) );
+  if( qh IStracing >= 4 && qh num_facets < 50 )
+    {
+    qh_printlists();
+    }
+  qh centrum_radius = maxcentrum;
+  qh cos_max = maxangle;
+  qh degen_mergeset = qh_settemp(qh TEMPsize);
+  qh facet_mergeset = qh_settemp(qh TEMPsize);
+  if( qh hull_dim >= 3 )
+    {
+    qh_mark_dupridges(qh newfacet_list);  /* facet_mergeset */
+    qh_mergecycle_all(qh newfacet_list, &othermerge);
+    qh_forcedmerges(&othermerge /* qh facet_mergeset */);
+    FORALLnew_facets {  /* test samecycle merges */
+      if( !newfacet->simplicial && !newfacet->mergeridge )
+        {
+        qh_degen_redundant_neighbors(newfacet, NULL);
+        }
+      }
+    if( qh_merge_degenredundant() )
+      {
+      othermerge = True;
+      }
+    }
+  else  /* qh hull_dim == 2 */
+    {
+    qh_mergecycle_all(qh newfacet_list, &othermerge);
+    }
+  qh_flippedmerges(qh newfacet_list, &othermerge);
+  if( !qh MERGEexact || zzval_(Ztotmerge) )
+    {
+    zinc_(Zpremergetot);
+    qh POSTmerging = False;
+    qh_getmergeset_initial(qh newfacet_list);
+    qh_all_merges(othermerge, False);
+    }
+  qh_settempfree(&qh facet_mergeset);
+  qh_settempfree(&qh degen_mergeset);
+} /* premerge */
+
+/*---------------------------------
+
+  qh_postmerge( reason, maxcentrum, maxangle, vneighbors )
+  post-merge nonconvex facets as defined by maxcentrum and maxangle
+  'reason' is for reporting progress
+  if vneighbors,
+  calls qh_test_vneighbors at end of qh_all_merge
+  if firstmerge,
+  calls qh_reducevertices before qh_getmergeset
+
+  returns:
+  if first call (qh.visible_list != qh.facet_list),
+  builds qh.facet_newlist, qh.newvertex_list
+  deleted facets added to qh.visible_list with facet->visible
+  qh.visible_list == qh.facet_list
+
+  notes:
+
+
+  design:
+  if first call
+  set qh.visible_list and qh.newfacet_list to qh.facet_list
+  add all facets to qh.newfacet_list
+  mark non-simplicial facets, facet->newmerge
+  set qh.newvertext_list to qh.vertex_list
+  add all vertices to qh.newvertex_list
+  if a pre-merge occured
+  set vertex->delridge {will retest the ridge}
+  if qh.MERGEexact
+  call qh_reducevertices()
+  if no pre-merging
+  merge flipped facets
+  determine non-convex facets
+  merge all non-convex facets
+*/
+void qh_postmerge(const char *reason, realT maxcentrum, realT maxangle,
+                  boolT vneighbors)
+{
+  facetT * newfacet;
+  boolT    othermerges = False;
+  vertexT *vertex;
+
+  if( qh REPORTfreq || qh IStracing )
+    {
+    qh_buildtracing(NULL, NULL);
+    qh_printsummary(qh ferr);
+    if( qh PRINTstatistics )
+      {
+      qh_printallstatistics(qh ferr, "reason");
+      }
+    fprintf(qh ferr, "\n%s with 'C%.2g' and 'A%.2g'\n",
+            reason, maxcentrum, maxangle);
+    }
+  trace2( (qh ferr, "qh_postmerge: postmerge.  test vneighbors? %d\n",
+           vneighbors) );
+  qh centrum_radius = maxcentrum;
+  qh cos_max = maxangle;
+  qh POSTmerging = True;
+  qh degen_mergeset = qh_settemp(qh TEMPsize);
+  qh facet_mergeset = qh_settemp(qh TEMPsize);
+  if( qh visible_list != qh facet_list )    /* first call */
+    {
+    qh NEWfacets = True;
+    qh visible_list = qh newfacet_list = qh facet_list;
+    FORALLnew_facets {
+      newfacet->newfacet = True;
+      if( !newfacet->simplicial )
+        {
+        newfacet->newmerge = True;
+        }
+      zinc_(Zpostfacets);
+      }
+    qh newvertex_list = qh vertex_list;
+    FORALLvertices
+    vertex-> newlist = True;
+    if( qh VERTEXneighbors )   /* a merge has occurred */
+      {
+      FORALLvertices
+      vertex-> delridge = True; /* test for redundant, needed? */
+      if( qh MERGEexact )
+        {
+        if( qh hull_dim <= qh_DIMreduceBuild )
+          {
+          qh_reducevertices(); /* was skipped during pre-merging */
+          }
+        }
+      }
+    if( !qh PREmerge && !qh MERGEexact )
+      {
+      qh_flippedmerges(qh newfacet_list, &othermerges);
+      }
+    }
+  qh_getmergeset_initial(qh newfacet_list);
+  qh_all_merges(False, vneighbors);
+  qh_settempfree(&qh facet_mergeset);
+  qh_settempfree(&qh degen_mergeset);
+} /* post_merge */
+
+/*---------------------------------
+
+  qh_all_merges( othermerge, vneighbors )
+  merge all non-convex facets
+
+  set othermerge if already merged facets (for qh_reducevertices)
+  if vneighbors
+  tests vertex neighbors for convexity at end
+  qh.facet_mergeset lists the non-convex ridges in qh_newfacet_list
+  qh.degen_mergeset is defined
+  if qh.MERGEexact && !qh.POSTmerging,
+  does not merge coplanar facets
+
+  returns:
+  deleted facets added to qh.visible_list with facet->visible
+  deleted vertices added qh.delvertex_list with vertex->delvertex
+
+  notes:
+  unless !qh.MERGEindependent,
+  merges facets in independent sets
+  uses qh.newfacet_list as argument since merges call qh_removefacet()
+
+  design:
+  while merges occur
+  for each merge in qh.facet_mergeset
+  unless one of the facets was already merged in this pass
+  merge the facets
+  test merged facets for additional merges
+  add merges to qh.facet_mergeset
+  if vertices record neighboring facets
+  rename redundant vertices
+  update qh.facet_mergeset
+  if vneighbors ??
+  tests vertex neighbors for convexity at end
+*/
+void qh_all_merges(boolT othermerge, boolT vneighbors)
+{
+  facetT *  facet1, *facet2;
+  mergeT *  merge;
+  boolT     wasmerge = True, isreduce;
+  void * *  freelistp; /* used !qh_NOmem */
+  vertexT * vertex;
+  mergeType mergetype;
+  int       numcoplanar = 0, numconcave = 0, numdegenredun = 0, numnewmerges = 0;
+
+  trace2( (qh ferr, "qh_all_merges: starting to merge facets beginning from f%d\n",
+           getid_(qh newfacet_list) ) );
+  while( True )
+    {
+    wasmerge = False;
+    while( qh_setsize(qh facet_mergeset) )
+      {
+      while( (merge = (mergeT *)qh_setdellast(qh facet_mergeset) ) )
+        {
+        facet1 = merge->facet1;
+        facet2 = merge->facet2;
+        mergetype = merge->type;
+        qh_memfree_(merge, sizeof(mergeT), freelistp);
+        if( facet1->visible || facet2->visible ) /*deleted facet*/
+          {
+          continue;
+          }
+        if( (facet1->newfacet && !facet1->tested)
+            || (facet2->newfacet && !facet2->tested) )
+          {
+          if( qh MERGEindependent && mergetype <= MRGanglecoplanar )
+            {
+            continue; /* perform independent sets of merges */
+            }
+          }
+        qh_merge_nonconvex(facet1, facet2, mergetype);
+        numdegenredun += qh_merge_degenredundant();
+        numnewmerges++;
+        wasmerge = True;
+        if( mergetype == MRGconcave )
+          {
+          numconcave++;
+          }
+        else /* MRGcoplanar or MRGanglecoplanar */
+          {
+          numcoplanar++;
+          }
+        } /* while setdellast */
+
+      if( qh POSTmerging && qh hull_dim <= qh_DIMreduceBuild
+          && numnewmerges > qh_MAXnewmerges )
+        {
+        numnewmerges = 0;
+        qh_reducevertices(); /* otherwise large post merges too slow */
+        }
+      qh_getmergeset(qh newfacet_list);  /* facet_mergeset */
+      } /* while mergeset */
+
+    if( qh VERTEXneighbors )
+      {
+      isreduce = False;
+      if( qh hull_dim >= 4 && qh POSTmerging )
+        {
+        FORALLvertices
+        vertex-> delridge = True;
+        isreduce = True;
+        }
+      if( (wasmerge || othermerge) && (!qh MERGEexact || qh POSTmerging)
+          && qh hull_dim <= qh_DIMreduceBuild )
+        {
+        othermerge = False;
+        isreduce = True;
+        }
+      if( isreduce )
+        {
+        if( qh_reducevertices() )
+          {
+          qh_getmergeset(qh newfacet_list); /* facet_mergeset */
+          continue;
+          }
+        }
+      }
+    if( vneighbors && qh_test_vneighbors(/* qh newfacet_list */) )
+      {
+      continue;
+      }
+    break;
+    } /* while (True) */
+
+  if( qh CHECKfrequently && !qh MERGEexact )
+    {
+    qh old_randomdist = qh RANDOMdist;
+    qh RANDOMdist = False;
+    qh_checkconvex(qh newfacet_list, qh_ALGORITHMfault);
+    /* qh_checkconnect (); [this is slow and it changes the facet order] */
+    qh RANDOMdist = qh old_randomdist;
+    }
+  trace1( (qh ferr, "qh_all_merges: merged %d coplanar facets %d concave facets and %d degen or redundant facets.\n",
+           numcoplanar, numconcave, numdegenredun) );
+  if( qh IStracing >= 4 && qh num_facets < 50 )
+    {
+    qh_printlists();
+    }
+} /* all_merges */
+
+/*---------------------------------
+
+  qh_appendmergeset( facet, neighbor, mergetype, angle )
+  appends an entry to qh.facet_mergeset or qh.degen_mergeset
+
+  angle ignored if NULL or !qh.ANGLEmerge
+
+  returns:
+  merge appended to facet_mergeset or degen_mergeset
+  sets ->degenerate or ->redundant if degen_mergeset
+
+  see:
+  qh_test_appendmerge()
+
+  design:
+  allocate merge entry
+  if regular merge
+  append to qh.facet_mergeset
+  else if degenerate merge and qh.facet_mergeset is all degenerate
+  append to qh.degen_mergeset
+  else if degenerate merge
+  prepend to qh.degen_mergeset
+  else if redundant merge
+  append to qh.degen_mergeset
+*/
+void qh_appendmergeset(facetT *facet, facetT *neighbor, mergeType mergetype, realT *angle)
+{
+  mergeT *merge, *lastmerge;
+  void * *freelistp; /* used !qh_NOmem */
+
+  if( facet->redundant )
+    {
+    return;
+    }
+  if( facet->degenerate && mergetype == MRGdegen )
+    {
+    return;
+    }
+  qh_memalloc_(sizeof(mergeT), freelistp, merge, mergeT);
+  merge->facet1 = facet;
+  merge->facet2 = neighbor;
+  merge->type = mergetype;
+  if( angle && qh ANGLEmerge )
+    {
+    merge->angle = *angle;
+    }
+  if( mergetype < MRGdegen )
+    {
+    qh_setappend(&(qh facet_mergeset), merge);
+    }
+  else if( mergetype == MRGdegen )
+    {
+    facet->degenerate = True;
+    if( !(lastmerge = (mergeT *)qh_setlast(qh degen_mergeset) )
+        || lastmerge->type == MRGdegen )
+      {
+      qh_setappend(&(qh degen_mergeset), merge);
+      }
+    else
+      {
+      qh_setaddnth(&(qh degen_mergeset), 0, merge);
+      }
+    }
+  else if( mergetype == MRGredundant )
+    {
+    facet->redundant = True;
+    qh_setappend(&(qh degen_mergeset), merge);
+    }
+  else  /* mergetype == MRGmirror */
+    {
+    if( facet->redundant || neighbor->redundant )
+      {
+      fprintf(qh ferr, "qhull error (qh_appendmergeset): facet f%d or f%d is already a mirrored facet\n",
+              facet->id, neighbor->id);
+      qh_errexit2(qh_ERRqhull, facet, neighbor);
+      }
+    if( !qh_setequal(facet->vertices, neighbor->vertices) )
+      {
+      fprintf(qh ferr, "qhull error (qh_appendmergeset): mirrored facets f%d and f%d do not have the same vertices\n",
+              facet->id, neighbor->id);
+      qh_errexit2(qh_ERRqhull, facet, neighbor);
+      }
+    facet->redundant = True;
+    neighbor->redundant = True;
+    qh_setappend(&(qh degen_mergeset), merge);
+    }
+} /* appendmergeset */
+
+/*---------------------------------
+
+  qh_basevertices( samecycle )
+  return temporary set of base vertices for samecycle
+  samecycle is first facet in the cycle
+  assumes apex is SETfirst_( samecycle->vertices )
+
+  returns:
+  vertices (settemp)
+  all ->seen are cleared
+
+  notes:
+  uses qh_vertex_visit;
+
+  design:
+  for each facet in samecycle
+  for each unseen vertex in facet->vertices
+  append to result
+*/
+setT * qh_basevertices(facetT *samecycle)
+{
+  facetT * same;
+  vertexT *apex, *vertex, * *vertexp;
+  setT *   vertices = qh_settemp(qh TEMPsize);
+
+  apex = SETfirstt_(samecycle->vertices, vertexT);
+  apex->visitid = ++qh vertex_visit;
+  FORALLsame_cycle_(samecycle) {
+    if( same->mergeridge )
+      {
+      continue;
+      }
+    FOREACHvertex_(same->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        qh_setappend(&vertices, vertex);
+        vertex->visitid = qh vertex_visit;
+        vertex->seen = False;
+        }
+      }
+    }
+  trace4( (qh ferr, "qh_basevertices: found %d vertices\n",
+           qh_setsize(vertices) ) );
+  return vertices;
+} /* basevertices */
+
+/*---------------------------------
+
+  qh_checkconnect()
+  check that new facets are connected
+  new facets are on qh.newfacet_list
+
+  notes:
+  this is slow and it changes the order of the facets
+  uses qh.visit_id
+
+  design:
+  move first new facet to end of qh.facet_list
+  for all newly appended facets
+  append unvisited neighbors to end of qh.facet_list
+  for all new facets
+  report error if unvisited
+*/
+void qh_checkconnect(void /* qh newfacet_list */)
+{
+  facetT *facet, *newfacet, *errfacet = NULL, *neighbor, * *neighborp;
+
+  facet = qh newfacet_list;
+  qh_removefacet(facet);
+  qh_appendfacet(facet);
+  facet->visitid = ++qh visit_id;
+  FORALLfacet_(facet) {
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid != qh visit_id )
+        {
+        qh_removefacet(neighbor);
+        qh_appendfacet(neighbor);
+        neighbor->visitid = qh visit_id;
+        }
+      }
+    }
+  FORALLnew_facets {
+    if( newfacet->visitid == qh visit_id )
+      {
+      break;
+      }
+    fprintf(qh ferr, "qhull error: f%d is not attached to the new facets\n",
+            newfacet->id);
+    errfacet = newfacet;
+    }
+  if( errfacet )
+    {
+    qh_errexit(qh_ERRqhull, errfacet, NULL);
+    }
+} /* checkconnect */
+
+/*---------------------------------
+
+  qh_checkzero( testall )
+  check that facets are clearly convex for qh.DISTround with qh.MERGEexact
+
+  if testall,
+  test all facets for qh.MERGEexact post-merging
+  else
+  test qh.newfacet_list
+
+  if qh.MERGEexact,
+  allows coplanar ridges
+  skips convexity test while qh.ZEROall_ok
+
+  returns:
+  True if all facets !flipped, !dupridge, normal
+  if all horizon facets are simplicial
+  if all vertices are clearly below neighbor
+  if all opposite vertices of horizon are below
+  clears qh.ZEROall_ok if any problems or coplanar facets
+
+  notes:
+  uses qh.vertex_visit
+  horizon facets may define multiple new facets
+
+  design:
+  for all facets in qh.newfacet_list or qh.facet_list
+  check for flagged faults (flipped, etc.)
+  for all facets in qh.newfacet_list or qh.facet_list
+  for each neighbor of facet
+  skip horizon facets for qh.newfacet_list
+  test the opposite vertex
+  if qh.newfacet_list
+  test the other vertices in the facet's horizon facet
+*/
+boolT qh_checkzero(boolT testall)
+{
+  facetT * facet, *neighbor, * *neighborp;
+  facetT * horizon, *facetlist;
+  int      neighbor_i;
+  vertexT *vertex, * *vertexp;
+  realT    dist;
+
+  if( testall )
+    {
+    facetlist = qh facet_list;
+    }
+  else
+    {
+    facetlist = qh newfacet_list;
+    FORALLfacet_(facetlist) {
+      horizon = SETfirstt_(facet->neighbors, facetT);
+      if( !horizon->simplicial )
+        {
+        goto LABELproblem;
+        }
+      if( facet->flipped || facet->dupridge || !facet->normal )
+        {
+        goto LABELproblem;
+        }
+      }
+    if( qh MERGEexact && qh ZEROall_ok )
+      {
+      trace2( (qh ferr, "qh_checkzero: skip convexity check until first pre-merge\n") );
+      return True;
+      }
+    }
+  FORALLfacet_(facetlist) {
+    qh vertex_visit++;
+
+    neighbor_i = 0;
+    horizon = NULL;
+    FOREACHneighbor_(facet) {
+      if( !neighbor_i && !testall )
+        {
+        horizon = neighbor;
+        neighbor_i++;
+        continue; /* horizon facet tested in qh_findhorizon */
+        }
+      vertex = SETelemt_(facet->vertices, neighbor_i++, vertexT);
+      vertex->visitid = qh vertex_visit;
+      zzinc_(Zdistzero);
+      qh_distplane(vertex->point, neighbor, &dist);
+      if( dist >= -qh DISTround )
+        {
+        qh ZEROall_ok = False;
+        if( !qh MERGEexact || testall || dist > qh DISTround )
+          {
+          goto LABELnonconvex;
+          }
+        }
+      }
+    if( !testall )
+      {
+      FOREACHvertex_(horizon->vertices) {
+        if( vertex->visitid != qh vertex_visit )
+          {
+          zzinc_(Zdistzero);
+          qh_distplane(vertex->point, facet, &dist);
+          if( dist >= -qh DISTround )
+            {
+            qh ZEROall_ok = False;
+            if( !qh MERGEexact || dist > qh DISTround )
+              {
+              goto LABELnonconvex;
+              }
+            }
+          break;
+          }
+        }
+      }
+    }
+  trace2( (qh ferr, "qh_checkzero: testall %d, facets are %s\n", testall,
+           (qh MERGEexact && !testall) ?
+           "not concave, flipped, or duplicate ridged" : "clearly convex") );
+  return True;
+
+LABELproblem:
+  qh ZEROall_ok = False;
+  trace2( (qh ferr, "qh_checkzero: facet f%d needs pre-merging\n",
+           facet->id) );
+  return False;
+
+LABELnonconvex:
+  trace2( (qh ferr, "qh_checkzero: facet f%d and f%d are not clearly convex.  v%d dist %.2g\n",
+           facet->id, neighbor->id, vertex->id, dist) );
+  return False;
+} /* checkzero */
+
+/*---------------------------------
+
+  qh_compareangle( angle1, angle2 )
+  used by qsort() to order merges by angle
+*/
+int qh_compareangle(const void *p1, const void *p2)
+{
+  const mergeT *a = *( (mergeT *const *)p1), *b = *( (mergeT *const *)p2);
+
+  return (a->angle > b->angle) ? 1 : -1;
+} /* compareangle */
+
+/*---------------------------------
+
+  qh_comparemerge( merge1, merge2 )
+  used by qsort() to order merges
+*/
+int qh_comparemerge(const void *p1, const void *p2)
+{
+  const mergeT *a = *( (mergeT *const *)p1), *b = *( (mergeT *const *)p2);
+
+  return a->type - b->type;
+} /* comparemerge */
+
+/*---------------------------------
+
+  qh_comparevisit( vertex1, vertex2 )
+  used by qsort() to order vertices by their visitid
+*/
+int qh_comparevisit(const void *p1, const void *p2)
+{
+  const vertexT *a = *( (vertexT *const *)p1), *b = *( (vertexT *const *)p2);
+
+  return a->visitid - b->visitid;
+} /* comparevisit */
+
+/*---------------------------------
+
+  qh_copynonconvex( atridge )
+  set non-convex flag on other ridges (if any) between same neighbors
+
+  notes:
+  may be faster if use smaller ridge set
+
+  design:
+  for each ridge of atridge's top facet
+  if ridge shares the same neighbor
+  set nonconvex flag
+*/
+void qh_copynonconvex(ridgeT *atridge)
+{
+  facetT *facet, *otherfacet;
+  ridgeT *ridge, * *ridgep;
+
+  facet = atridge->top;
+  otherfacet = atridge->bottom;
+  FOREACHridge_(facet->ridges) {
+    if( otherfacet == otherfacet_(ridge, facet) && ridge != atridge )
+      {
+      ridge->nonconvex = True;
+      trace4( (qh ferr, "qh_copynonconvex: moved nonconvex flag from r%d to r%d\n",
+               atridge->id, ridge->id) );
+      break;
+      }
+    }
+} /* copynonconvex */
+
+/*---------------------------------
+
+  qh_degen_redundant_facet( facet )
+  check facet for degen. or redundancy
+
+  notes:
+  bumps vertex_visit
+  called if a facet was redundant but no longer is (qh_merge_degenredundant)
+  qh_appendmergeset() only appends first reference to facet (i.e., redundant)
+
+  see:
+  qh_degen_redundant_neighbors()
+
+  design:
+  test for redundant neighbor
+  test for degenerate facet
+*/
+void qh_degen_redundant_facet(facetT *facet)
+{
+  vertexT *vertex, * *vertexp;
+  facetT * neighbor, * *neighborp;
+
+  trace4( (qh ferr, "qh_degen_redundant_facet: test facet f%d for degen/redundant\n",
+           facet->id) );
+  FOREACHneighbor_(facet) {
+    qh vertex_visit++;
+
+    FOREACHvertex_(neighbor->vertices)
+    vertex->visitid = qh vertex_visit;
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        break;
+        }
+      }
+    if( !vertex )
+      {
+      qh_appendmergeset(facet, neighbor, MRGredundant, NULL);
+      trace2( (qh ferr, "qh_degen_redundant_facet: f%d is contained in f%d.  merge\n", facet->id, neighbor->id) );
+      return;
+      }
+    }
+  if( qh_setsize(facet->neighbors) < qh hull_dim )
+    {
+    qh_appendmergeset(facet, facet, MRGdegen, NULL);
+    trace2( (qh ferr, "qh_degen_redundant_neighbors: f%d is degenerate.\n", facet->id) );
+    }
+} /* degen_redundant_facet */
+
+/*---------------------------------
+
+  qh_degen_redundant_neighbors( facet, delfacet,  )
+  append degenerate and redundant neighbors to facet_mergeset
+  if delfacet,
+  only checks neighbors of both delfacet and facet
+  also checks current facet for degeneracy
+
+  notes:
+  bumps vertex_visit
+  called for each qh_mergefacet() and qh_mergecycle()
+  merge and statistics occur in merge_nonconvex
+  qh_appendmergeset() only appends first reference to facet (i.e., redundant)
+  it appends redundant facets after degenerate ones
+
+  a degenerate facet has fewer than hull_dim neighbors
+  a redundant facet's vertices is a subset of its neighbor's vertices
+  tests for redundant merges first (appendmergeset is nop for others)
+  in a merge, only needs to test neighbors of merged facet
+
+  see:
+  qh_merge_degenredundant() and qh_degen_redundant_facet()
+
+  design:
+  test for degenerate facet
+  test for redundant neighbor
+  test for degenerate neighbor
+*/
+void qh_degen_redundant_neighbors(facetT *facet, facetT *delfacet)
+{
+  vertexT *vertex, * *vertexp;
+  facetT * neighbor, * *neighborp;
+  int      size;
+
+  trace4( (qh ferr, "qh_degen_redundant_neighbors: test neighbors of f%d with delfacet f%d\n",
+           facet->id, getid_(delfacet) ) );
+  if( (size = qh_setsize(facet->neighbors) ) < qh hull_dim )
+    {
+    qh_appendmergeset(facet, facet, MRGdegen, NULL);
+    trace2( (qh ferr, "qh_degen_redundant_neighbors: f%d is degenerate with %d neighbors.\n", facet->id, size) );
+    }
+  if( !delfacet )
+    {
+    delfacet = facet;
+    }
+  qh vertex_visit++;
+  FOREACHvertex_(facet->vertices)
+  vertex->visitid = qh vertex_visit;
+  FOREACHneighbor_(delfacet) {
+    /* uses early out instead of checking vertex count */
+    if( neighbor == facet )
+      {
+      continue;
+      }
+    FOREACHvertex_(neighbor->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        break;
+        }
+      }
+    if( !vertex )
+      {
+      qh_appendmergeset(neighbor, facet, MRGredundant, NULL);
+      trace2( (qh ferr, "qh_degen_redundant_neighbors: f%d is contained in f%d.  merge\n", neighbor->id, facet->id) );
+      }
+    }
+  FOREACHneighbor_(delfacet) {   /* redundant merges occur first */
+    if( neighbor == facet )
+      {
+      continue;
+      }
+    if( (size = qh_setsize(neighbor->neighbors) ) < qh hull_dim )
+      {
+      qh_appendmergeset(neighbor, neighbor, MRGdegen, NULL);
+      trace2( (qh ferr, "qh_degen_redundant_neighbors: f%d is degenerate with %d neighbors.  Neighbor of f%d.\n",
+               neighbor->id, size, facet->id) );
+      }
+    }
+} /* degen_redundant_neighbors */
+
+/*---------------------------------
+
+  qh_find_newvertex( oldvertex, vertices, ridges )
+  locate new vertex for renaming old vertex
+  vertices is a set of possible new vertices
+  vertices sorted by number of deleted ridges
+
+  returns:
+  newvertex or NULL
+  each ridge includes both vertex and oldvertex
+  vertices sorted by number of deleted ridges
+
+  notes:
+  modifies vertex->visitid
+  new vertex is in one of the ridges
+  renaming will not cause a duplicate ridge
+  renaming will minimize the number of deleted ridges
+  newvertex may not be adjacent in the dual (though unlikely)
+
+  design:
+  for each vertex in vertices
+  set vertex->visitid to number of references in ridges
+  remove unvisited vertices
+  set qh.vertex_visit above all possible values
+  sort vertices by number of references in ridges
+  add each ridge to qh.hash_table
+  for each vertex in vertices
+  look for a vertex that would not cause a duplicate ridge after a rename
+*/
+vertexT * qh_find_newvertex(vertexT *oldvertex, setT *vertices, setT *ridges)
+{
+  vertexT *vertex, * *vertexp;
+  setT *   newridges;
+  ridgeT * ridge, * *ridgep;
+  int      size, hashsize;
+  int      hash;
+
+#ifndef qh_NOtrace
+  if( qh IStracing >= 4 )
+    {
+    fprintf(qh ferr, "qh_find_newvertex: find new vertex for v%d from ",
+            oldvertex->id);
+    FOREACHvertex_(vertices)
+    fprintf(qh ferr, "v%d ", vertex->id);
+    FOREACHridge_(ridges)
+    fprintf(qh ferr, "r%d ", ridge->id);
+    fprintf(qh ferr, "\n");
+    }
+#endif
+  FOREACHvertex_(vertices)
+  vertex->visitid = 0;
+  FOREACHridge_(ridges) {
+    FOREACHvertex_(ridge->vertices)
+    vertex->visitid++;
+    }
+  FOREACHvertex_(vertices) {
+    if( !vertex->visitid )
+      {
+      qh_setdelnth(vertices, (size_t)SETindex_(vertices, vertex) );
+      vertexp--; /* repeat since deleted this vertex */
+      }
+    }
+  qh vertex_visit += qh_setsize(ridges);
+  if( !qh_setsize(vertices) )
+    {
+    trace4( (qh ferr, "qh_find_newvertex: vertices not in ridges for v%d\n",
+             oldvertex->id) );
+    return NULL;
+    }
+  qsort(SETaddr_(vertices, vertexT), (size_t)qh_setsize(vertices),
+        sizeof (vertexT *), qh_comparevisit);
+  /* can now use qh vertex_visit */
+  if( qh PRINTstatistics )
+    {
+    size = qh_setsize(vertices);
+    zinc_(Zintersect);
+    zadd_(Zintersecttot, size);
+    zmax_(Zintersectmax, size);
+    }
+  hashsize = qh_newhashtable(qh_setsize(ridges) );
+  FOREACHridge_(ridges)
+  qh_hashridge(qh hash_table, hashsize, ridge, oldvertex);
+  FOREACHvertex_(vertices) {
+    newridges = qh_vertexridges(vertex);
+    FOREACHridge_(newridges) {
+      if( qh_hashridge_find(qh hash_table, hashsize, ridge, vertex, oldvertex, &hash) )
+        {
+        zinc_(Zdupridge);
+        break;
+        }
+      }
+    qh_settempfree(&newridges);
+    if( !ridge )
+      {
+      break;  /* found a rename */
+      }
+    }
+  if( vertex )
+    {
+    /* counted in qh_renamevertex */
+    trace2( (qh ferr, "qh_find_newvertex: found v%d for old v%d from %d vertices and %d ridges.\n",
+             vertex->id, oldvertex->id, qh_setsize(vertices), qh_setsize(ridges) ) );
+    }
+  else
+    {
+    zinc_(Zfindfail);
+    trace0( (qh ferr, "qh_find_newvertex: no vertex for renaming v%d (all duplicated ridges) during p%d\n",
+             oldvertex->id, qh furthest_id) );
+    }
+  qh_setfree(&qh hash_table);
+  return vertex;
+} /* find_newvertex */
+
+/*---------------------------------
+
+  qh_findbest_test( testcentrum, facet, neighbor, bestfacet, dist, mindist, maxdist )
+  test neighbor of facet for qh_findbestneighbor()
+  if testcentrum,
+  tests centrum (assumes it is defined)
+  else
+  tests vertices
+
+  returns:
+  if a better facet (i.e., vertices/centrum of facet closer to neighbor)
+  updates bestfacet, dist, mindist, and maxdist
+*/
+void qh_findbest_test(boolT testcentrum, facetT *facet, facetT *neighbor,
+                      facetT * *bestfacet, realT *distp, realT *mindistp, realT *maxdistp)
+{
+  realT dist, mindist, maxdist;
+
+  if( testcentrum )
+    {
+    zzinc_(Zbestdist);
+    qh_distplane(facet->center, neighbor, &dist);
+    dist *= qh hull_dim; /* estimate furthest vertex */
+    if( dist < 0 )
+      {
+      maxdist = 0;
+      mindist = dist;
+      dist = -dist;
+      }
+    else
+      {
+      maxdist = dist;
+      }
+    }
+  else
+    {
+    dist = qh_getdistance(facet, neighbor, &mindist, &maxdist);
+    }
+  if( dist < *distp )
+    {
+    *bestfacet = neighbor;
+    *mindistp = mindist;
+    *maxdistp = maxdist;
+    *distp = dist;
+    }
+} /* findbest_test */
+
+/*---------------------------------
+
+  qh_findbestneighbor( facet, dist, mindist, maxdist )
+  finds best neighbor (least dist) of a facet for merging
+
+  returns:
+  returns min and max distances and their max absolute value
+
+  notes:
+  avoids merging old into new
+  assumes ridge->nonconvex only set on one ridge between a pair of facets
+  could use an early out predicate but not worth it
+
+  design:
+  if a large facet
+  will test centrum
+  else
+  will test vertices
+  if a large facet
+  test nonconvex neighbors for best merge
+  else
+  test all neighbors for the best merge
+  if testing centrum
+  get distance information
+*/
+facetT * qh_findbestneighbor(facetT *facet, realT *distp, realT *mindistp, realT *maxdistp)
+{
+  facetT *neighbor, * *neighborp, *bestfacet = NULL;
+  ridgeT *ridge, * *ridgep;
+  boolT   nonconvex = True, testcentrum = False;
+  int     size = qh_setsize(facet->vertices);
+
+  *distp = REALmax;
+  if( size > qh_BESTcentrum2 * qh hull_dim + qh_BESTcentrum )
+    {
+    testcentrum = True;
+    zinc_(Zbestcentrum);
+    if( !facet->center )
+      {
+      facet->center = qh_getcentrum(facet);
+      }
+    }
+  if( size > qh hull_dim + qh_BESTnonconvex )
+    {
+    FOREACHridge_(facet->ridges) {
+      if( ridge->nonconvex )
+        {
+        neighbor = otherfacet_(ridge, facet);
+        qh_findbest_test(testcentrum, facet, neighbor,
+                         &bestfacet, distp, mindistp, maxdistp);
+        }
+      }
+    }
+  if( !bestfacet )
+    {
+    nonconvex = False;
+    FOREACHneighbor_(facet)
+    qh_findbest_test(testcentrum, facet, neighbor,
+                     &bestfacet, distp, mindistp, maxdistp);
+    }
+  if( !bestfacet )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_findbestneighbor): no neighbors for f%d\n", facet->id);
+
+    qh_errexit(qh_ERRqhull, facet, NULL);
+    }
+  if( testcentrum )
+    {
+    qh_getdistance(facet, bestfacet, mindistp, maxdistp);
+    }
+  trace3( (qh ferr,
+           "qh_findbestneighbor: f%d is best neighbor for f%d testcentrum? %d nonconvex? %d dist %2.2g min %2.2g max %2.2g\n",
+           bestfacet->id, facet->id, testcentrum, nonconvex, *distp, *mindistp, *maxdistp) );
+  return bestfacet;
+} /* findbestneighbor */
+
+/*---------------------------------
+
+  qh_flippedmerges( facetlist, wasmerge )
+  merge flipped facets into best neighbor
+  assumes qh.facet_mergeset at top of temporary stack
+
+  returns:
+  no flipped facets on facetlist
+  sets wasmerge if merge occurred
+  degen/redundant merges passed through
+
+  notes:
+  othermerges not needed since qh.facet_mergeset is empty before & after
+  keep it in case of change
+
+  design:
+  append flipped facets to qh.facetmergeset
+  for each flipped merge
+  find best neighbor
+  merge facet into neighbor
+  merge degenerate and redundant facets
+  remove flipped merges from qh.facet_mergeset
+*/
+void qh_flippedmerges(facetT *facetlist, boolT *wasmerge)
+{
+  facetT *facet, *neighbor, *facet1;
+  realT   dist, mindist, maxdist;
+  mergeT *merge, * *mergep;
+  setT *  othermerges;
+  int     nummerge = 0;
+
+  trace4( (qh ferr, "qh_flippedmerges: begin\n") );
+  FORALLfacet_(facetlist) {
+    if( facet->flipped && !facet->visible )
+      {
+      qh_appendmergeset(facet, facet, MRGflip, NULL);
+      }
+    }
+  othermerges = qh_settemppop(); /* was facet_mergeset */
+  qh facet_mergeset = qh_settemp(qh TEMPsize);
+  qh_settemppush(othermerges);
+  FOREACHmerge_(othermerges) {
+    facet1 = merge->facet1;
+    if( merge->type != MRGflip || facet1->visible )
+      {
+      continue;
+      }
+    if( qh TRACEmerge - 1 == zzval_(Ztotmerge) )
+      {
+      qhmem.IStracing = qh IStracing = qh TRACElevel;
+      }
+    neighbor = qh_findbestneighbor(facet1, &dist, &mindist, &maxdist);
+    trace0( (qh ferr, "qh_flippedmerges: merge flipped f%d into f%d dist %2.2g during p%d\n",
+             facet1->id, neighbor->id, dist, qh furthest_id) );
+    qh_mergefacet(facet1, neighbor, &mindist, &maxdist, !qh_MERGEapex);
+    nummerge++;
+    if( qh PRINTstatistics )
+      {
+      zinc_(Zflipped);
+      wadd_(Wflippedtot, dist);
+      wmax_(Wflippedmax, dist);
+      }
+    qh_merge_degenredundant();
+    }
+  FOREACHmerge_(othermerges) {
+    if( merge->facet1->visible || merge->facet2->visible )
+      {
+      qh_memfree(merge, sizeof(mergeT) );
+      }
+    else
+      {
+      qh_setappend(&qh facet_mergeset, merge);
+      }
+    }
+  qh_settempfree(&othermerges);
+  if( nummerge )
+    {
+    *wasmerge = True;
+    }
+  trace1( (qh ferr, "qh_flippedmerges: merged %d flipped facets into a good neighbor\n", nummerge) );
+} /* flippedmerges */
+
+/*---------------------------------
+
+  qh_forcedmerges( wasmerge )
+  merge duplicated ridges
+
+  returns:
+  removes all duplicate ridges on facet_mergeset
+  wasmerge set if merge
+  qh.facet_mergeset may include non-forced merges (none for now)
+  qh.degen_mergeset includes degen/redun merges
+
+  notes:
+  duplicate ridges occur when the horizon is pinched,
+  i.e. a subridge occurs in more than two horizon ridges.
+  could rename vertices that pinch the horizon
+  assumes qh_merge_degenredundant() has not be called
+  othermerges isn't needed since facet_mergeset is empty afterwards
+  keep it in case of change
+
+  design:
+  for each duplicate ridge
+  find current facets by chasing f.replace links
+  determine best direction for facet
+  merge one facet into the other
+  remove duplicate ridges from qh.facet_mergeset
+*/
+void qh_forcedmerges(boolT *wasmerge)
+{
+  facetT *facet1, *facet2;
+  mergeT *merge, * *mergep;
+  realT   dist1, dist2, mindist1, mindist2, maxdist1, maxdist2;
+  setT *  othermerges;
+  int     nummerge = 0, numflip = 0;
+
+  if( qh TRACEmerge - 1 == zzval_(Ztotmerge) )
+    {
+    qhmem.IStracing = qh IStracing = qh TRACElevel;
+    }
+  trace4( (qh ferr, "qh_forcedmerges: begin\n") );
+  othermerges = qh_settemppop(); /* was facet_mergeset */
+  qh facet_mergeset = qh_settemp(qh TEMPsize);
+  qh_settemppush(othermerges);
+  FOREACHmerge_(othermerges) {
+    if( merge->type != MRGridge )
+      {
+      continue;
+      }
+    facet1 = merge->facet1;
+    facet2 = merge->facet2;
+    while( facet1->visible )      /* must exist, no qh_merge_degenredunant */
+      {
+      facet1 = facet1->f.replace; /* previously merged facet */
+      }
+
+    while( facet2->visible )
+      {
+      facet2 = facet2->f.replace; /* previously merged facet */
+      }
+
+    if( facet1 == facet2 )
+      {
+      continue;
+      }
+    if( !qh_setin(facet2->neighbors, facet1) )
+      {
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_forcedmerges): f%d and f%d had a duplicate ridge but as f%d and f%d they are no longer neighbors\n",
+        merge->facet1->id, merge->facet2->id, facet1->id, facet2->id);
+      qh_errexit2(qh_ERRqhull, facet1, facet2);
+      }
+    if( qh TRACEmerge - 1 == zzval_(Ztotmerge) )
+      {
+      qhmem.IStracing = qh IStracing = qh TRACElevel;
+      }
+    dist1 = qh_getdistance(facet1, facet2, &mindist1, &maxdist1);
+    dist2 = qh_getdistance(facet2, facet1, &mindist2, &maxdist2);
+    trace0( (qh ferr,
+             "qh_forcedmerges: duplicate ridge between f%d and f%d, dist %2.2g and reverse dist %2.2g during p%d\n",
+             facet1->id, facet2->id, dist1, dist2, qh furthest_id) );
+    if( dist1 < dist2 )
+      {
+      qh_mergefacet(facet1, facet2, &mindist1, &maxdist1, !qh_MERGEapex);
+      }
+    else
+      {
+      qh_mergefacet(facet2, facet1, &mindist2, &maxdist2, !qh_MERGEapex);
+      dist1 = dist2;
+      facet1 = facet2;
+      }
+    if( facet1->flipped )
+      {
+      zinc_(Zmergeflipdup);
+      numflip++;
+      }
+    else
+      {
+      nummerge++;
+      }
+    if( qh PRINTstatistics )
+      {
+      zinc_(Zduplicate);
+      wadd_(Wduplicatetot, dist1);
+      wmax_(Wduplicatemax, dist1);
+      }
+    }
+  FOREACHmerge_(othermerges) {
+    if( merge->type == MRGridge )
+      {
+      qh_memfree(merge, sizeof(mergeT) );
+      }
+    else
+      {
+      qh_setappend(&qh facet_mergeset, merge);
+      }
+    }
+  qh_settempfree(&othermerges);
+  if( nummerge )
+    {
+    *wasmerge = True;
+    }
+  trace1( (qh ferr, "qh_forcedmerges: merged %d facets and %d flipped facets across duplicated ridges\n",
+           nummerge, numflip) );
+} /* forcedmerges */
+
+/*---------------------------------
+
+  qh_getmergeset( facetlist )
+  determines nonconvex facets on facetlist
+  tests !tested ridges and nonconvex ridges of !tested facets
+
+  returns:
+  returns sorted qh.facet_mergeset of facet-neighbor pairs to be merged
+  all ridges tested
+
+  notes:
+  assumes no nonconvex ridges with both facets tested
+  uses facet->tested/ridge->tested to prevent duplicate tests
+  can not limit tests to modified ridges since the centrum changed
+  uses qh.visit_id
+
+  see:
+  qh_getmergeset_initial()
+
+  design:
+  for each facet on facetlist
+  for each ridge of facet
+  if untested ridge
+  test ridge for convexity
+  if non-convex
+  append ridge to qh.facet_mergeset
+  sort qh.facet_mergeset by angle
+*/
+void qh_getmergeset(facetT *facetlist)
+{
+  facetT *facet, *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+  int     nummerges;
+
+  nummerges = qh_setsize(qh facet_mergeset);
+  trace4( (qh ferr, "qh_getmergeset: started.\n") );
+  qh visit_id++;
+  FORALLfacet_(facetlist) {
+    if( facet->tested )
+      {
+      continue;
+      }
+    facet->visitid = qh visit_id;
+    facet->tested = True;  /* must be non-simplicial due to merge */
+    FOREACHneighbor_(facet)
+    neighbor->seen = False;
+    FOREACHridge_(facet->ridges) {
+      if( ridge->tested && !ridge->nonconvex )
+        {
+        continue;
+        }
+      /* if tested & nonconvex, need to append merge */
+      neighbor = otherfacet_(ridge, facet);
+      if( neighbor->seen )
+        {
+        ridge->tested = True;
+        ridge->nonconvex = False;
+        }
+      else if( neighbor->visitid != qh visit_id )
+        {
+        ridge->tested = True;
+        ridge->nonconvex = False;
+        neighbor->seen = True; /* only one ridge is marked nonconvex */
+        if( qh_test_appendmerge(facet, neighbor) )
+          {
+          ridge->nonconvex = True;
+          }
+        }
+      }
+    }
+  nummerges = qh_setsize(qh facet_mergeset);
+  if( qh ANGLEmerge )
+    {
+    qsort(SETaddr_(qh facet_mergeset, mergeT), (size_t)nummerges, sizeof(mergeT *), qh_compareangle);
+    }
+  else
+    {
+    qsort(SETaddr_(qh facet_mergeset, mergeT), (size_t)nummerges, sizeof(mergeT *), qh_comparemerge);
+    }
+  if( qh POSTmerging )
+    {
+    zadd_(Zmergesettot2, nummerges);
+    }
+  else
+    {
+    zadd_(Zmergesettot, nummerges);
+    zmax_(Zmergesetmax, nummerges);
+    }
+  trace2( (qh ferr, "qh_getmergeset: %d merges found\n", nummerges) );
+} /* getmergeset */
+
+/*---------------------------------
+
+  qh_getmergeset_initial( facetlist )
+  determine initial qh.facet_mergeset for facets
+  tests all facet/neighbor pairs on facetlist
+
+  returns:
+  sorted qh.facet_mergeset with nonconvex ridges
+  sets facet->tested, ridge->tested, and ridge->nonconvex
+
+  notes:
+  uses visit_id, assumes ridge->nonconvex is False
+
+  see:
+  qh_getmergeset()
+
+  design:
+  for each facet on facetlist
+  for each untested neighbor of facet
+  test facet and neighbor for convexity
+  if non-convex
+  append merge to qh.facet_mergeset
+  mark one of the ridges as nonconvex
+  sort qh.facet_mergeset by angle
+*/
+void qh_getmergeset_initial(facetT *facetlist)
+{
+  facetT *facet, *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+  int     nummerges;
+
+  qh visit_id++;
+
+  FORALLfacet_(facetlist) {
+    facet->visitid = qh visit_id;
+    facet->tested = True;
+    FOREACHneighbor_(facet) {
+      if( neighbor->visitid != qh visit_id )
+        {
+        if( qh_test_appendmerge(facet, neighbor) )
+          {
+          FOREACHridge_(neighbor->ridges) {
+            if( facet == otherfacet_(ridge, neighbor) )
+              {
+              ridge->nonconvex = True;
+              break;  /* only one ridge is marked nonconvex */
+              }
+            }
+          }
+        }
+      }
+    FOREACHridge_(facet->ridges)
+    ridge->tested = True;
+    }
+  nummerges = qh_setsize(qh facet_mergeset);
+  if( qh ANGLEmerge )
+    {
+    qsort(SETaddr_(qh facet_mergeset, mergeT), (size_t)nummerges, sizeof(mergeT *), qh_compareangle);
+    }
+  else
+    {
+    qsort(SETaddr_(qh facet_mergeset, mergeT), (size_t)nummerges, sizeof(mergeT *), qh_comparemerge);
+    }
+  if( qh POSTmerging )
+    {
+    zadd_(Zmergeinittot2, nummerges);
+    }
+  else
+    {
+    zadd_(Zmergeinittot, nummerges);
+    zmax_(Zmergeinitmax, nummerges);
+    }
+  trace2( (qh ferr, "qh_getmergeset_initial: %d merges found\n", nummerges) );
+} /* getmergeset_initial */
+
+/*---------------------------------
+
+  qh_hashridge( hashtable, hashsize, ridge, oldvertex )
+  add ridge to hashtable without oldvertex
+
+  notes:
+  assumes hashtable is large enough
+
+  design:
+  determine hash value for ridge without oldvertex
+  find next empty slot for ridge
+*/
+void qh_hashridge(setT *hashtable, int hashsize, ridgeT *ridge, vertexT *oldvertex)
+{
+  int     hash;
+  ridgeT *ridgeA;
+
+  hash = (int)qh_gethash(hashsize, ridge->vertices, qh hull_dim - 1, 0, oldvertex);
+  while( True )
+    {
+    if( !(ridgeA = SETelemt_(hashtable, hash, ridgeT) ) )
+      {
+      SETelem_(hashtable, hash) = ridge;
+      break;
+      }
+    else if( ridgeA == ridge )
+      {
+      break;
+      }
+    if( ++hash == hashsize )
+      {
+      hash = 0;
+      }
+    }
+} /* hashridge */
+
+/*---------------------------------
+
+  qh_hashridge_find( hashtable, hashsize, ridge, vertex, oldvertex, hashslot )
+  returns matching ridge without oldvertex in hashtable
+  for ridge without vertex
+  if oldvertex is NULL
+  matches with any one skip
+
+  returns:
+  matching ridge or NULL
+  if no match,
+  if ridge already in   table
+  hashslot= -1
+  else
+  hashslot= next NULL index
+
+  notes:
+  assumes hashtable is large enough
+  can't match ridge to itself
+
+  design:
+  get hash value for ridge without vertex
+  for each hashslot
+  return match if ridge matches ridgeA without oldvertex
+*/
+ridgeT * qh_hashridge_find(setT *hashtable, int hashsize, ridgeT *ridge,
+                           vertexT *vertex, vertexT *oldvertex, int *hashslot)
+{
+  int     hash;
+  ridgeT *ridgeA;
+
+  *hashslot = 0;
+  zinc_(Zhashridge);
+  hash = (int)qh_gethash(hashsize, ridge->vertices, qh hull_dim - 1, 0, vertex);
+  while( (ridgeA = SETelemt_(hashtable, hash, ridgeT) ) )
+    {
+    if( ridgeA == ridge )
+      {
+      *hashslot = -1;
+      }
+    else
+      {
+      zinc_(Zhashridgetest);
+      if( qh_setequal_except(ridge->vertices, vertex, ridgeA->vertices, oldvertex) )
+        {
+        return ridgeA;
+        }
+      }
+    if( ++hash == hashsize )
+      {
+      hash = 0;
+      }
+    }
+
+  if( !*hashslot )
+    {
+    *hashslot = hash;
+    }
+  return NULL;
+} /* hashridge_find */
+
+/*---------------------------------
+
+  qh_makeridges( facet )
+  creates explicit ridges between simplicial facets
+
+  returns:
+  facet with ridges and without qh_MERGEridge
+  ->simplicial is False
+
+  notes:
+  allows qh_MERGEridge flag
+  uses existing ridges
+  duplicate neighbors ok if ridges already exist (qh_mergecycle_ridges)
+
+  see:
+  qh_mergecycle_ridges()
+
+  design:
+  look for qh_MERGEridge neighbors
+  mark neighbors that already have ridges
+  for each unprocessed neighbor of facet
+  create a ridge for neighbor and facet
+  if any qh_MERGEridge neighbors
+  delete qh_MERGEridge flags (already handled by qh_mark_dupridges)
+*/
+void qh_makeridges(facetT *facet)
+{
+  facetT *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+  int     neighbor_i, neighbor_n;
+  boolT   toporient, mergeridge = False;
+
+  if( !facet->simplicial )
+    {
+    return;
+    }
+  trace4( (qh ferr, "qh_makeridges: make ridges for f%d\n", facet->id) );
+  facet->simplicial = False;
+  FOREACHneighbor_(facet) {
+    if( neighbor == qh_MERGEridge )
+      {
+      mergeridge = True;
+      }
+    else
+      {
+      neighbor->seen = False;
+      }
+    }
+  FOREACHridge_(facet->ridges)
+  otherfacet_(ridge, facet)->seen = True;
+  FOREACHneighbor_i_(facet) {
+    if( neighbor == qh_MERGEridge )
+      {
+      continue;  /* fixed by qh_mark_dupridges */
+      }
+    else if( !neighbor->seen )    /* no current ridges */
+      {
+      ridge = qh_newridge();
+      ridge->vertices = qh_setnew_delnthsorted(facet->vertices, qh hull_dim,
+                                               (size_t)neighbor_i, (size_t)0);
+      toporient = facet->toporient ^ (neighbor_i & 0x1);
+      if( toporient )
+        {
+        ridge->top = facet;
+        ridge->bottom = neighbor;
+        }
+      else
+        {
+        ridge->top = neighbor;
+        ridge->bottom = facet;
+        }
+#if 0 /* this also works */
+      flip = (facet->toporient ^ neighbor->toporient) ^ (skip1 & 0x1) ^ (skip2 & 0x1);
+      if( facet->toporient ^ (skip1 & 0x1) ^ flip )
+        {
+        ridge->top = neighbor;
+        ridge->bottom = facet;
+        }
+      else
+        {
+        ridge->top = facet;
+        ridge->bottom = neighbor;
+        }
+#endif
+      qh_setappend(&(facet->ridges), ridge);
+      qh_setappend(&(neighbor->ridges), ridge);
+      }
+    }
+  if( mergeridge )
+    {
+    while( qh_setdel(facet->neighbors, qh_MERGEridge) )
+      {
+      ; /* delete each one */
+      }
+    }
+} /* makeridges */
+
+/*---------------------------------
+
+  qh_mark_dupridges( facetlist )
+  add duplicated ridges to qh.facet_mergeset
+  facet->dupridge is true
+
+  returns:
+  duplicate ridges on qh.facet_mergeset
+  ->mergeridge/->mergeridge2 set
+  duplicate ridges marked by qh_MERGEridge and both sides facet->dupridge
+  no MERGEridges in neighbor sets
+
+  notes:
+  duplicate ridges occur when the horizon is pinched,
+  i.e. a subridge occurs in more than two horizon ridges.
+  could rename vertices that pinch the horizon
+  uses qh.visit_id
+
+  design:
+  for all facets on facetlist
+  if facet contains a duplicate ridge
+  for each neighbor of facet
+  if neighbor marked qh_MERGEridge (one side of the merge)
+  set facet->mergeridge
+  else
+  if neighbor contains a duplicate ridge
+  and the back link is qh_MERGEridge
+  append duplicate ridge to qh.facet_mergeset
+  for each duplicate ridge
+  make ridge sets in preparation for merging
+  remove qh_MERGEridge from neighbor set
+  for each duplicate ridge
+  restore the missing neighbor from the neighbor set that was qh_MERGEridge
+  add the missing ridge for this neighbor
+*/
+void qh_mark_dupridges(facetT *facetlist)
+{
+  facetT *facet, *neighbor, * *neighborp;
+  int     nummerge = 0;
+  mergeT *merge, * *mergep;
+
+  trace4( (qh ferr, "qh_mark_dupridges: identify duplicate ridges\n") );
+  FORALLfacet_(facetlist) {
+    if( facet->dupridge )
+      {
+      FOREACHneighbor_(facet) {
+        if( neighbor == qh_MERGEridge )
+          {
+          facet->mergeridge = True;
+          continue;
+          }
+        if( neighbor->dupridge
+            && !qh_setin(neighbor->neighbors, facet) ) /* qh_MERGEridge */
+          {
+          qh_appendmergeset(facet, neighbor, MRGridge, NULL);
+          facet->mergeridge2 = True;
+          facet->mergeridge = True;
+          nummerge++;
+          }
+        }
+      }
+    }
+  if( !nummerge )
+    {
+    return;
+    }
+  FORALLfacet_(facetlist) {            /* gets rid of qh_MERGEridge */
+    if( facet->mergeridge && !facet->mergeridge2 )
+      {
+      qh_makeridges(facet);
+      }
+    }
+  FOREACHmerge_(qh facet_mergeset) {   /* restore the missing neighbors */
+    if( merge->type == MRGridge )
+      {
+      qh_setappend(&merge->facet2->neighbors, merge->facet1);
+      qh_makeridges(merge->facet1);    /* and the missing ridges */
+      }
+    }
+  trace1( (qh ferr, "qh_mark_dupridges: found %d duplicated ridges\n",
+           nummerge) );
+} /* mark_dupridges */
+
+/*---------------------------------
+
+  qh_maydropneighbor( facet )
+  drop neighbor relationship if no ridge between facet and neighbor
+
+  returns:
+  neighbor sets updated
+  appends degenerate facets to qh.facet_mergeset
+
+  notes:
+  won't cause redundant facets since vertex inclusion is the same
+  may drop vertex and neighbor if no ridge
+  uses qh.visit_id
+
+  design:
+  visit all neighbors with ridges
+  for each unvisited neighbor of facet
+  delete neighbor and facet from the neighbor sets
+  if neighbor becomes degenerate
+  append neighbor to qh.degen_mergeset
+  if facet is degenerate
+  append facet to qh.degen_mergeset
+*/
+void qh_maydropneighbor(facetT *facet)
+{
+  ridgeT *ridge, * *ridgep;
+  realT   angledegen = qh_ANGLEdegen;
+  facetT *neighbor, * *neighborp;
+
+  qh visit_id++;
+
+  trace4( (qh ferr, "qh_maydropneighbor: test f%d for no ridges to a neighbor\n",
+           facet->id) );
+  FOREACHridge_(facet->ridges) {
+    ridge->top->visitid = qh visit_id;
+    ridge->bottom->visitid = qh visit_id;
+    }
+  FOREACHneighbor_(facet) {
+    if( neighbor->visitid != qh visit_id )
+      {
+      trace0( (qh ferr, "qh_maydropneighbor: facets f%d and f%d are no longer neighbors during p%d\n",
+               facet->id, neighbor->id, qh furthest_id) );
+      zinc_(Zdropneighbor);
+      qh_setdel(facet->neighbors, neighbor);
+      neighborp--;  /* repeat, deleted a neighbor */
+      qh_setdel(neighbor->neighbors, facet);
+      if( qh_setsize(neighbor->neighbors) < qh hull_dim )
+        {
+        zinc_(Zdropdegen);
+        qh_appendmergeset(neighbor, neighbor, MRGdegen, &angledegen);
+        trace2( (qh ferr, "qh_maydropneighbors: f%d is degenerate.\n", neighbor->id) );
+        }
+      }
+    }
+  if( qh_setsize(facet->neighbors) < qh hull_dim )
+    {
+    zinc_(Zdropdegen);
+    qh_appendmergeset(facet, facet, MRGdegen, &angledegen);
+    trace2( (qh ferr, "qh_maydropneighbors: f%d is degenerate.\n", facet->id) );
+    }
+} /* maydropneighbor */
+
+/*---------------------------------
+
+  qh_merge_degenredundant()
+  merge all degenerate and redundant facets
+  qh.degen_mergeset contains merges from qh_degen_redundant_neighbors()
+
+  returns:
+  number of merges performed
+  resets facet->degenerate/redundant
+  if deleted (visible) facet has no neighbors
+  sets ->f.replace to NULL
+
+  notes:
+  redundant merges happen before degenerate ones
+  merging and renaming vertices can result in degen/redundant facets
+
+  design:
+  for each merge on qh.degen_mergeset
+  if redundant merge
+  if non-redundant facet merged into redundant facet
+  recheck facet for redundancy
+  else
+  merge redundant facet into other facet
+*/
+int qh_merge_degenredundant(void)
+{
+  int       size;
+  mergeT *  merge;
+  facetT *  bestneighbor, *facet1, *facet2;
+  realT     dist, mindist, maxdist;
+  vertexT * vertex, * *vertexp;
+  int       nummerges = 0;
+  mergeType mergetype;
+
+  while( (merge = (mergeT *)qh_setdellast(qh degen_mergeset) ) )
+    {
+    facet1 = merge->facet1;
+    facet2 = merge->facet2;
+    mergetype = merge->type;
+    qh_memfree(merge, sizeof(mergeT) );
+    if( facet1->visible )
+      {
+      continue;
+      }
+    facet1->degenerate = False;
+    facet1->redundant = False;
+    if( qh TRACEmerge - 1 == zzval_(Ztotmerge) )
+      {
+      qhmem.IStracing = qh IStracing = qh TRACElevel;
+      }
+    if( mergetype == MRGredundant )
+      {
+      zinc_(Zneighbor);
+      while( facet2->visible )
+        {
+        if( !facet2->f.replace )
+          {
+          fprintf(qh ferr, "qhull internal error (qh_merge_degenredunant): f%d redundant but f%d has no replacement\n",
+                  facet1->id, facet2->id);
+          qh_errexit2(qh_ERRqhull, facet1, facet2);
+          }
+        facet2 = facet2->f.replace;
+        }
+
+      if( facet1 == facet2 )
+        {
+        qh_degen_redundant_facet(facet1); /* in case of others */
+        continue;
+        }
+      trace2( (qh ferr, "qh_merge_degenredundant: facet f%d is contained in f%d, will merge\n",
+               facet1->id, facet2->id) );
+      qh_mergefacet(facet1, facet2, NULL, NULL, !qh_MERGEapex);
+      /* merge distance is already accounted for */
+      nummerges++;
+      }
+    else     /* mergetype == MRGdegen, other merges may have fixed */
+      {
+      if( !(size = qh_setsize(facet1->neighbors) ) )
+        {
+        zinc_(Zdelfacetdup);
+        trace2( (qh ferr, "qh_merge_degenredundant: facet f%d has no neighbors.  Deleted\n", facet1->id) );
+        qh_willdelete(facet1, NULL);
+        FOREACHvertex_(facet1->vertices) {
+          qh_setdel(vertex->neighbors, facet1);
+          if( !SETfirst_(vertex->neighbors) )
+            {
+            zinc_(Zdegenvertex);
+            trace2( (qh ferr, "qh_merge_degenredundant: deleted v%d because f%d has no neighbors\n",
+                     vertex->id, facet1->id) );
+            vertex->deleted = True;
+            qh_setappend(&qh del_vertices, vertex);
+            }
+          }
+        nummerges++;
+        }
+      else if( size < qh hull_dim )
+        {
+        bestneighbor = qh_findbestneighbor(facet1, &dist, &mindist, &maxdist);
+        trace2( (qh ferr, "qh_merge_degenredundant: facet f%d has %d neighbors, merge into f%d dist %2.2g\n",
+                 facet1->id, size, bestneighbor->id, dist) );
+        qh_mergefacet(facet1, bestneighbor, &mindist, &maxdist, !qh_MERGEapex);
+        nummerges++;
+        if( qh PRINTstatistics )
+          {
+          zinc_(Zdegen);
+          wadd_(Wdegentot, dist);
+          wmax_(Wdegenmax, dist);
+          }
+        } /* else, another merge fixed the degeneracy and redundancy tested */
+      }
+    }
+
+  return nummerges;
+} /* merge_degenredundant */
+
+/*---------------------------------
+
+  qh_merge_nonconvex( facet1, facet2, mergetype )
+  remove non-convex ridge between facet1 into facet2
+  mergetype gives why the facet's are non-convex
+
+  returns:
+  merges one of the facets into the best neighbor
+
+  design:
+  if one of the facets is a new facet
+  prefer merging new facet into old facet
+  find best neighbors for both facets
+  merge the nearest facet into its best neighbor
+  update the statistics
+*/
+void qh_merge_nonconvex(facetT *facet1, facetT *facet2, mergeType mergetype)
+{
+  facetT *bestfacet, *bestneighbor, *neighbor;
+  realT   dist, dist2, mindist, mindist2, maxdist, maxdist2;
+
+  if( qh TRACEmerge - 1 == zzval_(Ztotmerge) )
+    {
+    qhmem.IStracing = qh IStracing = qh TRACElevel;
+    }
+  trace3( (qh ferr, "qh_merge_nonconvex: merge #%d for f%d and f%d type %d\n",
+           zzval_(Ztotmerge) + 1, facet1->id, facet2->id, mergetype) );
+  /* concave or coplanar */
+  if( !facet1->newfacet )
+    {
+    bestfacet = facet2;   /* avoid merging old facet if new is ok */
+    facet2 = facet1;
+    facet1 = bestfacet;
+    }
+  else
+    {
+    bestfacet = facet1;
+    }
+  bestneighbor = qh_findbestneighbor(bestfacet, &dist, &mindist, &maxdist);
+  neighbor = qh_findbestneighbor(facet2, &dist2, &mindist2, &maxdist2);
+  if( dist < dist2 )
+    {
+    qh_mergefacet(bestfacet, bestneighbor, &mindist, &maxdist, !qh_MERGEapex);
+    }
+  else if( qh AVOIDold && !facet2->newfacet
+           && ( (mindist >= -qh MAXcoplanar && maxdist <= qh max_outside)
+                || dist * 1.5 < dist2) )
+    {
+    zinc_(Zavoidold);
+    wadd_(Wavoidoldtot, dist);
+    wmax_(Wavoidoldmax, dist);
+    trace2( (qh ferr, "qh_merge_nonconvex: avoid merging old facet f%d dist %2.2g.  Use f%d dist %2.2g instead\n",
+             facet2->id, dist2, facet1->id, dist2) );
+    qh_mergefacet(bestfacet, bestneighbor, &mindist, &maxdist, !qh_MERGEapex);
+    }
+  else
+    {
+    qh_mergefacet(facet2, neighbor, &mindist2, &maxdist2, !qh_MERGEapex);
+    dist = dist2;
+    }
+  if( qh PRINTstatistics )
+    {
+    if( mergetype == MRGanglecoplanar )
+      {
+      zinc_(Zacoplanar);
+      wadd_(Wacoplanartot, dist);
+      wmax_(Wacoplanarmax, dist);
+      }
+    else if( mergetype == MRGconcave )
+      {
+      zinc_(Zconcave);
+      wadd_(Wconcavetot, dist);
+      wmax_(Wconcavemax, dist);
+      }
+    else    /* MRGcoplanar */
+      {
+      zinc_(Zcoplanar);
+      wadd_(Wcoplanartot, dist);
+      wmax_(Wcoplanarmax, dist);
+      }
+    }
+} /* merge_nonconvex */
+
+/*---------------------------------
+
+  qh_mergecycle( samecycle, newfacet )
+  merge a cycle of facets starting at samecycle into a newfacet
+  newfacet is a horizon facet with ->normal
+  samecycle facets are simplicial from an apex
+
+  returns:
+  initializes vertex neighbors on first merge
+  samecycle deleted (placed on qh.visible_list)
+  newfacet at end of qh.facet_list
+  deleted vertices on qh.del_vertices
+
+  see:
+  qh_mergefacet()
+  called by qh_mergecycle_all() for multiple, same cycle facets
+
+  design:
+  make vertex neighbors if necessary
+  make ridges for newfacet
+  merge neighbor sets of samecycle into newfacet
+  merge ridges of samecycle into newfacet
+  merge vertex neighbors of samecycle into newfacet
+  make apex of samecycle the apex of newfacet
+  if newfacet wasn't a new facet
+  add its vertices to qh.newvertex_list
+  delete samecycle facets a make newfacet a newfacet
+*/
+void qh_mergecycle(facetT *samecycle, facetT *newfacet)
+{
+  int      traceonce = False, tracerestore = 0;
+  vertexT *apex;
+
+#ifndef qh_NOtrace
+  facetT *same;
+#endif
+
+  if( newfacet->tricoplanar )
+    {
+    if( !qh TRInormals )
+      {
+      fprintf(qh ferr, "qh_mergecycle: does not work for tricoplanar facets.  Use option 'Q11'\n");
+      qh_errexit(qh_ERRqhull, newfacet, NULL);
+      }
+    newfacet->tricoplanar = False;
+    newfacet->keepcentrum = False;
+    }
+  if( !qh VERTEXneighbors )
+    {
+    qh_vertexneighbors();
+    }
+  zzinc_(Ztotmerge);
+  if( qh REPORTfreq2 && qh POSTmerging )
+    {
+    if( zzval_(Ztotmerge) > qh mergereport + qh REPORTfreq2 )
+      {
+      qh_tracemerging();
+      }
+    }
+#ifndef qh_NOtrace
+  if( qh TRACEmerge == zzval_(Ztotmerge) )
+    {
+    qhmem.IStracing = qh IStracing = qh TRACElevel;
+    }
+  trace2( (qh ferr, "qh_mergecycle: merge #%d for facets from cycle f%d into coplanar horizon f%d\n",
+           zzval_(Ztotmerge), samecycle->id, newfacet->id) );
+  if( newfacet == qh tracefacet )
+    {
+    tracerestore = qh IStracing;
+    qh IStracing = 4;
+    fprintf(qh ferr, "qh_mergecycle: ========= trace merge %d of samecycle %d into trace f%d, furthest is p%d\n",
+            zzval_(Ztotmerge), samecycle->id, newfacet->id,  qh furthest_id);
+    traceonce = True;
+    }
+  if( qh IStracing >= 4 )
+    {
+    fprintf(qh ferr, "  same cycle:");
+    FORALLsame_cycle_(samecycle)
+    fprintf(qh ferr, " f%d", same->id);
+    fprintf(qh ferr, "\n");
+    }
+  if( qh IStracing >= 4 )
+    {
+    qh_errprint("MERGING CYCLE", samecycle, newfacet, NULL, NULL);
+    }
+#endif /* !qh_NOtrace */
+  apex = SETfirstt_(samecycle->vertices, vertexT);
+  qh_makeridges(newfacet);
+  qh_mergecycle_neighbors(samecycle, newfacet);
+  qh_mergecycle_ridges(samecycle, newfacet);
+  qh_mergecycle_vneighbors(samecycle, newfacet);
+  if( SETfirstt_(newfacet->vertices, vertexT) != apex )
+    {
+    qh_setaddnth(&newfacet->vertices, 0, apex);   /* apex has last id */
+    }
+  if( !newfacet->newfacet )
+    {
+    qh_newvertices(newfacet->vertices);
+    }
+  qh_mergecycle_facets(samecycle, newfacet);
+  qh_tracemerge(samecycle, newfacet);
+  /* check for degen_redundant_neighbors after qh_forcedmerges() */
+  if( traceonce )
+    {
+    fprintf(qh ferr, "qh_mergecycle: end of trace facet\n");
+    qh IStracing = tracerestore;
+    }
+} /* mergecycle */
+
+/*---------------------------------
+
+  qh_mergecycle_all( facetlist, wasmerge )
+  merge all samecycles of coplanar facets into horizon
+  don't merge facets with ->mergeridge (these already have ->normal)
+  all facets are simplicial from apex
+  all facet->cycledone == False
+
+  returns:
+  all newfacets merged into coplanar horizon facets
+  deleted vertices on  qh.del_vertices
+  sets wasmerge if any merge
+
+  see:
+  calls qh_mergecycle for multiple, same cycle facets
+
+  design:
+  for each facet on facetlist
+  skip facets with duplicate ridges and normals
+  check that facet is in a samecycle (->mergehorizon)
+  if facet only member of samecycle
+  sets vertex->delridge for all vertices except apex
+  merge facet into horizon
+  else
+  mark all facets in samecycle
+  remove facets with duplicate ridges from samecycle
+  merge samecycle into horizon (deletes facets from facetlist)
+*/
+void qh_mergecycle_all(facetT *facetlist, boolT *wasmerge)
+{
+  facetT * facet, *same, *prev, *horizon;
+  facetT * samecycle = NULL, *nextfacet, *nextsame;
+  vertexT *apex, *vertex, * *vertexp;
+  int      cycles = 0, total = 0, facets, nummerge;
+
+  trace2( (qh ferr, "qh_mergecycle_all: begin\n") );
+  for( facet = facetlist; facet && (nextfacet = facet->next); facet = nextfacet )
+    {
+    if( facet->normal )
+      {
+      continue;
+      }
+    if( !facet->mergehorizon )
+      {
+      fprintf(qh ferr, "qh_mergecycle_all: f%d without normal\n", facet->id);
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    horizon = SETfirstt_(facet->neighbors, facetT);
+    if( facet->f.samecycle == facet )
+      {
+      zinc_(Zonehorizon);
+      /* merge distance done in qh_findhorizon */
+      apex = SETfirstt_(facet->vertices, vertexT);
+      FOREACHvertex_(facet->vertices) {
+        if( vertex != apex )
+          {
+          vertex->delridge = True;
+          }
+        }
+      horizon->f.newcycle = NULL;
+      qh_mergefacet(facet, horizon, NULL, NULL, qh_MERGEapex);
+      }
+    else
+      {
+      samecycle = facet;
+      facets = 0;
+      prev = facet;
+      for( same = facet->f.samecycle; same;           /*
+                                                        FORALLsame_cycle_(facet)
+                                                        */
+           same = (same == facet ? NULL : nextsame) ) /* ends at facet */
+        {
+        nextsame = same->f.samecycle;
+        if( same->cycledone || same->visible )
+          {
+          qh_infiniteloop(same);
+          }
+        same->cycledone = True;
+        if( same->normal )
+          {
+          prev->f.samecycle = same->f.samecycle; /* unlink ->mergeridge */
+          same->f.samecycle = NULL;
+          }
+        else
+          {
+          prev = same;
+          facets++;
+          }
+        }
+      while( nextfacet && nextfacet->cycledone )  /* will delete samecycle */
+        {
+        nextfacet = nextfacet->next;
+        }
+
+      horizon->f.newcycle = NULL;
+      qh_mergecycle(samecycle, horizon);
+      nummerge = horizon->nummerge + facets;
+      if( nummerge > qh_MAXnummerge )
+        {
+        horizon->nummerge = qh_MAXnummerge;
+        }
+      else
+        {
+        horizon->nummerge = nummerge;
+        }
+      zzinc_(Zcyclehorizon);
+      total += facets;
+      zzadd_(Zcyclefacettot, facets);
+      zmax_(Zcyclefacetmax, facets);
+      }
+    cycles++;
+    }
+  if( cycles )
+    {
+    *wasmerge = True;
+    }
+  trace1( (qh ferr, "qh_mergecycle_all: merged %d same cycles or facets into coplanar horizons\n", cycles) );
+} /* mergecycle_all */
+
+/*---------------------------------
+
+  qh_mergecycle_facets( samecycle, newfacet )
+  finish merge of samecycle into newfacet
+
+  returns:
+  samecycle prepended to visible_list for later deletion and partitioning
+  each facet->f.replace == newfacet
+
+  newfacet moved to end of qh.facet_list
+  makes newfacet a newfacet (get's facet1->id if it was old)
+  sets newfacet->newmerge
+  clears newfacet->center (unless merging into a large facet)
+  clears newfacet->tested and ridge->tested for facet1
+
+  adds neighboring facets to facet_mergeset if redundant or degenerate
+
+  design:
+  make newfacet a new facet and set its flags
+  move samecycle facets to qh.visible_list for later deletion
+  unless newfacet is large
+  remove its centrum
+*/
+void qh_mergecycle_facets(facetT *samecycle, facetT *newfacet)
+{
+  facetT *same, *next;
+
+  trace4( (qh ferr, "qh_mergecycle_facets: make newfacet new and samecycle deleted\n") );
+  qh_removefacet(newfacet);  /* append as a newfacet to end of qh facet_list */
+  qh_appendfacet(newfacet);
+  newfacet->newfacet = True;
+  newfacet->simplicial = False;
+  newfacet->newmerge = True;
+  for( same = samecycle->f.samecycle; same; same = (same == samecycle ?  NULL : next) )
+    {
+    next = same->f.samecycle;  /* reused by willdelete */
+    qh_willdelete(same, newfacet);
+    }
+  if( newfacet->center
+      && qh_setsize(newfacet->vertices) <= qh hull_dim + qh_MAXnewcentrum )
+    {
+    qh_memfree(newfacet->center, qh normal_size);
+    newfacet->center = NULL;
+    }
+  trace3( (qh ferr, "qh_mergecycle_facets: merged facets from cycle f%d into f%d\n",
+           samecycle->id, newfacet->id) );
+} /* mergecycle_facets */
+
+/*---------------------------------
+
+  qh_mergecycle_neighbors( samecycle, newfacet )
+  add neighbors for samecycle facets to newfacet
+
+  returns:
+  newfacet with updated neighbors and vice-versa
+  newfacet has ridges
+  all neighbors of newfacet marked with qh.visit_id
+  samecycle facets marked with qh.visit_id-1
+  ridges updated for simplicial neighbors of samecycle with a ridge
+
+  notes:
+  assumes newfacet not in samecycle
+  usually, samecycle facets are new, simplicial facets without internal ridges
+  not so if horizon facet is coplanar to two different samecycles
+
+  see:
+  qh_mergeneighbors()
+
+  design:
+  check samecycle
+  delete neighbors from newfacet that are also in samecycle
+  for each neighbor of a facet in samecycle
+  if neighbor is simplicial
+  if first visit
+  move the neighbor relation to newfacet
+  update facet links for its ridges
+  else
+  make ridges for neighbor
+  remove samecycle reference
+  else
+  update neighbor sets
+*/
+void qh_mergecycle_neighbors(facetT *samecycle, facetT *newfacet)
+{
+  facetT *     same, *neighbor, * *neighborp;
+  int          delneighbors = 0, newneighbors = 0;
+  unsigned int samevisitid;
+  ridgeT *     ridge, * *ridgep;
+
+  samevisitid = ++qh visit_id;
+  FORALLsame_cycle_(samecycle) {
+    if( same->visitid == samevisitid || same->visible )
+      {
+      qh_infiniteloop(samecycle);
+      }
+    same->visitid = samevisitid;
+    }
+  newfacet->visitid = ++qh visit_id;
+  trace4( (qh ferr, "qh_mergecycle_neighbors: delete shared neighbors from newfacet\n") );
+  FOREACHneighbor_(newfacet) {
+    if( neighbor->visitid == samevisitid )
+      {
+      SETref_(neighbor) = NULL;  /* samecycle neighbors deleted */
+      delneighbors++;
+      }
+    else
+      {
+      neighbor->visitid = qh visit_id;
+      }
+    }
+  qh_setcompact(newfacet->neighbors);
+
+  trace4( (qh ferr, "qh_mergecycle_neighbors: update neighbors\n") );
+  FORALLsame_cycle_(samecycle) {
+    FOREACHneighbor_(same) {
+      if( neighbor->visitid == samevisitid )
+        {
+        continue;
+        }
+      if( neighbor->simplicial )
+        {
+        if( neighbor->visitid != qh visit_id )
+          {
+          qh_setappend(&newfacet->neighbors, neighbor);
+          qh_setreplace(neighbor->neighbors, same, newfacet);
+          newneighbors++;
+          neighbor->visitid = qh visit_id;
+          FOREACHridge_(neighbor->ridges) { /* update ridge in case of
+                                              qh_makeridges */
+            if( ridge->top == same )
+              {
+              ridge->top = newfacet;
+              break;
+              }
+            else if( ridge->bottom == same )
+              {
+              ridge->bottom = newfacet;
+              break;
+              }
+            }
+          }
+        else
+          {
+          qh_makeridges(neighbor);
+          qh_setdel(neighbor->neighbors, same);
+          /* same can't be horizon facet for neighbor */
+          }
+        }
+      else    /* non-simplicial neighbor */
+        {
+        qh_setdel(neighbor->neighbors, same);
+        if( neighbor->visitid != qh visit_id )
+          {
+          qh_setappend(&neighbor->neighbors, newfacet);
+          qh_setappend(&newfacet->neighbors, neighbor);
+          neighbor->visitid = qh visit_id;
+          newneighbors++;
+          }
+        }
+      }
+    }
+  trace2( (qh ferr, "qh_mergecycle_neighbors: deleted %d neighbors and added %d\n",
+           delneighbors, newneighbors) );
+} /* mergecycle_neighbors */
+
+/*---------------------------------
+
+  qh_mergecycle_ridges( samecycle, newfacet )
+  add ridges/neighbors for facets in samecycle to newfacet
+  all new/old neighbors of newfacet marked with qh.visit_id
+  facets in samecycle marked with qh.visit_id-1
+  newfacet marked with qh.visit_id
+
+  returns:
+  newfacet has merged ridges
+
+  notes:
+  ridge already updated for simplicial neighbors of samecycle with a ridge
+
+  see:
+  qh_mergeridges()
+  qh_makeridges()
+
+  design:
+  remove ridges between newfacet and samecycle
+  for each facet in samecycle
+  for each ridge in facet
+  update facet pointers in ridge
+  skip ridges processed in qh_mergecycle_neighors
+  free ridges between newfacet and samecycle
+  free ridges between facets of samecycle (on 2nd visit)
+  append remaining ridges to newfacet
+  if simpilicial facet
+  for each neighbor of facet
+  if simplicial facet
+  and not samecycle facet or newfacet
+  make ridge between neighbor and newfacet
+*/
+void qh_mergecycle_ridges(facetT *samecycle, facetT *newfacet)
+{
+  facetT *     same, *neighbor = NULL;
+  int          numold = 0, numnew = 0;
+  int          neighbor_i, neighbor_n;
+  unsigned int samevisitid;
+  ridgeT *     ridge, * *ridgep;
+  boolT        toporient;
+  void * *     freelistp; /* used !qh_NOmem */
+
+  trace4( (qh ferr, "qh_mergecycle_ridges: delete shared ridges from newfacet\n") );
+  samevisitid = qh visit_id - 1;
+  FOREACHridge_(newfacet->ridges) {
+    neighbor = otherfacet_(ridge, newfacet);
+    if( neighbor->visitid == samevisitid )
+      {
+      SETref_(ridge) = NULL; /* ridge free'd below */
+      }
+    }
+  qh_setcompact(newfacet->ridges);
+
+  trace4( (qh ferr, "qh_mergecycle_ridges: add ridges to newfacet\n") );
+  FORALLsame_cycle_(samecycle) {
+    FOREACHridge_(same->ridges) {
+      if( ridge->top == same )
+        {
+        ridge->top = newfacet;
+        neighbor = ridge->bottom;
+        }
+      else if( ridge->bottom == same )
+        {
+        ridge->bottom = newfacet;
+        neighbor = ridge->top;
+        }
+      else if( ridge->top == newfacet || ridge->bottom == newfacet )
+        {
+        qh_setappend(&newfacet->ridges, ridge);
+        numold++;  /* already set by qh_mergecycle_neighbors */
+        continue;
+        }
+      else
+        {
+        fprintf(qh ferr, "qhull internal error (qh_mergecycle_ridges): bad ridge r%d\n", ridge->id);
+        qh_errexit(qh_ERRqhull, NULL, ridge);
+        }
+      if( neighbor == newfacet )
+        {
+        qh_setfree(&(ridge->vertices) );
+        qh_memfree_(ridge, sizeof(ridgeT), freelistp);
+        numold++;
+        }
+      else if( neighbor->visitid == samevisitid )
+        {
+        qh_setdel(neighbor->ridges, ridge);
+        qh_setfree(&(ridge->vertices) );
+        qh_memfree_(ridge, sizeof(ridgeT), freelistp);
+        numold++;
+        }
+      else
+        {
+        qh_setappend(&newfacet->ridges, ridge);
+        numold++;
+        }
+      }
+    if( same->ridges )
+      {
+      qh_settruncate(same->ridges, (size_t)0);
+      }
+    if( !same->simplicial )
+      {
+      continue;
+      }
+    FOREACHneighbor_i_(same) {       /* note: !newfact->simplicial */
+      if( neighbor->visitid != samevisitid && neighbor->simplicial )
+        {
+        ridge = qh_newridge();
+        ridge->vertices = qh_setnew_delnthsorted(same->vertices, qh hull_dim,
+                                                 (size_t)neighbor_i, (size_t)0);
+        toporient = same->toporient ^ (neighbor_i & 0x1);
+        if( toporient )
+          {
+          ridge->top = newfacet;
+          ridge->bottom = neighbor;
+          }
+        else
+          {
+          ridge->top = neighbor;
+          ridge->bottom = newfacet;
+          }
+        qh_setappend(&(newfacet->ridges), ridge);
+        qh_setappend(&(neighbor->ridges), ridge);
+        numnew++;
+        }
+      }
+    }
+
+  trace2( (qh ferr, "qh_mergecycle_ridges: found %d old ridges and %d new ones\n",
+           numold, numnew) );
+} /* mergecycle_ridges */
+
+/*---------------------------------
+
+  qh_mergecycle_vneighbors( samecycle, newfacet )
+  create vertex neighbors for newfacet from vertices of facets in samecycle
+  samecycle marked with visitid == qh.visit_id - 1
+
+  returns:
+  newfacet vertices with updated neighbors
+  marks newfacet with qh.visit_id-1
+  deletes vertices that are merged away
+  sets delridge on all vertices (faster here than in mergecycle_ridges)
+
+  see:
+  qh_mergevertex_neighbors()
+
+  design:
+  for each vertex of samecycle facet
+  set vertex->delridge
+  delete samecycle facets from vertex neighbors
+  append newfacet to vertex neighbors
+  if vertex only in newfacet
+  delete it from newfacet
+  add it to qh.del_vertices for later deletion
+*/
+void qh_mergecycle_vneighbors(facetT *samecycle, facetT *newfacet)
+{
+  facetT *     neighbor, * *neighborp;
+  unsigned int mergeid;
+  vertexT *    vertex, * *vertexp, *apex;
+  setT *       vertices;
+
+  trace4( (qh ferr, "qh_mergecycle_vneighbors: update vertex neighbors for newfacet\n") );
+  mergeid = qh visit_id - 1;
+  newfacet->visitid = mergeid;
+  vertices = qh_basevertices(samecycle); /* temp */
+  apex = SETfirstt_(samecycle->vertices, vertexT);
+  qh_setappend(&vertices, apex);
+  FOREACHvertex_(vertices) {
+    vertex->delridge = True;
+    FOREACHneighbor_(vertex) {
+      if( neighbor->visitid == mergeid )
+        {
+        SETref_(neighbor) = NULL;
+        }
+      }
+    qh_setcompact(vertex->neighbors);
+    qh_setappend(&vertex->neighbors, newfacet);
+    if( !SETsecond_(vertex->neighbors) )
+      {
+      zinc_(Zcyclevertex);
+      trace2( (qh ferr, "qh_mergecycle_vneighbors: deleted v%d when merging cycle f%d into f%d\n",
+               vertex->id, samecycle->id, newfacet->id) );
+      qh_setdelsorted(newfacet->vertices, vertex);
+      vertex->deleted = True;
+      qh_setappend(&qh del_vertices, vertex);
+      }
+    }
+  qh_settempfree(&vertices);
+  trace3( (qh ferr, "qh_mergecycle_vneighbors: merged vertices from cycle f%d into f%d\n",
+           samecycle->id, newfacet->id) );
+} /* mergecycle_vneighbors */
+
+/*---------------------------------
+
+  qh_mergefacet( facet1, facet2, mindist, maxdist, mergeapex )
+  merges facet1 into facet2
+  mergeapex==qh_MERGEapex if merging new facet into coplanar horizon
+
+  returns:
+  qh.max_outside and qh.min_vertex updated
+  initializes vertex neighbors on first merge
+
+  returns:
+  facet2 contains facet1's vertices, neighbors, and ridges
+  facet2 moved to end of qh.facet_list
+  makes facet2 a newfacet
+  sets facet2->newmerge set
+  clears facet2->center (unless merging into a large facet)
+  clears facet2->tested and ridge->tested for facet1
+
+  facet1 prepended to visible_list for later deletion and partitioning
+  facet1->f.replace == facet2
+
+  adds neighboring facets to facet_mergeset if redundant or degenerate
+
+  notes:
+  mindist/maxdist may be NULL
+  traces merge if fmax_(maxdist,-mindist) > TRACEdist
+
+  see:
+  qh_mergecycle()
+
+  design:
+  trace merge and check for degenerate simplex
+  make ridges for both facets
+  update qh.max_outside, qh.max_vertex, qh.min_vertex
+  update facet2->maxoutside and keepcentrum
+  update facet2->nummerge
+  update tested flags for facet2
+  if facet1 is simplicial
+  merge facet1 into facet2
+  else
+  merge facet1's neighbors into facet2
+  merge facet1's ridges into facet2
+  merge facet1's vertices into facet2
+  merge facet1's vertex neighbors into facet2
+  add facet2's vertices to qh.new_vertexlist
+  unless qh_MERGEapex
+  test facet2 for degenerate or redundant neighbors
+  move facet1 to qh.visible_list for later deletion
+  move facet2 to end of qh.newfacet_list
+*/
+void qh_mergefacet(facetT *facet1, facetT *facet2, realT *mindist, realT *maxdist, boolT mergeapex)
+{
+  boolT    traceonce = False;
+  vertexT *vertex, * *vertexp;
+  int      tracerestore = 0, nummerge;
+
+  if( facet1->tricoplanar || facet2->tricoplanar )
+    {
+    if( !qh TRInormals )
+      {
+      fprintf(qh ferr, "qh_mergefacet: does not work for tricoplanar facets.  Use option 'Q11'\n");
+      qh_errexit2(qh_ERRqhull, facet1, facet2);
+      }
+    if( facet2->tricoplanar )
+      {
+      facet2->tricoplanar = False;
+      facet2->keepcentrum = False;
+      }
+    }
+  zzinc_(Ztotmerge);
+  if( qh REPORTfreq2 && qh POSTmerging )
+    {
+    if( zzval_(Ztotmerge) > qh mergereport + qh REPORTfreq2 )
+      {
+      qh_tracemerging();
+      }
+    }
+#ifndef qh_NOtrace
+  if( qh build_cnt >= qh RERUN )
+    {
+    if( mindist && (-*mindist > qh TRACEdist || *maxdist > qh TRACEdist) )
+      {
+      tracerestore = 0;
+      qh IStracing = qh TRACElevel;
+      traceonce = True;
+      fprintf(qh ferr, "qh_mergefacet: ========= trace wide merge #%d (%2.2g) for f%d into f%d, last point was p%d\n",
+              zzval_(
+                Ztotmerge),
+              fmax_(-*mindist, *maxdist), facet1->id, facet2->id, qh furthest_id);
+      }
+    else if( facet1 == qh tracefacet || facet2 == qh tracefacet )
+      {
+      tracerestore = qh IStracing;
+      qh IStracing = 4;
+      traceonce = True;
+      fprintf(qh ferr, "qh_mergefacet: ========= trace merge #%d involving f%d, furthest is p%d\n",
+              zzval_(Ztotmerge), qh tracefacet_id,  qh furthest_id);
+      }
+    }
+  if( qh IStracing >= 2 )
+    {
+    realT mergemin = -2;
+    realT mergemax = -2;
+
+    if( mindist )
+      {
+      mergemin = *mindist;
+      mergemax = *maxdist;
+      }
+    fprintf(qh ferr, "qh_mergefacet: #%d merge f%d into f%d, mindist= %2.2g, maxdist= %2.2g\n",
+            zzval_(Ztotmerge), facet1->id, facet2->id, mergemin, mergemax);
+    }
+#endif /* !qh_NOtrace */
+  if( facet1 == facet2 || facet1->visible || facet2->visible )
+    {
+    fprintf(qh ferr,
+            "qhull internal error (qh_mergefacet): either f%d and f%d are the same or one is a visible facet\n",
+            facet1->id,
+            facet2->id);
+    qh_errexit2(qh_ERRqhull, facet1, facet2);
+    }
+  if( qh num_facets - qh num_visible <= qh hull_dim + 1 )
+    {
+    fprintf(
+      qh ferr,
+      "\n\
+qhull precision error: Only %d facets remain.  Can not merge another\n\
+pair.  The input is too degenerate or the convexity constraints are\n\
+too strong.\n"                                                                                                                                                          ,
+      qh hull_dim + 1);
+    if( qh hull_dim >= 5 && !qh MERGEexact )
+      {
+      fprintf(qh ferr, "Option 'Qx' may avoid this problem.\n");
+      }
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( !qh VERTEXneighbors )
+    {
+    qh_vertexneighbors();
+    }
+  qh_makeridges(facet1);
+  qh_makeridges(facet2);
+  if( qh IStracing >= 4 )
+    {
+    qh_errprint("MERGING", facet1, facet2, NULL, NULL);
+    }
+  if( mindist )
+    {
+    maximize_(qh max_outside, *maxdist);
+    maximize_(qh max_vertex, *maxdist);
+#if qh_MAXoutside
+    maximize_(facet2->maxoutside, *maxdist);
+#endif
+    minimize_(qh min_vertex, *mindist);
+    if( !facet2->keepcentrum
+        && (*maxdist > qh WIDEfacet || *mindist < -qh WIDEfacet) )
+      {
+      facet2->keepcentrum = True;
+      zinc_(Zwidefacet);
+      }
+    }
+  nummerge = facet1->nummerge + facet2->nummerge + 1;
+  if( nummerge >= qh_MAXnummerge )
+    {
+    facet2->nummerge = qh_MAXnummerge;
+    }
+  else
+    {
+    facet2->nummerge = nummerge;
+    }
+  facet2->newmerge = True;
+  facet2->dupridge = False;
+  qh_updatetested(facet1, facet2);
+  if( qh hull_dim > 2 && qh_setsize(facet1->vertices) == qh hull_dim )
+    {
+    qh_mergesimplex(facet1, facet2, mergeapex);
+    }
+  else
+    {
+    qh vertex_visit++;
+    FOREACHvertex_(facet2->vertices)
+    vertex->visitid = qh vertex_visit;
+    if( qh hull_dim == 2 )
+      {
+      qh_mergefacet2d(facet1, facet2);
+      }
+    else
+      {
+      qh_mergeneighbors(facet1, facet2);
+      qh_mergevertices(facet1->vertices, &facet2->vertices);
+      }
+    qh_mergeridges(facet1, facet2);
+    qh_mergevertex_neighbors(facet1, facet2);
+    if( !facet2->newfacet )
+      {
+      qh_newvertices(facet2->vertices);
+      }
+    }
+  if( !mergeapex )
+    {
+    qh_degen_redundant_neighbors(facet2, facet1);
+    }
+  if( facet2->coplanar || !facet2->newfacet )
+    {
+    zinc_(Zmergeintohorizon);
+    }
+  else if( !facet1->newfacet && facet2->newfacet )
+    {
+    zinc_(Zmergehorizon);
+    }
+  else
+    {
+    zinc_(Zmergenew);
+    }
+  qh_willdelete(facet1, facet2);
+  qh_removefacet(facet2);  /* append as a newfacet to end of qh facet_list */
+  qh_appendfacet(facet2);
+  facet2->newfacet = True;
+  facet2->tested = False;
+  qh_tracemerge(facet1, facet2);
+  if( traceonce )
+    {
+    fprintf(qh ferr, "qh_mergefacet: end of wide tracing\n");
+    qh IStracing = tracerestore;
+    }
+} /* mergefacet */
+
+/*---------------------------------
+
+  qh_mergefacet2d( facet1, facet2 )
+  in 2d, merges neighbors and vertices of facet1 into facet2
+
+  returns:
+  build ridges for neighbors if necessary
+  facet2 looks like a simplicial facet except for centrum, ridges
+  neighbors are opposite the corresponding vertex
+  maintains orientation of facet2
+
+  notes:
+  qh_mergefacet() retains non-simplicial structures
+  they are not needed in 2d, but later routines may use them
+  preserves qh.vertex_visit for qh_mergevertex_neighbors()
+
+  design:
+  get vertices and neighbors
+  determine new vertices and neighbors
+  set new vertices and neighbors and adjust orientation
+  make ridges for new neighbor if needed
+*/
+void qh_mergefacet2d(facetT *facet1, facetT *facet2)
+{
+  vertexT *vertex1A, *vertex1B, *vertex2A, *vertex2B, *vertexA, *vertexB;
+  facetT * neighbor1A, *neighbor1B, *neighbor2A, *neighbor2B, *neighborA, *neighborB;
+
+  vertex1A = SETfirstt_(facet1->vertices, vertexT);
+  vertex1B = SETsecondt_(facet1->vertices, vertexT);
+  vertex2A = SETfirstt_(facet2->vertices, vertexT);
+  vertex2B = SETsecondt_(facet2->vertices, vertexT);
+  neighbor1A = SETfirstt_(facet1->neighbors, facetT);
+  neighbor1B = SETsecondt_(facet1->neighbors, facetT);
+  neighbor2A = SETfirstt_(facet2->neighbors, facetT);
+  neighbor2B = SETsecondt_(facet2->neighbors, facetT);
+  if( vertex1A == vertex2A )
+    {
+    vertexA = vertex1B;
+    vertexB = vertex2B;
+    neighborA = neighbor2A;
+    neighborB = neighbor1A;
+    }
+  else if( vertex1A == vertex2B )
+    {
+    vertexA = vertex1B;
+    vertexB = vertex2A;
+    neighborA = neighbor2B;
+    neighborB = neighbor1A;
+    }
+  else if( vertex1B == vertex2A )
+    {
+    vertexA = vertex1A;
+    vertexB = vertex2B;
+    neighborA = neighbor2A;
+    neighborB = neighbor1B;
+    }
+  else    /* 1B == 2B */
+    {
+    vertexA = vertex1A;
+    vertexB = vertex2A;
+    neighborA = neighbor2B;
+    neighborB = neighbor1B;
+    }
+  /* vertexB always from facet2, neighborB always from facet1 */
+  if( vertexA->id > vertexB->id )
+    {
+    SETfirst_(facet2->vertices) = vertexA;
+    SETsecond_(facet2->vertices) = vertexB;
+    if( vertexB == vertex2A )
+      {
+      facet2->toporient = !facet2->toporient;
+      }
+    SETfirst_(facet2->neighbors) = neighborA;
+    SETsecond_(facet2->neighbors) = neighborB;
+    }
+  else
+    {
+    SETfirst_(facet2->vertices) = vertexB;
+    SETsecond_(facet2->vertices) = vertexA;
+    if( vertexB == vertex2B )
+      {
+      facet2->toporient = !facet2->toporient;
+      }
+    SETfirst_(facet2->neighbors) = neighborB;
+    SETsecond_(facet2->neighbors) = neighborA;
+    }
+  qh_makeridges(neighborB);
+  qh_setreplace(neighborB->neighbors, facet1, facet2);
+  trace4( (qh ferr, "qh_mergefacet2d: merged v%d and neighbor f%d of f%d into f%d\n",
+           vertexA->id, neighborB->id, facet1->id, facet2->id) );
+} /* mergefacet2d */
+
+/*---------------------------------
+
+  qh_mergeneighbors( facet1, facet2 )
+  merges the neighbors of facet1 into facet2
+
+  see:
+  qh_mergecycle_neighbors()
+
+  design:
+  for each neighbor of facet1
+  if neighbor is also a neighbor of facet2
+  if neighbor is simpilicial
+  make ridges for later deletion as a degenerate facet
+  update its neighbor set
+  else
+  move the neighbor relation to facet2
+  remove the neighbor relation for facet1 and facet2
+*/
+void qh_mergeneighbors(facetT *facet1, facetT *facet2)
+{
+  facetT *neighbor, * *neighborp;
+
+  trace4( (qh ferr, "qh_mergeneighbors: merge neighbors of f%d and f%d\n",
+           facet1->id, facet2->id) );
+  qh visit_id++;
+  FOREACHneighbor_(facet2) {
+    neighbor->visitid = qh visit_id;
+    }
+  FOREACHneighbor_(facet1) {
+    if( neighbor->visitid == qh visit_id )
+      {
+      if( neighbor->simplicial )    /* is degen, needs ridges */
+        {
+        qh_makeridges(neighbor);
+        }
+      if( SETfirstt_(neighbor->neighbors, facetT) != facet1 ) /*keep
+                                                                newfacet->horizon*/
+        {
+        qh_setdel(neighbor->neighbors, facet1);
+        }
+      else
+        {
+        qh_setdel(neighbor->neighbors, facet2);
+        qh_setreplace(neighbor->neighbors, facet1, facet2);
+        }
+      }
+    else if( neighbor != facet2 )
+      {
+      qh_setappend(&(facet2->neighbors), neighbor);
+      qh_setreplace(neighbor->neighbors, facet1, facet2);
+      }
+    }
+  qh_setdel(facet1->neighbors, facet2);  /* here for makeridges */
+  qh_setdel(facet2->neighbors, facet1);
+} /* mergeneighbors */
+
+/*---------------------------------
+
+  qh_mergeridges( facet1, facet2 )
+  merges the ridge set of facet1 into facet2
+
+  returns:
+  may delete all ridges for a vertex
+  sets vertex->delridge on deleted ridges
+
+  see:
+  qh_mergecycle_ridges()
+
+  design:
+  delete ridges between facet1 and facet2
+  mark (delridge) vertices on these ridges for later testing
+  for each remaining ridge
+  rename facet1 to facet2
+*/
+void qh_mergeridges(facetT *facet1, facetT *facet2)
+{
+  ridgeT * ridge, * *ridgep;
+  vertexT *vertex, * *vertexp;
+
+  trace4( (qh ferr, "qh_mergeridges: merge ridges of f%d and f%d\n",
+           facet1->id, facet2->id) );
+  FOREACHridge_(facet2->ridges) {
+    if( (ridge->top == facet1) || (ridge->bottom == facet1) )
+      {
+      FOREACHvertex_(ridge->vertices)
+      vertex->delridge = True;
+      qh_delridge(ridge); /* expensive in high-d, could rebuild */
+      ridgep--;           /*repeat*/
+      }
+    }
+  FOREACHridge_(facet1->ridges) {
+    if( ridge->top == facet1 )
+      {
+      ridge->top = facet2;
+      }
+    else
+      {
+      ridge->bottom = facet2;
+      }
+    qh_setappend(&(facet2->ridges), ridge);
+    }
+} /* mergeridges */
+
+/*---------------------------------
+
+  qh_mergesimplex( facet1, facet2, mergeapex )
+  merge simplicial facet1 into facet2
+  mergeapex==qh_MERGEapex if merging samecycle into horizon facet
+  vertex id is latest (most recently created)
+  facet1 may be contained in facet2
+  ridges exist for both facets
+
+  returns:
+  facet2 with updated vertices, ridges, neighbors
+  updated neighbors for facet1's vertices
+  facet1 not deleted
+  sets vertex->delridge on deleted ridges
+
+  notes:
+  special case code since this is the most common merge
+  called from qh_mergefacet()
+
+  design:
+  if qh_MERGEapex
+  add vertices of facet2 to qh.new_vertexlist if necessary
+  add apex to facet2
+  else
+  for each ridge between facet1 and facet2
+  set vertex->delridge
+  determine the apex for facet1 (i.e., vertex to be merged)
+  unless apex already in facet2
+  insert apex into vertices for facet2
+  add vertices of facet2 to qh.new_vertexlist if necessary
+  add apex to qh.new_vertexlist if necessary
+  for each vertex of facet1
+  if apex
+  rename facet1 to facet2 in its vertex neighbors
+  else
+  delete facet1 from vertex neighors
+  if only in facet2
+  add vertex to qh.del_vertices for later deletion
+  for each ridge of facet1
+  delete ridges between facet1 and facet2
+  append other ridges to facet2 after renaming facet to facet2
+*/
+void qh_mergesimplex(facetT *facet1, facetT *facet2, boolT mergeapex)
+{
+  vertexT *vertex, * *vertexp, *apex;
+  ridgeT * ridge, * *ridgep;
+  boolT    issubset = False;
+  int      vertex_i = -1, vertex_n;
+  facetT * neighbor, * *neighborp, *otherfacet;
+
+  if( mergeapex )
+    {
+    if( !facet2->newfacet )
+      {
+      qh_newvertices(facet2->vertices);   /* apex is new */
+      }
+    apex = SETfirstt_(facet1->vertices, vertexT);
+    if( SETfirstt_(facet2->vertices, vertexT) != apex )
+      {
+      qh_setaddnth(&facet2->vertices, 0, apex);   /* apex has last id */
+      }
+    else
+      {
+      issubset = True;
+      }
+    }
+  else
+    {
+    zinc_(Zmergesimplex);
+    FOREACHvertex_(facet1->vertices)
+    vertex->seen = False;
+    FOREACHridge_(facet1->ridges) {
+      if( otherfacet_(ridge, facet1) == facet2 )
+        {
+        FOREACHvertex_(ridge->vertices) {
+          vertex->seen = True;
+          vertex->delridge = True;
+          }
+        break;
+        }
+      }
+    FOREACHvertex_(facet1->vertices) {
+      if( !vertex->seen )
+        {
+        break; /* must occur */
+        }
+      }
+    apex = vertex;
+    trace4( (qh ferr, "qh_mergesimplex: merge apex v%d of f%d into facet f%d\n",
+             apex->id, facet1->id, facet2->id) );
+    FOREACHvertex_i_(facet2->vertices) {
+      if( vertex->id < apex->id )
+        {
+        break;
+        }
+      else if( vertex->id == apex->id )
+        {
+        issubset = True;
+        break;
+        }
+      }
+    if( !issubset )
+      {
+      qh_setaddnth(&facet2->vertices, vertex_i, apex);
+      }
+    if( !facet2->newfacet )
+      {
+      qh_newvertices(facet2->vertices);
+      }
+    else if( !apex->newlist )
+      {
+      qh_removevertex(apex);
+      qh_appendvertex(apex);
+      }
+    }
+  trace4( (qh ferr, "qh_mergesimplex: update vertex neighbors of f%d\n",
+           facet1->id) );
+  FOREACHvertex_(facet1->vertices) {
+    if( vertex == apex && !issubset )
+      {
+      qh_setreplace(vertex->neighbors, facet1, facet2);
+      }
+    else
+      {
+      qh_setdel(vertex->neighbors, facet1);
+      if( !SETsecond_(vertex->neighbors) )
+        {
+        qh_mergevertex_del(vertex, facet1, facet2);
+        }
+      }
+    }
+  trace4( (qh ferr, "qh_mergesimplex: merge ridges and neighbors of f%d into f%d\n",
+           facet1->id, facet2->id) );
+  qh visit_id++;
+  FOREACHneighbor_(facet2)
+  neighbor->visitid = qh visit_id;
+  FOREACHridge_(facet1->ridges) {
+    otherfacet = otherfacet_(ridge, facet1);
+    if( otherfacet == facet2 )
+      {
+      qh_setdel(facet2->ridges, ridge);
+      qh_setfree(&(ridge->vertices) );
+      qh_memfree(ridge, sizeof(ridgeT) );
+      qh_setdel(facet2->neighbors, facet1);
+      }
+    else
+      {
+      qh_setappend(&facet2->ridges, ridge);
+      if( otherfacet->visitid != qh visit_id )
+        {
+        qh_setappend(&facet2->neighbors, otherfacet);
+        qh_setreplace(otherfacet->neighbors, facet1, facet2);
+        otherfacet->visitid = qh visit_id;
+        }
+      else
+        {
+        if( otherfacet->simplicial ) /* is degen, needs ridges */
+          {
+          qh_makeridges(otherfacet);
+          }
+        if( SETfirstt_(otherfacet->neighbors, facetT) != facet1 )
+          {
+          qh_setdel(otherfacet->neighbors, facet1);
+          }
+        else /*keep newfacet->neighbors->horizon*/
+          {
+          qh_setdel(otherfacet->neighbors, facet2);
+          qh_setreplace(otherfacet->neighbors, facet1, facet2);
+          }
+        }
+      if( ridge->top == facet1 ) /* wait until after qh_makeridges */
+        {
+        ridge->top = facet2;
+        }
+      else
+        {
+        ridge->bottom = facet2;
+        }
+      }
+    }
+  SETfirst_(facet1->ridges) = NULL; /* it will be deleted */
+  trace3( (qh ferr, "qh_mergesimplex: merged simplex f%d apex v%d into facet f%d\n",
+           facet1->id, getid_(apex), facet2->id) );
+} /* mergesimplex */
+
+/*---------------------------------
+
+  qh_mergevertex_del( vertex, facet1, facet2 )
+  delete a vertex because of merging facet1 into facet2
+
+  returns:
+  deletes vertex from facet2
+  adds vertex to qh.del_vertices for later deletion
+*/
+void qh_mergevertex_del(vertexT *vertex, facetT *facet1, facetT *facet2)
+{
+
+  zinc_(Zmergevertex);
+  trace2( (qh ferr, "qh_mergevertex_del: deleted v%d when merging f%d into f%d\n",
+           vertex->id, facet1->id, facet2->id) );
+  qh_setdelsorted(facet2->vertices, vertex);
+  vertex->deleted = True;
+  qh_setappend(&qh del_vertices, vertex);
+} /* mergevertex_del */
+
+/*---------------------------------
+
+  qh_mergevertex_neighbors( facet1, facet2 )
+  merge the vertex neighbors of facet1 to facet2
+
+  returns:
+  if vertex is current qh.vertex_visit
+  deletes facet1 from vertex->neighbors
+  else
+  renames facet1 to facet2 in vertex->neighbors
+  deletes vertices if only one neighbor
+
+  notes:
+  assumes vertex neighbor sets are good
+*/
+void qh_mergevertex_neighbors(facetT *facet1, facetT *facet2)
+{
+  vertexT *vertex, * *vertexp;
+
+  trace4( (qh ferr, "qh_mergevertex_neighbors: merge vertex neighbors of f%d and f%d\n",
+           facet1->id, facet2->id) );
+  if( qh tracevertex )
+    {
+    fprintf(qh ferr, "qh_mergevertex_neighbors: of f%d and f%d at furthest p%d f0= %p\n",
+            facet1->id, facet2->id, qh furthest_id, qh tracevertex->neighbors->e[0].p);
+    qh_errprint("TRACE", NULL, NULL, NULL, qh tracevertex);
+    }
+  FOREACHvertex_(facet1->vertices) {
+    if( vertex->visitid != qh vertex_visit )
+      {
+      qh_setreplace(vertex->neighbors, facet1, facet2);
+      }
+    else
+      {
+      qh_setdel(vertex->neighbors, facet1);
+      if( !SETsecond_(vertex->neighbors) )
+        {
+        qh_mergevertex_del(vertex, facet1, facet2);
+        }
+      }
+    }
+  if( qh tracevertex )
+    {
+    qh_errprint("TRACE", NULL, NULL, NULL, qh tracevertex);
+    }
+} /* mergevertex_neighbors */
+
+/*---------------------------------
+
+  qh_mergevertices( vertices1, vertices2 )
+  merges the vertex set of facet1 into facet2
+
+  returns:
+  replaces vertices2 with merged set
+  preserves vertex_visit for qh_mergevertex_neighbors
+  updates qh.newvertex_list
+
+  design:
+  create a merged set of both vertices (in inverse id order)
+*/
+void qh_mergevertices(setT *vertices1, setT * *vertices2)
+{
+  int      newsize = qh_setsize(vertices1) + qh_setsize(*vertices2) - qh hull_dim + 1;
+  setT *   mergedvertices;
+  vertexT *vertex, * *vertexp, * *vertex2 = SETaddr_(*vertices2, vertexT);
+
+  mergedvertices = qh_settemp(newsize);
+  FOREACHvertex_(vertices1) {
+    if( !*vertex2 || vertex->id > (*vertex2)->id )
+      {
+      qh_setappend(&mergedvertices, vertex);
+      }
+    else
+      {
+      while( *vertex2 && (*vertex2)->id > vertex->id )
+        {
+        qh_setappend(&mergedvertices, *vertex2++);
+        }
+
+      if( !*vertex2 || (*vertex2)->id < vertex->id )
+        {
+        qh_setappend(&mergedvertices, vertex);
+        }
+      else
+        {
+        qh_setappend(&mergedvertices, *vertex2++);
+        }
+      }
+    }
+  while( *vertex2 )
+    {
+    qh_setappend(&mergedvertices, *vertex2++);
+    }
+
+  if( newsize < qh_setsize(mergedvertices) )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_mergevertices): facets did not share a ridge\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  qh_setfree(vertices2);
+  *vertices2 = mergedvertices;
+  qh_settemppop();
+} /* mergevertices */
+
+/*---------------------------------
+
+  qh_neighbor_intersections( vertex )
+  return intersection of all vertices in vertex->neighbors except for vertex
+
+  returns:
+  returns temporary set of vertices
+  does not include vertex
+  NULL if a neighbor is simplicial
+  NULL if empty set
+
+  notes:
+  used for renaming vertices
+
+  design:
+  initialize the intersection set with vertices of the first two neighbors
+  delete vertex from the intersection
+  for each remaining neighbor
+  intersect its vertex set with the intersection set
+  return NULL if empty
+  return the intersection set
+*/
+setT * qh_neighbor_intersections(vertexT *vertex)
+{
+  facetT *neighbor, * *neighborp, *neighborA, *neighborB;
+  setT *  intersect;
+  int     neighbor_i, neighbor_n;
+
+  FOREACHneighbor_(vertex) {
+    if( neighbor->simplicial )
+      {
+      return NULL;
+      }
+    }
+  neighborA = SETfirstt_(vertex->neighbors, facetT);
+  neighborB = SETsecondt_(vertex->neighbors, facetT);
+  zinc_(Zintersectnum);
+  if( !neighborA )
+    {
+    return NULL;
+    }
+  if( !neighborB )
+    {
+    intersect = qh_setcopy(neighborA->vertices, 0);
+    }
+  else
+    {
+    intersect = qh_vertexintersect_new(neighborA->vertices, neighborB->vertices);
+    }
+  qh_settemppush(intersect);
+  qh_setdelsorted(intersect, vertex);
+  FOREACHneighbor_i_(vertex) {
+    if( neighbor_i >= 2 )
+      {
+      zinc_(Zintersectnum);
+      qh_vertexintersect(&intersect, neighbor->vertices);
+      if( !SETfirst_(intersect) )
+        {
+        zinc_(Zintersectfail);
+        qh_settempfree(&intersect);
+        return NULL;
+        }
+      }
+    }
+  trace3( (qh ferr, "qh_neighbor_intersections: %d vertices in neighbor intersection of v%d\n",
+           qh_setsize(intersect), vertex->id) );
+  return intersect;
+} /* neighbor_intersections */
+
+/*---------------------------------
+
+  qh_newvertices( vertices )
+  add vertices to end of qh.vertex_list (marks as new vertices)
+
+  returns:
+  vertices on qh.newvertex_list
+  vertex->newlist set
+*/
+void qh_newvertices(setT *vertices)
+{
+  vertexT *vertex, * *vertexp;
+
+  FOREACHvertex_(vertices) {
+    if( !vertex->newlist )
+      {
+      qh_removevertex(vertex);
+      qh_appendvertex(vertex);
+      }
+    }
+} /* newvertices */
+
+/*---------------------------------
+
+  qh_reducevertices()
+  reduce extra vertices, shared vertices, and redundant vertices
+  facet->newmerge is set if merged since last call
+  if !qh.MERGEvertices, only removes extra vertices
+
+  returns:
+  True if also merged degen_redundant facets
+  vertices are renamed if possible
+  clears facet->newmerge and vertex->delridge
+
+  notes:
+  ignored if 2-d
+
+  design:
+  merge any degenerate or redundant facets
+  for each newly merged facet
+  remove extra vertices
+  if qh.MERGEvertices
+  for each newly merged facet
+  for each vertex
+  if vertex was on a deleted ridge
+  rename vertex if it is shared
+  remove delridge flag from new vertices
+*/
+boolT qh_reducevertices(void)
+{
+  int      numshare = 0, numrename = 0;
+  boolT    degenredun = False;
+  facetT * newfacet;
+  vertexT *vertex, * *vertexp;
+
+  if( qh hull_dim == 2 )
+    {
+    return False;
+    }
+  if( qh_merge_degenredundant() )
+    {
+    degenredun = True;
+    }
+LABELrestart:
+  FORALLnew_facets {
+    if( newfacet->newmerge )
+      {
+      if( !qh MERGEvertices )
+        {
+        newfacet->newmerge = False;
+        }
+      qh_remove_extravertices(newfacet);
+      }
+    }
+  if( !qh MERGEvertices )
+    {
+    return False;
+    }
+  FORALLnew_facets {
+    if( newfacet->newmerge )
+      {
+      newfacet->newmerge = False;
+      FOREACHvertex_(newfacet->vertices) {
+        if( vertex->delridge )
+          {
+          if( qh_rename_sharedvertex(vertex, newfacet) )
+            {
+            numshare++;
+            vertexp--; /* repeat since deleted vertex */
+            }
+          }
+        }
+      }
+    }
+  FORALLvertex_(qh newvertex_list) {
+    if( vertex->delridge && !vertex->deleted )
+      {
+      vertex->delridge = False;
+      if( qh hull_dim >= 4 && qh_redundant_vertex(vertex) )
+        {
+        numrename++;
+        if( qh_merge_degenredundant() )
+          {
+          degenredun = True;
+          goto LABELrestart;
+          }
+        }
+      }
+    }
+  trace1( (qh ferr, "qh_reducevertices: renamed %d shared vertices and %d redundant vertices. Degen? %d\n",
+           numshare, numrename, degenredun) );
+  return degenredun;
+} /* reducevertices */
+
+/*---------------------------------
+
+  qh_redundant_vertex( vertex )
+  detect and rename a redundant vertex
+  vertices have full vertex->neighbors
+
+  returns:
+  returns true if find a redundant vertex
+  deletes vertex (vertex->deleted)
+
+  notes:
+  only needed if vertex->delridge and hull_dim >= 4
+  may add degenerate facets to qh.facet_mergeset
+  doesn't change vertex->neighbors or create redundant facets
+
+  design:
+  intersect vertices of all facet neighbors of vertex
+  determine ridges for these vertices
+  if find a new vertex for vertex amoung these ridges and vertices
+  rename vertex to the new vertex
+*/
+vertexT * qh_redundant_vertex(vertexT *vertex)
+{
+  vertexT *newvertex = NULL;
+  setT *   vertices, *ridges;
+
+  trace3( (qh ferr, "qh_redundant_vertex: check if v%d can be renamed\n", vertex->id) );
+  if( (vertices = qh_neighbor_intersections(vertex) ) )
+    {
+    ridges = qh_vertexridges(vertex);
+    if( (newvertex = qh_find_newvertex(vertex, vertices, ridges) ) )
+      {
+      qh_renamevertex(vertex, newvertex, ridges, NULL, NULL);
+      }
+    qh_settempfree(&ridges);
+    qh_settempfree(&vertices);
+    }
+  return newvertex;
+} /* redundant_vertex */
+
+/*---------------------------------
+
+  qh_remove_extravertices( facet )
+  remove extra vertices from non-simplicial facets
+
+  returns:
+  returns True if it finds them
+
+  design:
+  for each vertex in facet
+  if vertex not in a ridge (i.e., no longer used)
+  delete vertex from facet
+  delete facet from vertice's neighbors
+  unless vertex in another facet
+  add vertex to qh.del_vertices for later deletion
+*/
+boolT qh_remove_extravertices(facetT *facet)
+{
+  ridgeT * ridge, * *ridgep;
+  vertexT *vertex, * *vertexp;
+  boolT    foundrem = False;
+
+  trace4( (qh ferr, "qh_remove_extravertices: test f%d for extra vertices\n",
+           facet->id) );
+  FOREACHvertex_(facet->vertices)
+  vertex->seen = False;
+  FOREACHridge_(facet->ridges) {
+    FOREACHvertex_(ridge->vertices)
+    vertex->seen = True;
+    }
+  FOREACHvertex_(facet->vertices) {
+    if( !vertex->seen )
+      {
+      foundrem = True;
+      zinc_(Zremvertex);
+      qh_setdelsorted(facet->vertices, vertex);
+      qh_setdel(vertex->neighbors, facet);
+      if( !qh_setsize(vertex->neighbors) )
+        {
+        vertex->deleted = True;
+        qh_setappend(&qh del_vertices, vertex);
+        zinc_(Zremvertexdel);
+        trace2( (qh ferr, "qh_remove_extravertices: v%d deleted because it's lost all ridges\n", vertex->id) );
+        }
+      else
+        {
+        trace3( (qh ferr, "qh_remove_extravertices: v%d removed from f%d because it's lost all ridges\n", vertex->id,
+                 facet->id) );
+        }
+      vertexp--; /*repeat*/
+      }
+    }
+  return foundrem;
+} /* remove_extravertices */
+
+/*---------------------------------
+
+  qh_rename_sharedvertex( vertex, facet )
+  detect and rename if shared vertex in facet
+  vertices have full ->neighbors
+
+  returns:
+  newvertex or NULL
+  the vertex may still exist in other facets (i.e., a neighbor was pinched)
+  does not change facet->neighbors
+  updates vertex->neighbors
+
+  notes:
+  a shared vertex for a facet is only in ridges to one neighbor
+  this may undo a pinched facet
+
+  it does not catch pinches involving multiple facets.  These appear
+  to be difficult to detect, since an exhaustive search is too expensive.
+
+  design:
+  if vertex only has two neighbors
+  determine the ridges that contain the vertex
+  determine the vertices shared by both neighbors
+  if can find a new vertex in this set
+  rename the vertex to the new vertex
+*/
+vertexT * qh_rename_sharedvertex(vertexT *vertex, facetT *facet)
+{
+  facetT * neighbor, * *neighborp, *neighborA = NULL;
+  setT *   vertices, *ridges;
+  vertexT *newvertex;
+
+  if( qh_setsize(vertex->neighbors) == 2 )
+    {
+    neighborA = SETfirstt_(vertex->neighbors, facetT);
+    if( neighborA == facet )
+      {
+      neighborA = SETsecondt_(vertex->neighbors, facetT);
+      }
+    }
+  else if( qh hull_dim == 3 )
+    {
+    return NULL;
+    }
+  else
+    {
+    qh visit_id++;
+    FOREACHneighbor_(facet)
+    neighbor->visitid = qh visit_id;
+    FOREACHneighbor_(vertex) {
+      if( neighbor->visitid == qh visit_id )
+        {
+        if( neighborA )
+          {
+          return NULL;
+          }
+        neighborA = neighbor;
+        }
+      }
+    if( !neighborA )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_rename_sharedvertex): v%d's neighbors not in f%d\n",
+              vertex->id, facet->id);
+      qh_errprint("ERRONEOUS", facet, NULL, NULL, vertex);
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    }
+  /* the vertex is shared by facet and neighborA */
+  ridges = qh_settemp(qh TEMPsize);
+  neighborA->visitid = ++qh visit_id;
+  qh_vertexridges_facet(vertex, facet, &ridges);
+  trace2( (qh ferr, "qh_rename_sharedvertex: p%d (v%d) is shared by f%d (%d ridges) and f%d\n",
+           qh_pointid(vertex->point), vertex->id, facet->id, qh_setsize(ridges), neighborA->id) );
+  zinc_(Zintersectnum);
+  vertices = qh_vertexintersect_new(facet->vertices, neighborA->vertices);
+  qh_setdel(vertices, vertex);
+  qh_settemppush(vertices);
+  if( (newvertex = qh_find_newvertex(vertex, vertices, ridges) ) )
+    {
+    qh_renamevertex(vertex, newvertex, ridges, facet, neighborA);
+    }
+  qh_settempfree(&vertices);
+  qh_settempfree(&ridges);
+  return newvertex;
+} /* rename_sharedvertex */
+
+/*---------------------------------
+
+  qh_renameridgevertex( ridge, oldvertex, newvertex )
+  renames oldvertex as newvertex in ridge
+
+  returns:
+
+  design:
+  delete oldvertex from ridge
+  if newvertex already in ridge
+  copy ridge->noconvex to another ridge if possible
+  delete the ridge
+  else
+  insert newvertex into the ridge
+  adjust the ridge's orientation
+*/
+void qh_renameridgevertex(ridgeT *ridge, vertexT *oldvertex, vertexT *newvertex)
+{
+  int      nth = 0, oldnth;
+  facetT * temp;
+  vertexT *vertex, * *vertexp;
+
+  oldnth = qh_setindex(ridge->vertices, oldvertex);
+  qh_setdelnthsorted(ridge->vertices, (size_t)oldnth);
+  FOREACHvertex_(ridge->vertices) {
+    if( vertex == newvertex )
+      {
+      zinc_(Zdelridge);
+      if( ridge->nonconvex ) /* only one ridge has nonconvex set */
+        {
+        qh_copynonconvex(ridge);
+        }
+      qh_delridge(ridge);
+      trace2( (qh ferr, "qh_renameridgevertex: ridge r%d deleted.  It contained both v%d and v%d\n",
+               ridge->id, oldvertex->id, newvertex->id) );
+      return;
+      }
+    if( vertex->id < newvertex->id )
+      {
+      break;
+      }
+    nth++;
+    }
+  qh_setaddnth(&ridge->vertices, nth, newvertex);
+  if( abs(oldnth - nth) % 2 )
+    {
+    trace3( (qh ferr, "qh_renameridgevertex: swapped the top and bottom of ridge r%d\n",
+             ridge->id) );
+    temp = ridge->top;
+    ridge->top = ridge->bottom;
+    ridge->bottom = temp;
+    }
+} /* renameridgevertex */
+
+/*---------------------------------
+
+  qh_renamevertex( oldvertex, newvertex, ridges, oldfacet, neighborA )
+  renames oldvertex as newvertex in ridges
+  gives oldfacet/neighborA if oldvertex is shared between two facets
+
+  returns:
+  oldvertex may still exist afterwards
+
+
+  notes:
+  can not change neighbors of newvertex (since it's a subset)
+
+  design:
+  for each ridge in ridges
+  rename oldvertex to newvertex and delete degenerate ridges
+  if oldfacet not defined
+  for each neighbor of oldvertex
+  delete oldvertex from neighbor's vertices
+  remove extra vertices from neighbor
+  add oldvertex to qh.del_vertices
+  else if oldvertex only between oldfacet and neighborA
+  delete oldvertex from oldfacet and neighborA
+  add oldvertex to qh.del_vertices
+  else oldvertex is in oldfacet and neighborA and other facets (i.e., pinched)
+  delete oldvertex from oldfacet
+  delete oldfacet from oldvertice's neighbors
+  remove extra vertices (e.g., oldvertex) from neighborA
+*/
+void qh_renamevertex(vertexT *oldvertex, vertexT *newvertex, setT *ridges, facetT *oldfacet, facetT *neighborA)
+{
+  facetT *neighbor, * *neighborp;
+  ridgeT *ridge, * *ridgep;
+  boolT   istrace = False;
+
+  if( qh IStracing >= 2 || oldvertex->id == qh tracevertex_id ||
+      newvertex->id == qh tracevertex_id )
+    {
+    istrace = True;
+    }
+  FOREACHridge_(ridges)
+  qh_renameridgevertex(ridge, oldvertex, newvertex);
+  if( !oldfacet )
+    {
+    zinc_(Zrenameall);
+    if( istrace )
+      {
+      fprintf(qh ferr, "qh_renamevertex: renamed v%d to v%d in several facets\n",
+              oldvertex->id, newvertex->id);
+      }
+    FOREACHneighbor_(oldvertex) {
+      qh_maydropneighbor(neighbor);
+      qh_setdelsorted(neighbor->vertices, oldvertex);
+      if( qh_remove_extravertices(neighbor) )
+        {
+        neighborp--; /* neighbor may be deleted */
+        }
+      }
+    if( !oldvertex->deleted )
+      {
+      oldvertex->deleted = True;
+      qh_setappend(&qh del_vertices, oldvertex);
+      }
+    }
+  else if( qh_setsize(oldvertex->neighbors) == 2 )
+    {
+    zinc_(Zrenameshare);
+    if( istrace )
+      {
+      fprintf(qh ferr, "qh_renamevertex: renamed v%d to v%d in oldfacet f%d\n",
+              oldvertex->id, newvertex->id, oldfacet->id);
+      }
+    FOREACHneighbor_(oldvertex)
+    qh_setdelsorted(neighbor->vertices, oldvertex);
+    oldvertex->deleted = True;
+    qh_setappend(&qh del_vertices, oldvertex);
+    }
+  else
+    {
+    zinc_(Zrenamepinch);
+    if( istrace || qh IStracing )
+      {
+      fprintf(qh ferr, "qh_renamevertex: renamed pinched v%d to v%d between f%d and f%d\n",
+              oldvertex->id, newvertex->id, oldfacet->id, neighborA->id);
+      }
+    qh_setdelsorted(oldfacet->vertices, oldvertex);
+    qh_setdel(oldvertex->neighbors, oldfacet);
+    qh_remove_extravertices(neighborA);
+    }
+} /* renamevertex */
+
+/*---------------------------------
+
+  qh_test_appendmerge( facet, neighbor )
+  tests facet/neighbor for convexity
+  appends to mergeset if non-convex
+  if pre-merging,
+  nop if qh.SKIPconvex, or qh.MERGEexact and coplanar
+
+  returns:
+  true if appends facet/neighbor to mergeset
+  sets facet->center as needed
+  does not change facet->seen
+
+  design:
+  if qh.cos_max is defined
+  if the angle between facet normals is too shallow
+  append an angle-coplanar merge to qh.mergeset
+  return True
+  make facet's centrum if needed
+  if facet's centrum is above the neighbor
+  set isconcave
+  else
+  if facet's centrum is not below the neighbor
+  set iscoplanar
+  make neighbor's centrum if needed
+  if neighbor's centrum is above the facet
+  set isconcave
+  else if neighbor's centrum is not below the facet
+  set iscoplanar
+  if isconcave or iscoplanar
+  get angle if needed
+  append concave or coplanar merge to qh.mergeset
+*/
+boolT qh_test_appendmerge(facetT *facet, facetT *neighbor)
+{
+  realT dist, dist2 = -REALmax, angle = -REALmax;
+  boolT isconcave = False, iscoplanar = False, okangle = False;
+
+  if( qh SKIPconvex && !qh POSTmerging )
+    {
+    return False;
+    }
+  if( (!qh MERGEexact || qh POSTmerging) && qh cos_max < REALmax / 2 )
+    {
+    angle = qh_getangle(facet->normal, neighbor->normal);
+    zinc_(Zangletests);
+    if( angle > qh cos_max )
+      {
+      zinc_(Zcoplanarangle);
+      qh_appendmergeset(facet, neighbor, MRGanglecoplanar, &angle);
+      trace2( (qh ferr, "qh_test_appendmerge: coplanar angle %4.4g between f%d and f%d\n",
+               angle, facet->id, neighbor->id) );
+      return True;
+      }
+    else
+      {
+      okangle = True;
+      }
+    }
+  if( !facet->center )
+    {
+    facet->center = qh_getcentrum(facet);
+    }
+  zzinc_(Zcentrumtests);
+  qh_distplane(facet->center, neighbor, &dist);
+  if( dist > qh centrum_radius )
+    {
+    isconcave = True;
+    }
+  else
+    {
+    if( dist > -qh centrum_radius )
+      {
+      iscoplanar = True;
+      }
+    if( !neighbor->center )
+      {
+      neighbor->center = qh_getcentrum(neighbor);
+      }
+    zzinc_(Zcentrumtests);
+    qh_distplane(neighbor->center, facet, &dist2);
+    if( dist2 > qh centrum_radius )
+      {
+      isconcave = True;
+      }
+    else if( !iscoplanar && dist2 > -qh centrum_radius )
+      {
+      iscoplanar = True;
+      }
+    }
+  if( !isconcave && (!iscoplanar || (qh MERGEexact && !qh POSTmerging) ) )
+    {
+    return False;
+    }
+  if( !okangle && qh ANGLEmerge )
+    {
+    angle = qh_getangle(facet->normal, neighbor->normal);
+    zinc_(Zangletests);
+    }
+  if( isconcave )
+    {
+    zinc_(Zconcaveridge);
+    if( qh ANGLEmerge )
+      {
+      angle += qh_ANGLEconcave + 0.5;
+      }
+    qh_appendmergeset(facet, neighbor, MRGconcave, &angle);
+    trace0( (qh ferr,
+             "qh_test_appendmerge: concave f%d to f%d dist %4.4g and reverse dist %4.4g angle %4.4g during p%d\n",
+             facet->id, neighbor->id, dist, dist2, angle, qh furthest_id) );
+    }
+  else  /* iscoplanar */
+    {
+    zinc_(Zcoplanarcentrum);
+    qh_appendmergeset(facet, neighbor, MRGcoplanar, &angle);
+    trace2( (qh ferr, "qh_test_appendmerge: coplanar f%d to f%d dist %4.4g, reverse dist %4.4g angle %4.4g\n",
+             facet->id, neighbor->id, dist, dist2, angle) );
+    }
+  return True;
+} /* test_appendmerge */
+
+/*---------------------------------
+
+  qh_test_vneighbors()
+  test vertex neighbors for convexity
+  tests all facets on qh.newfacet_list
+
+  returns:
+  true if non-convex vneighbors appended to qh.facet_mergeset
+  initializes vertex neighbors if needed
+
+  notes:
+  assumes all facet neighbors have been tested
+  this can be expensive
+  this does not guarantee that a centrum is below all facets
+  but it is unlikely
+  uses qh.visit_id
+
+  design:
+  build vertex neighbors if necessary
+  for all new facets
+  for all vertices
+  for each unvisited facet neighbor of the vertex
+  test new facet and neighbor for convexity
+*/
+boolT qh_test_vneighbors(void /* qh newfacet_list */)
+{
+  facetT * newfacet, *neighbor, * *neighborp;
+  vertexT *vertex, * *vertexp;
+  int      nummerges = 0;
+
+  trace1( (qh ferr, "qh_test_vneighbors: testing vertex neighbors for convexity\n") );
+  if( !qh VERTEXneighbors )
+    {
+    qh_vertexneighbors();
+    }
+  FORALLnew_facets
+  newfacet-> seen = False;
+  FORALLnew_facets {
+    newfacet->seen = True;
+    newfacet->visitid = qh visit_id++;
+    FOREACHneighbor_(newfacet)
+    newfacet->visitid = qh visit_id;
+    FOREACHvertex_(newfacet->vertices) {
+      FOREACHneighbor_(vertex) {
+        if( neighbor->seen || neighbor->visitid == qh visit_id )
+          {
+          continue;
+          }
+        if( qh_test_appendmerge(newfacet, neighbor) )
+          {
+          nummerges++;
+          }
+        }
+      }
+    }
+  zadd_(Ztestvneighbor, nummerges);
+  trace1( (qh ferr, "qh_test_vneighbors: found %d non-convex, vertex neighbors\n",
+           nummerges) );
+  return nummerges > 0;
+} /* test_vneighbors */
+
+/*---------------------------------
+
+  qh_tracemerge( facet1, facet2 )
+  print trace message after merge
+*/
+void qh_tracemerge(facetT *facet1, facetT *facet2)
+{
+  boolT waserror = False;
+
+#ifndef qh_NOtrace
+  if( qh IStracing >= 4 )
+    {
+    qh_errprint("MERGED", facet2, NULL, NULL, NULL);
+    }
+  if( facet2 == qh tracefacet || (qh tracevertex && qh tracevertex->newlist) )
+    {
+    fprintf(qh ferr, "qh_tracemerge: trace facet and vertex after merge of f%d and f%d, furthest p%d\n", facet1->id,
+            facet2->id,
+            qh furthest_id);
+    if( facet2 != qh tracefacet )
+      {
+      qh_errprint("TRACE", qh tracefacet,
+                  (qh tracevertex && qh tracevertex->neighbors) ?
+                  SETfirstt_(qh tracevertex->neighbors, facetT) : NULL,
+                  NULL, qh tracevertex);
+      }
+    }
+  if( qh tracevertex )
+    {
+    if( qh tracevertex->deleted )
+      {
+      fprintf(qh ferr, "qh_tracemerge: trace vertex deleted at furthest p%d\n",
+              qh furthest_id);
+      }
+    else
+      {
+      qh_checkvertex(qh tracevertex);
+      }
+    }
+  if( qh tracefacet )
+    {
+    qh_checkfacet(qh tracefacet, True, &waserror);
+    if( waserror )
+      {
+      qh_errexit(qh_ERRqhull, qh tracefacet, NULL);
+      }
+    }
+#endif /* !qh_NOtrace */
+  if( qh CHECKfrequently || qh IStracing >= 4 )   /* can't check polygon here */
+    {
+    qh_checkfacet(facet2, True, &waserror);
+    if( waserror )
+      {
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    }
+} /* tracemerge */
+
+/*---------------------------------
+
+  qh_tracemerging()
+  print trace message during POSTmerging
+
+  returns:
+  updates qh.mergereport
+
+  notes:
+  called from qh_mergecycle() and qh_mergefacet()
+
+  see:
+  qh_buildtracing()
+*/
+void qh_tracemerging(void)
+{
+  realT      cpu;
+  int        total;
+  time_t     timedata;
+  struct tm *tp;
+
+  qh mergereport = zzval_(Ztotmerge);
+
+  time(&timedata);
+  tp = localtime(&timedata);
+  cpu = qh_CPUclock;
+  cpu /= qh_SECticks;
+  total = zzval_(Ztotmerge) - zzval_(Zcyclehorizon) + zzval_(Zcyclefacettot);
+  fprintf(
+    qh ferr,
+    "\n\
+At %d:%d:%d & %2.5g CPU secs, qhull has merged %d facets.  The hull\n\
+  contains %d facets and %d vertices.\n"                                                                                ,
+    tp->tm_hour, tp->tm_min, tp->tm_sec, cpu,
+    total, qh num_facets - qh num_visible,
+    qh num_vertices - qh_setsize(
+      qh del_vertices) );
+} /* tracemerging */
+
+/*---------------------------------
+
+  qh_updatetested( facet1, facet2 )
+  clear facet2->tested and facet1->ridge->tested for merge
+
+  returns:
+  deletes facet2->center unless it's already large
+  if so, clears facet2->ridge->tested
+
+  design:
+  clear facet2->tested
+  clear ridge->tested for facet1's ridges
+  if facet2 has a centrum
+  if facet2 is large
+  set facet2->keepcentrum
+  else if facet2 has 3 vertices due to many merges, or not large and post merging
+  clear facet2->keepcentrum
+  unless facet2->keepcentrum
+  clear facet2->center to recompute centrum later
+  clear ridge->tested for facet2's ridges
+*/
+void qh_updatetested(facetT *facet1, facetT *facet2)
+{
+  ridgeT *ridge, * *ridgep;
+  int     size;
+
+  facet2->tested = False;
+  FOREACHridge_(facet1->ridges)
+  ridge->tested = False;
+  if( !facet2->center )
+    {
+    return;
+    }
+  size = qh_setsize(facet2->vertices);
+  if( !facet2->keepcentrum )
+    {
+    if( size > qh hull_dim + qh_MAXnewcentrum )
+      {
+      facet2->keepcentrum = True;
+      zinc_(Zwidevertices);
+      }
+    }
+  else if( size <= qh hull_dim + qh_MAXnewcentrum )
+    {
+    /* center and keepcentrum was set */
+    if( size == qh hull_dim || qh POSTmerging )
+      {
+      facet2->keepcentrum = False; /* if many merges need to recompute centrum
+                                     */
+      }
+    }
+  if( !facet2->keepcentrum )
+    {
+    qh_memfree(facet2->center, qh normal_size);
+    facet2->center = NULL;
+    FOREACHridge_(facet2->ridges)
+    ridge->tested = False;
+    }
+} /* updatetested */
+
+/*---------------------------------
+
+  qh_vertexridges( vertex )
+  return temporary set of ridges adjacent to a vertex
+  vertex->neighbors defined
+
+  ntoes:
+  uses qh.visit_id
+  does not include implicit ridges for simplicial facets
+
+  design:
+  for each neighbor of vertex
+  add ridges that include the vertex to ridges
+*/
+setT * qh_vertexridges(vertexT *vertex)
+{
+  facetT *neighbor, * *neighborp;
+  setT *  ridges = qh_settemp(qh TEMPsize);
+  int     size;
+
+  qh visit_id++;
+
+  FOREACHneighbor_(vertex)
+  neighbor->visitid = qh visit_id;
+  FOREACHneighbor_(vertex) {
+    if( *neighborp )   /* no new ridges in last neighbor */
+      {
+      qh_vertexridges_facet(vertex, neighbor, &ridges);
+      }
+    }
+  if( qh PRINTstatistics || qh IStracing )
+    {
+    size = qh_setsize(ridges);
+    zinc_(Zvertexridge);
+    zadd_(Zvertexridgetot, size);
+    zmax_(Zvertexridgemax, size);
+    trace3( (qh ferr, "qh_vertexridges: found %d ridges for v%d\n",
+             size, vertex->id) );
+    }
+  return ridges;
+} /* vertexridges */
+
+/*---------------------------------
+
+  qh_vertexridges_facet( vertex, facet, ridges )
+  add adjacent ridges for vertex in facet
+  neighbor->visitid==qh.visit_id if it hasn't been visited
+
+  returns:
+  ridges updated
+  sets facet->visitid to qh.visit_id-1
+
+  design:
+  for each ridge of facet
+  if ridge of visited neighbor (i.e., unprocessed)
+  if vertex in ridge
+  append ridge to vertex
+  mark facet processed
+*/
+void qh_vertexridges_facet(vertexT *vertex, facetT *facet, setT * *ridges)
+{
+  ridgeT *ridge, * *ridgep;
+  facetT *neighbor;
+
+  FOREACHridge_(facet->ridges) {
+    neighbor = otherfacet_(ridge, facet);
+    if( neighbor->visitid == qh visit_id
+        && qh_setin(ridge->vertices, vertex) )
+      {
+      qh_setappend(ridges, ridge);
+      }
+    }
+  facet->visitid = qh visit_id - 1;
+} /* vertexridges_facet */
+
+/*---------------------------------
+
+  qh_willdelete( facet, replace )
+  moves facet to visible list
+  sets facet->f.replace to replace (may be NULL)
+
+  returns:
+  bumps qh.num_visible
+*/
+void qh_willdelete(facetT *facet, facetT *replace)
+{
+
+  qh_removefacet(facet);
+  qh_prependfacet(facet, &qh visible_list);
+  qh num_visible++;
+  facet->visible = True;
+  facet->f.replace = replace;
+} /* willdelete */
+
+#else /* qh_NOmerge */
+void qh_premerge(vertexT *apex, realT maxcentrum, realT maxangle)
+{
+}
+
+void qh_postmerge(const char *reason, realT maxcentrum, realT maxangle,
+                  boolT vneighbors)
+{
+}
+
+boolT qh_checkzero(boolT testall)
+{
+}
+
+#endif /* qh_NOmerge */
+
diff --git a/BRAINSABC/qhull/merge.h b/BRAINSABC/qhull/merge.h
new file mode 100644
index 00000000..e2310a79
--- /dev/null
+++ b/BRAINSABC/qhull/merge.h
@@ -0,0 +1,300 @@
+/*
  ---------------------------------
+
+   merge.h
+   header file for merge.c
+
+   see qh-merge.htm and merge.c
+
+   copyright (c) 1993-2003, The Geometry Center
+*/
+
+#ifndef qhDEFmerge
+#define qhDEFmerge 1
+
+/*============ -constants- ==============*/
+
+/*----------------------------------
+
+  qh_ANGLEredundant
+    indicates redundant merge in mergeT->angle
+*/
+#define qh_ANGLEredundant 6.0
+
+/*----------------------------------
+
+  qh_ANGLEdegen
+    indicates degenerate facet in mergeT->angle
+*/
+#define qh_ANGLEdegen     5.0
+
+/*----------------------------------
+
+  qh_ANGLEconcave
+    offset to indicate concave facets in mergeT->angle
+
+  notes:
+    concave facets are assigned the range of [2,4] in mergeT->angle
+    roundoff error may make the angle less than 2
+*/
+#define qh_ANGLEconcave  1.5
+
+/*----------------------------------
+
+  MRG... (mergeType)
+    indicates the type of a merge (mergeT->type)
+*/
+typedef enum    /* in sort order for facet_mergeset */
+                                                             { MRGnone = 0,
+                                                             MRGcoplanar,      /*
+                                                                                 centrum
+                                                                                 coplanar
+                                                                                 */
+                                                             MRGanglecoplanar, /*
+                                                                                 angle
+                                                                                 coplanar
+                                                                                 */
+                                                                               /*
+                                                                                 could
+                                                                                 detect
+                                                                                 half
+                                                                                 concave
+                                                                                 ridges
+                                                                                 */
+                                                             MRGconcave,       /*
+                                                                                 concave
+                                                                                 ridge
+                                                                                 */
+                                                             MRGflip,          /*
+                                                                                 flipped
+                                                                                 facet.
+                                                                                 facet1
+                                                                                 ==
+                                                                                 facet2
+                                                                                 */
+                                                             MRGridge,         /*
+                                                                                 duplicate
+                                                                                 ridge
+                                                                                 (qh_MERGEridge)
+                                                                                 */
+                                                                               /*
+                                                                                 degen
+                                                                                 and
+                                                                                 redundant
+                                                                                 go
+                                                                                 onto
+                                                                                 degen_mergeset
+                                                                                 */
+                                                             MRGdegen,         /*
+                                                                                 degenerate
+                                                                                 facet
+                                                                                 (not
+                                                                                 enough
+                                                                                 neighbors)
+                                                                                 facet1
+                                                                                 ==
+                                                                                 facet2
+                                                                                 */
+                                                             MRGredundant,     /*
+                                                                                 redundant
+                                                                                 facet
+                                                                                 (vertex
+                                                                                 subset)
+                                                                                 */
+                                                                               /*
+                                                                                 merge_degenredundant
+                                                                                 assumes
+                                                                                 degen
+                                                                                 <
+                                                                                 redundant
+                                                                                 */
+                                                             MRGmirror,        /*
+                                                                                 mirror
+                                                                                 facet
+                                                                                 from
+                                                                                 qh_triangulate
+                                                                                 */
+                                                             ENDmrg } mergeType;
+
+/*----------------------------------
+
+  qh_MERGEapex
+    flag for qh_mergefacet() to indicate an apex merge
+*/
+#define qh_MERGEapex     True
+
+/*============ -structures- ====================*/
+
+/*----------------------------------
+
+  mergeT
+    structure used to merge facets
+*/
+
+typedef struct mergeT mergeT;
+struct mergeT                                                                 /*
+                                                                                initialize
+                                                                                in
+                                                                                qh_appendmergeset
+                                                                                */
+                                                              { realT angle;  /*
+                                                                                angle
+                                                                                between
+                                                                                normals
+                                                                                of
+                                                                                facet1
+                                                                                and
+                                                                                facet2
+                                                                                */
+                                                              facetT *facet1; /*
+                                                                                will
+                                                                                merge
+                                                                                facet1
+                                                                                into
+                                                                                facet2
+                                                                                */
+                                                              facetT *facet2;
+                                                              mergeType type; };
+
+/*=========== -macros- =========================*/
+
+/*----------------------------------
+
+  FOREACHmerge_( merges ) {...}
+    assign 'merge' to each merge in merges
+
+  notes:
+    uses 'mergeT *merge, **mergep;'
+    if qh_mergefacet(),
+      restart since qh.facet_mergeset may change
+    see FOREACHsetelement_
+*/
+#define FOREACHmerge_( merges ) FOREACHsetelement_(mergeT, merges, merge)
+
+/*============ prototypes in alphabetical order after pre/postmerge =======*/
+
+void    qh_premerge(vertexT *apex, realT maxcentrum, realT maxangle);
+
+void    qh_postmerge(const char *reason, realT maxcentrum, realT maxangle, boolT vneighbors);
+
+void    qh_all_merges(boolT othermerge, boolT vneighbors);
+
+void    qh_appendmergeset(facetT *facet, facetT *neighbor, mergeType mergetype, realT *angle);
+
+setT   * qh_basevertices( facetT *samecycle);
+
+void    qh_checkconnect(void /* qh new_facets */);
+
+boolT   qh_checkzero(boolT testall);
+
+int     qh_compareangle(const void *p1, const void *p2);
+
+int     qh_comparemerge(const void *p1, const void *p2);
+
+int     qh_comparevisit(const void *p1, const void *p2);
+
+void    qh_copynonconvex(ridgeT *atridge);
+
+void    qh_degen_redundant_facet(facetT *facet);
+
+void    qh_degen_redundant_neighbors(facetT *facet, facetT *delfacet);
+
+vertexT * qh_find_newvertex(vertexT *oldvertex, setT *vertices, setT *ridges);
+
+void    qh_findbest_test(boolT testcentrum, facetT *facet, facetT *neighbor, facetT * *bestfacet, realT *distp,
+                         realT *mindistp,
+                         realT *maxdistp);
+
+facetT * qh_findbestneighbor(facetT *facet, realT *distp, realT *mindistp, realT *maxdistp);
+
+void  qh_flippedmerges(facetT *facetlist, boolT *wasmerge);
+
+void  qh_forcedmerges( boolT *wasmerge);
+
+void  qh_getmergeset(facetT *facetlist);
+
+void  qh_getmergeset_initial(facetT *facetlist);
+
+void    qh_hashridge(setT *hashtable, int hashsize, ridgeT *ridge, vertexT *oldvertex);
+
+ridgeT * qh_hashridge_find(setT *hashtable, int hashsize, ridgeT *ridge, vertexT *vertex, vertexT *oldvertex,
+                           int *hashslot);
+
+void  qh_makeridges(facetT *facet);
+
+void    qh_mark_dupridges(facetT *facetlist);
+
+void    qh_maydropneighbor(facetT *facet);
+
+int     qh_merge_degenredundant(void);
+
+void    qh_merge_nonconvex( facetT *facet1, facetT *facet2, mergeType mergetype);
+
+void    qh_mergecycle(facetT *samecycle, facetT *newfacet);
+
+void    qh_mergecycle_all(facetT *facetlist, boolT *wasmerge);
+
+void    qh_mergecycle_facets( facetT *samecycle, facetT *newfacet);
+
+void    qh_mergecycle_neighbors(facetT *samecycle, facetT *newfacet);
+
+void    qh_mergecycle_ridges(facetT *samecycle, facetT *newfacet);
+
+void    qh_mergecycle_vneighbors( facetT *samecycle, facetT *newfacet);
+
+void  qh_mergefacet(facetT *facet1, facetT *facet2, realT *mindist, realT *maxdist, boolT mergeapex);
+
+void    qh_mergefacet2d(facetT *facet1, facetT *facet2);
+
+void  qh_mergeneighbors(facetT *facet1, facetT *facet2);
+
+void  qh_mergeridges(facetT *facet1, facetT *facet2);
+
+void    qh_mergesimplex(facetT *facet1, facetT *facet2, boolT mergeapex);
+
+void    qh_mergevertex_del(vertexT *vertex, facetT *facet1, facetT *facet2);
+
+void    qh_mergevertex_neighbors(facetT *facet1, facetT *facet2);
+
+void  qh_mergevertices(setT *vertices1, setT * *vertices);
+
+setT   * qh_neighbor_intersections(vertexT *vertex);
+
+void    qh_newvertices(setT *vertices);
+
+boolT   qh_reducevertices(void);
+
+vertexT * qh_redundant_vertex(vertexT *vertex);
+
+boolT   qh_remove_extravertices(facetT *facet);
+
+vertexT * qh_rename_sharedvertex(vertexT *vertex, facetT *facet);
+
+void  qh_renameridgevertex(ridgeT *ridge, vertexT *oldvertex, vertexT *newvertex);
+
+void    qh_renamevertex(vertexT *oldvertex, vertexT *newvertex, setT *ridges, facetT *oldfacet, facetT *neighborA);
+
+boolT   qh_test_appendmerge(facetT *facet, facetT *neighbor);
+
+boolT   qh_test_vneighbors(void /* qh newfacet_list */);
+
+void    qh_tracemerge(facetT *facet1, facetT *facet2);
+
+void    qh_tracemerging(void);
+
+void    qh_updatetested( facetT *facet1, facetT *facet2);
+
+setT   * qh_vertexridges(vertexT *vertex);
+
+void    qh_vertexridges_facet(vertexT *vertex, facetT *facet, setT * *ridges);
+
+void    qh_willdelete(facetT *facet, facetT *replace);
+
+#endif /* qhDEFmerge */
diff --git a/BRAINSABC/qhull/poly.c b/BRAINSABC/qhull/poly.c
new file mode 100644
index 00000000..0e3dc61b
--- /dev/null
+++ b/BRAINSABC/qhull/poly.c
@@ -0,0 +1,1431 @@
+/*
  ---------------------------------
+
+  poly.c
+  implements polygons and simplices
+
+  see qh-poly.htm, poly.h and qhull.h
+
+  infrequent code is in poly2.c
+  (all but top 50 and their callers 12/3/95)
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*======== functions in alphabetical order ==========*/
+
+/*---------------------------------
+
+  qh_appendfacet( facet )
+  appends facet to end of qh.facet_list,
+
+  returns:
+  updates qh.newfacet_list, facet_next, facet_list
+  increments qh.numfacets
+
+  notes:
+  assumes qh.facet_list/facet_tail is defined (createsimplex)
+
+  see:
+  qh_removefacet()
+
+*/
+void qh_appendfacet(facetT *facet)
+{
+  facetT *tail = qh facet_tail;
+
+  if( tail == qh newfacet_list )
+    {
+    qh newfacet_list = facet;
+    }
+  if( tail == qh facet_next )
+    {
+    qh facet_next = facet;
+    }
+  facet->previous = tail->previous;
+  facet->next = tail;
+  if( tail->previous )
+    {
+    tail->previous->next = facet;
+    }
+  else
+    {
+    qh facet_list = facet;
+    }
+  tail->previous = facet;
+  qh num_facets++;
+  trace4( (qh ferr, "qh_appendfacet: append f%d to facet_list\n", facet->id) );
+} /* appendfacet */
+
+/*---------------------------------
+
+  qh_appendvertex( vertex )
+  appends vertex to end of qh.vertex_list,
+
+  returns:
+  sets vertex->newlist
+  updates qh.vertex_list, newvertex_list
+  increments qh.num_vertices
+
+  notes:
+  assumes qh.vertex_list/vertex_tail is defined (createsimplex)
+
+*/
+void qh_appendvertex(vertexT *vertex)
+{
+  vertexT *tail = qh vertex_tail;
+
+  if( tail == qh newvertex_list )
+    {
+    qh newvertex_list = vertex;
+    }
+  vertex->newlist = True;
+  vertex->previous = tail->previous;
+  vertex->next = tail;
+  if( tail->previous )
+    {
+    tail->previous->next = vertex;
+    }
+  else
+    {
+    qh vertex_list = vertex;
+    }
+  tail->previous = vertex;
+  qh num_vertices++;
+  trace4( (qh ferr, "qh_appendvertex: append v%d to vertex_list\n", vertex->id) );
+} /* appendvertex */
+
+/*---------------------------------
+
+  qh_attachnewfacets( )
+  attach horizon facets to new facets in qh.newfacet_list
+  newfacets have neighbor and ridge links to horizon but not vice versa
+  only needed for qh.ONLYgood
+
+  returns:
+  set qh.NEWfacets
+  horizon facets linked to new facets
+  ridges changed from visible facets to new facets
+  simplicial ridges deleted
+  qh.visible_list, no ridges valid
+  facet->f.replace is a newfacet (if any)
+
+  design:
+  delete interior ridges and neighbor sets by
+  for each visible, non-simplicial facet
+  for each ridge
+  if last visit or if neighbor is simplicial
+  if horizon neighbor
+  delete ridge for horizon's ridge set
+  delete ridge
+  erase neighbor set
+  attach horizon facets and new facets by
+  for all new facets
+  if corresponding horizon facet is simplicial
+  locate corresponding visible facet {may be more than one}
+  link visible facet to new facet
+  replace visible facet with new facet in horizon
+  else it's non-simplicial
+  for all visible neighbors of the horizon facet
+  link visible neighbor to new facet
+  delete visible neighbor from horizon facet
+  append new facet to horizon's neighbors
+  the first ridge of the new facet is the horizon ridge
+  link the new facet into the horizon ridge
+*/
+void qh_attachnewfacets(void )
+{
+  facetT *newfacet = NULL, *neighbor, * *neighborp, *horizon, *visible;
+  ridgeT *ridge, * *ridgep;
+
+  qh NEWfacets = True;
+
+  trace3( (qh ferr, "qh_attachnewfacets: delete interior ridges\n") );
+  qh visit_id++;
+  FORALLvisible_facets {
+    visible->visitid = qh visit_id;
+    if( visible->ridges )
+      {
+      FOREACHridge_(visible->ridges) {
+        neighbor = otherfacet_(ridge, visible);
+        if( neighbor->visitid == qh visit_id
+            || (!neighbor->visible && neighbor->simplicial) )
+          {
+          if( !neighbor->visible ) /* delete ridge for simplicial horizon */
+            {
+            qh_setdel(neighbor->ridges, ridge);
+            }
+          qh_setfree(&(ridge->vertices) ); /* delete on 2nd visit */
+          qh_memfree(ridge, sizeof(ridgeT) );
+          }
+        }
+      SETfirst_(visible->ridges) = NULL;
+      }
+    SETfirst_(visible->neighbors) = NULL;
+    }
+  trace1( (qh ferr, "qh_attachnewfacets: attach horizon facets to new facets\n") );
+  FORALLnew_facets {
+    horizon = SETfirstt_(newfacet->neighbors, facetT);
+    if( horizon->simplicial )
+      {
+      visible = NULL;
+      FOREACHneighbor_(horizon) {   /* may have more than one horizon ridge */
+        if( neighbor->visible )
+          {
+          if( visible )
+            {
+            if( qh_setequal_skip(newfacet->vertices, 0, horizon->vertices,
+                                 (int)SETindex_(horizon->neighbors, neighbor) ) )
+              {
+              visible = neighbor;
+              break;
+              }
+            }
+          else
+            {
+            visible = neighbor;
+            }
+          }
+        }
+      if( visible )
+        {
+        visible->f.replace = newfacet;
+        qh_setreplace(horizon->neighbors, visible, newfacet);
+        }
+      else
+        {
+        fprintf(
+          qh ferr,
+          "qhull internal error (qh_attachnewfacets): couldn't find visible facet for horizon f%d of newfacet f%d\n",
+          horizon->id, newfacet->id);
+        qh_errexit2(qh_ERRqhull, horizon, newfacet);
+        }
+      }
+    else    /* non-simplicial, with a ridge for newfacet */
+      {
+      FOREACHneighbor_(horizon) {    /* may hold for many new facets */
+        if( neighbor->visible )
+          {
+          neighbor->f.replace = newfacet;
+          qh_setdelnth(horizon->neighbors,
+                       (size_t)SETindex_(horizon->neighbors, neighbor) );
+          neighborp--; /* repeat */
+          }
+        }
+      qh_setappend(&horizon->neighbors, newfacet);
+      ridge = SETfirstt_(newfacet->ridges, ridgeT);
+      if( ridge->top == horizon )
+        {
+        ridge->bottom = newfacet;
+        }
+      else
+        {
+        ridge->top = newfacet;
+        }
+      }
+    } /* newfacets */
+  if( qh PRINTstatistics )
+    {
+    FORALLvisible_facets {
+      if( !visible->f.replace )
+        {
+        zinc_(Zinsidevisible);
+        }
+      }
+    }
+} /* attachnewfacets */
+
+/*---------------------------------
+
+  qh_checkflipped( facet, dist, allerror )
+  checks facet orientation to interior point
+
+  if allerror set,
+  tests against qh.DISTround
+  else
+  tests against 0 since tested against DISTround before
+
+  returns:
+  False if it flipped orientation (sets facet->flipped)
+  distance if non-NULL
+*/
+boolT qh_checkflipped(facetT *facet, realT *distp, boolT allerror)
+{
+  realT dist;
+
+  if( facet->flipped && !distp )
+    {
+    return False;
+    }
+  zzinc_(Zdistcheck);
+  qh_distplane(qh interior_point, facet, &dist);
+  if( distp )
+    {
+    *distp = dist;
+    }
+  if( (allerror && dist > -qh DISTround) || (!allerror && dist >= 0.0) )
+    {
+    facet->flipped = True;
+    zzinc_(Zflippedfacets);
+    trace0( (qh ferr, "qh_checkflipped: facet f%d is flipped, distance= %6.12g during p%d\n",
+             facet->id, dist, qh furthest_id) );
+    qh_precision("flipped facet");
+    return False;
+    }
+  return True;
+} /* checkflipped */
+
+/*---------------------------------
+
+  qh_delfacet( facet )
+  removes facet from facet_list and frees up its memory
+
+  notes:
+  assumes vertices and ridges already freed
+*/
+void qh_delfacet(facetT *facet)
+{
+  void * *freelistp; /* used !qh_NOmem */
+
+  trace4( (qh ferr, "qh_delfacet: delete f%d\n", facet->id) );
+  if( facet == qh tracefacet )
+    {
+    qh tracefacet = NULL;
+    }
+  if( facet == qh GOODclosest )
+    {
+    qh GOODclosest = NULL;
+    }
+  qh_removefacet(facet);
+  if( !facet->tricoplanar || facet->keepcentrum )
+    {
+    qh_memfree_(facet->normal, qh normal_size, freelistp);
+    if( qh CENTERtype == qh_ASvoronoi )     /* uses macro calls */
+      {
+      qh_memfree_(facet->center, qh center_size, freelistp);
+      }
+    else  /* AScentrum */
+      {
+      qh_memfree_(facet->center, qh normal_size, freelistp);
+      }
+    }
+  qh_setfree(&(facet->neighbors) );
+  if( facet->ridges )
+    {
+    qh_setfree(&(facet->ridges) );
+    }
+  qh_setfree(&(facet->vertices) );
+  if( facet->outsideset )
+    {
+    qh_setfree(&(facet->outsideset) );
+    }
+  if( facet->coplanarset )
+    {
+    qh_setfree(&(facet->coplanarset) );
+    }
+  qh_memfree_(facet, sizeof(facetT), freelistp);
+} /* delfacet */
+
+/*---------------------------------
+
+  qh_deletevisible()
+  delete visible facets and vertices
+
+  returns:
+  deletes each facet and removes from facetlist
+  at exit, qh.visible_list empty (== qh.newfacet_list)
+
+  notes:
+  ridges already deleted
+  horizon facets do not reference facets on qh.visible_list
+  new facets in qh.newfacet_list
+  uses   qh.visit_id;
+*/
+void qh_deletevisible(void /*qh visible_list*/)
+{
+  facetT * visible, *nextfacet;
+  vertexT *vertex, * *vertexp;
+  int      numvisible = 0, numdel = qh_setsize(qh del_vertices);
+
+  trace1( (qh ferr, "qh_deletevisible: delete %d visible facets and %d vertices\n",
+           qh num_visible, numdel) );
+  for( visible = qh visible_list; visible && visible->visible;
+       visible = nextfacet )   /* deleting current */
+    {
+    nextfacet = visible->next;
+    numvisible++;
+    qh_delfacet(visible);
+    }
+  if( numvisible != qh num_visible )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_deletevisible): qh num_visible %d is not number of visible facets %d\n",
+            qh num_visible, numvisible);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  qh num_visible = 0;
+  zadd_(Zvisfacettot, numvisible);
+  zmax_(Zvisfacetmax, numvisible);
+  zzadd_(Zdelvertextot, numdel);
+  zmax_(Zdelvertexmax, numdel);
+  FOREACHvertex_(qh del_vertices)
+  qh_delvertex(vertex);
+  qh_settruncate(qh del_vertices, (size_t)0);
+} /* deletevisible */
+
+/*---------------------------------
+
+  qh_facetintersect( facetA, facetB, skipa, skipB, prepend )
+  return vertices for intersection of two simplicial facets
+  may include 1 prepended entry (if more, need to settemppush)
+
+  returns:
+  returns set of qh.hull_dim-1 + prepend vertices
+  returns skipped index for each test and checks for exactly one
+
+  notes:
+  does not need settemp since set in quick memory
+
+  see also:
+  qh_vertexintersect and qh_vertexintersect_new
+  use qh_setnew_delnthsorted to get nth ridge (no skip information)
+
+  design:
+  locate skipped vertex by scanning facet A's neighbors
+  locate skipped vertex by scanning facet B's neighbors
+  intersect the vertex sets
+*/
+setT * qh_facetintersect(facetT *facetA, facetT *facetB,
+                         int *skipA, int *skipB, int prepend)
+{
+  setT *    intersect;
+  int       dim = qh hull_dim, i, j;
+  facetT * *neighborsA, * *neighborsB;
+
+  neighborsA = SETaddr_(facetA->neighbors, facetT);
+  neighborsB = SETaddr_(facetB->neighbors, facetT);
+  i = j = 0;
+  if( facetB == *neighborsA++ )
+    {
+    *skipA = 0;
+    }
+  else if( facetB == *neighborsA++ )
+    {
+    *skipA = 1;
+    }
+  else if( facetB == *neighborsA++ )
+    {
+    *skipA = 2;
+    }
+  else
+    {
+    for( i = 3; i < dim; i++ )
+      {
+      if( facetB == *neighborsA++ )
+        {
+        *skipA = i;
+        break;
+        }
+      }
+    }
+  if( facetA == *neighborsB++ )
+    {
+    *skipB = 0;
+    }
+  else if( facetA == *neighborsB++ )
+    {
+    *skipB = 1;
+    }
+  else if( facetA == *neighborsB++ )
+    {
+    *skipB = 2;
+    }
+  else
+    {
+    for( j = 3; j < dim; j++ )
+      {
+      if( facetA == *neighborsB++ )
+        {
+        *skipB = j;
+        break;
+        }
+      }
+    }
+  if( i >= dim || j >= dim )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_facetintersect): f%d or f%d not in others neighbors\n",
+            facetA->id, facetB->id);
+    qh_errexit2(qh_ERRqhull, facetA, facetB);
+    }
+  intersect = qh_setnew_delnthsorted(facetA->vertices, qh hull_dim, (size_t)*skipA, (size_t)prepend);
+  trace4( (qh ferr, "qh_facetintersect: f%d skip %d matches f%d skip %d\n",
+           facetA->id, *skipA, facetB->id, *skipB) );
+  return intersect;
+} /* facetintersect */
+
+/*---------------------------------
+
+  qh_gethash( hashsize, set, size, firstindex, skipelem )
+  return hashvalue for a set with firstindex and skipelem
+
+  notes:
+  assumes at least firstindex+1 elements
+  assumes skipelem is NULL, in set, or part of hash
+
+  hashes memory addresses which may change over different runs of the same data
+  using sum for hash does badly in high d
+*/
+unsigned qh_gethash(int hashsize, setT *set, int size, int firstindex, void *skipelem)
+{
+  void * * elemp = SETelemaddr_(set, firstindex, void);
+  ptr_intT hash = 0, elem;
+  int      i;
+
+  switch( size - firstindex )
+    {
+    case 1:
+      hash = (ptr_intT)(*elemp) - (ptr_intT) skipelem;
+      break;
+    case 2:
+      hash = (ptr_intT)(*elemp) + (ptr_intT)elemp[1] - (ptr_intT) skipelem;
+      break;
+    case 3:
+      hash = (ptr_intT)(*elemp) + (ptr_intT)elemp[1] + (ptr_intT)elemp[2]
+        - (ptr_intT) skipelem;
+      break;
+    case 4:
+      hash = (ptr_intT)(*elemp) + (ptr_intT)elemp[1] + (ptr_intT)elemp[2]
+        + (ptr_intT)elemp[3] - (ptr_intT) skipelem;
+      break;
+    case 5:
+      hash = (ptr_intT)(*elemp) + (ptr_intT)elemp[1] + (ptr_intT)elemp[2]
+        + (ptr_intT)elemp[3] + (ptr_intT)elemp[4] - (ptr_intT) skipelem;
+      break;
+    case 6:
+      hash = (ptr_intT)(*elemp) + (ptr_intT)elemp[1] + (ptr_intT)elemp[2]
+        + (ptr_intT)elemp[3] + (ptr_intT)elemp[4] + (ptr_intT)elemp[5]
+        - (ptr_intT) skipelem;
+      break;
+    default:
+      hash = 0;
+      i = 3;
+
+      do     /* this is about 10% in 10-d */
+        {
+        if( (elem = (ptr_intT) * elemp++) != (ptr_intT)skipelem )
+          {
+          hash ^= (elem << i) + (elem >> (32 - i) );
+          i += 3;
+          if( i >= 32 )
+            {
+            i -= 32;
+            }
+          }
+        }
+      while( *elemp );
+
+      break;
+    }
+  hash %= (ptr_intT) hashsize;
+  /* hash= 0; for debugging purposes */
+  return hash;
+} /* gethash */
+
+/*---------------------------------
+
+  qh_makenewfacet( vertices, toporient, horizon )
+  creates a toporient? facet from vertices
+
+  returns:
+  returns newfacet
+  adds newfacet to qh.facet_list
+  newfacet->vertices= vertices
+  if horizon
+  newfacet->neighbor= horizon, but not vice versa
+  newvertex_list updated with vertices
+*/
+facetT * qh_makenewfacet(setT *vertices, boolT toporient, facetT *horizon)
+{
+  facetT * newfacet;
+  vertexT *vertex, * *vertexp;
+
+  FOREACHvertex_(vertices) {
+    if( !vertex->newlist )
+      {
+      qh_removevertex(vertex);
+      qh_appendvertex(vertex);
+      }
+    }
+  newfacet = qh_newfacet();
+  newfacet->vertices = vertices;
+  newfacet->toporient = toporient;
+  if( horizon )
+    {
+    qh_setappend(&(newfacet->neighbors), horizon);
+    }
+  qh_appendfacet(newfacet);
+  return newfacet;
+} /* makenewfacet */
+
+/*---------------------------------
+
+  qh_makenewplanes()
+  make new hyperplanes for facets on qh.newfacet_list
+
+  returns:
+  all facets have hyperplanes or are marked for   merging
+  doesn't create hyperplane if horizon is coplanar (will merge)
+  updates qh.min_vertex if qh.JOGGLEmax
+
+  notes:
+  facet->f.samecycle is defined for facet->mergehorizon facets
+*/
+void qh_makenewplanes(void /* newfacet_list */)
+{
+  facetT *newfacet;
+
+  FORALLnew_facets {
+    if( !newfacet->mergehorizon )
+      {
+      qh_setfacetplane(newfacet);
+      }
+    }
+  if( qh JOGGLEmax < REALmax / 2 )
+    {
+    minimize_(qh min_vertex, -wwval_(Wnewvertexmax) );
+    }
+} /* makenewplanes */
+
+/*---------------------------------
+
+  qh_makenew_nonsimplicial( visible, apex, numnew )
+  make new facets for ridges of a visible facet
+
+  returns:
+  first newfacet, bumps numnew as needed
+  attaches new facets if !qh.ONLYgood
+  marks ridge neighbors for simplicial visible
+  if (qh.ONLYgood)
+  ridges on newfacet, horizon, and visible
+  else
+  ridge and neighbors between newfacet and   horizon
+  visible facet's ridges are deleted
+
+  notes:
+  qh.visit_id if visible has already been processed
+  sets neighbor->seen for building f.samecycle
+  assumes all 'seen' flags initially false
+
+  design:
+  for each ridge of visible facet
+  get neighbor of visible facet
+  if neighbor was already processed
+  delete the ridge (will delete all visible facets later)
+  if neighbor is a horizon facet
+  create a new facet
+  if neighbor coplanar
+  adds newfacet to f.samecycle for later merging
+  else
+  updates neighbor's neighbor set
+  (checks for non-simplicial facet with multiple ridges to visible facet)
+  updates neighbor's ridge set
+  (checks for simplicial neighbor to non-simplicial visible facet)
+  (deletes ridge if neighbor is simplicial)
+
+*/
+#ifndef qh_NOmerge
+facetT * qh_makenew_nonsimplicial(facetT *visible, vertexT *apex, int *numnew)
+{
+  void * *freelistp; /* used !qh_NOmem */
+  ridgeT *ridge, * *ridgep;
+  facetT *neighbor, *newfacet = NULL, *samecycle;
+  setT *  vertices;
+  boolT   toporient;
+  int     ridgeid;
+
+  FOREACHridge_(visible->ridges) {
+    ridgeid = ridge->id;
+    neighbor = otherfacet_(ridge, visible);
+    if( neighbor->visible )
+      {
+      if( !qh ONLYgood )
+        {
+        if( neighbor->visitid == qh visit_id )
+          {
+          qh_setfree(&(ridge->vertices) );  /* delete on 2nd visit */
+          qh_memfree_(ridge, sizeof(ridgeT), freelistp);
+          }
+        }
+      }
+    else     /* neighbor is an horizon facet */
+      {
+      toporient = (ridge->top == visible);
+      vertices = qh_setnew(qh hull_dim); /* makes sure this is quick */
+      qh_setappend(&vertices, apex);
+      qh_setappend_set(&vertices, ridge->vertices);
+      newfacet = qh_makenewfacet(vertices, toporient, neighbor);
+      (*numnew)++;
+      if( neighbor->coplanar )
+        {
+        newfacet->mergehorizon = True;
+        if( !neighbor->seen )
+          {
+          newfacet->f.samecycle = newfacet;
+          neighbor->f.newcycle = newfacet;
+          }
+        else
+          {
+          samecycle = neighbor->f.newcycle;
+          newfacet->f.samecycle = samecycle->f.samecycle;
+          samecycle->f.samecycle = newfacet;
+          }
+        }
+      if( qh ONLYgood )
+        {
+        if( !neighbor->simplicial )
+          {
+          qh_setappend(&(newfacet->ridges), ridge);
+          }
+        }
+      else     /* qh_attachnewfacets */
+        {
+        if( neighbor->seen )
+          {
+          if( neighbor->simplicial )
+            {
+            fprintf(qh ferr,
+                    "qhull internal error (qh_makenew_nonsimplicial): simplicial f%d sharing two ridges with f%d\n",
+                    neighbor->id,
+                    visible->id);
+            qh_errexit2(qh_ERRqhull, neighbor, visible);
+            }
+          qh_setappend(&(neighbor->neighbors), newfacet);
+          }
+        else
+          {
+          qh_setreplace(neighbor->neighbors, visible, newfacet);
+          }
+        if( neighbor->simplicial )
+          {
+          qh_setdel(neighbor->ridges, ridge);
+          qh_setfree(&(ridge->vertices) );
+          qh_memfree(ridge, sizeof(ridgeT) );
+          }
+        else
+          {
+          qh_setappend(&(newfacet->ridges), ridge);
+          if( toporient )
+            {
+            ridge->top = newfacet;
+            }
+          else
+            {
+            ridge->bottom = newfacet;
+            }
+          }
+        trace4( (qh ferr, "qh_makenew_nonsimplicial: created facet f%d from v%d and r%d of horizon f%d\n",
+                 newfacet->id, apex->id, ridgeid, neighbor->id) );
+        }
+      }
+    neighbor->seen = True;
+    } /* for each ridge */
+  if( !qh ONLYgood )
+    {
+    SETfirst_(visible->ridges) = NULL;
+    }
+  return newfacet;
+} /* makenew_nonsimplicial */
+
+#else /* qh_NOmerge */
+facetT * qh_makenew_nonsimplicial(facetT *visible, vertexT *apex, int *numnew)
+{
+  return NULL;
+}
+
+#endif /* qh_NOmerge */
+
+/*---------------------------------
+
+  qh_makenew_simplicial( visible, apex, numnew )
+  make new facets for simplicial visible facet and apex
+
+  returns:
+  attaches new facets if (!qh.ONLYgood)
+  neighbors between newfacet and horizon
+
+  notes:
+  nop if neighbor->seen or neighbor->visible (see qh_makenew_nonsimplicial)
+
+  design:
+  locate neighboring horizon facet for visible facet
+  determine vertices and orientation
+  create new facet
+  if coplanar,
+  add new facet to f.samecycle
+  update horizon facet's neighbor list
+*/
+facetT * qh_makenew_simplicial(facetT *visible, vertexT *apex, int *numnew)
+{
+  facetT *neighbor, * *neighborp, *newfacet = NULL;
+  setT *  vertices;
+  boolT   flip, toporient;
+  int     horizonskip, visibleskip;
+
+  FOREACHneighbor_(visible) {
+    if( !neighbor->seen && !neighbor->visible )
+      {
+      vertices = qh_facetintersect(neighbor, visible, &horizonskip, &visibleskip, 1);
+      SETfirst_(vertices) = apex;
+      flip = ( (horizonskip & 0x1) ^ (visibleskip & 0x1) );
+      if( neighbor->toporient )
+        {
+        toporient = horizonskip & 0x1;
+        }
+      else
+        {
+        toporient = (horizonskip & 0x1) ^ 0x1;
+        }
+      newfacet = qh_makenewfacet(vertices, toporient, neighbor);
+      (*numnew)++;
+      if( neighbor->coplanar && (qh PREmerge || qh MERGEexact) )
+        {
+#ifndef qh_NOmerge
+        newfacet->f.samecycle = newfacet;
+        newfacet->mergehorizon = True;
+#endif
+        }
+      if( !qh ONLYgood )
+        {
+        SETelem_(neighbor->neighbors, horizonskip) = newfacet;
+        }
+      trace4( (qh ferr,
+               "qh_makenew_simplicial: create facet f%d top %d from v%d and horizon f%d skip %d top %d and visible f%d skip %d, flip? %d\n",
+               newfacet->id, toporient, apex->id, neighbor->id, horizonskip,
+               neighbor->toporient, visible->id, visibleskip, flip) );
+      }
+    }
+  return newfacet;
+} /* makenew_simplicial */
+
+/*---------------------------------
+
+  qh_matchneighbor( newfacet, newskip, hashsize, hashcount )
+  either match subridge of newfacet with neighbor or add to hash_table
+
+  returns:
+  duplicate ridges are unmatched and marked by qh_DUPLICATEridge
+
+  notes:
+  ridge is newfacet->vertices w/o newskip vertex
+  do not allocate memory (need to free hash_table cleanly)
+  uses linear hash chains
+
+  see also:
+  qh_matchduplicates
+
+  design:
+  for each possible matching facet in qh.hash_table
+  if vertices match
+  set ismatch, if facets have opposite orientation
+  if ismatch and matching facet doesn't have a match
+  match the facets by updating their neighbor sets
+  else
+  indicate a duplicate ridge
+  set facet hyperplane for later testing
+  add facet to hashtable
+  unless the other facet was already a duplicate ridge
+  mark both facets with a duplicate ridge
+  add other facet (if defined) to hash table
+*/
+void qh_matchneighbor(facetT *newfacet, int newskip, int hashsize, int *hashcount)
+{
+  boolT    newfound = False; /* True, if new facet is already in hash chain */
+  boolT    same, ismatch;
+  unsigned hash; int scan;
+  facetT * facet, *matchfacet;
+  int      skip, matchskip;
+
+  hash = (int)qh_gethash(hashsize, newfacet->vertices, qh hull_dim, 1,
+                         SETelem_(newfacet->vertices, newskip) );
+  trace4( (qh ferr, "qh_matchneighbor: newfacet f%d skip %d hash %d hashcount %d\n",
+           newfacet->id, newskip, hash, *hashcount) );
+  zinc_(Zhashlookup);
+  for( scan = hash; (facet = SETelemt_(qh hash_table, scan, facetT) );
+       scan = (++scan >= hashsize ? 0 : scan) )
+    {
+    if( facet == newfacet )
+      {
+      newfound = True;
+      continue;
+      }
+    zinc_(Zhashtests);
+    if( qh_matchvertices(1, newfacet->vertices, newskip, facet->vertices, &skip, &same) )
+      {
+      if( SETelem_(newfacet->vertices, newskip) ==
+          SETelem_(facet->vertices, skip) )
+        {
+        qh_precision("two facets with the same vertices");
+        fprintf(qh ferr, "qhull precision error: Vertex sets are the same for f%d and f%d.  Can not force output.\n",
+                facet->id, newfacet->id);
+        qh_errexit2(qh_ERRprec, facet, newfacet);
+        }
+      ismatch = (same == (boolT)(newfacet->toporient ^ facet->toporient) );
+      matchfacet = SETelemt_(facet->neighbors, skip, facetT);
+      if( ismatch && !matchfacet )
+        {
+        SETelem_(facet->neighbors, skip) = newfacet;
+        SETelem_(newfacet->neighbors, newskip) = facet;
+        (*hashcount)--;
+        trace4( (qh ferr, "qh_matchneighbor: f%d skip %d matched with new f%d skip %d\n",
+                 facet->id, skip, newfacet->id, newskip) );
+        return;
+        }
+      if( !qh PREmerge && !qh MERGEexact )
+        {
+        qh_precision("a ridge with more than two neighbors");
+        fprintf(
+          qh ferr,
+          "qhull precision error: facets f%d, f%d and f%d meet at a ridge with more than 2 neighbors.  Can not continue.\n",
+          facet->id, newfacet->id, getid_(matchfacet) );
+        qh_errexit2(qh_ERRprec, facet, newfacet);
+        }
+      SETelem_(newfacet->neighbors, newskip) = qh_DUPLICATEridge;
+      newfacet->dupridge = True;
+      if( !newfacet->normal )
+        {
+        qh_setfacetplane(newfacet);
+        }
+      qh_addhash(newfacet, qh hash_table, hashsize, hash);
+      (*hashcount)++;
+      if( !facet->normal )
+        {
+        qh_setfacetplane(facet);
+        }
+      if( matchfacet != qh_DUPLICATEridge )
+        {
+        SETelem_(facet->neighbors, skip) = qh_DUPLICATEridge;
+        facet->dupridge = True;
+        if( !facet->normal )
+          {
+          qh_setfacetplane(facet);
+          }
+        if( matchfacet )
+          {
+          matchskip = qh_setindex(matchfacet->neighbors, facet);
+          SETelem_(matchfacet->neighbors, matchskip) = qh_DUPLICATEridge;
+          matchfacet->dupridge = True;
+          if( !matchfacet->normal )
+            {
+            qh_setfacetplane(matchfacet);
+            }
+          qh_addhash(matchfacet, qh hash_table, hashsize, hash);
+          *hashcount += 2;
+          }
+        }
+      trace4( (qh ferr,
+               "qh_matchneighbor: new f%d skip %d duplicates ridge for f%d skip %d matching f%d ismatch %d at hash %d\n",
+               newfacet->id, newskip, facet->id, skip,
+               (matchfacet == qh_DUPLICATEridge ? -2 : getid_(matchfacet) ),
+               ismatch, hash) );
+      return; /* end of duplicate ridge */
+      }
+    }
+  if( !newfound )
+    {
+    SETelem_(qh hash_table, scan) = newfacet;  /* same as qh_addhash */
+    }
+  (*hashcount)++;
+  trace4( (qh ferr, "qh_matchneighbor: no match for f%d skip %d at hash %d\n",
+           newfacet->id, newskip, hash) );
+} /* matchneighbor */
+
+/*---------------------------------
+
+  qh_matchnewfacets()
+  match newfacets in qh.newfacet_list to their newfacet neighbors
+
+  returns:
+  qh.newfacet_list with full neighbor sets
+  get vertices with nth neighbor by deleting nth vertex
+  if qh.PREmerge/MERGEexact or qh.FORCEoutput
+  sets facet->flippped if flipped normal (also prevents point partitioning)
+  if duplicate ridges and qh.PREmerge/MERGEexact
+  sets facet->dupridge
+  missing neighbor links identifies extra ridges to be merging (qh_MERGEridge)
+
+  notes:
+  newfacets already have neighbor[0] (horizon facet)
+  assumes qh.hash_table is NULL
+  vertex->neighbors has not been updated yet
+  do not allocate memory after qh.hash_table (need to free it cleanly)
+
+  design:
+  delete neighbor sets for all new facets
+  initialize a hash table
+  for all new facets
+  match facet with neighbors
+  if unmatched facets (due to duplicate ridges)
+  for each new facet with a duplicate ridge
+  match it with a facet
+  check for flipped facets
+*/
+void qh_matchnewfacets(void /* qh newfacet_list */)
+{
+  int     numnew = 0, hashcount = 0, newskip;
+  facetT *newfacet, *neighbor;
+  int     dim = qh hull_dim, hashsize, neighbor_i, neighbor_n;
+  setT *  neighbors;
+
+#ifndef qh_NOtrace
+  int     facet_i, facet_n, numfree = 0;
+  facetT *facet;
+#endif
+
+  trace1( (qh ferr, "qh_matchnewfacets: match neighbors for new facets.\n") );
+  FORALLnew_facets {
+    numnew++;
+      { /* inline qh_setzero (newfacet->neighbors, 1, qh hull_dim); */
+      neighbors = newfacet->neighbors;
+      neighbors->e[neighbors->maxsize].i = dim + 1; /*may be overwritten*/
+      memset( (char *)SETelemaddr_(neighbors, 1, void), 0, dim * SETelemsize);
+      }
+    }
+  qh_newhashtable(numnew * (qh hull_dim - 1) ); /* twice what is normally needed,
+                 but every ridge could be DUPLICATEridge */
+  hashsize = qh_setsize(qh hash_table);
+  FORALLnew_facets {
+    for( newskip = 1; newskip < qh hull_dim; newskip++ ) /* furthest/horizon
+                                                           already matched */
+      {
+      qh_matchneighbor(newfacet, newskip, hashsize, &hashcount);
+      }
+#if 0   /* use the following to trap hashcount errors */
+      {
+      int     count = 0, k;
+      facetT *facet, *neighbor;
+
+      count = 0;
+      FORALLfacet_(qh newfacet_list) {  /* newfacet already in use */
+        for( k = 1; k < qh hull_dim; k++ )
+          {
+          neighbor = SETelemt_(facet->neighbors, k, facetT);
+          if( !neighbor || neighbor == qh_DUPLICATEridge )
+            {
+            count++;
+            }
+          }
+        if( facet == newfacet )
+          {
+          break;
+          }
+        }
+      if( count != hashcount )
+        {
+        fprintf(qh ferr, "qh_matchnewfacets: after adding facet %d, hashcount %d != count %d\n",
+                newfacet->id, hashcount, count);
+        qh_errexit(qh_ERRqhull, newfacet, NULL);
+        }
+      }
+#endif  /* end of trap code */
+    }
+  if( hashcount )
+    {
+    FORALLnew_facets {
+      if( newfacet->dupridge )
+        {
+        FOREACHneighbor_i_(newfacet) {
+          if( neighbor == qh_DUPLICATEridge )
+            {
+            qh_matchduplicates(newfacet, neighbor_i, hashsize, &hashcount);
+            /* this may report MERGEfacet */
+            }
+          }
+        }
+      }
+    }
+  if( hashcount )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_matchnewfacets): %d neighbors did not match up\n",
+            hashcount);
+    qh_printhashtable(qh ferr);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+#ifndef qh_NOtrace
+  if( qh IStracing >= 2 )
+    {
+    FOREACHfacet_i_(qh hash_table) {
+      if( !facet )
+        {
+        numfree++;
+        }
+      }
+    fprintf(qh ferr, "qh_matchnewfacets: %d new facets, %d unused hash entries .  hashsize %d\n",
+            numnew, numfree, qh_setsize(qh hash_table) );
+    }
+#endif /* !qh_NOtrace */
+  qh_setfree(&qh hash_table);
+  if( qh PREmerge || qh MERGEexact )
+    {
+    if( qh IStracing >= 4 )
+      {
+      qh_printfacetlist(qh newfacet_list, NULL, qh_ALL);
+      }
+    FORALLnew_facets {
+      if( newfacet->normal )
+        {
+        qh_checkflipped(newfacet, NULL, qh_ALL);
+        }
+      }
+    }
+  else if( qh FORCEoutput )
+    {
+    qh_checkflipped_all(qh newfacet_list);   /* prints warnings for flipped */
+    }
+} /* matchnewfacets */
+
+/*---------------------------------
+
+  qh_matchvertices( firstindex, verticesA, skipA, verticesB, skipB, same )
+  tests whether vertices match with a single skip
+  starts match at firstindex since all new facets have a common vertex
+
+  returns:
+  true if matched vertices
+  skip index for each set
+  sets same iff vertices have the same orientation
+
+  notes:
+  assumes skipA is in A and both sets are the same size
+
+  design:
+  set up pointers
+  scan both sets checking for a match
+  test orientation
+*/
+boolT qh_matchvertices(int firstindex, setT *verticesA, int skipA,
+                       setT *verticesB, int *skipB, boolT *same)
+{
+  vertexT * *elemAp, * *elemBp, * *skipBp = NULL, * *skipAp;
+
+  elemAp = SETelemaddr_(verticesA, firstindex, vertexT);
+  elemBp = SETelemaddr_(verticesB, firstindex, vertexT);
+  skipAp = SETelemaddr_(verticesA, skipA, vertexT);
+
+  do
+    {
+    if( elemAp != skipAp )
+      {
+      while( *elemAp != *elemBp++ )
+        {
+        if( skipBp )
+          {
+          return False;
+          }
+        skipBp = elemBp; /* one extra like FOREACH */
+        }
+      }
+    }
+  while( *(++elemAp) );
+
+  if( !skipBp )
+    {
+    skipBp = ++elemBp;
+    }
+  *skipB = SETindex_(verticesB, skipB);
+  *same = !( ( (ptr_intT)skipA & 0x1) ^ ( (ptr_intT) * skipB & 0x1) );
+  trace4( (qh ferr, "qh_matchvertices: matched by skip %d (v%d) and skip %d (v%d) same? %d\n",
+           skipA, (*skipAp)->id, *skipB, (*(skipBp - 1) )->id, *same) );
+  return True;
+} /* matchvertices */
+
+/*---------------------------------
+
+  qh_newfacet()
+  return a new facet
+
+  returns:
+  all fields initialized or cleared   (NULL)
+  preallocates neighbors set
+*/
+facetT * qh_newfacet(void)
+{
+  facetT *facet;
+  void * *freelistp; /* used !qh_NOmem */
+
+  qh_memalloc_(sizeof(facetT), freelistp, facet, facetT);
+  memset( (char *)facet, 0, sizeof(facetT) );
+  if( qh facet_id == qh tracefacet_id )
+    {
+    qh tracefacet = facet;
+    }
+  facet->id = qh facet_id++;
+  facet->neighbors = qh_setnew(qh hull_dim);
+#if !qh_COMPUTEfurthest
+  facet->furthestdist = 0.0;
+#endif
+#if qh_MAXoutside
+  if( qh FORCEoutput && qh APPROXhull )
+    {
+    facet->maxoutside = qh MINoutside;
+    }
+  else
+    {
+    facet->maxoutside = qh DISTround;
+    }
+#endif
+  facet->simplicial = True;
+  facet->good = True;
+  facet->newfacet = True;
+  trace4( (qh ferr, "qh_newfacet: created facet f%d\n", facet->id) );
+  return facet;
+} /* newfacet */
+
+/*---------------------------------
+
+  qh_newridge()
+  return a new ridge
+*/
+ridgeT * qh_newridge(void)
+{
+  ridgeT *ridge;
+  void * *freelistp;   /* used !qh_NOmem */
+
+  qh_memalloc_(sizeof(ridgeT), freelistp, ridge, ridgeT);
+  memset( (char *)ridge, 0, sizeof(ridgeT) );
+  zinc_(Ztotridges);
+  if( qh ridge_id == 0xFFFFFF )
+    {
+    fprintf(
+      qh ferr,
+      "\
+qhull warning: more than %d ridges.  ID field overflows and two ridges\n\
+may have the same identifier.  Otherwise output ok.\n"                                                                                   ,
+      0xFFFFFF);
+    }
+  ridge->id = qh ridge_id++;
+  trace4( (qh ferr, "qh_newridge: created ridge r%d\n", ridge->id) );
+  return ridge;
+} /* newridge */
+
+/*---------------------------------
+
+  qh_pointid(  )
+  return id for a point,
+  returns -3 if null, -2 if interior, or -1 if not known
+
+  alternative code:
+  unsigned long id;
+  id= ((unsigned long)point - (unsigned long)qh.first_point)/qh.normal_size;
+
+  notes:
+  if point not in point array
+  the code does a comparison of unrelated pointers.
+*/
+int qh_pointid(pointT *point)
+{
+  long offset, id;
+
+  if( !point )
+    {
+    id = -3;
+    }
+  else if( point == qh interior_point )
+    {
+    id = -2;
+    }
+  else if( point >= qh first_point
+           && point < qh first_point + qh num_points * qh hull_dim )
+    {
+    offset = point - qh first_point;
+    id = offset / qh hull_dim;
+    }
+  else if( (id = qh_setindex(qh other_points, point) ) != -1 )
+    {
+    id += qh num_points;
+    }
+  else
+    {
+    id = -1;
+    }
+  return (int) id;
+} /* pointid */
+
+/*---------------------------------
+
+  qh_removefacet( facet )
+  unlinks facet from qh.facet_list,
+
+  returns:
+  updates qh.facet_list .newfacet_list .facet_next visible_list
+  decrements qh.num_facets
+
+  see:
+  qh_appendfacet
+*/
+void qh_removefacet(facetT *facet)
+{
+  facetT *next = facet->next, *previous = facet->previous;
+
+  if( facet == qh newfacet_list )
+    {
+    qh newfacet_list = next;
+    }
+  if( facet == qh facet_next )
+    {
+    qh facet_next = next;
+    }
+  if( facet == qh visible_list )
+    {
+    qh visible_list = next;
+    }
+  if( previous )
+    {
+    previous->next = next;
+    next->previous = previous;
+    }
+  else     /* 1st facet in qh facet_list */
+    {
+    qh              facet_list = next;
+    qh facet_list-> previous = NULL;
+    }
+  qh num_facets--;
+  trace4( (qh ferr, "qh_removefacet: remove f%d from facet_list\n", facet->id) );
+} /* removefacet */
+
+/*---------------------------------
+
+  qh_removevertex( vertex )
+  unlinks vertex from qh.vertex_list,
+
+  returns:
+  updates qh.vertex_list .newvertex_list
+  decrements qh.num_vertices
+*/
+void qh_removevertex(vertexT *vertex)
+{
+  vertexT *next = vertex->next, *previous = vertex->previous;
+
+  if( vertex == qh newvertex_list )
+    {
+    qh newvertex_list = next;
+    }
+  if( previous )
+    {
+    previous->next = next;
+    next->previous = previous;
+    }
+  else     /* 1st vertex in qh vertex_list */
+    {
+    qh               vertex_list = vertex->next;
+    qh vertex_list-> previous = NULL;
+    }
+  qh num_vertices--;
+  trace4( (qh ferr, "qh_removevertex: remove v%d from vertex_list\n", vertex->id) );
+} /* removevertex */
+
+/*---------------------------------
+
+  qh_updatevertices()
+  update vertex neighbors and delete interior vertices
+
+  returns:
+  if qh.VERTEXneighbors, updates neighbors for each vertex
+  if qh.newvertex_list,
+  removes visible neighbors  from vertex neighbors
+  if qh.newfacet_list
+  adds new facets to vertex neighbors
+  if qh.visible_list
+  interior vertices added to qh.del_vertices for later partitioning
+
+  design:
+  if qh.VERTEXneighbors
+  deletes references to visible facets from vertex neighbors
+  appends new facets to the neighbor list for each vertex
+  checks all vertices of visible facets
+  removes visible facets from neighbor lists
+  marks unused vertices for deletion
+*/
+void qh_updatevertices(void /*qh newvertex_list, newfacet_list, visible_list*/)
+{
+  facetT * newfacet = NULL, *neighbor, * *neighborp, *visible;
+  vertexT *vertex, * *vertexp;
+
+  trace3( (qh ferr, "qh_updatevertices: delete interior vertices and update vertex->neighbors\n") );
+  if( qh VERTEXneighbors )
+    {
+    FORALLvertex_(qh newvertex_list) {
+      FOREACHneighbor_(vertex) {
+        if( neighbor->visible )
+          {
+          SETref_(neighbor) = NULL;
+          }
+        }
+      qh_setcompact(vertex->neighbors);
+      }
+    FORALLnew_facets {
+      FOREACHvertex_(newfacet->vertices)
+      qh_setappend(&vertex->neighbors, newfacet);
+      }
+    FORALLvisible_facets {
+      FOREACHvertex_(visible->vertices) {
+        if( !vertex->newlist && !vertex->deleted )
+          {
+          FOREACHneighbor_(vertex) { /* this can happen under merging */
+            if( !neighbor->visible )
+              {
+              break;
+              }
+            }
+          if( neighbor )
+            {
+            qh_setdel(vertex->neighbors, visible);
+            }
+          else
+            {
+            vertex->deleted = True;
+            qh_setappend(&qh del_vertices, vertex);
+            trace2( (qh ferr, "qh_updatevertices: delete vertex p%d (v%d) in f%d\n",
+                     qh_pointid(vertex->point), vertex->id, visible->id) );
+            }
+          }
+        }
+      }
+    }
+  else     /* !VERTEXneighbors */
+    {
+    FORALLvisible_facets {
+      FOREACHvertex_(visible->vertices) {
+        if( !vertex->newlist && !vertex->deleted )
+          {
+          vertex->deleted = True;
+          qh_setappend(&qh del_vertices, vertex);
+          trace2( (qh ferr, "qh_updatevertices: delete vertex p%d (v%d) in f%d\n",
+                   qh_pointid(vertex->point), vertex->id, visible->id) );
+          }
+        }
+      }
+    }
+} /* updatevertices */
+
diff --git a/BRAINSABC/qhull/poly.h b/BRAINSABC/qhull/poly.h
new file mode 100644
index 00000000..cf995a0f
--- /dev/null
+++ b/BRAINSABC/qhull/poly.h
@@ -0,0 +1,361 @@
+/*
  ---------------------------------
+
+   poly.h
+   header file for poly.c and poly2.c
+
+   see qh-poly.htm, qhull.h and poly.c
+
+   copyright (c) 1993-2003, The Geometry Center
+*/
+
+#ifndef qhDEFpoly
+#define qhDEFpoly 1
+
+/*===============   constants ========================== */
+
+/*----------------------------------
+
+  ALGORITHMfault
+    use as argument to checkconvex() to report errors during buildhull
+*/
+#define qh_ALGORITHMfault 0
+
+/*----------------------------------
+
+  DATAfault
+    use as argument to checkconvex() to report errors during initialhull
+*/
+#define qh_DATAfault 1
+
+/*----------------------------------
+
+  DUPLICATEridge
+    special value for facet->neighbor to indicate a duplicate ridge
+
+  notes:
+    set by matchneighbor, used by matchmatch and mark_dupridge
+*/
+#define qh_DUPLICATEridge (facetT *)1L
+
+/*----------------------------------
+
+  MERGEridge       flag in facet
+    special value for facet->neighbor to indicate a merged ridge
+
+  notes:
+    set by matchneighbor, used by matchmatch and mark_dupridge
+*/
+#define qh_MERGEridge (facetT *)2L
+
+/*============ -structures- ====================*/
+
+/*=========== -macros- =========================*/
+
+/*----------------------------------
+
+  FORALLfacet_( facetlist ) { ... }
+    assign 'facet' to each facet in facetlist
+
+  notes:
+    uses 'facetT *facet;'
+    assumes last facet is a sentinel
+
+  see:
+    FORALLfacets
+*/
+#define FORALLfacet_( facetlist ) if( facetlist ) for( facet = ( facetlist ); \
+                                                       facet && facet->next; \
+                                                       facet = facet->next )
+
+/*----------------------------------
+
+  FORALLnew_facets { ... }
+    assign 'newfacet' to each facet in qh.newfacet_list
+
+  notes:
+    uses 'facetT *newfacet;'
+    at exit, newfacet==NULL
+*/
+#define FORALLnew_facets for( newfacet = qh newfacet_list; newfacet && newfacet->next; newfacet = newfacet->next )
+
+/*----------------------------------
+
+  FORALLvertex_( vertexlist ) { ... }
+    assign 'vertex' to each vertex in vertexlist
+
+  notes:
+    uses 'vertexT *vertex;'
+    at exit, vertex==NULL
+*/
+#define FORALLvertex_( vertexlist ) for( vertex = ( vertexlist ); vertex && vertex->next; vertex = vertex->next )
+
+/*----------------------------------
+
+  FORALLvisible_facets { ... }
+    assign 'visible' to each visible facet in qh.visible_list
+
+  notes:
+    uses 'vacetT *visible;'
+    at exit, visible==NULL
+*/
+#define FORALLvisible_facets for( visible = qh visible_list; visible && visible->visible; visible = visible->next )
+
+/*----------------------------------
+
+  FORALLsame_( newfacet ) { ... }
+    assign 'same' to each facet in newfacet->f.samecycle
+
+  notes:
+    uses 'facetT *same;'
+    stops when it returns to newfacet
+*/
+#define FORALLsame_(newfacet) for( same = newfacet->f.samecycle; same != newfacet; same = same->f.samecycle )
+
+/*----------------------------------
+
+  FORALLsame_cycle_( newfacet ) { ... }
+    assign 'same' to each facet in newfacet->f.samecycle
+
+  notes:
+    uses 'facetT *same;'
+    at exit, same == NULL
+*/
+#define FORALLsame_cycle_(newfacet)                                     \
+  for( same = newfacet->f.samecycle;                                   \
+       same; same = ( same == newfacet ?  NULL : same->f.samecycle ) )
+
+/*----------------------------------
+
+  FOREACHneighborA_( facet ) { ... }
+    assign 'neighborA' to each neighbor in facet->neighbors
+
+  FOREACHneighborA_( vertex ) { ... }
+    assign 'neighborA' to each neighbor in vertex->neighbors
+
+  declare:
+    facetT *neighborA, **neighborAp;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHneighborA_(facet)  FOREACHsetelement_(facetT, facet->neighbors, neighborA)
+
+/*----------------------------------
+
+  FOREACHvisible_( facets ) { ... }
+    assign 'visible' to each facet in facets
+
+  notes:
+    uses 'facetT *facet, *facetp;'
+    see FOREACHsetelement_
+*/
+#define FOREACHvisible_(facets) FOREACHsetelement_(facetT, facets, visible)
+
+/*----------------------------------
+
+  FOREACHnewfacet_( facets ) { ... }
+    assign 'newfacet' to each facet in facets
+
+  notes:
+    uses 'facetT *newfacet, *newfacetp;'
+    see FOREACHsetelement_
+*/
+#define FOREACHnewfacet_(facets) FOREACHsetelement_(facetT, facets, newfacet)
+
+/*----------------------------------
+
+  FOREACHvertexA_( vertices ) { ... }
+    assign 'vertexA' to each vertex in vertices
+
+  notes:
+    uses 'vertexT *vertexA, *vertexAp;'
+    see FOREACHsetelement_
+*/
+#define FOREACHvertexA_(vertices) FOREACHsetelement_(vertexT, vertices, vertexA)
+
+/*----------------------------------
+
+  FOREACHvertexreverse12_( vertices ) { ... }
+    assign 'vertex' to each vertex in vertices
+    reverse order of first two vertices
+
+  notes:
+    uses 'vertexT *vertex, *vertexp;'
+    see FOREACHsetelement_
+*/
+#define FOREACHvertexreverse12_(vertices) FOREACHsetelementreverse12_(vertexT, vertices, vertex)
+
+/*=============== prototypes poly.c in alphabetical order ================*/
+
+void    qh_appendfacet(facetT *facet);
+
+void    qh_appendvertex(vertexT *vertex);
+
+void  qh_attachnewfacets(void);
+
+boolT   qh_checkflipped(facetT *facet, realT *dist, boolT allerror);
+
+void  qh_delfacet(facetT *facet);
+
+void  qh_deletevisible(void /*qh visible_list, qh horizon_list*/);
+
+setT   * qh_facetintersect(facetT *facetA, facetT *facetB, int *skipAp, int *skipBp, int extra);
+
+unsigned qh_gethash(int hashsize, setT *set, int size, int firstindex, void *skipelem);
+
+facetT * qh_makenewfacet(setT *vertices, boolT toporient, facetT *facet);
+
+void    qh_makenewplanes( void /* newfacet_list */);
+
+facetT * qh_makenew_nonsimplicial(facetT *visible, vertexT *apex, int *numnew);
+
+facetT * qh_makenew_simplicial(facetT *visible, vertexT *apex, int *numnew);
+
+void    qh_matchneighbor(facetT *newfacet, int newskip, int hashsize, int *hashcount);
+
+void  qh_matchnewfacets(void);
+
+boolT   qh_matchvertices(int firstindex, setT *verticesA, int skipA, setT *verticesB, int *skipB, boolT *same);
+
+facetT * qh_newfacet(void);
+
+ridgeT * qh_newridge(void);
+
+int     qh_pointid(pointT *point);
+
+void  qh_removefacet(facetT *facet);
+
+void  qh_removevertex(vertexT *vertex);
+
+void    qh_updatevertices(void);
+
+/*========== -prototypes poly2.c in alphabetical order ===========*/
+
+void    qh_addhash(void *newelem, setT *hashtable, int hashsize, unsigned hash);
+
+void  qh_check_bestdist(void);
+
+void    qh_check_maxout(void);
+
+void    qh_check_output(void);
+
+void    qh_check_point(pointT *point, facetT *facet, realT *maxoutside, realT *maxdist, facetT * *errfacet1,
+                       facetT * *errfacet2);
+
+void    qh_check_points(void);
+
+void  qh_checkconvex(facetT *facetlist, int fault);
+
+void    qh_checkfacet(facetT *facet, boolT newmerge, boolT *waserrorp);
+
+void  qh_checkflipped_all(facetT *facetlist);
+
+void  qh_checkpolygon(facetT *facetlist);
+
+void    qh_checkvertex(vertexT *vertex);
+
+void  qh_clearcenters(qh_CENTER type);
+
+void  qh_createsimplex(setT *vertices);
+
+void  qh_delridge(ridgeT *ridge);
+
+void    qh_delvertex(vertexT *vertex);
+
+setT   * qh_facet3vertex(facetT *facet);
+
+facetT * qh_findbestfacet(pointT *point, boolT bestoutside, realT *bestdist, boolT *isoutside);
+
+facetT * qh_findbestlower(facetT *upperfacet, pointT *point, realT *bestdistp, int *numpart);
+
+facetT * qh_findfacet_all(pointT *point, realT *bestdist, boolT *isoutside, int *numpart);
+
+int   qh_findgood(facetT *facetlist, int goodhorizon);
+
+void  qh_findgood_all(facetT *facetlist);
+
+void    qh_furthestnext(void /* qh facet_list */);
+
+void    qh_furthestout(facetT *facet);
+
+void    qh_infiniteloop(facetT *facet);
+
+void  qh_initbuild(void);
+
+void  qh_initialhull(setT *vertices);
+
+setT   * qh_initialvertices(int dim, setT *maxpoints, pointT *points, int numpoints);
+
+vertexT * qh_isvertex(pointT *point, setT *vertices);
+
+vertexT * qh_makenewfacets(pointT *point /*horizon_list, visible_list*/);
+
+void    qh_matchduplicates(facetT *atfacet, int atskip, int hashsize, int *hashcount);
+
+void    qh_nearcoplanar( void /* qh.facet_list */);
+
+vertexT * qh_nearvertex(facetT *facet, pointT *point, realT *bestdistp);
+
+int   qh_newhashtable(int newsize);
+
+vertexT * qh_newvertex(pointT *point);
+
+ridgeT * qh_nextridge3d(ridgeT *atridge, facetT *facet, vertexT * *vertexp);
+
+void    qh_outcoplanar(void /* facet_list */);
+
+pointT * qh_point(int id);
+
+void  qh_point_add(setT *set, pointT *point, void *elem);
+
+setT   * qh_pointfacet(void /*qh facet_list*/);
+
+setT   * qh_pointvertex(void /*qh facet_list*/);
+
+void  qh_prependfacet(facetT *facet, facetT * *facetlist);
+
+void  qh_printhashtable(FILE *fp);
+
+void    qh_printlists(void);
+
+void    qh_resetlists(boolT stats, boolT resetVisible /*qh newvertex_list
+                                                         newfacet_list
+                                                         visible_list*/);
+
+void    qh_setvoronoi_all(void);
+
+void  qh_triangulate(void /*qh facet_list*/);
+
+void    qh_triangulate_facet(facetT *facetA, vertexT * *first_vertex);
+
+void    qh_triangulate_link(facetT *oldfacetA, facetT *facetA, facetT *oldfacetB, facetT *facetB);
+
+void  qh_triangulate_mirror(facetT *facetA, facetT *facetB);
+
+void    qh_triangulate_null(facetT *facetA);
+
+void    qh_vertexintersect(setT * *vertexsetA, setT *vertexsetB);
+
+setT   * qh_vertexintersect_new(setT *vertexsetA, setT *vertexsetB);
+
+void    qh_vertexneighbors(void /*qh facet_list*/);
+
+boolT   qh_vertexsubset(setT *vertexsetA, setT *vertexsetB);
+
+#endif /* qhDEFpoly */
diff --git a/BRAINSABC/qhull/poly2.c b/BRAINSABC/qhull/poly2.c
new file mode 100644
index 00000000..1c9632f5
--- /dev/null
+++ b/BRAINSABC/qhull/poly2.c
@@ -0,0 +1,3888 @@
+/*
  ---------------------------------
+
+  poly2.c
+  implements polygons and simplices
+
+  see qh-poly.htm, poly.h and qhull.h
+
+  frequently used code is in poly.c
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*======== functions in alphabetical order ==========*/
+
+/*---------------------------------
+
+  qh_addhash( newelem, hashtable, hashsize, hash )
+  add newelem to linear hash table at hash if not already there
+*/
+void qh_addhash(void* newelem, setT *hashtable, int hashsize, unsigned hash)
+{
+  int   scan;
+  void *elem;
+  for( scan = (int)hash; (elem = SETelem_(hashtable, scan) );
+       scan = (++scan >= hashsize ? 0 : scan) )
+    {
+    if( elem == newelem )
+      {
+      break;
+      }
+    }
+  /* loop terminates because qh_HASHfactor >= 1.1 by qh_initbuffers */
+  if( !elem )
+    {
+    SETelem_(hashtable, scan) = newelem;
+    }
+} /* addhash */
+
+/*---------------------------------
+
+  qh_check_bestdist()
+  check that all points are within max_outside of the nearest facet
+  if qh.ONLYgood,
+  ignores !good facets
+
+  see:
+  qh_check_maxout(), qh_outerinner()
+
+  notes:
+  only called from qh_check_points()
+  seldom used since qh.MERGING is almost always set
+  if notverified>0 at end of routine
+  some points were well inside the hull.  If the hull contains
+  a lens-shaped component, these points were not verified.  Use
+  options 'Qi Tv' to verify all points.  (Exhaustive check also verifies)
+
+  design:
+  determine facet for each point (if any)
+  for each point
+  start with the assigned facet or with the first facet
+  find the best facet for the point and check all coplanar facets
+  error if point is outside of facet
+*/
+void qh_check_bestdist(void)
+{
+  boolT   waserror = False, unassigned;
+  facetT *facet, *bestfacet, *errfacet1 = NULL, *errfacet2 = NULL;
+  facetT *facetlist;
+  realT   dist, maxoutside, maxdist = -REALmax;
+  pointT *point;
+  int     numpart = 0, facet_i, facet_n, notgood = 0, notverified = 0;
+  setT *  facets;
+
+  trace1( (qh ferr, "qh_check_bestdist: check points below nearest facet.  Facet_list f%d\n",
+           qh facet_list->id) );
+  maxoutside = qh_maxouter();
+  maxoutside += qh DISTround;
+  /* one more qh.DISTround for check computation */
+  trace1( (qh ferr, "qh_check_bestdist: check that all points are within %2.2g of best facet\n", maxoutside) );
+  facets = qh_pointfacet(/*qh facet_list*/);
+  if( !qh_QUICKhelp && qh PRINTprecision )
+    {
+    fprintf(qh ferr,
+            "\n\
+qhull output completed.  Verifying that %d points are\n\
+below %2.2g of the nearest %sfacet.\n"                                                                          ,
+            qh_setsize(
+              facets), maxoutside, (qh ONLYgood ?  "good " : "") );
+    }
+  FOREACHfacet_i_(facets) {  /* for each point with facet assignment */
+    if( facet )
+      {
+      unassigned = False;
+      }
+    else
+      {
+      unassigned = True;
+      facet = qh facet_list;
+      }
+    point = qh_point(facet_i);
+    if( point == qh GOODpointp )
+      {
+      continue;
+      }
+    qh_distplane(point, facet, &dist);
+    numpart++;
+    bestfacet = qh_findbesthorizon(!qh_IScheckmax, point, facet, qh_NOupper, &dist, &numpart);
+    /* occurs after statistics reported */
+    maximize_(maxdist, dist);
+    if( dist > maxoutside )
+      {
+      if( qh ONLYgood && !bestfacet->good
+          && !( (bestfacet = qh_findgooddist(point, bestfacet, &dist, &facetlist) )
+                && dist > maxoutside) )
+        {
+        notgood++;
+        }
+      else
+        {
+        waserror = True;
+        fprintf(qh ferr, "qhull precision error: point p%d is outside facet f%d, distance= %6.8g maxoutside= %6.8g\n",
+                facet_i, bestfacet->id, dist, maxoutside);
+        if( errfacet1 != bestfacet )
+          {
+          errfacet2 = errfacet1;
+          errfacet1 = bestfacet;
+          }
+        }
+      }
+    else if( unassigned && dist < -qh MAXcoplanar )
+      {
+      notverified++;
+      }
+    }
+  qh_settempfree(&facets);
+  if( notverified && !qh DELAUNAY && !qh_QUICKhelp && qh PRINTprecision )
+    {
+    fprintf(
+      qh ferr,
+      "\n%d points were well inside the hull.  If the hull contains\n\
+a lens-shaped component, these points were not verified.  Use\n\
+options 'Qci Tv' to verify all points.\n"                                                                                                                                        ,
+      notverified);
+    }
+  if( maxdist > qh outside_err )
+    {
+    fprintf(
+      qh ferr,
+      "qhull precision error (qh_check_bestdist): a coplanar point is %6.2g from convex hull.  The maximum value (qh.outside_err) is %6.2g\n",
+      maxdist, qh outside_err);
+    qh_errexit2(qh_ERRprec, errfacet1, errfacet2);
+    }
+  else if( waserror && qh outside_err > REALmax / 2 )
+    {
+    qh_errexit2(qh_ERRprec, errfacet1, errfacet2);
+    }
+  /*  else if (waserror)
+      ;                       ?* the error was logged to qh.ferr but does not effect the output */
+  trace0( (qh ferr, "qh_check_bestdist: max distance outside %2.2g\n", maxdist) );
+} /* check_bestdist */
+
+/*---------------------------------
+
+  qh_check_maxout()
+  updates qh.max_outside by checking all points against bestfacet
+  if qh.ONLYgood, ignores !good facets
+
+  returns:
+  updates facet->maxoutside via qh_findbesthorizon()
+  sets qh.maxoutdone
+  if printing qh.min_vertex (qh_outerinner),
+  it is updated to the current vertices
+  removes inside/coplanar points from coplanarset as needed
+
+  notes:
+  defines coplanar as min_vertex instead of MAXcoplanar
+  may not need to check near-inside points because of qh.MAXcoplanar
+  and qh.KEEPnearinside (before it was -DISTround)
+
+  see also:
+  qh_check_bestdist()
+
+  design:
+  if qh.min_vertex is needed
+  for all neighbors of all vertices
+  test distance from vertex to neighbor
+  determine facet for each point (if any)
+  for each point with an assigned facet
+  find the best facet for the point and check all coplanar facets
+  (updates outer planes)
+  remove near-inside points from coplanar sets
+*/
+#ifndef qh_NOmerge
+void qh_check_maxout(void)
+{
+  facetT * facet, *bestfacet, *neighbor, * *neighborp, *facetlist;
+  realT    dist, maxoutside, minvertex, old_maxoutside;
+  pointT * point;
+  int      numpart = 0, facet_i, facet_n, notgood = 0;
+  setT *   facets, *vertices;
+  vertexT *vertex;
+
+  trace1( (qh ferr, "qh_check_maxout: check and update maxoutside for each facet.\n") );
+  maxoutside = minvertex = 0;
+  if( qh VERTEXneighbors
+      && (qh PRINTsummary || qh KEEPinside || qh KEEPcoplanar
+          || qh TRACElevel || qh PRINTstatistics
+          || qh PRINTout[0] == qh_PRINTsummary || qh PRINTout[0] == qh_PRINTnone) )
+    {
+    trace1( (qh ferr, "qh_check_maxout: determine actual maxoutside and minvertex\n") );
+    vertices = qh_pointvertex(/*qh facet_list*/);
+    FORALLvertices {
+      FOREACHneighbor_(vertex) {
+        zinc_(Zdistvertex);  /* distance also computed by main loop below */
+        qh_distplane(vertex->point, neighbor, &dist);
+        minimize_(minvertex, dist);
+        if( -dist > qh TRACEdist || dist > qh TRACEdist
+            || neighbor == qh tracefacet || vertex == qh tracevertex )
+          {
+          fprintf(qh ferr, "qh_check_maxout: p%d (v%d) is %.2g from f%d\n",
+                  qh_pointid(vertex->point), vertex->id, dist, neighbor->id);
+          }
+        }
+      }
+    if( qh MERGING )
+      {
+      wmin_(Wminvertex, qh min_vertex);
+      }
+    qh min_vertex = minvertex;
+    qh_settempfree(&vertices);
+    }
+  facets = qh_pointfacet(/*qh facet_list*/);
+
+  do
+    {
+    old_maxoutside = fmax_(qh max_outside, maxoutside);
+    FOREACHfacet_i_(facets) {     /* for each point with facet assignment */
+      if( facet )
+        {
+        point = qh_point(facet_i);
+        if( point == qh GOODpointp )
+          {
+          continue;
+          }
+        zinc_(Ztotcheck);
+        qh_distplane(point, facet, &dist);
+        numpart++;
+        bestfacet = qh_findbesthorizon(qh_IScheckmax, point, facet, !qh_NOupper, &dist, &numpart);
+        if( bestfacet && dist > maxoutside )
+          {
+          if( qh ONLYgood && !bestfacet->good
+              && !( (bestfacet = qh_findgooddist(point, bestfacet, &dist, &facetlist) )
+                    && dist > maxoutside) )
+            {
+            notgood++;
+            }
+          else
+            {
+            maxoutside = dist;
+            }
+          }
+        if( dist > qh TRACEdist || (bestfacet && bestfacet == qh tracefacet) )
+          {
+          fprintf(qh ferr, "qh_check_maxout: p%d is %.2g above f%d\n",
+                  qh_pointid(point), dist, bestfacet->id);
+          }
+        }
+      }
+    }
+  while
+  ( maxoutside > 2 * old_maxoutside );
+
+  /* if qh.maxoutside increases substantially, qh_SEARCHdist is not valid
+     e.g., RBOX 5000 s Z1 G1e-13 t1001200614 | qhull */
+  zzadd_(Zcheckpart, numpart);
+  qh_settempfree(&facets);
+  wval_(Wmaxout) = maxoutside - qh max_outside;
+  wmax_(Wmaxoutside, qh max_outside);
+  qh max_outside = maxoutside;
+  qh_nearcoplanar(/*qh.facet_list*/);
+  qh maxoutdone = True;
+  trace1( (qh ferr, "qh_check_maxout: maxoutside %2.2g, min_vertex %2.2g, outside of not good %d\n",
+           maxoutside, qh min_vertex, notgood) );
+} /* check_maxout */
+
+#else /* qh_NOmerge */
+void qh_check_maxout(void)
+{
+}
+
+#endif
+
+/*---------------------------------
+
+  qh_check_output()
+  performs the checks at the end of qhull algorithm
+  Maybe called after voronoi output.  Will recompute otherwise centrums are Voronoi centers instead
+*/
+void qh_check_output(void)
+{
+  int i;
+
+  if( qh STOPcone )
+    {
+    return;
+    }
+  if( qh VERIFYoutput | qh IStracing | qh CHECKfrequently )
+    {
+    qh_checkpolygon(qh facet_list);
+    qh_checkflipped_all(qh facet_list);
+    qh_checkconvex(qh facet_list, qh_ALGORITHMfault);
+    }
+  else if( !qh MERGING && qh_newstats(qhstat precision, &i) )
+    {
+    qh_checkflipped_all(qh facet_list);
+    qh_checkconvex(qh facet_list, qh_ALGORITHMfault);
+    }
+} /* check_output */
+
+/*---------------------------------
+
+  qh_check_point( point, facet, maxoutside, maxdist, errfacet1, errfacet2 )
+  check that point is less than maxoutside from facet
+*/
+void qh_check_point(pointT *point, facetT *facet, realT *maxoutside, realT *maxdist, facetT * *errfacet1,
+                    facetT * *errfacet2)
+{
+  realT dist;
+
+  /* occurs after statistics reported */
+  qh_distplane(point, facet, &dist);
+  if( dist > *maxoutside )
+    {
+    if( *errfacet1 != facet )
+      {
+      *errfacet2 = *errfacet1;
+      *errfacet1 = facet;
+      }
+    fprintf(qh ferr, "qhull precision error: point p%d is outside facet f%d, distance= %6.8g maxoutside= %6.8g\n",
+            qh_pointid(point), facet->id, dist, *maxoutside);
+    }
+  maximize_(*maxdist, dist);
+} /* qh_check_point */
+
+/*---------------------------------
+
+  qh_check_points()
+  checks that all points are inside all facets
+
+  notes:
+  if many points and qh_check_maxout not called (i.e., !qh.MERGING),
+  calls qh_findbesthorizon (seldom done).
+  ignores flipped facets
+  maxoutside includes 2 qh.DISTrounds
+  one qh.DISTround for the computed distances in qh_check_points
+  qh_printafacet and qh_printsummary needs only one qh.DISTround
+  the computation for qh.VERIFYdirect does not account for qh.other_points
+
+  design:
+  if many points
+  use qh_check_bestdist()
+  else
+  for all facets
+  for all points
+  check that point is inside facet
+*/
+void qh_check_points(void)
+{
+  facetT *facet, *errfacet1 = NULL, *errfacet2 = NULL;
+  realT   total, maxoutside, maxdist = -REALmax;
+  pointT *point, * *pointp, *pointtemp;
+  boolT   testouter;
+
+  maxoutside = qh_maxouter();
+  maxoutside += qh DISTround;
+  /* one more qh.DISTround for check computation */
+  trace1( (qh ferr, "qh_check_points: check all points below %2.2g of all facet planes\n",
+           maxoutside) );
+  if( qh num_good )   /* miss counts other_points and !good facets */
+    {
+    total = (float) qh num_good * qh num_points;
+    }
+  else
+    {
+    total = (float) qh num_facets * qh num_points;
+    }
+  if( total >= qh_VERIFYdirect && !qh maxoutdone )
+    {
+    if( !qh_QUICKhelp && qh SKIPcheckmax && qh MERGING )
+      {
+      fprintf(
+        qh ferr,
+        "\n\
+qhull input warning: merging without checking outer planes ('Q5' or 'Po').\n\
+Verify may report that a point is outside of a facet.\n"                                                                                           );
+      }
+    qh_check_bestdist();
+    }
+  else
+    {
+    if( qh_MAXoutside && qh maxoutdone )
+      {
+      testouter = True;
+      }
+    else
+      {
+      testouter = False;
+      }
+    if( !qh_QUICKhelp )
+      {
+      if( qh MERGEexact )
+        {
+        fprintf(
+          qh ferr,
+          "\n\
+qhull input warning: exact merge ('Qx').  Verify may report that a point\n\
+is outside of a facet.  See qh-optq.htm#Qx\n"                                                                                           );
+        }
+      else if( qh SKIPcheckmax || qh NOnearinside )
+        {
+        fprintf(
+          qh ferr,
+          "\n\
+qhull input warning: no outer plane check ('Q5') or no processing of\n\
+near-inside points ('Q8').  Verify may report that a point is outside\n\
+of a facet.\n"                                                                                                                                                                );
+        }
+      }
+    if( qh PRINTprecision )
+      {
+      if( testouter )
+        {
+        fprintf(
+          qh ferr,
+          "\n\
+Output completed.  Verifying that all points are below outer planes of\n\
+all %sfacets.  Will make %2.0f distance computations.\n"                                                                                         ,
+          (qh ONLYgood ?  "good " : ""),
+          total);
+        }
+      else
+        {
+        fprintf(
+          qh ferr,
+          "\n\
+Output completed.  Verifying that all points are below %2.2g of\n\
+all %sfacets.  Will make %2.0f distance computations.\n"                                                                                  ,
+          maxoutside, (qh ONLYgood ?  "good " : ""),
+          total);
+        }
+      }
+    FORALLfacets {
+      if( !facet->good && qh ONLYgood )
+        {
+        continue;
+        }
+      if( facet->flipped )
+        {
+        continue;
+        }
+      if( !facet->normal )
+        {
+        fprintf( qh ferr, "qhull warning (qh_check_points): missing normal for facet f%d\n", facet->id);
+        continue;
+        }
+      if( testouter )
+        {
+#if qh_MAXoutside
+        maxoutside = facet->maxoutside + 2 * qh DISTround;
+        /* one DISTround to actual point and another to computed point */
+#endif
+        }
+      FORALLpoints {
+        if( point != qh GOODpointp )
+          {
+          qh_check_point(point, facet, &maxoutside, &maxdist, &errfacet1, &errfacet2);
+          }
+        }
+      FOREACHpoint_(qh other_points) {
+        if( point != qh GOODpointp )
+          {
+          qh_check_point(point, facet, &maxoutside, &maxdist, &errfacet1, &errfacet2);
+          }
+        }
+      }
+    if( maxdist > qh outside_err )
+      {
+      fprintf(
+        qh ferr,
+        "qhull precision error (qh_check_points): a coplanar point is %6.2g from convex hull.  The maximum value (qh.outside_err) is %6.2g\n",
+        maxdist, qh outside_err );
+      qh_errexit2( qh_ERRprec, errfacet1, errfacet2 );
+      }
+    else if( errfacet1 && qh outside_err > REALmax / 2 )
+      {
+      qh_errexit2( qh_ERRprec, errfacet1, errfacet2 );
+      }
+    /*    else if (errfacet1)
+    ;  ?* the error was logged to qh.ferr but does not effect the output */
+    trace0( (qh ferr, "qh_check_points: max distance outside %2.2g\n", maxdist) );
+    }
+} /* check_points */
+
+/*---------------------------------
+
+  qh_checkconvex( facetlist, fault )
+  check that each ridge in facetlist is convex
+  fault = qh_DATAfault if reporting errors
+  = qh_ALGORITHMfault otherwise
+
+  returns:
+  counts Zconcaveridges and Zcoplanarridges
+  errors if concaveridge or if merging an coplanar ridge
+
+  note:
+  if not merging,
+  tests vertices for neighboring simplicial facets
+  else if ZEROcentrum,
+  tests vertices for neighboring simplicial   facets
+  else
+  tests centrums of neighboring facets
+
+  design:
+  for all facets
+  report flipped facets
+  if ZEROcentrum and simplicial neighbors
+  test vertices for neighboring simplicial facets
+  else
+  test centrum against all neighbors
+*/
+void qh_checkconvex(facetT *facetlist, int fault)
+{
+  facetT * facet, *neighbor, * *neighborp, *errfacet1 = NULL, *errfacet2 = NULL;
+  vertexT *vertex;
+  realT    dist;
+  pointT * centrum;
+  boolT    waserror = False, centrum_warning = False, tempcentrum = False, allsimplicial;
+  int      neighbor_i;
+
+  trace1( (qh ferr, "qh_checkconvex: check all ridges are convex\n") );
+  if( !qh RERUN )
+    {
+    zzval_(Zconcaveridges) = 0;
+    zzval_(Zcoplanarridges) = 0;
+    }
+  FORALLfacet_(facetlist) {
+    if( facet->flipped )
+      {
+      qh_precision("flipped facet");
+      fprintf(qh ferr, "qhull precision error: f%d is flipped (interior point is outside)\n",
+              facet->id);
+      errfacet1 = facet;
+      waserror = True;
+      continue;
+      }
+    if( qh MERGING && (!qh ZEROcentrum || !facet->simplicial || facet->tricoplanar) )
+      {
+      allsimplicial = False;
+      }
+    else
+      {
+      allsimplicial = True;
+      neighbor_i = 0;
+      FOREACHneighbor_(facet) {
+        vertex = SETelemt_(facet->vertices, neighbor_i++, vertexT);
+        if( !neighbor->simplicial || neighbor->tricoplanar )
+          {
+          allsimplicial = False;
+          continue;
+          }
+        qh_distplane(vertex->point, neighbor, &dist);
+        if( dist > -qh DISTround )
+          {
+          if( fault == qh_DATAfault )
+            {
+            qh_precision("coplanar or concave ridge");
+            fprintf(qh ferr, "qhull precision error: initial simplex is not convex. Distance=%.2g\n", dist);
+            qh_errexit(qh_ERRsingular, NULL, NULL);
+            }
+          if( dist > qh DISTround )
+            {
+            zzinc_(Zconcaveridges);
+            qh_precision("concave ridge");
+            fprintf(qh ferr, "qhull precision error: f%d is concave to f%d, since p%d (v%d) is %6.4g above\n",
+                    facet->id, neighbor->id, qh_pointid(vertex->point), vertex->id, dist);
+            errfacet1 = facet;
+            errfacet2 = neighbor;
+            waserror = True;
+            }
+          else if( qh ZEROcentrum )
+            {
+            if( dist > 0 )       /* qh_checkzero checks that dist < - qh
+                                   DISTround */
+              {
+              zzinc_(Zcoplanarridges);
+              qh_precision("coplanar ridge");
+              fprintf(qh ferr,
+                      "qhull precision error: f%d is clearly not convex to f%d, since p%d (v%d) is %6.4g above\n",
+                      facet->id, neighbor->id, qh_pointid(
+                        vertex->point), vertex->id, dist);
+              errfacet1 = facet;
+              errfacet2 = neighbor;
+              waserror = True;
+              }
+            }
+          else
+            {
+            zzinc_(Zcoplanarridges);
+            qh_precision("coplanar ridge");
+            trace0( (qh ferr,
+                     "qhull precision error: f%d may be coplanar to f%d, since p%d (v%d) is within %6.4g during p%d\n",
+                     facet->id, neighbor->id, qh_pointid(vertex->point), vertex->id, dist, qh furthest_id) );
+            }
+          }
+        }
+      }
+    if( !allsimplicial )
+      {
+      if( qh CENTERtype == qh_AScentrum )
+        {
+        if( !facet->center )
+          {
+          facet->center = qh_getcentrum(facet);
+          }
+        centrum = facet->center;
+        }
+      else
+        {
+        if( !centrum_warning && (!facet->simplicial || facet->tricoplanar) )
+          {
+          centrum_warning = True;
+          fprintf(qh ferr,
+                  "qhull note: recomputing centrums for convexity test.  This may lead to false, precision errors.\n");
+          }
+        centrum = qh_getcentrum(facet);
+        tempcentrum = True;
+        }
+      FOREACHneighbor_(facet) {
+        if( qh ZEROcentrum && facet->simplicial && neighbor->simplicial )
+          {
+          continue;
+          }
+        if( facet->tricoplanar || neighbor->tricoplanar )
+          {
+          continue;
+          }
+        zzinc_(Zdistconvex);
+        qh_distplane(centrum, neighbor, &dist);
+        if( dist > qh DISTround )
+          {
+          zzinc_(Zconcaveridges);
+          qh_precision("concave ridge");
+          fprintf(qh ferr, "qhull precision error: f%d is concave to f%d.  Centrum of f%d is %6.4g above f%d\n",
+                  facet->id, neighbor->id, facet->id, dist, neighbor->id);
+          errfacet1 = facet;
+          errfacet2 = neighbor;
+          waserror = True;
+          }
+        else if( dist >= 0.0 ) /* if arithmetic always rounds the same,
+              can test against centrum radius instead */
+          {
+          zzinc_(Zcoplanarridges);
+          qh_precision("coplanar ridge");
+          fprintf(qh ferr,
+                  "qhull precision error: f%d is coplanar or concave to f%d.  Centrum of f%d is %6.4g above f%d\n",
+                  facet->id, neighbor->id, facet->id, dist,
+                  neighbor->id);
+          errfacet1 = facet;
+          errfacet2 = neighbor;
+          waserror = True;
+          }
+        }
+      if( tempcentrum )
+        {
+        qh_memfree(centrum, qh normal_size);
+        }
+      }
+    }
+  if( waserror && !qh FORCEoutput )
+    {
+    qh_errexit2(qh_ERRprec, errfacet1, errfacet2);
+    }
+} /* checkconvex */
+
+/*---------------------------------
+
+  qh_checkfacet( facet, newmerge, waserror )
+  checks for consistency errors in facet
+  newmerge set if from merge.c
+
+  returns:
+  sets waserror if any error occurs
+
+  checks:
+  vertex ids are inverse sorted
+  unless newmerge, at least hull_dim neighbors and vertices (exactly if simplicial)
+  if non-simplicial, at least as many ridges as neighbors
+  neighbors are not duplicated
+  ridges are not duplicated
+  in 3-d, ridges=verticies
+  (qh.hull_dim-1) ridge vertices
+  neighbors are reciprocated
+  ridge neighbors are facet neighbors and a ridge for every neighbor
+  simplicial neighbors match facetintersect
+  vertex intersection matches vertices of common ridges
+  vertex neighbors and facet vertices agree
+  all ridges have distinct vertex sets
+
+  notes:
+  uses neighbor->seen
+
+  design:
+  check sets
+  check vertices
+  check sizes of neighbors and vertices
+  check for qh_MERGEridge and qh_DUPLICATEridge flags
+  check neighbor set
+  check ridge set
+  check ridges, neighbors, and vertices
+*/
+void qh_checkfacet(facetT *facet, boolT newmerge, boolT *waserrorp)
+{
+  facetT * neighbor, * *neighborp, *errother = NULL;
+  ridgeT * ridge, * *ridgep, *errridge = NULL, *ridge2;
+  vertexT *vertex, * *vertexp;
+  unsigned previousid = INT_MAX;
+  int      numneighbors, numvertices, numridges = 0, numRvertices = 0;
+  boolT    waserror = False;
+  int      skipA, skipB, ridge_i, ridge_n, i;
+  setT *   intersection;
+
+  if( facet->visible )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d is on the visible_list\n",
+            facet->id);
+    qh_errexit(qh_ERRqhull, facet, NULL);
+    }
+  if( !facet->normal )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d does not have  a normal\n",
+            facet->id);
+    waserror = True;
+    }
+  qh_setcheck(facet->vertices, "vertices for f", facet->id);
+  qh_setcheck(facet->ridges, "ridges for f", facet->id);
+  qh_setcheck(facet->outsideset, "outsideset for f", facet->id);
+  qh_setcheck(facet->coplanarset, "coplanarset for f", facet->id);
+  qh_setcheck(facet->neighbors, "neighbors for f", facet->id);
+  FOREACHvertex_(facet->vertices) {
+    if( vertex->deleted )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): deleted vertex v%d in f%d\n", vertex->id, facet->id);
+      qh_errprint("ERRONEOUS", NULL, NULL, NULL, vertex);
+      waserror = True;
+      }
+    if( vertex->id >= previousid )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): vertices of f%d are not in descending id order at v%d\n",
+              facet->id,
+              vertex->id);
+      waserror = True;
+      break;
+      }
+    previousid = vertex->id;
+    }
+  numneighbors = qh_setsize(facet->neighbors);
+  numvertices = qh_setsize(facet->vertices);
+  numridges = qh_setsize(facet->ridges);
+  if( facet->simplicial )
+    {
+    if( numvertices + numneighbors != 2 * qh hull_dim
+        && !facet->degenerate && !facet->redundant )
+      {
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_checkfacet): for simplicial facet f%d, #vertices %d + #neighbors %d != 2*qh hull_dim\n",
+        facet->id, numvertices, numneighbors);
+      qh_setprint(qh ferr, "", facet->neighbors);
+      waserror = True;
+      }
+    }
+  else    /* non-simplicial */
+    {
+    if( !newmerge
+        && (numvertices < qh hull_dim || numneighbors < qh hull_dim)
+        && !facet->degenerate && !facet->redundant )
+      {
+      fprintf(qh ferr,
+              "qhull internal error (qh_checkfacet): for facet f%d, #vertices %d or #neighbors %d < qh hull_dim\n",
+              facet->id, numvertices,
+              numneighbors);
+      waserror = True;
+      }
+    /* in 3-d, can get a vertex twice in an edge list, e.g., RBOX 1000 s W1e-13
+      t995849315 D2 | QHULL d Tc Tv TP624 TW1e-13 T4 */
+    if( numridges < numneighbors
+        || (qh hull_dim == 3 && numvertices > numridges && !qh NEWfacets)
+        || (qh hull_dim == 2 && numridges + numvertices + numneighbors != 6) )
+      {
+      if( !facet->degenerate && !facet->redundant )
+        {
+        fprintf(
+          qh ferr,
+          "qhull internal error (qh_checkfacet): for facet f%d, #ridges %d < #neighbors %d or (3-d) > #vertices %d or (2-d) not all 2\n",
+          facet->id, numridges, numneighbors, numvertices);
+        waserror = True;
+        }
+      }
+    }
+  FOREACHneighbor_(facet) {
+    if( neighbor == qh_MERGEridge || neighbor == qh_DUPLICATEridge )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d still has a MERGE or DUP neighbor\n", facet->id);
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    neighbor->seen = True;
+    }
+  FOREACHneighbor_(facet) {
+    if( !qh_setin(neighbor->neighbors, facet) )
+      {
+      fprintf(qh ferr,
+              "qhull internal error (qh_checkfacet): facet f%d has neighbor f%d, but f%d does not have neighbor f%d\n",
+              facet->id, neighbor->id, neighbor->id,
+              facet->id);
+      errother = neighbor;
+      waserror = True;
+      }
+    if( !neighbor->seen )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d has a duplicate neighbor f%d\n",
+              facet->id, neighbor->id);
+      errother = neighbor;
+      waserror = True;
+      }
+    neighbor->seen = False;
+    }
+  FOREACHridge_(facet->ridges) {
+    qh_setcheck(ridge->vertices, "vertices for r", ridge->id);
+    ridge->seen = False;
+    }
+  FOREACHridge_(facet->ridges) {
+    if( ridge->seen )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d has a duplicate ridge r%d\n",
+              facet->id, ridge->id);
+      errridge = ridge;
+      waserror = True;
+      }
+    ridge->seen = True;
+    numRvertices = qh_setsize(ridge->vertices);
+    if( numRvertices != qh hull_dim - 1 )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): ridge between f%d and f%d has %d vertices\n",
+              ridge->top->id, ridge->bottom->id, numRvertices);
+      errridge = ridge;
+      waserror = True;
+      }
+    neighbor = otherfacet_(ridge, facet);
+    neighbor->seen = True;
+    if( !qh_setin(facet->neighbors, neighbor) )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkfacet): for facet f%d, neighbor f%d of ridge r%d not in facet\n",
+              facet->id, neighbor->id, ridge->id);
+      errridge = ridge;
+      waserror = True;
+      }
+    }
+  if( !facet->simplicial )
+    {
+    FOREACHneighbor_(facet) {
+      if( !neighbor->seen )
+        {
+        fprintf(qh ferr, "qhull internal error (qh_checkfacet): facet f%d does not have a ridge for neighbor f%d\n",
+                facet->id, neighbor->id);
+        errother = neighbor;
+        waserror = True;
+        }
+      intersection = qh_vertexintersect_new(facet->vertices, neighbor->vertices);
+      qh_settemppush(intersection);
+      FOREACHvertex_(facet->vertices) {
+        vertex->seen = False;
+        vertex->seen2 = False;
+        }
+      FOREACHvertex_(intersection)
+      vertex->seen = True;
+      FOREACHridge_(facet->ridges) {
+        if( neighbor != otherfacet_(ridge, facet) )
+          {
+          continue;
+          }
+        FOREACHvertex_(ridge->vertices) {
+          if( !vertex->seen )
+            {
+            fprintf(qh ferr, "qhull internal error (qh_checkfacet): vertex v%d in r%d not in f%d intersect f%d\n",
+                    vertex->id, ridge->id, facet->id, neighbor->id);
+            qh_errexit(qh_ERRqhull, facet, ridge);
+            }
+          vertex->seen2 = True;
+          }
+        }
+      if( !newmerge )
+        {
+        FOREACHvertex_(intersection) {
+          if( !vertex->seen2 )
+            {
+            if( qh IStracing >= 3 || !qh MERGING )
+              {
+              fprintf(
+                qh ferr,
+                "qhull precision error (qh_checkfacet): vertex v%d in f%d intersect f%d but\n\
+ not in a ridge.  This is ok under merging.  Last point was p%d\n"                                                                                               ,
+                vertex->id, facet->id, neighbor->id,
+                qh furthest_id);
+              if( !qh FORCEoutput && !qh MERGING )
+                {
+                qh_errprint("ERRONEOUS", facet, neighbor, NULL, vertex);
+                if( !qh MERGING )
+                  {
+                  qh_errexit(qh_ERRqhull, NULL, NULL);
+                  }
+                }
+              }
+            }
+          }
+        }
+      qh_settempfree(&intersection);
+      }
+    }
+  else    /* simplicial */
+    {
+    FOREACHneighbor_(facet) {
+      if( neighbor->simplicial )
+        {
+        skipA = SETindex_(facet->neighbors, neighbor);
+        skipB = qh_setindex(neighbor->neighbors, facet);
+        if( !qh_setequal_skip(facet->vertices, skipA, neighbor->vertices, skipB) )
+          {
+          fprintf(qh ferr,
+                  "qhull internal error (qh_checkfacet): facet f%d skip %d and neighbor f%d skip %d do not match \n",
+                  facet->id, skipA, neighbor->id,
+                  skipB);
+          errother = neighbor;
+          waserror = True;
+          }
+        }
+      }
+    }
+  if( qh hull_dim < 5 && (qh IStracing > 2 || qh CHECKfrequently) )
+    {
+    FOREACHridge_i_(facet->ridges) {           /* expensive */
+      for( i = ridge_i + 1; i < ridge_n; i++ )
+        {
+        ridge2 = SETelemt_(facet->ridges, i, ridgeT);
+        if( qh_setequal(ridge->vertices, ridge2->vertices) )
+          {
+          fprintf(qh ferr, "qh_checkfacet: ridges r%d and r%d have the same vertices\n",
+                  ridge->id, ridge2->id);
+          errridge = ridge;
+          waserror = True;
+          }
+        }
+      }
+    }
+  if( waserror )
+    {
+    qh_errprint("ERRONEOUS", facet, errother, errridge, NULL);
+    *waserrorp = True;
+    }
+} /* checkfacet */
+
+/*---------------------------------
+
+  qh_checkflipped_all( facetlist )
+  checks orientation of facets in list against interior point
+*/
+void qh_checkflipped_all(facetT *facetlist)
+{
+  facetT *facet;
+  boolT   waserror = False;
+  realT   dist;
+
+  if( facetlist == qh facet_list )
+    {
+    zzval_(Zflippedfacets) = 0;
+    }
+  FORALLfacet_(facetlist) {
+    if( facet->normal && !qh_checkflipped(facet, &dist, !qh_ALL) )
+      {
+      fprintf(qh ferr, "qhull precision error: facet f%d is flipped, distance= %6.12g\n",
+              facet->id, dist);
+      if( !qh FORCEoutput )
+        {
+        qh_errprint("ERRONEOUS", facet, NULL, NULL, NULL);
+        waserror = True;
+        }
+      }
+    }
+  if( waserror )
+    {
+    fprintf(
+      qh ferr,
+      "\n\
+A flipped facet occurs when its distance to the interior point is\n\
+greater than %2.2g, the maximum roundoff error.\n"                                                                                ,
+      -qh DISTround);
+    qh_errexit(qh_ERRprec, NULL, NULL);
+    }
+} /* checkflipped_all */
+
+/*---------------------------------
+
+  qh_checkpolygon( facetlist )
+  checks the correctness of the structure
+
+  notes:
+  call with either qh.facet_list or qh.newfacet_list
+  checks num_facets and num_vertices if qh.facet_list
+
+  design:
+  for each facet
+  checks facet and outside set
+  initializes vertexlist
+  for each facet
+  checks vertex set
+  if checking all facets (qh.facetlist)
+  check facet count
+  if qh.VERTEXneighbors
+  check vertex neighbors and count
+  check vertex count
+*/
+void qh_checkpolygon(facetT *facetlist)
+{
+  facetT * facet;
+  vertexT *vertex, * *vertexp, *vertexlist;
+  int      numfacets = 0, numvertices = 0, numridges = 0;
+  int      totvneighbors = 0, totvertices = 0;
+  boolT    waserror = False, nextseen = False, visibleseen = False;
+
+  trace1( (qh ferr, "qh_checkpolygon: check all facets from f%d\n", facetlist->id) );
+  if( facetlist != qh facet_list || qh ONLYgood )
+    {
+    nextseen = True;
+    }
+  FORALLfacet_(facetlist) {
+    if( facet == qh visible_list )
+      {
+      visibleseen = True;
+      }
+    if( !facet->visible )
+      {
+      if( !nextseen )
+        {
+        if( facet == qh facet_next )
+          {
+          nextseen = True;
+          }
+        else if( qh_setsize(facet->outsideset) )
+          {
+          if( !qh NARROWhull
+#if !qh_COMPUTEfurthest
+              || facet->furthestdist >= qh MINoutside
+#endif
+              )
+            {
+            fprintf(qh ferr, "qhull internal error (qh_checkpolygon): f%d has outside points before qh facet_next\n",
+                    facet->id);
+            qh_errexit(qh_ERRqhull, facet, NULL);
+            }
+          }
+        }
+      numfacets++;
+      qh_checkfacet(facet, False, &waserror);
+      }
+    }
+  if( qh visible_list && !visibleseen && facetlist == qh facet_list )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_checkpolygon): visible list f%d no longer on facet list\n",
+            qh visible_list->id);
+    qh_printlists();
+    qh_errexit(qh_ERRqhull, qh visible_list, NULL);
+    }
+  if( facetlist == qh facet_list )
+    {
+    vertexlist = qh vertex_list;
+    }
+  else if( facetlist == qh newfacet_list )
+    {
+    vertexlist = qh newvertex_list;
+    }
+  else
+    {
+    vertexlist = NULL;
+    }
+  FORALLvertex_(vertexlist) {
+    vertex->seen = False;
+    vertex->visitid = 0;
+    }
+  FORALLfacet_(facetlist) {
+    if( facet->visible )
+      {
+      continue;
+      }
+    if( facet->simplicial )
+      {
+      numridges += qh hull_dim;
+      }
+    else
+      {
+      numridges += qh_setsize(facet->ridges);
+      }
+    FOREACHvertex_(facet->vertices) {
+      vertex->visitid++;
+      if( !vertex->seen )
+        {
+        vertex->seen = True;
+        numvertices++;
+        if( qh_pointid(vertex->point) == -1 )
+          {
+          fprintf(qh ferr, "qhull internal error (qh_checkpolygon): unknown point %p for vertex v%d first_point %p\n",
+                  vertex->point, vertex->id, qh first_point);
+          waserror = True;
+          }
+        }
+      }
+    }
+  qh vertex_visit += numfacets;
+  if( facetlist == qh facet_list )
+    {
+    if( numfacets != qh num_facets - qh num_visible )
+      {
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_checkpolygon): actual number of facets is %d, cumulative facet count is %d - %d visible facets\n",
+        numfacets, qh num_facets, qh num_visible);
+      waserror = True;
+      }
+    qh vertex_visit++;
+    if( qh VERTEXneighbors )
+      {
+      FORALLvertices {
+        qh_setcheck(vertex->neighbors, "neighbors for v", vertex->id);
+        if( vertex->deleted )
+          {
+          continue;
+          }
+        totvneighbors += qh_setsize(vertex->neighbors);
+        }
+      FORALLfacet_(facetlist)
+      totvertices += qh_setsize(facet->vertices);
+      if( totvneighbors != totvertices )
+        {
+        fprintf(
+          qh ferr,
+          "qhull internal error (qh_checkpolygon): vertex neighbors inconsistent.  Totvneighbors %d, totvertices %d\n",
+          totvneighbors, totvertices);
+        waserror = True;
+        }
+      }
+    if( numvertices != qh num_vertices - qh_setsize(qh del_vertices) )
+      {
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_checkpolygon): actual number of vertices is %d, cumulative vertex count is %d\n",
+        numvertices, qh num_vertices - qh_setsize(qh del_vertices) );
+      waserror = True;
+      }
+    if( qh hull_dim == 2 && numvertices != numfacets )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_checkpolygon): #vertices %d != #facets %d\n",
+              numvertices, numfacets);
+      waserror = True;
+      }
+    if( qh hull_dim == 3 && numvertices + numfacets - numridges / 2 != 2 )
+      {
+      fprintf(
+        qh ferr,
+        "qhull warning: #vertices %d + #facets %d - #edges %d != 2\n\
+	A vertex appears twice in a edge list.  May occur during merging."                                                                     ,
+        numvertices, numfacets,
+        numridges / 2);
+      /* occurs if lots of merging and a vertex ends up twice in an edge list.
+         e.g., RBOX 1000 s W1e-13 t995849315 D2 | QHULL d Tc Tv */
+      }
+    }
+  if( waserror )
+    {
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+} /* checkpolygon */
+
+/*---------------------------------
+
+  qh_checkvertex( vertex )
+  check vertex for consistency
+  checks vertex->neighbors
+
+  notes:
+  neighbors checked efficiently in checkpolygon
+*/
+void qh_checkvertex(vertexT *vertex)
+{
+  boolT   waserror = False;
+  facetT *neighbor, * *neighborp, *errfacet = NULL;
+
+  if( qh_pointid(vertex->point) == -1 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_checkvertex): unknown point id %p\n", vertex->point);
+    waserror = True;
+    }
+  if( vertex->id >= qh vertex_id )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_checkvertex): unknown vertex id %d\n", vertex->id);
+    waserror = True;
+    }
+  if( !waserror && !vertex->deleted )
+    {
+    if( qh_setsize(vertex->neighbors) )
+      {
+      FOREACHneighbor_(vertex) {
+        if( !qh_setin(neighbor->vertices, vertex) )
+          {
+          fprintf(qh ferr, "qhull internal error (qh_checkvertex): neighbor f%d does not contain v%d\n", neighbor->id,
+                  vertex->id);
+          errfacet = neighbor;
+          waserror = True;
+          }
+        }
+      }
+    }
+  if( waserror )
+    {
+    qh_errprint("ERRONEOUS", NULL, NULL, NULL, vertex);
+    qh_errexit(qh_ERRqhull, errfacet, NULL);
+    }
+} /* checkvertex */
+
+/*---------------------------------
+
+  qh_clearcenters( type )
+  clear old data from facet->center
+
+  notes:
+  sets new centertype
+  nop if CENTERtype is the same
+*/
+void qh_clearcenters(qh_CENTER type)
+{
+  facetT *facet;
+
+  if( qh CENTERtype != type )
+    {
+    FORALLfacets {
+      if( qh CENTERtype == qh_ASvoronoi )
+        {
+        if( facet->center )
+          {
+          qh_memfree(facet->center, qh center_size);
+          facet->center = NULL;
+          }
+        }
+      else  /* qh CENTERtype == qh_AScentrum */
+        {
+        if( facet->center )
+          {
+          qh_memfree(facet->center, qh normal_size);
+          facet->center = NULL;
+          }
+        }
+      }
+    qh CENTERtype = type;
+    }
+  trace2( (qh ferr, "qh_clearcenters: switched to center type %d\n", type) );
+} /* clearcenters */
+
+/*---------------------------------
+
+  qh_createsimplex( vertices )
+  creates a simplex from a set of vertices
+
+  returns:
+  initializes qh.facet_list to the simplex
+  initializes qh.newfacet_list, .facet_tail
+  initializes qh.vertex_list, .newvertex_list, .vertex_tail
+
+  design:
+  initializes lists
+  for each vertex
+  create a new facet
+  for each new facet
+  create its neighbor set
+*/
+void qh_createsimplex(setT *vertices)
+{
+  facetT * facet = NULL, *newfacet;
+  boolT    toporient = True;
+  int      vertex_i, vertex_n, nth;
+  setT *   newfacets = qh_settemp(qh hull_dim + 1);
+  vertexT *vertex;
+
+  qh facet_list = qh newfacet_list = qh facet_tail = qh_newfacet();
+  qh num_facets = qh num_vertices = qh num_visible = 0;
+  qh vertex_list = qh newvertex_list = qh vertex_tail = qh_newvertex(NULL);
+
+  FOREACHvertex_i_(vertices) {
+    newfacet = qh_newfacet();
+    newfacet->vertices = qh_setnew_delnthsorted(vertices, vertex_n,
+                                                (size_t)vertex_i, (size_t)0);
+    newfacet->toporient = toporient;
+    qh_appendfacet(newfacet);
+    newfacet->newfacet = True;
+    qh_appendvertex(vertex);
+    qh_setappend(&newfacets, newfacet);
+    toporient ^= True;
+    }
+  FORALLnew_facets {
+    nth = 0;
+    FORALLfacet_(qh newfacet_list) {
+      if( facet != newfacet )
+        {
+        SETelem_(newfacet->neighbors, nth++) = facet;
+        }
+      }
+    qh_settruncate(newfacet->neighbors, (size_t) qh hull_dim);
+    }
+  qh_settempfree(&newfacets);
+  trace1( (qh ferr, "qh_createsimplex: created simplex\n") );
+} /* createsimplex */
+
+/*---------------------------------
+
+  qh_delridge( ridge )
+  deletes ridge from data structures it belongs to
+  frees up its memory
+
+  notes:
+  in merge.c, caller sets vertex->delridge for each vertex
+  ridges also freed in qh_freeqhull
+*/
+void qh_delridge(ridgeT *ridge)
+{
+  void * *freelistp; /* used !qh_NOmem */
+
+  qh_setdel(ridge->top->ridges, ridge);
+  qh_setdel(ridge->bottom->ridges, ridge);
+  qh_setfree(&(ridge->vertices) );
+  qh_memfree_(ridge, sizeof(ridgeT), freelistp);
+} /* delridge */
+
+/*---------------------------------
+
+  qh_delvertex( vertex )
+  deletes a vertex and frees its memory
+
+  notes:
+  assumes vertex->adjacencies have been updated if needed
+  unlinks from vertex_list
+*/
+void qh_delvertex(vertexT *vertex)
+{
+
+  if( vertex == qh tracevertex )
+    {
+    qh tracevertex = NULL;
+    }
+  qh_removevertex(vertex);
+  qh_setfree(&vertex->neighbors);
+  qh_memfree(vertex, sizeof(vertexT) );
+} /* delvertex */
+
+/*---------------------------------
+
+  qh_facet3vertex(  )
+  return temporary set of 3-d vertices in qh_ORIENTclock order
+
+  design:
+  if simplicial facet
+  build set from facet->vertices with facet->toporient
+  else
+  for each ridge in order
+  build set from ridge's vertices
+*/
+setT * qh_facet3vertex(facetT *facet)
+{
+  ridgeT * ridge, *firstridge;
+  vertexT *vertex;
+  int      cntvertices, cntprojected = 0;
+  setT *   vertices;
+
+  cntvertices = qh_setsize(facet->vertices);
+  vertices = qh_settemp(cntvertices);
+  if( facet->simplicial )
+    {
+    if( cntvertices != 3 )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_facet3vertex): only %d vertices for simplicial facet f%d\n",
+              cntvertices, facet->id);
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    qh_setappend(&vertices, SETfirst_(facet->vertices) );
+    if( facet->toporient ^ qh_ORIENTclock )
+      {
+      qh_setappend(&vertices, SETsecond_(facet->vertices) );
+      }
+    else
+      {
+      qh_setaddnth(&vertices, 0, SETsecond_(facet->vertices) );
+      }
+    qh_setappend(&vertices, SETelem_(facet->vertices, 2) );
+    }
+  else
+    {
+    ridge = firstridge = SETfirstt_(facet->ridges, ridgeT);   /* no infinite */
+    while( (ridge = qh_nextridge3d(ridge, facet, &vertex) ) )
+      {
+      qh_setappend(&vertices, vertex);
+      if( ++cntprojected > cntvertices || ridge == firstridge )
+        {
+        break;
+        }
+      }
+
+    if( !ridge || cntprojected != cntvertices )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_facet3vertex): ridges for facet %d don't match up.  got at least %d\n",
+              facet->id, cntprojected);
+      qh_errexit(qh_ERRqhull, facet, ridge);
+      }
+    }
+  return vertices;
+} /* facet3vertex */
+
+/*---------------------------------
+
+  qh_findbestfacet( point, bestoutside, bestdist, isoutside )
+  find facet that is furthest below a point
+
+  for Delaunay triangulations,
+  Use qh_setdelaunay() to lift point to paraboloid and scale by 'Qbb' if needed
+  Do not use options 'Qbk', 'QBk', or 'QbB' since they scale the coordinates.
+
+  returns:
+  if bestoutside is set (e.g., qh_ALL)
+  returns best facet that is not upperdelaunay
+  if Delaunay and inside, point is outside circumsphere of bestfacet
+  else
+  returns first facet below point
+  if point is inside, returns nearest, !upperdelaunay facet
+  distance to facet
+  isoutside set if outside of facet
+
+  notes:
+  For tricoplanar facets, this finds one of the tricoplanar facets closest
+  to the point.  For Delaunay triangulations, the point may be inside a
+  different tricoplanar facet. See locate a facet with qh_findbestfacet()
+
+  If inside, qh_findbestfacet performs an exhaustive search
+  this may be too conservative.  Sometimes it is clearly required.
+
+  qh_findbestfacet is not used by qhull.
+  uses qh.visit_id and qh.coplanarset
+
+  see:
+  qh_findbest
+*/
+facetT * qh_findbestfacet(pointT *point, boolT bestoutside,
+                          realT *bestdist, boolT *isoutside)
+{
+  facetT *bestfacet = NULL;
+  int     numpart, totpart = 0;
+
+  bestfacet = qh_findbest(point, qh facet_list,
+                          bestoutside, !qh_ISnewfacets, bestoutside /*
+                                                                      qh_NOupper
+                                                                      */            ,
+                          bestdist, isoutside, &totpart);
+  if( *bestdist < -qh DISTround )
+    {
+    bestfacet = qh_findfacet_all(point, bestdist, isoutside, &numpart);
+    totpart += numpart;
+    if( (isoutside && bestoutside)
+        || (!isoutside && bestfacet->upperdelaunay) )
+      {
+      bestfacet = qh_findbest(point, bestfacet,
+                              bestoutside, False, bestoutside,
+                              bestdist, isoutside, &totpart);
+      totpart += numpart;
+      }
+    }
+  trace3( (qh ferr, "qh_findbestfacet: f%d dist %2.2g isoutside %d totpart %d\n",
+           bestfacet->id, *bestdist, *isoutside, totpart) );
+  return bestfacet;
+} /* findbestfacet */
+
+/*---------------------------------
+
+  qh_findbestlower( facet, point, bestdist, numpart )
+  returns best non-upper, non-flipped neighbor of facet for point
+  if needed, searches vertex neighbors
+
+  returns:
+  returns bestdist and updates numpart
+
+  notes:
+  if Delaunay and inside, point is outside of circumsphere of bestfacet
+  called by qh_findbest() for points above an upperdelaunay facet
+
+*/
+facetT * qh_findbestlower(facetT *upperfacet, pointT *point, realT *bestdistp, int *numpart)
+{
+  facetT * neighbor, * *neighborp, *bestfacet = NULL;
+  realT    bestdist = -REALmax / 2 /* avoid underflow */;
+  realT    dist;
+  vertexT *vertex;
+
+  zinc_(Zbestlower);
+  FOREACHneighbor_(upperfacet) {
+    if( neighbor->upperdelaunay || neighbor->flipped )
+      {
+      continue;
+      }
+    (*numpart)++;
+    qh_distplane(point, neighbor, &dist);
+    if( dist > bestdist )
+      {
+      bestfacet = neighbor;
+      bestdist = dist;
+      }
+    }
+  if( !bestfacet )
+    {
+    zinc_(Zbestlowerv);
+    /* rarely called, numpart does not count nearvertex computations */
+    vertex = qh_nearvertex(upperfacet, point, &dist);
+    qh_vertexneighbors();
+    FOREACHneighbor_(vertex) {
+      if( neighbor->upperdelaunay || neighbor->flipped )
+        {
+        continue;
+        }
+      (*numpart)++;
+      qh_distplane(point, neighbor, &dist);
+      if( dist > bestdist )
+        {
+        bestfacet = neighbor;
+        bestdist = dist;
+        }
+      }
+    }
+  if( !bestfacet )
+    {
+    fprintf(
+      qh ferr,
+      "\n\
+qh_findbestlower: all neighbors of facet %d are flipped or upper Delaunay.\n\
+Please report this error to qhull_bug@qhull.org with the input and all of the output.\n"                                                                                         ,
+      upperfacet->id);
+    qh_errexit(qh_ERRqhull, upperfacet, NULL);
+    }
+  *bestdistp = bestdist;
+  trace3( (qh ferr, "qh_findbestlower: f%d dist %2.2g for f%d p%d\n",
+           bestfacet->id, bestdist, upperfacet->id, qh_pointid(point) ) );
+  return bestfacet;
+} /* findbestlower */
+
+/*---------------------------------
+
+  qh_findfacet_all( point, bestdist, isoutside, numpart )
+  exhaustive search for facet below a point
+
+  for Delaunay triangulations,
+  Use qh_setdelaunay() to lift point to paraboloid and scale by 'Qbb' if needed
+  Do not use options 'Qbk', 'QBk', or 'QbB' since they scale the coordinates.
+
+  returns:
+  returns first facet below point
+  if point is inside,
+  returns nearest facet
+  distance to facet
+  isoutside if point is outside of the hull
+  number of distance tests
+*/
+facetT * qh_findfacet_all(pointT *point, realT *bestdist, boolT *isoutside,
+                          int *numpart)
+{
+  facetT *bestfacet = NULL, *facet;
+  realT   dist;
+  int     totpart = 0;
+
+  *bestdist = REALmin;
+  *isoutside = False;
+  FORALLfacets {
+    if( facet->flipped || !facet->normal )
+      {
+      continue;
+      }
+    totpart++;
+    qh_distplane(point, facet, &dist);
+    if( dist > *bestdist )
+      {
+      *bestdist = dist;
+      bestfacet = facet;
+      if( dist > qh MINoutside )
+        {
+        *isoutside = True;
+        break;
+        }
+      }
+    }
+  *numpart = totpart;
+  trace3( (qh ferr, "qh_findfacet_all: f%d dist %2.2g isoutside %d totpart %d\n",
+           getid_(bestfacet), *bestdist, *isoutside, totpart) );
+  return bestfacet;
+} /* findfacet_all */
+
+/*---------------------------------
+
+  qh_findgood( facetlist, goodhorizon )
+  identify good facets for qh.PRINTgood
+  if qh.GOODvertex>0
+  facet includes point as vertex
+  if !match, returns goodhorizon
+  inactive if qh.MERGING
+  if qh.GOODpoint
+  facet is visible or coplanar (>0) or not visible (<0)
+  if qh.GOODthreshold
+  facet->normal matches threshold
+  if !goodhorizon and !match,
+  selects facet with closest angle
+  sets GOODclosest
+
+  returns:
+  number of new, good facets found
+  determines facet->good
+  may update qh.GOODclosest
+
+  notes:
+  qh_findgood_all further reduces the good region
+
+  design:
+  count good facets
+  mark good facets for qh.GOODpoint
+  mark good facets for qh.GOODthreshold
+  if necessary
+  update qh.GOODclosest
+*/
+int qh_findgood(facetT *facetlist, int goodhorizon)
+{
+  facetT *facet, *bestfacet = NULL;
+  realT   angle, bestangle = REALmax, dist;
+  int     numgood = 0;
+
+  FORALLfacet_(facetlist) {
+    if( facet->good )
+      {
+      numgood++;
+      }
+    }
+  if( qh GOODvertex > 0 && !qh MERGING )
+    {
+    FORALLfacet_(facetlist) {
+      if( !qh_isvertex(qh GOODvertexp, facet->vertices) )
+        {
+        facet->good = False;
+        numgood--;
+        }
+      }
+    }
+  if( qh GOODpoint && numgood )
+    {
+    FORALLfacet_(facetlist) {
+      if( facet->good && facet->normal )
+        {
+        zinc_(Zdistgood);
+        qh_distplane(qh GOODpointp, facet, &dist);
+        if( (qh GOODpoint > 0) ^ (dist > 0.0) )
+          {
+          facet->good = False;
+          numgood--;
+          }
+        }
+      }
+    }
+  if( qh GOODthreshold && (numgood || goodhorizon || qh GOODclosest) )
+    {
+    FORALLfacet_(facetlist) {
+      if( facet->good && facet->normal )
+        {
+        if( !qh_inthresholds(facet->normal, &angle) )
+          {
+          facet->good = False;
+          numgood--;
+          if( angle < bestangle )
+            {
+            bestangle = angle;
+            bestfacet = facet;
+            }
+          }
+        }
+      }
+    if( !numgood && (!goodhorizon || qh GOODclosest) )
+      {
+      if( qh GOODclosest )
+        {
+        if( qh GOODclosest->visible )
+          {
+          qh GOODclosest = NULL;
+          }
+        else
+          {
+          qh_inthresholds(qh GOODclosest->normal, &angle);
+          if( angle < bestangle )
+            {
+            bestfacet = qh GOODclosest;
+            }
+          }
+        }
+      if( bestfacet && bestfacet != qh GOODclosest )
+        {
+        if( qh GOODclosest )
+          {
+          qh GOODclosest-> good = False;
+          }
+        qh GOODclosest = bestfacet;
+        bestfacet->good = True;
+        numgood++;
+        trace2( (qh ferr, "qh_findgood: f%d is closest (%2.2g) to thresholds\n",
+                 bestfacet->id, bestangle) );
+        return numgood;
+        }
+      }
+    else if( qh GOODclosest )   /* numgood > 0 */
+      {
+      qh GOODclosest-> good = False;
+      qh               GOODclosest = NULL;
+      }
+    }
+  zadd_(Zgoodfacet, numgood);
+  trace2( (qh ferr, "qh_findgood: found %d good facets with %d good horizon\n",
+           numgood, goodhorizon) );
+  if( !numgood && qh GOODvertex > 0 && !qh MERGING )
+    {
+    return goodhorizon;
+    }
+  return numgood;
+} /* findgood */
+
+/*---------------------------------
+
+  qh_findgood_all( facetlist )
+  apply other constraints for good facets (used by qh.PRINTgood)
+  if qh.GOODvertex
+  facet includes (>0) or doesn't include (<0) point as vertex
+  if last good facet and ONLYgood, prints warning and continues
+  if qh.SPLITthresholds
+  facet->normal matches threshold, or if none, the closest one
+  calls qh_findgood
+  nop if good not used
+
+  returns:
+  clears facet->good if not good
+  sets qh.num_good
+
+  notes:
+  this is like qh_findgood but more restrictive
+
+  design:
+  uses qh_findgood to mark good facets
+  marks facets for qh.GOODvertex
+  marks facets for qh.SPLITthreholds
+*/
+void qh_findgood_all(facetT *facetlist)
+{
+  facetT *facet, *bestfacet = NULL;
+  realT   angle, bestangle = REALmax;
+  int     numgood = 0, startgood;
+
+  if( !qh GOODvertex && !qh GOODthreshold && !qh GOODpoint
+      && !qh SPLITthresholds )
+    {
+    return;
+    }
+  if( !qh ONLYgood )
+    {
+    qh_findgood(qh facet_list, 0);
+    }
+  FORALLfacet_(facetlist) {
+    if( facet->good )
+      {
+      numgood++;
+      }
+    }
+  if( qh GOODvertex < 0 || (qh GOODvertex > 0 && qh MERGING) )
+    {
+    FORALLfacet_(facetlist) {
+      if( facet->good && ( (qh GOODvertex > 0) ^ !!qh_isvertex(qh GOODvertexp, facet->vertices) ) )
+        {
+        if( !--numgood )
+          {
+          if( qh ONLYgood )
+            {
+            fprintf(qh ferr, "qhull warning: good vertex p%d does not match last good facet f%d.  Ignored.\n",
+                    qh_pointid(qh GOODvertexp), facet->id);
+            return;
+            }
+          else if( qh GOODvertex > 0 )
+            {
+            fprintf(qh ferr, "qhull warning: point p%d is not a vertex ('QV%d').\n",
+                    qh GOODvertex - 1, qh GOODvertex - 1);
+            }
+          else
+            {
+            fprintf(qh ferr, "qhull warning: point p%d is a vertex for every facet ('QV-%d').\n",
+                    -qh GOODvertex - 1, -qh GOODvertex - 1);
+            }
+          }
+        facet->good = False;
+        }
+      }
+    }
+  startgood = numgood;
+  if( qh SPLITthresholds )
+    {
+    FORALLfacet_(facetlist) {
+      if( facet->good )
+        {
+        if( !qh_inthresholds(facet->normal, &angle) )
+          {
+          facet->good = False;
+          numgood--;
+          if( angle < bestangle )
+            {
+            bestangle = angle;
+            bestfacet = facet;
+            }
+          }
+        }
+      }
+    if( !numgood && bestfacet )
+      {
+      bestfacet->good = True;
+      numgood++;
+      trace0( (qh ferr, "qh_findgood_all: f%d is closest (%2.2g) to thresholds\n",
+               bestfacet->id, bestangle) );
+      return;
+      }
+    }
+  qh num_good = numgood;
+  trace0( (qh ferr, "qh_findgood_all: %d good facets remain out of %d facets\n",
+           numgood, startgood) );
+} /* findgood_all */
+
+/*---------------------------------
+
+  qh_furthestnext()
+  set qh.facet_next to facet with furthest of all furthest points
+  searches all facets on qh.facet_list
+
+  notes:
+  this may help avoid precision problems
+*/
+void qh_furthestnext(void /* qh facet_list */)
+{
+  facetT *facet, *bestfacet = NULL;
+  realT   dist, bestdist = -REALmax;
+
+  FORALLfacets {
+    if( facet->outsideset )
+      {
+#if qh_COMPUTEfurthest
+      pointT *furthest;
+      furthest = (pointT *)qh_setlast(facet->outsideset);
+      zinc_(Zcomputefurthest);
+      qh_distplane(furthest, facet, &dist);
+#else
+      dist = facet->furthestdist;
+#endif
+      if( dist > bestdist )
+        {
+        bestfacet = facet;
+        bestdist = dist;
+        }
+      }
+    }
+  if( bestfacet )
+    {
+    qh_removefacet(bestfacet);
+    qh_prependfacet(bestfacet, &qh facet_next);
+    trace1( (qh ferr, "qh_furthestnext: made f%d next facet (dist %.2g)\n",
+             bestfacet->id, bestdist) );
+    }
+} /* furthestnext */
+
+/*---------------------------------
+
+  qh_furthestout( facet )
+  make furthest outside point the last point of outsideset
+
+  returns:
+  updates facet->outsideset
+  clears facet->notfurthest
+  sets facet->furthestdist
+
+  design:
+  determine best point of outsideset
+  make it the last point of outsideset
+*/
+void qh_furthestout(facetT *facet)
+{
+  pointT *point, * *pointp, *bestpoint = NULL;
+  realT   dist, bestdist = -REALmax;
+
+  FOREACHpoint_(facet->outsideset) {
+    qh_distplane(point, facet, &dist);
+    zinc_(Zcomputefurthest);
+    if( dist > bestdist )
+      {
+      bestpoint = point;
+      bestdist = dist;
+      }
+    }
+  if( bestpoint )
+    {
+    qh_setdel(facet->outsideset, point);
+    qh_setappend(&facet->outsideset, point);
+#if !qh_COMPUTEfurthest
+    facet->furthestdist = bestdist;
+#endif
+    }
+  facet->notfurthest = False;
+  trace3( (qh ferr, "qh_furthestout: p%d is furthest outside point of f%d\n",
+           qh_pointid(point), facet->id) );
+} /* furthestout */
+
+/*---------------------------------
+
+  qh_infiniteloop( facet )
+  report infinite loop error due to facet
+*/
+void qh_infiniteloop(facetT *facet)
+{
+
+  fprintf(qh ferr, "qhull internal error (qh_infiniteloop): potential infinite loop detected\n");
+  qh_errexit(qh_ERRqhull, facet, NULL);
+} /* qh_infiniteloop */
+
+/*---------------------------------
+
+  qh_initbuild()
+  initialize hull and outside sets with point array
+  qh.FIRSTpoint/qh.NUMpoints is point array
+  if qh.GOODpoint
+  adds qh.GOODpoint to initial hull
+
+  returns:
+  qh_facetlist with initial hull
+  points partioned into outside sets, coplanar sets, or inside
+  initializes qh.GOODpointp, qh.GOODvertexp,
+
+  design:
+  initialize global variables used during qh_buildhull
+  determine precision constants and points with max/min coordinate values
+  if qh.SCALElast, scale last coordinate (for 'd')
+  build initial simplex
+  partition input points into facets of initial simplex
+  set up lists
+  if qh.ONLYgood
+  check consistency
+  add qh.GOODvertex if defined
+*/
+void qh_initbuild( void)
+{
+  setT *  maxpoints, *vertices;
+  facetT *facet;
+  int     i, numpart;
+  realT   dist;
+  boolT   isoutside;
+
+  qh furthest_id = -1;
+  qh lastreport = 0;
+  qh facet_id = qh vertex_id = qh ridge_id = 0;
+  qh visit_id = qh vertex_visit = 0;
+  qh maxoutdone = False;
+
+  if( qh GOODpoint > 0 )
+    {
+    qh GOODpointp = qh_point(qh GOODpoint - 1);
+    }
+  else if( qh GOODpoint < 0 )
+    {
+    qh GOODpointp = qh_point(-qh GOODpoint - 1);
+    }
+  if( qh GOODvertex > 0 )
+    {
+    qh GOODvertexp = qh_point(qh GOODvertex - 1);
+    }
+  else if( qh GOODvertex < 0 )
+    {
+    qh GOODvertexp = qh_point(-qh GOODvertex - 1);
+    }
+  if( (qh GOODpoint
+       && (qh GOODpointp < qh first_point  /* also catches !GOODpointp */
+           || qh GOODpointp > qh_point(qh num_points - 1) ) )
+      || (qh GOODvertex
+          && (qh GOODvertexp < qh first_point /* also catches !GOODvertexp */
+              || qh GOODvertexp > qh_point(qh num_points - 1) ) ) )
+    {
+    fprintf(qh ferr, "qhull input error: either QGn or QVn point is > p%d\n",
+            qh num_points - 1);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  maxpoints = qh_maxmin(qh first_point, qh num_points, qh hull_dim);
+  if( qh SCALElast )
+    {
+    qh_scalelast(qh first_point, qh num_points, qh hull_dim,
+                 qh MINlastcoord, qh MAXlastcoord, qh MAXwidth);
+    }
+  qh_detroundoff();
+  if( qh DELAUNAY && qh upper_threshold[qh hull_dim - 1] > REALmax / 2
+      && qh lower_threshold[qh hull_dim - 1] < -REALmax / 2 )
+    {
+    for( i = qh_PRINTEND; i--; )
+      {
+      if( qh PRINTout[i] == qh_PRINTgeom && qh DROPdim < 0
+          && !qh GOODthreshold && !qh SPLITthresholds )
+        {
+        break; /* in this case, don't set upper_threshold */
+        }
+      }
+    if( i < 0 )
+      {
+      if( qh UPPERdelaunay )   /* matches qh.upperdelaunay in qh_setfacetplane
+                                 */
+        {
+        qh lower_threshold[qh hull_dim - 1] = qh ANGLEround * qh_ZEROdelaunay;
+        qh GOODthreshold = True;
+        }
+      else
+        {
+        qh upper_threshold[qh hull_dim - 1] = -qh ANGLEround * qh_ZEROdelaunay;
+        if( !qh GOODthreshold )
+          {
+          qh SPLITthresholds = True; /* build upper-convex hull even if Qg */
+          }
+        /* qh_initqhull_globals errors if Qg without Pdk/etc. */
+        }
+      }
+    }
+  vertices = qh_initialvertices(qh hull_dim, maxpoints, qh first_point, qh num_points);
+  qh_initialhull(vertices);   /* initial qh facet_list */
+  qh_partitionall(vertices, qh first_point, qh num_points);
+  if( qh PRINToptions1st || qh TRACElevel || qh IStracing )
+    {
+    if( qh TRACElevel || qh IStracing )
+      {
+      fprintf(qh ferr, "\nTrace level %d for %s | %s\n",
+              qh IStracing ? qh IStracing : qh TRACElevel, qh rbox_command, qh qhull_command);
+      }
+    fprintf(qh ferr, "Options selected for Qhull %s:\n%s\n", qh_version, qh qhull_options);
+    }
+  qh_resetlists(False, qh_RESETvisible /*qh visible_list newvertex_list
+                                         newfacet_list */                               );
+  qh facet_next = qh facet_list;
+  qh_furthestnext(/* qh facet_list */);
+  if( qh PREmerge )
+    {
+    qh cos_max = qh premerge_cos;
+    qh centrum_radius = qh premerge_centrum;
+    }
+  if( qh ONLYgood )
+    {
+    if( qh GOODvertex > 0 && qh MERGING )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input error: 'Qg QVn' (only good vertex) does not work with merging.\nUse 'QJ' to joggle the input or 'Q0' to turn off merging.\n");
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    if( !(qh GOODthreshold || qh GOODpoint
+          || (!qh MERGEexact && !qh PREmerge && qh GOODvertexp) ) )
+      {
+      fprintf(
+        qh ferr,
+        "qhull input error: 'Qg' (ONLYgood) needs a good threshold ('Pd0D0'), a\n\
+good point (QGn or QG-n), or a good vertex with 'QJ' or 'Q0' (QVn).\n"                                                                                   );
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    if( qh GOODvertex > 0  && !qh MERGING  /* matches qh_partitionall */
+        && !qh_isvertex(qh GOODvertexp, vertices) )
+      {
+      facet = qh_findbestnew(qh GOODvertexp, qh facet_list,
+                             &dist, !qh_ALL, &isoutside, &numpart);
+      zadd_(Zdistgood, numpart);
+      if( !isoutside )
+        {
+        fprintf(qh ferr, "qhull input error: point for QV%d is inside initial simplex.  It can not be made a vertex.\n",
+                qh_pointid(qh GOODvertexp) );
+        qh_errexit(qh_ERRinput, NULL, NULL);
+        }
+      if( !qh_addpoint(qh GOODvertexp, facet, False) )
+        {
+        qh_settempfree(&vertices);
+        qh_settempfree(&maxpoints);
+        return;
+        }
+      }
+    qh_findgood(qh facet_list, 0);
+    }
+  qh_settempfree(&vertices);
+  qh_settempfree(&maxpoints);
+  trace1( (qh ferr, "qh_initbuild: initial hull created and points partitioned\n") );
+} /* initbuild */
+
+/*---------------------------------
+
+  qh_initialhull( vertices )
+  constructs the initial hull as a DIM3 simplex of vertices
+
+  design:
+  creates a simplex (initializes lists)
+  determines orientation of simplex
+  sets hyperplanes for facets
+  doubles checks orientation (in case of axis-parallel facets with Gaussian elimination)
+  checks for flipped facets and qh.NARROWhull
+  checks the result
+*/
+void qh_initialhull(setT *vertices)
+{
+  facetT *facet, *firstfacet, *neighbor, * *neighborp;
+  realT   dist, angle, minangle = REALmax;
+
+#ifndef qh_NOtrace
+  int k;
+#endif
+
+  qh_createsimplex(vertices);  /* qh facet_list */
+  qh_resetlists(False, qh_RESETvisible);
+  qh facet_next = qh facet_list;      /* advance facet when processed */
+  qh interior_point = qh_getcenter(vertices);
+  firstfacet = qh facet_list;
+  qh_setfacetplane(firstfacet);
+  zinc_(Znumvisibility); /* needs to be in printsummary */
+  qh_distplane(qh interior_point, firstfacet, &dist);
+  if( dist > 0 )
+    {
+    FORALLfacets
+    facet-> toporient ^= True;
+    }
+  FORALLfacets
+  qh_setfacetplane(facet);
+  FORALLfacets {
+    if( !qh_checkflipped(facet, NULL, qh_ALL) )  /* due to axis-parallel facet
+                                                   */
+      {
+      trace1( (qh ferr, "qh_initialhull: initial orientation incorrect.  Correct all facets\n") );
+      facet->flipped = False;
+      FORALLfacets {
+        facet->toporient ^= True;
+        qh_orientoutside(facet);
+        }
+      break;
+      }
+    }
+  FORALLfacets {
+    if( !qh_checkflipped(facet, NULL, !qh_ALL) )    /* can happen with 'R0.1' */
+      {
+      qh_precision("initial facet is coplanar with interior point");
+      fprintf(qh ferr, "qhull precision error: initial facet %d is coplanar with the interior point\n",
+              facet->id);
+      qh_errexit(qh_ERRsingular, facet, NULL);
+      }
+    FOREACHneighbor_(facet) {
+      angle = qh_getangle(facet->normal, neighbor->normal);
+      minimize_( minangle, angle);
+      }
+    }
+  if( minangle < qh_MAXnarrow && !qh NOnarrow )
+    {
+    realT diff = 1.0 + minangle;
+
+    qh NARROWhull = True;
+    qh_option("_narrow-hull", NULL, &diff);
+    if( minangle < qh_WARNnarrow && !qh RERUN && qh PRINTprecision )
+      {
+      fprintf(
+        qh ferr,
+        "qhull precision warning: \n\
+The initial hull is narrow (cosine of min. angle is %.16f).\n\
+A coplanar point may lead to a wide facet.  Options 'QbB' (scale to unit box)\n\
+or 'Qbb' (scale last coordinate) may remove this warning.  Use 'Pp' to skip\n\
+this warning.  See 'Limitations' in qh-impre.htm.\n"                                                                                                                                                                                                                                                                     ,
+        -minangle);    /* convert from angle between normals to angle between
+                         facets */
+      }
+    }
+  zzval_(Zprocessed) = qh hull_dim + 1;
+  qh_checkpolygon(qh facet_list);
+  qh_checkconvex(qh facet_list,   qh_DATAfault);
+#ifndef qh_NOtrace
+  if( qh IStracing >= 1 )
+    {
+    fprintf(qh ferr, "qh_initialhull: simplex constructed, interior point:");
+    for( k = 0; k < qh hull_dim; k++ )
+      {
+      fprintf(qh ferr, " %6.4g", qh interior_point[k]);
+      }
+    fprintf(qh ferr, "\n");
+    }
+#endif
+} /* initialhull */
+
+/*---------------------------------
+
+  qh_initialvertices( dim, maxpoints, points, numpoints )
+  determines a non-singular set of initial vertices
+  maxpoints may include duplicate points
+
+  returns:
+  temporary set of dim+1 vertices in descending order by vertex id
+  if qh.RANDOMoutside && !qh.ALLpoints
+  picks random points
+  if dim >= qh_INITIALmax,
+  uses min/max x and max points with non-zero determinants
+
+  notes:
+  unless qh.ALLpoints,
+  uses maxpoints as long as determinate is non-zero
+*/
+setT * qh_initialvertices(int dim, setT *maxpoints, pointT *points, int numpoints)
+{
+  pointT *point, * *pointp;
+  setT *  vertices, *simplex, *tested;
+  realT   randr;
+  int     idx, point_i, point_n, k;
+  boolT   nearzero = False;
+
+  vertices = qh_settemp(dim + 1);
+  simplex = qh_settemp(dim + 1);
+  if( qh ALLpoints )
+    {
+    qh_maxsimplex(dim, NULL, points, numpoints, &simplex);
+    }
+  else if( qh RANDOMoutside )
+    {
+    while( qh_setsize(simplex) != dim + 1 )
+      {
+      randr = qh_RANDOMint;
+      randr = randr / (qh_RANDOMmax + 1);
+      idx = (int)floor(qh num_points * randr);
+      while( qh_setin(simplex, qh_point(idx) ) )
+        {
+        idx++; /* in case qh_RANDOMint always returns the same value */
+        idx = idx < qh num_points ? idx : 0;
+        }
+
+      qh_setappend(&simplex, qh_point(idx) );
+      }
+    }
+  else if( qh hull_dim >= qh_INITIALmax )
+    {
+    tested = qh_settemp(dim + 1);
+    qh_setappend(&simplex, SETfirst_(maxpoints) );   /* max and min X coord */
+    qh_setappend(&simplex, SETsecond_(maxpoints) );
+    qh_maxsimplex(fmin_(qh_INITIALsearch, dim), maxpoints, points, numpoints, &simplex);
+    k = qh_setsize(simplex);
+    FOREACHpoint_i_(maxpoints) {
+      if( point_i & 0x1 )       /* first pick up max. coord. points */
+        {
+        if( !qh_setin(simplex, point) && !qh_setin(tested, point) )
+          {
+          qh_detsimplex(point, simplex, k, &nearzero);
+          if( nearzero )
+            {
+            qh_setappend(&tested, point);
+            }
+          else
+            {
+            qh_setappend(&simplex, point);
+            if( ++k == dim )  /* use search for last point */
+              {
+              break;
+              }
+            }
+          }
+        }
+      }
+    while( k != dim && (point = (pointT *)qh_setdellast(maxpoints) ) )
+      {
+      if( !qh_setin(simplex, point) && !qh_setin(tested, point) )
+        {
+        qh_detsimplex(point, simplex, k, &nearzero);
+        if( nearzero )
+          {
+          qh_setappend(&tested, point);
+          }
+        else
+          {
+          qh_setappend(&simplex, point);
+          k++;
+          }
+        }
+      }
+
+    idx = 0;
+    while( k != dim && (point = qh_point(idx++) ) )
+      {
+      if( !qh_setin(simplex, point) && !qh_setin(tested, point) )
+        {
+        qh_detsimplex(point, simplex, k, &nearzero);
+        if( !nearzero )
+          {
+          qh_setappend(&simplex, point);
+          k++;
+          }
+        }
+      }
+
+    qh_settempfree(&tested);
+    qh_maxsimplex(dim, maxpoints, points, numpoints, &simplex);
+    }
+  else
+    {
+    qh_maxsimplex(dim, maxpoints, points, numpoints, &simplex);
+    }
+  FOREACHpoint_(simplex)
+  qh_setaddnth(&vertices, 0, qh_newvertex(point) );   /* descending order */
+  qh_settempfree(&simplex);
+  return vertices;
+} /* initialvertices */
+
+/*---------------------------------
+
+  qh_isvertex(  )
+  returns vertex if point is in vertex set, else returns NULL
+
+  notes:
+  for qh.GOODvertex
+*/
+vertexT * qh_isvertex(pointT *point, setT *vertices)
+{
+  vertexT *vertex, * *vertexp;
+
+  FOREACHvertex_(vertices) {
+    if( vertex->point == point )
+      {
+      return vertex;
+      }
+    }
+  return NULL;
+} /* isvertex */
+
+/*---------------------------------
+
+  qh_makenewfacets( point )
+  make new facets from point and qh.visible_list
+
+  returns:
+  qh.newfacet_list= list of new facets with hyperplanes and ->newfacet
+  qh.newvertex_list= list of vertices in new facets with ->newlist set
+
+  if (qh.ONLYgood)
+  newfacets reference horizon facets, but not vice versa
+  ridges reference non-simplicial horizon ridges, but not vice versa
+  does not change existing facets
+  else
+  sets qh.NEWfacets
+  new facets attached to horizon facets and ridges
+  for visible facets,
+  visible->r.replace is corresponding new facet
+
+  see also:
+  qh_makenewplanes() -- make hyperplanes for facets
+  qh_attachnewfacets() -- attachnewfacets if not done here (qh ONLYgood)
+  qh_matchnewfacets() -- match up neighbors
+  qh_updatevertices() -- update vertex neighbors and delvertices
+  qh_deletevisible() -- delete visible facets
+  qh_checkpolygon() --check the result
+  qh_triangulate() -- triangulate a non-simplicial facet
+
+  design:
+  for each visible facet
+  make new facets to its horizon facets
+  update its f.replace
+  clear its neighbor set
+*/
+vertexT * qh_makenewfacets(pointT *point /*visible_list*/)
+{
+  facetT * visible, *newfacet = NULL, *newfacet2 = NULL, *neighbor, * *neighborp;
+  vertexT *apex;
+  int      numnew = 0;
+
+  qh newfacet_list = qh facet_tail;
+  qh newvertex_list = qh vertex_tail;
+
+  apex = qh_newvertex(point);
+  qh_appendvertex(apex);
+  qh visit_id++;
+  if( !qh ONLYgood )
+    {
+    qh NEWfacets = True;
+    }
+  FORALLvisible_facets {
+    FOREACHneighbor_(visible)
+    neighbor->seen = False;
+    if( visible->ridges )
+      {
+      visible->visitid = qh visit_id;
+      newfacet2 = qh_makenew_nonsimplicial(visible, apex, &numnew);
+      }
+    if( visible->simplicial )
+      {
+      newfacet = qh_makenew_simplicial(visible, apex, &numnew);
+      }
+    if( !qh ONLYgood )
+      {
+      if( newfacet2 )  /* newfacet is null if all ridges defined */
+        {
+        newfacet = newfacet2;
+        }
+      if( newfacet )
+        {
+        visible->f.replace = newfacet;
+        }
+      else
+        {
+        zinc_(Zinsidevisible);
+        }
+      SETfirst_(visible->neighbors) = NULL;
+      }
+    }
+  trace1( (qh ferr, "qh_makenewfacets: created %d new facets from point p%d to horizon\n",
+           numnew, qh_pointid(point) ) );
+  if( qh IStracing >= 4 )
+    {
+    qh_printfacetlist(qh newfacet_list, NULL, qh_ALL);
+    }
+  return apex;
+} /* makenewfacets */
+
+/*---------------------------------
+
+  qh_matchduplicates( atfacet, atskip, hashsize, hashcount )
+  match duplicate ridges in qh.hash_table for atfacet/atskip
+  duplicates marked with ->dupridge and qh_DUPLICATEridge
+
+  returns:
+  picks match with worst merge (min distance apart)
+  updates hashcount
+
+  see also:
+  qh_matchneighbor
+
+  notes:
+
+  design:
+  compute hash value for atfacet and atskip
+  repeat twice -- once to make best matches, once to match the rest
+  for each possible facet in qh.hash_table
+  if it is a matching facet and pass 2
+  make match
+  unless tricoplanar, mark match for merging (qh_MERGEridge)
+  [e.g., tricoplanar RBOX s 1000 t993602376 | QHULL C-1e-3 d Qbb FA Qt]
+  if it is a matching facet and pass 1
+  test if this is a better match
+  if pass 1,
+  make best match (it will not be merged)
+*/
+#ifndef qh_NOmerge
+void qh_matchduplicates(facetT *atfacet, int atskip, int hashsize, int *hashcount)
+{
+  boolT   same, ismatch;
+  int     hash, scan;
+  facetT *facet, *newfacet, *maxmatch = NULL, *maxmatch2 = NULL, *nextfacet;
+  int     skip, newskip, nextskip = 0, maxskip = 0, maxskip2 = 0, makematch;
+  realT   maxdist = -REALmax, mindist, dist2, low, high;
+
+  hash = (int)qh_gethash(hashsize, atfacet->vertices, qh hull_dim, 1,
+                         SETelem_(atfacet->vertices, atskip) );
+  trace2( (qh ferr, "qh_matchduplicates: find duplicate matches for f%d skip %d hash %d hashcount %d\n",
+           atfacet->id, atskip, hash, *hashcount) );
+  for( makematch = 0; makematch < 2; makematch++ )
+    {
+    qh visit_id++;
+    for( newfacet = atfacet, newskip = atskip; newfacet; newfacet = nextfacet, newskip = nextskip )
+      {
+      zinc_(Zhashlookup);
+      nextfacet = NULL;
+      newfacet->visitid = qh visit_id;
+      for( scan = hash; (facet = SETelemt_(qh hash_table, scan, facetT) );
+           scan = (++scan >= hashsize ? 0 : scan) )
+        {
+        if( !facet->dupridge || facet->visitid == qh visit_id )
+          {
+          continue;
+          }
+        zinc_(Zhashtests);
+        if( qh_matchvertices(1, newfacet->vertices, newskip, facet->vertices, &skip, &same) )
+          {
+          ismatch = (same == (boolT)(newfacet->toporient ^ facet->toporient) );
+          if( SETelemt_(facet->neighbors, skip, facetT) != qh_DUPLICATEridge )
+            {
+            if( !makematch )
+              {
+              fprintf(
+                qh ferr,
+                "qhull internal error (qh_matchduplicates): missing dupridge at f%d skip %d for new f%d skip %d hash %d\n",
+                facet->id, skip, newfacet->id, newskip, hash);
+              qh_errexit2(qh_ERRqhull, facet, newfacet);
+              }
+            }
+          else if( ismatch && makematch )
+            {
+            if( SETelemt_(newfacet->neighbors, newskip, facetT) == qh_DUPLICATEridge )
+              {
+              SETelem_(facet->neighbors, skip) = newfacet;
+              if( newfacet->tricoplanar )
+                {
+                SETelem_(newfacet->neighbors, newskip) = facet;
+                }
+              else
+                {
+                SETelem_(newfacet->neighbors, newskip) = qh_MERGEridge;
+                }
+              *hashcount -= 2; /* removed two unmatched facets */
+              trace4( (qh ferr, "qh_matchduplicates: duplicate f%d skip %d matched with new f%d skip %d merge\n",
+                       facet->id, skip, newfacet->id, newskip) );
+              }
+            }
+          else if( ismatch )
+            {
+            mindist = qh_getdistance(facet, newfacet, &low, &high);
+            dist2 = qh_getdistance(newfacet, facet, &low, &high);
+            minimize_(mindist, dist2);
+            if( mindist > maxdist )
+              {
+              maxdist = mindist;
+              maxmatch = facet;
+              maxskip = skip;
+              maxmatch2 = newfacet;
+              maxskip2 = newskip;
+              }
+            trace3( (qh ferr,
+                     "qh_matchduplicates: duplicate f%d skip %d new f%d skip %d at dist %2.2g, max is now f%d f%d\n",
+                     facet->id, skip, newfacet->id, newskip, mindist,
+                     maxmatch->id, maxmatch2->id) );
+            }
+          else /* !ismatch */
+            {
+            nextfacet = facet;
+            nextskip = skip;
+            }
+          }
+        if( makematch && !facet
+            && SETelemt_(facet->neighbors, skip, facetT) == qh_DUPLICATEridge )
+          {
+          fprintf(
+            qh ferr,
+            "qhull internal error (qh_matchduplicates): no MERGEridge match for duplicate f%d skip %d at hash %d\n",
+            newfacet->id, newskip, hash);
+          qh_errexit(qh_ERRqhull, newfacet, NULL);
+          }
+        }
+      } /* end of for each new facet at hash */
+    if( !makematch )
+      {
+      if( !maxmatch )
+        {
+        fprintf(qh ferr,
+                "qhull internal error (qh_matchduplicates): no maximum match at duplicate f%d skip %d at hash %d\n",
+                atfacet->id, atskip,
+                hash);
+        qh_errexit(qh_ERRqhull, atfacet, NULL);
+        }
+      SETelem_(maxmatch->neighbors, maxskip) = maxmatch2;
+      SETelem_(maxmatch2->neighbors, maxskip2) = maxmatch;
+      *hashcount -= 2; /* removed two unmatched facets */
+      zzinc_(Zmultiridge);
+      trace0( (qh ferr, "qh_matchduplicates: duplicate f%d skip %d matched with new f%d skip %d keep\n",
+               maxmatch->id, maxskip, maxmatch2->id, maxskip2) );
+      qh_precision("ridge with multiple neighbors");
+      if( qh IStracing >= 4 )
+        {
+        qh_errprint("DUPLICATED/MATCH", maxmatch, maxmatch2, NULL, NULL);
+        }
+      }
+    }
+} /* matchduplicates */
+
+/*---------------------------------
+
+  qh_nearcoplanar()
+  for all facets, remove near-inside points from facet->coplanarset
+  coplanar points defined by innerplane from qh_outerinner()
+
+  returns:
+  if qh KEEPcoplanar && !qh KEEPinside
+  facet->coplanarset only contains coplanar points
+  if qh.JOGGLEmax
+  drops inner plane by another qh.JOGGLEmax diagonal since a
+  vertex could shift out while a coplanar point shifts in
+
+  notes:
+  used for qh.PREmerge and qh.JOGGLEmax
+  must agree with computation of qh.NEARcoplanar in qh_detroundoff()
+  design:
+  if not keeping coplanar or inside points
+  free all coplanar sets
+  else if not keeping both coplanar and inside points
+  remove !coplanar or !inside points from coplanar sets
+*/
+void qh_nearcoplanar( void /* qh.facet_list */)
+{
+  facetT *facet;
+  pointT *point, * *pointp;
+  int     numpart;
+  realT   dist, innerplane;
+
+  if( !qh KEEPcoplanar && !qh KEEPinside )
+    {
+    FORALLfacets {
+      if( facet->coplanarset )
+        {
+        qh_setfree( &facet->coplanarset);
+        }
+      }
+    }
+  else if( !qh KEEPcoplanar || !qh KEEPinside )
+    {
+    qh_outerinner(NULL, NULL, &innerplane);
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      innerplane -= qh JOGGLEmax * sqrt( (double)qh hull_dim);
+      }
+    numpart = 0;
+    FORALLfacets {
+      if( facet->coplanarset )
+        {
+        FOREACHpoint_(facet->coplanarset) {
+          numpart++;
+          qh_distplane(point, facet, &dist);
+          if( dist < innerplane )
+            {
+            if( !qh KEEPinside )
+              {
+              SETref_(point) = NULL;
+              }
+            }
+          else if( !qh KEEPcoplanar )
+            {
+            SETref_(point) = NULL;
+            }
+          }
+        qh_setcompact(facet->coplanarset);
+        }
+      }
+    zzadd_(Zcheckpart, numpart);
+    }
+} /* nearcoplanar */
+
+/*---------------------------------
+
+  qh_nearvertex( facet, point, bestdist )
+  return nearest vertex in facet to point
+
+  returns:
+  vertex and its distance
+
+  notes:
+  if qh.DELAUNAY
+  distance is measured in the input set
+  searches neighboring tricoplanar facets (requires vertexneighbors)
+  Slow implementation.  Recomputes vertex set for each point.
+  The vertex set could be stored in the qh.keepcentrum facet.
+*/
+vertexT * qh_nearvertex(facetT *facet, pointT *point, realT *bestdistp)
+{
+  realT    bestdist = REALmax, dist;
+  vertexT *bestvertex = NULL, *vertex, * *vertexp, *apex;
+  coordT * center;
+  facetT * neighbor, * *neighborp;
+  setT *   vertices;
+  int      dim = qh hull_dim;
+
+  if( qh DELAUNAY )
+    {
+    dim--;
+    }
+  if( facet->tricoplanar )
+    {
+    if( !qh VERTEXneighbors || !facet->center )
+      {
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_nearvertex): qh.VERTEXneighbors and facet->center required for tricoplanar facets\n");
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    vertices = qh_settemp(qh TEMPsize);
+    apex = SETfirst_(facet->vertices);
+    center = facet->center;
+    FOREACHneighbor_(apex) {
+      if( neighbor->center == center )
+        {
+        FOREACHvertex_(neighbor->vertices)
+        qh_setappend(&vertices, vertex);
+        }
+      }
+    }
+  else
+    {
+    vertices = facet->vertices;
+    }
+  FOREACHvertex_(vertices) {
+    dist = qh_pointdist(vertex->point, point, -dim);
+    if( dist < bestdist )
+      {
+      bestdist = dist;
+      bestvertex = vertex;
+      }
+    }
+  if( facet->tricoplanar )
+    {
+    qh_settempfree(&vertices);
+    }
+  *bestdistp = sqrt(bestdist);
+  trace3( (qh ferr, "qh_nearvertex: v%d dist %2.2g for f%d p%d\n",
+           bestvertex->id, *bestdistp, facet->id, qh_pointid(point) ) );
+  return bestvertex;
+} /* nearvertex */
+
+/*---------------------------------
+
+  qh_newhashtable( newsize )
+  returns size of qh.hash_table of at least newsize slots
+
+  notes:
+  assumes qh.hash_table is NULL
+  qh_HASHfactor determines the number of extra slots
+  size is not divisible by 2, 3, or 5
+*/
+int qh_newhashtable(int newsize)
+{
+  int size;
+
+  size = ( (newsize + 1) * qh_HASHfactor) | 0x1;  /* odd number */
+  while( True )
+    {
+    if( (size % 3) && (size % 5) )
+      {
+      break;
+      }
+    size += 2;
+    /* loop terminates because there is an infinite number of primes */
+    }
+
+  qh hash_table = qh_setnew(size);
+  qh_setzero(qh hash_table, 0, size);
+  return size;
+} /* newhashtable */
+
+/*---------------------------------
+
+  qh_newvertex( point )
+  returns a new vertex for point
+*/
+vertexT * qh_newvertex(pointT *point)
+{
+  vertexT *vertex;
+
+  zinc_(Ztotvertices);
+  vertex = (vertexT *)qh_memalloc(sizeof(vertexT) );
+  memset( (char *) vertex, 0, sizeof (vertexT) );
+  if( qh vertex_id == 0xFFFFFF )
+    {
+    fprintf(
+      qh ferr,
+      "qhull input error: more than %d vertices.  ID field overflows and two vertices\n\
+may have the same identifier.  Vertices not sorted correctly.\n"                                                                                         ,
+      0xFFFFFF);
+    qh_errexit(qh_ERRinput, NULL, NULL);
+    }
+  if( qh vertex_id == qh tracevertex_id )
+    {
+    qh tracevertex = vertex;
+    }
+  vertex->id = qh vertex_id++;
+  vertex->point = point;
+  trace4( (qh ferr, "qh_newvertex: vertex p%d (v%d) created\n", qh_pointid(vertex->point),
+           vertex->id) );
+  return vertex;
+} /* newvertex */
+
+/*---------------------------------
+
+  qh_nextridge3d( atridge, facet, vertex )
+  return next ridge and vertex for a 3d facet
+
+  notes:
+  in qh_ORIENTclock order
+  this is a O(n^2) implementation to trace all ridges
+  be sure to stop on any 2nd visit
+
+  design:
+  for each ridge
+  exit if it is the ridge after atridge
+*/
+ridgeT * qh_nextridge3d(ridgeT *atridge, facetT *facet, vertexT * *vertexp)
+{
+  vertexT *atvertex, *vertex, *othervertex;
+  ridgeT * ridge, * *ridgep;
+
+  if( (atridge->top == facet) ^ qh_ORIENTclock )
+    {
+    atvertex = SETsecondt_(atridge->vertices, vertexT);
+    }
+  else
+    {
+    atvertex = SETfirstt_(atridge->vertices, vertexT);
+    }
+  FOREACHridge_(facet->ridges) {
+    if( ridge == atridge )
+      {
+      continue;
+      }
+    if( (ridge->top == facet) ^ qh_ORIENTclock )
+      {
+      othervertex = SETsecondt_(ridge->vertices, vertexT);
+      vertex = SETfirstt_(ridge->vertices, vertexT);
+      }
+    else
+      {
+      vertex = SETsecondt_(ridge->vertices, vertexT);
+      othervertex = SETfirstt_(ridge->vertices, vertexT);
+      }
+    if( vertex == atvertex )
+      {
+      if( vertexp )
+        {
+        *vertexp = othervertex;
+        }
+      return ridge;
+      }
+    }
+  return NULL;
+} /* nextridge3d */
+
+#else /* qh_NOmerge */
+void qh_matchduplicates(facetT *atfacet, int atskip, int hashsize, int *hashcount)
+{
+}
+
+ridgeT * qh_nextridge3d(ridgeT *atridge, facetT *facet, vertexT * *vertexp)
+{
+
+  return NULL;
+}
+
+#endif /* qh_NOmerge */
+
+/*---------------------------------
+
+  qh_outcoplanar()
+  move points from all facets' outsidesets to their coplanarsets
+
+  notes:
+  for post-processing under qh.NARROWhull
+
+  design:
+  for each facet
+  for each outside point for facet
+  partition point into coplanar set
+*/
+void qh_outcoplanar(void /* facet_list */)
+{
+  pointT *point, * *pointp;
+  facetT *facet;
+  realT   dist;
+
+  trace1( (qh ferr, "qh_outcoplanar: move outsideset to coplanarset for qh NARROWhull\n") );
+  FORALLfacets {
+    FOREACHpoint_(facet->outsideset) {
+      qh num_outside--;
+
+      if( qh KEEPcoplanar || qh KEEPnearinside )
+        {
+        qh_distplane(point, facet, &dist);
+        zinc_(Zpartition);
+        qh_partitioncoplanar(point, facet, &dist);
+        }
+      }
+    qh_setfree(&facet->outsideset);
+    }
+} /* outcoplanar */
+
+/*---------------------------------
+
+  qh_point( id )
+  return point for a point id, or NULL if unknown
+
+  alternative code:
+  return ((pointT *)((unsigned   long)qh.first_point
+  + (unsigned long)((id)*qh.normal_size)));
+*/
+pointT * qh_point(int id)
+{
+
+  if( id < 0 )
+    {
+    return NULL;
+    }
+  if( id < qh num_points )
+    {
+    return qh first_point + id * qh hull_dim;
+    }
+  id -= qh num_points;
+  if( id < qh_setsize(qh other_points) )
+    {
+    return SETelemt_(qh other_points, id, pointT);
+    }
+  return NULL;
+} /* point */
+
+/*---------------------------------
+
+  qh_point_add( set, point, elem )
+  stores elem at set[point.id]
+
+  returns:
+  access function for qh_pointfacet and qh_pointvertex
+
+  notes:
+  checks point.id
+*/
+void qh_point_add(setT *set, pointT *point, void *elem)
+{
+  int id, size;
+
+  SETreturnsize_(set, size);
+  if( (id = qh_pointid(point) ) < 0 )
+    {
+    fprintf(qh ferr, "qhull internal warning (point_add): unknown point %p id %d\n",
+            point, id);
+    }
+  else if( id >= size )
+    {
+    fprintf(qh ferr, "qhull internal errror (point_add): point p%d is out of bounds (%d)\n",
+            id, size);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  else
+    {
+    SETelem_(set, id) = elem;
+    }
+} /* point_add */
+
+/*---------------------------------
+
+  qh_pointfacet()
+  return temporary set of facet for each point
+  the set is indexed by point id
+
+  notes:
+  vertices assigned to one of the facets
+  coplanarset assigned to the facet
+  outside set assigned to the facet
+  NULL if no facet for point (inside)
+  includes qh.GOODpointp
+
+  access:
+  FOREACHfacet_i_(facets) { ... }
+  SETelem_(facets, i)
+
+  design:
+  for each facet
+  add each vertex
+  add each coplanar point
+  add each outside point
+*/
+setT * qh_pointfacet(void /*qh facet_list*/)
+{
+  int      numpoints = qh num_points + qh_setsize(qh other_points);
+  setT *   facets;
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+  pointT * point, * *pointp;
+
+  facets = qh_settemp(numpoints);
+  qh_setzero(facets, 0, numpoints);
+  qh vertex_visit++;
+  FORALLfacets {
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        vertex->visitid = qh vertex_visit;
+        qh_point_add(facets, vertex->point, facet);
+        }
+      }
+    FOREACHpoint_(facet->coplanarset)
+    qh_point_add(facets, point, facet);
+    FOREACHpoint_(facet->outsideset)
+    qh_point_add(facets, point, facet);
+    }
+  return facets;
+} /* pointfacet */
+
+/*---------------------------------
+
+  qh_pointvertex(  )
+  return temporary set of vertices indexed by point id
+  entry is NULL if no vertex for a point
+  this will include qh.GOODpointp
+
+  access:
+  FOREACHvertex_i_(vertices) { ... }
+  SETelem_(vertices, i)
+*/
+setT * qh_pointvertex(void /*qh facet_list*/)
+{
+  int      numpoints = qh num_points + qh_setsize(qh other_points);
+  setT *   vertices;
+  vertexT *vertex;
+
+  vertices = qh_settemp(numpoints);
+  qh_setzero(vertices, 0, numpoints);
+  FORALLvertices
+  qh_point_add(vertices, vertex->point, vertex);
+  return vertices;
+} /* pointvertex */
+
+/*---------------------------------
+
+  qh_prependfacet( facet, facetlist )
+  prepend facet to the start of a facetlist
+
+  returns:
+  increments qh.numfacets
+  updates facetlist, qh.facet_list, facet_next
+
+  notes:
+  be careful of prepending since it can lose a pointer.
+  e.g., can lose _next by deleting and then prepending before _next
+*/
+void qh_prependfacet(facetT *facet, facetT * *facetlist)
+{
+  facetT *prevfacet, *list;
+
+  trace4( (qh ferr, "qh_prependfacet: prepend f%d before f%d\n",
+           facet->id, getid_(*facetlist) ) );
+  if( !*facetlist )
+    {
+    (*facetlist) = qh facet_tail;
+    }
+  list = *facetlist;
+  prevfacet = list->previous;
+  facet->previous = prevfacet;
+  if( prevfacet )
+    {
+    prevfacet->next = facet;
+    }
+  list->previous = facet;
+  facet->next = *facetlist;
+  if( qh facet_list == list )  /* this may change *facetlist */
+    {
+    qh facet_list = facet;
+    }
+  if( qh facet_next == list )
+    {
+    qh facet_next = facet;
+    }
+  *facetlist = facet;
+  qh num_facets++;
+} /* prependfacet */
+
+/*---------------------------------
+
+  qh_printhashtable( fp )
+  print hash table to fp
+
+  notes:
+  not in I/O to avoid bringing io.c in
+
+  design:
+  for each hash entry
+  if defined
+  if unmatched or will merge (NULL, qh_MERGEridge, qh_DUPLICATEridge)
+  print entry and neighbors
+*/
+void qh_printhashtable(FILE *fp)
+{
+  facetT * facet, *neighbor;
+  int      id, facet_i, facet_n, neighbor_i = 0, neighbor_n = 0;
+  vertexT *vertex, * *vertexp;
+
+  FOREACHfacet_i_(qh hash_table) {
+    if( facet )
+      {
+      FOREACHneighbor_i_(facet) {
+        if( !neighbor || neighbor == qh_MERGEridge || neighbor == qh_DUPLICATEridge )
+          {
+          break;
+          }
+        }
+      if( neighbor_i == neighbor_n )
+        {
+        continue;
+        }
+      fprintf(fp, "hash %d f%d ", facet_i, facet->id);
+      FOREACHvertex_(facet->vertices)
+      fprintf(fp, "v%d ", vertex->id);
+      fprintf(fp, "\n neighbors:");
+      FOREACHneighbor_i_(facet) {
+        if( neighbor == qh_MERGEridge )
+          {
+          id = -3;
+          }
+        else if( neighbor == qh_DUPLICATEridge )
+          {
+          id = -2;
+          }
+        else
+          {
+          id = getid_(neighbor);
+          }
+        fprintf(fp, " %d", id);
+        }
+      fprintf(fp, "\n");
+      }
+    }
+} /* printhashtable */
+
+/*---------------------------------
+
+  qh_printlists( fp )
+  print out facet and vertex list for debugging (without 'f/v' tags)
+*/
+void qh_printlists(void)
+{
+  facetT * facet;
+  vertexT *vertex;
+  int      count = 0;
+
+  fprintf(qh ferr, "qh_printlists: facets:");
+  FORALLfacets {
+    if( ++count % 100 == 0 )
+      {
+      fprintf(qh ferr, "\n     ");
+      }
+    fprintf(qh ferr, " %d", facet->id);
+    }
+  fprintf(qh ferr, "\n  new facets %d visible facets %d next facet for qh_addpoint %d\n  vertices (new %d):",
+          getid_(qh newfacet_list), getid_(qh visible_list), getid_(qh facet_next),
+          getid_(qh newvertex_list) );
+  count = 0;
+  FORALLvertices {
+    if( ++count % 100 == 0 )
+      {
+      fprintf(qh ferr, "\n     ");
+      }
+    fprintf(qh ferr, " %d", vertex->id);
+    }
+  fprintf(qh ferr, "\n");
+} /* printlists */
+
+/*---------------------------------
+
+  qh_resetlists( stats, qh_RESETvisible )
+  reset newvertex_list, newfacet_list, visible_list
+  if stats,
+  maintains statistics
+
+  returns:
+  visible_list is empty if qh_deletevisible was called
+*/
+void qh_resetlists(boolT stats, boolT resetVisible /*qh newvertex_list
+                                                     newfacet_list
+                                                     visible_list*/                                )
+{
+  vertexT *vertex;
+  facetT * newfacet, *visible;
+  int      totnew = 0, totver = 0;
+
+  if( stats )
+    {
+    FORALLvertex_(qh newvertex_list)
+    totver++;
+    FORALLnew_facets
+      totnew++;
+    zadd_(Zvisvertextot, totver);
+    zmax_(Zvisvertexmax, totver);
+    zadd_(Znewfacettot, totnew);
+    zmax_(Znewfacetmax, totnew);
+    }
+  FORALLvertex_(qh newvertex_list)
+  vertex->newlist = False;
+  qh newvertex_list = NULL;
+  FORALLnew_facets
+  newfacet-> newfacet = False;
+  qh         newfacet_list = NULL;
+  if( resetVisible )
+    {
+    FORALLvisible_facets {
+      visible->f.replace = NULL;
+      visible->visible = False;
+      }
+    qh num_visible = 0;
+    }
+  qh visible_list = NULL; /* may still have visible facets via qh_triangulate */
+  qh NEWfacets = False;
+} /* resetlists */
+
+/*---------------------------------
+
+  qh_setvoronoi_all()
+  compute Voronoi centers for all facets
+  includes upperDelaunay facets if qh.UPPERdelaunay ('Qu')
+
+  returns:
+  facet->center is the Voronoi center
+
+  notes:
+  this is unused/untested code
+  please email bradb@shore.net if this works ok for you
+
+  use:
+  FORALLvertices {...} to locate the vertex for a point.
+  FOREACHneighbor_(vertex) {...} to visit the Voronoi centers for a Voronoi cell.
+*/
+void qh_setvoronoi_all(void)
+{
+  facetT *facet;
+
+  qh_clearcenters(qh_ASvoronoi);
+  qh_vertexneighbors();
+
+  FORALLfacets {
+    if( !facet->normal || !facet->upperdelaunay || qh UPPERdelaunay )
+      {
+      if( !facet->center )
+        {
+        facet->center = qh_facetcenter(facet->vertices);
+        }
+      }
+    }
+} /* setvoronoi_all */
+
+#ifndef qh_NOmerge
+
+/*---------------------------------
+
+  qh_triangulate()
+  triangulate non-simplicial facets on qh.facet_list,
+  if qh.CENTERtype=qh_ASvoronoi, sets Voronoi centers of non-simplicial facets
+
+  returns:
+  all facets simplicial
+  each tricoplanar facet has ->f.triowner == owner of ->center,normal,etc.
+
+  notes:
+  call after qh_check_output since may switch to Voronoi centers
+  Output may overwrite ->f.triowner with ->f.area
+*/
+void qh_triangulate(void /*qh facet_list*/)
+{
+  facetT *  facet, *nextfacet, *owner;
+  int       onlygood = qh ONLYgood;
+  facetT *  neighbor, *visible = NULL, *facet1, *facet2, *new_facet_list = NULL;
+  facetT *  orig_neighbor = NULL, *otherfacet;
+  vertexT * new_vertex_list = NULL;
+  mergeT *  merge;
+  mergeType mergetype;
+  int       neighbor_i, neighbor_n;
+
+  trace1( (qh ferr, "qh_triangulate: triangulate non-simplicial facets\n") );
+  if( qh hull_dim == 2 )
+    {
+    return;
+    }
+  if( qh VORONOI )    /* otherwise lose Voronoi centers [could rebuild vertex
+                        set from tricoplanar] */
+    {
+    qh_clearcenters(qh_ASvoronoi);
+    qh_vertexneighbors();
+    }
+  qh ONLYgood = False; /* for makenew_nonsimplicial */
+  qh visit_id++;
+  qh NEWfacets = True;
+  qh degen_mergeset = qh_settemp(qh TEMPsize);
+  qh newvertex_list = qh vertex_tail;
+  for( facet = qh facet_list; facet && facet->next; facet = nextfacet )   /*
+                                                                            non-simplicial
+                                                                            facets
+                                                                            moved
+                                                                            to
+                                                                            end
+                                                                            */
+    {
+    nextfacet = facet->next;
+    if( facet->visible || facet->simplicial )
+      {
+      continue;
+      }
+    /* triangulate all non-simplicial facets, otherwise merging does not work,
+      e.g., RBOX c P-0.1 P+0.1 P+0.1 D3 | QHULL d Qt Tv */
+    if( !new_facet_list )
+      {
+      new_facet_list = facet;  /* will be moved to end */
+      }
+    qh_triangulate_facet(facet, &new_vertex_list);
+    }
+  trace2( (qh ferr, "qh_triangulate: delete null facets from f%d -- apex same as second vertex\n",
+           getid_(new_facet_list) ) );
+  for( facet = new_facet_list; facet && facet->next; facet = nextfacet )   /*
+                                                                             null
+                                                                             facets
+                                                                             moved
+                                                                             to
+                                                                             end
+                                                                             */
+    {
+    nextfacet = facet->next;
+    if( facet->visible )
+      {
+      continue;
+      }
+    if( facet->ridges )
+      {
+      if( qh_setsize(facet->ridges) > 0 )
+        {
+        fprintf( qh ferr, "qhull error (qh_triangulate): ridges still defined for f%d\n", facet->id);
+        qh_errexit(qh_ERRqhull, facet, NULL);
+        }
+      qh_setfree(&facet->ridges);
+      }
+    if( SETfirst_(facet->vertices) == SETsecond_(facet->vertices) )
+      {
+      zinc_(Ztrinull);
+      qh_triangulate_null(facet);
+      }
+    }
+  trace2( (qh ferr, "qh_triangulate: delete %d or more mirror facets -- same vertices and neighbors\n",
+           qh_setsize(qh degen_mergeset) ) );
+  qh visible_list = qh facet_tail;
+  while( (merge = (mergeT *)qh_setdellast(qh degen_mergeset) ) )
+    {
+    facet1 = merge->facet1;
+    facet2 = merge->facet2;
+    mergetype = merge->type;
+    qh_memfree(merge, sizeof(mergeT) );
+    if( mergetype == MRGmirror )
+      {
+      zinc_(Ztrimirror);
+      qh_triangulate_mirror(facet1, facet2);
+      }
+    }
+
+  qh_settempfree(&qh degen_mergeset);
+  trace2( (qh ferr, "qh_triangulate: update neighbor lists for vertices from v%d\n", getid_(new_vertex_list) ) );
+  qh newvertex_list = new_vertex_list;  /* all vertices of new facets */
+  qh visible_list = NULL;
+  qh_updatevertices(/*qh newvertex_list, empty newfacet_list and
+                      visible_list*/                                           );
+  qh_resetlists(False, !qh_RESETvisible /*qh newvertex_list, empty newfacet_list
+                                          and visible_list*/                                       );
+
+  trace2( (qh ferr, "qh_triangulate: identify degenerate tricoplanar facets from f%d\n", getid_(new_facet_list) ) );
+  trace2( (qh ferr,
+           "qh_triangulate: and replace facet->f.triowner with tricoplanar facets that own center, normal, etc.\n") );
+  FORALLfacet_(new_facet_list) {
+    if( facet->tricoplanar && !facet->visible )
+      {
+      FOREACHneighbor_i_(facet) {
+        if( neighbor_i == 0 ) /* first iteration */
+          {
+          if( neighbor->tricoplanar )
+            {
+            orig_neighbor = neighbor->f.triowner;
+            }
+          else
+            {
+            orig_neighbor = neighbor;
+            }
+          }
+        else
+          {
+          if( neighbor->tricoplanar )
+            {
+            otherfacet = neighbor->f.triowner;
+            }
+          else
+            {
+            otherfacet = neighbor;
+            }
+          if( orig_neighbor == otherfacet )
+            {
+            zinc_(Ztridegen);
+            facet->degenerate = True;
+            break;
+            }
+          }
+        }
+      }
+    }
+
+  trace2( (qh ferr, "qh_triangulate: delete visible facets -- non-simplicial, null, and mirrored facets\n") );
+  owner = NULL;
+  visible = NULL;
+  for( facet = new_facet_list; facet && facet->next; facet = nextfacet )   /*
+                                                                             may
+                                                                             delete
+                                                                             facet
+                                                                             */
+    {
+    nextfacet = facet->next;
+    if( facet->visible )
+      {
+      if( facet->tricoplanar )   /* a null or mirrored facet */
+        {
+        qh_delfacet(facet);
+        qh num_visible--;
+        }
+      else     /* a non-simplicial facet followed by its tricoplanars */
+        {
+        if( visible && !owner )
+          {
+          /*  RBOX 200 s D5 t1001471447 | QHULL Qt C-0.01 Qx Qc Tv Qt -- f4483
+            had 6 vertices/neighbors and 8 ridges */
+          trace2( (qh ferr, "qh_triangulate: all tricoplanar facets degenerate for non-simplicial facet f%d\n",
+                   visible->id) );
+          qh_delfacet(visible);
+          qh num_visible--;
+          }
+        visible = facet;
+        owner = NULL;
+        }
+      }
+    else if( facet->tricoplanar )
+      {
+      if( facet->f.triowner != visible )
+        {
+        fprintf(
+          qh ferr,
+          "qhull error (qh_triangulate): tricoplanar facet f%d not owned by its visible, non-simplicial facet f%d\n",
+          facet->id, getid_(visible) );
+        qh_errexit2(qh_ERRqhull, facet, visible);
+        }
+      if( owner )
+        {
+        facet->f.triowner = owner;
+        }
+      else if( !facet->degenerate )
+        {
+        owner = facet;
+        nextfacet = visible->next; /* rescan tricoplanar facets with owner */
+        facet->keepcentrum = True; /* one facet owns ->normal, etc. */
+        facet->coplanarset = visible->coplanarset;
+        facet->outsideset = visible->outsideset;
+        visible->coplanarset = NULL;
+        visible->outsideset = NULL;
+        if( !qh TRInormals )   /* center and normal copied to tricoplanar facets
+                                 */
+          {
+          visible->center = NULL;
+          visible->normal = NULL;
+          }
+        qh_delfacet(visible);
+        qh num_visible--;
+        }
+      }
+    }
+  if( visible && !owner )
+    {
+    trace2( (qh ferr, "qh_triangulate: all tricoplanar facets degenerate for last non-simplicial facet f%d\n",
+             visible->id) );
+    qh_delfacet(visible);
+    qh num_visible--;
+    }
+  qh NEWfacets = False;
+  qh ONLYgood = onlygood; /* restore value */
+  if( qh CHECKfrequently )
+    {
+    qh_checkpolygon(qh facet_list);
+    }
+} /* triangulate */
+
+/*---------------------------------
+
+  qh_triangulate_facet (facetA)
+  triangulate a non-simplicial facet
+  if qh.CENTERtype=qh_ASvoronoi, sets its Voronoi center
+  returns:
+  qh.newfacet_list == simplicial facets
+  facet->tricoplanar set and ->keepcentrum false
+  facet->degenerate set if duplicated apex
+  facet->f.trivisible set to facetA
+  facet->center copied from facetA (created if qh_ASvoronoi)
+  qh_eachvoronoi, qh_detvridge, qh_detvridge3 assume centers copied
+  facet->normal,offset,maxoutside copied from facetA
+
+  notes:
+  qh_makenew_nonsimplicial uses neighbor->seen for the same
+
+  see also:
+  qh_addpoint() -- add a point
+  qh_makenewfacets() -- construct a cone of facets for a new vertex
+
+  design:
+  if qh_ASvoronoi,
+  compute Voronoi center (facet->center)
+  select first vertex (highest ID to preserve ID ordering of ->vertices)
+  triangulate from vertex to ridges
+  copy facet->center, normal, offset
+  update vertex neighbors
+*/
+void qh_triangulate_facet(facetT *facetA, vertexT * *first_vertex)
+{
+  facetT * newfacet;
+  facetT * neighbor, * *neighborp;
+  vertexT *apex;
+  int      numnew = 0;
+
+  trace3( (qh ferr, "qh_triangulate_facet: triangulate facet f%d\n", facetA->id) );
+
+  if( qh IStracing >= 4 )
+    {
+    qh_printfacet(qh ferr, facetA);
+    }
+  FOREACHneighbor_(facetA) {
+    neighbor->seen = False;
+    neighbor->coplanar = False;
+    }
+  if( qh CENTERtype == qh_ASvoronoi && !facetA->center  /* matches upperdelaunay
+                                                          in qh_setfacetplane()
+                                                          */
+      && fabs_(facetA->normal[qh hull_dim - 1]) >= qh ANGLEround * qh_ZEROdelaunay )
+    {
+    facetA->center = qh_facetcenter(facetA->vertices);
+    }
+  qh_willdelete(facetA, NULL);
+  qh newfacet_list = qh facet_tail;
+  facetA->visitid = qh visit_id;
+  apex = SETfirst_(facetA->vertices);
+  qh_makenew_nonsimplicial(facetA, apex, &numnew);
+  SETfirst_(facetA->neighbors) = NULL;
+  FORALLnew_facets {
+    newfacet->tricoplanar = True;
+    newfacet->f.trivisible = facetA;
+    newfacet->degenerate = False;
+    newfacet->upperdelaunay = facetA->upperdelaunay;
+    newfacet->good = facetA->good;
+    if( qh TRInormals )
+      {
+      newfacet->keepcentrum = True;
+      newfacet->normal = qh_copypoints(facetA->normal, 1, qh hull_dim);
+      if( qh CENTERtype == qh_AScentrum )
+        {
+        newfacet->center = qh_getcentrum(newfacet);
+        }
+      else
+        {
+        newfacet->center = qh_copypoints(facetA->center, 1, qh hull_dim);
+        }
+      }
+    else
+      {
+      newfacet->keepcentrum = False;
+      newfacet->normal = facetA->normal;
+      newfacet->center = facetA->center;
+      }
+    newfacet->offset = facetA->offset;
+#if qh_MAXoutside
+    newfacet->maxoutside = facetA->maxoutside;
+#endif
+    }
+  qh_matchnewfacets(/*qh newfacet_list*/);
+  zinc_(Ztricoplanar);
+  zadd_(Ztricoplanartot, numnew);
+  zmax_(Ztricoplanarmax, numnew);
+  qh visible_list = NULL;
+  if( !(*first_vertex) )
+    {
+    (*first_vertex) = qh newvertex_list;
+    }
+  qh newvertex_list = NULL;
+  qh_updatevertices(/*qh newfacet_list, empty visible_list and
+                      newvertex_list*/                                         );
+  qh_resetlists(False, !qh_RESETvisible /*qh newfacet_list, empty visible_list
+                                          and newvertex_list*/                                     );
+} /* triangulate_facet */
+
+/*---------------------------------
+
+  qh_triangulate_link (oldfacetA, facetA, oldfacetB, facetB)
+  relink facetA to facetB via oldfacets
+  returns:
+  adds mirror facets to qh degen_mergeset (4-d and up only)
+  design:
+  if they are already neighbors, the opposing neighbors become MRGmirror facets
+*/
+void qh_triangulate_link(facetT *oldfacetA, facetT *facetA, facetT *oldfacetB, facetT *facetB)
+{
+  int errmirror = False;
+
+  trace3( (qh ferr, "qh_triangulate_link: relink old facets f%d and f%d between neighbors f%d and f%d\n",
+           oldfacetA->id, oldfacetB->id, facetA->id, facetB->id) );
+  if( qh_setin(facetA->neighbors, facetB) )
+    {
+    if( !qh_setin(facetB->neighbors, facetA) )
+      {
+      errmirror = True;
+      }
+    else
+      {
+      qh_appendmergeset(facetA, facetB, MRGmirror, NULL);
+      }
+    }
+  else if( qh_setin(facetB->neighbors, facetA) )
+    {
+    errmirror = True;
+    }
+  if( errmirror )
+    {
+    fprintf( qh ferr,
+             "qhull error (qh_triangulate_link): mirror facets f%d and f%d do not match for old facets f%d and f%d\n",
+             facetA->id, facetB->id, oldfacetA->id,
+             oldfacetB->id);
+    qh_errexit2(qh_ERRqhull, facetA, facetB);
+    }
+  qh_setreplace(facetB->neighbors, oldfacetB, facetA);
+  qh_setreplace(facetA->neighbors, oldfacetA, facetB);
+} /* triangulate_link */
+
+/*---------------------------------
+
+  qh_triangulate_mirror (facetA, facetB)
+  delete mirrored facets from qh_triangulate_null() and qh_triangulate_mirror
+  a mirrored facet shares the same vertices of a logical ridge
+  design:
+  since a null facet duplicates the first two vertices, the opposing neighbors absorb the null facet
+  if they are already neighbors, the opposing neighbors become MRGmirror facets
+*/
+void qh_triangulate_mirror(facetT *facetA, facetT *facetB)
+{
+  facetT *neighbor, *neighborB;
+  int     neighbor_i, neighbor_n;
+
+  trace3( (qh ferr, "qh_triangulate_mirror: delete mirrored facets f%d and f%d\n",
+           facetA->id, facetB->id) );
+  FOREACHneighbor_i_(facetA) {
+    neighborB = SETelemt_(facetB->neighbors, neighbor_i, facetT);
+    if( neighbor == neighborB )
+      {
+      continue; /* occurs twice */
+      }
+    qh_triangulate_link(facetA, neighbor, facetB, neighborB);
+    }
+  qh_willdelete(facetA, NULL);
+  qh_willdelete(facetB, NULL);
+} /* triangulate_mirror */
+
+/*---------------------------------
+
+  qh_triangulate_null (facetA)
+  remove null facetA from qh_triangulate_facet()
+  a null facet has vertex #1 (apex) == vertex #2
+  returns:
+  adds facetA to ->visible for deletion after qh_updatevertices
+  qh degen_mergeset contains mirror facets (4-d and up only)
+  design:
+  since a null facet duplicates the first two vertices, the opposing neighbors absorb the null facet
+  if they are already neighbors, the opposing neighbors become MRGmirror facets
+*/
+void qh_triangulate_null(facetT *facetA)
+{
+  facetT *neighbor, *otherfacet;
+
+  trace3( (qh ferr, "qh_triangulate_null: delete null facet f%d\n", facetA->id) );
+  neighbor = SETfirst_(facetA->neighbors);
+  otherfacet = SETsecond_(facetA->neighbors);
+  qh_triangulate_link(facetA, neighbor, facetA, otherfacet);
+  qh_willdelete(facetA, NULL);
+} /* triangulate_null */
+
+#else /* qh_NOmerge */
+void qh_triangulate(void)
+{
+}
+
+#endif /* qh_NOmerge */
+
+/*---------------------------------
+
+  qh_vertexintersect( vertexsetA, vertexsetB )
+  intersects two vertex sets (inverse id ordered)
+  vertexsetA is a temporary set at the top of qhmem.tempstack
+
+  returns:
+  replaces vertexsetA with the intersection
+
+  notes:
+  could overwrite vertexsetA if currently too slow
+*/
+void qh_vertexintersect(setT * *vertexsetA, setT *vertexsetB)
+{
+  setT *intersection;
+
+  intersection = qh_vertexintersect_new(*vertexsetA, vertexsetB);
+  qh_settempfree(vertexsetA);
+  *vertexsetA = intersection;
+  qh_settemppush(intersection);
+} /* vertexintersect */
+
+/*---------------------------------
+
+  qh_vertexintersect_new(  )
+  intersects two vertex sets (inverse id ordered)
+
+  returns:
+  a new set
+*/
+setT * qh_vertexintersect_new(setT *vertexsetA, setT *vertexsetB)
+{
+  setT *     intersection = qh_setnew(qh hull_dim - 1);
+  vertexT * *vertexA = SETaddr_(vertexsetA, vertexT);
+  vertexT * *vertexB = SETaddr_(vertexsetB, vertexT);
+
+  while( *vertexA && *vertexB )
+    {
+    if( *vertexA  == *vertexB )
+      {
+      qh_setappend(&intersection, *vertexA);
+      vertexA++; vertexB++;
+      }
+    else
+      {
+      if( (*vertexA)->id > (*vertexB)->id )
+        {
+        vertexA++;
+        }
+      else
+        {
+        vertexB++;
+        }
+      }
+    }
+
+  return intersection;
+} /* vertexintersect_new */
+
+/*---------------------------------
+
+  qh_vertexneighbors()
+  for each vertex in qh.facet_list,
+  determine its neighboring facets
+
+  returns:
+  sets qh.VERTEXneighbors
+  nop if qh.VERTEXneighbors already set
+  qh_addpoint() will maintain them
+
+  notes:
+  assumes all vertex->neighbors are NULL
+
+  design:
+  for each facet
+  for each vertex
+  append facet to vertex->neighbors
+*/
+void qh_vertexneighbors(void /*qh facet_list*/)
+{
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+
+  if( qh VERTEXneighbors )
+    {
+    return;
+    }
+  trace1( (qh ferr, "qh_vertexneighbors: determing neighboring facets for each vertex\n") );
+  qh vertex_visit++;
+  FORALLfacets {
+    if( facet->visible )
+      {
+      continue;
+      }
+    FOREACHvertex_(facet->vertices) {
+      if( vertex->visitid != qh vertex_visit )
+        {
+        vertex->visitid = qh vertex_visit;
+        vertex->neighbors = qh_setnew(qh hull_dim);
+        }
+      qh_setappend(&vertex->neighbors, facet);
+      }
+    }
+  qh VERTEXneighbors = True;
+} /* vertexneighbors */
+
+/*---------------------------------
+
+  qh_vertexsubset( vertexsetA, vertexsetB )
+  returns True if vertexsetA is a subset of vertexsetB
+  assumes vertexsets are sorted
+
+  note:
+  empty set is a subset of any other set
+*/
+boolT qh_vertexsubset(setT *vertexsetA, setT *vertexsetB)
+{
+  vertexT * *vertexA = (vertexT * *) SETaddr_(vertexsetA, vertexT);
+  vertexT * *vertexB = (vertexT * *) SETaddr_(vertexsetB, vertexT);
+
+  while( True )
+    {
+    if( !*vertexA )
+      {
+      return True;
+      }
+    if( !*vertexB )
+      {
+      return False;
+      }
+    if( (*vertexA)->id > (*vertexB)->id )
+      {
+      return False;
+      }
+    if( *vertexA  == *vertexB )
+      {
+      vertexA++;
+      }
+    vertexB++;
+    }
+
+  return False; /* avoid warnings */
+} /* vertexsubset */
+
diff --git a/BRAINSABC/qhull/qconvex.c b/BRAINSABC/qhull/qconvex.c
new file mode 100644
index 00000000..a0136361
--- /dev/null
+++ b/BRAINSABC/qhull/qconvex.c
@@ -0,0 +1,364 @@
+/*
  ---------------------------------
+
+  qconvex.c
+  compute convex hulls using qhull
+
+  see unix.c for full interface
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+
+#if __MWERKS__ && __POWERPC__
+#include 
+#include 
+#include 
+#include 
+
+#elif __cplusplus
+extern "C" {
+int isatty(int);
+
+}
+
+#elif _MSC_VER
+#include 
+#define isatty _isatty
+
+#else
+int isatty(int);   /* returns 1 if stdin is a tty
+          if "Undefined symbol" this can be deleted along with call in main() */
+
+#endif
+
+/*---------------------------------
+
+  qh_prompt
+  long prompt for qconvex
+
+  notes:
+  restricted version of qhull.c
+
+  see:
+  concise prompt below
+*/
+
+/* duplicated in qconvex.htm */
+char hidden_options[] = " d v H Qbb Qf Qg Qm Qr Qu Qv Qx Qz TR E V Fp Gt Q0 Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 ";
+
+char qh_prompta[] =
+  "\n\
+qconvex- compute the convex hull\n\
+    http://www.qhull.org  %s\n\
+\n\
+input (stdin):\n\
+    first lines: dimension and number of points (or vice-versa).\n\
+    other lines: point coordinates, best if one point per line\n\
+    comments:    start with a non-numeric character\n\
+\n\
+options:\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Qc   - keep coplanar points with nearest facet\n\
+    Qi   - keep interior points with nearest facet\n\
+\n\
+Qhull control options:\n\
+    Qbk:n   - scale coord k so that low bound is n\n\
+      QBk:n - scale coord k so that upper bound is n (QBk is %2.2g)\n\
+    QbB  - scale input to unit cube centered at the origin\n\
+    Qbk:0Bk:0 - remove k-th coordinate from input\n\
+    QJn  - randomly joggle input in range [-n,n]\n\
+    QRn  - random rotation (n=seed, n=0 time, n=-1 time/no rotate)\n\
+%s%s%s%s"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ; /*
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      split
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      up
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      qh_prompt
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      for
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Visual
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      C++
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      */
+char qh_promptb[] =
+  "\
+    Qs   - search all points for the initial simplex\n\
+    QGn  - good facet if visible from point n, -n for not visible\n\
+    QVn  - good facet if it includes point n, -n if not\n\
+\n\
+"                                                                                                                                                                                                 ;
+char qh_promptc[] =
+  "\
+Trace options:\n\
+    T4   - trace at level n, 4=all, 5=mem/gauss, -1= events\n\
+    Tc   - check frequently during execution\n\
+    Ts   - print statistics\n\
+    Tv   - verify result: structure, convexity, and point inclusion\n\
+    Tz   - send all output to stdout\n\
+    TFn  - report summary when n or more facets created\n\
+    TI file - input data from file, no spaces or single quotes\n\
+    TO file - output results to file, may be enclosed in single quotes\n\
+    TPn  - turn on tracing when point n added to hull\n\
+     TMn - turn on tracing at merge n\n\
+     TWn - trace merge facets when width > n\n\
+    TVn  - stop qhull after adding point n, -n for before (see TCn)\n\
+     TCn - stop qhull after building cone for point n (see TVn)\n\
+\n\
+Precision options:\n\
+    Cn   - radius of centrum (roundoff added).  Merge facets if non-convex\n\
+     An  - cosine of maximum angle.  Merge facets if cosine > n or non-convex\n\
+           C-0 roundoff, A-0.99/C-0.01 pre-merge, A0.99/C0.01 post-merge\n\
+    Rn   - randomly perturb computations by a factor of [1-n,1+n]\n\
+    Un   - max distance below plane for a new, coplanar point\n\
+    Wn   - min facet width for outside point (before roundoff)\n\
+\n\
+Output formats (may be combined; if none, produces a summary to stdout):\n\
+    f    - facet dump\n\
+    G    - Geomview output (see below)\n\
+    i    - vertices incident to each facet\n\
+    m    - Mathematica output (2-d and 3-d)\n\
+    n    - normals with offsets\n\
+    o    - OFF file format (dim, points and facets; Voronoi regions)\n\
+    p    - point coordinates \n\
+    s    - summary (stderr)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ;
+char qh_promptd[] =
+  "\
+More formats:\n\
+    Fa   - area for each facet\n\
+    FA   - compute total area and volume for option 's'\n\
+    Fc   - count plus coplanar points for each facet\n\
+           use 'Qc' (default) for coplanar and 'Qi' for interior\n\
+    FC   - centrum for each facet\n\
+    Fd   - use cdd format for input (homogeneous with offset first)\n\
+    FD   - use cdd format for numeric output (offset first)\n\
+    FF   - facet dump without ridges\n\
+    Fi   - inner plane for each facet\n\
+    FI   - ID for each facet\n\
+    Fm   - merge count for each facet (511 max)\n\
+    Fn   - count plus neighboring facets for each facet\n\
+    FN   - count plus neighboring facets for each point\n\
+    Fo   - outer plane (or max_outside) for each facet\n\
+    FO   - options and precision constants\n\
+    FP   - nearest vertex for each coplanar point\n\
+    FQ   - command used for qconvex\n\
+    Fs   - summary: #int (8), dimension, #points, tot vertices, tot facets,\n\
+                      for output: #vertices, #facets,\n\
+                                  #coplanar points, #non-simplicial facets\n\
+                    #real (2), max outer plane, min vertex\n\
+    FS   - sizes:   #int (0) \n\
+                    #real(2) tot area, tot volume\n\
+    Ft   - triangulation with centrums for non-simplicial facets (OFF format)\n\
+    Fv   - count plus vertices for each facet\n\
+    FV   - average of vertices (a feasible point for 'H')\n\
+    Fx   - extreme points (in order for 2-d)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ;
+char qh_prompte[] =
+  "\
+Geomview output (2-d, 3-d, and 4-d)\n\
+    Ga   - all points as dots\n\
+     Gp  -  coplanar points and vertices as radii\n\
+     Gv  -  vertices as spheres\n\
+    Gi   - inner planes only\n\
+     Gn  -  no planes\n\
+     Go  -  outer planes only\n\
+    Gc   - centrums\n\
+    Gh   - hyperplane intersections\n\
+    Gr   - ridges\n\
+    GDn  - drop dimension n in 3-d and 4-d output\n\
+\n\
+Print options:\n\
+    PAn  - keep n largest facets by area\n\
+    Pdk:n - drop facet if normal[k] <= n (default 0.0)\n\
+    PDk:n - drop facet if normal[k] >= n\n\
+    Pg   - print good facets (needs 'QGn' or 'QVn')\n\
+    PFn  - keep facets whose area is at least n\n\
+    PG   - print neighbors of good facets\n\
+    PMn  - keep n facets with most merges\n\
+    Po   - force output.  If error, output neighborhood of facet\n\
+    Pp   - do not report precision problems\n\
+\n\
+    .    - list of all options\n\
+    -    - one line descriptions of all options\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt2
+  synopsis for qhull
+*/
+char qh_prompt2[] =
+  "\n\
+qconvex- compute the convex hull.  Qhull %s\n\
+    input (stdin): dimension, number of points, point coordinates\n\
+    comments start with a non-numeric character\n\
+\n\
+options (qconvex.htm):\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Tv   - verify result: structure, convexity, and point inclusion\n\
+    .    - concise list of all options\n\
+    -    - one-line description of all options\n\
+\n\
+output options (subset):\n\
+    s    - summary of results (default)\n\
+    i    - vertices incident to each facet\n\
+    n    - normals with offsets\n\
+    p    - vertex coordinates (includes coplanar points if 'Qc')\n\
+    Fx   - extreme points (convex hull vertices)\n\
+    FA   - compute total area and volume\n\
+    o    - OFF format (dim, n, points, facets)\n\
+    G    - Geomview output (2-d, 3-d, and 4-d)\n\
+    m    - Mathematica output (2-d and 3-d)\n\
+    QVn  - print facets that include point n, -n if not\n\
+    TO file- output results to file, may be enclosed in single quotes\n\
+\n\
+examples:\n\
+    rbox c D2 | qconvex s n                    rbox c D2 | qconvex i\n\
+    rbox c D2 | qconvex o                      rbox 1000 s | qconvex s Tv FA\n\
+    rbox c d D2 | qconvex s Qc Fx              rbox y 1000 W0 | qconvex s n\n\
+    rbox y 1000 W0 | qconvex s QJ              rbox d G1 D12 | qconvex QR0 FA Pp\n\
+    rbox c D7 | qconvex FA TF1000\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt3
+  concise prompt for qhull
+*/
+char qh_prompt3[] =
+  "\n\
+Qhull %s.\n\
+Except for 'F.' and 'PG', upper-case options take an argument.\n\
+\n\
+ incidences     mathematica    normals        OFF_format     points\n\
+ summary        facet_dump\n\
+\n\
+ Farea          FArea_total    Fcoplanars     FCentrums      Fd_cdd_in\n\
+ FD_cdd_out     FFacet_xridge  Finner         FIDs           Fmerges\n\
+ Fneighbors     FNeigh_vertex  Fouter         FOptions       FPoint_near\n\
+ FQhull         Fsummary       FSize          Fvertices      FVertex_ave\n\
+ Fxtremes       FMaple\n\
+\n\
+ Gvertices      Gpoints        Gall_points    Gno_planes     Ginner\n\
+ Gcentrums      Ghyperplanes   Gridges        Gouter         GDrop_dim\n\
+\n\
+ PArea_keep     Pdrop d0:0D0   PFacet_area_keep Pgood        PGood_neighbors\n\
+ PMerge_keep    Poutput_forced Pprecision_not\n\
+\n\
+ QbBound 0:0.5  QbB_scale_box  Qcoplanar      QGood_point    Qinterior\n\
+ QJoggle        Qrandom        QRotate        Qsearch_1st    Qtriangulate\n\
+ QVertex_good\n\
+\n\
+ T4_trace       Tcheck_often   Tstatistics    Tverify        Tz_stdout\n\
+ TFacet_log     TInput_file    TPoint_trace   TMerge_trace   TOutput_file\n\
+ TWide_trace    TVertex_stop   TCone_stop\n\
+\n\
+ Angle_max      Centrum_size   Random_dist    Ucoplanar_max  Wide_outside\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ;
+
+/*---------------------------------
+
+  main( argc, argv )
+  processes the command line, calls qhull() to do the work, and exits
+
+  design:
+  initializes data structures
+  reads points
+  finishes initialization
+  computes convex hull and other structures
+  checks the result
+  writes the output
+  frees memory
+*/
+int main(int argc, char *argv[])
+{
+  int     curlong, totlong; /* used !qh_NOmem */
+  int     exitcode, numpoints, dim;
+  coordT *points;
+  boolT   ismalloc;
+
+#if __MWERKS__ && __POWERPC__
+  char inBuf[BUFSIZ], outBuf[BUFSIZ], errBuf[BUFSIZ];
+  SIOUXSettings.showstatusline = false;
+  SIOUXSettings.tabspaces = 1;
+  SIOUXSettings.rows = 40;
+  if( setvbuf(stdin, inBuf, _IOFBF, sizeof(inBuf) ) < 0   /* w/o, SIOUX I/O is
+                                                            slow*/
+      || setvbuf(stdout, outBuf, _IOFBF, sizeof(outBuf) ) < 0
+      || (stdout != stderr && setvbuf(stderr, errBuf, _IOFBF, sizeof(errBuf) ) < 0) )
+    {
+    fprintf(stderr, "qhull internal warning (main): could not change stdio to fully buffered.\n");
+    }
+  argc = ccommand(&argv);
+#endif
+
+  if( (argc == 1) && isatty( 0 /*stdin*/) )
+    {
+    fprintf(stdout, qh_prompt2, qh_version);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '-' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompta, qh_version, qh_DEFAULTbox,
+            qh_promptb, qh_promptc, qh_promptd, qh_prompte);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '.' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompt3, qh_version);
+    exit(qh_ERRnone);
+    }
+  qh_init_A(stdin, stdout, stderr, argc, argv); /* sets qh qhull_command */
+  exitcode = setjmp(qh errexit);                /* simple statement for CRAY
+                                                  J916 */
+  if( !exitcode )
+    {
+    qh_checkflags(qh qhull_command, hidden_options);
+    qh_initflags(qh qhull_command);
+    points = qh_readpoints(&numpoints, &dim, &ismalloc);
+    if( dim >= 5 )
+      {
+      qh_option("Qxact_merge", NULL, NULL);
+      qh MERGEexact = True; /* 'Qx' always */
+      }
+    qh_init_B(points, numpoints, dim, ismalloc);
+    qh_qhull();
+    qh_check_output();
+    qh_produce_output();
+    if( qh VERIFYoutput && !qh FORCEoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    exitcode = qh_ERRnone;
+    }
+  qh NOerrexit = True;  /* no more setjmp */
+#ifdef qh_NOmem
+  qh_freeqhull( True);
+#else
+  qh_freeqhull( False);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(stderr, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+#endif
+  return exitcode;
+} /* main */
+
diff --git a/BRAINSABC/qhull/qdelaun.c b/BRAINSABC/qhull/qdelaun.c
new file mode 100644
index 00000000..bf989e05
--- /dev/null
+++ b/BRAINSABC/qhull/qdelaun.c
@@ -0,0 +1,355 @@
+/*
  ---------------------------------
+
+  qdelaun.c
+  compute Delaunay triangulations and furthest-point Delaunay
+  triangulations using qhull
+
+  see unix.c for full interface
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+
+#if __MWERKS__ && __POWERPC__
+#include 
+#include 
+#include 
+#include 
+
+#elif __cplusplus
+extern "C" {
+int isatty(int);
+
+}
+
+#elif _MSC_VER
+#include 
+#define isatty _isatty
+
+#else
+int isatty(int);   /* returns 1 if stdin is a tty
+          if "Undefined symbol" this can be deleted along with call in main() */
+
+#endif
+
+/*---------------------------------
+
+  qh_prompt
+  long prompt for qhull
+
+  notes:
+  restricted version of qhull.c
+
+  see:
+  concise prompt below
+*/
+
+/* duplicated in qdelau_f.htm and qdelaun.htm */
+char hidden_options[] =
+  " d n v H U Qb QB Qc Qf Qg Qi Qm Qr QR Qv Qx TR E V FC Fi Fo Ft Fp FV Q0 Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 ";
+
+char qh_prompta[] =
+  "\n\
+qdelaunay- compute the Delaunay triangulation\n\
+    http://www.qhull.org  %s\n\
+\n\
+input (stdin):\n\
+    first lines: dimension and number of points (or vice-versa).\n\
+    other lines: point coordinates, best if one point per line\n\
+    comments:    start with a non-numeric character\n\
+\n\
+options:\n\
+    Qu   - compute furthest-site Delaunay triangulation\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+\n\
+Qhull control options:\n\
+    QJn  - randomly joggle input in range [-n,n]\n\
+%s%s%s%s"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ; /*
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            split
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            up
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            qh_prompt
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            for
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Visual
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            C++
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            */
+char qh_promptb[] =
+  "\
+    Qs   - search all points for the initial simplex\n\
+    Qz   - add point-at-infinity to Delaunay triangulation\n\
+    QGn  - print Delaunay region if visible from point n, -n if not\n\
+    QVn  - print Delaunay regions that include point n, -n if not\n\
+\n\
+"                                                                                                                                                                                                                                                                           ;
+char qh_promptc[] =
+  "\
+Trace options:\n\
+    T4   - trace at level n, 4=all, 5=mem/gauss, -1= events\n\
+    Tc   - check frequently during execution\n\
+    Ts   - print statistics\n\
+    Tv   - verify result: structure, convexity, and in-circle test\n\
+    Tz   - send all output to stdout\n\
+    TFn  - report summary when n or more facets created\n\
+    TI file - input data from file, no spaces or single quotes\n\
+    TO file - output results to file, may be enclosed in single quotes\n\
+    TPn  - turn on tracing when point n added to hull\n\
+     TMn - turn on tracing at merge n\n\
+     TWn - trace merge facets when width > n\n\
+    TVn  - stop qhull after adding point n, -n for before (see TCn)\n\
+     TCn - stop qhull after building cone for point n (see TVn)\n\
+\n\
+Precision options:\n\
+    Cn   - radius of centrum (roundoff added).  Merge facets if non-convex\n\
+     An  - cosine of maximum angle.  Merge facets if cosine > n or non-convex\n\
+           C-0 roundoff, A-0.99/C-0.01 pre-merge, A0.99/C0.01 post-merge\n\
+    Rn   - randomly perturb computations by a factor of [1-n,1+n]\n\
+    Wn   - min facet width for outside point (before roundoff)\n\
+\n\
+Output formats (may be combined; if none, produces a summary to stdout):\n\
+    f    - facet dump\n\
+    G    - Geomview output (see below)\n\
+    i    - vertices incident to each Delaunay region\n\
+    m    - Mathematica output (2-d only, lifted to a paraboloid)\n\
+    o    - OFF format (dim, points, and facets as a paraboloid)\n\
+    p    - point coordinates (lifted to a paraboloid)\n\
+    s    - summary (stderr)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ;
+char qh_promptd[] =
+  "\
+More formats:\n\
+    Fa   - area for each Delaunay region\n\
+    FA   - compute total area for option 's'\n\
+    Fc   - count plus coincident points for each Delaunay region\n\
+    Fd   - use cdd format for input (homogeneous with offset first)\n\
+    FD   - use cdd format for numeric output (offset first)\n\
+    FF   - facet dump without ridges\n\
+    FI   - ID of each Delaunay region\n\
+    Fm   - merge count for each Delaunay region (511 max)\n\
+    FM   - Maple output (2-d only, lifted to a paraboloid)\n\
+    Fn   - count plus neighboring region for each Delaunay region\n\
+    FN   - count plus neighboring region for each point\n\
+    FO   - options and precision constants\n\
+    FP   - nearest point and distance for each coincident point\n\
+    FQ   - command used for qdelaunay\n\
+    Fs   - summary: #int (8), dimension, #points, tot vertices, tot facets,\n\
+                    for output: #vertices, #Delaunay regions,\n\
+                                #coincident points, #non-simplicial regions\n\
+                    #real (2), max outer plane, min vertex\n\
+    FS   - sizes:   #int (0)\n\
+                    #real(2) tot area, 0\n\
+    Fv   - count plus vertices for each Delaunay region\n\
+    Fx   - extreme points of Delaunay triangulation (on convex hull)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ;
+char qh_prompte[] =
+  "\
+Geomview options (2-d and 3-d)\n\
+    Ga   - all points as dots\n\
+     Gp  -  coplanar points and vertices as radii\n\
+     Gv  -  vertices as spheres\n\
+    Gi   - inner planes only\n\
+     Gn  -  no planes\n\
+     Go  -  outer planes only\n\
+    Gc	   - centrums\n\
+    Gh   - hyperplane intersections\n\
+    Gr   - ridges\n\
+    GDn  - drop dimension n in 3-d and 4-d output\n\
+    Gt   - transparent outer ridges to view 3-d Delaunay\n\
+\n\
+Print options:\n\
+    PAn  - keep n largest Delaunay regions by area\n\
+    Pdk:n - drop facet if normal[k] <= n (default 0.0)\n\
+    PDk:n - drop facet if normal[k] >= n\n\
+    Pg   - print good Delaunay regions (needs 'QGn' or 'QVn')\n\
+    PFn  - keep Delaunay regions whose area is at least n\n\
+    PG   - print neighbors of good regions (needs 'QGn' or 'QVn')\n\
+    PMn  - keep n Delaunay regions with most merges\n\
+    Po   - force output.  If error, output neighborhood of facet\n\
+    Pp   - do not report precision problems\n\
+\n\
+    .    - list of all options\n\
+    -    - one line descriptions of all options\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt2
+  synopsis for qhull
+*/
+char qh_prompt2[] =
+  "\n\
+qdelaunay- compute the Delaunay triangulation.  Qhull %s\n\
+    input (stdin): dimension, number of points, point coordinates\n\
+    comments start with a non-numeric character\n\
+\n\
+options (qdelaun.htm):\n\
+    Qu   - furthest-site Delaunay triangulation\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Tv   - verify result: structure, convexity, and in-circle test\n\
+    .    - concise list of all options\n\
+    -    - one-line description of all options\n\
+\n\
+output options (subset):\n\
+    s    - summary of results (default)\n\
+    i    - vertices incident to each Delaunay region\n\
+    Fx   - extreme points (vertices of the convex hull)\n\
+    o    - OFF format (shows the points lifted to a paraboloid)\n\
+    G    - Geomview output (2-d and 3-d points lifted to a paraboloid)\n\
+    m    - Mathematica output (2-d inputs lifted to a paraboloid)\n\
+    QVn  - print Delaunay regions that include point n, -n if not\n\
+    TO file- output results to file, may be enclosed in single quotes\n\
+\n\
+examples:\n\
+    rbox c P0 D2 | qdelaunay s o          rbox c P0 D2 | qdelaunay i\n\
+    rbox c P0 D2 | qdelaunay Fv           rbox c P0 D2 | qdelaunay s Qu Fv\n\
+    rbox c G1 d D2 | qdelaunay s i        rbox c G1 d D2 | qdelaunay Qt\n\
+    rbox M3,4 z 100 D2 | qdelaunay s      rbox M3,4 z 100 D2 | qdelaunay s Qt\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt3
+  concise prompt for qhull
+*/
+char qh_prompt3[] =
+  "\n\
+Qhull %s.\n\
+Except for 'F.' and 'PG', upper-case options take an argument.\n\
+\n\
+ incidences     mathematica    OFF_format     points_lifted  summary\n\
+ facet_dump\n\
+\n\
+ Farea          FArea_total    Fcoincident    Fd_cdd_in      FD_cdd_out\n\
+ FF_dump_xridge FIDs           Fmerges        Fneighbors     FNeigh_vertex\n\
+ FOptions       FPoint_near    FQdelaun       Fsummary       FSize\n\
+ Fvertices      Fxtremes       FMaple\n\
+\n\
+ Gvertices      Gpoints        Gall_points    Gno_planes     Ginner\n\
+ Gcentrums      Ghyperplanes   Gridges        Gouter         GDrop_dim\n\
+ Gtransparent\n\
+\n\
+ PArea_keep     Pdrop d0:0D0   Pgood          PFacet_area_keep\n\
+ PGood_neighbors PMerge_keep   Poutput_forced Pprecision_not\n\
+\n\
+ QGood_point    QJoggle        Qsearch_1st    Qtriangulate   QupperDelaunay\n\
+ QVertex_good   Qzinfinite\n\
+\n\
+ T4_trace       Tcheck_often   Tstatistics    Tverify        Tz_stdout\n\
+ TFacet_log     TInput_file    TPoint_trace   TMerge_trace   TOutput_file\n\
+ TWide_trace    TVertex_stop   TCone_stop\n\
+\n\
+ Angle_max      Centrum_size   Random_dist    Wide_outside\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ;
+
+/*---------------------------------
+
+  main( argc, argv )
+  processes the command line, calls qhull() to do the work, and exits
+
+  design:
+  initializes data structures
+  reads points
+  finishes initialization
+  computes convex hull and other structures
+  checks the result
+  writes the output
+  frees memory
+*/
+int main(int argc, char *argv[])
+{
+  int     curlong, totlong; /* used !qh_NOmem */
+  int     exitcode, numpoints, dim;
+  coordT *points;
+  boolT   ismalloc;
+
+#if __MWERKS__ && __POWERPC__
+  char inBuf[BUFSIZ], outBuf[BUFSIZ], errBuf[BUFSIZ];
+  SIOUXSettings.showstatusline = false;
+  SIOUXSettings.tabspaces = 1;
+  SIOUXSettings.rows = 40;
+  if( setvbuf(stdin, inBuf, _IOFBF, sizeof(inBuf) ) < 0   /* w/o, SIOUX I/O is
+                                                            slow*/
+      || setvbuf(stdout, outBuf, _IOFBF, sizeof(outBuf) ) < 0
+      || (stdout != stderr && setvbuf(stderr, errBuf, _IOFBF, sizeof(errBuf) ) < 0) )
+    {
+    fprintf(stderr, "qhull internal warning (main): could not change stdio to fully buffered.\n");
+    }
+  argc = ccommand(&argv);
+#endif
+
+  if( (argc == 1) && isatty( 0 /*stdin*/) )
+    {
+    fprintf(stdout, qh_prompt2, qh_version);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '-' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompta, qh_version,
+            qh_promptb, qh_promptc, qh_promptd, qh_prompte);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '.' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompt3, qh_version);
+    exit(qh_ERRnone);
+    }
+  qh_init_A(stdin, stdout, stderr, argc, argv); /* sets qh qhull_command */
+  exitcode = setjmp(qh errexit);                /* simple statement for CRAY
+                                                  J916 */
+  if( !exitcode )
+    {
+    qh_option("delaunay  Qbbound-last", NULL, NULL);
+    qh DELAUNAY = True;     /* 'd'   */
+    qh SCALElast = True;    /* 'Qbb' */
+    qh KEEPcoplanar = True; /* 'Qc', to keep coplanars in 'p' */
+    qh_checkflags(qh qhull_command, hidden_options);
+    qh_initflags(qh qhull_command);
+    points = qh_readpoints(&numpoints, &dim, &ismalloc);
+    if( dim >= 5 )
+      {
+      qh_option("Qxact_merge", NULL, NULL);
+      qh MERGEexact = True; /* 'Qx' always */
+      }
+    qh_init_B(points, numpoints, dim, ismalloc);
+    qh_qhull();
+    qh_check_output();
+    qh_produce_output();
+    if( qh VERIFYoutput && !qh FORCEoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    exitcode = qh_ERRnone;
+    }
+  qh NOerrexit = True;  /* no more setjmp */
+#ifdef qh_NOmem
+  qh_freeqhull( True);
+#else
+  qh_freeqhull( False);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(stderr, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+#endif
+  return exitcode;
+} /* main */
+
diff --git a/BRAINSABC/qhull/qhalf.c b/BRAINSABC/qhull/qhalf.c
new file mode 100644
index 00000000..74bd8c47
--- /dev/null
+++ b/BRAINSABC/qhull/qhalf.c
@@ -0,0 +1,359 @@
+/*
  ---------------------------------
+
+  qhalf.c
+  compute the intersection of halfspaces about a point
+
+  see unix.c for full interface
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+
+#if __MWERKS__ && __POWERPC__
+#include 
+#include 
+#include 
+#include 
+
+#elif __cplusplus
+extern "C" {
+int isatty(int);
+
+}
+
+#elif _MSC_VER
+#include 
+#define isatty _isatty
+
+#else
+int isatty(int);   /* returns 1 if stdin is a tty
+          if "Undefined symbol" this can be deleted along with call in main() */
+
+#endif
+
+/*---------------------------------
+
+  qh_prompt
+  long prompt for qhull
+
+  notes:
+  restricted version of qhull.c
+
+  see:
+  concise prompt below
+*/
+
+/* duplicated in qhalf.htm */
+char hidden_options[] =
+  " d n v Qbb QbB Qf Qg Qm Qr QR Qv Qx Qz TR E V Fa FA FC FD FS Ft FV Gt Q0 Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 ";
+
+char qh_prompta[] =
+  "\n\
+qhalf- compute the intersection of halfspaces about a point\n\
+    http://www.qhull.org  %s\n\
+\n\
+input (stdin):\n\
+    optional interior point: dimension, 1, coordinates\n\
+    first lines: dimension+1 and number of halfspaces\n\
+    other lines: halfspace coefficients followed by offset\n\
+    comments:    start with a non-numeric character\n\
+\n\
+options:\n\
+    Hn,n - specify coordinates of interior point\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Qc   - keep coplanar halfspaces\n\
+    Qi   - keep other redundant halfspaces\n\
+\n\
+Qhull control options:\n\
+    QJn  - randomly joggle input in range [-n,n]\n\
+%s%s%s%s"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ; /*
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   split
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   up
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   qh_prompt
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   for
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Visual
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   C++
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   */
+char qh_promptb[] =
+  "\
+    Qbk:0Bk:0 - remove k-th coordinate from input\n\
+    Qs   - search all halfspaces for the initial simplex\n\
+    QGn  - print intersection if visible to halfspace n, -n for not\n\
+    QVn  - print intersections for halfspace n, -n if not\n\
+\n\
+"                                                                                                                                                                                                                                                              ;
+char qh_promptc[] =
+  "\
+Trace options:\n\
+    T4   - trace at level n, 4=all, 5=mem/gauss, -1= events\n\
+    Tc   - check frequently during execution\n\
+    Ts   - print statistics\n\
+    Tv   - verify result: structure, convexity, and redundancy\n\
+    Tz   - send all output to stdout\n\
+    TFn  - report summary when n or more facets created\n\
+    TI file - input data from file, no spaces or single quotes\n\
+    TO file - output results to file, may be enclosed in single quotes\n\
+    TPn  - turn on tracing when halfspace n added to intersection\n\
+    TMn  - turn on tracing at merge n\n\
+    TWn  - trace merge facets when width > n\n\
+    TVn  - stop qhull after adding halfspace n, -n for before (see TCn)\n\
+    TCn  - stop qhull after building cone for halfspace n (see TVn)\n\
+\n\
+Precision options:\n\
+    Cn   - radius of centrum (roundoff added).  Merge facets if non-convex\n\
+     An  - cosine of maximum angle.  Merge facets if cosine > n or non-convex\n\
+           C-0 roundoff, A-0.99/C-0.01 pre-merge, A0.99/C0.01 post-merge\n\
+    Rn   - randomly perturb computations by a factor of [1-n,1+n]\n\
+    Un   - max distance below plane for a new, coplanar halfspace\n\
+    Wn   - min facet width for outside halfspace (before roundoff)\n\
+\n\
+Output formats (may be combined; if none, produces a summary to stdout):\n\
+    f    - facet dump\n\
+    G    - Geomview output (dual convex hull)\n\
+    i    - non-redundant halfspaces incident to each intersection\n\
+    m    - Mathematica output (dual convex hull)\n\
+    o    - OFF format (dual convex hull: dimension, points, and facets)\n\
+    p    - vertex coordinates of dual convex hull (coplanars if 'Qc' or 'Qi')\n\
+    s    - summary (stderr)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ;
+char qh_promptd[] =
+  "\
+More formats:\n\
+    Fc   - count plus redundant halfspaces for each intersection\n\
+         -   Qc (default) for coplanar and Qi for other redundant\n\
+    Fd   - use cdd format for input (homogeneous with offset first)\n\
+    FF   - facet dump without ridges\n\
+    FI   - ID of each intersection\n\
+    Fm   - merge count for each intersection (511 max)\n\
+    FM   - Maple output (dual convex hull)\n\
+    Fn   - count plus neighboring intersections for each intersection\n\
+    FN   - count plus intersections for each non-redundant halfspace\n\
+    FO   - options and precision constants\n\
+    Fp   - dim, count, and intersection coordinates\n\
+    FP   - nearest halfspace and distance for each redundant halfspace\n\
+    FQ   - command used for qhalf\n\
+    Fs   - summary: #int (8), dim, #halfspaces, #non-redundant, #intersections\n\
+                      for output: #non-redundant, #intersections, #coplanar\n\
+                                  halfspaces, #non-simplicial intersections\n\
+                    #real (2), max outer plane, min vertex\n\
+    Fv   - count plus non-redundant halfspaces for each intersection\n\
+    Fx   - non-redundant halfspaces\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ;
+char qh_prompte[] =
+  "\
+Geomview output (2-d, 3-d and 4-d; dual convex hull)\n\
+    Ga   - all points (i.e., transformed halfspaces) as dots\n\
+     Gp  -  coplanar points and vertices as radii\n\
+     Gv  -  vertices (i.e., non-redundant halfspaces) as spheres\n\
+    Gi   - inner planes (i.e., halfspace intersections) only\n\
+     Gn  -  no planes\n\
+     Go  -  outer planes only\n\
+    Gc	 - centrums\n\
+    Gh   - hyperplane intersections\n\
+    Gr   - ridges\n\
+    GDn  - drop dimension n in 3-d and 4-d output\n\
+\n\
+Print options:\n\
+    PAn  - keep n largest facets (i.e., intersections) by area\n\
+    Pdk:n- drop facet if normal[k] <= n (default 0.0)\n\
+    PDk:n- drop facet if normal[k] >= n\n\
+    Pg   - print good facets (needs 'QGn' or 'QVn')\n\
+    PFn  - keep facets whose area is at least n\n\
+    PG   - print neighbors of good facets\n\
+    PMn  - keep n facets with most merges\n\
+    Po   - force output.  If error, output neighborhood of facet\n\
+    Pp   - do not report precision problems\n\
+\n\
+    .    - list of all options\n\
+    -    - one line descriptions of all options\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt2
+  synopsis for qhull
+*/
+char qh_prompt2[] =
+  "\n\
+qhalf- halfspace intersection about a point.  Qhull %s\n\
+    input (stdin): [dim, 1, interior point], dim+1, n, coefficients+offset\n\
+    comments start with a non-numeric character\n\
+\n\
+options (qhalf.htm):\n\
+    Hn,n - specify coordinates of interior point\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Tv   - verify result: structure, convexity, and redundancy\n\
+    .    - concise list of all options\n\
+    -    - one-line description of all options\n\
+\n\
+output options (subset):\n\
+    s    - summary of results (default)\n\
+    Fp   - intersection coordinates\n\
+    Fv   - non-redundant halfspaces incident to each intersection\n\
+    Fx   - non-redundant halfspaces\n\
+    o    - OFF file format (dual convex hull)\n\
+    G    - Geomview output (dual convex hull)\n\
+    m    - Mathematica output (dual convex hull)\n\
+    QVn  - print intersections for halfspace n, -n if not\n\
+    TO file - output results to file, may be enclosed in single quotes\n\
+\n\
+examples:\n\
+    rbox d | qconvex FQ n | qhalf s H0,0,0 Fp\n\
+    rbox c | qconvex FQ FV n | qhalf s i\n\
+    rbox c | qconvex FQ FV n | qhalf s o\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt3
+  concise prompt for qhull
+*/
+char qh_prompt3[] =
+  "\n\
+Qhull %s.\n\
+Except for 'F.' and 'PG', upper_case options take an argument.\n\
+\n\
+ incidences     Geomview       mathematica    OFF_format     point_dual\n\
+ summary        facet_dump\n\
+\n\
+ Fc_redundant   Fd_cdd_in      FF_dump_xridge FIDs           Fmerges\n\
+ Fneighbors     FN_intersect   FOptions       Fp_coordinates FP_nearest\n\
+ FQhalf         Fsummary       Fv_halfspace   FMaple         Fx_non_redundant\n\
+\n\
+ Gvertices      Gpoints        Gall_points    Gno_planes     Ginner\n\
+ Gcentrums      Ghyperplanes   Gridges        Gouter         GDrop_dim\n\
+\n\
+ PArea_keep     Pdrop d0:0D0   Pgood          PFacet_area_keep\n\
+ PGood_neighbors PMerge_keep   Poutput_forced Pprecision_not\n\
+\n\
+ Qbk:0Bk:0_drop Qcoplanar      QG_half_good   Qi_redundant   QJoggle\n\
+ Qsearch_1st    Qtriangulate   QVertex_good\n\
+\n\
+ T4_trace       Tcheck_often   Tstatistics    Tverify        Tz_stdout\n\
+ TFacet_log     TInput_file    TPoint_trace   TMerge_trace   TOutput_file\n\
+ TWide_trace    TVertex_stop   TCone_stop\n\
+\n\
+ Angle_max      Centrum_size   Random_dist    Ucoplanar_max  Wide_outside\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ;
+
+/*---------------------------------
+
+  main( argc, argv )
+  processes the command line, calls qhull() to do the work, and exits
+
+  design:
+  initializes data structures
+  reads points
+  finishes initialization
+  computes convex hull and other structures
+  checks the result
+  writes the output
+  frees memory
+*/
+int main(int argc, char *argv[])
+{
+  int     curlong, totlong; /* used !qh_NOmem */
+  int     exitcode, numpoints, dim;
+  coordT *points;
+  boolT   ismalloc;
+
+#if __MWERKS__ && __POWERPC__
+  char inBuf[BUFSIZ], outBuf[BUFSIZ], errBuf[BUFSIZ];
+  SIOUXSettings.showstatusline = false;
+  SIOUXSettings.tabspaces = 1;
+  SIOUXSettings.rows = 40;
+  if( setvbuf(stdin, inBuf, _IOFBF, sizeof(inBuf) ) < 0   /* w/o, SIOUX I/O is
+                                                            slow*/
+      || setvbuf(stdout, outBuf, _IOFBF, sizeof(outBuf) ) < 0
+      || (stdout != stderr && setvbuf(stderr, errBuf, _IOFBF, sizeof(errBuf) ) < 0) )
+    {
+    fprintf(stderr, "qhull internal warning (main): could not change stdio to fully buffered.\n");
+    }
+  argc = ccommand(&argv);
+#endif
+
+  if( (argc == 1) && isatty( 0 /*stdin*/) )
+    {
+    fprintf(stdout, qh_prompt2, qh_version);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '-' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompta, qh_version,
+            qh_promptb, qh_promptc, qh_promptd, qh_prompte);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '.' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompt3, qh_version);
+    exit(qh_ERRnone);
+    }
+  qh_init_A(stdin, stdout, stderr, argc, argv); /* sets qh qhull_command */
+  exitcode = setjmp(qh errexit);                /* simple statement for CRAY
+                                                  J916 */
+  if( !exitcode )
+    {
+    qh_option("Halfspace", NULL, NULL);
+    qh HALFspace = True;    /* 'H'   */
+    qh_checkflags(qh qhull_command, hidden_options);
+    qh_initflags(qh qhull_command);
+    if( qh SCALEinput )
+      {
+      fprintf(
+        qh ferr,
+        "\
+qhull error: options 'Qbk:n' and 'QBk:n' are not used with qhalf.\n\
+             Use 'Qbk:0Bk:0 to drop dimension k.\n"                                                                                );
+      qh_errexit(qh_ERRinput, NULL, NULL);
+      }
+    points = qh_readpoints(&numpoints, &dim, &ismalloc);
+    if( dim >= 5 )
+      {
+      qh_option("Qxact_merge", NULL, NULL);
+      qh MERGEexact = True; /* 'Qx' always */
+      }
+    qh_init_B(points, numpoints, dim, ismalloc);
+    qh_qhull();
+    qh_check_output();
+    qh_produce_output();
+    if( qh VERIFYoutput && !qh FORCEoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    exitcode = qh_ERRnone;
+    }
+  qh NOerrexit = True;  /* no more setjmp */
+#ifdef qh_NOmem
+  qh_freeqhull( True);
+#else
+  qh_freeqhull( False);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(stderr, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+#endif
+  return exitcode;
+} /* main */
+
diff --git a/BRAINSABC/qhull/qhull.c b/BRAINSABC/qhull/qhull.c
new file mode 100644
index 00000000..cb10f23b
--- /dev/null
+++ b/BRAINSABC/qhull/qhull.c
@@ -0,0 +1,1808 @@
+/*
  ---------------------------------
+
+  qhull.c
+  Quickhull algorithm for convex hulls
+
+  qhull() and top-level routines
+
+  see qh-qhull.htm, qhull.h, unix.c
+
+  see qhull_a.h for internal functions
+
+  copyright (c) 1993-2003 The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*============= functions in alphabetic order after qhull() =======*/
+
+/*---------------------------------
+
+  qh_qhull()
+  compute DIM3 convex hull of qh.num_points starting at qh.first_point
+  qh contains all global options and variables
+
+  returns:
+  returns polyhedron
+  qh.facet_list, qh.num_facets, qh.vertex_list, qh.num_vertices,
+
+  returns global variables
+  qh.hulltime, qh.max_outside, qh.interior_point, qh.max_vertex, qh.min_vertex
+
+  returns precision constants
+  qh.ANGLEround, centrum_radius, cos_max, DISTround, MAXabs_coord, ONEmerge
+
+  notes:
+  unless needed for output
+  qh.max_vertex and qh.min_vertex are max/min due to merges
+
+  see:
+  to add individual points to either qh.num_points
+  use qh_addpoint()
+
+  if qh.GETarea
+  qh_produceoutput() returns qh.totarea and qh.totvol via qh_getarea()
+
+  design:
+  record starting time
+  initialize hull and partition points
+  build convex hull
+  unless early termination
+  update facet->maxoutside for vertices, coplanar, and near-inside points
+  error if temporary sets exist
+  record end time
+*/
+
+void qh_qhull(void)
+{
+  int numoutside;
+
+  qh hulltime = qh_CPUclock;
+
+  if( qh RERUN || qh JOGGLEmax < REALmax / 2 )
+    {
+    qh_build_withrestart();
+    }
+  else
+    {
+    qh_initbuild();
+    qh_buildhull();
+    }
+  if( !qh STOPpoint && !qh STOPcone )
+    {
+    if( qh ZEROall_ok && !qh TESTvneighbors && qh MERGEexact )
+      {
+      qh_checkzero( qh_ALL);
+      }
+    if( qh ZEROall_ok && !qh TESTvneighbors && !qh WAScoplanar )
+      {
+      trace2( (qh ferr,
+               "qh_qhull: all facets are clearly convex and no coplanar points.  Post-merging and check of maxout not needed.\n") );
+      qh DOcheckmax = False;
+      }
+    else
+      {
+      if( qh MERGEexact || (qh hull_dim > qh_DIMreduceBuild && qh PREmerge) )
+        {
+        qh_postmerge("First post-merge", qh premerge_centrum, qh premerge_cos,
+                     (qh POSTmerge ? False : qh TESTvneighbors) );
+        }
+      else if( !qh POSTmerge && qh TESTvneighbors )
+        {
+        qh_postmerge("For testing vertex neighbors", qh premerge_centrum,
+                     qh premerge_cos, True);
+        }
+      if( qh POSTmerge )
+        {
+        qh_postmerge("For post-merging", qh postmerge_centrum,
+                     qh postmerge_cos, qh TESTvneighbors);
+        }
+      if( qh visible_list == qh facet_list )   /* i.e., merging done */
+        {
+        qh findbestnew = True;
+        qh_partitionvisible(/*visible_list, newfacet_list*/ !qh_ALL, &numoutside);
+        qh findbestnew = False;
+        qh_deletevisible(/*qh visible_list*/);
+        qh_resetlists(False, qh_RESETvisible /*qh visible_list newvertex_list
+                                               newfacet_list */                               );
+        }
+      }
+    if( qh DOcheckmax )
+      {
+      if( qh REPORTfreq )
+        {
+        qh_buildtracing(NULL, NULL);
+        fprintf(qh ferr, "\nTesting all coplanar points.\n");
+        }
+      qh_check_maxout();
+      }
+    if( qh KEEPnearinside && !qh maxoutdone )
+      {
+      qh_nearcoplanar();
+      }
+    }
+  if( qh_setsize( (setT *)qhmem.tempstack) != 0 )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_qhull): temporary sets not empty (%d)\n",
+            qh_setsize( (setT *)qhmem.tempstack) );
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  qh hulltime = qh_CPUclock - qh hulltime;
+  qh QHULLfinished = True;
+  trace1( (qh ferr, "qh_qhull: algorithm completed\n") );
+} /* qhull */
+
+/*---------------------------------
+
+  qh_addpoint( furthest, facet, checkdist )
+  add point (usually furthest point) above facet to hull
+  if checkdist,
+  check that point is above facet.
+  if point is not outside of the hull, uses qh_partitioncoplanar()
+  assumes that facet is defined by qh_findbestfacet()
+  else if facet specified,
+  assumes that point is above facet (major damage if below)
+  for Delaunay triangulations,
+  Use qh_setdelaunay() to lift point to paraboloid and scale by 'Qbb' if needed
+  Do not use options 'Qbk', 'QBk', or 'QbB' since they scale the coordinates.
+
+  returns:
+  returns False if user requested an early termination
+  qh.visible_list, newfacet_list, delvertex_list, NEWfacets may be defined
+  updates qh.facet_list, qh.num_facets, qh.vertex_list, qh.num_vertices
+  clear qh.maxoutdone (will need to call qh_check_maxout() for facet->maxoutside)
+  if unknown point, adds a pointer to qh.other_points
+  do not deallocate the point's coordinates
+
+  notes:
+  assumes point is near its best facet and not at a local minimum of a lens
+  distributions.  Use qh_findbestfacet to avoid this case.
+  uses qh.visible_list, qh.newfacet_list, qh.delvertex_list, qh.NEWfacets
+
+  see also:
+  qh_triangulate() -- triangulate non-simplicial facets
+
+  design:
+  check point in qh.first_point/.num_points
+  if checkdist
+  if point not above facet
+  partition coplanar point
+  exit
+  exit if pre STOPpoint requested
+  find horizon and visible facets for point
+  make new facets for point to horizon
+  make hyperplanes for point
+  compute balance statistics
+  match neighboring new facets
+  update vertex neighbors and delete interior vertices
+  exit if STOPcone requested
+  merge non-convex new facets
+  if merge found, many merges, or 'Qf'
+  use qh_findbestnew() instead of qh_findbest()
+  partition outside points from visible facets
+  delete visible facets
+  check polyhedron if requested
+  exit if post STOPpoint requested
+  reset working lists of facets and vertices
+*/
+boolT qh_addpoint(pointT *furthest, facetT *facet, boolT checkdist)
+{
+  int      goodvisible, goodhorizon;
+  vertexT *vertex;
+  facetT * newfacet;
+  realT    dist, newbalance, pbalance;
+  boolT    isoutside = False;
+  int      numpart, numpoints, numnew, firstnew;
+
+  qh maxoutdone = False;
+
+  if( qh_pointid(furthest) == -1 )
+    {
+    qh_setappend(&qh other_points, furthest);
+    }
+  if( !facet )
+    {
+    fprintf(qh ferr, "qh_addpoint: NULL facet.  Need to call qh_findbestfacet first\n");
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  if( checkdist )
+    {
+    facet = qh_findbest(furthest, facet, !qh_ALL, !qh_ISnewfacets, !qh_NOupper,
+                        &dist, &isoutside, &numpart);
+    zzadd_(Zpartition, numpart);
+    if( !isoutside )
+      {
+      zinc_(Znotmax);  /* last point of outsideset is no longer furthest. */
+      facet->notfurthest = True;
+      qh_partitioncoplanar(furthest, facet, &dist);
+      return True;
+      }
+    }
+  qh_buildtracing(furthest, facet);
+  if( qh STOPpoint < 0 && qh furthest_id == -qh STOPpoint - 1 )
+    {
+    facet->notfurthest = True;
+    return False;
+    }
+  qh_findhorizon(furthest, facet, &goodvisible, &goodhorizon);
+  if( qh ONLYgood && !(goodvisible + goodhorizon) && !qh GOODclosest )
+    {
+    zinc_(Znotgood);
+    facet->notfurthest = True;
+    /* last point of outsideset is no longer furthest.  This is ok
+       since all points of the outside are likely to be bad */
+    qh_resetlists(False, qh_RESETvisible /*qh visible_list newvertex_list
+                                           newfacet_list */                               );
+    return True;
+    }
+  zzinc_(Zprocessed);
+  firstnew = qh facet_id;
+  vertex = qh_makenewfacets(furthest /*visible_list, attaches if !ONLYgood */);
+  qh_makenewplanes(/* newfacet_list */);
+  numnew = qh facet_id - firstnew;
+  newbalance = numnew - (realT) (qh num_facets - qh num_visible)
+    * qh hull_dim / qh num_vertices;
+  wadd_(Wnewbalance, newbalance);
+  wadd_(Wnewbalance2, newbalance * newbalance);
+  if( qh ONLYgood
+      && !qh_findgood(qh newfacet_list, goodhorizon) && !qh GOODclosest )
+    {
+    FORALLnew_facets
+    qh_delfacet(newfacet);
+    qh_delvertex(vertex);
+    qh_resetlists(True, qh_RESETvisible /*qh visible_list newvertex_list
+                                          newfacet_list */                               );
+    zinc_(Znotgoodnew);
+    facet->notfurthest = True;
+    return True;
+    }
+  if( qh ONLYgood )
+    {
+    qh_attachnewfacets(/*visible_list*/);
+    }
+  qh_matchnewfacets();
+  qh_updatevertices();
+  if( qh STOPcone && qh furthest_id == qh STOPcone - 1 )
+    {
+    facet->notfurthest = True;
+    return False;  /* visible_list etc. still defined */
+    }
+  qh findbestnew = False;
+  if( qh PREmerge || qh MERGEexact )
+    {
+    qh_premerge(vertex, qh premerge_centrum, qh premerge_cos);
+    if( qh_USEfindbestnew )
+      {
+      qh findbestnew = True;
+      }
+    else
+      {
+      FORALLnew_facets {
+        if( !newfacet->simplicial )
+          {
+          qh findbestnew = True; /* use qh_findbestnew instead of qh_findbest*/
+          break;
+          }
+        }
+      }
+    }
+  else if( qh BESToutside )
+    {
+    qh findbestnew = True;
+    }
+  qh_partitionvisible(/*visible_list, newfacet_list*/ !qh_ALL, &numpoints);
+  qh findbestnew = False;
+  qh findbest_notsharp = False;
+  zinc_(Zpbalance);
+  pbalance = numpoints - (realT) qh hull_dim /* assumes all points extreme */
+    * (qh num_points - qh num_vertices) / qh num_vertices;
+  wadd_(Wpbalance, pbalance);
+  wadd_(Wpbalance2, pbalance * pbalance);
+  qh_deletevisible(/*qh visible_list*/);
+  zmax_(Zmaxvertex, qh num_vertices);
+  qh NEWfacets = False;
+  if( qh IStracing >= 4 )
+    {
+    if( qh num_facets < 2000 )
+      {
+      qh_printlists();
+      }
+    qh_printfacetlist(qh newfacet_list, NULL, True);
+    qh_checkpolygon(qh facet_list);
+    }
+  else if( qh CHECKfrequently )
+    {
+    if( qh num_facets < 50 )
+      {
+      qh_checkpolygon(qh facet_list);
+      }
+    else
+      {
+      qh_checkpolygon(qh newfacet_list);
+      }
+    }
+  if( qh STOPpoint > 0 && qh furthest_id == qh STOPpoint - 1 )
+    {
+    return False;
+    }
+  qh_resetlists(True, qh_RESETvisible /*qh visible_list newvertex_list
+                                        newfacet_list */                               );
+  /* qh_triangulate(); to test qh.TRInormals */
+  trace2( (qh ferr, "qh_addpoint: added p%d new facets %d new balance %2.2g point balance %2.2g\n",
+           qh_pointid(furthest), numnew, newbalance, pbalance) );
+  return True;
+} /* addpoint */
+
+/*---------------------------------
+
+  qh_build_withrestart()
+  allow restarts due to qh.JOGGLEmax while calling qh_buildhull()
+  qh.FIRSTpoint/qh.NUMpoints is point array
+  it may be moved by qh_joggleinput()
+*/
+void qh_build_withrestart(void)
+{
+  int restart;
+
+  qh ALLOWrestart = True;
+
+  while( True )
+    {
+    restart = setjmp(qh restartexit); /* simple statement for CRAY J916 */
+    if( restart )                     /* only from qh_precision() */
+      {
+      zzinc_(Zretry);
+      wmax_(Wretrymax, qh JOGGLEmax);
+      qh ERREXITcalled = False;
+      qh STOPcone = True; /* if break, prevents normal output */
+      }
+    if( !qh RERUN && qh JOGGLEmax < REALmax / 2 )
+      {
+      if( qh build_cnt > qh_JOGGLEmaxretry )
+        {
+        fprintf(
+          qh ferr,
+          "\n\
+qhull precision error: %d attempts to construct a convex hull\n\
+        with joggled input.  Increase joggle above 'QJ%2.2g'\n\
+	or modify qh_JOGGLE... parameters in user.h\n"                                                                                                                                               ,
+          qh build_cnt,
+          qh JOGGLEmax);
+        qh_errexit(qh_ERRqhull, NULL, NULL);
+        }
+      if( qh build_cnt && !restart )
+        {
+        break;
+        }
+      }
+    else if( qh build_cnt && qh build_cnt >= qh RERUN )
+      {
+      break;
+      }
+    qh STOPcone = False;
+    qh_freebuild(True);   /* first call is a nop */
+    qh build_cnt++;
+    if( !qh qhull_optionsiz )
+      {
+      qh qhull_optionsiz = strlen(qh qhull_options);
+      }
+    else
+      {
+      qh qhull_options[qh qhull_optionsiz] = '\0';
+      qh qhull_optionlen = 80;
+      }
+    qh_option("_run", &qh build_cnt, NULL);
+    if( qh build_cnt == qh RERUN )
+      {
+      qh IStracing = qh TRACElastrun;  /* duplicated from qh_initqhull_globals
+                                         */
+      if( qh TRACEpoint != -1 || qh TRACEdist < REALmax / 2 || qh TRACEmerge )
+        {
+        qh TRACElevel = (qh IStracing ? qh IStracing : 3);
+        qh IStracing = 0;
+        }
+      qhmem.IStracing = qh IStracing;
+      }
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      qh_joggleinput();
+      }
+    qh_initbuild();
+    qh_buildhull();
+    if( qh JOGGLEmax < REALmax / 2 && !qh MERGING )
+      {
+      qh_checkconvex(qh facet_list, qh_ALGORITHMfault);
+      }
+    }
+
+  qh ALLOWrestart = False;
+} /* qh_build_withrestart */
+
+/*---------------------------------
+
+  qh_buildhull()
+  construct a convex hull by adding outside points one at a time
+
+  returns:
+
+  notes:
+  may be called multiple times
+  checks facet and vertex lists for incorrect flags
+  to recover from STOPcone, call qh_deletevisible and qh_resetlists
+
+  design:
+  check visible facet and newfacet flags
+  check newlist vertex flags and qh.STOPcone/STOPpoint
+  for each facet with a furthest outside point
+  add point to facet
+  exit if qh.STOPcone or qh.STOPpoint requested
+  if qh.NARROWhull for initial simplex
+  partition remaining outside points to coplanar sets
+*/
+void qh_buildhull(void)
+{
+  facetT * facet;
+  pointT * furthest;
+  vertexT *vertex;
+  int      id;
+
+  trace1( (qh ferr, "qh_buildhull: start build hull\n") );
+  FORALLfacets {
+    if( facet->visible || facet->newfacet )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_buildhull): visible or new facet f%d in facet list\n",
+              facet->id);
+      qh_errexit(qh_ERRqhull, facet, NULL);
+      }
+    }
+  FORALLvertices {
+    if( vertex->newlist )
+      {
+      fprintf(qh ferr, "qhull internal error (qh_buildhull): new vertex f%d in vertex list\n",
+              vertex->id);
+      qh_errprint("ERRONEOUS", NULL, NULL, NULL, vertex);
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    id = qh_pointid(vertex->point);
+    if( (qh STOPpoint > 0 && id == qh STOPpoint - 1) ||
+        (qh STOPpoint < 0 && id == -qh STOPpoint - 1) ||
+        (qh STOPcone > 0 && id == qh STOPcone - 1) )
+      {
+      trace1( (qh ferr, "qh_buildhull: stop point or cone P%d in initial hull\n", id) );
+      return;
+      }
+    }
+  qh facet_next = qh facet_list;      /* advance facet when processed */
+  while( (furthest = qh_nextfurthest(&facet) ) )
+    {
+    qh num_outside--;  /* if ONLYmax, furthest may not be outside */
+    if( !qh_addpoint(furthest, facet, qh ONLYmax) )
+      {
+      break;
+      }
+    }
+
+  if( qh NARROWhull ) /* move points from outsideset to coplanarset */
+    {
+    qh_outcoplanar( /* facet_list */ );
+    }
+  if( qh num_outside && !furthest )
+    {
+    fprintf(qh ferr, "qhull internal error (qh_buildhull): %d outside points were never processed.\n", qh num_outside);
+    qh_errexit(qh_ERRqhull, NULL, NULL);
+    }
+  trace1( (qh ferr, "qh_buildhull: completed the hull construction\n") );
+} /* buildhull */
+
+/*---------------------------------
+
+  qh_buildtracing( furthest, facet )
+  trace an iteration of qh_buildhull() for furthest point and facet
+  if !furthest, prints progress message
+
+  returns:
+  tracks progress with qh.lastreport
+  updates qh.furthest_id (-3 if furthest is NULL)
+  also resets visit_id, vertext_visit on wrap around
+
+  see:
+  qh_tracemerging()
+
+  design:
+  if !furthest
+  print progress message
+  exit
+  if 'TFn' iteration
+  print progress message
+  else if tracing
+  trace furthest point and facet
+  reset qh.visit_id and qh.vertex_visit if overflow may occur
+  set qh.furthest_id for tracing
+*/
+void qh_buildtracing(pointT *furthest, facetT *facet)
+{
+  realT      dist = 0;
+  float      cpu;
+  int        total, furthestid;
+  time_t     timedata;
+  struct tm *tp;
+  vertexT *  vertex;
+
+  qh old_randomdist = qh RANDOMdist;
+  qh RANDOMdist = False;
+
+  if( !furthest )
+    {
+    time(&timedata);
+    tp = localtime(&timedata);
+    cpu = qh_CPUclock - qh hulltime;
+    cpu /= qh_SECticks;
+    total = zzval_(Ztotmerge) - zzval_(Zcyclehorizon) + zzval_(Zcyclefacettot);
+    fprintf(
+      qh ferr,
+      "\n\
+At %02d:%02d:%02d & %2.5g CPU secs, qhull has created %d facets and merged %d.\n\
+ The current hull contains %d facets and %d vertices.  Last point was p%d\n"                                                                                             ,
+      tp->tm_hour, tp->tm_min, tp->tm_sec, cpu, qh facet_id - 1,
+      total, qh num_facets, qh num_vertices,
+      qh furthest_id);
+    return;
+    }
+  furthestid = qh_pointid(furthest);
+  if( qh TRACEpoint == furthestid )
+    {
+    qh IStracing = qh TRACElevel;
+    qhmem.IStracing = qh TRACElevel;
+    }
+  else if( qh TRACEpoint != -1 && qh TRACEdist < REALmax / 2 )
+    {
+    qh IStracing = 0;
+    qhmem.IStracing = 0;
+    }
+  if( qh REPORTfreq && (qh facet_id - 1 > qh lastreport + qh REPORTfreq) )
+    {
+    qh lastreport = qh facet_id - 1;
+    time(&timedata);
+    tp = localtime(&timedata);
+    cpu = qh_CPUclock - qh hulltime;
+    cpu /= qh_SECticks;
+    total = zzval_(Ztotmerge) - zzval_(Zcyclehorizon) + zzval_(Zcyclefacettot);
+    zinc_(Zdistio);
+    qh_distplane(furthest, facet, &dist);
+    fprintf(
+      qh ferr,
+      "\n\
+At %02d:%02d:%02d & %2.5g CPU secs, qhull has created %d facets and merged %d.\n\
+ The current hull contains %d facets and %d vertices.  There are %d\n\
+ outside points.  Next is point p%d (v%d), %2.2g above f%d.\n"                                                                                                                                                                    ,
+      tp->tm_hour, tp->tm_min, tp->tm_sec, cpu, qh facet_id - 1,
+      total, qh num_facets, qh num_vertices, qh num_outside + 1,
+      furthestid, qh vertex_id, dist, getid_(
+        facet) );
+    }
+  else if( qh IStracing >= 1 )
+    {
+    cpu = qh_CPUclock - qh hulltime;
+    cpu /= qh_SECticks;
+    qh_distplane(furthest, facet, &dist);
+    fprintf(
+      qh ferr,
+      "qh_addpoint: add p%d (v%d) to hull of %d facets (%2.2g above f%d) and %d outside at %4.4g CPU secs.  Previous was p%d.\n",
+      furthestid, qh vertex_id, qh num_facets, dist,
+      getid_(facet), qh num_outside + 1, cpu, qh furthest_id);
+    }
+  if( qh visit_id > (unsigned) INT_MAX )
+    {
+    qh visit_id = 0;
+    FORALLfacets
+    facet-> visitid = qh visit_id;
+    }
+  if( qh vertex_visit > (unsigned) INT_MAX )
+    {
+    qh vertex_visit = 0;
+    FORALLvertices
+    vertex-> visitid = qh vertex_visit;
+    }
+  qh furthest_id = furthestid;
+  qh RANDOMdist = qh old_randomdist;
+} /* buildtracing */
+
+/*---------------------------------
+
+  qh_errexit2( exitcode, facet, otherfacet )
+  return exitcode to system after an error
+  report two facets
+
+  returns:
+  assumes exitcode non-zero
+
+  see:
+  normally use qh_errexit() in user.c (reports a facet and a ridge)
+*/
+void qh_errexit2(int exitcode, facetT *facet, facetT *otherfacet)
+{
+
+  qh_errprint("ERRONEOUS", facet, otherfacet, NULL, NULL);
+  qh_errexit(exitcode, NULL, NULL);
+} /* errexit2 */
+
+/*---------------------------------
+
+  qh_findhorizon( point, facet, goodvisible, goodhorizon )
+  given a visible facet, find the point's horizon and visible facets
+  for all facets, !facet-visible
+
+  returns:
+  returns qh.visible_list/num_visible with all visible facets
+  marks visible facets with ->visible
+  updates count of good visible and good horizon facets
+  updates qh.max_outside, qh.max_vertex, facet->maxoutside
+
+  see:
+  similar to qh_delpoint()
+
+  design:
+  move facet to qh.visible_list at end of qh.facet_list
+  for all visible facets
+  for each unvisited neighbor of a visible facet
+  compute distance of point to neighbor
+  if point above neighbor
+  move neighbor to end of qh.visible_list
+  else if point is coplanar with neighbor
+  update qh.max_outside, qh.max_vertex, neighbor->maxoutside
+  mark neighbor coplanar (will create a samecycle later)
+  update horizon statistics
+*/
+void qh_findhorizon(pointT *point, facetT *facet, int *goodvisible, int *goodhorizon)
+{
+  facetT *neighbor, * *neighborp, *visible;
+  int     numhorizon = 0, coplanar = 0;
+  realT   dist;
+
+  trace1( (qh ferr, "qh_findhorizon: find horizon for point p%d facet f%d\n", qh_pointid(point), facet->id) );
+  *goodvisible = *goodhorizon = 0;
+  zinc_(Ztotvisible);
+  qh_removefacet(facet);  /* visible_list at end of qh facet_list */
+  qh_appendfacet(facet);
+  qh num_visible = 1;
+  if( facet->good )
+    {
+    (*goodvisible)++;
+    }
+  qh visible_list = facet;
+  facet->visible = True;
+  facet->f.replace = NULL;
+  if( qh IStracing >= 4 )
+    {
+    qh_errprint("visible", facet, NULL, NULL, NULL);
+    }
+  qh visit_id++;
+  FORALLvisible_facets {
+    if( visible->tricoplanar && !qh TRInormals )
+      {
+      fprintf(qh ferr, "qh_findhorizon: does not work for tricoplanar facets.  Use option 'Q11'\n");
+      qh_errexit(qh_ERRqhull, visible, NULL);
+      }
+    visible->visitid = qh visit_id;
+    FOREACHneighbor_(visible) {
+      if( neighbor->visitid == qh visit_id )
+        {
+        continue;
+        }
+      neighbor->visitid = qh visit_id;
+      zzinc_(Znumvisibility);
+      qh_distplane(point, neighbor, &dist);
+      if( dist > qh MINvisible )
+        {
+        zinc_(Ztotvisible);
+        qh_removefacet(neighbor); /* append to end of qh visible_list */
+        qh_appendfacet(neighbor);
+        neighbor->visible = True;
+        neighbor->f.replace = NULL;
+        qh num_visible++;
+        if( neighbor->good )
+          {
+          (*goodvisible)++;
+          }
+        if( qh IStracing >= 4 )
+          {
+          qh_errprint("visible", neighbor, NULL, NULL, NULL);
+          }
+        }
+      else
+        {
+        if( dist > -qh MAXcoplanar )
+          {
+          neighbor->coplanar = True;
+          zzinc_(Zcoplanarhorizon);
+          qh_precision("coplanar horizon");
+          coplanar++;
+          if( qh MERGING )
+            {
+            if( dist > 0 )
+              {
+              maximize_(qh max_outside, dist);
+              maximize_(qh max_vertex, dist);
+#if qh_MAXoutside
+              maximize_(neighbor->maxoutside, dist);
+#endif
+              }
+            else
+              {
+              minimize_(qh min_vertex, dist); /* due to merge later */
+              }
+            }
+          trace2( (qh ferr,
+                   "qh_findhorizon: point p%d is coplanar to horizon f%d, dist=%2.7g < qh MINvisible (%2.7g)\n",
+                   qh_pointid(point), neighbor->id, dist, qh MINvisible) );
+          }
+        else
+          {
+          neighbor->coplanar = False;
+          }
+        zinc_(Ztothorizon);
+        numhorizon++;
+        if( neighbor->good )
+          {
+          (*goodhorizon)++;
+          }
+        if( qh IStracing >= 4 )
+          {
+          qh_errprint("horizon", neighbor, NULL, NULL, NULL);
+          }
+        }
+      }
+    }
+  if( !numhorizon )
+    {
+    qh_precision("empty horizon");
+    fprintf(qh ferr, "qhull precision error (qh_findhorizon): empty horizon\n\
+Point p%d was above all facets.\n", qh_pointid(point) );
+    qh_printfacetlist(qh facet_list, NULL, True);
+    qh_errexit(qh_ERRprec, NULL, NULL);
+    }
+  trace1( (qh ferr, "qh_findhorizon: %d horizon facets (good %d), %d visible (good %d), %d coplanar\n",
+           numhorizon, *goodhorizon, qh num_visible, *goodvisible, coplanar) );
+  if( qh IStracing >= 4 && qh num_facets < 50 )
+    {
+    qh_printlists();
+    }
+} /* findhorizon */
+
+/*---------------------------------
+
+  qh_nextfurthest( visible )
+  returns next furthest point and visible facet for qh_addpoint()
+  starts search at qh.facet_next
+
+  returns:
+  removes furthest point from outside set
+  NULL if none available
+  advances qh.facet_next over facets with empty outside sets
+
+  design:
+  for each facet from qh.facet_next
+  if empty outside set
+  advance qh.facet_next
+  else if qh.NARROWhull
+  determine furthest outside point
+  if furthest point is not outside
+  advance qh.facet_next (point will be coplanar)
+  remove furthest point from outside set
+*/
+pointT * qh_nextfurthest(facetT * *visible)
+{
+  facetT *facet;
+  int     size, idx;
+  realT   randr, dist;
+  pointT *furthest;
+
+  while( (facet = qh facet_next) != qh facet_tail )
+    {
+    if( !facet->outsideset )
+      {
+      qh facet_next = facet->next;
+      continue;
+      }
+    SETreturnsize_(facet->outsideset, size);
+    if( !size )
+      {
+      qh_setfree(&facet->outsideset);
+      qh facet_next = facet->next;
+      continue;
+      }
+    if( qh NARROWhull )
+      {
+      if( facet->notfurthest )
+        {
+        qh_furthestout(facet);
+        }
+      furthest = (pointT *)qh_setlast(facet->outsideset);
+#if qh_COMPUTEfurthest
+      qh_distplane(furthest, facet, &dist);
+      zinc_(Zcomputefurthest);
+#else
+      dist = facet->furthestdist;
+#endif
+      if( dist < qh MINoutside )   /* remainder of outside set is coplanar for
+                                     qh_outcoplanar */
+        {
+        qh facet_next = facet->next;
+        continue;
+        }
+      }
+    if( !qh RANDOMoutside && !qh VIRTUALmemory )
+      {
+      if( qh PICKfurthest )
+        {
+        qh_furthestnext(/* qh facet_list */);
+        facet = qh facet_next;
+        }
+      *visible = facet;
+      return (pointT *)qh_setdellast(facet->outsideset);
+      }
+    if( qh RANDOMoutside )
+      {
+      int outcoplanar = 0;
+      if( qh NARROWhull )
+        {
+        FORALLfacets {
+          if( facet == qh facet_next )
+            {
+            break;
+            }
+          if( facet->outsideset )
+            {
+            outcoplanar += qh_setsize( facet->outsideset);
+            }
+          }
+        }
+      randr = qh_RANDOMint;
+      randr = randr / (qh_RANDOMmax + 1);
+      idx = (int)floor( (qh num_outside - outcoplanar) * randr);
+      FORALLfacet_(qh facet_next) {
+        if( facet->outsideset )
+          {
+          SETreturnsize_(facet->outsideset, size);
+          if( !size )
+            {
+            qh_setfree(&facet->outsideset);
+            }
+          else if( size > idx )
+            {
+            *visible = facet;
+            return (pointT *)qh_setdelnth(facet->outsideset, (size_t)idx);
+            }
+          else
+            {
+            idx -= size;
+            }
+          }
+        }
+      fprintf(
+        qh ferr,
+        "qhull internal error (qh_nextfurthest): num_outside %d is too low\nby at least %d, or a random real %g >= 1.0\n",
+        qh num_outside, idx + 1, randr);
+      qh_errexit(qh_ERRqhull, NULL, NULL);
+      }
+    else    /* VIRTUALmemory */
+      {
+      facet = qh facet_tail->previous;
+      if( !(furthest = (pointT *)qh_setdellast(facet->outsideset) ) )
+        {
+        if( facet->outsideset )
+          {
+          qh_setfree(&facet->outsideset);
+          }
+        qh_removefacet(facet);
+        qh_prependfacet(facet, &qh facet_list);
+        continue;
+        }
+      *visible = facet;
+      return furthest;
+      }
+    }
+
+  return NULL;
+} /* nextfurthest */
+
+/*---------------------------------
+
+  qh_partitionall( vertices, points, numpoints )
+  partitions all points in points/numpoints to the outsidesets of facets
+  vertices= vertices in qh.facet_list (not partitioned)
+
+  returns:
+  builds facet->outsideset
+  does not partition qh.GOODpoint
+  if qh.ONLYgood && !qh.MERGING,
+  does not partition qh.GOODvertex
+
+  notes:
+  faster if qh.facet_list sorted by anticipated size of outside set
+
+  design:
+  initialize pointset with all points
+  remove vertices from pointset
+  remove qh.GOODpointp from pointset (unless it's qh.STOPcone or qh.STOPpoint)
+  for all facets
+  for all remaining points in pointset
+  compute distance from point to facet
+  if point is outside facet
+  remove point from pointset (by not reappending)
+  update bestpoint
+  append point or old bestpoint to facet's outside set
+  append bestpoint to facet's outside set (furthest)
+  for all points remaining in pointset
+  partition point into facets' outside sets and coplanar sets
+*/
+void qh_partitionall(setT *vertices, pointT *points, int numpoints)
+{
+  setT *   pointset;
+  vertexT *vertex, * *vertexp;
+  pointT * point, * *pointp, *bestpoint;
+  int      size, point_i, point_n, point_end, remaining, i, id;
+  facetT * facet;
+  realT    bestdist = -REALmax, dist, distoutside;
+
+  trace1( (qh ferr, "qh_partitionall: partition all points into outside sets\n") );
+  pointset = qh_settemp(numpoints);
+  qh num_outside = 0;
+  pointp = SETaddr_(pointset, pointT);
+  for( i = numpoints, point = points; i--; point += qh hull_dim )
+    {
+    *(pointp++) = point;
+    }
+  qh_settruncate(pointset, (size_t)numpoints);
+  FOREACHvertex_(vertices) {
+    if( (id = qh_pointid(vertex->point) ) >= 0 )
+      {
+      SETelem_(pointset, id) = NULL;
+      }
+    }
+  id = qh_pointid(qh GOODpointp);
+  if( id >= 0 && qh STOPcone - 1 != id && -qh STOPpoint - 1 != id )
+    {
+    SETelem_(pointset, id) = NULL;
+    }
+  if( qh GOODvertexp && qh ONLYgood && !qh MERGING )   /* matches qhull()*/
+    {
+    if( (id = qh_pointid(qh GOODvertexp) ) >= 0 )
+      {
+      SETelem_(pointset, id) = NULL;
+      }
+    }
+  if( !qh BESToutside )    /* matches conditional for qh_partitionpoint below */
+    {
+    distoutside = qh_DISToutside;                           /* multiple of
+                                                              qh.MINoutside &
+                                                              qh.max_outside,
+                                                              see user.h */
+    zval_(Ztotpartition) = qh num_points - qh hull_dim - 1; /*misses GOOD... */
+    remaining = qh num_facets;
+    point_end = numpoints;
+    FORALLfacets {
+      size = point_end / (remaining--) + 100;
+      facet->outsideset = qh_setnew(size);
+      bestpoint = NULL;
+      point_end = 0;
+      FOREACHpoint_i_(pointset) {
+        if( point )
+          {
+          zzinc_(Zpartitionall);
+          qh_distplane(point, facet, &dist);
+          if( dist < distoutside )
+            {
+            SETelem_(pointset, point_end++) = point;
+            }
+          else
+            {
+            qh num_outside++;
+            if( !bestpoint )
+              {
+              bestpoint = point;
+              bestdist = dist;
+              }
+            else if( dist > bestdist )
+              {
+              qh_setappend(&facet->outsideset, bestpoint);
+              bestpoint = point;
+              bestdist = dist;
+              }
+            else
+              {
+              qh_setappend(&facet->outsideset, point);
+              }
+            }
+          }
+        }
+      if( bestpoint )
+        {
+        qh_setappend(&facet->outsideset, bestpoint);
+#if !qh_COMPUTEfurthest
+        facet->furthestdist = bestdist;
+#endif
+        }
+      else
+        {
+        qh_setfree(&facet->outsideset);
+        }
+      qh_settruncate(pointset, (size_t)point_end);
+      }
+    }
+  /* if !qh BESToutside, pointset contains points not assigned to outsideset */
+  if( qh BESToutside || qh MERGING || qh KEEPcoplanar || qh KEEPinside )
+    {
+    qh findbestnew = True;
+    FOREACHpoint_i_(pointset) {
+      if( point )
+        {
+        qh_partitionpoint(point, qh facet_list);
+        }
+      }
+    qh findbestnew = False;
+    }
+  zzadd_(Zpartitionall, zzval_(Zpartition) );
+  zzval_(Zpartition) = 0;
+  qh_settempfree(&pointset);
+  if( qh IStracing >= 4 )
+    {
+    qh_printfacetlist(qh facet_list, NULL, True);
+    }
+} /* partitionall */
+
+/*---------------------------------
+
+  qh_partitioncoplanar( point, facet, dist )
+  partition coplanar point to a facet
+  dist is distance from point to facet
+  if dist NULL,
+  searches for bestfacet and does nothing if inside
+  if qh.findbestnew set,
+  searches new facets instead of using qh_findbest()
+
+  returns:
+  qh.max_ouside updated
+  if qh.KEEPcoplanar or qh.KEEPinside
+  point assigned to best coplanarset
+
+  notes:
+  facet->maxoutside is updated at end by qh_check_maxout
+
+  design:
+  if dist undefined
+  find best facet for point
+  if point sufficiently below facet (depends on qh.NEARinside and qh.KEEPinside)
+  exit
+  if keeping coplanar/nearinside/inside points
+  if point is above furthest coplanar point
+  append point to coplanar set (it is the new furthest)
+  update qh.max_outside
+  else
+  append point one before end of coplanar set
+  else if point is clearly outside of qh.max_outside and bestfacet->coplanarset
+  and bestfacet is more than perpendicular to facet
+  repartition the point using qh_findbest() -- it may be put on an outsideset
+  else
+  update qh.max_outside
+*/
+void qh_partitioncoplanar(pointT *point, facetT *facet, realT *dist)
+{
+  facetT *bestfacet;
+  pointT *oldfurthest;
+  realT   bestdist, dist2, angle;
+  int     numpart = 0, oldfindbest;
+  boolT   isoutside;
+
+  qh WAScoplanar = True;
+
+  if( !dist )
+    {
+    if( qh findbestnew )
+      {
+      bestfacet = qh_findbestnew(point, facet, &bestdist, qh_ALL, &isoutside, &numpart);
+      }
+    else
+      {
+      bestfacet = qh_findbest(point, facet, qh_ALL, !qh_ISnewfacets, qh DELAUNAY,
+                              &bestdist, &isoutside, &numpart);
+      }
+    zinc_(Ztotpartcoplanar);
+    zzadd_(Zpartcoplanar, numpart);
+    if( !qh DELAUNAY && !qh KEEPinside )   /*  for 'd', bestdist skips
+                                             upperDelaunay facets */
+      {
+      if( qh KEEPnearinside )
+        {
+        if( bestdist < -qh NEARinside )
+          {
+          zinc_(Zcoplanarinside);
+          trace4( (qh ferr,
+                   "qh_partitioncoplanar: point p%d is more than near-inside facet f%d dist %2.2g findbestnew %d\n",
+                   qh_pointid(point), bestfacet->id, bestdist, qh findbestnew) );
+          return;
+          }
+        }
+      else if( bestdist < -qh MAXcoplanar )
+        {
+        trace4( (qh ferr, "qh_partitioncoplanar: point p%d is inside facet f%d dist %2.2g findbestnew %d\n",
+                 qh_pointid(point), bestfacet->id, bestdist, qh findbestnew) );
+        zinc_(Zcoplanarinside);
+        return;
+        }
+      }
+    }
+  else
+    {
+    bestfacet = facet;
+    bestdist = *dist;
+    }
+  if( bestdist > qh max_outside )
+    {
+    if( !dist && facet != bestfacet )
+      {
+      zinc_(Zpartangle);
+      angle = qh_getangle(facet->normal, bestfacet->normal);
+      if( angle < 0 )
+        {
+        /* typically due to deleted vertex and coplanar facets, e.g.,
+           RBOX 1000 s Z1 G1e-13 t1001185205 | QHULL Tv */
+        zinc_(Zpartflip);
+        trace2( (qh ferr,
+                 "qh_partitioncoplanar: repartition point p%d from f%d.  It is above flipped facet f%d dist %2.2g\n",
+                 qh_pointid(point), facet->id, bestfacet->id, bestdist) );
+        oldfindbest = qh findbestnew;
+        qh findbestnew = False;
+        qh_partitionpoint(point, bestfacet);
+        qh findbestnew = oldfindbest;
+        return;
+        }
+      }
+    qh max_outside = bestdist;
+    if( bestdist > qh TRACEdist )
+      {
+      fprintf(qh ferr, "qh_partitioncoplanar: ====== p%d from f%d increases max_outside to %2.2g of f%d last p%d\n",
+              qh_pointid(point), facet->id, bestdist, bestfacet->id, qh furthest_id);
+      qh_errprint("DISTANT", facet, bestfacet, NULL, NULL);
+      }
+    }
+  if( qh KEEPcoplanar + qh KEEPinside + qh KEEPnearinside )
+    {
+    oldfurthest = (pointT *)qh_setlast(bestfacet->coplanarset);
+    if( oldfurthest )
+      {
+      zinc_(Zcomputefurthest);
+      qh_distplane(oldfurthest, bestfacet, &dist2);
+      }
+    if( !oldfurthest || dist2 < bestdist )
+      {
+      qh_setappend(&bestfacet->coplanarset, point);
+      }
+    else
+      {
+      qh_setappend2ndlast(&bestfacet->coplanarset, point);
+      }
+    }
+  trace4( (qh ferr, "qh_partitioncoplanar: point p%d is coplanar with facet f%d (or inside) dist %2.2g\n",
+           qh_pointid(point), bestfacet->id, bestdist) );
+} /* partitioncoplanar */
+
+/*---------------------------------
+
+  qh_partitionpoint( point, facet )
+  assigns point to an outside set, coplanar set, or inside set (i.e., dropt)
+  if qh.findbestnew
+  uses qh_findbestnew() to search all new facets
+  else
+  uses qh_findbest()
+
+  notes:
+  after qh_distplane(), this and qh_findbest() are most expensive in 3-d
+
+  design:
+  find best facet for point
+  (either exhaustive search of new facets or directed search from facet)
+  if qh.NARROWhull
+  retain coplanar and nearinside points as outside points
+  if point is outside bestfacet
+  if point above furthest point for bestfacet
+  append point to outside set (it becomes the new furthest)
+  if outside set was empty
+  move bestfacet to end of qh.facet_list (i.e., after qh.facet_next)
+  update bestfacet->furthestdist
+  else
+  append point one before end of outside set
+  else if point is coplanar to bestfacet
+  if keeping coplanar points or need to update qh.max_outside
+  partition coplanar point into bestfacet
+  else if near-inside point
+  partition as coplanar point into bestfacet
+  else is an inside point
+  if keeping inside points
+  partition as coplanar point into bestfacet
+*/
+void qh_partitionpoint(pointT *point, facetT *facet)
+{
+  realT   bestdist;
+  boolT   isoutside;
+  facetT *bestfacet;
+  int     numpart;
+
+#if qh_COMPUTEfurthest
+  realT dist;
+#endif
+
+  if( qh findbestnew )
+    {
+    bestfacet = qh_findbestnew(point, facet, &bestdist, qh BESToutside, &isoutside, &numpart);
+    }
+  else
+    {
+    bestfacet = qh_findbest(point, facet, qh BESToutside, qh_ISnewfacets, !qh_NOupper,
+                            &bestdist, &isoutside, &numpart);
+    }
+  zinc_(Ztotpartition);
+  zzadd_(Zpartition, numpart);
+  if( qh NARROWhull )
+    {
+    if( qh DELAUNAY && !isoutside && bestdist >= -qh MAXcoplanar )
+      {
+      qh_precision("nearly incident point (narrow hull)");
+      }
+    if( qh KEEPnearinside )
+      {
+      if( bestdist >= -qh NEARinside )
+        {
+        isoutside = True;
+        }
+      }
+    else if( bestdist >= -qh MAXcoplanar )
+      {
+      isoutside = True;
+      }
+    }
+
+  if( isoutside )
+    {
+    if( !bestfacet->outsideset
+        || !qh_setlast(bestfacet->outsideset) )
+      {
+      qh_setappend(&(bestfacet->outsideset), point);
+      if( !bestfacet->newfacet )
+        {
+        qh_removefacet(bestfacet);   /* make sure it's after qh facet_next */
+        qh_appendfacet(bestfacet);
+        }
+#if !qh_COMPUTEfurthest
+      bestfacet->furthestdist = bestdist;
+#endif
+      }
+    else
+      {
+#if qh_COMPUTEfurthest
+      zinc_(Zcomputefurthest);
+      qh_distplane(oldfurthest, bestfacet, &dist);
+      if( dist < bestdist )
+        {
+        qh_setappend(&(bestfacet->outsideset), point);
+        }
+      else
+        {
+        qh_setappend2ndlast(&(bestfacet->outsideset), point);
+        }
+#else
+      if( bestfacet->furthestdist < bestdist )
+        {
+        qh_setappend(&(bestfacet->outsideset), point);
+        bestfacet->furthestdist = bestdist;
+        }
+      else
+        {
+        qh_setappend2ndlast(&(bestfacet->outsideset), point);
+        }
+#endif
+      }
+    qh num_outside++;
+    trace4( (qh ferr, "qh_partitionpoint: point p%d is outside facet f%d new? %d(or narrowhull)\n",
+             qh_pointid(point), bestfacet->id, bestfacet->newfacet) );
+    }
+  else if( qh DELAUNAY || bestdist >= -qh MAXcoplanar )   /* for 'd', bestdist
+                                                            skips upperDelaunay
+                                                            facets */
+    {
+    zzinc_(Zcoplanarpart);
+    if( qh DELAUNAY )
+      {
+      qh_precision("nearly incident point");
+      }
+    if( (qh KEEPcoplanar + qh KEEPnearinside) || bestdist > qh max_outside )
+      {
+      qh_partitioncoplanar(point, bestfacet, &bestdist);
+      }
+    else
+      {
+      trace4( (qh ferr, "qh_partitionpoint: point p%d is coplanar to facet f%d (dropped)\n",
+               qh_pointid(point), bestfacet->id) );
+      }
+    }
+  else if( qh KEEPnearinside && bestdist > -qh NEARinside )
+    {
+    zinc_(Zpartnear);
+    qh_partitioncoplanar(point, bestfacet, &bestdist);
+    }
+  else
+    {
+    zinc_(Zpartinside);
+    trace4( (qh ferr, "qh_partitionpoint: point p%d is inside all facets, closest to f%d dist %2.2g\n",
+             qh_pointid(point), bestfacet->id, bestdist) );
+    if( qh KEEPinside )
+      {
+      qh_partitioncoplanar(point, bestfacet, &bestdist);
+      }
+    }
+} /* partitionpoint */
+
+/*---------------------------------
+
+  qh_partitionvisible( allpoints, numoutside )
+  partitions points in visible facets to qh.newfacet_list
+  qh.visible_list= visible facets
+  for visible facets
+  1st neighbor (if any) points to a horizon facet or a new facet
+  if allpoints (not used),
+  repartitions coplanar points
+
+  returns:
+  updates outside sets and coplanar sets of qh.newfacet_list
+  updates qh.num_outside (count of outside points)
+
+  notes:
+  qh.findbest_notsharp should be clear (extra work if set)
+
+  design:
+  for all visible facets with outside set or coplanar set
+  select a newfacet for visible facet
+  if outside set
+  partition outside set into new facets
+  if coplanar set and keeping coplanar/near-inside/inside points
+  if allpoints
+  partition coplanar set into new facets, may be assigned outside
+  else
+  partition coplanar set into coplanar sets of new facets
+  for each deleted vertex
+  if allpoints
+  partition vertex into new facets, may be assigned outside
+  else
+  partition vertex into coplanar sets of new facets
+*/
+void qh_partitionvisible(/*visible_list*/ boolT allpoints, int *numoutside)
+{
+  facetT * visible, *newfacet;
+  pointT * point, * *pointp;
+  int      coplanar = 0, size;
+  unsigned count;
+  vertexT *vertex, * *vertexp;
+
+  if( qh ONLYmax )
+    {
+    maximize_(qh MINoutside, qh max_vertex);
+    }
+  *numoutside = 0;
+  FORALLvisible_facets {
+    if( !visible->outsideset && !visible->coplanarset )
+      {
+      continue;
+      }
+    newfacet = visible->f.replace;
+    count = 0;
+    while( newfacet && newfacet->visible )
+      {
+      newfacet = newfacet->f.replace;
+      if( count++ > qh facet_id )
+        {
+        qh_infiniteloop(visible);
+        }
+      }
+
+    if( !newfacet )
+      {
+      newfacet = qh newfacet_list;
+      }
+    if( newfacet == qh facet_tail )
+      {
+      fprintf(
+        qh ferr,
+        "qhull precision error (qh_partitionvisible): all new facets deleted as\n        degenerate facets. Can not continue.\n");
+      qh_errexit(qh_ERRprec, NULL, NULL);
+      }
+    if( visible->outsideset )
+      {
+      size = qh_setsize(visible->outsideset);
+      *numoutside += size;
+      qh num_outside -= size;
+      FOREACHpoint_(visible->outsideset)
+      qh_partitionpoint(point, newfacet);
+      }
+    if( visible->coplanarset && (qh KEEPcoplanar + qh KEEPinside + qh KEEPnearinside) )
+      {
+      size = qh_setsize(visible->coplanarset);
+      coplanar += size;
+      FOREACHpoint_(visible->coplanarset) {
+        if( allpoints ) /* not used */
+          {
+          qh_partitionpoint(point, newfacet);
+          }
+        else
+          {
+          qh_partitioncoplanar(point, newfacet, NULL);
+          }
+        }
+      }
+    }
+  FOREACHvertex_(qh del_vertices) {
+    if( vertex->point )
+      {
+      if( allpoints ) /* not used */
+        {
+        qh_partitionpoint(vertex->point, qh newfacet_list);
+        }
+      else
+        {
+        qh_partitioncoplanar(vertex->point, qh newfacet_list, NULL);
+        }
+      }
+    }
+  trace1( (qh ferr, "qh_partitionvisible: partitioned %d points from outsidesets and %d points from coplanarsets\n",
+           *numoutside, coplanar) );
+} /* partitionvisible */
+
+/*---------------------------------
+
+  qh_precision( reason )
+  restart on precision errors if not merging and if 'QJn'
+*/
+void qh_precision(const char *reason)
+{
+
+  if( qh ALLOWrestart && !qh PREmerge && !qh MERGEexact )
+    {
+    if( qh JOGGLEmax < REALmax / 2 )
+      {
+      trace0( (qh ferr, "qh_precision: qhull restart because of %s\n", reason) );
+      longjmp(qh restartexit, qh_ERRprec);
+      }
+    }
+} /* qh_precision */
+
+/*---------------------------------
+
+  qh_printsummary( fp )
+  prints summary to fp
+
+  notes:
+  not in io.c so that user_eg.c can prevent io.c from loading
+  qh_printsummary and qh_countfacets must match counts
+
+  design:
+  determine number of points, vertices, and coplanar points
+  print summary
+*/
+void qh_printsummary(FILE *fp)
+{
+  realT       ratio, outerplane, innerplane;
+  float       cpu;
+  int         size, id, nummerged, numvertices, numcoplanars = 0, nonsimplicial = 0;
+  int         goodused;
+  facetT *    facet;
+  const char *s;
+  int         numdel = zzval_(Zdelvertextot);
+  int         numtricoplanars = 0;
+
+  size = qh num_points + qh_setsize(qh other_points);
+  numvertices = qh num_vertices - qh_setsize(qh del_vertices);
+  id = qh_pointid(qh GOODpointp);
+  FORALLfacets {
+    if( facet->coplanarset )
+      {
+      numcoplanars += qh_setsize( facet->coplanarset);
+      }
+    if( facet->good )
+      {
+      if( facet->simplicial )
+        {
+        if( facet->keepcentrum && facet->tricoplanar )
+          {
+          numtricoplanars++;
+          }
+        }
+      else if( qh_setsize(facet->vertices) != qh hull_dim )
+        {
+        nonsimplicial++;
+        }
+      }
+    }
+  if( id >= 0 && qh STOPcone - 1 != id && -qh STOPpoint - 1 != id )
+    {
+    size--;
+    }
+  if( qh STOPcone || qh STOPpoint )
+    {
+    fprintf(fp, "\nAt a premature exit due to 'TVn', 'TCn', 'TRn', or precision error.");
+    }
+  if( qh UPPERdelaunay )
+    {
+    goodused = qh GOODvertex + qh GOODpoint + qh SPLITthresholds;
+    }
+  else if( qh DELAUNAY )
+    {
+    goodused = qh GOODvertex + qh GOODpoint + qh GOODthreshold;
+    }
+  else
+    {
+    goodused = qh num_good;
+    }
+  nummerged = zzval_(Ztotmerge) - zzval_(Zcyclehorizon) + zzval_(Zcyclefacettot);
+  if( qh VORONOI )
+    {
+    if( qh UPPERdelaunay )
+      {
+      fprintf(fp, "\n\
+Furthest-site Voronoi vertices by the convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+      }
+    else
+      {
+      fprintf(fp, "\n\
+Voronoi diagram by the convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+      }
+    fprintf(fp, "  Number of Voronoi regions%s: %d\n",
+            qh ATinfinity ? " and at-infinity" : "", numvertices);
+    if( numdel )
+      {
+      fprintf(fp, "  Total number of deleted points due to merging: %d\n", numdel);
+      }
+    if( numcoplanars - numdel > 0 )
+      {
+      fprintf(fp, "  Number of nearly incident points: %d\n", numcoplanars - numdel);
+      }
+    else if( size - numvertices - numdel > 0 )
+      {
+      fprintf(fp, "  Total number of nearly incident points: %d\n", size - numvertices - numdel);
+      }
+    fprintf(fp, "  Number of%s Voronoi vertices: %d\n",
+            goodused ? " 'good'" : "", qh num_good);
+    if( nonsimplicial )
+      {
+      fprintf(fp, "  Number of%s non-simplicial Voronoi vertices: %d\n",
+              goodused ? " 'good'" : "", nonsimplicial);
+      }
+    }
+  else if( qh DELAUNAY )
+    {
+    if( qh UPPERdelaunay )
+      {
+      fprintf(fp, "\n\
+Furthest-site Delaunay triangulation by the convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+      }
+    else
+      {
+      fprintf(fp, "\n\
+Delaunay triangulation by the convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+      }
+    fprintf(fp, "  Number of input sites%s: %d\n",
+            qh ATinfinity ? " and at-infinity" : "", numvertices);
+    if( numdel )
+      {
+      fprintf(fp, "  Total number of deleted points due to merging: %d\n", numdel);
+      }
+    if( numcoplanars - numdel > 0 )
+      {
+      fprintf(fp, "  Number of nearly incident points: %d\n", numcoplanars - numdel);
+      }
+    else if( size - numvertices - numdel > 0 )
+      {
+      fprintf(fp, "  Total number of nearly incident points: %d\n", size - numvertices - numdel);
+      }
+    fprintf(fp, "  Number of%s Delaunay regions: %d\n",
+            goodused ? " 'good'" : "", qh num_good);
+    if( nonsimplicial )
+      {
+      fprintf(fp, "  Number of%s non-simplicial Delaunay regions: %d\n",
+              goodused ? " 'good'" : "", nonsimplicial);
+      }
+    }
+  else if( qh HALFspace )
+    {
+    fprintf(fp, "\n\
+Halfspace intersection by the convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+    fprintf(fp, "  Number of halfspaces: %d\n", size);
+    fprintf(fp, "  Number of non-redundant halfspaces: %d\n", numvertices);
+    if( numcoplanars )
+      {
+      if( qh KEEPinside && qh KEEPcoplanar )
+        {
+        s = "similar and redundant";
+        }
+      else if( qh KEEPinside )
+        {
+        s = "redundant";
+        }
+      else
+        {
+        s = "similar";
+        }
+      fprintf(fp, "  Number of %s halfspaces: %d\n", s, numcoplanars);
+      }
+    fprintf(fp, "  Number of intersection points: %d\n", qh num_facets - qh num_visible);
+    if( goodused )
+      {
+      fprintf(fp, "  Number of 'good' intersection points: %d\n", qh num_good);
+      }
+    if( nonsimplicial )
+      {
+      fprintf(fp, "  Number of%s non-simplicial intersection points: %d\n",
+              goodused ? " 'good'" : "", nonsimplicial);
+      }
+    }
+  else
+    {
+    fprintf(fp, "\n\
+Convex hull of %d points in %d-d:\n\n", size, qh hull_dim);
+    fprintf(fp, "  Number of vertices: %d\n", numvertices);
+    if( numcoplanars )
+      {
+      if( qh KEEPinside && qh KEEPcoplanar )
+        {
+        s = "coplanar and interior";
+        }
+      else if( qh KEEPinside )
+        {
+        s = "interior";
+        }
+      else
+        {
+        s = "coplanar";
+        }
+      fprintf(fp, "  Number of %s points: %d\n", s, numcoplanars);
+      }
+    fprintf(fp, "  Number of facets: %d\n", qh num_facets - qh num_visible);
+    if( goodused )
+      {
+      fprintf(fp, "  Number of 'good' facets: %d\n", qh num_good);
+      }
+    if( nonsimplicial )
+      {
+      fprintf(fp, "  Number of%s non-simplicial facets: %d\n",
+              goodused ? " 'good'" : "", nonsimplicial);
+      }
+    }
+  if( numtricoplanars )
+    {
+    fprintf(fp, "  Number of triangulated facets: %d\n", numtricoplanars);
+    }
+  fprintf(fp, "\nStatistics for: %s | %s",
+          qh rbox_command, qh qhull_command);
+  if( qh ROTATErandom != INT_MIN )
+    {
+    fprintf(fp, " QR%d\n\n", qh ROTATErandom);
+    }
+  else
+    {
+    fprintf(fp, "\n\n");
+    }
+  fprintf(fp, "  Number of points processed: %d\n", zzval_(Zprocessed) );
+  fprintf(fp, "  Number of hyperplanes created: %d\n", zzval_(Zsetplane) );
+  if( qh DELAUNAY )
+    {
+    fprintf(fp, "  Number of facets in hull: %d\n", qh num_facets - qh num_visible);
+    }
+  fprintf(fp, "  Number of distance tests for qhull: %d\n", zzval_(Zpartition)
+          + zzval_(Zpartitionall) + zzval_(Znumvisibility) + zzval_(Zpartcoplanar) );
+#if 0  /* NOTE: must print before printstatistics() */
+      {realT stddev, ave;
+      fprintf(fp, "  average new facet balance: %2.2g\n",
+              wval_(Wnewbalance) / zval_(Zprocessed) );
+      stddev = qh_stddev(zval_(Zprocessed), wval_(Wnewbalance),
+                         wval_(Wnewbalance2), &ave);
+      fprintf(fp, "  new facet standard deviation: %2.2g\n", stddev);
+      fprintf(fp, "  average partition balance: %2.2g\n",
+              wval_(Wpbalance) / zval_(Zpbalance) );
+      stddev = qh_stddev(zval_(Zpbalance), wval_(Wpbalance),
+                         wval_(Wpbalance2), &ave);
+      fprintf(fp, "  partition standard deviation: %2.2g\n", stddev); }
+#endif
+  if( nummerged )
+    {
+    fprintf(fp, "  Number of distance tests for merging: %d\n", zzval_(Zbestdist)
+            + zzval_(Zcentrumtests) + zzval_(Zdistconvex) + zzval_(Zdistcheck)
+            + zzval_(Zdistzero) );
+    fprintf(fp, "  Number of distance tests for checking: %d\n", zzval_(Zcheckpart) );
+    fprintf(fp, "  Number of merged facets: %d\n", nummerged);
+    }
+  if( !qh RANDOMoutside && qh QHULLfinished )
+    {
+    cpu = qh hulltime;
+    cpu /= qh_SECticks;
+    wval_(Wcpu) = cpu;
+    fprintf(fp, "  CPU seconds to compute hull (after input): %2.4g\n", cpu);
+    }
+  if( qh RERUN )
+    {
+    if( !qh PREmerge && !qh MERGEexact )
+      {
+      fprintf(fp, "  Percentage of runs with precision errors: %4.1f\n",
+              zzval_(Zretry) * 100.0 / qh build_cnt); /* careful of order */
+      }
+    }
+  else if( qh JOGGLEmax < REALmax / 2 )
+    {
+    if( zzval_(Zretry) )
+      {
+      fprintf(fp, "  After %d retries, input joggled by: %2.2g\n",
+              zzval_(Zretry), qh JOGGLEmax);
+      }
+    else
+      {
+      fprintf(fp, "  Input joggled by: %2.2g\n", qh JOGGLEmax);
+      }
+    }
+  if( qh totarea != 0.0 )
+    {
+    fprintf(fp, "  %s facet area:   %2.8g\n",
+            zzval_(Ztotmerge) ? "Approximate" : "Total", qh totarea);
+    }
+  if( qh totvol != 0.0 )
+    {
+    fprintf(fp, "  %s volume:       %2.8g\n",
+            zzval_(Ztotmerge) ? "Approximate" : "Total", qh totvol);
+    }
+  if( qh MERGING )
+    {
+    qh_outerinner(NULL, &outerplane, &innerplane);
+    if( outerplane > 2 * qh DISTround )
+      {
+      fprintf(fp, "  Maximum distance of %spoint above facet: %2.2g",
+              (qh QHULLfinished ? "" : "merged "), outerplane);
+      ratio = outerplane / (qh ONEmerge + qh DISTround);
+      /* don't report ratio if MINoutside is large */
+      if( ratio > 0.05 && 2 * qh ONEmerge > qh MINoutside && qh JOGGLEmax > REALmax / 2 )
+        {
+        fprintf(fp, " (%.1fx)\n", ratio);
+        }
+      else
+        {
+        fprintf(fp, "\n");
+        }
+      }
+    if( innerplane < -2 * qh DISTround )
+      {
+      fprintf(fp, "  Maximum distance of %svertex below facet: %2.2g",
+              (qh QHULLfinished ? "" : "merged "), innerplane);
+      ratio = -innerplane / (qh ONEmerge + qh DISTround);
+      if( ratio > 0.05 && qh JOGGLEmax > REALmax / 2 )
+        {
+        fprintf(fp, " (%.1fx)\n", ratio);
+        }
+      else
+        {
+        fprintf(fp, "\n");
+        }
+      }
+    }
+  fprintf(fp, "\n");
+} /* printsummary */
+
diff --git a/BRAINSABC/qhull/qhull.h b/BRAINSABC/qhull/qhull.h
new file mode 100644
index 00000000..a4645aae
--- /dev/null
+++ b/BRAINSABC/qhull/qhull.h
@@ -0,0 +1,1165 @@
+/*
  ---------------------------------
+
+   qhull.h
+   user-level header file for using qhull.a library
+
+   see qh-qhull.htm, qhull_a.h
+
+   copyright (c) 1993-2003, The Geometry Center
+
+   NOTE: access to qh_qh is via the 'qh' macro.  This allows
+   qh_qh to be either a pointer or a structure.  An example
+   of using qh is "qh DROPdim" which accesses the DROPdim
+   field of qh_qh.  Similarly, access to qh_qhstat is via
+   the 'qhstat' macro.
+
+   includes function prototypes for qhull.c, geom.c, global.c, io.c, user.c
+
+   use mem.h for mem.c
+   use qset.h for qset.c
+
+   see unix.c for an example of using qhull.h
+
+   recompile qhull if you change this file
+*/
+
+#ifndef qhDEFqhull
+#define qhDEFqhull 1
+
+/*=========================== -included files ==============*/
+
+#include 
+#include 
+#include 
+
+#if __MWERKS__ && __POWERPC__
+#include  
+#include  
+#include  
+#endif
+
+#ifndef __STDC__
+#ifndef __cplusplus
+#if     !_MSC_VER
+#error  Neither __STDC__ nor __cplusplus is defined.  Please use strict ANSI C or C++ to compile
+#error  Qhull.  You may need to turn off compiler extensions in your project configuration.  If
+#error  your compiler is a standard C compiler, you can delete this warning from qhull.h
+#endif
+#endif
+#endif
+
+#include "user.h"      /* user defineable constants */
+
+/*============ constants and basic types ====================*/
+
+extern const char *qh_version; /* defined in global.c */
+
+/*----------------------------------
+
+  coordT
+    coordinates and coefficients are stored as realT (i.e., double)
+
+  notes:
+    could use 'float' for data and 'double' for calculations (realT vs. coordT)
+      This requires many type casts, and adjusted error bounds.
+      Also C compilers may do expressions in double anyway.
+*/
+#define coordT realT
+
+/*----------------------------------
+
+  pointT
+    a point is an array of DIM3 coordinates
+*/
+#define pointT coordT
+
+/*----------------------------------
+
+  flagT
+    Boolean flag as a bit
+*/
+#define flagT unsigned int
+
+/*----------------------------------
+
+  boolT
+    boolean value, either True or False
+
+  notes:
+    needed for portability
+*/
+#define boolT unsigned int
+#ifdef False
+#undef False
+#endif
+#ifdef True
+#undef True
+#endif
+#define False 0
+#define True 1
+
+/*----------------------------------
+
+  qh_CENTER
+    to distinguish facet->center
+*/
+typedef enum
+  {
+  qh_ASnone = 0, qh_ASvoronoi, qh_AScentrum
+  }
+qh_CENTER;
+
+/*----------------------------------
+
+  qh_PRINT
+    output formats for printing (qh.PRINTout).
+    'Fa' 'FV' 'Fc' 'FC'
+
+
+   notes:
+   some of these names are similar to qh names.  The similar names are only
+   used in switch statements in qh_printbegin() etc.
+*/
+typedef enum { qh_PRINTnone = 0,
+               qh_PRINTarea, qh_PRINTaverage, /* 'Fa' 'FV' 'Fc' 'FC' */
+               qh_PRINTcoplanars, qh_PRINTcentrums,
+               qh_PRINTfacets, qh_PRINTfacets_xridge, /* 'f' 'FF' 'G' 'FI' 'Fi'
+                                                       'Fn' */
+               qh_PRINTgeom, qh_PRINTids, qh_PRINTinner, qh_PRINTneighbors,
+               qh_PRINTnormals, qh_PRINTouter, qh_PRINTmaple, /* 'n' 'Fo' 'i' 'm'
+                                                               'Fm' 'FM', 'o' */
+               qh_PRINTincidences, qh_PRINTmathematica, qh_PRINTmerges, qh_PRINToff,
+               qh_PRINToptions, qh_PRINTpointintersect, /* 'FO' 'Fp' 'FP' 'p'
+                                                         'FQ' 'FS' */
+               qh_PRINTpointnearest, qh_PRINTpoints, qh_PRINTqhull, qh_PRINTsize,
+               qh_PRINTsummary, qh_PRINTtriangles, /* 'Fs' 'Ft' 'Fv' 'FN' 'Fx'
+                                                     */
+               qh_PRINTvertices, qh_PRINTvneighbors, qh_PRINTextremes,
+               qh_PRINTEND } qh_PRINT;
+
+/*----------------------------------
+
+  qh_ALL
+    argument flag for selecting everything
+*/
+#define qh_ALL      True
+#define qh_NOupper  True      /* argument for qh_findbest */
+#define qh_IScheckmax  True   /* argument for qh_findbesthorizon */
+#define qh_ISnewfacets  True  /* argument for qh_findbest */
+#define qh_RESETvisible  True /* argument for qh_resetlists */
+
+/*----------------------------------
+
+  qh_ERR
+    Qhull exit codes, for indicating errors
+*/
+#define qh_ERRnone  0    /* no error occurred during qhull */
+#define qh_ERRinput 1    /* input inconsistency */
+#define qh_ERRsingular 2 /* singular input data */
+#define qh_ERRprec  3    /* precision error */
+#define qh_ERRmem   4    /* insufficient memory, matches mem.h */
+#define qh_ERRqhull 5    /* internal error detected, matches mem.h */
+
+/* ============ -structures- ====================
+   each of the following structures is defined by a typedef
+   all realT and coordT fields occur at the beginning of a structure
+        (otherwise space may be wasted due to alignment)
+   define all flags together and pack into 32-bit number
+*/
+
+typedef struct vertexT vertexT;
+typedef struct ridgeT  ridgeT;
+typedef struct facetT  facetT;
+#ifndef DEFsetT
+#define DEFsetT 1
+typedef struct setT setT;          /* defined in qset.h */
+#endif
+
+/*----------------------------------
+
+  facetT
+    defines a facet
+
+  notes:
+   qhull() generates the hull as a list of facets.
+
+  topological information:
+    f.previous,next     doubly-linked list of facets
+    f.vertices          set of vertices
+    f.ridges            set of ridges
+    f.neighbors         set of neighbors
+    f.toporient         True if facet has top-orientation (else bottom)
+
+  geometric information:
+    f.offset,normal     hyperplane equation
+    f.maxoutside        offset to outer plane -- all points inside
+    f.center            centrum for testing convexity
+    f.simplicial        True if facet is simplicial
+    f.flipped           True if facet does not include qh.interior_point
+
+  for constructing hull:
+    f.visible           True if facet on list of visible facets (will be deleted)
+    f.newfacet          True if facet on list of newly created facets
+    f.coplanarset       set of points coplanar with this facet
+                        (includes near-inside points for later testing)
+    f.outsideset        set of points outside of this facet
+    f.furthestdist      distance to furthest point of outside set
+    f.visitid           marks visited facets during a loop
+    f.replace           replacement facet for to-be-deleted, visible facets
+    f.samecycle,newcycle cycle of facets for merging into horizon facet
+
+  see below for other flags and fields
+*/
+struct facetT
+  {
+#if !qh_COMPUTEfurthest
+  coordT furthestdist;  /* distance to furthest point of outsideset */
+#endif
+#if qh_MAXoutside
+  coordT maxoutside;    /* max computed distance of point to facet
+        Before QHULLfinished this is an approximation
+        since maxdist not always set for mergefacet
+      Actual outer plane is +DISTround and
+      computed outer plane is +2*DISTround */
+#endif
+  coordT offset;        /* exact offset of hyperplane from origin */
+  coordT *normal;       /* normal of hyperplane, hull_dim coefficients */
+  /*   if tricoplanar, shared with a neighbor */
+  union                                                                     /*
+                                                                              in
+                                                                              order
+                                                                              of
+                                                                              testing
+                                                                              */
+                                                        { realT area;       /*
+                                                                              area
+                                                                              of
+                                                                              facet,
+                                                                              only
+                                                                              in
+                                                                              io.c
+                                                                              if
+
+                                                                              ->isarea
+                                                                              */
+                                                        facetT *replace;    /*  replacement facet if ->visible and NEWfacets
+             is NULL only if qh_mergedegen_redundant or interior */
+                                                        facetT *samecycle;  /*  cycle of facets from the same visible/horizon intersection,
+             if ->newfacet */
+                                                        facetT *newcycle;   /*
+
+                                                                              in
+                                                                              horizon
+                                                                              facet,
+                                                                              current
+                                                                              samecycle
+                                                                              of
+                                                                              new
+                                                                              facets
+                                                                              */
+                                                        facetT *trivisible; /* visible facet for ->tricoplanar facets during
+                          qh_triangulate() */
+                                                        facetT *triowner;   /* owner facet for ->tricoplanar, !isarea facets w/
+                          ->keepcentrum */
+                                                        } f;
+  coordT *center;       /*  centrum for convexity, qh CENTERtype == qh_AScentrum
+                          */
+  /*  Voronoi center, qh CENTERtype == qh_ASvoronoi */
+  /*   if tricoplanar, shared with a neighbor */
+  facetT *previous;        /* previous facet in the facet_list */
+  facetT *next;            /* next facet in the facet_list */
+  setT *vertices;          /* vertices for this facet, inverse sorted by ID
+                           if simplicial, 1st vertex was apex/furthest */
+  setT *ridges;            /* explicit ridges for nonsimplicial facets.
+           for simplicial facets, neighbors defines ridge */
+  setT *neighbors;         /* neighbors of the facet.  If simplicial, the kth
+         neighbor is opposite the kth vertex, and the first
+         neighbor is the horizon facet for the first vertex*/
+  setT *outsideset;        /* set of points outside this facet
+               if non-empty, last point is furthest
+         if NARROWhull, includes coplanars for partitioning*/
+  setT *coplanarset;       /* set of points coplanar with this facet
+           > qh.min_vertex and <= facet->max_outside
+                           a point is assigned to the furthest facet
+               if non-empty, last point is furthest away */
+  unsigned visitid;        /* visit_id, for visiting all neighbors,
+         all uses are independent */
+  unsigned id;             /* unique identifier from qh facet_id */
+  unsigned nummerge : 9;   /* number of merges */
+#define qh_MAXnummerge 511 /*     2^9-1, 32 flags total, see "flags:" in io.c */
+  flagT tricoplanar : 1;   /* True if TRIangulate and simplicial and coplanar
+                             with a neighbor */
+  /*   all tricoplanars share the same ->center, ->normal, ->offset,
+    ->maxoutside */
+  /*   all tricoplanars share the same apex */
+  /*   if ->degenerate, does not span facet (one logical ridge) */
+  /*   one tricoplanar has ->keepcentrum and ->coplanarset */
+  /*   during qh_triangulate, f.trivisible points to original facet */
+  flagT newfacet : 1;      /* True if facet on qh newfacet_list (new or merged)
+                             */
+  flagT visible : 1;       /* True if visible facet (will be deleted) */
+  flagT toporient : 1;     /* True if created with top orientation
+         after merging, use ridge orientation */
+  flagT simplicial : 1;    /* True if simplicial facet, ->ridges may be implicit
+                             */
+  flagT seen : 1;          /* used to perform operations only once, like visitid
+                             */
+  flagT seen2 : 1;         /* used to perform operations only once, like visitid
+                             */
+  flagT flipped : 1;       /* True if facet is flipped */
+  flagT upperdelaunay : 1; /* True if facet is upper envelope of Delaunay
+                             triangulation */
+  flagT notfurthest : 1;   /* True if last point of outsideset is not furthest*/
+
+  /*-------- flags primarily for output ---------*/
+  flagT good : 1;       /* True if a facet marked good for output */
+  flagT isarea : 1;     /* True if facet->f.area is defined */
+
+  /*-------- flags for merging ------------------*/
+  flagT dupridge : 1;     /* True if duplicate ridge in facet */
+  flagT mergeridge : 1;   /* True if facet or neighbor contains a qh_MERGEridge
+                            ->normal defined (also defined for mergeridge2) */
+  flagT mergeridge2 : 1;  /* True if neighbor contains a qh_MERGEridge
+                            (mark_dupridges */
+  flagT coplanar : 1;     /* True if horizon facet is coplanar at last use */
+  flagT mergehorizon : 1; /* True if will merge into horizon (->coplanar) */
+  flagT cycledone : 1;    /* True if mergecycle_all already done */
+  flagT tested : 1;       /* True if facet convexity has been tested (false
+                            after merge */
+  flagT keepcentrum : 1;  /* True if keep old centrum after a merge, or marks
+                            owner for ->tricoplanar */
+  flagT newmerge : 1;     /* True if facet is newly merged for reducevertices */
+  flagT degenerate : 1;   /* True if facet is degenerate (degen_mergeset or
+                            ->tricoplanar) */
+  flagT redundant : 1;    /* True if facet is redundant (degen_mergeset) */
+  };
+
+/*----------------------------------
+
+  ridgeT
+    defines a ridge
+
+  notes:
+  a ridge is DIM3-1 simplex between two neighboring facets.  If the
+  facets are non-simplicial, there may be more than one ridge between
+  two facets.  E.G. a 4-d hypercube has two triangles between each pair
+  of neighboring facets.
+
+  topological information:
+    vertices            a set of vertices
+    top,bottom          neighboring facets with orientation
+
+  geometric information:
+    tested              True if ridge is clearly convex
+    nonconvex           True if ridge is non-convex
+*/
+struct ridgeT
+  {
+  setT *vertices;       /* vertices belonging to this ridge, inverse sorted by ID
+                           NULL if a degen ridge (matchsame) */
+  facetT *top;          /* top facet this ridge is part of */
+  facetT *bottom;       /* bottom facet this ridge is part of */
+  unsigned id : 24;     /* unique identifier, =>room for 8 flags */
+  flagT seen : 1;       /* used to perform operations only once */
+  flagT tested : 1;     /* True when ridge is tested for convexity */
+  flagT nonconvex : 1;  /* True if getmergeset detected a non-convex neighbor
+         only one ridge between neighbors may have nonconvex */
+  };
+
+/*----------------------------------
+
+  vertexT
+     defines a vertex
+
+  topological information:
+    next,previous       doubly-linked list of all vertices
+    neighbors           set of adjacent facets (only if qh.VERTEXneighbors)
+
+  geometric information:
+    point               array of DIM3 coordinates
+*/
+struct vertexT
+  {
+  vertexT *next;      /* next vertex in vertex_list */
+  vertexT *previous;  /* previous vertex in vertex_list */
+  pointT *point;      /* hull_dim coordinates (coordT) */
+  setT *neighbors;    /* neighboring facets of vertex, qh_vertexneighbors()
+         inits in io.c or after first merge */
+  unsigned visitid;   /* for use with qh vertex_visit */
+  unsigned id : 24;   /* unique identifier, =>room for 8 flags */
+  flagT seen : 1;     /* used to perform operations only once */
+  flagT seen2 : 1;    /* another seen flag */
+  flagT delridge : 1; /* vertex was part of a deleted ridge */
+  flagT deleted : 1;  /* true if vertex on qh del_vertices */
+  flagT newlist : 1;  /* true if vertex on qh newvertex_list */
+  };
+
+/*======= -global variables -qh ============================*/
+
+/*----------------------------------
+
+  qh
+   all global variables for qhull are in qh, qhmem, and qhstat
+
+  notes:
+   qhmem is defined in mem.h and qhstat is defined in stat.h
+   Access to qh_qh is via the "qh" macro.  See qh_QHpointer in user.h
+*/
+typedef struct qhT qhT;
+#if qh_QHpointer
+#define qh qh_qh->
+extern qhT *qh_qh;     /* allocated in global.c */
+#else
+#define qh qh_qh.
+extern qhT qh_qh;
+#endif
+
+struct qhT
+  {
+  /*----------------------------------
+
+    qh constants
+      configuration flags and constants for Qhull
+
+    notes:
+      The user configures Qhull by defining flags.  They are
+      copied into qh by qh_setflags().  qh-quick.htm#options defines the flags.
+  */
+  boolT ALLpoints;         /* true 'Qs' if search all points for initial simplex
+                             */
+  boolT ANGLEmerge;        /* true 'Qa' if sort potential merges by angle */
+  boolT APPROXhull;        /* true 'Wn' if MINoutside set */
+  realT MINoutside;        /*   'Wn' min. distance for an outside point */
+  boolT ATinfinity;        /* true 'Qz' if point num_points-1 is "at-infinity"
+                             for improving precision in Delaunay triangulations */
+  boolT AVOIDold;          /* true 'Q4' if avoid old->new merges */
+  boolT BESToutside;       /* true 'Qf' if partition points into best outsideset
+                             */
+  boolT CDDinput;          /* true 'Pc' if input uses CDD format (1.0/offset
+                             first) */
+  boolT CDDoutput;         /* true 'PC' if print normals in CDD format (offset
+                             first) */
+  boolT CHECKfrequently;   /* true 'Tc' if checking frequently */
+  realT premerge_cos;      /*   'A-n'   cos_max when pre merging */
+  realT postmerge_cos;     /*   'An'    cos_max when post merging */
+  boolT DELAUNAY;          /* true 'd' if computing DELAUNAY triangulation */
+  boolT DOintersections;   /* true 'Gh' if print hyperplane intersections */
+  int DROPdim;             /* drops dim 'GDn' for 4-d -> 3-d output */
+  boolT FORCEoutput;       /* true 'Po' if forcing output despite degeneracies
+                             */
+  int GOODpoint;           /* 1+n for 'QGn', good facet if visible/not(-) from
+                             point n*/
+  pointT *GOODpointp;      /*   the actual point */
+  boolT GOODthreshold;     /* true if qh lower_threshold/upper_threshold defined
+             false if qh SPLITthreshold */
+  int GOODvertex;          /* 1+n, good facet if vertex for point n */
+  pointT *GOODvertexp;     /*   the actual point */
+  boolT HALFspace;         /* true 'Hn,n,n' if halfspace intersection */
+  int IStracing;           /* trace execution, 0=none, 1=least, 4=most,
+                             -1=events */
+  int KEEParea;            /* 'PAn' number of largest facets to keep */
+  boolT KEEPcoplanar;      /* true 'Qc' if keeping nearest facet for coplanar
+                             points */
+  boolT KEEPinside;        /* true 'Qi' if keeping nearest facet for inside points
+            set automatically if 'd Qc' */
+  int KEEPmerge;           /* 'PMn' number of facets to keep with most merges */
+  realT KEEPminArea;       /* 'PFn' minimum facet area to keep */
+  realT MAXcoplanar;       /* 'Un' max distance below a facet to be coplanar*/
+  boolT MERGEexact;        /* true 'Qx' if exact merges (coplanar, degen,
+                             dupridge, flipped) */
+  boolT MERGEindependent;  /* true 'Q2' if merging independent sets */
+  boolT MERGING;           /* true if exact-, pre- or post-merging, with angle
+                             and centrum tests */
+  realT premerge_centrum;  /*   'C-n' centrum_radius when pre merging.  Default
+                             is round-off */
+  realT postmerge_centrum; /*   'Cn' centrum_radius when post merging.  Default
+                             is round-off */
+  boolT MERGEvertices;     /* true 'Q3' if merging redundant vertices */
+  realT MINvisible;        /* 'Vn' min. distance for a facet to be visible */
+  boolT NOnarrow;          /* true 'Q10' if no special processing for narrow
+                             distributions */
+  boolT NOnearinside;      /* true 'Q8' if ignore near-inside points when
+                             partitioning */
+  boolT NOpremerge;        /* true 'Q0' if no defaults for C-0 or Qx */
+  boolT ONLYgood;          /* true 'Qg' if process points with good visible or
+                             horizon facets */
+  boolT ONLYmax;           /* true 'Qm' if only process points that increase
+                             max_outside */
+  boolT PICKfurthest;      /* true 'Q9' if process furthest of furthest points*/
+  boolT POSTmerge;         /* true if merging after buildhull (Cn or An) */
+  boolT PREmerge;          /* true if merging during buildhull (C-n or A-n) */
+  /* NOTE: some of these names are similar to qh_PRINT names */
+  boolT PRINTcentrums;            /* true 'Gc' if printing centrums */
+  boolT PRINTcoplanar;            /* true 'Gp' if printing coplanar points */
+  int PRINTdim;                   /* print dimension for Geomview output */
+  boolT PRINTdots;                /* true 'Ga' if printing all points as dots */
+  boolT PRINTgood;                /* true 'Pg' if printing good facets */
+  boolT PRINTinner;               /* true 'Gi' if printing inner planes */
+  boolT PRINTneighbors;           /* true 'PG' if printing neighbors of good
+                                    facets */
+  boolT PRINTnoplanes;            /* true 'Gn' if printing no planes */
+  boolT PRINToptions1st;          /* true 'FO' if printing options to stderr */
+  boolT PRINTouter;               /* true 'Go' if printing outer planes */
+  boolT PRINTprecision;           /* false 'Pp' if not reporting precision
+                                    problems */
+  qh_PRINT PRINTout[qh_PRINTEND]; /* list of output formats to print */
+  boolT PRINTridges;              /* true 'Gr' if print ridges */
+  boolT PRINTspheres;             /* true 'Gv' if print vertices as spheres */
+  boolT PRINTstatistics;          /* true 'Ts' if printing statistics to stderr
+                                    */
+  boolT PRINTsummary;             /* true 's' if printing summary to stderr */
+  boolT PRINTtransparent;         /* true 'Gt' if print transparent outer ridges
+                                    */
+  boolT PROJECTdelaunay;          /* true if DELAUNAY, no readpoints() and
+           need projectinput() for Delaunay in qh_init_B */
+  int PROJECTinput;               /* number of projected dimensions 'bn:0Bn:0'
+                                    */
+  boolT QUICKhelp;                /* true if quick help message for degen input
+                                    */
+  boolT RANDOMdist;               /* true if randomly change distplane and
+                                    setfacetplane */
+  realT RANDOMfactor;             /*    maximum random perturbation */
+  realT RANDOMa;                  /*  qh_randomfactor is randr * RANDOMa +
+                                    RANDOMb */
+  realT RANDOMb;
+  boolT RANDOMoutside;   /* true if select a random outside point */
+  int REPORTfreq;        /* buildtracing reports every n facets */
+  int REPORTfreq2;       /* tracemerging reports every REPORTfreq/2 facets */
+  int RERUN;             /* 'TRn' rerun qhull n times (qh.build_cnt) */
+  int ROTATErandom;      /* 'QRn' seed, 0 time, >= rotate input */
+  boolT SCALEinput;      /* true 'Qbk' if scaling input */
+  boolT SCALElast;       /* true 'Qbb' if scale last coord to max prev coord */
+  boolT SETroundoff;     /* true 'E' if qh DISTround is predefined */
+  boolT SKIPcheckmax;    /* true 'Q5' if skip qh_check_maxout */
+  boolT SKIPconvex;      /* true 'Q6' if skip convexity testing during pre-merge
+                           */
+  boolT SPLITthresholds; /* true if upper_/lower_threshold defines a region
+                               used only for printing (not for qh ONLYgood) */
+  int STOPcone;          /* 'TCn' 1+n for stopping after cone for point n*/
+  /*       also used by qh_build_withresart for err exit*/
+  int STOPpoint;        /* 'TVn' 'TV-n' 1+n for stopping after/before(-)
+                      adding point n */
+  int TESTpoints;       /* 'QTn' num of test points after qh.num_points.  Test
+                          points always coplanar. */
+  boolT TESTvneighbors; /*  true 'Qv' if test vertex neighbors at end */
+  int TRACElevel;       /* 'Tn' conditional IStracing level */
+  int TRACElastrun;     /*  qh.TRACElevel applies to last qh.RERUN */
+  int TRACEpoint;       /* 'TPn' start tracing when point n is a vertex */
+  realT TRACEdist;      /* 'TWn' start tracing when merge distance too big */
+  int TRACEmerge;       /* 'TMn' start tracing before this merge */
+  boolT TRIangulate;    /* true 'Qt' if triangulate non-simplicial facets */
+  boolT TRInormals;     /* true 'Q11' if triangulate duplicates normals (sets
+                          Qt) */
+  boolT UPPERdelaunay;  /* true 'Qu' if computing furthest-site Delaunay */
+  boolT VERIFYoutput;   /* true 'Tv' if verify output at end of qhull */
+  boolT VIRTUALmemory;  /* true 'Q7' if depth-first processing in buildhull */
+  boolT VORONOI;        /* true 'v' if computing Voronoi diagram */
+
+  /*--------input constants ---------*/
+  realT AREAfactor;        /* 1/(hull_dim-1)! for converting det's to area */
+  boolT DOcheckmax;        /* true if calling qh_check_maxout
+                             (qh_initqhull_globals) */
+  char *feasible_string;   /* feasible point 'Hn,n,n' for halfspace intersection
+                             */
+  coordT *feasible_point;  /*    as coordinates, both malloc'd */
+  boolT GETarea;           /* true 'Fa', 'FA', 'FS', 'PAn', 'PFn' if compute
+                             facet area/Voronoi volume in io.c */
+  boolT KEEPnearinside;    /* true if near-inside points in coplanarset */
+  int hull_dim;            /* dimension of hull, set by initbuffers */
+  int input_dim;           /* dimension of input, set by initbuffers */
+  int num_points;          /* number of input points */
+  pointT *first_point;     /* array of input points, see POINTSmalloc */
+  boolT POINTSmalloc;      /*   true if qh first_point/num_points allocated */
+  pointT *input_points;    /* copy of original qh.first_point for input points
+                             for qh_joggleinput */
+  boolT input_malloc;      /* true if qh input_points malloc'd */
+  char qhull_command[256]; /* command line that invoked this program */
+  char rbox_command[256];  /* command line that produced the input points */
+  char qhull_options[512]; /* descriptive list of options */
+  int qhull_optionlen;     /*    length of last line */
+  int qhull_optionsiz;     /*     size of qhull_options before qh_initbuild */
+  boolT VERTEXneighbors;   /* true if maintaining vertex neighbors */
+  boolT ZEROcentrum;       /* true if 'C-0' or 'C-0 Qx'.  sets ZEROall_ok */
+  realT *upper_threshold;  /* don't print if facet->normal[k]>=upper_threshold[k]
+                             must set either GOODthreshold or SPLITthreshold
+             if Delaunay, default is 0.0 for upper envelope */
+  realT *lower_threshold;  /* don't print if facet->normal[k]
+                             <=lower_threshold[k] */
+  realT *upper_bound;      /* scale point[k] to new upper bound */
+  realT *lower_bound;      /* scale point[k] to new lower bound
+             project if both upper_ and lower_bound == 0 */
+
+  /*----------------------------------
+
+    qh precision constants
+      precision constants for Qhull
+
+    notes:
+      qh_detroundoff() computes the maximum roundoff error for distance
+      and other computations.  It also sets default values for the
+      qh constants above.
+  */
+  realT ANGLEround;     /* max round off error for angles */
+  realT centrum_radius; /* max centrum radius for convexity (roundoff added) */
+  realT cos_max;        /* max cosine for convexity (roundoff added) */
+  realT DISTround;      /* max round off error for distances, 'E' overrides */
+  realT MAXabs_coord;   /* max absolute coordinate */
+  realT MAXlastcoord;   /* max last coordinate for qh_scalelast */
+  realT MAXsumcoord;    /* max sum of coordinates */
+  realT MAXwidth;       /* max rectilinear width of point coordinates */
+  realT MINdenom_1;     /* min. abs. value for 1/x */
+  realT MINdenom;       /*    use divzero if denominator < MINdenom */
+  realT MINdenom_1_2;   /* min. abs. val for 1/x that allows normalization */
+  realT MINdenom_2;     /*    use divzero if denominator < MINdenom_2 */
+  realT MINlastcoord;   /* min. last coordinate for qh_scalelast */
+  boolT NARROWhull;     /* set in qh_initialhull if angle < qh_MAXnarrow */
+  realT *NEARzero;      /* hull_dim array for near zero in gausselim */
+  realT NEARinside;     /* keep points for qh_check_maxout if close to facet */
+  realT ONEmerge;       /* max distance for merging simplicial facets */
+  realT outside_err;    /* application's epsilon for coplanar points
+                             qh_check_bestdist() qh_check_points() reports error if point outside */
+  realT WIDEfacet;      /* size of wide facet for skipping ridge in
+           area computation and locking centrum */
+
+  /*----------------------------------
+
+    qh internal constants
+      internal constants for Qhull
+  */
+  char qhull[sizeof( "qhull" )]; /* for checking ownership */
+  void *old_stat;                /* pointer to saved qh_qhstat, qh_save_qhull */
+  jmp_buf errexit;               /* exit label for qh_errexit, defined by
+                                   setjmp() */
+  char jmpXtra[40];              /* extra bytes in case jmp_buf is defined wrong
+                                   by compiler */
+  jmp_buf restartexit;           /* restart label for qh_errexit, defined by
+                                   setjmp() */
+  char jmpXtra2[40];             /* extra bytes in case jmp_buf is defined wrong
+                                   by compiler*/
+  FILE *fin;                     /* pointer to input file, init by qh_meminit */
+  FILE *fout;                    /* pointer to output file */
+  FILE *ferr;                    /* pointer to error file */
+  pointT *interior_point;        /* center point of the initial simplex*/
+  size_t normal_size;            /* size in bytes for facet normals and point
+                                   coords*/
+  size_t center_size;            /* size in bytes for Voronoi centers */
+  int TEMPsize;                  /* size for small, temporary sets (in quick
+                                   mem) */
+
+  /*----------------------------------
+
+    qh facet and vertex lists
+      defines lists of facets, new facets, visible facets, vertices, and
+      new vertices.  Includes counts, next ids, and trace ids.
+    see:
+      qh_resetlists()
+  */
+  facetT *facet_list;      /* first facet */
+  facetT *facet_tail;      /* end of facet_list (dummy facet) */
+  facetT *facet_next;      /* next facet for buildhull()
+               previous facets do not have outside sets
+                             NARROWhull: previous facets may have coplanar outside sets for qh_outcoplanar */
+  facetT *newfacet_list;   /* list of new facets to end of facet_list */
+  facetT *visible_list;    /* list of visible facets preceeding newfacet_list,
+                             facet->visible set */
+  int num_visible;         /* current number of visible facets */
+  unsigned tracefacet_id;  /* set at init, then can print whenever */
+  facetT *tracefacet;      /*   set in newfacet/mergefacet, undone in delfacet*/
+  unsigned tracevertex_id; /* set at buildtracing, can print whenever */
+  vertexT *tracevertex;    /*   set in newvertex, undone in delvertex*/
+  vertexT *vertex_list;    /* list of all vertices, to vertex_tail */
+  vertexT *vertex_tail;    /*      end of vertex_list (dummy vertex) */
+  vertexT *newvertex_list; /* list of vertices in newfacet_list, to vertex_tail
+                             all vertices have 'newlist' set */
+  int num_facets;          /* number of facets in facet_list
+           includes visble faces (num_visible) */
+  int num_vertices;        /* number of vertices in facet_list */
+  int num_outside;         /* number of points in outsidesets (for tracing and RANDOMoutside)
+                               includes coplanar outsideset points for NARROWhull/qh_outcoplanar() */
+  int num_good;            /* number of good facets (after findgood_all) */
+  unsigned facet_id;       /* ID of next, new facet from newfacet() */
+  unsigned ridge_id;       /* ID of next, new ridge from newridge() */
+  unsigned vertex_id;      /* ID of next, new vertex from newvertex() */
+
+  /*----------------------------------
+
+    qh global variables
+      defines minimum and maximum distances, next visit ids, several flags,
+      and other global variables.
+      initialize in qh_initbuild or qh_maxmin if used in qh_buildhull
+  */
+  unsigned long hulltime;    /* ignore time to set up input and randomize */
+                             /*   use unsigned to avoid wrap-around errors */
+  boolT ALLOWrestart;        /* true if qh_precision can use qh.restartexit */
+  int build_cnt;             /* number of calls to qh_initbuild */
+  qh_CENTER CENTERtype;      /* current type of facet->center, qh_CENTER */
+  int furthest_id;           /* pointid of furthest point, for tracing */
+  facetT *GOODclosest;       /* closest facet to GOODthreshold in qh_findgood */
+  realT JOGGLEmax;           /* set 'QJn' if randomly joggle input */
+  boolT maxoutdone;          /* set qh_check_maxout(), cleared by qh_addpoint()
+                               */
+  realT max_outside;         /* maximum distance from a point to a facet,
+             before roundoff, not simplicial vertices
+             actual outer plane is +DISTround and
+             computed outer plane is +2*DISTround */
+  realT max_vertex;          /* maximum distance (>0) from vertex to a facet,
+             before roundoff, due to a merge */
+  realT min_vertex;          /* minimum distance (<0) from vertex to a facet,
+             before roundoff, due to a merge
+             if qh.JOGGLEmax, qh_makenewplanes sets it
+               recomputed if qh.DOcheckmax, default -qh.DISTround */
+  boolT NEWfacets;           /* true while visible facets invalid due to new or merge
+            from makecone/attachnewfacets to deletevisible */
+  boolT findbestnew;         /* true if partitioning calls qh_findbestnew */
+  boolT findbest_notsharp;   /* true if new facets are at least 90 degrees */
+  boolT NOerrexit;           /* true if qh.errexit is not available */
+  realT PRINTcradius;        /* radius for printing centrums */
+  realT PRINTradius;         /* radius for printing vertex spheres and points */
+  boolT POSTmerging;         /* true when post merging */
+  int printoutvar;           /* temporary variable for qh_printbegin, etc. */
+  int printoutnum;           /* number of facets printed */
+  boolT QHULLfinished;       /* True after qhull() is finished */
+  realT totarea;             /* 'FA': total facet area computed by qh_getarea */
+  realT totvol;              /* 'FA': total volume computed by qh_getarea */
+  unsigned int visit_id;     /* unique ID for searching neighborhoods, */
+  unsigned int vertex_visit; /* unique ID for searching vertices */
+  boolT ZEROall_ok;          /* True if qh_checkzero always succeeds */
+  boolT WAScoplanar;         /* True if qh_partitioncoplanar (qh_check_maxout)
+                               */
+
+  /*----------------------------------
+
+    qh global sets
+      defines sets for merging, initial simplex, hashing, extra input points,
+      and deleted vertices
+  */
+  setT *facet_mergeset; /* temporary set of merges to be done */
+  setT *degen_mergeset; /* temporary set of degenerate and redundant merges */
+  setT *hash_table;     /* hash table for matching ridges in qh_matchfacets
+                             size is setsize() */
+  setT *other_points;   /* additional points (first is qh interior_point) */
+  setT *del_vertices;   /* vertices to partition and delete with visible
+                             facets.  Have deleted set for checkfacet */
+
+  /*----------------------------------
+
+    qh global buffers
+      defines buffers for maxtrix operations, input, and error messages
+  */
+  coordT *gm_matrix;      /* (dim+1)Xdim matrix for geom.c */
+  coordT * *gm_row;       /* array of gm_matrix rows */
+  char *line;             /* malloc'd input line of maxline+1 chars */
+  int maxline;
+  coordT *half_space;     /* malloc'd input array for halfspace (qh
+                            normal_size+coordT) */
+  coordT *temp_malloc;    /* malloc'd input array for points */
+
+  /*----------------------------------
+
+    qh static variables
+      defines static variables for individual functions
+
+    notes:
+      do not use 'static' within a function.  Multiple instances of qhull
+      may exist.
+
+      do not assume zero initialization, 'QPn' may cause a restart
+  */
+  boolT ERREXITcalled;    /* true during errexit (prevents duplicate calls */
+  boolT firstcentrum;     /* for qh_printcentrum */
+  realT last_low;         /* qh_scalelast parameters for qh_setdelaunay */
+  realT last_high;
+  realT last_newhigh;
+  unsigned lastreport;    /* for qh_buildtracing */
+  int mergereport;        /* for qh_tracemerging */
+  boolT old_randomdist;   /* save RANDOMdist when io, tracing, or statistics */
+  int ridgeoutnum;        /* number of ridges in 4OFF output */
+  void *old_qhstat;       /* for saving qh_qhstat in save_qhull() */
+  setT *old_tempstack;    /* for saving qhmem.tempstack in save_qhull */
+  setT *coplanarset;      /* set of coplanar facets for searching
+                            qh_findbesthorizon() */
+  };
+
+/*=========== -macros- =========================*/
+
+/*----------------------------------
+
+  otherfacet_(ridge, facet)
+    return neighboring facet for a ridge in facet
+*/
+#define otherfacet_(ridge, facet)                                       \
+  ( ( ( ridge )->top == ( facet ) ) ? ( ridge )->bottom : ( ridge )->top )
+
+/*----------------------------------
+
+  getid_(p)
+    return ID for facet, ridge, or vertex
+    return MAXINT if NULL (-1 causes type conversion error )
+*/
+#define getid_(p)       ( ( p ) ? (int)( ( p )->id ) : -1 )
+
+/*============== FORALL macros ===================*/
+
+/*----------------------------------
+
+  FORALLfacets { ... }
+    assign 'facet' to each facet in qh.facet_list
+
+  notes:
+    uses 'facetT *facet;'
+    assumes last facet is a sentinel
+
+  see:
+    FORALLfacet_( facetlist )
+*/
+#define FORALLfacets for( facet = qh facet_list; facet && facet->next; facet = facet->next )
+
+/*----------------------------------
+
+  FORALLpoints { ... }
+    assign 'point' to each point in qh.first_point, qh.num_points
+
+  declare:
+    coordT *point, *pointtemp;
+*/
+#define FORALLpoints FORALLpoint_(qh first_point, qh num_points)
+
+/*----------------------------------
+
+  FORALLpoint_( points, num) { ... }
+    assign 'point' to each point in points array of num points
+
+  declare:
+    coordT *point, *pointtemp;
+*/
+#define FORALLpoint_(points, num)                                       \
+  for( point = ( points ),                                             \
+       pointtemp = ( points ) + qh hull_dim * ( num ); point < pointtemp; point += qh hull_dim )
+
+/*----------------------------------
+
+  FORALLvertices { ... }
+    assign 'vertex' to each vertex in qh.vertex_list
+
+  declare:
+    vertexT *vertex;
+
+  notes:
+    assumes qh.vertex_list terminated with a sentinel
+*/
+#define FORALLvertices for( vertex = qh vertex_list; vertex && vertex->next; vertex = vertex->next )
+
+/*----------------------------------
+
+  FOREACHfacet_( facets ) { ... }
+    assign 'facet' to each facet in facets
+
+  declare:
+    facetT *facet, **facetp;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHfacet_(facets)    FOREACHsetelement_(facetT, facets, facet)
+
+/*----------------------------------
+
+  FOREACHneighbor_( facet ) { ... }
+    assign 'neighbor' to each neighbor in facet->neighbors
+
+  FOREACHneighbor_( vertex ) { ... }
+    assign 'neighbor' to each neighbor in vertex->neighbors
+
+  declare:
+    facetT *neighbor, **neighborp;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHneighbor_(facet)  FOREACHsetelement_(facetT, facet->neighbors, neighbor)
+
+/*----------------------------------
+
+  FOREACHpoint_( points ) { ... }
+    assign 'point' to each point in points set
+
+  declare:
+    pointT *point, **pointp;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHpoint_(points)    FOREACHsetelement_(pointT, points, point)
+
+/*----------------------------------
+
+  FOREACHridge_( ridges ) { ... }
+    assign 'ridge' to each ridge in ridges set
+
+  declare:
+    ridgeT *ridge, **ridgep;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHridge_(ridges)    FOREACHsetelement_(ridgeT, ridges, ridge)
+
+/*----------------------------------
+
+  FOREACHvertex_( vertices ) { ... }
+    assign 'vertex' to each vertex in vertices set
+
+  declare:
+    vertexT *vertex, **vertexp;
+
+  see:
+    FOREACHsetelement_
+*/
+#define FOREACHvertex_(vertices) FOREACHsetelement_(vertexT, vertices, vertex)
+
+/*----------------------------------
+
+  FOREACHfacet_i_( facets ) { ... }
+    assign 'facet' and 'facet_i' for each facet in facets set
+
+  declare:
+    facetT *facet;
+    int     facet_n, facet_i;
+
+  see:
+    FOREACHsetelement_i_
+*/
+#define FOREACHfacet_i_(facets)    FOREACHsetelement_i_(facetT, facets, facet)
+
+/*----------------------------------
+
+  FOREACHneighbor_i_( facet ) { ... }
+    assign 'neighbor' and 'neighbor_i' for each neighbor in facet->neighbors
+
+  FOREACHneighbor_i_( vertex ) { ... }
+    assign 'neighbor' and 'neighbor_i' for each neighbor in vertex->neighbors
+
+  declare:
+    facetT *neighbor;
+    int     neighbor_n, neighbor_i;
+
+  see:
+    FOREACHsetelement_i_
+*/
+#define FOREACHneighbor_i_(facet)  FOREACHsetelement_i_(facetT, facet->neighbors, neighbor)
+
+/*----------------------------------
+
+  FOREACHpoint_i_( points ) { ... }
+    assign 'point' and 'point_i' for each point in points set
+
+  declare:
+    pointT *point;
+    int     point_n, point_i;
+
+  see:
+    FOREACHsetelement_i_
+*/
+#define FOREACHpoint_i_(points)    FOREACHsetelement_i_(pointT, points, point)
+
+/*----------------------------------
+
+  FOREACHridge_i_( ridges ) { ... }
+    assign 'ridge' and 'ridge_i' for each ridge in ridges set
+
+  declare:
+    ridgeT *ridge;
+    int     ridge_n, ridge_i;
+
+  see:
+    FOREACHsetelement_i_
+*/
+#define FOREACHridge_i_(ridges)    FOREACHsetelement_i_(ridgeT, ridges, ridge)
+
+/*----------------------------------
+
+  FOREACHvertex_i_( vertices ) { ... }
+    assign 'vertex' and 'vertex_i' for each vertex in vertices set
+
+  declare:
+    vertexT *vertex;
+    int     vertex_n, vertex_i;
+
+  see:
+    FOREACHsetelement_i_
+ */
+#define FOREACHvertex_i_(vertices) FOREACHsetelement_i_(vertexT, vertices, vertex)
+
+/********* -qhull.c prototypes (duplicated from qhull_a.h)
+  **********************/
+
+void    qh_qhull(void);
+
+boolT   qh_addpoint(pointT *furthest, facetT *facet, boolT checkdist);
+
+void  qh_printsummary(FILE *fp);
+
+/********* -user.c prototypes (alphabetical) **********************/
+
+void  qh_errexit(int exitcode, facetT *facet, ridgeT *ridge);
+
+void  qh_errprint(const char *string, facetT *atfacet, facetT *otherfacet, ridgeT *atridge, vertexT *atvertex);
+
+int     qh_new_qhull(int dim, int numpoints, coordT *points, boolT ismalloc, char *qhull_cmd, FILE *outfile,
+                     FILE *errfile);
+
+void    qh_printfacetlist(facetT *facetlist, setT *facets, boolT printall);
+
+void  qh_user_memsizes(void);
+
+/***** -geom.c/geom2.c prototypes (duplicated from geom.h) ****************/
+
+facetT * qh_findbest(pointT *point, facetT *startfacet, boolT bestoutside, boolT newfacets, boolT noupper, realT *dist,
+                     boolT *isoutside,
+                     int *numpart);
+
+facetT * qh_findbestnew(pointT *point, facetT *startfacet, realT *dist, boolT bestoutside, boolT *isoutside,
+                        int *numpart);
+
+boolT   qh_gram_schmidt(int dim, realT * *rows);
+
+void    qh_outerinner(facetT *facet, realT *outerplane, realT *innerplane);
+
+void  qh_printsummary(FILE *fp);
+
+void    qh_projectinput(void);
+
+void    qh_randommatrix(realT *buffer, int dim, realT * *row);
+
+void    qh_rotateinput(realT * *rows);
+
+void    qh_scaleinput(void);
+
+void    qh_setdelaunay(int dim, int count, pointT *points);
+
+coordT  * qh_sethalfspace_all(int dim, int count, coordT *halfspaces, pointT *feasible);
+
+/***** -global.c prototypes (alphabetical) ***********************/
+
+unsigned long qh_clock(void);
+
+void  qh_checkflags(char *command, char *hiddenflags);
+
+void  qh_freebuffers(void);
+
+void    qh_freeqhull(boolT allmem);
+
+void qh_init_A(FILE * infile, FILE * outfile, FILE * errfile, int argc, char *argv[]);
+void    qh_init_B(coordT *points, int numpoints, int dim, boolT ismalloc);
+
+void qh_init_qhull_command(int argc, char *argv[]);
+void    qh_initbuffers(coordT *points, int numpoints, int dim, boolT ismalloc);
+
+void  qh_initflags(char *command);
+
+void  qh_initqhull_buffers(void);
+
+void  qh_initqhull_globals(coordT *points, int numpoints, int dim, boolT ismalloc);
+
+void    qh_initqhull_mem(void);
+
+void  qh_initqhull_start(FILE *infile, FILE *outfile, FILE *errfile);
+
+void  qh_initthresholds(char *command);
+
+void    qh_option(const char *option, int *i, realT *r);
+
+#if qh_QHpointer
+void  qh_restore_qhull(qhT * *oldqh);
+
+qhT    * qh_save_qhull(void);
+
+#endif
+
+/***** -io.c prototypes (duplicated from io.h) ***********************/
+
+void    dfacet( unsigned id);
+
+void    dvertex( unsigned id);
+
+void  qh_printneighborhood(FILE *fp, qh_PRINT format, facetT *facetA, facetT *facetB, boolT printall);
+
+void  qh_produce_output(void);
+
+coordT * qh_readpoints(int *numpoints, int *dimension, boolT *ismalloc);
+
+/********* -mem.c prototypes (duplicated from mem.h) **********************/
+
+void qh_meminit(FILE *ferr);
+
+void qh_memfreeshort(int *curlong, int *totlong);
+
+/********* -poly.c/poly2.c prototypes (duplicated from poly.h)
+  **********************/
+
+void    qh_check_output(void);
+
+void    qh_check_points(void);
+
+setT   * qh_facetvertices(facetT *facetlist, setT *facets, boolT allfacets);
+
+facetT * qh_findbestfacet(pointT *point, boolT bestoutside, realT *bestdist, boolT *isoutside);
+
+vertexT * qh_nearvertex(facetT *facet, pointT *point, realT *bestdistp);
+
+pointT * qh_point(int id);
+
+setT   * qh_pointfacet(void /*qh.facet_list*/);
+
+int     qh_pointid(pointT *point);
+
+setT   * qh_pointvertex(void /*qh.facet_list*/);
+
+void    qh_setvoronoi_all(void);
+
+void  qh_triangulate(void /*qh facet_list*/);
+
+/********* -stat.c prototypes (duplicated from stat.h) **********************/
+
+void    qh_collectstatistics(void);
+
+void    qh_printallstatistics(FILE *fp, const char *string);
+
+#endif /* qhDEFqhull */
diff --git a/BRAINSABC/qhull/qhull_a.h b/BRAINSABC/qhull/qhull_a.h
new file mode 100644
index 00000000..cd6ef04b
--- /dev/null
+++ b/BRAINSABC/qhull/qhull_a.h
@@ -0,0 +1,155 @@
+/*
  ---------------------------------
+
+   qhull_a.h
+   all header files for compiling qhull
+
+   see qh-qhull.htm
+
+   see qhull.h for user-level definitions
+
+   see user.h for user-defineable constants
+
+   defines internal functions for qhull.c global.c
+
+   copyright (c) 1993-2003, The Geometry Center
+
+   Notes:  grep for ((" and (" to catch fprintf("lkasdjf");
+           full parens around (x?y:z)
+     use '#include qhull/qhull_a.h' to avoid name clashes
+*/
+
+#ifndef qhDEFqhulla
+#define qhDEFqhulla
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include     /* some compilers will not need float.h */
+#include 
+#include 
+#include 
+/*** uncomment here and qset.c
+     if string.h does not define memcpy()
+#include 
+*/
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+#include "geom.h"
+#include "merge.h"
+#include "poly.h"
+#include "io.h"
+#include "stat.h"
+
+#if qh_CLOCKtype == 2  /* defined in user.h from qhull.h */
+#include 
+#include 
+#include 
+#endif
+
+#ifdef _MSC_VER  /* Microsoft Visual C++ */
+#pragma warning( disable : 4056)  /* float constant expression.  Looks like a compiler bug */
+#pragma warning( disable : 4146)  /* unary minus applied to unsigned type */
+#pragma warning( disable : 4244)  /* conversion from 'unsigned long' to 'real' */
+#pragma warning( disable : 4305)  /* conversion from 'const double' to 'float' */
+#endif
+
+/* ======= -macros- =========== */
+
+/*----------------------------------
+
+  traceN((fp.ferr, "format\n", vars));
+    calls fprintf if qh.IStracing >= N
+
+  notes:
+    removing tracing reduces code size but doesn't change execution speed
+*/
+#ifndef qh_NOtrace
+#define trace0(args) {if( qh IStracing ) {fprintf args; }}
+#define trace1(args) {if( qh IStracing >= 1 ) {fprintf args; }}
+#define trace2(args) {if( qh IStracing >= 2 ) {fprintf args; }}
+#define trace3(args) {if( qh IStracing >= 3 ) {fprintf args; }}
+#define trace4(args) {if( qh IStracing >= 4 ) {fprintf args; }}
+#define trace5(args) {if( qh IStracing >= 5 ) {fprintf args; }}
+#else /* qh_NOtrace */
+#define trace0(args) {}
+#define trace1(args) {}
+#define trace2(args) {}
+#define trace3(args) {}
+#define trace4(args) {}
+#define trace5(args) {}
+#endif /* qh_NOtrace */
+
+/***** -qhull.c prototypes (alphabetical after qhull) ********************/
+
+void  qh_qhull(void);
+
+boolT   qh_addpoint(pointT *furthest, facetT *facet, boolT checkdist);
+
+void  qh_buildhull(void);
+
+void    qh_buildtracing(pointT *furthest, facetT *facet);
+
+void    qh_build_withrestart(void);
+
+void  qh_errexit2(int exitcode, facetT *facet, facetT *otherfacet);
+
+void    qh_findhorizon(pointT *point, facetT *facet, int *goodvisible, int *goodhorizon);
+
+pointT * qh_nextfurthest(facetT * *visible);
+
+void  qh_partitionall(setT *vertices, pointT *points, int npoints);
+
+void    qh_partitioncoplanar(pointT *point, facetT *facet, realT *dist);
+
+void    qh_partitionpoint(pointT *point, facetT *facet);
+
+void  qh_partitionvisible(boolT allpoints, int *numpoints);
+
+void    qh_precision(const char *reason);
+
+void  qh_printsummary(FILE *fp);
+
+/***** -global.c internal prototypes (alphabetical) ***********************/
+
+void    qh_appendprint(qh_PRINT format);
+
+void  qh_freebuild(boolT allmem);
+
+void  qh_freebuffers(void);
+
+void    qh_initbuffers(coordT *points, int numpoints, int dim, boolT ismalloc);
+
+int     qh_strtol(const char *s, char * *endp);
+
+double  qh_strtod(const char *s, char * *endp);
+
+/***** -stat.c internal prototypes (alphabetical) ***********************/
+
+void  qh_allstatA(void);
+
+void  qh_allstatB(void);
+
+void  qh_allstatC(void);
+
+void  qh_allstatD(void);
+
+void  qh_allstatE(void);
+
+void  qh_allstatE2(void);
+
+void  qh_allstatF(void);
+
+void  qh_allstatG(void);
+
+void  qh_allstatH(void);
+
+void  qh_freebuffers(void);
+
+void    qh_initbuffers(coordT *points, int numpoints, int dim, boolT ismalloc);
+
+#endif /* qhDEFqhulla */
diff --git a/BRAINSABC/qhull/qhull_interface.cpp b/BRAINSABC/qhull/qhull_interface.cpp
new file mode 100644
index 00000000..38d1faa5
--- /dev/null
+++ b/BRAINSABC/qhull/qhull_interface.cpp
@@ -0,0 +1,102 @@
+/*
  ---------------------------------
+*/
+
+#include 
+#include 
+
+// --- Include qhull, so it works from with in a C++ source file
+// ---
+// --- In MVC one cannot just do:
+// ---
+// ---    extern "C"
+// ---    {
+// ---      #include "qhull_a.h"
+// ---    }
+// ---
+// --- Because qhull_a.h includes math.h, which can not appear
+// --- inside a extern "C" declaration.
+// ---
+// --- Maybe that why Numerical recipes in C avoid this problem, by removing
+// --- standard include headers from its header files and add them in the
+// --- respective source files instead.
+// ---
+// --- [K. Erleben]
+
+#if defined(__cplusplus)
+extern "C"
+{
+#endif
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#if defined(__cplusplus)
+}
+#endif
+
+/*********************************************************************/
+/*                                                                   */
+/*                                                                   */
+/*                                                                   */
+/*                                                                   */
+/*********************************************************************/
+
+void compute_convex_hull(void)
+{
+  int     dim;                  /* dimension of points */
+  int     numpoints;            /* number of points */
+  coordT *points;               /* array of coordinates for each point */
+  boolT   ismalloc;             /* True if qhull should free points in
+                                  qh_freeqhull() or reallocation */
+  char    flags[] = "qhull Tv"; /* option flags for qhull, see qh_opt.htm */
+  FILE *  outfile = stdout;     /* output from qh_produce_output()
+                                     use NULL to skip qh_produce_output() */
+  FILE *  errfile = stderr;     /* error messages from qhull code */
+  int     exitcode;             /* 0 if no error from qhull */
+  facetT *facet;                /* set by FORALLfacets */
+  int     curlong, totlong;     /* memory remaining after qh_memfreeshort */
+
+  /* initialize dim, numpoints, points[], ismalloc here */
+  exitcode = qh_new_qhull(dim, numpoints, points, ismalloc,
+                          flags, outfile, errfile);
+  if( !exitcode )   /* if no error */
+    { /* 'qh facet_list' contains the convex hull */
+    FORALLfacets {
+      /* ... your code ... */
+      }
+    }
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+};
+
+/*********************************************************************/
+/*                                                                   */
+/*                                                                   */
+/*                                                                   */
+/*                                                                   */
+/*********************************************************************/
+
+void main()
+{
+  cout << "Hello world" << endl;
+
+  cout << "Press any key..." << endl;
+
+  while( !_kbhit() )
+    {
+    ;
+    }
+
+};
diff --git a/BRAINSABC/qhull/qset.c b/BRAINSABC/qhull/qset.c
new file mode 100644
index 00000000..1cded77c
--- /dev/null
+++ b/BRAINSABC/qhull/qset.c
@@ -0,0 +1,1489 @@
+/*
  ---------------------------------
+
+  qset.c
+  implements set manipulations needed for quickhull
+
+  see qh-set.htm and qset.h
+
+  copyright (c) 1993-2003 The Geometry Center
+*/
+
+#include 
+#include 
+/*** uncomment here and qhull_a.h
+     if string.h does not define memcpy()
+     #include 
+*/
+#include "qset.h"
+#include "mem.h"
+
+#ifndef qhDEFqhull
+typedef struct ridgeT ridgeT;
+typedef struct facetT facetT;
+void    qh_errexit(int exitcode, facetT *, ridgeT *);
+
+#endif
+
+/*=============== internal macros ===========================*/
+
+/*---------------------------------
+
+  SETsizeaddr_(set)
+  return pointer to actual size+1 of set (set CANNOT be NULL!!)
+
+  notes:
+  *SETsizeaddr==NULL or e[*SETsizeaddr-1].p==NULL
+  */
+#define SETsizeaddr_(set) (&( (set)->e[(set)->maxsize].i) )
+
+/*============ functions in alphabetical order ===================*/
+
+/*----------------------------------
+
+  qh_setaddnth( setp, nth, newelem)
+  adds newelem as n'th element of sorted or unsorted *setp
+
+  notes:
+  *setp and newelem must be defined
+  *setp may be a temp set
+  nth=0 is first element
+  errors if nth is out of bounds
+
+  design:
+  expand *setp if empty or full
+  move tail of *setp up one
+  insert newelem
+*/
+void qh_setaddnth(setT * *setp, int nth, void *newelem)
+{
+  int *   sizep, oldsize, i;
+  void * *oldp, * *newp;
+
+  if( !*setp || !*(sizep = SETsizeaddr_(*setp) ) )
+    {
+    qh_setlarger(setp);
+    sizep = SETsizeaddr_(*setp);
+    }
+  oldsize = *sizep - 1;
+  if( nth < 0 || nth > oldsize )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setaddnth): nth %d is out-of-bounds for set:\n", nth);
+    qh_setprint(qhmem.ferr, "", *setp);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  (*sizep)++;
+  oldp = SETelemaddr_(*setp, oldsize, void);   /* NULL */
+  newp = oldp + 1;
+  for( i = oldsize - nth + 1; i--; )  /* move at least NULL  */
+    {
+    *(newp--) = *(oldp--);       /* may overwrite *sizep */
+    }
+  *newp = newelem;
+} /* setaddnth */
+
+/*----------------------------------
+
+  setaddsorted( setp, newelem )
+  adds an newelem into sorted *setp
+
+  notes:
+  *setp and newelem must be defined
+  *setp may be a temp set
+  nop if newelem already in set
+
+  design:
+  find newelem's position in *setp
+  insert newelem
+*/
+void qh_setaddsorted(setT * *setp, void *newelem)
+{
+  int   newindex = 0;
+  void *elem, * *elemp;
+
+  FOREACHelem_(*setp) {          /* could use binary search instead */
+    if( elem < newelem )
+      {
+      newindex++;
+      }
+    else if( elem == newelem )
+      {
+      return;
+      }
+    else
+      {
+      break;
+      }
+    }
+  qh_setaddnth(setp, newindex, newelem);
+} /* setaddsorted */
+
+/*---------------------------------
+
+  qh_setappend( setp, newelem)
+  append newelem to *setp
+
+  notes:
+  *setp may be a temp set
+  *setp and newelem may be NULL
+
+  design:
+  expand *setp if empty or full
+  append newelem to *setp
+
+*/
+void qh_setappend(setT * *setp, void *newelem)
+{
+  int *   sizep;
+  void * *endp;
+
+  if( !newelem )
+    {
+    return;
+    }
+  if( !*setp || !*(sizep = SETsizeaddr_(*setp) ) )
+    {
+    qh_setlarger(setp);
+    sizep = SETsizeaddr_(*setp);
+    }
+  *(endp = &( (*setp)->e[(*sizep)++ - 1].p) ) = newelem;
+  *(++endp) = NULL;
+} /* setappend */
+
+/*---------------------------------
+
+  qh_setappend_set( setp, setA)
+  appends setA to *setp
+
+  notes:
+  *setp can not be a temp set
+  *setp and setA may be NULL
+
+  design:
+  setup for copy
+  expand *setp if it is too small
+  append all elements of setA to *setp
+*/
+void qh_setappend_set(setT * *setp, setT *setA)
+{
+  int * sizep, sizeA, size;
+  setT *oldset;
+
+  if( !setA )
+    {
+    return;
+    }
+  SETreturnsize_(setA, sizeA);
+  if( !*setp )
+    {
+    *setp = qh_setnew(sizeA);
+    }
+  sizep = SETsizeaddr_(*setp);
+  if( !(size = *sizep) )
+    {
+    size = (*setp)->maxsize;
+    }
+  else
+    {
+    size--;
+    }
+  if( size + sizeA > (*setp)->maxsize )
+    {
+    oldset = *setp;
+    *setp = qh_setcopy(oldset, sizeA);
+    qh_setfree(&oldset);
+    sizep = SETsizeaddr_(*setp);
+    }
+  *sizep = size + sizeA + 1;   /* memcpy may overwrite */
+  if( sizeA > 0 )
+    {
+    memcpy( (char *)&( (*setp)->e[size].p), (char *)&(setA->e[0].p), SETelemsize * (sizeA + 1) );
+    }
+} /* setappend_set */
+
+/*---------------------------------
+
+  qh_setappend2ndlast( setp, newelem )
+  makes newelem the next to the last element in *setp
+
+  notes:
+  *setp must have at least one element
+  newelem must be defined
+  *setp may be a temp set
+
+  design:
+  expand *setp if empty or full
+  move last element of *setp up one
+  insert newelem
+*/
+void qh_setappend2ndlast(setT * *setp, void *newelem)
+{
+  int *   sizep;
+  void * *endp, * *lastp;
+
+  if( !*setp || !*(sizep = SETsizeaddr_(*setp) ) )
+    {
+    qh_setlarger(setp);
+    sizep = SETsizeaddr_(*setp);
+    }
+  endp = SETelemaddr_(*setp, (*sizep)++ - 1, void); /* NULL */
+  lastp = endp - 1;
+  *(endp++) = *lastp;
+  *endp = NULL;    /* may overwrite *sizep */
+  *lastp = newelem;
+} /* setappend2ndlast */
+
+/*---------------------------------
+
+  qh_setcheck( set, typename, id )
+  check set for validity
+  report errors with typename and id
+
+  design:
+  checks that maxsize, actual size, and NULL terminator agree
+*/
+void qh_setcheck(setT *set, const char *tname, unsigned id)
+{
+  int maxsize, size;
+  int waserr = 0;
+
+  if( !set )
+    {
+    return;
+    }
+  SETreturnsize_(set, size);
+  maxsize = set->maxsize;
+  if( size > maxsize || !maxsize )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setcheck): actual size %d of %s%d is greater than max size %d\n",
+            size, tname, id, maxsize);
+    waserr = 1;
+    }
+  else if( set->e[size].p )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setcheck): %s%d (size %d max %d) is not null terminated.\n",
+            tname, id, maxsize, size - 1);
+    waserr = 1;
+    }
+  if( waserr )
+    {
+    qh_setprint(qhmem.ferr, "ERRONEOUS", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+} /* setcheck */
+
+/*---------------------------------
+
+  qh_setcompact( set )
+  remove internal NULLs from an unsorted set
+
+  returns:
+  updated set
+
+  notes:
+  set may be NULL
+  it would be faster to swap tail of set into holes, like qh_setdel
+
+  design:
+  setup pointers into set
+  skip NULLs while copying elements to start of set
+  update the actual size
+*/
+void qh_setcompact(setT *set)
+{
+  int     size;
+  void * *destp, * *elemp, * *endp, * *firstp;
+
+  if( !set )
+    {
+    return;
+    }
+  SETreturnsize_(set, size);
+  destp = elemp = firstp = SETaddr_(set, void);
+  endp = destp + size;
+  while( 1 )
+    {
+    if( !(*destp++ = *elemp++) )
+      {
+      destp--;
+      if( elemp > endp )
+        {
+        break;
+        }
+      }
+    }
+
+  qh_settruncate(set, (size_t)(destp - firstp) );
+} /* setcompact */
+
+/*---------------------------------
+
+  qh_setcopy( set, extra )
+  make a copy of a sorted or unsorted set with extra slots
+
+  returns:
+  new set
+
+  design:
+  create a newset with extra slots
+  copy the elements to the newset
+
+*/
+setT * qh_setcopy(setT *set, int extra)
+{
+  setT *newset;
+  int   size;
+
+  if( extra < 0 )
+    {
+    extra = 0;
+    }
+  SETreturnsize_(set, size);
+  newset = qh_setnew(size + extra);
+  *SETsizeaddr_(newset) = size + 1;    /* memcpy may overwrite */
+  memcpy( (char *)&(newset->e[0].p), (char *)&(set->e[0].p), SETelemsize * (size + 1) );
+  return newset;
+} /* setcopy */
+
+/*---------------------------------
+
+  qh_setdel( set, oldelem )
+  delete oldelem from an unsorted set
+
+  returns:
+  returns oldelem if found
+  returns NULL otherwise
+
+  notes:
+  set may be NULL
+  oldelem must not be NULL;
+  only deletes one copy of oldelem in set
+
+  design:
+  locate oldelem
+  update actual size if it was full
+  move the last element to the oldelem's location
+*/
+void * qh_setdel(setT *set, void *oldelem)
+{
+  void * *elemp, * *lastp;
+  int *   sizep;
+
+  if( !set )
+    {
+    return NULL;
+    }
+  elemp = SETaddr_(set, void);
+  while( *elemp != oldelem && *elemp )
+    {
+    elemp++;
+    }
+
+  if( *elemp )
+    {
+    sizep = SETsizeaddr_(set);
+    if( !(*sizep)-- )         /*  if was a full set */
+      {
+      *sizep = set->maxsize;  /*     *sizep= (maxsize-1)+ 1 */
+      }
+    lastp = SETelemaddr_(set, *sizep - 1, void);
+    *elemp = *lastp;      /* may overwrite itself */
+    *lastp = NULL;
+    return oldelem;
+    }
+  return NULL;
+} /* setdel */
+
+/*---------------------------------
+
+  qh_setdellast( set)
+  return last element of set or NULL
+
+  notes:
+  deletes element from set
+  set may be NULL
+
+  design:
+  return NULL if empty
+  if full set
+  delete last element and set actual size
+  else
+  delete last element and update actual size
+*/
+void * qh_setdellast(setT *set)
+{
+  int   setsize; /* actually, actual_size + 1 */
+  int   maxsize;
+  int * sizep;
+  void *returnvalue;
+
+  if( !set || !(set->e[0].p) )
+    {
+    return NULL;
+    }
+  sizep = SETsizeaddr_(set);
+  if( (setsize = *sizep) )
+    {
+    returnvalue = set->e[setsize - 2].p;
+    set->e[setsize - 2].p = NULL;
+    (*sizep)--;
+    }
+  else
+    {
+    maxsize = set->maxsize;
+    returnvalue = set->e[maxsize - 1].p;
+    set->e[maxsize - 1].p = NULL;
+    *sizep = maxsize;
+    }
+  return returnvalue;
+} /* setdellast */
+
+/*---------------------------------
+
+  qh_setdelnth( set, nth )
+  deletes nth element from unsorted set
+  0 is first element
+
+  returns:
+  returns the element (needs type conversion)
+
+  notes:
+  errors if nth invalid
+
+  design:
+  setup points and check nth
+  delete nth element and overwrite with last element
+*/
+void * qh_setdelnth(setT *set, size_t nth)
+{
+  void * *elemp, * *lastp, *elem;
+  int *   sizep;
+
+  elemp = SETelemaddr_(set, nth, void);
+  sizep = SETsizeaddr_(set);
+  if( !(*sizep)-- )         /*  if was a full set */
+    {
+    *sizep = set->maxsize;  /*     *sizep= (maxsize-1)+ 1 */
+    }
+  if( /* nth < 0 || */ nth >= (size_t)*sizep )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setaddnth): nth %lu is out-of-bounds for set:\n",
+            (unsigned long)nth);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  lastp = SETelemaddr_(set, *sizep - 1, void);
+  elem = *elemp;
+  *elemp = *lastp;      /* may overwrite itself */
+  *lastp = NULL;
+  return elem;
+} /* setdelnth */
+
+/*---------------------------------
+
+  qh_setdelnthsorted( set, nth )
+  deletes nth element from sorted set
+
+  returns:
+  returns the element (use type conversion)
+
+  notes:
+  errors if nth invalid
+
+  see also:
+  setnew_delnthsorted
+
+  design:
+  setup points and check nth
+  copy remaining elements down one
+  update actual size
+*/
+void * qh_setdelnthsorted(setT *set, size_t nth)
+{
+  void * *newp, * *oldp, *elem;
+  int *   sizep;
+
+  sizep = SETsizeaddr_(set);
+  if( /* nth < 0 || */ (*sizep && nth >= (size_t)*sizep - 1) || nth >= (size_t)set->maxsize )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setaddnth): nth %lu is out-of-bounds for set:\n",
+            (unsigned long)nth);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  newp = SETelemaddr_(set, nth, void);
+  elem = *newp;
+  oldp = newp + 1;
+  while( (*(newp++) = *(oldp++) ) )
+    {
+    ; /* copy remaining elements and NULL */
+    }
+
+  if( !(*sizep)-- )         /*  if was a full set */
+    {
+    *sizep = set->maxsize;  /*     *sizep= (max size-1)+ 1 */
+    }
+  return elem;
+} /* setdelnthsorted */
+
+/*---------------------------------
+
+  qh_setdelsorted( set, oldelem )
+  deletes oldelem from sorted set
+
+  returns:
+  returns oldelem if it was deleted
+
+  notes:
+  set may be NULL
+
+  design:
+  locate oldelem in set
+  copy remaining elements down one
+  update actual size
+*/
+void * qh_setdelsorted(setT *set, void *oldelem)
+{
+  void * *newp, * *oldp;
+  int *   sizep;
+
+  if( !set )
+    {
+    return NULL;
+    }
+  newp = SETaddr_(set, void);
+  while( *newp != oldelem && *newp )
+    {
+    newp++;
+    }
+
+  if( *newp )
+    {
+    oldp = newp + 1;
+    while( (*(newp++) = *(oldp++) ) )
+      {
+      ; /* copy remaining elements */
+      }
+
+    sizep = SETsizeaddr_(set);
+    if( !(*sizep)-- )    /*  if was a full set */
+      {
+      *sizep = set->maxsize;  /*     *sizep= (max size-1)+ 1 */
+      }
+    return oldelem;
+    }
+  return NULL;
+} /* setdelsorted */
+
+/*---------------------------------
+
+  qh_setduplicate( set, elemsize )
+  duplicate a set of elemsize elements
+
+  notes:
+  use setcopy if retaining old elements
+
+  design:
+  create a new set
+  for each elem of the old set
+  create a newelem
+  append newelem to newset
+*/
+setT * qh_setduplicate(setT *set, int elemsize)
+{
+  void *elem, * *elemp, *newElem;
+  setT *newSet;
+  int   size;
+
+  if( !(size = qh_setsize(set) ) )
+    {
+    return NULL;
+    }
+  newSet = qh_setnew(size);
+  FOREACHelem_(set) {
+    newElem = qh_memalloc( (size_t)elemsize);
+    memcpy(newElem, elem, (size_t)elemsize);
+    qh_setappend(&newSet, newElem);
+    }
+  return newSet;
+} /* setduplicate */
+
+/*---------------------------------
+
+  qh_setequal(  )
+  returns 1 if two sorted sets are equal, otherwise returns 0
+
+  notes:
+  either set may be NULL
+
+  design:
+  check size of each set
+  setup pointers
+  compare elements of each set
+*/
+int qh_setequal(setT *setA, setT *setB)
+{
+  void * *elemAp, * *elemBp;
+  int     sizeA, sizeB;
+
+  SETreturnsize_(setA, sizeA);
+  SETreturnsize_(setB, sizeB);
+  if( sizeA != sizeB )
+    {
+    return 0;
+    }
+  if( !sizeA )
+    {
+    return 1;
+    }
+  elemAp = SETaddr_(setA, void);
+  elemBp = SETaddr_(setB, void);
+  if( !memcmp( (char *)elemAp, (char *)elemBp, sizeA * SETelemsize) )
+    {
+    return 1;
+    }
+  return 0;
+} /* setequal */
+
+/*---------------------------------
+
+  qh_setequal_except( setA, skipelemA, setB, skipelemB )
+  returns 1 if sorted setA and setB are equal except for skipelemA & B
+
+  returns:
+  false if either skipelemA or skipelemB are missing
+
+  notes:
+  neither set may be NULL
+
+  if skipelemB is NULL,
+  can skip any one element of setB
+
+  design:
+  setup pointers
+  search for skipelemA, skipelemB, and mismatches
+  check results
+*/
+int qh_setequal_except(setT *setA, void *skipelemA, setT *setB, void *skipelemB)
+{
+  void * *elemA, * *elemB;
+  int     skip = 0;
+
+  elemA = SETaddr_(setA, void);
+  elemB = SETaddr_(setB, void);
+  while( 1 )
+    {
+    if( *elemA == skipelemA )
+      {
+      skip++;
+      elemA++;
+      }
+    if( skipelemB )
+      {
+      if( *elemB == skipelemB )
+        {
+        skip++;
+        elemB++;
+        }
+      }
+    else if( *elemA != *elemB )
+      {
+      skip++;
+      if( !(skipelemB = *elemB++) )
+        {
+        return 0;
+        }
+      }
+    if( !*elemA )
+      {
+      break;
+      }
+    if( *elemA++ != *elemB++ )
+      {
+      return 0;
+      }
+    }
+
+  if( skip != 2 || *elemB )
+    {
+    return 0;
+    }
+  return 1;
+} /* setequal_except */
+
+/*---------------------------------
+
+  qh_setequal_skip( setA, skipA, setB, skipB )
+  returns 1 if sorted setA and setB are equal except for elements skipA & B
+
+  returns:
+  false if different size
+
+  notes:
+  neither set may be NULL
+
+  design:
+  setup pointers
+  search for mismatches while skipping skipA and skipB
+*/
+int qh_setequal_skip(setT *setA, int skipA, setT *setB, int skipB)
+{
+  void * *elemA, * *elemB, * *skipAp, * *skipBp;
+
+  elemA = SETaddr_(setA, void);
+  elemB = SETaddr_(setB, void);
+  skipAp = SETelemaddr_(setA, skipA, void);
+  skipBp = SETelemaddr_(setB, skipB, void);
+  while( 1 )
+    {
+    if( elemA == skipAp )
+      {
+      elemA++;
+      }
+    if( elemB == skipBp )
+      {
+      elemB++;
+      }
+    if( !*elemA )
+      {
+      break;
+      }
+    if( *elemA++ != *elemB++ )
+      {
+      return 0;
+      }
+    }
+
+  if( *elemB )
+    {
+    return 0;
+    }
+  return 1;
+} /* setequal_skip */
+
+/*---------------------------------
+
+  qh_setfree( setp )
+  frees the space occupied by a sorted or unsorted set
+
+  returns:
+  sets setp to NULL
+
+  notes:
+  set may be NULL
+
+  design:
+  free array
+  free set
+*/
+void qh_setfree(setT * *setp)
+{
+  void * *freelistp;  /* used !qh_NOmem */
+
+  if( *setp )
+    {
+    const int size = sizeof(setT) + ( (*setp)->maxsize) * SETelemsize;
+    if( size <= qhmem.LASTsize )
+      {
+      qh_memfree_(*setp, size, freelistp);
+      }
+    else
+      {
+      qh_memfree(*setp, (size_t)size);
+      }
+    *setp = NULL;
+    }
+} /* setfree */
+
+/*---------------------------------
+
+  qh_setfree2( setp, elemsize )
+  frees the space occupied by a set and its elements
+
+  notes:
+  set may be NULL
+
+  design:
+  free each element
+  free set
+*/
+void qh_setfree2(setT * *setp, int elemsize)
+{
+  void *elem, * *elemp;
+
+  FOREACHelem_(*setp)
+  qh_memfree(elem, (size_t)elemsize);
+  qh_setfree(setp);
+} /* setfree2 */
+
+/*---------------------------------
+
+  qh_setfreelong( setp )
+  frees a set only if it's in long memory
+
+  returns:
+  sets setp to NULL if it is freed
+
+  notes:
+  set may be NULL
+
+  design:
+  if set is large
+  free it
+*/
+void qh_setfreelong(setT * *setp)
+{
+  if( *setp )
+    {
+    const int size = sizeof(setT) + ( (*setp)->maxsize) * SETelemsize;
+    if( size > qhmem.LASTsize )
+      {
+      qh_memfree(*setp, (size_t)size);
+      *setp = NULL;
+      }
+    }
+} /* setfreelong */
+
+/*---------------------------------
+
+  qh_setin( set, setelem )
+  returns 1 if setelem is in a set, 0 otherwise
+
+  notes:
+  set may be NULL or unsorted
+
+  design:
+  scans set for setelem
+*/
+int qh_setin(setT *set, void *setelem)
+{
+  void *elem, * *elemp;
+
+  FOREACHelem_(set) {
+    if( elem == setelem )
+      {
+      return 1;
+      }
+    }
+  return 0;
+} /* setin */
+
+/*---------------------------------
+
+  qh_setindex( set, atelem )
+  returns the index of atelem in set.
+  returns -1, if not in set or maxsize wrong
+
+  notes:
+  set may be NULL and may contain nulls.
+
+  design:
+  checks maxsize
+  scans set for atelem
+*/
+int qh_setindex(setT *set, void *atelem)
+{
+  void * *elem;
+  int     size, i;
+
+  SETreturnsize_(set, size);
+  if( size > set->maxsize )
+    {
+    return -1;
+    }
+  elem = SETaddr_(set, void);
+  for( i = 0; i < size; i++ )
+    {
+    if( *elem++ == atelem )
+      {
+      return i;
+      }
+    }
+  return -1;
+} /* setindex */
+
+/*---------------------------------
+
+  qh_setlarger( oldsetp )
+  returns a larger set that contains all elements of *oldsetp
+
+  notes:
+  the set is at least twice as large
+  if temp set, updates qhmem.tempstack
+
+  design:
+  creates a new set
+  copies the old set to the new set
+  updates pointers in tempstack
+  deletes the old set
+*/
+void qh_setlarger(setT * *oldsetp)
+{
+  int *sizep;
+  setT *  newset, *set, * *setp, *oldset;
+  void * *oldp, * *newp;
+
+  if( *oldsetp )
+    {
+    int size = 1;
+    oldset = *oldsetp;
+    SETreturnsize_(oldset, size);
+    qhmem.cntlarger++;
+    qhmem.totlarger += size + 1;
+    newset = qh_setnew(2 * size);
+    oldp = SETaddr_(oldset, void);
+    newp = SETaddr_(newset, void);
+    memcpy( (char *)newp, (char *)oldp, (size + 1) * SETelemsize);
+    sizep = SETsizeaddr_(newset);
+    *sizep = size + 1;
+    FOREACHset_( (setT *)qhmem.tempstack) {
+      if( set == oldset )
+        {
+        *(setp - 1) = newset;
+        }
+      }
+    qh_setfree(oldsetp);
+    }
+  else
+    {
+    newset = qh_setnew(3);
+    }
+  *oldsetp = newset;
+} /* setlarger */
+
+/*---------------------------------
+
+  qh_setlast(  )
+  return last element of set or NULL (use type conversion)
+
+  notes:
+  set may be NULL
+
+  design:
+  return last element
+*/
+void * qh_setlast(setT *set)
+{
+  if( set )
+    {
+    const int size = *SETsizeaddr_(set);
+    if( !size )
+      {
+      return SETelem_(set, set->maxsize - 1);
+      }
+    else if( size > 1 )
+      {
+      return SETelem_(set, size - 2);
+      }
+    }
+  return NULL;
+} /* setlast */
+
+/*---------------------------------
+
+  qh_setnew( setsize )
+  creates and allocates space for a set
+
+  notes:
+  setsize means the number of elements (NOT including the NULL terminator)
+  use qh_settemp/qh_setfreetemp if set is temporary
+
+  design:
+  allocate memory for set
+  roundup memory if small set
+  initialize as empty set
+*/
+setT * qh_setnew(int setsize)
+{
+  setT *  set;
+  int     size;
+  void * *freelistp; /* used !qh_NOmem */
+
+  if( !setsize )
+    {
+    setsize++;
+    }
+  size = sizeof(setT) + setsize * SETelemsize;
+  if( (unsigned) size <= (unsigned) qhmem.LASTsize )
+    {
+    qh_memalloc_( (size_t)size, freelistp, set, setT);
+#ifndef qh_NOmem
+    const int sizereceived = qhmem.sizetable[qhmem.indextable[size]];
+    if( sizereceived > size )
+      {
+      setsize += (sizereceived - size) / SETelemsize;
+      }
+#endif
+    }
+  else
+    {
+    set = (setT *)qh_memalloc( (size_t)size);
+    }
+  set->maxsize = setsize;
+  set->e[setsize].i = 1;
+  set->e[0].p = NULL;
+  return set;
+} /* setnew */
+
+/*---------------------------------
+
+  qh_setnew_delnthsorted( set, size, nth, prepend )
+  creates a sorted set not containing nth element
+  if prepend, the first prepend elements are undefined
+
+  notes:
+  set must be defined
+  checks nth
+  see also: setdelnthsorted
+
+  design:
+  create new set
+  setup pointers and allocate room for prepend'ed entries
+  append head of old set to new set
+  append tail of old set to new set
+*/
+setT * qh_setnew_delnthsorted(setT *set, int size, size_t nth, size_t prepend)
+{
+  setT *  newset;
+  void * *oldp, * *newp;
+  int     tailsize = size - nth - 1, newsize;
+
+  if( tailsize < 0 )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setaddnth): nth %lu is out-of-bounds for set:\n",
+            (unsigned long)nth);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  newsize = size - 1 + prepend;
+  newset = qh_setnew(newsize);
+  newset->e[newset->maxsize].i = newsize + 1;  /* may be overwritten */
+  oldp = SETaddr_(set, void);
+  newp = SETaddr_(newset, void) + prepend;
+
+  switch( nth )
+    {
+    case 0:
+      break;
+    case 1:
+      *(newp++) = *oldp++;
+      break;
+    case 2:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    case 3:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    case 4:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    default:
+      memcpy( (char *)newp, (char *)oldp, nth * SETelemsize);
+      newp += nth;
+      oldp += nth;
+      break;
+    }
+  oldp++;
+
+  switch( tailsize )
+    {
+    case 0:
+      break;
+    case 1:
+      *(newp++) = *oldp++;
+      break;
+    case 2:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    case 3:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    case 4:
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      *(newp++) = *oldp++;
+      break;
+    default:
+      memcpy( (char *)newp, (char *)oldp, tailsize * SETelemsize);
+      newp += tailsize;
+    }
+  *newp = NULL;
+  return newset;
+} /* setnew_delnthsorted */
+
+/*---------------------------------
+
+  qh_setprint( fp, string, set )
+  print set elements to fp with identifying string
+
+  notes:
+  never errors
+*/
+void qh_setprint(FILE *fp, const char* string, setT *set)
+{
+  if( !set )
+    {
+    fprintf(fp, "%s set is null\n", string);
+    }
+  else
+    {
+    int size;
+    SETreturnsize_(set, size);
+    fprintf(fp, "%s set=%p maxsize=%d size=%d elems=",
+            string, set, set->maxsize, size);
+    if( size > set->maxsize )
+      {
+      size = set->maxsize + 1;
+      }
+    for( int k = 0; k < size; k++ )
+      {
+      fprintf(fp, " %p", set->e[k].p);
+      }
+    fprintf(fp, "\n");
+    }
+} /* setprint */
+
+/*---------------------------------
+
+  qh_setreplace( set, oldelem, newelem )
+  replaces oldelem in set with newelem
+
+  notes:
+  errors if oldelem not in the set
+  newelem may be NULL, but it turns the set into an indexed set (no FOREACH)
+
+  design:
+  find oldelem
+  replace with newelem
+*/
+void qh_setreplace(setT *set, void *oldelem, void *newelem)
+{
+  void * *elemp;
+
+  elemp = SETaddr_(set, void);
+  while( *elemp != oldelem && *elemp )
+    {
+    elemp++;
+    }
+
+  if( *elemp )
+    {
+    *elemp = newelem;
+    }
+  else
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setreplace): elem %p not found in set\n",
+            oldelem);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+} /* setreplace */
+
+/*---------------------------------
+
+  qh_setsize( set )
+  returns the size of a set
+
+  notes:
+  errors if set's maxsize is incorrect
+  same as SETreturnsize_(set)
+
+  design:
+  determine actual size of set from maxsize
+*/
+int qh_setsize(setT *set)
+{
+  int size, *sizep;
+
+  if( !set )
+    {
+    return 0;
+    }
+  sizep = SETsizeaddr_(set);
+  if( (size = *sizep) )
+    {
+    size--;
+    if( size > set->maxsize )
+      {
+      fprintf(qhmem.ferr, "qhull internal error (qh_setsize): current set size %d is greater than maximum size %d\n",
+              size, set->maxsize);
+      qh_setprint(qhmem.ferr, "set: ", set);
+      qh_errexit(qhmem_ERRqhull, NULL, NULL);
+      }
+    }
+  else
+    {
+    size = set->maxsize;
+    }
+  return size;
+} /* setsize */
+
+/*---------------------------------
+
+  qh_settemp( setsize )
+  return a stacked, temporary set of upto setsize elements
+
+  notes:
+  use settempfree or settempfree_all to release from qhmem.tempstack
+  see also qh_setnew
+
+  design:
+  allocate set
+  append to qhmem.tempstack
+
+*/
+setT * qh_settemp(int setsize)
+{
+  setT *newset;
+
+  newset = qh_setnew(setsize);
+  qh_setappend( (setT * *)&qhmem.tempstack, newset);
+  if( qhmem.IStracing >= 5 )
+    {
+    fprintf(qhmem.ferr, "qh_settemp: temp set %p of %d elements, depth %d\n",
+            newset, newset->maxsize, qh_setsize( (setT *)qhmem.tempstack) );
+    }
+  return newset;
+} /* settemp */
+
+/*---------------------------------
+
+  qh_settempfree( set )
+  free temporary set at top of qhmem.tempstack
+
+  notes:
+  nop if set is NULL
+  errors if set not from previous   qh_settemp
+
+  to locate errors:
+  use 'T2' to find source and then find mis-matching qh_settemp
+
+  design:
+  check top of qhmem.tempstack
+  free it
+*/
+void qh_settempfree(setT * *set)
+{
+  setT *stackedset;
+
+  if( !*set )
+    {
+    return;
+    }
+  stackedset = qh_settemppop();
+  if( stackedset != *set )
+    {
+    qh_settemppush(stackedset);
+    fprintf(
+      qhmem.ferr,
+      "qhull internal error (qh_settempfree): set %p (size %d) was not last temporary allocated (depth %d, set %p, size %d)\n",
+      *set, qh_setsize(*set), qh_setsize( (setT *)qhmem.tempstack) + 1,
+      stackedset, qh_setsize(stackedset) );
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  qh_setfree(set);
+} /* settempfree */
+
+/*---------------------------------
+
+  qh_settempfree_all(  )
+  free all temporary sets in qhmem.tempstack
+
+  design:
+  for each set in tempstack
+  free set
+  free qhmem.tempstack
+*/
+void qh_settempfree_all(void)
+{
+  setT *set, * *setp;
+
+  FOREACHset_( (setT *)qhmem.tempstack)
+  qh_setfree(&set);
+  qh_setfree( (setT * *)&qhmem.tempstack);
+} /* settempfree_all */
+
+/*---------------------------------
+
+  qh_settemppop(  )
+  pop and return temporary set from qhmem.tempstack
+
+  notes:
+  the returned set is permanent
+
+  design:
+  pop and check top of qhmem.tempstack
+*/
+setT * qh_settemppop(void)
+{
+  setT *stackedset;
+
+  stackedset = (setT *)qh_setdellast( (setT *)qhmem.tempstack);
+  if( !stackedset )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_settemppop): pop from empty temporary stack\n");
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  if( qhmem.IStracing >= 5 )
+    {
+    fprintf(qhmem.ferr, "qh_settemppop: depth %d temp set %p of %d elements\n",
+            qh_setsize( (setT *)qhmem.tempstack) + 1, stackedset, qh_setsize(stackedset) );
+    }
+  return stackedset;
+} /* settemppop */
+
+/*---------------------------------
+
+  qh_settemppush( set )
+  push temporary set unto qhmem.tempstack (makes it temporary)
+
+  notes:
+  duplicates settemp() for tracing
+
+  design:
+  append set to tempstack
+*/
+void qh_settemppush(setT *set)
+{
+
+  qh_setappend( (setT * *)&qhmem.tempstack, set);
+  if( qhmem.IStracing >= 5 )
+    {
+    fprintf(qhmem.ferr, "qh_settemppush: depth %d temp set %p of %d elements\n",
+            qh_setsize( (setT *)qhmem.tempstack), set, qh_setsize(set) );
+    }
+} /* settemppush */
+
+/*---------------------------------
+
+  qh_settruncate( set, size )
+  truncate set to size elements
+
+  notes:
+  set must be defined
+
+  see:
+  SETtruncate_
+
+  design:
+  check size
+  update actual size of set
+*/
+void qh_settruncate(setT *set, size_t size)
+{
+
+  if( /* size < 0 || */ size > (size_t)set->maxsize )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_settruncate): size %lu out of bounds for set:\n",
+            (unsigned long)size);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  set->e[set->maxsize].i = size + 1;   /* maybe overwritten */
+  set->e[size].p = NULL;
+} /* settruncate */
+
+/*---------------------------------
+
+  qh_setunique( set, elem )
+  add elem to unsorted set unless it is already in set
+
+  notes:
+  returns 1 if it is appended
+
+  design:
+  if elem not in set
+  append elem to set
+*/
+int qh_setunique(setT * *set, void *elem)
+{
+
+  if( !qh_setin(*set, elem) )
+    {
+    qh_setappend(set, elem);
+    return 1;
+    }
+  return 0;
+} /* setunique */
+
+/*---------------------------------
+
+  qh_setzero( set, index, size )
+  zero elements from index on
+  set actual size of set to size
+
+  notes:
+  set must be defined
+  the set becomes an indexed set (can not use FOREACH...)
+
+  see also:
+  qh_settruncate
+
+  design:
+  check index and size
+  update actual size
+  zero elements starting at e[index]
+*/
+void qh_setzero(setT *set, int idx, int size)
+{
+  int count;
+
+  if( idx < 0 || idx >= size || size > set->maxsize )
+    {
+    fprintf(qhmem.ferr, "qhull internal error (qh_setzero): index %d or size %d out of bounds for set:\n", idx, size);
+    qh_setprint(qhmem.ferr, "", set);
+    qh_errexit(qhmem_ERRqhull, NULL, NULL);
+    }
+  set->e[set->maxsize].i =  size + 1; /* may be overwritten */
+  count = size - idx + 1;             /* +1 for NULL terminator */
+  memset( (char *)SETelemaddr_(set, idx, void), 0, count * SETelemsize);
+} /* setzero */
+
diff --git a/BRAINSABC/qhull/qset.h b/BRAINSABC/qhull/qset.h
new file mode 100644
index 00000000..8fa10319
--- /dev/null
+++ b/BRAINSABC/qhull/qset.h
@@ -0,0 +1,514 @@
+/*
  ---------------------------------
+
+   qset.h
+     header file for qset.c that implements set
+
+   see qh-set.htm and qset.c
+
+   only uses mem.c, malloc/free
+
+   for error handling, writes message and calls
+      qh_errexit (qhmem_ERRqhull, NULL, NULL);
+
+   set operations satisfy the following properties:
+    - sets have a max size, the actual size (if different) is stored at the end
+    - every set is NULL terminated
+    - sets may be sorted or unsorted, the caller must distinguish this
+
+   copyright (c) 1993-2003, The Geometry Center
+*/
+
+#ifndef qhDEFset
+#define qhDEFset 1
+
+/*================= -structures- ===============*/
+
+#ifndef DEFsetT
+#define DEFsetT 1
+typedef struct setT setT;   /* a set is a sorted or unsorted array of pointers
+                              */
+#endif
+
+/*------------------------------------------
+
+setT
+  a set or list of pointers with maximum size and actual size.
+
+variations:
+  unsorted, unique   -- a list of unique pointers with NULL terminator
+           user guarantees uniqueness
+  sorted             -- a sorted list of unique pointers with NULL terminator
+           qset.c guarantees uniqueness
+  unsorted           -- a list of pointers terminated with NULL
+  indexed        -- an array of pointers with NULL elements
+
+structure for set of n elements:
+
+  --------------
+  |  maxsize
+  --------------
+  |  e[0] - a pointer, may be NULL for indexed sets
+  --------------
+  |  e[1]
+
+  --------------
+  |  ...
+  --------------
+  |  e[n-1]
+  --------------
+  |  e[n] = NULL
+  --------------
+  |  ...
+  --------------
+  |  e[maxsize] - n+1 or NULL (determines actual size of set)
+  --------------
+
+*/
+
+/*-- setelemT -- internal type to allow both pointers and indices
+*/
+typedef union setelemT setelemT;
+union setelemT
+  {
+  void *p;
+  int i;              /* integer used for e[maxSize] */
+  };
+
+struct setT
+  {
+  int maxsize;          /* maximum number of elements (except NULL) */
+  setelemT e[1];        /* array of pointers, tail is NULL */
+                        /* last slot (unless NULL) is actual size+1
+                           e[maxsize]==NULL or e[e[maxsize]-1]==NULL */
+                        /* this may generate a warning since e[] contains
+         maxsize elements */
+  };
+
+/*=========== -constants- =========================*/
+
+/*-------------------------------------
+
+  SETelemsize
+    size of a set element in bytes
+*/
+#define SETelemsize sizeof( setelemT )
+
+/*=========== -macros- =========================*/
+
+/*-------------------------------------
+
+   FOREACHsetelement_(type, set, variable)
+     define FOREACH iterator
+
+   declare:
+     assumes *variable and **variablep are declared
+     no space in "variable)" [DEC Alpha cc compiler]
+
+   each iteration:
+     variable is set element
+     variablep is one beyond variable.
+
+   to repeat an element:
+     variablep--; / *repeat* /
+
+   at exit:
+     variable is NULL at end of loop
+
+   example:
+     #define FOREACHfacet_( facets ) FOREACHsetelement_( facetT, facets, facet )
+
+   notes:
+     use FOREACHsetelement_i_() if need index or include NULLs
+
+   WARNING:
+     nested loops can't use the same variable (define another FOREACH)
+
+     needs braces if nested inside another FOREACH
+     this includes intervening blocks, e.g. FOREACH...{ if () FOREACH...} )
+*/
+#define FOREACHsetelement_(type, set, variable)         \
+  if( ( ( variable = NULL ), set ) ) for(             \
+      variable##p = (type * *)&( ( set )->e[0].p );      \
+      ( variable = *variable##p++ ); )
+
+/*------------------------------------------
+
+   FOREACHsetelement_i_(type, set, variable)
+     define indexed FOREACH iterator
+
+   declare:
+     type *variable, variable_n, variable_i;
+
+   each iteration:
+     variable is set element, may be NULL
+     variable_i is index, variable_n is qh_setsize()
+
+   to repeat an element:
+     variable_i--; variable_n-- repeats for deleted element
+
+   at exit:
+     variable==NULL and variable_i==variable_n
+
+   example:
+     #define FOREACHfacet_i_( facets ) FOREACHsetelement_i_( facetT, facets, facet )
+
+   WARNING:
+     nested loops can't use the same variable (define another FOREACH)
+
+     needs braces if nested inside another FOREACH
+     this includes intervening blocks, e.g. FOREACH...{ if () FOREACH...} )
+*/
+#define FOREACHsetelement_i_(type, set, variable)               \
+  if( ( ( variable = NULL ), set ) ) for(                     \
+      variable##_i = 0, variable = (type *)( ( set )->e[0].p ), \
+      variable##_n = qh_setsize(set);                         \
+      variable##_i < variable##_n;                            \
+      variable = (type *)( ( set )->e[++variable##_i].p ) )
+
+/*----------------------------------------
+
+   FOREACHsetelementreverse_(type, set, variable)-
+     define FOREACH iterator in reverse order
+
+   declare:
+     assumes *variable and **variablep are declared
+     also declare 'int variabletemp'
+
+   each iteration:
+     variable is set element
+
+   to repeat an element:
+     variabletemp++; / *repeat* /
+
+   at exit:
+     variable is NULL
+
+   example:
+     #define FOREACHvertexreverse_( vertices ) FOREACHsetelementreverse_( vertexT, vertices, vertex )
+
+   notes:
+     use FOREACHsetelementreverse12_() to reverse first two elements
+     WARNING: needs braces if nested inside another FOREACH
+*/
+#define FOREACHsetelementreverse_(type, set, variable)                  \
+  if( ( ( variable = NULL ), set ) ) for(                             \
+      variable##temp = qh_setsize(set) - 1, variable = qh_setlast(set); \
+      variable; variable                                                  \
+        = ( ( --variable##temp >= 0 ) ? SETelemt_(set, variable##temp, type) : NULL ) )
+
+/*-------------------------------------
+
+   FOREACHsetelementreverse12_(type, set, variable)-
+     define FOREACH iterator with e[1] and e[0] reversed
+
+   declare:
+     assumes *variable and **variablep are declared
+
+   each iteration:
+     variable is set element
+     variablep is one after variable.
+
+   to repeat an element:
+     variablep--; / *repeat* /
+
+   at exit:
+     variable is NULL at end of loop
+
+   example
+     #define FOREACHvertexreverse12_( vertices ) FOREACHsetelementreverse12_( vertexT, vertices, vertex )
+
+   notes:
+     WARNING: needs braces if nested inside another FOREACH
+*/
+#define FOREACHsetelementreverse12_(type, set, variable)                \
+  if( ( ( variable = NULL ), set ) ) for(                             \
+      variable##p = (type * *)&( ( set )->e[1].p );                      \
+      ( variable = *variable##p );                                      \
+      variable##p == ( (type * *)&( ( set )->e[0].p ) ) ? variable##p += 2 : \
+        ( variable##p ==                                                \
+          ( (type * *)&( ( set )->e[1].p ) ) ?                             \
+          variable##p-- : variable##p++ ) )
+
+/*-------------------------------------
+
+   FOREACHelem_( set )-
+     iterate elements in a set
+
+   declare:
+     void *elem, *elemp;
+
+   each iteration:
+     elem is set element
+     elemp is one beyond
+
+   to repeat an element:
+     elemp--; / *repeat* /
+
+   at exit:
+     elem == NULL at end of loop
+
+   example:
+     FOREACHelem_(set) {
+
+   notes:
+     WARNING: needs braces if nested inside another FOREACH
+*/
+#define FOREACHelem_(set) FOREACHsetelement_(void, set, elem)
+
+/*-------------------------------------
+
+   FOREACHset_( set )-
+     iterate a set of sets
+
+   declare:
+     setT *set, **setp;
+
+   each iteration:
+     set is set element
+     setp is one beyond
+
+   to repeat an element:
+     setp--; / *repeat* /
+
+   at exit:
+     set == NULL at end of loop
+
+   example
+     FOREACHset_(sets) {
+
+   notes:
+     WARNING: needs braces if nested inside another FOREACH
+*/
+#define FOREACHset_(sets) FOREACHsetelement_(setT, sets, set)
+
+/*-------------------------------------------
+
+   SETindex_( set, elem )
+     return index of elem in set
+
+   notes:
+     for use with FOREACH iteration
+
+   example:
+     i= SETindex_(ridges, ridge)
+*/
+#define SETindex_(set, elem) ( (void * *)elem##p - (void * *)&( set )->e[1].p )
+
+/*-----------------------------------------
+
+   SETref_( elem )
+     l.h.s. for modifying the current element in a FOREACH iteration
+
+   example:
+     SETref_(ridge)= anotherridge;
+*/
+#define SETref_(elem) ( elem##p[-1] )
+
+/*-----------------------------------------
+
+   SETelem_(set, n)
+     return the n'th element of set
+
+   notes:
+      assumes that n is valid [0..size] and that set is defined
+      use SETelemt_() for type cast
+*/
+#define SETelem_(set, n)           ( ( set )->e[n].p )
+
+/*-----------------------------------------
+
+   SETelemt_(set, n, type)
+     return the n'th element of set as a type
+
+   notes:
+      assumes that n is valid [0..size] and that set is defined
+*/
+#define SETelemt_(set, n, type)    ( (type *)( ( set )->e[n].p ) )
+
+/*-----------------------------------------
+
+   SETelemaddr_(set, n, type)
+     return address of the n'th element of a set
+
+   notes:
+      assumes that n is valid [0..size] and set is defined
+*/
+#define SETelemaddr_(set, n, type) ( (type * *)( &( ( set )->e[n].p ) ) )
+
+/*-----------------------------------------
+
+   SETfirst_(set)
+     return first element of set
+
+*/
+#define SETfirst_(set)             ( ( set )->e[0].p )
+
+/*-----------------------------------------
+
+   SETfirstt_(set, type)
+     return first element of set as a type
+
+*/
+#define SETfirstt_(set, type)      ( (type *)( ( set )->e[0].p ) )
+
+/*-----------------------------------------
+
+   SETsecond_(set)
+     return second element of set
+
+*/
+#define SETsecond_(set)            ( ( set )->e[1].p )
+
+/*-----------------------------------------
+
+   SETsecondt_(set, type)
+     return second element of set as a type
+*/
+#define SETsecondt_(set, type)     ( (type *)( ( set )->e[1].p ) )
+
+/*-----------------------------------------
+
+   SETaddr_(set, type)
+       return address of set's elements
+*/
+#define SETaddr_(set, type)     ( (type * *)( &( ( set )->e[0].p ) ) )
+
+/*-----------------------------------------
+
+   SETreturnsize_(set, size)
+     return size of a set
+
+   notes:
+      set must be defined
+      use qh_setsize(set) unless speed is critical
+*/
+#define SETreturnsize_(set,                                             \
+                       size) ( ( ( size ) = ( ( set )->e[( set )->maxsize].i ) ) ? ( --( size ) ) : ( ( size ) \
+                                                                                                        = ( set )-> \
+                                                                                                          maxsize ) )
+
+/*-----------------------------------------
+
+   SETempty_(set)
+     return true (1) if set is empty
+
+   notes:
+      set may be NULL
+*/
+#define SETempty_(set)            ( !set || ( SETfirst_(set) ? 0 : 1 ) )
+
+/*-----------------------------------------
+
+   SETtruncate_(set)
+     return first element of set
+
+   see:
+     qh_settruncate()
+
+*/
+#define SETtruncate_(set, size)                 \
+    {set->e[set->maxsize].i = size + 1; /*
+                                                                           maybe
+                                                                           overwritten
+                                                                           */ \
+    set->e[size].p = NULL; }
+
+/*======= prototypes in alphabetical order ============*/
+
+void  qh_setaddsorted(setT * *setp, void *elem);
+
+void  qh_setaddnth(setT * *setp, int nth, void *newelem);
+
+void  qh_setappend(setT * *setp, void *elem);
+
+void  qh_setappend_set(setT * *setp, setT *setA);
+
+void  qh_setappend2ndlast(setT * *setp, void *elem);
+
+void  qh_setcheck(setT *set, const char *tname, unsigned id);
+
+void  qh_setcompact(setT *set);
+
+setT * qh_setcopy(setT *set, int extra);
+
+void * qh_setdel(setT *set, void *elem);
+
+void * qh_setdellast(setT *set);
+
+void * qh_setdelnth(setT *set, size_t nth);
+
+void * qh_setdelnthsorted(setT *set, size_t nth);
+
+void * qh_setdelsorted(setT *set, void *newelem);
+
+setT * qh_setduplicate( setT *set, int elemsize);
+
+int   qh_setequal(setT *setA, setT *setB);
+
+int   qh_setequal_except(setT *setA, void *skipelemA, setT *setB, void *skipelemB);
+
+int   qh_setequal_skip(setT *setA, int skipA, setT *setB, int skipB);
+
+void  qh_setfree(setT * *set);
+
+void  qh_setfree2( setT * *setp, int elemsize);
+
+void  qh_setfreelong(setT * *set);
+
+int   qh_setin(setT *set, void *setelem);
+
+int   qh_setindex(setT *set, void *setelem);
+
+void  qh_setlarger(setT * *setp);
+
+void * qh_setlast(setT *set);
+
+setT * qh_setnew(int size);
+
+setT * qh_setnew_delnthsorted(setT *set, int size, size_t nth, size_t prepend);
+
+void  qh_setprint(FILE *fp, const char *string, setT *set);
+
+void  qh_setreplace(setT *set, void *oldelem, void *newelem);
+
+int   qh_setsize(setT *set);
+
+setT * qh_settemp(int setsize);
+
+void  qh_settempfree(setT * *set);
+
+void  qh_settempfree_all(void);
+
+setT * qh_settemppop(void);
+
+void  qh_settemppush(setT *set);
+
+void  qh_settruncate(setT *set, size_t size);
+
+int   qh_setunique(setT * *set, void *elem);
+
+void  qh_setzero(setT *set, int idx, int size);
+
+#endif /* qhDEFset */
diff --git a/BRAINSABC/qhull/qvoronoi.c b/BRAINSABC/qhull/qvoronoi.c
new file mode 100644
index 00000000..8f20b839
--- /dev/null
+++ b/BRAINSABC/qhull/qvoronoi.c
@@ -0,0 +1,349 @@
+/*
  ---------------------------------
+
+  qvoronoi.c
+  compute Voronoi diagrams and furthest-point Voronoi
+  diagrams using qhull
+
+  see unix.c for full interface
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+
+#if __MWERKS__ && __POWERPC__
+#include 
+#include 
+#include 
+#include 
+
+#elif __cplusplus
+extern "C" {
+int isatty(int);
+
+}
+
+#elif _MSC_VER
+#include 
+#define isatty _isatty
+
+#else
+int isatty(int);   /* returns 1 if stdin is a tty
+          if "Undefined symbol" this can be deleted along with call in main() */
+
+#endif
+
+/*---------------------------------
+
+  qh_prompt
+  long prompt for qhull
+
+  notes:
+  restricted version of qhull.c
+
+  see:
+  concise prompt below
+*/
+
+/* duplicated in qvoron_f.htm and qvoronoi.htm */
+char hidden_options[] =
+  " d n m v H U Qb QB Qc Qf Qg Qi Qm Qr QR Qv Qx TR E V Fa FA FC Fp FS Ft FV Pv Gt Q0 Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 ";
+
+char qh_prompta[] =
+  "\n\
+qvoronoi- compute the Voronoi diagram\n\
+    http://www.qhull.org  %s\n\
+\n\
+input (stdin):\n\
+    first lines: dimension and number of points (or vice-versa).\n\
+    other lines: point coordinates, best if one point per line\n\
+    comments:    start with a non-numeric character\n\
+\n\
+options:\n\
+    Qu   - compute furthest-site Voronoi diagram\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+\n\
+Qhull control options:\n\
+    Qz   - add point-at-infinity to Voronoi diagram\n\
+    QJn  - randomly joggle input in range [-n,n]\n\
+%s%s%s%s"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ; /*
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    split
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    up
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    qh_prompt
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    for
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Visual
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    C++
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    */
+char qh_promptb[] =
+  "\
+    Qs   - search all points for the initial simplex\n\
+    QGn  - Voronoi vertices if visible from point n, -n if not\n\
+    QVn  - Voronoi vertices for input point n, -n if not\n\
+\n\
+"                                                                                                                                                                                               ;
+char qh_promptc[] =
+  "\
+Trace options:\n\
+    T4   - trace at level n, 4=all, 5=mem/gauss, -1= events\n\
+    Tc   - check frequently during execution\n\
+    Ts   - statistics\n\
+    Tv   - verify result: structure, convexity, and in-circle test\n\
+    Tz   - send all output to stdout\n\
+    TFn  - report summary when n or more facets created\n\
+    TI file - input data from file, no spaces or single quotes\n\
+    TO file - output results to file, may be enclosed in single quotes\n\
+    TPn  - turn on tracing when point n added to hull\n\
+     TMn - turn on tracing at merge n\n\
+     TWn - trace merge facets when width > n\n\
+    TVn  - stop qhull after adding point n, -n for before (see TCn)\n\
+     TCn - stop qhull after building cone for point n (see TVn)\n\
+\n\
+Precision options:\n\
+    Cn   - radius of centrum (roundoff added).  Merge facets if non-convex\n\
+     An  - cosine of maximum angle.  Merge facets if cosine > n or non-convex\n\
+           C-0 roundoff, A-0.99/C-0.01 pre-merge, A0.99/C0.01 post-merge\n\
+    Rn   - randomly perturb computations by a factor of [1-n,1+n]\n\
+    Wn   - min facet width for non-coincident point (before roundoff)\n\
+\n\
+Output formats (may be combined; if none, produces a summary to stdout):\n\
+    s    - summary to stderr\n\
+    p    - Voronoi vertices\n\
+    o    - OFF format (dim, Voronoi vertices, and Voronoi regions)\n\
+    i    - Delaunay regions (use 'Pp' to avoid warning)\n\
+    f    - facet dump\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ;
+char qh_promptd[] =
+  "\
+More formats:\n\
+    Fc   - count plus coincident points (by Voronoi vertex)\n\
+    Fd   - use cdd format for input (homogeneous with offset first)\n\
+    FD   - use cdd format for output (offset first)\n\
+    FF   - facet dump without ridges\n\
+    Fi   - separating hyperplanes for bounded Voronoi regions\n\
+    FI   - ID for each Voronoi vertex\n\
+    Fm   - merge count for each Voronoi vertex (511 max)\n\
+    Fn   - count plus neighboring Voronoi vertices for each Voronoi vertex\n\
+    FN   - count and Voronoi vertices for each Voronoi region\n\
+    Fo   - separating hyperplanes for unbounded Voronoi regions\n\
+    FO   - options and precision constants\n\
+    FP   - nearest point and distance for each coincident point\n\
+    FQ   - command used for qvoronoi\n\
+    Fs   - summary: #int (8), dimension, #points, tot vertices, tot facets,\n\
+                    for output: #Voronoi regions, #Voronoi vertices,\n\
+                                #coincident points, #non-simplicial regions\n\
+                    #real (2), max outer plane and min vertex\n\
+    Fv   - Voronoi diagram as Voronoi vertices between adjacent input sites\n\
+    Fx   - extreme points of Delaunay triangulation (on convex hull)\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ;
+char qh_prompte[] =
+  "\
+Geomview options (2-d only)\n\
+    Ga   - all points as dots\n\
+     Gp  -  coplanar points and vertices as radii\n\
+     Gv  -  vertices as spheres\n\
+    Gi   - inner planes only\n\
+     Gn  -  no planes\n\
+     Go  -  outer planes only\n\
+    Gc	 - centrums\n\
+    Gh   - hyperplane intersections\n\
+    Gr   - ridges\n\
+    GDn  - drop dimension n in 3-d and 4-d output\n\
+\n\
+Print options:\n\
+    PAn  - keep n largest Voronoi vertices by 'area'\n\
+    Pdk:n - drop facet if normal[k] <= n (default 0.0)\n\
+    PDk:n - drop facet if normal[k] >= n\n\
+    Pg   - print good Voronoi vertices (needs 'QGn' or 'QVn')\n\
+    PFn  - keep Voronoi vertices whose 'area' is at least n\n\
+    PG   - print neighbors of good Voronoi vertices\n\
+    PMn  - keep n Voronoi vertices with most merges\n\
+    Po   - force output.  If error, output neighborhood of facet\n\
+    Pp   - do not report precision problems\n\
+\n\
+    .    - list of all options\n\
+    -    - one line descriptions of all options\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt2
+  synopsis for qhull
+*/
+char qh_prompt2[] =
+  "\n\
+qvoronoi- compute the Voronoi diagram.  Qhull %s\n\
+    input (stdin): dimension, number of points, point coordinates\n\
+    comments start with a non-numeric character\n\
+\n\
+options (qvoronoi.htm):\n\
+    Qu   - compute furthest-site Voronoi diagram\n\
+    Qt   - triangulated output\n\
+    QJ   - joggled input instead of merged facets\n\
+    Tv   - verify result: structure, convexity, and in-circle test\n\
+    .    - concise list of all options\n\
+    -    - one-line description of all options\n\
+\n\
+output options (subset):\n\
+    s    - summary of results (default)\n\
+    p    - Voronoi vertices\n\
+    o    - OFF file format (dim, Voronoi vertices, and Voronoi regions)\n\
+    FN   - count and Voronoi vertices for each Voronoi region\n\
+    Fv   - Voronoi diagram as Voronoi vertices between adjacent input sites\n\
+    Fi   - separating hyperplanes for bounded regions, 'Fo' for unbounded\n\
+    G    - Geomview output (2-d only)\n\
+    QVn  - Voronoi vertices for input point n, -n if not\n\
+    TO file- output results to file, may be enclosed in single quotes\n\
+\n\
+examples:\n\
+rbox c P0 D2 | qvoronoi s o         rbox c P0 D2 | qvoronoi Fi\n\
+rbox c P0 D2 | qvoronoi Fo          rbox c P0 D2 | qvoronoi Fv\n\
+rbox c P0 D2 | qvoronoi s Qu Fv     rbox c P0 D2 | qvoronoi Qu Fo\n\
+rbox c G1 d D2 | qvoronoi s p       rbox c G1 d D2 | qvoronoi QJ s p\n\
+rbox c P0 D2 | qvoronoi s Fv QV0\n\
+\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ;
+/* for opts, don't assign 'e' or 'E' to a flag (already used for exponent) */
+
+/*---------------------------------
+
+  qh_prompt3
+  concise prompt for qhull
+*/
+char qh_prompt3[] =
+  "\n\
+Qhull %s.\n\
+Except for 'F.' and 'PG', upper-case options take an argument.\n\
+\n\
+ OFF_format     p_vertices     i_delaunay     summary        facet_dump\n\
+\n\
+ Fcoincident    Fd_cdd_in      FD_cdd_out     FF-dump-xridge Fi_bounded\n\
+ Fxtremes       Fmerges        Fneighbors     FNeigh_region  FOptions\n\
+ Fo_unbounded   FPoint_near    FQvoronoi      Fsummary       Fvoronoi\n\
+ FIDs\n\
+\n\
+ Gvertices      Gpoints        Gall_points    Gno_planes     Ginner\n\
+ Gcentrums      Ghyperplanes   Gridges        Gouter         GDrop_dim\n\
+\n\
+ PArea_keep     Pdrop d0:0D0   Pgood          PFacet_area_keep\n\
+ PGood_neighbors PMerge_keep   Poutput_forced Pprecision_not\n\
+\n\
+ QG_vertex_good QJoggle        Qsearch_1st    Qtriangulate   Qupper_voronoi\n\
+ QV_point_good  Qzinfinite\n\
+\n\
+ T4_trace       Tcheck_often   Tstatistics    Tverify        Tz_stdout\n\
+ TFacet_log     TInput_file    TPoint_trace   TMerge_trace   TOutput_file\n\
+ TWide_trace    TVertex_stop   TCone_stop\n\
+\n\
+ Angle_max      Centrum_size   Random_dist    Wide_outside\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ;
+
+/*---------------------------------
+
+  main( argc, argv )
+  processes the command line, calls qhull() to do the work, and exits
+
+  design:
+  initializes data structures
+  reads points
+  finishes initialization
+  computes convex hull and other structures
+  checks the result
+  writes the output
+  frees memory
+*/
+int main(int argc, char *argv[])
+{
+  int     curlong, totlong; /* used !qh_NOmem */
+  int     exitcode, numpoints, dim;
+  coordT *points;
+  boolT   ismalloc;
+
+#if __MWERKS__ && __POWERPC__
+  char inBuf[BUFSIZ], outBuf[BUFSIZ], errBuf[BUFSIZ];
+  SIOUXSettings.showstatusline = false;
+  SIOUXSettings.tabspaces = 1;
+  SIOUXSettings.rows = 40;
+  if( setvbuf(stdin, inBuf, _IOFBF, sizeof(inBuf) ) < 0   /* w/o, SIOUX I/O is
+                                                            slow*/
+      || setvbuf(stdout, outBuf, _IOFBF, sizeof(outBuf) ) < 0
+      || (stdout != stderr && setvbuf(stderr, errBuf, _IOFBF, sizeof(errBuf) ) < 0) )
+    {
+    fprintf(stderr, "qhull internal warning (main): could not change stdio to fully buffered.\n");
+    }
+  argc = ccommand(&argv);
+#endif
+
+  if( (argc == 1) && isatty( 0 /*stdin*/) )
+    {
+    fprintf(stdout, qh_prompt2, qh_version);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '-' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompta, qh_version,
+            qh_promptb, qh_promptc, qh_promptd, qh_prompte);
+    exit(qh_ERRnone);
+    }
+  if( argc > 1 && *argv[1] == '.' && !*(argv[1] + 1) )
+    {
+    fprintf(stdout, qh_prompt3, qh_version);
+    exit(qh_ERRnone);
+    }
+  qh_init_A(stdin, stdout, stderr, argc, argv); /* sets qh qhull_command */
+  exitcode = setjmp(qh errexit);                /* simple statement for CRAY
+                                                  J916 */
+  if( !exitcode )
+    {
+    qh_option("voronoi  _bbound-last  _coplanar-keep", NULL, NULL);
+    qh DELAUNAY = True;     /* 'v'   */
+    qh VORONOI = True;
+    qh SCALElast = True;    /* 'Qbb' */
+    qh_checkflags(qh qhull_command, hidden_options);
+    qh_initflags(qh qhull_command);
+    points = qh_readpoints(&numpoints, &dim, &ismalloc);
+    if( dim >= 5 )
+      {
+      qh_option("_merge-exact", NULL, NULL);
+      qh MERGEexact = True; /* 'Qx' always */
+      }
+    qh_init_B(points, numpoints, dim, ismalloc);
+    qh_qhull();
+    qh_check_output();
+    qh_produce_output();
+    if( qh VERIFYoutput && !qh FORCEoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    exitcode = qh_ERRnone;
+    }
+  qh NOerrexit = True;  /* no more setjmp */
+#ifdef qh_NOmem
+  qh_freeqhull( True);
+#else
+  qh_freeqhull( False);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(stderr, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+#endif
+  return exitcode;
+} /* main */
+
diff --git a/BRAINSABC/qhull/stat.c b/BRAINSABC/qhull/stat.c
new file mode 100644
index 00000000..1a6abdca
--- /dev/null
+++ b/BRAINSABC/qhull/stat.c
@@ -0,0 +1,838 @@
+/*
  ---------------------------------
+
+  stat.c
+  contains all statistics that are collected for qhull
+
+  see qh-stat.htm and stat.h
+
+  copyright (c) 1993-2003, The Geometry Center
+*/
+
+#include "qhull_a.h"
+
+/*============ global data structure ==========*/
+
+#if qh_QHpointer
+qhstatT *qh_qhstat = NULL;  /* global data structure */
+#else
+qhstatT qh_qhstat;   /* add "={0}" if this causes a compiler error */
+#endif
+
+/*========== functions in alphabetic order ================*/
+
+/*---------------------------------
+
+  qh_allstatA()
+  define statistics in groups of 20
+
+  notes:
+  (otherwise, 'gcc -O2' uses too much memory)
+  uses qhstat.next
+*/
+void qh_allstatA(void)
+{
+
+  /* zdef_(type,name,doc,average) */
+  zzdef_(zdoc, Zdoc2, "precision statistics", -1);
+  zdef_(zinc, Znewvertex, NULL, -1);
+  zdef_(wadd, Wnewvertex, "ave. distance of a new vertex to a facet (not 0s)", Znewvertex);
+  zzdef_(wmax, Wnewvertexmax, "max. distance of a new vertex to a facet", -1);
+  zdef_(wmax, Wvertexmax, "max. distance of an output vertex to a facet", -1);
+  zdef_(wmin, Wvertexmin, "min. distance of an output vertex to a facet", -1);
+  zdef_(wmin, Wmindenom, "min. denominator in hyperplane computation", -1);
+
+  qhstat precision = qhstat next;  /* call qh_precision for each of these */
+  zzdef_(zdoc, Zdoc3, "precision problems (corrected unless 'Q0' or an error)", -1);
+  zzdef_(zinc, Zcoplanarridges, "coplanar half ridges in output", -1);
+  zzdef_(zinc, Zconcaveridges, "concave half ridges in output", -1);
+  zzdef_(zinc, Zflippedfacets, "flipped facets", -1);
+  zzdef_(zinc, Zcoplanarhorizon, "coplanar horizon facets for new vertices", -1);
+  zzdef_(zinc, Zcoplanarpart, "coplanar points during partitioning", -1);
+  zzdef_(zinc, Zminnorm, "degenerate hyperplanes recomputed with gaussian elimination", -1);
+  zzdef_(zinc, Znearlysingular, "nearly singular or axis-parallel hyperplanes", -1);
+  zzdef_(zinc, Zback0, "zero divisors during back substitute", -1);
+  zzdef_(zinc, Zgauss0, "zero divisors during gaussian elimination", -1);
+  zzdef_(zinc, Zmultiridge, "ridges with multiple neighbors", -1);
+}
+
+void qh_allstatB(void)
+{
+  zzdef_(zdoc, Zdoc1, "summary information", -1);
+  zdef_(zinc, Zvertices, "number of vertices in output", -1);
+  zdef_(zinc, Znumfacets, "number of facets in output", -1);
+  zdef_(zinc, Znonsimplicial, "number of non-simplicial facets in output", -1);
+  zdef_(zinc, Znowsimplicial, "number of simplicial facets that were merged", -1);
+  zdef_(zinc, Znumridges, "number of ridges in output", -1);
+  zdef_(zadd, Znumridges, "average number of ridges per facet", Znumfacets);
+  zdef_(zmax, Zmaxridges, "maximum number of ridges", -1);
+  zdef_(zadd, Znumneighbors, "average number of neighbors per facet", Znumfacets);
+  zdef_(zmax, Zmaxneighbors, "maximum number of neighbors", -1);
+  zdef_(zadd, Znumvertices, "average number of vertices per facet", Znumfacets);
+  zdef_(zmax, Zmaxvertices, "maximum number of vertices", -1);
+  zdef_(zadd, Znumvneighbors, "average number of neighbors per vertex", Zvertices);
+  zdef_(zmax, Zmaxvneighbors, "maximum number of neighbors", -1);
+  zdef_(wadd, Wcpu, "cpu seconds for qhull after input", -1);
+  zdef_(zinc, Ztotvertices, "vertices created altogether", -1);
+  zzdef_(zinc, Zsetplane, "facets created altogether", -1);
+  zdef_(zinc, Ztotridges, "ridges created altogether", -1);
+  zdef_(zinc, Zpostfacets, "facets before post merge", -1);
+  zdef_(zadd, Znummergetot, "average merges per facet (at most 511)", Znumfacets);
+  zdef_(zmax, Znummergemax, "  maximum merges for a facet (at most 511)", -1);
+  zdef_(zinc, Zangle, NULL, -1);
+  zdef_(wadd, Wangle, "average angle (cosine) of facet normals for all ridges", Zangle);
+  zdef_(wmax, Wanglemax, "  maximum angle (cosine) of facet normals across a ridge", -1);
+  zdef_(wmin, Wanglemin, "  minimum angle (cosine) of facet normals across a ridge", -1);
+  zdef_(wadd, Wareatot, "total area of facets", -1);
+  zdef_(wmax, Wareamax, "  maximum facet area", -1);
+  zdef_(wmin, Wareamin, "  minimum facet area", -1);
+}
+
+void qh_allstatC(void)
+{
+  zdef_(zdoc, Zdoc9, "build hull statistics", -1);
+  zzdef_(zinc, Zprocessed, "points processed", -1);
+  zzdef_(zinc, Zretry, "retries due to precision problems", -1);
+  zdef_(wmax, Wretrymax, "  max. random joggle", -1);
+  zdef_(zmax, Zmaxvertex, "max. vertices at any one time", -1);
+  zdef_(zinc, Ztotvisible, "ave. visible facets per iteration", Zprocessed);
+  zdef_(zinc, Zinsidevisible, "  ave. visible facets without an horizon neighbor", Zprocessed);
+  zdef_(zadd, Zvisfacettot,  "  ave. facets deleted per iteration", Zprocessed);
+  zdef_(zmax, Zvisfacetmax,  "    maximum", -1);
+  zdef_(zadd, Zvisvertextot, "ave. visible vertices per iteration", Zprocessed);
+  zdef_(zmax, Zvisvertexmax, "    maximum", -1);
+  zdef_(zinc, Ztothorizon, "ave. horizon facets per iteration", Zprocessed);
+  zdef_(zadd, Znewfacettot,  "ave. new or merged facets per iteration", Zprocessed);
+  zdef_(zmax, Znewfacetmax,  "    maximum (includes initial simplex)", -1);
+  zdef_(wadd, Wnewbalance, "average new facet balance", Zprocessed);
+  zdef_(wadd, Wnewbalance2, "  standard deviation", -1);
+  zdef_(wadd, Wpbalance, "average partition balance", Zpbalance);
+  zdef_(wadd, Wpbalance2, "  standard deviation", -1);
+  zdef_(zinc, Zpbalance, "  number of trials", -1);
+  zdef_(zinc, Zsearchpoints, "searches of all points for initial simplex", -1);
+  zdef_(zinc, Zdetsimplex, "determinants computed (area & initial hull)", -1);
+  zdef_(zinc, Znoarea, "determinants not computed because vertex too low", -1);
+  zdef_(zinc, Znotmax, "points ignored (not above max_outside)", -1);
+  zdef_(zinc, Znotgood, "points ignored (not above a good facet)", -1);
+  zdef_(zinc, Znotgoodnew, "points ignored (didn't create a good new facet)", -1);
+  zdef_(zinc, Zgoodfacet, "good facets found", -1);
+  zzdef_(zinc, Znumvisibility, "distance tests for facet visibility", -1);
+  zdef_(zinc, Zdistvertex, "distance tests to report minimum vertex", -1);
+  zdef_(zinc, Ztotcheck, "points checked for facets' outer planes", -1);
+  zzdef_(zinc, Zcheckpart, "  ave. distance tests per check", Ztotcheck);
+}
+
+void qh_allstatD(void)
+{
+  zdef_(zdoc, Zdoc4, "partitioning statistics (see previous for outer planes)", -1);
+  zzdef_(zadd, Zdelvertextot, "total vertices deleted", -1);
+  zdef_(zmax, Zdelvertexmax, "    maximum vertices deleted per iteration", -1);
+  zdef_(zinc, Zfindbest, "calls to findbest", -1);
+  zdef_(zadd, Zfindbesttot, " ave. facets tested", Zfindbest);
+  zdef_(zmax, Zfindbestmax, " max. facets tested", -1);
+  zdef_(zadd, Zfindcoplanar, " ave. coplanar search", Zfindbest);
+  zdef_(zinc, Zfindnew, "calls to findbestnew", -1);
+  zdef_(zadd, Zfindnewtot, " ave. facets tested", Zfindnew);
+  zdef_(zmax, Zfindnewmax, " max. facets tested", -1);
+  zdef_(zinc, Zfindnewjump, " ave. clearly better", Zfindnew);
+  zdef_(zinc, Zfindnewsharp, " calls due to qh_sharpnewfacets", -1);
+  zdef_(zinc, Zfindhorizon, "calls to findhorizon", -1);
+  zdef_(zadd, Zfindhorizontot, " ave. facets tested", Zfindhorizon);
+  zdef_(zmax, Zfindhorizonmax, " max. facets tested", -1);
+  zdef_(zinc, Zfindjump,       " ave. clearly better", Zfindhorizon);
+  zdef_(zinc, Zparthorizon, " horizon facets better than bestfacet", -1);
+  zdef_(zinc, Zpartangle, "angle tests for repartitioned coplanar points", -1);
+  zdef_(zinc, Zpartflip, "  repartitioned coplanar points for flipped orientation", -1);
+}
+
+void qh_allstatE(void)
+{
+  zdef_(zinc, Zpartinside, "inside points", -1);
+  zdef_(zinc, Zpartnear, "  inside points kept with a facet", -1);
+  zdef_(zinc, Zcoplanarinside, "  inside points that were coplanar with a facet", -1);
+  zdef_(zinc, Zbestlower, "calls to findbestlower", -1);
+  zdef_(zinc, Zbestlowerv, "  with search of vertex neighbors", -1);
+  zdef_(wadd, Wmaxout, "difference in max_outside at final check", -1);
+  zzdef_(zinc, Zpartitionall, "distance tests for initial partition", -1);
+  zdef_(zinc, Ztotpartition, "partitions of a point", -1);
+  zzdef_(zinc, Zpartition, "distance tests for partitioning", -1);
+  zzdef_(zinc, Zdistcheck, "distance tests for checking flipped facets", -1);
+  zzdef_(zinc, Zdistconvex, "distance tests for checking convexity", -1);
+  zdef_(zinc, Zdistgood, "distance tests for checking good point", -1);
+  zdef_(zinc, Zdistio, "distance tests for output", -1);
+  zdef_(zinc, Zdiststat, "distance tests for statistics", -1);
+  zdef_(zinc, Zdistplane, "total number of distance tests", -1);
+  zdef_(zinc, Ztotpartcoplanar, "partitions of coplanar points or deleted vertices", -1);
+  zzdef_(zinc, Zpartcoplanar, "   distance tests for these partitions", -1);
+  zdef_(zinc, Zcomputefurthest, "distance tests for computing furthest", -1);
+}
+
+void qh_allstatE2(void)
+{
+  zdef_(zdoc, Zdoc5, "statistics for matching ridges", -1);
+  zdef_(zinc, Zhashlookup, "total lookups for matching ridges of new facets", -1);
+  zdef_(zinc, Zhashtests, "average number of tests to match a ridge", Zhashlookup);
+  zdef_(zinc, Zhashridge, "total lookups of subridges (duplicates and boundary)", -1);
+  zdef_(zinc, Zhashridgetest, "average number of tests per subridge", Zhashridge);
+  zdef_(zinc, Zdupsame, "duplicated ridges in same merge cycle", -1);
+  zdef_(zinc, Zdupflip, "duplicated ridges with flipped facets", -1);
+
+  zdef_(zdoc, Zdoc6, "statistics for determining merges", -1);
+  zdef_(zinc, Zangletests, "angles computed for ridge convexity", -1);
+  zdef_(zinc, Zbestcentrum, "best merges used centrum instead of vertices", -1);
+  zzdef_(zinc, Zbestdist, "distance tests for best merge", -1);
+  zzdef_(zinc, Zcentrumtests, "distance tests for centrum convexity", -1);
+  zzdef_(zinc, Zdistzero, "distance tests for checking simplicial convexity", -1);
+  zdef_(zinc, Zcoplanarangle, "coplanar angles in getmergeset", -1);
+  zdef_(zinc, Zcoplanarcentrum, "coplanar centrums in getmergeset", -1);
+  zdef_(zinc, Zconcaveridge, "concave ridges in getmergeset", -1);
+}
+
+void qh_allstatF(void)
+{
+  zdef_(zdoc, Zdoc7, "statistics for merging", -1);
+  zdef_(zinc, Zpremergetot, "merge iterations", -1);
+  zdef_(zadd, Zmergeinittot, "ave. initial non-convex ridges per iteration", Zpremergetot);
+  zdef_(zadd, Zmergeinitmax, "  maximum", -1);
+  zdef_(zadd, Zmergesettot, "  ave. additional non-convex ridges per iteration", Zpremergetot);
+  zdef_(zadd, Zmergesetmax, "  maximum additional in one pass", -1);
+  zdef_(zadd, Zmergeinittot2, "initial non-convex ridges for post merging", -1);
+  zdef_(zadd, Zmergesettot2, "  additional non-convex ridges", -1);
+  zdef_(wmax, Wmaxoutside, "max distance of vertex or coplanar point above facet (w/roundoff)", -1);
+  zdef_(wmin, Wminvertex, "max distance of merged vertex below facet (or roundoff)", -1);
+  zdef_(zinc, Zwidefacet, "centrums frozen due to a wide merge", -1);
+  zdef_(zinc, Zwidevertices, "centrums frozen due to extra vertices", -1);
+  zzdef_(zinc, Ztotmerge, "total number of facets or cycles of facets merged", -1);
+  zdef_(zinc, Zmergesimplex, "merged a simplex", -1);
+  zdef_(zinc, Zonehorizon, "simplices merged into coplanar horizon", -1);
+  zzdef_(zinc, Zcyclehorizon, "cycles of facets merged into coplanar horizon", -1);
+  zzdef_(zadd, Zcyclefacettot, "  ave. facets per cycle", Zcyclehorizon);
+  zdef_(zmax, Zcyclefacetmax, "  max. facets", -1);
+  zdef_(zinc, Zmergeintohorizon, "new facets merged into horizon", -1);
+  zdef_(zinc, Zmergenew, "new facets merged", -1);
+  zdef_(zinc, Zmergehorizon, "horizon facets merged into new facets", -1);
+  zdef_(zinc, Zmergevertex, "vertices deleted by merging", -1);
+  zdef_(zinc, Zcyclevertex, "vertices deleted by merging into coplanar horizon", -1);
+  zdef_(zinc, Zdegenvertex, "vertices deleted by degenerate facet", -1);
+  zdef_(zinc, Zmergeflipdup, "merges due to flipped facets in duplicated ridge", -1);
+  zdef_(zinc, Zneighbor, "merges due to redundant neighbors", -1);
+  zdef_(zadd, Ztestvneighbor, "non-convex vertex neighbors", -1);
+}
+
+void qh_allstatG(void)
+{
+  zdef_(zinc, Zacoplanar, "merges due to angle coplanar facets", -1);
+  zdef_(wadd, Wacoplanartot, "  average merge distance", Zacoplanar);
+  zdef_(wmax, Wacoplanarmax, "  maximum merge distance", -1);
+  zdef_(zinc, Zcoplanar, "merges due to coplanar facets", -1);
+  zdef_(wadd, Wcoplanartot, "  average merge distance", Zcoplanar);
+  zdef_(wmax, Wcoplanarmax, "  maximum merge distance", -1);
+  zdef_(zinc, Zconcave, "merges due to concave facets", -1);
+  zdef_(wadd, Wconcavetot, "  average merge distance", Zconcave);
+  zdef_(wmax, Wconcavemax, "  maximum merge distance", -1);
+  zdef_(zinc, Zavoidold, "coplanar/concave merges due to avoiding old merge", -1);
+  zdef_(wadd, Wavoidoldtot, "  average merge distance", Zavoidold);
+  zdef_(wmax, Wavoidoldmax, "  maximum merge distance", -1);
+  zdef_(zinc, Zdegen, "merges due to degenerate facets", -1);
+  zdef_(wadd, Wdegentot, "  average merge distance", Zdegen);
+  zdef_(wmax, Wdegenmax, "  maximum merge distance", -1);
+  zdef_(zinc, Zflipped, "merges due to removing flipped facets", -1);
+  zdef_(wadd, Wflippedtot, "  average merge distance", Zflipped);
+  zdef_(wmax, Wflippedmax, "  maximum merge distance", -1);
+  zdef_(zinc, Zduplicate, "merges due to duplicated ridges", -1);
+  zdef_(wadd, Wduplicatetot, "  average merge distance", Zduplicate);
+  zdef_(wmax, Wduplicatemax, "  maximum merge distance", -1);
+}
+
+void qh_allstatH(void)
+{
+  zdef_(zdoc, Zdoc8, "renamed vertex statistics", -1);
+  zdef_(zinc, Zrenameshare, "renamed vertices shared by two facets", -1);
+  zdef_(zinc, Zrenamepinch, "renamed vertices in a pinched facet", -1);
+  zdef_(zinc, Zrenameall, "renamed vertices shared by multiple facets", -1);
+  zdef_(zinc, Zfindfail, "rename failures due to duplicated ridges", -1);
+  zdef_(zinc, Zdupridge, "  duplicate ridges detected", -1);
+  zdef_(zinc, Zdelridge, "deleted ridges due to renamed vertices", -1);
+  zdef_(zinc, Zdropneighbor, "dropped neighbors due to renamed vertices", -1);
+  zdef_(zinc, Zdropdegen, "degenerate facets due to dropped neighbors", -1);
+  zdef_(zinc, Zdelfacetdup, "  facets deleted because of no neighbors", -1);
+  zdef_(zinc, Zremvertex, "vertices removed from facets due to no ridges", -1);
+  zdef_(zinc, Zremvertexdel, "  deleted", -1);
+  zdef_(zinc, Zintersectnum, "vertex intersections for locating redundant vertices", -1);
+  zdef_(zinc, Zintersectfail, "intersections failed to find a redundant vertex", -1);
+  zdef_(zinc, Zintersect, "intersections found redundant vertices", -1);
+  zdef_(zadd, Zintersecttot, "   ave. number found per vertex", Zintersect);
+  zdef_(zmax, Zintersectmax, "   max. found for a vertex", -1);
+  zdef_(zinc, Zvertexridge, NULL, -1);
+  zdef_(zadd, Zvertexridgetot, "  ave. number of ridges per tested vertex", Zvertexridge);
+  zdef_(zmax, Zvertexridgemax, "  max. number of ridges per tested vertex", -1);
+
+  zdef_(zdoc, Zdoc10, "memory usage statistics (in bytes)", -1);
+  zdef_(zadd, Zmemfacets, "for facets and their normals, neighbor and vertex sets", -1);
+  zdef_(zadd, Zmemvertices, "for vertices and their neighbor sets", -1);
+  zdef_(zadd, Zmempoints, "for input points and outside and coplanar sets", -1);
+  zdef_(zadd, Zmemridges, "for ridges and their vertex sets", -1);
+} /* allstat */
+
+void qh_allstatI(void)
+{
+  qhstat vridges = qhstat next;
+
+  zzdef_(zdoc, Zdoc11, "Voronoi ridge statistics", -1);
+  zzdef_(zinc, Zridge, "non-simplicial Voronoi vertices for all ridges", -1);
+  zzdef_(wadd, Wridge, "  ave. distance to ridge", Zridge);
+  zzdef_(wmax, Wridgemax, "  max. distance to ridge", -1);
+  zzdef_(zinc, Zridgemid, "bounded ridges", -1);
+  zzdef_(wadd, Wridgemid, "  ave. distance of midpoint to ridge", Zridgemid);
+  zzdef_(wmax, Wridgemidmax, "  max. distance of midpoint to ridge", -1);
+  zzdef_(zinc, Zridgeok, "bounded ridges with ok normal", -1);
+  zzdef_(wadd, Wridgeok, "  ave. angle to ridge", Zridgeok);
+  zzdef_(wmax, Wridgeokmax, "  max. angle to ridge", -1);
+  zzdef_(zinc, Zridge0, "bounded ridges with near-zero normal", -1);
+  zzdef_(wadd, Wridge0, "  ave. angle to ridge", Zridge0);
+  zzdef_(wmax, Wridge0max, "  max. angle to ridge", -1);
+
+  zdef_(zdoc, Zdoc12, "Triangulation statistics (Qt)", -1);
+  zdef_(zinc, Ztricoplanar, "non-simplicial facets triangulated", -1);
+  zdef_(zadd, Ztricoplanartot, "  ave. new facets created (may be deleted)", Ztricoplanar);
+  zdef_(zmax, Ztricoplanarmax, "  max. new facets created", -1);
+  zdef_(zinc, Ztrinull, "null new facets deleted (duplicated vertex)", -1);
+  zdef_(zinc, Ztrimirror, "mirrored pairs of new facets deleted (same vertices)", -1);
+  zdef_(zinc, Ztridegen, "degenerate new facets in output (same ridge)", -1);
+} /* allstat */
+
+/*---------------------------------
+
+  qh_allstatistics()
+  reset printed flag for all statistics
+*/
+void qh_allstatistics(void)
+{
+  int i;
+  for( i = ZEND; i--; )
+    {
+    qhstat printed[i] = False;
+    }
+} /* allstatistics */
+
+#if qh_KEEPstatistics
+/*---------------------------------
+
+  qh_collectstatistics()
+  collect statistics for qh.facet_list
+
+*/
+void qh_collectstatistics(void)
+{
+  facetT * facet, *neighbor, * *neighborp;
+  vertexT *vertex, * *vertexp;
+  realT    dotproduct, dist;
+  int      sizneighbors, sizridges, sizvertices, i;
+
+  qh old_randomdist = qh RANDOMdist;
+  qh RANDOMdist = False;
+
+  zval_(Zmempoints) = qh num_points * qh normal_size
+    + sizeof (qhT) + sizeof (qhstatT);
+  zval_(Zmemfacets) = 0;
+  zval_(Zmemridges) = 0;
+  zval_(Zmemvertices) = 0;
+  zval_(Zangle) = 0;
+  wval_(Wangle) = 0.0;
+  zval_(Znumridges) = 0;
+  zval_(Znumfacets) = 0;
+  zval_(Znumneighbors) = 0;
+  zval_(Znumvertices) = 0;
+  zval_(Znumvneighbors) = 0;
+  zval_(Znummergetot) = 0;
+  zval_(Znummergemax) = 0;
+  zval_(Zvertices) = qh num_vertices - qh_setsize(qh del_vertices);
+  if( qh MERGING || qh APPROXhull || qh JOGGLEmax < REALmax / 2 )
+    {
+    wmax_(Wmaxoutside, qh max_outside);
+    }
+  if( qh MERGING )
+    {
+    wmin_(Wminvertex, qh min_vertex);
+    }
+  FORALLfacets
+  facet-> seen = False;
+  if( qh DELAUNAY )
+    {
+    FORALLfacets {
+      if( facet->upperdelaunay != qh UPPERdelaunay )
+        {
+        facet->seen = True; /* remove from angle statistics */
+        }
+      }
+    }
+  FORALLfacets {
+    if( facet->visible && qh NEWfacets )
+      {
+      continue;
+      }
+    sizvertices = qh_setsize(facet->vertices);
+    sizneighbors = qh_setsize(facet->neighbors);
+    sizridges = qh_setsize(facet->ridges);
+    zinc_(Znumfacets);
+    zadd_(Znumvertices, sizvertices);
+    zmax_(Zmaxvertices, sizvertices);
+    zadd_(Znumneighbors, sizneighbors);
+    zmax_(Zmaxneighbors, sizneighbors);
+    zadd_(Znummergetot, facet->nummerge);
+    i = facet->nummerge; /* avoid warnings */
+    zmax_(Znummergemax, i);
+    if( !facet->simplicial )
+      {
+      if( sizvertices == qh hull_dim )
+        {
+        zinc_(Znowsimplicial);
+        }
+      else
+        {
+        zinc_(Znonsimplicial);
+        }
+      }
+    if( sizridges )
+      {
+      zadd_(Znumridges, sizridges);
+      zmax_(Zmaxridges, sizridges);
+      }
+    zadd_(Zmemfacets, sizeof (facetT) + qh normal_size + 2 * sizeof (setT)
+          + SETelemsize * (sizneighbors + sizvertices) );
+    if( facet->ridges )
+      {
+      zadd_(Zmemridges,
+            sizeof (setT) + SETelemsize * sizridges + sizridges
+            * (sizeof (ridgeT) + sizeof (setT) + SETelemsize * (qh hull_dim - 1) ) / 2);
+      }
+    if( facet->outsideset )
+      {
+      zadd_(Zmempoints, sizeof (setT) + SETelemsize * qh_setsize(facet->outsideset) );
+      }
+    if( facet->coplanarset )
+      {
+      zadd_(Zmempoints, sizeof (setT) + SETelemsize * qh_setsize(facet->coplanarset) );
+      }
+    if( facet->seen ) /* Delaunay upper envelope */
+      {
+      continue;
+      }
+    facet->seen = True;
+    FOREACHneighbor_(facet) {
+      if( neighbor == qh_DUPLICATEridge || neighbor == qh_MERGEridge
+          || neighbor->seen || !facet->normal || !neighbor->normal )
+        {
+        continue;
+        }
+      dotproduct = qh_getangle(facet->normal, neighbor->normal);
+      zinc_(Zangle);
+      wadd_(Wangle, dotproduct);
+      wmax_(Wanglemax, dotproduct)
+      wmin_(Wanglemin, dotproduct)
+      }
+    if( facet->normal )
+      {
+      FOREACHvertex_(facet->vertices) {
+        zinc_(Zdiststat);
+        qh_distplane(vertex->point, facet, &dist);
+        wmax_(Wvertexmax, dist);
+        wmin_(Wvertexmin, dist);
+        }
+      }
+    }
+  FORALLvertices {
+    if( vertex->deleted )
+      {
+      continue;
+      }
+    zadd_(Zmemvertices, sizeof (vertexT) );
+    if( vertex->neighbors )
+      {
+      sizneighbors = qh_setsize(vertex->neighbors);
+      zadd_(Znumvneighbors, sizneighbors);
+      zmax_(Zmaxvneighbors, sizneighbors);
+      zadd_(Zmemvertices, sizeof (vertexT) + SETelemsize * sizneighbors);
+      }
+    }
+  qh RANDOMdist = qh old_randomdist;
+} /* collectstatistics */
+
+#endif /* qh_KEEPstatistics */
+
+/*---------------------------------
+
+  qh_freestatistics(  )
+  free memory used for statistics
+*/
+void qh_freestatistics(void)
+{
+
+#if qh_QHpointer
+  free(qh_qhstat);
+  qh_qhstat = NULL;
+#endif
+} /* freestatistics */
+
+/*---------------------------------
+
+  qh_initstatistics(  )
+  allocate and initialize statistics
+
+  notes:
+  uses malloc() instead of qh_memalloc() since mem.c not set up yet
+*/
+void qh_initstatistics(void)
+{
+  int   i;
+  realT realx;
+  int   intx;
+
+#if qh_QHpointer
+  if( !(qh_qhstat = (qhstatT *)malloc(sizeof(qhstatT) ) ) )
+    {
+    fprintf(qhmem.ferr, "qhull error (qh_initstatistics): insufficient memory\n");
+    exit(1);   /* can not use qh_errexit() */
+    }
+#endif
+
+  qhstat next = 0;
+  qh_allstatA();
+  qh_allstatB();
+  qh_allstatC();
+  qh_allstatD();
+  qh_allstatE();
+  qh_allstatE2();
+  qh_allstatF();
+  qh_allstatG();
+  qh_allstatH();
+  qh_allstatI();
+  if( qhstat next > (int)sizeof(qhstat id) )
+    {
+    fprintf(
+      qhmem.ferr,
+      "qhull error (qh_initstatistics): increase size of qhstat.id[].\n\
+      qhstat.next %d should be <= sizeof(qhstat id) %lu\n"                                                                         ,
+      qhstat next,
+      sizeof(qhstat id) );
+#if 0 /* for locating error, Znumridges should be duplicated */
+    for( i = 0; i < ZEND; i++ )
+      {
+      int j;
+      for( j = i + 1; j < ZEND; j++ )
+        {
+        if( qhstat id[i] == qhstat id[j] )
+          {
+          fprintf(qhmem.ferr, "qhull error (qh_initstatistics): duplicated statistic %d at indices %d and %d\n",
+                  qhstat id[i], i, j);
+          }
+        }
+      }
+#endif
+    exit(1);   /* can not use qh_errexit() */
+    }
+  qhstat init[zinc].i = 0;
+  qhstat init[zadd].i = 0;
+  qhstat init[zmin].i = INT_MAX;
+  qhstat init[zmax].i = INT_MIN;
+  qhstat init[wadd].r = 0;
+  qhstat init[wmin].r = REALmax;
+  qhstat init[wmax].r = -REALmax;
+  for( i = 0; i < ZEND; i++ )
+    {
+    if( qhstat type[i] > ZTYPEreal )
+      {
+      realx = qhstat init[(unsigned char)(qhstat type[i])].r;
+      qhstat stats[i].r = realx;
+      }
+    else if( qhstat type[i] != zdoc )
+      {
+      intx = qhstat init[(unsigned char)(qhstat type[i])].i;
+      qhstat stats[i].i = intx;
+      }
+    }
+} /* initstatistics */
+
+/*---------------------------------
+
+  qh_newstats(  )
+  returns True if statistics for zdoc
+
+  returns:
+  next zdoc
+*/
+boolT qh_newstats(int idx, int *nextindex)
+{
+  boolT isnew = False;
+  int   start, i;
+
+  if( qhstat type[qhstat id[idx]] == zdoc )
+    {
+    start = idx + 1;
+    }
+  else
+    {
+    start = idx;
+    }
+  for( i = start; i < qhstat next && qhstat type[qhstat id[i]] != zdoc; i++ )
+    {
+    if( !qh_nostatistic(qhstat id[i]) && !qhstat printed[qhstat id[i]] )
+      {
+      isnew = True;
+      }
+    }
+  *nextindex = i;
+  return isnew;
+} /* newstats */
+
+/*---------------------------------
+
+  qh_nostatistic( index )
+  true if no statistic to print
+*/
+boolT qh_nostatistic(int i)
+{
+
+  if( (qhstat type[i] > ZTYPEreal
+       && qhstat stats[i].r == qhstat init[(unsigned char)(qhstat type[i])].r)
+      || (qhstat type[i] < ZTYPEreal
+          && qhstat stats[i].i == qhstat init[(unsigned char)(qhstat type[i])].i) )
+    {
+    return True;
+    }
+  return False;
+} /* nostatistic */
+
+#if qh_KEEPstatistics
+/*---------------------------------
+
+  qh_printallstatistics( fp, string )
+  print all statistics with header 'string'
+*/
+void qh_printallstatistics(FILE *fp, const char *string)
+{
+
+  qh_allstatistics();
+  qh_collectstatistics();
+  qh_printstatistics(fp, string);
+  qh_memstatistics(fp);
+}
+
+/*---------------------------------
+
+  qh_printstatistics( fp, string )
+  print statistics to a file with header 'string'
+  skips statistics with qhstat.printed[] (reset with qh_allstatistics)
+
+  see:
+  qh_printallstatistics()
+*/
+void qh_printstatistics(FILE *fp, const char *string)
+{
+  int   i, k;
+  realT ave;
+
+  if( qh num_points != qh num_vertices )
+    {
+    wval_(Wpbalance) = 0;
+    wval_(Wpbalance2) = 0;
+    }
+  else
+    {
+    wval_(Wpbalance2) = qh_stddev(zval_(Zpbalance), wval_(Wpbalance),
+                                  wval_(Wpbalance2), &ave);
+    }
+  wval_(Wnewbalance2) = qh_stddev(zval_(Zprocessed), wval_(Wnewbalance),
+                                  wval_(Wnewbalance2), &ave);
+  fprintf(fp, "\n\
+%s\n\
+ qhull invoked by: %s | %s\n%s with options:\n%s\n", string, qh rbox_command,
+          qh qhull_command, qh_version, qh qhull_options);
+  fprintf(
+    fp,
+    "\nprecision constants:\n\
+ %6.2g max. abs. coordinate in the (transformed) input ('Qbd:n')\n\
+ %6.2g max. roundoff error for distance computation ('En')\n\
+ %6.2g max. roundoff error for angle computations\n\
+ %6.2g min. distance for outside points ('Wn')\n\
+ %6.2g min. distance for visible facets ('Vn')\n\
+ %6.2g max. distance for coplanar facets ('Un')\n\
+ %6.2g max. facet width for recomputing centrum and area\n\
+"                                                                                                                                                                                                                                                                                                                                                                                                                                         ,
+    qh MAXabs_coord, qh DISTround, qh ANGLEround, qh MINoutside,
+    qh MINvisible, qh MAXcoplanar,
+    qh WIDEfacet);
+  if( qh KEEPnearinside )
+    {
+    fprintf(fp, "\
+ %6.2g max. distance for near-inside points\n", qh NEARinside);
+    }
+  if( qh premerge_cos < REALmax / 2 )
+    {
+    fprintf(fp, "\
+ %6.2g max. cosine for pre-merge angle\n", qh premerge_cos);
+    }
+  if( qh PREmerge )
+    {
+    fprintf(fp, "\
+ %6.2g radius of pre-merge centrum\n", qh premerge_centrum);
+    }
+  if( qh postmerge_cos < REALmax / 2 )
+    {
+    fprintf(fp, "\
+ %6.2g max. cosine for post-merge angle\n", qh postmerge_cos);
+    }
+  if( qh POSTmerge )
+    {
+    fprintf(fp, "\
+ %6.2g radius of post-merge centrum\n", qh postmerge_centrum);
+    }
+  fprintf(
+    fp,
+    "\
+ %6.2g max. distance for merging two simplicial facets\n\
+ %6.2g max. roundoff error for arithmetic operations\n\
+ %6.2g min. denominator for divisions\n\
+  zero diagonal for Gauss: "                                                                                                                                                                  ,
+    qh ONEmerge, REALepsilon,
+    qh MINdenom);
+  for( k = 0; k < qh hull_dim; k++ )
+    {
+    fprintf(fp, "%6.2e ", qh NEARzero[k]);
+    }
+  fprintf(fp, "\n\n");
+  for( i = 0; i < qhstat next; )
+    {
+    qh_printstats(fp, i, &i);
+    }
+} /* printstatistics */
+
+#endif /* qh_KEEPstatistics */
+
+/*---------------------------------
+
+  qh_printstatlevel( fp, id )
+  print level information for a statistic
+
+  notes:
+  nop if id >= ZEND, printed, or same as initial value
+*/
+void qh_printstatlevel(FILE *fp, int id, int start)
+{
+#define NULLfield "       "
+
+  if( id >= ZEND || qhstat printed[id] )
+    {
+    return;
+    }
+  if( qhstat type[id] == zdoc )
+    {
+    fprintf(fp, "%s\n", qhstat doc[id]);
+    return;
+    }
+  start = 0; /* not used */
+  if( qh_nostatistic(id) || !qhstat doc[id] )
+    {
+    return;
+    }
+  qhstat printed[id] = True;
+  if( qhstat count[id] != -1
+      && qhstat stats[(unsigned char)(qhstat count[id])].i == 0 )
+    {
+    fprintf(fp, " *0 cnt*");
+    }
+  else if( qhstat type[id] >= ZTYPEreal && qhstat count[id] == -1 )
+    {
+    fprintf(fp, "%7.2g", qhstat stats[id].r);
+    }
+  else if( qhstat type[id] >= ZTYPEreal && qhstat count[id] != -1 )
+    {
+    fprintf(fp, "%7.2g", qhstat stats[id].r / qhstat stats[(unsigned char)(qhstat count[id])].i);
+    }
+  else if( qhstat type[id] < ZTYPEreal && qhstat count[id] == -1 )
+    {
+    fprintf(fp, "%7d", qhstat stats[id].i);
+    }
+  else if( qhstat type[id] < ZTYPEreal && qhstat count[id] != -1 )
+    {
+    fprintf(fp, "%7.3g", (realT) qhstat stats[id].i / qhstat stats[(unsigned char)(qhstat count[id])].i);
+    }
+  fprintf(fp, " %s\n", qhstat doc[id]);
+} /* printstatlevel */
+
+/*---------------------------------
+
+  qh_printstats( fp, index, nextindex )
+  print statistics for a zdoc group
+
+  returns:
+  next zdoc if non-null
+*/
+void qh_printstats(FILE *fp, int idx, int *nextindex)
+{
+  int j, nexti;
+
+  if( qh_newstats(idx, &nexti) )
+    {
+    fprintf(fp, "\n");
+    for( j = idx; j < nexti; j++ )
+      {
+      qh_printstatlevel(fp, qhstat id[j], 0);
+      }
+    }
+  if( nextindex )
+    {
+    *nextindex = nexti;
+    }
+} /* printstats */
+
+#if qh_KEEPstatistics
+
+/*---------------------------------
+
+  qh_stddev( num, tot, tot2, ave )
+  compute the standard deviation and average from statistics
+
+  tot2 is the sum of the squares
+  notes:
+  computes r.m.s.:
+  (x-ave)^2
+  == x^2 - 2x tot/num +   (tot/num)^2
+  == tot2 - 2 tot tot/num + tot tot/num
+  == tot2 - tot ave
+*/
+realT qh_stddev(int num, realT tot, realT tot2, realT *ave)
+{
+  realT stddev;
+
+  *ave = tot / num;
+  stddev = sqrt(tot2 / num - *ave * *ave);
+  return stddev;
+} /* stddev */
+
+#endif /* qh_KEEPstatistics */
+
+#if !qh_KEEPstatistics
+void    qh_collectstatistics(void)
+{
+}
+void    qh_printallstatistics(FILE *fp, char *string)
+{
+};
+void    qh_printstatistics(FILE *fp, char *string)
+{
+}
+#endif
+
diff --git a/BRAINSABC/qhull/stat.h b/BRAINSABC/qhull/stat.h
new file mode 100644
index 00000000..da8f467a
--- /dev/null
+++ b/BRAINSABC/qhull/stat.h
@@ -0,0 +1,544 @@
+/*
  ---------------------------------
+
+   stat.h
+     contains all statistics that are collected for qhull
+
+   see qh-stat.htm and stat.c
+
+   copyright (c) 1993-2003, The Geometry Center
+
+   recompile qhull if you change this file
+
+   Integer statistics are Z* while real statistics are W*.
+
+   define maydebugx to call a routine at every statistic event
+
+*/
+
+#ifndef qhDEFstat
+#define qhDEFstat 1
+
+/*---------------------------------
+
+  qh_KEEPstatistics
+    0 turns off statistic gathering (except zzdef/zzinc/zzadd/zzval/wwval)
+*/
+#ifndef qh_KEEPstatistics
+#define qh_KEEPstatistics 1
+#endif
+
+/*---------------------------------
+
+  Zxxx for integers, Wxxx for reals
+
+  notes:
+    be sure that all statistics are defined in stat.c
+      otherwise initialization may core dump
+    can pick up all statistics by:
+      grep '[zw].*_[(][ZW]' *.c >z.x
+    remove trailers with query">-
+    remove leaders with  query-replace-regexp [ ^I]+  (
+*/
+#if qh_KEEPstatistics
+enum statistics       /* alphabetical after Z/W */
+                                                       { Zacoplanar,
+                                                       Wacoplanarmax,
+                                                       Wacoplanartot,
+                                                       Zangle,
+                                                       Wangle,
+                                                       Wanglemax,
+                                                       Wanglemin,
+                                                       Zangletests,
+                                                       Wareatot,
+                                                       Wareamax,
+                                                       Wareamin,
+                                                       Zavoidold,
+                                                       Wavoidoldmax,
+                                                       Wavoidoldtot,
+                                                       Zback0,
+                                                       Zbestcentrum,
+                                                       Zbestdist,
+                                                       Zbestlower,
+                                                       Zbestlowerv,
+                                                       Zcentrumtests,
+                                                       Zcheckpart,
+                                                       Zcomputefurthest,
+                                                       Zconcave,
+                                                       Wconcavemax,
+                                                       Wconcavetot,
+                                                       Zconcaveridges,
+                                                       Zconcaveridge,
+                                                       Zcoplanar,
+                                                       Wcoplanarmax,
+                                                       Wcoplanartot,
+                                                       Zcoplanarangle,
+                                                       Zcoplanarcentrum,
+                                                       Zcoplanarhorizon,
+                                                       Zcoplanarinside,
+                                                       Zcoplanarpart,
+                                                       Zcoplanarridges,
+                                                       Wcpu,
+                                                       Zcyclefacetmax,
+                                                       Zcyclefacettot,
+                                                       Zcyclehorizon,
+                                                       Zcyclevertex,
+                                                       Zdegen,
+                                                       Wdegenmax,
+                                                       Wdegentot,
+                                                       Zdegenvertex,
+                                                       Zdelfacetdup,
+                                                       Zdelridge,
+                                                       Zdelvertextot,
+                                                       Zdelvertexmax,
+                                                       Zdetsimplex,
+                                                       Zdistcheck,
+                                                       Zdistconvex,
+                                                       Zdistgood,
+                                                       Zdistio,
+                                                       Zdistplane,
+                                                       Zdiststat,
+                                                       Zdistvertex,
+                                                       Zdistzero,
+                                                       Zdoc1,
+                                                       Zdoc2,
+                                                       Zdoc3,
+                                                       Zdoc4,
+                                                       Zdoc5,
+                                                       Zdoc6,
+                                                       Zdoc7,
+                                                       Zdoc8,
+                                                       Zdoc9,
+                                                       Zdoc10,
+                                                       Zdoc11,
+                                                       Zdoc12,
+                                                       Zdropdegen,
+                                                       Zdropneighbor,
+                                                       Zdupflip,
+                                                       Zduplicate,
+                                                       Wduplicatemax,
+                                                       Wduplicatetot,
+                                                       Zdupridge,
+                                                       Zdupsame,
+                                                       Zflipped,
+                                                       Wflippedmax,
+                                                       Wflippedtot,
+                                                       Zflippedfacets,
+                                                       Zfindbest,
+                                                       Zfindbestmax,
+                                                       Zfindbesttot,
+                                                       Zfindcoplanar,
+                                                       Zfindfail,
+                                                       Zfindhorizon,
+                                                       Zfindhorizonmax,
+                                                       Zfindhorizontot,
+                                                       Zfindjump,
+                                                       Zfindnew,
+                                                       Zfindnewmax,
+                                                       Zfindnewtot,
+                                                       Zfindnewjump,
+                                                       Zfindnewsharp,
+                                                       Zgauss0,
+                                                       Zgoodfacet,
+                                                       Zhashlookup,
+                                                       Zhashridge,
+                                                       Zhashridgetest,
+                                                       Zhashtests,
+                                                       Zinsidevisible,
+                                                       Zintersect,
+                                                       Zintersectfail,
+                                                       Zintersectmax,
+                                                       Zintersectnum,
+                                                       Zintersecttot,
+                                                       Zmaxneighbors,
+                                                       Wmaxout,
+                                                       Wmaxoutside,
+                                                       Zmaxridges,
+                                                       Zmaxvertex,
+                                                       Zmaxvertices,
+                                                       Zmaxvneighbors,
+                                                       Zmemfacets,
+                                                       Zmempoints,
+                                                       Zmemridges,
+                                                       Zmemvertices,
+                                                       Zmergeflipdup,
+                                                       Zmergehorizon,
+                                                       Zmergeinittot,
+                                                       Zmergeinitmax,
+                                                       Zmergeinittot2,
+                                                       Zmergeintohorizon,
+                                                       Zmergenew,
+                                                       Zmergesettot,
+                                                       Zmergesetmax,
+                                                       Zmergesettot2,
+                                                       Zmergesimplex,
+                                                       Zmergevertex,
+                                                       Wmindenom,
+                                                       Wminvertex,
+                                                       Zminnorm,
+                                                       Zmultiridge,
+                                                       Znearlysingular,
+                                                       Zneighbor,
+                                                       Wnewbalance,
+                                                       Wnewbalance2,
+                                                       Znewfacettot,
+                                                       Znewfacetmax,
+                                                       Znewvertex,
+                                                       Wnewvertex,
+                                                       Wnewvertexmax,
+                                                       Znoarea,
+                                                       Znonsimplicial,
+                                                       Znowsimplicial,
+                                                       Znotgood,
+                                                       Znotgoodnew,
+                                                       Znotmax,
+                                                       Znumfacets,
+                                                       Znummergemax,
+                                                       Znummergetot,
+                                                       Znumneighbors,
+                                                       Znumridges,
+                                                       Znumvertices,
+                                                       Znumvisibility,
+                                                       Znumvneighbors,
+                                                       Zonehorizon,
+                                                       Zpartangle,
+                                                       Zpartcoplanar,
+                                                       Zpartflip,
+                                                       Zparthorizon,
+                                                       Zpartinside,
+                                                       Zpartition,
+                                                       Zpartitionall,
+                                                       Zpartnear,
+                                                       Zpbalance,
+                                                       Wpbalance,
+                                                       Wpbalance2,
+                                                       Zpostfacets,
+                                                       Zpremergetot,
+                                                       Zprocessed,
+                                                       Zremvertex,
+                                                       Zremvertexdel,
+                                                       Zrenameall,
+                                                       Zrenamepinch,
+                                                       Zrenameshare,
+                                                       Zretry,
+                                                       Wretrymax,
+                                                       Zridge,
+                                                       Wridge,
+                                                       Wridgemax,
+                                                       Zridge0,
+                                                       Wridge0,
+                                                       Wridge0max,
+                                                       Zridgemid,
+                                                       Wridgemid,
+                                                       Wridgemidmax,
+                                                       Zridgeok,
+                                                       Wridgeok,
+                                                       Wridgeokmax,
+                                                       Zsearchpoints,
+                                                       Zsetplane,
+                                                       Ztestvneighbor,
+                                                       Ztotcheck,
+                                                       Ztothorizon,
+                                                       Ztotmerge,
+                                                       Ztotpartcoplanar,
+                                                       Ztotpartition,
+                                                       Ztotridges,
+                                                       Ztotvertices,
+                                                       Ztotvisible,
+                                                       Ztricoplanar,
+                                                       Ztricoplanarmax,
+                                                       Ztricoplanartot,
+                                                       Ztridegen,
+                                                       Ztrimirror,
+                                                       Ztrinull,
+                                                       Wvertexmax,
+                                                       Wvertexmin,
+                                                       Zvertexridge,
+                                                       Zvertexridgetot,
+                                                       Zvertexridgemax,
+                                                       Zvertices,
+                                                       Zvisfacettot,
+                                                       Zvisfacetmax,
+                                                       Zvisvertextot,
+                                                       Zvisvertexmax,
+                                                       Zwidefacet,
+                                                       Zwidevertices,
+                                                       ZEND };
+
+/*---------------------------------
+
+  Zxxx/Wxxx statistics that remain defined if qh_KEEPstatistics=0
+
+  notes:
+    be sure to use zzdef, zzinc, etc. with these statistics (no double checking!)
+*/
+#else
+enum statistics       /* for zzdef etc. macros */
+                                                      { Zback0,
+                                                      Zbestdist,
+                                                      Zcentrumtests,
+                                                      Zcheckpart,
+                                                      Zconcaveridges,
+                                                      Zcoplanarhorizon,
+                                                      Zcoplanarpart,
+                                                      Zcoplanarridges,
+                                                      Zcyclefacettot,
+                                                      Zcyclehorizon,
+                                                      Zdelvertextot,
+                                                      Zdistcheck,
+                                                      Zdistconvex,
+                                                      Zdistzero,
+                                                      Zdoc1,
+                                                      Zdoc2,
+                                                      Zdoc3,
+                                                      Zdoc11,
+                                                      Zflippedfacets,
+                                                      Zgauss0,
+                                                      Zminnorm,
+                                                      Zmultiridge,
+                                                      Znearlysingular,
+                                                      Wnewvertexmax,
+                                                      Znumvisibility,
+                                                      Zpartcoplanar,
+                                                      Zpartition,
+                                                      Zpartitionall,
+                                                      Zprocessed,
+                                                      Zretry,
+                                                      Zridge,
+                                                      Wridge,
+                                                      Wridgemax,
+                                                      Zridge0,
+                                                      Wridge0,
+                                                      Wridge0max,
+                                                      Zridgemid,
+                                                      Wridgemid,
+                                                      Wridgemidmax,
+                                                      Zridgeok,
+                                                      Wridgeok,
+                                                      Wridgeokmax,
+                                                      Zsetplane,
+                                                      Ztotmerge,
+                                                      ZEND };
+#endif
+
+/*---------------------------------
+
+  ztype
+    the type of a statistic sets its initial value.
+
+  notes:
+    The type should be the same as the macro for collecting the statistic
+*/
+enum ztypes { zdoc, zinc, zadd, zmax, zmin, ZTYPEreal, wadd, wmax, wmin, ZTYPEend };
+
+/*========== macros and constants =============*/
+
+/*----------------------------------
+
+  MAYdebugx
+    define as maydebug() to be called frequently for error trapping
+*/
+#define MAYdebugx
+
+/*----------------------------------
+
+  zzdef_, zdef_( type, name, doc, -1)
+    define a statistic (assumes 'qhstat.next= 0;')
+
+  zdef_( type, name, doc, count)
+    define an averaged statistic
+    printed as name/count
+*/
+#define zzdef_(stype, name, string, cnt)                                \
+  qhstat id[qhstat next++] = name;                                      \
+  qhstat doc[name] = string; qhstat count[name] = cnt; qhstat type[name] = stype
+#if qh_KEEPstatistics
+#define zdef_(stype, name, string, cnt)                                 \
+  qhstat id[qhstat next++] = name;                                      \
+  qhstat doc[name] = string; qhstat count[name] = cnt; qhstat type[name] = stype
+#else
+#define zdef_(type, name, doc, count)
+#endif
+
+/*----------------------------------
+
+  zzinc_( name ), zinc_( name)
+    increment an integer statistic
+*/
+#define zzinc_(id) {MAYdebugx; qhstat stats[id].i++; }
+#if qh_KEEPstatistics
+#define zinc_(id) {MAYdebugx; qhstat stats[id].i++; }
+#else
+#define zinc_(id) {}
+#endif
+
+/*----------------------------------
+
+  zzadd_( name, value ), zadd_( name, value ), wadd_( name, value )
+    add value to an integer or real statistic
+*/
+#define zzadd_(id, val) {MAYdebugx; qhstat stats[id].i += ( val ); }
+#define wwadd_(id, val) {MAYdebugx; qhstat stats[id].r += ( val ); }
+#if qh_KEEPstatistics
+#define zadd_(id, val) {MAYdebugx; qhstat stats[id].i += ( val ); }
+#define wadd_(id, val) {MAYdebugx; qhstat stats[id].r += ( val ); }
+#else
+#define zadd_(id, val) {}
+#define wadd_(id, val) {}
+#endif
+
+/*----------------------------------
+
+  zzval_( name ), zval_( name ), wwval_( name )
+    set or return value of a statistic
+*/
+#define zzval_(id) ( ( qhstat stats[id] ).i )
+#define wwval_(id) ( ( qhstat stats[id] ).r )
+#if qh_KEEPstatistics
+#define zval_(id) ( ( qhstat stats[id] ).i )
+#define wval_(id) ( ( qhstat stats[id] ).r )
+#else
+#define zval_(id) qhstat tempi
+#define wval_(id) qhstat tempr
+#endif
+
+/*----------------------------------
+
+  zmax_( id, val ), wmax_( id, value )
+    maximize id with val
+*/
+#define wwmax_(id, val) {MAYdebugx; maximize_( qhstat stats[id].r, ( val ) ); }
+#if qh_KEEPstatistics
+#define zmax_(id, val) {MAYdebugx; maximize_( qhstat stats[id].i, ( val ) ); }
+#define wmax_(id, val) {MAYdebugx; maximize_( qhstat stats[id].r, ( val ) ); }
+#else
+#define zmax_(id, val) {}
+#define wmax_(id, val) {}
+#endif
+
+/*----------------------------------
+
+  zmin_( id, val ), wmin_( id, value )
+    minimize id with val
+*/
+#if qh_KEEPstatistics
+#define zmin_(id, val) {MAYdebugx; minimize_( qhstat stats[id].i, ( val ) ); }
+#define wmin_(id, val) {MAYdebugx; minimize_( qhstat stats[id].r, ( val ) ); }
+#else
+#define zmin_(id, val) {}
+#define wmin_(id, val) {}
+#endif
+
+/*================== stat.h types ==============*/
+
+/*----------------------------------
+
+  intrealT
+    union of integer and real, used for statistics
+*/
+typedef union intrealT intrealT;    /* union of int and realT */
+union intrealT
+  {
+  int i;
+  realT r;
+  };
+
+/*----------------------------------
+
+  qhstat
+    global data structure for statistics
+
+  notes:
+   access to qh_qhstat is via the "qhstat" macro.  There are two choices
+   qh_QHpointer = 1     access globals via a pointer
+                        enables qh_saveqhull() and qh_restoreqhull()
+    = 0     qh_qhstat is a static data structure
+            only one instance of qhull() can be active at a time
+      default value
+   qh_QHpointer is defined in qhull.h
+
+   allocated in stat.c
+*/
+typedef struct qhstatT qhstatT;
+#if qh_QHpointer
+#define qhstat qh_qhstat->
+extern qhstatT *qh_qhstat;
+#else
+#define qhstat qh_qhstat.
+extern qhstatT qh_qhstat;
+#endif
+struct qhstatT
+  {
+  intrealT stats[ZEND];        /* integer and real statistics */
+  unsigned char id[ZEND + 10]; /* id's in print order */
+  const char *doc[ZEND];       /* array of documentation strings */
+  short int count[ZEND];       /* -1 if none, else index of count to use */
+  char type[ZEND];             /* type, see ztypes above */
+  char printed[ZEND];          /* true, if statistic has been printed */
+  intrealT init[ZTYPEend];     /* initial values by types, set initstatistics */
+
+  int next;                   /* next index for zdef_ */
+  int precision;              /* index for precision problems */
+  int vridges;                /* index for Voronoi ridges */
+  int tempi;
+  realT tempr;
+  };
+
+/*========== function prototypes ===========*/
+
+void    qh_allstatA(void);
+
+void    qh_allstatB(void);
+
+void    qh_allstatC(void);
+
+void    qh_allstatD(void);
+
+void    qh_allstatE(void);
+
+void    qh_allstatE2(void);
+
+void    qh_allstatF(void);
+
+void    qh_allstatG(void);
+
+void    qh_allstatH(void);
+
+void    qh_allstatI(void);
+
+void    qh_allstatistics(void);
+
+void    qh_collectstatistics(void);
+
+void  qh_freestatistics(void);
+
+void    qh_initstatistics(void);
+
+boolT   qh_newstats(int idx, int *nextindex);
+
+boolT   qh_nostatistic(int i);
+
+void    qh_printallstatistics(FILE *fp, const char *string);
+
+void    qh_printstatistics(FILE *fp, const char *string);
+
+void    qh_printstatlevel(FILE *fp, int id, int start);
+
+void    qh_printstats(FILE *fp, int idx, int *nextindex);
+
+realT   qh_stddev(int num, realT tot, realT tot2, realT *ave);
+
+#endif   /* qhDEFstat */
diff --git a/BRAINSABC/qhull/testqh.cxx b/BRAINSABC/qhull/testqh.cxx
new file mode 100644
index 00000000..02f906b4
--- /dev/null
+++ b/BRAINSABC/qhull/testqh.cxx
@@ -0,0 +1,40 @@
+#include "vtkQhullDelaunay3D.h"
+
+#include "vtkUnstructuredGridWriter.h"
+
+int main(int argc, char * *argv)
+{
+  vtkPoints *pts = vtkPoints::New();
+
+  double c = 2.0;
+  /*
+    for (double x = -c; x <= c; x += 1.0)
+      for (double y = -c; y <= c; y += 1.0)
+        for (double z = -c; z <= c; z += 1.0)
+  */
+  for( double x = 0; x <= c; x += 1.0 )
+    {
+    for( double y = 0; y <= c; y += 1.0 )
+      {
+      for( double z = 0; z <= c; z += 1.0 )
+        {
+        double p[3];
+        p[0] = x;
+        p[1] = y;
+        p[2] = z;
+        pts->InsertNextPoint(p);
+        }
+      }
+    }
+
+  vtkUnstructuredGrid *mesh = vtkQhullDelaunay3D(pts);
+
+  vtkUnstructuredGridWriter *meshWriter = vtkUnstructuredGridWriter::New();
+  meshWriter->SetFileTypeToBinary();
+  meshWriter->SetFileName("testqh.vtk");
+  meshWriter->SetInput(mesh);
+  meshWriter->Update();
+
+  return 0;
+}
+
diff --git a/BRAINSABC/qhull/user.c b/BRAINSABC/qhull/user.c
new file mode 100644
index 00000000..72f6c54b
--- /dev/null
+++ b/BRAINSABC/qhull/user.c
@@ -0,0 +1,382 @@
+/*
  ---------------------------------
+
+  user.c
+  user redefinable functions
+
+  see README.txt  see COPYING.txt for copyright information.
+
+  see qhull.h for data structures, macros, and user-callable functions.
+
+  see user_eg.c, unix.c, and qhull_interface.cpp for examples.
+
+  see user.h for user-definable constants
+
+  use qh_NOmem in mem.h to turn off memory management
+  use qh_NOmerge in user.h to turn off facet merging
+  set qh_KEEPstatistics in user.h to 0 to turn off statistics
+
+  This is unsupported software.  You're welcome to make changes,
+  but you're on your own if something goes wrong.  Use 'Tc' to
+  check frequently.  Usually qhull will report an error if
+  a data structure becomes inconsistent.  If so, it also reports
+  the last point added to the hull, e.g., 102.  You can then trace
+  the execution of qhull with "T4P102".
+
+  Please report any errors that you fix to qhull@qhull.org
+
+  call_qhull is a template for calling qhull from within your application
+
+  if you recompile and load this module, then user.o will not be loaded
+  from qhull.a
+
+  you can add additional quick allocation sizes in qh_user_memsizes
+
+  if the other functions here are redefined to not use qh_print...,
+  then io.o will not be loaded from qhull.a.  See user_eg.c for an
+  example.  We recommend keeping io.o for the extra debugging
+  information it supplies.
+*/
+
+#include "qhull_a.h"
+
+/*---------------------------------
+
+  qh_call_qhull( void )
+  template for calling qhull from inside your program
+  remove #if 0, #endif to compile
+
+  returns:
+  exit code (see qh_ERR... in qhull.h)
+  all memory freed
+
+  notes:
+  This can be called any number of times.
+
+  see:
+  qh_call_qhull_once()
+
+*/
+#if 0
+  {
+  int     dim;                  /* dimension of points */
+  int     numpoints;            /* number of points */
+  coordT *points;               /* array of coordinates for each point */
+  boolT   ismalloc;             /* True if qhull should free points in
+                                  qh_freeqhull() or reallocation */
+  char    flags[] = "qhull Tv"; /* option flags for qhull, see qh_opt.htm */
+  FILE *  outfile = stdout;     /* output from qh_produce_output()
+             use NULL to skip qh_produce_output() */
+  FILE *  errfile = stderr;     /* error messages from qhull code */
+  int     exitcode;             /* 0 if no error from qhull */
+  facetT *facet;                /* set by FORALLfacets */
+  int     curlong, totlong;     /* memory remaining after qh_memfreeshort */
+
+  /* initialize dim, numpoints, points[], ismalloc here */
+  exitcode = qh_new_qhull(dim, numpoints, points, ismalloc,
+                          flags, outfile, errfile);
+  if( !exitcode )                    /* if no error */
+    { /* 'qh facet_list' contains the convex hull */
+    FORALLfacets {
+      /* ... your code ... */
+      }
+    }
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )
+    {
+    fprintf(errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n", totlong,
+            curlong);
+    }
+  }
+#endif
+
+/*---------------------------------
+
+  qh_new_qhull( dim, numpoints, points, ismalloc, qhull_cmd, outfile, errfile )
+  build new qhull data structure and return exitcode (0 if no errors)
+
+  notes:
+  do not modify points until finished with results.
+  The qhull data structure contains pointers into the points array.
+  do not call qhull functions before qh_new_qhull().
+  The qhull data structure is not initialized until qh_new_qhull().
+
+  outfile may be null
+  qhull_cmd must start with "qhull "
+  projects points to a new point array for Delaunay triangulations ('d' and 'v')
+  transforms points into a new point array for halfspace intersection ('H')
+
+
+  To allow multiple, concurrent calls to qhull()
+  - set qh_QHpointer in user.h
+  - use qh_save_qhull and qh_restore_qhull to swap the global data structure between calls.
+  - use qh_freeqhull(qh_ALL) to free intermediate convex hulls
+
+  see:
+  user_eg.c for an example
+*/
+int qh_new_qhull(int dim, int numpoints, coordT *points, boolT ismalloc,
+                 char *qhull_cmd, FILE *outfile, FILE *errfile)
+{
+  int          exitcode, hulldim;
+  boolT        new_ismalloc;
+  static boolT firstcall = True;
+  coordT *     new_points;
+
+  if( firstcall )
+    {
+    qh_meminit(errfile);
+    firstcall = False;
+    }
+  if( strncmp(qhull_cmd, "qhull ", (size_t)6) )
+    {
+    fprintf(errfile, "qh_new_qhull: start qhull_cmd argument with \"qhull \"\n");
+    exit(1);
+    }
+  qh_initqhull_start(NULL, outfile, errfile);
+  trace1( ( qh ferr, "qh_new_qhull: build new Qhull for %d %d-d points with %s\n", numpoints, dim, qhull_cmd) );
+  exitcode = setjmp(qh errexit);
+  if( !exitcode )
+    {
+    qh NOerrexit = False;
+    qh_initflags(qhull_cmd);
+    if( qh DELAUNAY )
+      {
+      qh PROJECTdelaunay = True;
+      }
+    if( qh HALFspace )
+      {
+      /* points is an array of halfspaces,
+         the last coordinate of each halfspace is its offset */
+      hulldim = dim - 1;
+      qh_setfeasible(hulldim);
+      new_points = qh_sethalfspace_all(dim, numpoints, points, qh feasible_point);
+      new_ismalloc = True;
+      if( ismalloc )
+        {
+        free(points);
+        }
+      }
+    else
+      {
+      hulldim = dim;
+      new_points = points;
+      new_ismalloc = ismalloc;
+      }
+    qh_init_B(new_points, numpoints, hulldim, new_ismalloc);
+    qh_qhull();
+    qh_check_output();
+    if( outfile )
+      {
+      qh_produce_output();
+      }
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    }
+  qh NOerrexit = True;
+  return exitcode;
+} /* new_qhull */
+
+/*---------------------------------
+
+  qh_errexit( exitcode, facet, ridge )
+  report and exit from an error
+  report facet and ridge if non-NULL
+  reports useful information such as last point processed
+  set qh.FORCEoutput to print neighborhood of facet
+
+  see:
+  qh_errexit2() in qhull.c for printing 2 facets
+
+  design:
+  check for error within error processing
+  compute qh.hulltime
+  print facet and ridge (if any)
+  report commandString, options, qh.furthest_id
+  print summary and statistics (including precision statistics)
+  if qh_ERRsingular
+  print help text for singular data set
+  exit program via long jump (if defined) or exit()
+*/
+void qh_errexit(int exitcode, facetT *facet, ridgeT *ridge)
+{
+
+  if( qh ERREXITcalled )
+    {
+    fprintf(qh ferr, "\nqhull error while processing previous error.  Exit program\n");
+    exit(1);
+    }
+  qh ERREXITcalled = True;
+  if( !qh QHULLfinished )
+    {
+    qh hulltime = qh_CPUclock - qh hulltime;
+    }
+  qh_errprint("ERRONEOUS", facet, NULL, ridge, NULL);
+  fprintf(qh ferr, "\nWhile executing: %s | %s\n", qh rbox_command, qh qhull_command);
+  fprintf(qh ferr, "Options selected for Qhull %s:\n%s\n", qh_version, qh qhull_options);
+  if( qh furthest_id >= 0 )
+    {
+    fprintf(qh ferr, "Last point added to hull was p%d.", qh furthest_id);
+    if( zzval_(Ztotmerge) )
+      {
+      fprintf(qh ferr, "  Last merge was #%d.", zzval_(Ztotmerge) );
+      }
+    if( qh QHULLfinished )
+      {
+      fprintf(qh ferr, "\nQhull has finished constructing the hull.");
+      }
+    else if( qh POSTmerging )
+      {
+      fprintf(qh ferr, "\nQhull has started post-merging.");
+      }
+    fprintf(qh ferr, "\n");
+    }
+  if( qh FORCEoutput && (qh QHULLfinished || (!facet && !ridge) ) )
+    {
+    qh_produce_output();
+    }
+  else
+    {
+    if( exitcode != qh_ERRsingular && zzval_(Zsetplane) > qh hull_dim + 1 )
+      {
+      fprintf(qh ferr, "\nAt error exit:\n");
+      qh_printsummary(qh ferr);
+      if( qh PRINTstatistics )
+        {
+        qh_collectstatistics();
+        qh_printstatistics(qh ferr, "at error exit");
+        qh_memstatistics(qh ferr);
+        }
+      }
+    if( qh PRINTprecision )
+      {
+      qh_printstats(qh ferr, qhstat precision, NULL);
+      }
+    }
+  if( !exitcode )
+    {
+    exitcode = qh_ERRqhull;
+    }
+  else if( exitcode == qh_ERRsingular )
+    {
+    qh_printhelp_singular(qh ferr);
+    }
+  else if( exitcode == qh_ERRprec && !qh PREmerge )
+    {
+    qh_printhelp_degenerate(qh ferr);
+    }
+  if( qh NOerrexit )
+    {
+    fprintf(qh ferr, "qhull error while ending program.  Exit program\n");
+    exit(1);
+    }
+  qh NOerrexit = True;
+  longjmp(qh errexit, exitcode);
+} /* errexit */
+
+/*---------------------------------
+
+  qh_errprint( fp, string, atfacet, otherfacet, atridge, atvertex )
+  prints out the information of facets and ridges to fp
+  also prints neighbors and geomview output
+
+  notes:
+  except for string, any parameter may be NULL
+*/
+void qh_errprint(const char *string, facetT *atfacet, facetT *otherfacet, ridgeT *atridge, vertexT *atvertex)
+{
+  int i;
+
+  if( atfacet )
+    {
+    fprintf(qh ferr, "%s FACET:\n", string);
+    qh_printfacet(qh ferr, atfacet);
+    }
+  if( otherfacet )
+    {
+    fprintf(qh ferr, "%s OTHER FACET:\n", string);
+    qh_printfacet(qh ferr, otherfacet);
+    }
+  if( atridge )
+    {
+    fprintf(qh ferr, "%s RIDGE:\n", string);
+    qh_printridge(qh ferr, atridge);
+    if( atridge->top && atridge->top != atfacet && atridge->top != otherfacet )
+      {
+      qh_printfacet(qh ferr, atridge->top);
+      }
+    if( atridge->bottom
+        && atridge->bottom != atfacet && atridge->bottom != otherfacet )
+      {
+      qh_printfacet(qh ferr, atridge->bottom);
+      }
+    if( !atfacet )
+      {
+      atfacet = atridge->top;
+      }
+    if( !otherfacet )
+      {
+      otherfacet = otherfacet_(atridge, atfacet);
+      }
+    }
+  if( atvertex )
+    {
+    fprintf(qh ferr, "%s VERTEX:\n", string);
+    qh_printvertex(qh ferr, atvertex);
+    }
+  if( qh fout && qh FORCEoutput && atfacet && !qh QHULLfinished && !qh IStracing )
+    {
+    fprintf(qh ferr, "ERRONEOUS and NEIGHBORING FACETS to output\n");
+    for( i = 0; i < qh_PRINTEND; i++ )  /* use fout for geomview output */
+      {
+      qh_printneighborhood(qh fout, qh PRINTout[i], atfacet, otherfacet,
+                           !qh_ALL);
+      }
+    }
+} /* errprint */
+
+/*---------------------------------
+
+  qh_printfacetlist( fp, facetlist, facets, printall )
+  print all fields for a facet list and/or set of facets to fp
+  if !printall,
+  only prints good facets
+
+  notes:
+  also prints all vertices
+*/
+void qh_printfacetlist(facetT *facetlist, setT *facets, boolT printall)
+{
+  facetT *facet, * *facetp;
+
+  qh_printbegin(qh ferr, qh_PRINTfacets, facetlist, facets, printall);
+  FORALLfacet_(facetlist)
+  qh_printafacet(qh ferr, qh_PRINTfacets, facet, printall);
+  FOREACHfacet_(facets)
+  qh_printafacet(qh ferr, qh_PRINTfacets, facet, printall);
+  qh_printend(qh ferr, qh_PRINTfacets, facetlist, facets, printall);
+} /* printfacetlist */
+
+/*---------------------------------
+
+  qh_user_memsizes()
+  allocate up to 10 additional, quick allocation sizes
+
+  notes:
+  increase maximum number of allocations in qh_initqhull_mem()
+*/
+void qh_user_memsizes(void)
+{
+
+  /* qh_memsize (size); */
+} /* user_memsizes */
+
diff --git a/BRAINSABC/qhull/user.h b/BRAINSABC/qhull/user.h
new file mode 100644
index 00000000..fd451cef
--- /dev/null
+++ b/BRAINSABC/qhull/user.h
@@ -0,0 +1,762 @@
+/*
  ---------------------------------
+
+   user.h
+   user redefinable constants
+
+   see qh-user.htm.  see COPYING for copyright information.
+
+   before reading any code, review qhull.h for data structure definitions and
+   the "qh" macro.
+*/
+
+#ifndef qhDEFuser
+#define qhDEFuser 1
+
+/*============= data types and configuration macros ==========*/
+
+/*----------------------------------
+
+  realT
+    set the size of floating point numbers
+
+  qh_REALdigits
+    maximimum number of significant digits
+
+  qh_REAL_1, qh_REAL_2n, qh_REAL_3n
+    format strings for printf
+
+  qh_REALmax, qh_REALmin
+    maximum and minimum (near zero) values
+
+  qh_REALepsilon
+    machine roundoff.  Maximum roundoff error for addition and multiplication.
+
+  notes:
+   Select whether to store floating point numbers in single precision (float)
+   or double precision (double).
+
+   Use 'float' to save about 8% in time and 25% in space.  This is particularly
+   help if high-d where convex hulls are space limited.  Using 'float' also
+   reduces the printed size of Qhull's output since numbers have 8 digits of
+   precision.
+
+   Use 'double' when greater arithmetic precision is needed.  This is needed
+   for Delaunay triangulations and Voronoi diagrams when you are not merging
+   facets.
+
+   If 'double' gives insufficient precision, your data probably includes
+   degeneracies.  If so you should use facet merging (done by default)
+   or exact arithmetic (see imprecision section of manual, qh-impre.htm).
+   You may also use option 'Po' to force output despite precision errors.
+
+   You may use 'long double', but many format statements need to be changed
+   and you may need a 'long double' square root routine.  S. Grundmann
+   (sg@eeiwzb.et.tu-dresden.de) has done this.  He reports that the code runs
+   much slower with little gain in precision.
+
+   WARNING: on some machines,    int f(){realT a= REALmax;return (a == REALmax);}
+      returns False.  Use (a > REALmax/2) instead of (a == REALmax).
+
+   REALfloat =   1      all numbers are 'float' type
+             =   0      all numbers are 'double' type
+*/
+#define REALfloat 0
+
+#if ( REALfloat == 1 )
+#define realT float
+#define REALmax FLT_MAX
+#define REALmin FLT_MIN
+#define REALepsilon FLT_EPSILON
+#define qh_REALdigits 8   /* maximum number of significant digits */
+#define qh_REAL_1 "%6.8g "
+#define qh_REAL_2n "%6.8g %6.8g\n"
+#define qh_REAL_3n "%6.8g %6.8g %6.8g\n"
+
+#elif ( REALfloat == 0 )
+#define realT double
+#define REALmax DBL_MAX
+#define REALmin DBL_MIN
+#define REALepsilon DBL_EPSILON
+#define qh_REALdigits 16    /* maximum number of significant digits */
+#define qh_REAL_1 "%6.16g "
+#define qh_REAL_2n "%6.16g %6.16g\n"
+#define qh_REAL_3n "%6.16g %6.16g %6.16g\n"
+
+#else
+#error unknown float option
+#endif
+
+/*----------------------------------
+
+  qh_CPUclock
+    define the clock() function for reporting the total time spent by Qhull
+    returns CPU ticks as a 'long int'
+    qh_CPUclock is only used for reporting the total time spent by Qhull
+
+  qh_SECticks
+    the number of clock ticks per second
+
+  notes:
+    looks for CLOCKS_PER_SEC, CLOCKS_PER_SECOND, or assumes microseconds
+    to define a custom clock, set qh_CLOCKtype to 0
+
+    if your system does not use clock() to return CPU ticks, replace
+    qh_CPUclock with the corresponding function.  It is converted
+    to unsigned long to prevent wrap-around during long runs.
+
+
+   Set qh_CLOCKtype to
+
+     1      for CLOCKS_PER_SEC, CLOCKS_PER_SECOND, or microsecond
+                Note:  may fail if more than 1 hour elapsed time
+
+     2      use qh_clock() with POSIX times() (see global.c)
+*/
+#define qh_CLOCKtype 1  /* change to the desired number */
+
+#if ( qh_CLOCKtype == 1 )
+
+#if defined( CLOCKS_PER_SECOND )
+#define qh_CPUclock    ( (unsigned long)clock() )  /* return CPU clock */
+#define qh_SECticks CLOCKS_PER_SECOND
+
+#elif defined( CLOCKS_PER_SEC )
+#define qh_CPUclock    ( (unsigned long)clock() )  /* return CPU clock */
+#define qh_SECticks CLOCKS_PER_SEC
+
+#elif defined( CLK_TCK )
+#define qh_CPUclock    ( (unsigned long)clock() )  /* return CPU clock */
+#define qh_SECticks CLK_TCK
+
+#else
+#define qh_CPUclock    ( (unsigned long)clock() )  /* return CPU clock */
+#define qh_SECticks 1E6
+#endif
+
+#elif ( qh_CLOCKtype == 2 )
+#define qh_CPUclock    qh_clock()  /* return CPU clock */
+#define qh_SECticks 100
+
+#else /* qh_CLOCKtype == ? */
+#error unknown clock option
+#endif
+
+/*----------------------------------
+
+  qh_RANDOMtype, qh_RANDOMmax, qh_RANDOMseed
+    define random number generator
+
+    qh_RANDOMint generates a random integer between 0 and qh_RANDOMmax.
+    qh_RANDOMseed sets the random number seed for qh_RANDOMint
+
+  Set qh_RANDOMtype (default 5) to:
+    1       for random() with 31 bits (UCB)
+    2       for rand() with RAND_MAX or 15 bits (system 5)
+    3       for rand() with 31 bits (Sun)
+    4       for lrand48() with 31 bits (Solaris)
+    5       for qh_rand() with 31 bits (included with Qhull)
+
+  notes:
+    Random numbers are used by rbox to generate point sets.  Random
+    numbers are used by Qhull to rotate the input ('QRn' option),
+    simulate a randomized algorithm ('Qr' option), and to simulate
+    roundoff errors ('Rn' option).
+
+    Random number generators differ between systems.  Most systems provide
+    rand() but the period varies.  The period of rand() is not critical
+    since qhull does not normally use random numbers.
+
+    The default generator is Park & Miller's minimal standard random
+    number generator [CACM 31:1195 '88].  It is included with Qhull.
+
+    If qh_RANDOMmax is wrong, qhull will report a warning and Geomview
+    output will likely be invisible.
+*/
+#define qh_RANDOMtype 5   /* *** change to the desired number *** */
+
+#if ( qh_RANDOMtype == 1 )
+#define qh_RANDOMmax ( (realT)0x7fffffffUL )  /* 31 bits, random()/MAX */
+#define qh_RANDOMint random()
+#define qh_RANDOMseed_(seed) srandom(seed);
+
+#elif ( qh_RANDOMtype == 2 )
+#ifdef RAND_MAX
+#define qh_RANDOMmax ( (realT)RAND_MAX )
+#else
+#define qh_RANDOMmax ( (realT)32767 )   /* 15 bits (System 5) */
+#endif
+#define qh_RANDOMint  rand()
+#define qh_RANDOMseed_(seed) srand( (unsigned)seed );
+
+#elif ( qh_RANDOMtype == 3 )
+#define qh_RANDOMmax ( (realT)0x7fffffffUL )  /* 31 bits, Sun */
+#define qh_RANDOMint  rand()
+#define qh_RANDOMseed_(seed) srand( (unsigned)seed );
+
+#elif ( qh_RANDOMtype == 4 )
+#define qh_RANDOMmax ( (realT)0x7fffffffUL )  /* 31 bits, lrand38()/MAX */
+#define qh_RANDOMint lrand48()
+#define qh_RANDOMseed_(seed) srand48(seed);
+
+#elif ( qh_RANDOMtype == 5 )
+#define qh_RANDOMmax ( (realT)2147483646UL )  /* 31 bits, qh_rand/MAX */
+#define qh_RANDOMint qh_rand()
+#define qh_RANDOMseed_(seed) qh_srand(seed);
+/* unlike rand(), never returns 0 */
+
+#else
+#error : unknown random option
+#endif
+
+/*----------------------------------
+
+  qh_ORIENTclock
+    0 for inward pointing normals by Geomview convention
+*/
+#define qh_ORIENTclock 0
+
+/*========= performance related constants =========*/
+
+/*----------------------------------
+
+  qh_HASHfactor
+    total hash slots / used hash slots.  Must be at least 1.1.
+
+  notes:
+    =2 for at worst 50% occupancy for qh hash_table and normally 25% occupancy
+*/
+#define qh_HASHfactor 2
+
+/*----------------------------------
+
+  qh_VERIFYdirect
+    with 'Tv' verify all points against all facets if op count is smaller
+
+  notes:
+    if greater, calls qh_check_bestdist() instead
+*/
+#define qh_VERIFYdirect 1000000
+
+/*----------------------------------
+
+  qh_INITIALsearch
+     if qh_INITIALmax, search points up to this dimension
+*/
+#define qh_INITIALsearch 6
+
+/*----------------------------------
+
+  qh_INITIALmax
+    if dim >= qh_INITIALmax, use min/max coordinate points for initial simplex
+
+  notes:
+    from points with non-zero determinants
+    use option 'Qs' to override (much slower)
+*/
+#define qh_INITIALmax 8
+
+/*----------------------------------
+
+  qh_JOGGLEdefault
+    default qh.JOGGLEmax is qh.DISTround * qh_JOGGLEdefault
+
+  notes:
+    rbox s r 100 | qhull QJ1e-15 QR0 generates 90% faults at distround 7e-16
+    rbox s r 100 | qhull QJ1e-14 QR0 generates 70% faults
+    rbox s r 100 | qhull QJ1e-13 QR0 generates 35% faults
+    rbox s r 100 | qhull QJ1e-12 QR0 generates 8% faults
+    rbox s r 100 | qhull QJ1e-11 QR0 generates 1% faults
+    rbox s r 100 | qhull QJ1e-10 QR0 generates 0% faults
+    rbox 1000 W0 | qhull QJ1e-12 QR0 generates 86% faults
+    rbox 1000 W0 | qhull QJ1e-11 QR0 generates 20% faults
+    rbox 1000 W0 | qhull QJ1e-10 QR0 generates 2% faults
+    the later have about 20 points per facet, each of which may interfere
+
+    pick a value large enough to avoid retries on most inputs
+*/
+#define qh_JOGGLEdefault 30000.0
+
+/*----------------------------------
+
+  qh_JOGGLEincrease
+    factor to increase qh.JOGGLEmax on qh_JOGGLEretry or qh_JOGGLEagain
+*/
+#define qh_JOGGLEincrease 10.0
+
+/*----------------------------------
+
+  qh_JOGGLEretry
+    if ZZretry = qh_JOGGLEretry, increase qh.JOGGLEmax
+
+  notes:
+    try twice at the original value in case of bad luck the first time
+*/
+#define qh_JOGGLEretry 2
+
+/*----------------------------------
+
+  qh_JOGGLEagain
+    every following qh_JOGGLEagain, increase qh.JOGGLEmax
+
+  notes:
+    1 is OK since it's already failed qh_JOGGLEretry times
+*/
+#define qh_JOGGLEagain 1
+
+/*----------------------------------
+
+  qh_JOGGLEmaxincrease
+    maximum qh.JOGGLEmax due to qh_JOGGLEincrease
+    relative to qh.MAXwidth
+
+  notes:
+    qh.joggleinput will retry at this value until qh_JOGGLEmaxretry
+*/
+#define qh_JOGGLEmaxincrease 1e-2
+
+/*----------------------------------
+
+  qh_JOGGLEmaxretry
+    stop after qh_JOGGLEmaxretry attempts
+*/
+#define qh_JOGGLEmaxretry 100
+
+/*========= memory constants =========*/
+
+/*----------------------------------
+
+  qh_MEMalign
+    memory alignment for qh_meminitbuffers() in global.c
+
+  notes:
+    to avoid bus errors, memory allocation must consider alignment requirements.
+    malloc() automatically takes care of alignment.   Since mem.c manages
+    its own memory, we need to explicitly specify alignment in
+    qh_meminitbuffers().
+
+    A safe choice is sizeof(double).  sizeof(float) may be used if doubles
+    do not occur in data structures and pointers are the same size.  Be careful
+    of machines (e.g., DEC Alpha) with large pointers.
+
+    If using gcc, best alignment is
+              #define qh_MEMalign fmax_(__alignof__(realT),__alignof__(void *))
+*/
+#define qh_MEMalign fmax_( sizeof( realT ), sizeof( void * ) )
+
+/*----------------------------------
+
+  qh_MEMbufsize
+    size of additional memory buffers
+
+  notes:
+    used for qh_meminitbuffers() in global.c
+*/
+#define qh_MEMbufsize 0x10000       /* allocate 64K memory buffers */
+
+/*----------------------------------
+
+  qh_MEMinitbuf
+    size of initial memory buffer
+
+  notes:
+    use for qh_meminitbuffers() in global.c
+*/
+#define qh_MEMinitbuf 0x20000      /* initially allocate 128K buffer */
+
+/*----------------------------------
+
+  qh_INFINITE
+    on output, indicates Voronoi center at infinity
+*/
+#define qh_INFINITE  -10.101
+
+/*----------------------------------
+
+  qh_DEFAULTbox
+    default box size (Geomview expects 0.5)
+*/
+#define qh_DEFAULTbox 0.5
+
+/*======= conditional compilation ============================*/
+
+/*----------------------------------
+
+  __cplusplus
+    defined by C++ compilers
+
+  __MSC_VER
+    defined by Microsoft Visual C++
+
+  __MWERKS__ && __POWERPC__
+    defined by Metrowerks when compiling for the Power Macintosh
+
+  __STDC__
+    defined for strict ANSI C
+*/
+
+/*----------------------------------
+
+  qh_COMPUTEfurthest
+    compute furthest distance to an outside point instead of storing it with the facet
+    =1 to compute furthest
+
+  notes:
+    computing furthest saves memory but costs time
+      about 40% more distance tests for partitioning
+      removes facet->furthestdist
+*/
+#define qh_COMPUTEfurthest 0
+
+/*----------------------------------
+
+  qh_KEEPstatistics
+    =0 removes most of statistic gathering and reporting
+
+  notes:
+    if 0, code size is reduced by about 4%.
+*/
+#define qh_KEEPstatistics 1
+
+/*----------------------------------
+
+  qh_MAXoutside
+    record outer plane for each facet
+    =1 to record facet->maxoutside
+
+  notes:
+    this takes a realT per facet and slightly slows down qhull
+    it produces better outer planes for geomview output
+*/
+#define qh_MAXoutside 1
+
+/*----------------------------------
+
+  qh_NOmerge
+    disables facet merging if defined
+
+  notes:
+    This saves about 10% space.
+
+    Unless 'Q0'
+      qh_NOmerge sets 'QJ' to avoid precision errors
+
+    #define qh_NOmerge
+
+  see:
+    qh_NOmem in mem.c
+
+    see user.c/user_eg.c for removing io.o
+*/
+
+/*----------------------------------
+
+  qh_NOtrace
+    no tracing if defined
+
+  notes:
+    This saves about 5% space.
+
+    #define qh_NOtrace
+*/
+
+/*----------------------------------
+
+  qh_QHpointer
+    access global data with pointer or static structure
+
+  qh_QHpointer  = 1     access globals via a pointer to allocated memory
+                        enables qh_saveqhull() and qh_restoreqhull()
+      costs about 8% in time and 2% in space
+
+    = 0     qh_qh and qh_qhstat are static data structures
+            only one instance of qhull() can be active at a time
+      default value
+
+  notes:
+    all global variables for qhull are in qh, qhmem, and qhstat
+    qh is defined in qhull.h
+    qhmem is defined in mem.h
+    qhstat is defined in stat.h
+
+  see:
+    user_eg.c for an example
+*/
+#define qh_QHpointer 0
+#if 0  /* sample code */
+qhT *oldqhA, *oldqhB;
+
+exitcode = qh_new_qhull(dim, numpoints, points, ismalloc,
+                        flags, outfile, errfile);
+/* use results from first call to qh_new_qhull */
+oldqhA = qh_save_qhull();
+exitcode = qh_new_qhull(dimB, numpointsB, pointsB, ismalloc,
+                        flags, outfile, errfile);
+/* use results from second call to qh_new_qhull */
+oldqhB = qh_save_qhull();
+qh_restore_qhull(&oldqhA);
+/* use results from first call to qh_new_qhull */
+qh_freeqhull(qh_ALL);       /* frees all memory used by first call */
+qh_restore_qhull(&oldqhB);
+/* use results from second call to qh_new_qhull */
+qh_freeqhull(!qh_ALL);                /* frees long memory used by second call
+                                        */
+qh_memfreeshort(&curlong, &totlong);  /* frees short memory and memory allocator
+                                        */
+#endif
+
+/*----------------------------------
+
+  qh_QUICKhelp
+    =1 to use abbreviated help messages, e.g., for degenerate inputs
+*/
+#define qh_QUICKhelp    0
+
+/* ============ -merge constants- ====================
+
+   These constants effect facet merging.  You probably will not need
+   to modify these.  They effect the performance of facet merging.
+*/
+
+/*----------------------------------
+
+  qh_DIMmergeVertex
+    max dimension for vertex merging (it is not effective in high-d)
+*/
+#define qh_DIMmergeVertex 6
+
+/*----------------------------------
+
+  qh_DIMreduceBuild
+     max dimension for vertex reduction during build (slow in high-d)
+*/
+#define qh_DIMreduceBuild 5
+
+/*----------------------------------
+
+  qh_BESTcentrum
+     if > 2*dim+n vertices, qh_findbestneighbor() tests centrums (faster)
+     else, qh_findbestneighbor() tests all vertices (much better merges)
+
+  qh_BESTcentrum2
+     if qh_BESTcentrum2 * DIM3 + BESTcentrum < #vertices tests centrums
+*/
+#define qh_BESTcentrum 20
+#define qh_BESTcentrum2 2
+
+/*----------------------------------
+
+  qh_BESTnonconvex
+    if > dim+n neighbors, qh_findbestneighbor() tests nonconvex ridges.
+
+  notes:
+    It is needed because qh_findbestneighbor is slow for large facets
+*/
+#define qh_BESTnonconvex 15
+
+/*----------------------------------
+
+  qh_MAXnewmerges
+    if >n newmerges, qh_merge_nonconvex() calls qh_reducevertices_centrums.
+
+  notes:
+    It is needed because postmerge can merge many facets at once
+*/
+#define qh_MAXnewmerges 2
+
+/*----------------------------------
+
+  qh_MAXnewcentrum
+    if <= dim+n vertices (n approximates the number of merges),
+      reset the centrum in qh_updatetested() and qh_mergecycle_facets()
+
+  notes:
+    needed to reduce cost and because centrums may move too much if
+    many vertices in high-d
+*/
+#define qh_MAXnewcentrum 5
+
+/*----------------------------------
+
+  qh_COPLANARratio
+    for 3-d+ merging, qh.MINvisible is n*premerge_centrum
+
+  notes:
+    for non-merging, it's DISTround
+*/
+#define qh_COPLANARratio 3
+
+/*----------------------------------
+
+  qh_DISToutside
+    When is a point clearly outside of a facet?
+    Stops search in qh_findbestnew or qh_partitionall
+    qh_findbest uses qh.MINoutside since since it is only called if no merges.
+
+  notes:
+    'Qf' always searches for best facet
+    if !qh.MERGING, same as qh.MINoutside.
+    if qh_USEfindbestnew, increase value since neighboring facets may be ill-behaved
+      [Note: Zdelvertextot occurs normally with interior points]
+            RBOX 1000 s Z1 G1e-13 t1001188774 | QHULL Tv
+    When there is a sharp edge, need to move points to a
+    clearly good facet; otherwise may be lost in another partitioning.
+    if too big then O(n^2) behavior for partitioning in cone
+    if very small then important points not processed
+    Needed in qh_partitionall for
+      RBOX 1000 s Z1 G1e-13 t1001032651 | QHULL Tv
+    Needed in qh_findbestnew for many instances of
+      RBOX 1000 s Z1 G1e-13 t | QHULL Tv
+
+  See:
+    qh_DISToutside -- when is a point clearly outside of a facet
+    qh_SEARCHdist -- when is facet coplanar with the best facet?
+    qh_USEfindbestnew -- when to use qh_findbestnew for qh_partitionpoint()
+*/
+#define qh_DISToutside                                                  \
+  ( ( qh_USEfindbestnew ? 2 : 1 )                                       \
+    * fmax_( ( qh MERGING ? 2 : 1 ) * qh MINoutside, qh max_outside ) )
+
+/*----------------------------------
+
+  qh_RATIOnearinside
+    ratio of qh.NEARinside to qh.ONEmerge for retaining inside points for
+    qh_check_maxout().
+
+  notes:
+    This is overkill since do not know the correct value.
+    It effects whether 'Qc' reports all coplanar points
+    Not used for 'd' since non-extreme points are coplanar
+*/
+#define qh_RATIOnearinside 5
+
+/*----------------------------------
+
+  qh_SEARCHdist
+    When is a facet coplanar with the best facet?
+    qh_findbesthorizon: all coplanar facets of the best facet need to be searched.
+
+  See:
+    qh_DISToutside -- when is a point clearly outside of a facet
+    qh_SEARCHdist -- when is facet coplanar with the best facet?
+    qh_USEfindbestnew -- when to use qh_findbestnew for qh_partitionpoint()
+*/
+#define qh_SEARCHdist                                                   \
+  ( ( qh_USEfindbestnew ? 2 : 1 )                                       \
+    * ( qh max_outside + 2 * qh DISTround + fmax_( qh MINvisible, qh MAXcoplanar) ) );
+
+/*----------------------------------
+
+  qh_USEfindbestnew
+     Always use qh_findbestnew for qh_partitionpoint, otherwise use
+     qh_findbestnew if merged new facet or sharpnewfacets.
+
+  See:
+    qh_DISToutside -- when is a point clearly outside of a facet
+    qh_SEARCHdist -- when is facet coplanar with the best facet?
+    qh_USEfindbestnew -- when to use qh_findbestnew for qh_partitionpoint()
+*/
+#define qh_USEfindbestnew ( zzval_(Ztotmerge) > 50 )
+
+/*----------------------------------
+
+  qh_WIDEcoplanar
+    n*MAXcoplanar or n*MINvisible for a WIDEfacet
+
+    if vertex is further than qh.WIDEfacet from the hyperplane
+    then its ridges are not counted in computing the area, and
+    the facet's centrum is frozen.
+
+  notes:
+   qh.WIDEfacet= max(qh.MAXoutside,qh_WIDEcoplanar*qh.MAXcoplanar,
+      qh_WIDEcoplanar * qh.MINvisible);
+*/
+#define qh_WIDEcoplanar 6
+
+/*----------------------------------
+
+  qh_MAXnarrow
+    max. cosine in initial hull that sets qh.NARROWhull
+
+  notes:
+    If qh.NARROWhull, the initial partition does not make
+    coplanar points.  If narrow, a coplanar point can be
+    coplanar to two facets of opposite orientations and
+    distant from the exact convex hull.
+
+    Conservative estimate.  Don't actually see problems until it is -1.0
+*/
+#define qh_MAXnarrow -0.99999999
+
+/*----------------------------------
+
+  qh_WARNnarrow
+    max. cosine in initial hull to warn about qh.NARROWhull
+
+  notes:
+    this is a conservative estimate.
+    Don't actually see problems until it is -1.0.  See qh-impre.htm
+*/
+#define qh_WARNnarrow -0.999999999999999
+
+/*----------------------------------
+
+  qh_ZEROdelaunay
+    a zero Delaunay facet occurs for input sites coplanar with their convex hull
+    the last normal coefficient of a zero Delaunay facet is within
+        qh_ZEROdelaunay * qh.ANGLEround of 0
+
+  notes:
+    qh_ZEROdelaunay does not allow for joggled input ('QJ').
+
+    You can avoid zero Delaunay facets by surrounding the input with a box.
+
+    Use option 'PDk:-n' to explicitly define zero Delaunay facets
+      k= dimension of input sites (e.g., 3 for 3-d Delaunay triangulation)
+      n= the cutoff for zero Delaunay facets (e.g., 'PD3:-1e-12')
+*/
+#define qh_ZEROdelaunay 2
+
+#endif /* qh_DEFuser */
diff --git a/BRAINSABC/qhull/user_eg.c b/BRAINSABC/qhull/user_eg.c
new file mode 100644
index 00000000..78ae1fce
--- /dev/null
+++ b/BRAINSABC/qhull/user_eg.c
@@ -0,0 +1,375 @@
+/*
  ---------------------------------
+
+  user_eg.c
+  sample code for calling qhull() from an application
+
+  call with:
+
+  user_eg "cube/diamond options" "delaunay options" "halfspace options"
+
+  for example:
+
+  user_eg                             #return summaries
+
+  user_eg "n" "o" "Fp"                #return normals, OFF, points
+
+  user_eg "n Qt" "o" "Fp"             #triangulated cube
+
+  user_eg "QR0 p" "QR0 v p" "QR0 Fp"  #rotate input and return points
+  #'v' returns Voronoi
+  #transform is rotated for halfspaces
+
+  main() makes three runs of qhull.
+
+  1) compute the convex hull of a cube
+
+  2a) compute the Delaunay triangulation of random points
+
+  2b) find the Delaunay triangle closest to a point.
+
+  3) compute the halfspace intersection of a diamond
+
+  notes:
+
+  For another example, see main() in unix.c and user_eg2.c.
+  These examples, call qh_qhull() directly.  They allow
+  tighter control on the code loaded with Qhull.
+
+  For a simple C++ example, see qhull_interface.cpp
+
+  Summaries are sent to stderr if other output formats are used
+
+  compiled by 'make user_eg'
+
+  see qhull.h for data structures, macros, and user-callable functions.
+*/
+
+#include "qhull_a.h"
+
+/*-------------------------------------------------
+  -internal function prototypes
+*/
+void print_summary(void);
+
+void makecube(coordT *points, int numpoints, int dim);
+
+void makeDelaunay(coordT *points, int numpoints, int dim, int seed);
+
+void findDelaunay(int dim);
+
+void makehalf(coordT *points, int numpoints, int dim);
+
+/*-------------------------------------------------
+  -print_summary()
+*/
+void print_summary(void)
+{
+  facetT *facet;
+  int     k;
+
+  printf("\n%d vertices and %d facets with normals:\n",
+         qh num_vertices, qh num_facets);
+  FORALLfacets {
+    for( k = 0; k < qh hull_dim; k++ )
+      {
+      printf("%6.2g ", facet->normal[k]);
+      }
+    printf("\n");
+    }
+}
+
+/*--------------------------------------------------
+  -makecube- set points to vertices of cube
+  points is numpoints X dim
+*/
+void makecube(coordT *points, int numpoints, int dim)
+{
+  int     j, k;
+  coordT *point;
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * dim;
+    for( k = dim; k--; )
+      {
+      if( j & ( 1 << k) )
+        {
+        point[k] = 1.0;
+        }
+      else
+        {
+        point[k] = -1.0;
+        }
+      }
+    }
+} /*.makecube.*/
+
+/*--------------------------------------------------
+  -makeDelaunay- set points for dim Delaunay triangulation of random points
+  points is numpoints X dim.
+  notes:
+  makeDelaunay() in user_eg2.c uses qh_setdelaunay() to project points in place.
+*/
+void makeDelaunay(coordT *points, int numpoints, int dim, int seed)
+{
+  int     j, k;
+  coordT *point, realr;
+
+  printf("seed: %d\n", seed);
+  qh_RANDOMseed_( seed);
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * dim;
+    for( k = 0; k < dim; k++ )
+      {
+      realr = qh_RANDOMint;
+      point[k] = 2.0 * realr / (qh_RANDOMmax + 1) - 1.0;
+      }
+    }
+} /*.makeDelaunay.*/
+
+/*--------------------------------------------------
+  -findDelaunay- find Delaunay triangle for [0.5,0.5,...]
+  assumes dim < 100
+  notes:
+  calls qh_setdelaunay() to project the point to a parabaloid
+  warning:
+  This is not implemented for tricoplanar facets ('Qt'),
+  See locate a facet with qh_findbestfacet()
+*/
+void findDelaunay(int dim)
+{
+  int      k;
+  coordT   point[100];
+  boolT    isoutside;
+  realT    bestdist;
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+  for( k = 0; k < dim; k++ )
+    {
+    point[k] = 0.5;
+    }
+  qh_setdelaunay(dim + 1, 1, point);
+  facet = qh_findbestfacet(point, qh_ALL, &bestdist, &isoutside);
+  if( facet->tricoplanar )
+    {
+    fprintf(
+      stderr,
+      "findDelaunay: not implemented for triangulated, non-simplicial Delaunay regions (tricoplanar facet, f%d).\n",
+      facet->id);
+    qh_errexit(qh_ERRqhull, facet, NULL);
+    }
+  FOREACHvertex_(facet->vertices) {
+    for( k = 0; k < dim; k++ )
+      {
+      printf("%5.2f ", vertex->point[k]);
+      }
+    printf("\n");
+    }
+} /*.findDelaunay.*/
+
+/*--------------------------------------------------
+  -makehalf- set points to halfspaces for a (dim)-dimensional diamond
+  points is numpoints X dim+1
+
+  each halfspace consists of dim coefficients followed by an offset
+*/
+void makehalf(coordT *points, int numpoints, int dim)
+{
+  int     j, k;
+  coordT *point;
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * (dim + 1);
+    point[dim] = -1.0; /* offset */
+    for( k = dim; k--; )
+      {
+      if( j & ( 1 << k) )
+        {
+        point[k] = 1.0;
+        }
+      else
+        {
+        point[k] = -1.0;
+        }
+      }
+    }
+} /*.makehalf.*/
+
+#define DIM 3     /* dimension of points, must be < 31 for SIZEcube */
+#define SIZEcube (1 << DIM)
+#define SIZEdiamond (2 * DIM)
+#define TOTpoints (SIZEcube + SIZEdiamond)
+
+/*--------------------------------------------------
+  -main- derived from call_qhull in user.c
+
+  see program header
+
+  this contains three runs of Qhull for convex hull, Delaunay
+  triangulation or Voronoi vertices, and halfspace intersection
+
+*/
+int main(int argc, char *argv[])
+{
+  int     dim = DIM;                     /* dimension of points */
+  int     numpoints;                     /* number of points */
+  coordT  points[(DIM + 1) * TOTpoints]; /* array of coordinates for each point
+                                           */
+  coordT *rows[TOTpoints];
+  boolT   ismalloc = False; /* True if qhull should free points in
+                              qh_freeqhull() or reallocation */
+  char    flags[250];       /* option flags for qhull, see qh_opt.htm */
+  FILE *  outfile = stdout; /* output from qh_produce_output()
+             use NULL to skip qh_produce_output() */
+  FILE *  errfile = stderr; /* error messages from qhull code */
+  int     exitcode;         /* 0 if no error from qhull */
+  facetT *facet;            /* set by FORALLfacets */
+  int     curlong, totlong; /* memory remaining after qh_memfreeshort */
+  int     i;
+
+  printf(
+    "This is the output from user_eg.c\n\n\
+It shows how qhull() may be called from an application.  It is not part\n\
+of qhull itself.  If it appears accidently, please remove user_eg.c from\n\
+your project.\n\n"                                                                                                                                                                                                   );
+
+  /*
+    Run 1: convex hull
+  */
+  printf( "\ncompute convex hull of cube after rotating input\n");
+  sprintf(flags, "qhull s Tcv %s", argc >= 2 ? argv[1] : "");
+  numpoints = SIZEcube;
+  makecube(points, numpoints, DIM);
+  for( i = numpoints; i--; )
+    {
+    rows[i] = points + dim * i;
+    }
+  qh_printmatrix(outfile, "input", rows, numpoints, dim);
+  exitcode = qh_new_qhull(dim, numpoints, points, ismalloc,
+                          flags, outfile, errfile);
+  if( !exitcode )                    /* if no error */
+    { /* 'qh facet_list' contains the convex hull */
+    print_summary();
+    FORALLfacets {
+      /* ... your code ... */
+      }
+    }
+  qh_freeqhull(!qh_ALL);                   /* free long memory  */
+  qh_memfreeshort(&curlong, &totlong);     /* free short memory and memory
+                                             allocator */
+  if( curlong || totlong )
+    {
+    fprintf(errfile, "qhull internal warning (user_eg, #1): did not free %d bytes of long memory (%d pieces)\n",
+            totlong,
+            curlong);
+    }
+
+  /*
+    Run 2: Delaunay triangulation
+  */
+
+  printf( "\ncompute %d-d Delaunay triangulation\n", dim);
+  sprintf(flags, "qhull s d Tcv %s", argc >= 3 ? argv[2] : "");
+  numpoints = SIZEcube;
+  makeDelaunay(points, numpoints, dim, time(NULL) );
+  for( i = numpoints; i--; )
+    {
+    rows[i] = points + dim * i;
+    }
+  qh_printmatrix(outfile, "input", rows, numpoints, dim);
+  exitcode = qh_new_qhull(dim, numpoints, points, ismalloc,
+                          flags, outfile, errfile);
+  if( !exitcode )                    /* if no error */
+    { /* 'qh facet_list' contains the convex hull */
+     /* If you want a Voronoi diagram ('v') and do not request output (i.e., outfile=NULL),
+        call qh_setvoronoi_all() after qh_new_qhull(). */
+    print_summary();
+    FORALLfacets {
+      /* ... your code ... */
+      }
+    printf( "\nfind %d-d Delaunay triangle closest to [0.5, 0.5, ...]\n", dim);
+    exitcode = setjmp(qh errexit);
+    if( !exitcode )
+      {
+      /* Trap Qhull errors in findDelaunay().  Without the setjmp(), Qhull
+         will exit() after reporting an error */
+      qh NOerrexit = False;
+      findDelaunay(DIM);
+      }
+    qh NOerrexit = True;
+    }
+#if qh_QHpointer  /* see user.h */
+    {
+    qhT *  oldqhA, *oldqhB;
+    coordT pointsB[DIM * TOTpoints]; /* array of coordinates for each point */
+
+    printf( "\nsave first triangulation and compute a new triangulation\n");
+    oldqhA = qh_save_qhull();
+    sprintf(flags, "qhull s d Tcv %s", argc >= 3 ? argv[2] : "");
+    numpoints = SIZEcube;
+    makeDelaunay(pointsB, numpoints, dim, time(NULL) + 1);
+    for( i = numpoints; i--; )
+      {
+      rows[i] = pointsB + dim * i;
+      }
+    qh_printmatrix(outfile, "input", rows, numpoints, dim);
+    exitcode = qh_new_qhull(dim, numpoints, pointsB, ismalloc,
+                            flags, outfile, errfile);
+    if( !exitcode )
+      {
+      print_summary();
+      }
+    printf( "\nsave second triangulation and restore first one\n");
+    oldqhB = qh_save_qhull();
+    qh_restore_qhull(&oldqhA);
+    print_summary();
+    printf( "\nfree first triangulation and restore second one.\n");
+    qh_freeqhull(qh_ALL);                /* free short and long memory used by
+                                           first call */
+    /* do not use qh_memfreeshort */
+    qh_restore_qhull(&oldqhB);
+    print_summary();
+    }
+#endif
+  qh_freeqhull(!qh_ALL);                 /* free long memory */
+  qh_memfreeshort(&curlong, &totlong);   /* free short memory and memory
+                                           allocator */
+  if( curlong || totlong )
+    {
+    fprintf(errfile, "qhull internal warning (user_eg, #2): did not free %d bytes of long memory (%d pieces)\n",
+            totlong,
+            curlong);
+    }
+
+  /*
+    Run 3: halfspace intersection about the origin
+  */
+  printf( "\ncompute halfspace intersection about the origin for a diamond\n");
+  sprintf(flags, "qhull H0 s Tcv %s", argc >= 4 ? argv[3] : "Fp");
+  numpoints = SIZEcube;
+  makehalf(points, numpoints, dim);
+  for( i = numpoints; i--; )
+    {
+    rows[i] = points + (dim + 1) * i;
+    }
+  qh_printmatrix(outfile, "input as halfspace coefficients + offsets", rows, numpoints, dim + 1);
+  /* use qh_sethalfspace_all to transform the halfspaces yourself.
+     If so, set 'qh feasible_point and do not use option 'Hn,...' [it would retransform the halfspaces]
+  */
+  exitcode = qh_new_qhull(dim + 1, numpoints, points, ismalloc,
+                          flags, outfile, errfile);
+  if( !exitcode )
+    {
+    print_summary();
+    }
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )  /* could also check previous runs */
+    {
+    fprintf(stderr, "qhull internal warning (user_eg, #3): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+  return exitcode;
+} /* main */
+
diff --git a/BRAINSABC/qhull/user_eg2.c b/BRAINSABC/qhull/user_eg2.c
new file mode 100644
index 00000000..92c9da8c
--- /dev/null
+++ b/BRAINSABC/qhull/user_eg2.c
@@ -0,0 +1,647 @@
+/*
  ---------------------------------
+
+  user_eg2.c
+
+  sample code for calling qhull() from an application.
+
+  See user_eg.c for a simpler method using qh_new_qhull().
+  The method used here and in unix.c gives you additional
+  control over Qhull.
+
+  call with:
+
+  user_eg2 "triangulated cube/diamond options" "delaunay options" "halfspace options"
+
+  for example:
+
+  user_eg2                             #return summaries
+
+  user_eg2 "n" "o" "Fp"                #return normals, OFF, points
+
+  user_eg2 "QR0 p" "QR0 v p" "QR0 Fp"  #rotate input and return points
+  #'v' returns Voronoi
+  #transform is rotated for halfspaces
+
+  main() makes three runs of qhull.
+
+  1) compute the convex hull of a cube, and incrementally add a diamond
+
+  2a) compute the Delaunay triangulation of random points, and add points.
+
+  2b) find the Delaunay triangle closest to a point.
+
+  3) compute the halfspace intersection of a diamond, and add a cube
+
+  notes:
+
+  summaries are sent to stderr if other output formats are used
+
+  derived from unix.c and compiled by 'make user_eg2'
+
+  see qhull.h for data structures, macros, and user-callable functions.
+
+  If you want to control all output to stdio and input to stdin,
+  set the #if below to "1" and delete all lines that contain "io.c".
+  This prevents the loading of io.o.  Qhull will
+  still write to 'qh ferr' (stderr) for error reporting and tracing.
+
+  Defining #if 1, also prevents user.o from being loaded.
+*/
+
+#include "qhull_a.h"
+
+/*-------------------------------------------------
+  -internal function prototypes
+*/
+void print_summary(void);
+
+void makecube(coordT *points, int numpoints, int dim);
+
+void adddiamond(coordT *points, int numpoints, int numnew, int dim);
+
+void makeDelaunay(coordT *points, int numpoints, int dim);
+
+void addDelaunay(coordT *points, int numpoints, int numnew, int dim);
+
+void findDelaunay(int dim);
+
+void makehalf(coordT *points, int numpoints, int dim);
+
+void addhalf(coordT *points, int numpoints, int numnew, int dim, coordT *feasible);
+
+/*-------------------------------------------------
+  -print_summary()
+*/
+void print_summary(void)
+{
+  facetT *facet;
+  int     k;
+
+  printf("\n%d vertices and %d facets with normals:\n",
+         qh num_vertices, qh num_facets);
+  FORALLfacets {
+    for( k = 0; k < qh hull_dim; k++ )
+      {
+      printf("%6.2g ", facet->normal[k]);
+      }
+    printf("\n");
+    }
+}
+
+/*--------------------------------------------------
+  -makecube- set points to vertices of cube
+  points is numpoints X dim
+*/
+void makecube(coordT *points, int numpoints, int dim)
+{
+  int     j, k;
+  coordT *point;
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * dim;
+    for( k = dim; k--; )
+      {
+      if( j & ( 1 << k) )
+        {
+        point[k] = 1.0;
+        }
+      else
+        {
+        point[k] = -1.0;
+        }
+      }
+    }
+} /*.makecube.*/
+
+/*--------------------------------------------------
+  -adddiamond- add diamond to convex hull
+  points is numpoints+numnew X dim.
+
+  notes:
+  qh_addpoint() does not make a copy of the point coordinates.
+
+  For inside points and some outside points, qh_findbestfacet performs
+  an exhaustive search for a visible facet.  Algorithms that retain
+  previously constructed hulls should be faster for on-line construction
+  of the convex hull.
+*/
+void adddiamond(coordT *points, int numpoints, int numnew, int dim)
+{
+  int     j, k;
+  coordT *point;
+  facetT *facet;
+  boolT   isoutside;
+  realT   bestdist;
+  for( j = 0; j < numnew; j++ )
+    {
+    point = points + (numpoints + j) * dim;
+    if( points == qh first_point )  /* in case of 'QRn' */
+      {
+      qh num_points = numpoints + j + 1;
+      }
+    /* qh num_points sets the size of the points array.  You may
+       allocate the points elsewhere.  If so, qh_addpoint records
+       the point's address in qh other_points
+    */
+    for( k = dim; k--; )
+      {
+      if( j / 2 == k )
+        {
+        point[k] = (j & 1) ? 2.0 : -2.0;
+        }
+      else
+        {
+        point[k] = 0.0;
+        }
+      }
+    facet = qh_findbestfacet(point, !qh_ALL, &bestdist, &isoutside);
+    if( isoutside )
+      {
+      if( !qh_addpoint(point, facet, False) )
+        {
+        break; /* user requested an early exit with 'TVn' or 'TCn' */
+        }
+      }
+    printf("%d vertices and %d facets\n",
+           qh num_vertices, qh num_facets);
+    /* qh_produce_output(); */
+    }
+  if( qh DOcheckmax )
+    {
+    qh_check_maxout();
+    }
+  else if( qh KEEPnearinside )
+    {
+    qh_nearcoplanar();
+    }
+} /*.adddiamond.*/
+
+/*--------------------------------------------------
+  -makeDelaunay- set points for dim-1 Delaunay triangulation of random points
+  points is numpoints X dim.  Each point is projected to a paraboloid.
+*/
+void makeDelaunay(coordT *points, int numpoints, int dim)
+{
+  int     j, k, seed;
+  coordT *point, realr;
+
+  seed = time(NULL);
+  printf("seed: %d\n", seed);
+  qh_RANDOMseed_( seed);
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * dim;
+    for( k = 0; k < dim - 1; k++ )
+      {
+      realr = qh_RANDOMint;
+      point[k] = 2.0 * realr / (qh_RANDOMmax + 1) - 1.0;
+      }
+    }
+  qh_setdelaunay(dim, numpoints, points);
+} /*.makeDelaunay.*/
+
+/*--------------------------------------------------
+  -addDelaunay- add points to dim-1 Delaunay triangulation
+  points is numpoints+numnew X dim.  Each point is projected to a paraboloid.
+  notes:
+  qh_addpoint() does not make a copy of the point coordinates.
+
+  Since qh_addpoint() is not given a visible facet, it performs a directed
+  search of all facets.  Algorithms that retain previously
+  constructed hulls may be faster.
+*/
+void addDelaunay(coordT *points, int numpoints, int numnew, int dim)
+{
+  int     j, k;
+  coordT *point, realr;
+  facetT *facet;
+  realT   bestdist;
+  boolT   isoutside;
+  for( j = 0; j < numnew; j++ )
+    {
+    point = points + (numpoints + j) * dim;
+    if( points == qh first_point )  /* in case of 'QRn' */
+      {
+      qh num_points = numpoints + j + 1;
+      }
+    /* qh num_points sets the size of the points array.  You may
+       allocate the point elsewhere.  If so, qh_addpoint records
+       the point's address in qh other_points
+    */
+    for( k = 0; k < dim - 1; k++ )
+      {
+      realr = qh_RANDOMint;
+      point[k] = 2.0 * realr / (qh_RANDOMmax + 1) - 1.0;
+      }
+    qh_setdelaunay(dim, 1, point);
+    facet = qh_findbestfacet(point, !qh_ALL, &bestdist, &isoutside);
+    if( isoutside )
+      {
+      if( !qh_addpoint(point, facet, False) )
+        {
+        break; /* user requested an early exit with 'TVn' or 'TCn' */
+        }
+      }
+    qh_printpoint(stdout, "added point", point);
+    printf("%d points, %d extra points, %d vertices, and %d facets in total\n",
+           qh num_points, qh_setsize(qh other_points),
+           qh num_vertices, qh num_facets);
+
+    /* qh_produce_output(); */
+    }
+  if( qh DOcheckmax )
+    {
+    qh_check_maxout();
+    }
+  else if( qh KEEPnearinside )
+    {
+    qh_nearcoplanar();
+    }
+} /*.addDelaunay.*/
+
+/*--------------------------------------------------
+  -findDelaunay- find Delaunay triangle for [0.5,0.5,...]
+  assumes dim < 100
+  notes:
+  calls qh_setdelaunay() to project the point to a parabaloid
+  warning:
+  This is not implemented for tricoplanar facets ('Qt'),
+  See locate a facet with qh_findbestfacet()
+*/
+void findDelaunay(int dim)
+{
+  int      k;
+  coordT   point[100];
+  boolT    isoutside;
+  realT    bestdist;
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+  for( k = 0; k < dim - 1; k++ )
+    {
+    point[k] = 0.5;
+    }
+  qh_setdelaunay(dim, 1, point);
+  facet = qh_findbestfacet(point, qh_ALL, &bestdist, &isoutside);
+  if( facet->tricoplanar )
+    {
+    fprintf(
+      stderr,
+      "findDelaunay: not implemented for triangulated, non-simplicial Delaunay regions (tricoplanar facet, f%d).\n",
+      facet->id);
+    qh_errexit(qh_ERRqhull, facet, NULL);
+    }
+  FOREACHvertex_(facet->vertices) {
+    for( k = 0; k < dim - 1; k++ )
+      {
+      printf("%5.2f ", vertex->point[k]);
+      }
+    printf("\n");
+    }
+} /*.findDelaunay.*/
+
+/*--------------------------------------------------
+  -makehalf- set points to halfspaces for a (dim)-d diamond
+  points is numpoints X dim+1
+
+  each halfspace consists of dim coefficients followed by an offset
+*/
+void makehalf(coordT *points, int numpoints, int dim)
+{
+  int     j, k;
+  coordT *point;
+  for( j = 0; j < numpoints; j++ )
+    {
+    point = points + j * (dim + 1);
+    point[dim] = -1.0; /* offset */
+    for( k = dim; k--; )
+      {
+      if( j & ( 1 << k) )
+        {
+        point[k] = 1.0;
+        }
+      else
+        {
+        point[k] = -1.0;
+        }
+      }
+    }
+} /*.makehalf.*/
+
+/*--------------------------------------------------
+  -addhalf- add halfspaces for a (dim)-d cube to the intersection
+  points is numpoints+numnew X dim+1
+  notes:
+  assumes dim < 100.
+
+  For makehalf(), points is the initial set of halfspaces with offsets.
+  It is transformed by qh_sethalfspace_all into a
+  (dim)-d set of newpoints.  Qhull computed the convex hull of newpoints -
+  this is equivalent to the halfspace intersection of the
+  orginal halfspaces.
+
+  For addhalf(), the remainder of points stores the transforms of
+  the added halfspaces.  Qhull computes the convex hull of newpoints
+  and the added points.  qh_addpoint() does not make a copy of these points.
+
+  Since halfspace intersection is equivalent to a convex hull,
+  qh_findbestfacet may perform an exhaustive search
+  for a visible facet.  Algorithms that retain previously constructed
+  intersections should be faster for on-line construction.
+*/
+void addhalf(coordT *points, int numpoints, int numnew, int dim, coordT *feasible)
+{
+  int     j, k;
+  coordT *point, normal[100], offset, *next;
+  facetT *facet;
+  boolT   isoutside;
+  realT   bestdist;
+  for( j = 0; j < numnew; j++ )
+    {
+    offset = -1.0;
+    for( k = dim; k--; )
+      {
+      if( j / 2 == k )
+        {
+        normal[k] = sqrt(dim); /* to normalize as in makehalf */
+        if( j & 1 )
+          {
+          normal[k] = -normal[k];
+          }
+        }
+      else
+        {
+        normal[k] = 0.0;
+        }
+      }
+    point = points + (numpoints + j) * (dim + 1);  /* does not use point[dim] */
+    qh_sethalfspace(dim, point, &next, normal, &offset, feasible);
+    facet = qh_findbestfacet(point, !qh_ALL, &bestdist, &isoutside);
+    if( isoutside )
+      {
+      if( !qh_addpoint(point, facet, False) )
+        {
+        break; /* user requested an early exit with 'TVn' or 'TCn' */
+        }
+      }
+    qh_printpoint(stdout, "added offset -1 and normal", normal);
+    printf("%d points, %d extra points, %d vertices, and %d facets in total\n",
+           qh num_points, qh_setsize(qh other_points),
+           qh num_vertices, qh num_facets);
+    /* qh_produce_output(); */
+    }
+  if( qh DOcheckmax )
+    {
+    qh_check_maxout();
+    }
+  else if( qh KEEPnearinside )
+    {
+    qh_nearcoplanar();
+    }
+} /*.addhalf.*/
+
+#define DIM 3     /* dimension of points, must be < 31 for SIZEcube */
+#define SIZEcube (1 << DIM)
+#define SIZEdiamond (2 * DIM)
+#define TOTpoints (SIZEcube + SIZEdiamond)
+
+/*--------------------------------------------------
+  -main- derived from call_qhull in user.c
+
+  see program header
+
+  this contains three runs of Qhull for convex hull, Delaunay
+  triangulation or Voronoi vertices, and halfspace intersection
+
+*/
+int main(int argc, char *argv[])
+{
+  boolT ismalloc;
+  int   curlong, totlong, exitcode;
+  char  options[2000];
+
+  printf(
+    "This is the output from user_eg2.c\n\n\
+It shows how qhull() may be called from an application.  It is not part\n\
+of qhull itself.  If it appears accidently, please remove user_eg2.c from\n\
+your project.\n\n"                                                                                                                                                                                                     );
+  ismalloc = False;  /* True if qh_freeqhull should 'free(array)' */
+  /*
+    Run 1: convex hull
+  */
+  qh_init_A(stdin, stdout, stderr, 0, NULL);
+  exitcode = setjmp(qh errexit);
+  if( !exitcode )
+    {
+    coordT array[TOTpoints][DIM];
+
+    strcat(qh rbox_command, "user_eg cube");
+    sprintf(options, "qhull s Tcv Q11 %s ", argc >= 2 ? argv[1] : "");
+    qh_initflags(options);
+    printf( "\ncompute triangulated convex hull of cube after rotating input\n");
+    makecube(array[0], SIZEcube, DIM);
+    qh_init_B(array[0], SIZEcube, DIM, ismalloc);
+    qh_qhull();
+    qh_check_output();
+    qh_triangulate();  /* requires option 'Q11' if want to add points */
+    print_summary();
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    printf( "\nadd points in a diamond\n");
+    adddiamond(array[0], SIZEcube, SIZEdiamond, DIM);
+    qh_check_output();
+    print_summary();
+    qh_produce_output();  /* delete this line to help avoid io.c */
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    }
+  qh NOerrexit = True;
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  /*
+    Run 2: Delaunay triangulation
+  */
+  qh_init_A(stdin, stdout, stderr, 0, NULL);
+  exitcode = setjmp(qh errexit);
+  if( !exitcode )
+    {
+    coordT array[TOTpoints][DIM];
+
+    strcat(qh rbox_command, "user_eg Delaunay");
+    sprintf(options, "qhull s d Tcv %s", argc >= 3 ? argv[2] : "");
+    qh_initflags(options);
+    printf( "\ncompute %d-d Delaunay triangulation\n", DIM - 1);
+    makeDelaunay(array[0], SIZEcube, DIM);
+    /* Instead of makeDelaunay with qh_setdelaunay, you may
+       produce a 2-d array of points, set DIM to 2, and set
+       qh PROJECTdelaunay to True.  qh_init_B will call
+       qh_projectinput to project the points to the paraboloid
+       and add a point "at-infinity".
+    */
+    qh_init_B(array[0], SIZEcube, DIM, ismalloc);
+    qh_qhull();
+    /* If you want Voronoi ('v') without qh_produce_output(), call
+       qh_setvoronoi_all() after qh_qhull() */
+    qh_check_output();
+    print_summary();
+    qh_produce_output();  /* delete this line to help avoid io.c */
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    printf( "\nadd points to triangulation\n");
+    addDelaunay(array[0], SIZEcube, SIZEdiamond, DIM);
+    qh_check_output();
+    qh_produce_output();  /* delete this line to help avoid io.c */
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    printf( "\nfind Delaunay triangle closest to [0.5, 0.5, ...]\n");
+    findDelaunay(DIM);
+    }
+  qh NOerrexit = True;
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  /*
+    Run 3: halfspace intersection
+  */
+  qh_init_A(stdin, stdout, stderr, 0, NULL);
+  exitcode = setjmp(qh errexit);
+  if( !exitcode )
+    {
+    coordT  array[TOTpoints][DIM + 1]; /* +1 for halfspace offset */
+    pointT *points;
+
+    strcat(qh rbox_command, "user_eg halfspaces");
+    sprintf(options, "qhull H0 s Tcv %s", argc >= 4 ? argv[3] : "");
+    qh_initflags(options);
+    printf( "\ncompute halfspace intersection about the origin for a diamond\n");
+    makehalf(array[0], SIZEcube, DIM);
+    qh_setfeasible(DIM);  /* from io.c, sets qh feasible_point from 'Hn,n' */
+    /* you may malloc and set qh feasible_point directly.  It is only used for
+       option 'Fp' */
+    points = qh_sethalfspace_all( DIM + 1, SIZEcube, array[0], qh feasible_point);
+    qh_init_B(points, SIZEcube, DIM, True);  /* qh_freeqhull frees points */
+    qh_qhull();
+    qh_check_output();
+    qh_produce_output();  /* delete this line to help avoid io.c */
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    printf( "\nadd halfspaces for cube to intersection\n");
+    addhalf(array[0], SIZEcube, SIZEdiamond, DIM, qh feasible_point);
+    qh_check_output();
+    qh_produce_output();  /* delete this line to help avoid io.c */
+    if( qh VERIFYoutput && !qh STOPpoint && !qh STOPcone )
+      {
+      qh_check_points();
+      }
+    }
+  qh NOerrexit = True;
+  qh NOerrexit = True;
+  qh_freeqhull(!qh_ALL);
+  qh_memfreeshort(&curlong, &totlong);
+  if( curlong || totlong )  /* could also check previous runs */
+    {
+    fprintf(stderr, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
+            totlong, curlong);
+    }
+  return exitcode;
+} /* main */
+
+#if 1    /* use 1 to prevent loading of io.o and user.o */
+/*-------------------------------------------
+  -errexit- return exitcode to system after an error
+  assumes exitcode non-zero
+  prints useful information
+  see qh_errexit2() in qhull.c for 2 facets
+*/
+void qh_errexit(int exitcode, facetT *facet, ridgeT *ridge)
+{
+
+  if( qh ERREXITcalled )
+    {
+    fprintf(qh ferr, "qhull error while processing previous error.  Exit program\n");
+    exit(1);
+    }
+  qh ERREXITcalled = True;
+  if( !qh QHULLfinished )
+    {
+    qh hulltime = (unsigned)clock() - qh hulltime;
+    }
+  fprintf(qh ferr, "\nWhile executing: %s | %s\n", qh rbox_command, qh qhull_command);
+  fprintf(qh ferr, "Options selected:\n%s\n", qh qhull_options);
+  if( qh furthest_id >= 0 )
+    {
+    fprintf(qh ferr, "\nLast point added to hull was p%d", qh furthest_id);
+    if( zzval_(Ztotmerge) )
+      {
+      fprintf(qh ferr, "  Last merge was #%d.", zzval_(Ztotmerge) );
+      }
+    if( qh QHULLfinished )
+      {
+      fprintf(qh ferr, "\nQhull has finished constructing the hull.");
+      }
+    else if( qh POSTmerging )
+      {
+      fprintf(qh ferr, "\nQhull has started post-merging");
+      }
+    fprintf(qh ferr, "\n\n");
+    }
+  if( qh NOerrexit )
+    {
+    fprintf(qh ferr, "qhull error while ending program.  Exit program\n");
+    exit(1);
+    }
+  if( !exitcode )
+    {
+    exitcode = qh_ERRqhull;
+    }
+  qh NOerrexit = True;
+  longjmp(qh errexit, exitcode);
+} /* errexit */
+
+/*-------------------------------------------
+  -errprint- prints out the information of the erroneous object
+  any parameter may be NULL, also prints neighbors and geomview output
+*/
+void qh_errprint(const char *string, facetT *atfacet, facetT *otherfacet, ridgeT *atridge, vertexT *atvertex)
+{
+
+  fprintf(qh ferr, "%s facets f%d f%d ridge r%d vertex v%d\n",
+          string, getid_(atfacet), getid_(otherfacet), getid_(atridge),
+          getid_(atvertex) );
+} /* errprint */
+
+void qh_printfacetlist(facetT *facetlist, setT *facets, boolT printall)
+{
+  facetT *facet, * *facetp;
+
+  /* remove these calls to help avoid io.c */
+  qh_printbegin(qh ferr, qh_PRINTfacets, facetlist, facets, printall); /*io.c*/
+  FORALLfacet_(facetlist)                                              /*io.c*/
+  qh_printafacet(qh ferr, qh_PRINTfacets, facet, printall);            /*io.c*/
+  FOREACHfacet_(facets)                                                /*io.c*/
+  qh_printafacet(qh ferr, qh_PRINTfacets, facet, printall);            /*io.c*/
+  qh_printend(qh ferr, qh_PRINTfacets, facetlist, facets, printall);   /*io.c*/
+
+  FORALLfacet_(facetlist)
+  fprintf( qh ferr, "facet f%d\n", facet->id);
+} /* printfacetlist */
+
+/*-----------------------------------------
+  -user_memsizes- allocate up to 10 additional, quick allocation sizes
+*/
+void qh_user_memsizes(void)
+{
+
+  /* qh_memsize (size); */
+} /* user_memsizes */
+
+#endif
diff --git a/BRAINSABC/qhull/vtkQhullDelaunay3D.cxx b/BRAINSABC/qhull/vtkQhullDelaunay3D.cxx
new file mode 100644
index 00000000..770ddef6
--- /dev/null
+++ b/BRAINSABC/qhull/vtkQhullDelaunay3D.cxx
@@ -0,0 +1,165 @@
+// From MathLink Delaunay qhull interface
+// Original header:
+/*
+
+  qh-math.c -- MathLink(TM) interface to Qhull's Delaunay Triangulation
+
+  Original work Copyright (c) 1998 by Alban P.M. Tsui 
+  Modifications Copyright (c) 2000 by P.J. Hinton 
+
+  Author: Alban P.M. Tsui
+  Date:   Jan 19, 1998
+  Tested: Unix, Windows95
+
+  Revised by P.J. Hinton, July 5, 2000
+  Ported: Linux (glibc 2.1), Windows 95, MacOS System 8.6
+
+  Use of this source code implies consent to the license in the file
+  COPYING that accompanies this source code archive.
+
+*/
+
+#include "vtkQhullDelaunay3D.h"
+
+#include 
+#include 
+#include 
+
+extern "C"
+{
+#include "qhull.h"
+#include "mem.h"
+#include "qset.h"
+}
+
+#include "vtkCellArray.h"
+#include "vtkCellType.h"
+#include "vtkIdList.h"
+#include "vtkPoints.h"
+#include "vtkSmartPointer.h"
+#include "vtkUnstructuredGrid.h"
+
+#define BUF_SIZE 2048
+// #define QHULL_COMMAND "qhull d QJ Tv "
+#define QHULL_COMMAND "qhull d QJ "
+
+vtkSmartPointer
+vtkQhullDelaunay3D(vtkPoints *inputPoints)
+{
+  int     curlong, totlong, exitcode;
+  char    options[BUF_SIZE];
+  coordT *points;
+
+  facetT * facet;
+  vertexT *vertex, * *vertexp;
+
+  vtkSmartPointer outMesh
+    = vtkSmartPointer::New();
+  outMesh->SetPoints(inputPoints);
+
+  const unsigned int dim = 3;
+
+  unsigned int numPoints = inputPoints->GetNumberOfPoints();
+
+  /* Allocate memory to store elements of the list */
+
+  points = (coordT *)malloc( ( dim + 1 ) * numPoints * sizeof( coordT ) );
+  /* Store each coordinate in an array element. */
+  for( unsigned int k = 0; k < numPoints; k++ )
+    {
+    double x[3];
+    inputPoints->GetPoint(k, x);
+
+    long pos = k * ( dim + 1 );
+
+#if 1
+    double sumS = 0;
+    for( unsigned int j = 0; j < dim; j++ )
+      {
+      points[pos + j] = x[j];
+      sumS += x[j] * x[j];
+      }
+    points[pos + dim] = sumS;
+#else
+    points[pos + dim] = 0.0;
+#endif
+    }
+
+  /* Call out to qhull library to compute DeLaunay triangulation. */
+  qh_init_A(stdin, stdout, stderr, 0, NULL);
+  exitcode = setjmp(qh errexit);
+
+  if( !exitcode )
+    {
+    // Add extra options here
+    strcpy(options, QHULL_COMMAND);
+
+    qh_initflags(options);
+    qh_setdelaunay(dim + 1, numPoints, points);
+    qh_init_B(points, numPoints, dim + 1, False);
+    qh_qhull();
+    qh_check_output();
+
+    /*
+        long numfacets = 0;
+
+        FORALLfacets
+        {
+          if (!facet->upperdelaunay)
+          {
+            numfacets++;
+          }
+        }
+    */
+
+    FORALLfacets
+      {
+      if( !facet->upperdelaunay )
+        {
+        vtkIdType    ptIds[4];
+        unsigned int k = 0;
+        bool         validCell = true;
+        FOREACHvertex_(facet->vertices)
+          {
+          if( k >= 4 )
+            {
+            validCell = false;
+            break;
+            }
+          vtkIdType id = qh_pointid(vertex->point);
+          if( id < 0 || id >= numPoints )
+            {
+            validCell = false;
+            std::cerr << ">->->- WARNING: qhull attempted to insert point id : " <<  id << " with " << numPoints
+                      << "points" << std::endl;
+            break;
+            }
+          ptIds[k++] = id;
+          }
+        if( !validCell )
+          {
+          continue;
+          }
+        outMesh->InsertNextCell(VTK_TETRA, 4, ptIds);
+        }
+      }
+    }
+
+  // Free allocated memory
+
+  qh NOerrexit = True;
+  qh_freeqhull(False);
+  qh_memfreeshort(&curlong, &totlong);
+  free(points);
+
+  if( curlong || totlong )
+    {
+    fprintf(stderr, "qhull internal warning (main): did not \
+      free %d bytes of long memory (%d pieces)\n", totlong, curlong);
+    }
+
+  outMesh->BuildLinks();
+
+  return outMesh;
+}
+
diff --git a/BRAINSABC/qhull/vtkQhullDelaunay3D.h b/BRAINSABC/qhull/vtkQhullDelaunay3D.h
new file mode 100644
index 00000000..5f84b9e0
--- /dev/null
+++ b/BRAINSABC/qhull/vtkQhullDelaunay3D.h
@@ -0,0 +1,10 @@
+#ifndef _vtkQhullDelaunay3D_h
+#define _vtkQhullDelaunay3D_h
+
+#include "vtkPoints.h"
+#include "vtkSmartPointer.h"
+#include "vtkUnstructuredGrid.h"
+
+vtkSmartPointer vtkQhullDelaunay3D(vtkPoints *inputPoints);
+
+#endif
diff --git a/BRAINSCommonLib/ApplicationBase.h b/BRAINSCommonLib/ApplicationBase.h
new file mode 100644
index 00000000..54d73bda
--- /dev/null
+++ b/BRAINSCommonLib/ApplicationBase.h
@@ -0,0 +1,92 @@
+#ifndef __ApplicationBase_h
+#define __ApplicationBase_h
+
+#include "itkObjectFactory.h"
+#include "itkObject.h"
+
+namespace itk
+{
+/** \class ApplicationBase
+  *
+  * This class ties together an input parser, a preprocessor,
+  * a registrator components to
+  * form a deformable registration/atlas segmentation application.
+  *
+  */
+template 
+class ApplicationBase : public Object
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef ApplicationBase          Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(MIMApplication, Object);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Input parser type. */
+  typedef TParser                      ParserType;
+  typedef typename ParserType::Pointer ParserPointer;
+
+  /** Preprocessor type. */
+  typedef TPreprocessor                      PreprocessorType;
+  typedef typename PreprocessorType::Pointer PreprocessorPointer;
+
+  /** Registrator type. */
+  typedef TRegistrator                      RegistratorType;
+  typedef typename RegistratorType::Pointer RegistratorPointer;
+
+  /** Set Debug mode */
+  itkSetMacro(OutDebug, bool);
+  itkGetConstMacro(OutDebug, bool);
+
+  RegistratorType * GetRegistratorType(void)
+  {
+    return m_Registrator;
+  }
+
+  /** Execute the application. */
+  virtual void Execute();
+
+protected:
+
+  ApplicationBase();
+  virtual ~ApplicationBase()
+  {
+  }
+
+  /** Initialize the input parser. */
+  virtual void InitializeParser()
+  {
+  }
+
+  /*** Initialize the preprocessor */
+  virtual void InitializePreprocessor()
+  {
+  }
+
+  /*** Initialize the registrator  */
+  virtual void InitializeRegistrator()
+  {
+  }
+
+  ParserPointer       m_Parser;
+  PreprocessorPointer m_Preprocessor;
+  RegistratorPointer  m_Registrator;
+  bool                m_OutDebug;
+};
+}   // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "ApplicationBase.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/ApplicationBase.hxx b/BRAINSCommonLib/ApplicationBase.hxx
new file mode 100644
index 00000000..57d15d6a
--- /dev/null
+++ b/BRAINSCommonLib/ApplicationBase.hxx
@@ -0,0 +1,118 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *
+ *  Copyright (c) 2002 Insight Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __ApplicationBase_hxx
+#define __ApplicationBase_hxx
+
+#include "ApplicationBase.h"
+
+namespace itk
+{
+template 
+ApplicationBase
+::ApplicationBase()
+{
+  m_Parser       = ParserType::New();
+  m_Preprocessor = PreprocessorType::New();
+  m_Registrator  = RegistratorType::New();
+  m_OutDebug  = false;
+}
+
+template 
+void
+ApplicationBase
+::Execute()
+{
+  /**************************
+    * Parse input
+    */
+  if( this->GetOutDebug() )
+    {
+    std::cout << "Parsing input ... " << std::endl;
+    }
+
+  try
+    {
+    this->InitializeParser();
+    m_Parser->Execute();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "Error occurred during input parsing." << std::endl;
+    throw;
+    }
+
+  /**************************
+    * Preprocess the images before registration
+    */
+
+  if( this->GetOutDebug() )
+    {
+    std::cout << "Preprocess the images ... " << std::endl;
+    }
+
+  try
+    {
+    this->InitializePreprocessor();
+    m_Preprocessor->Execute();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "Error occured during preprocessing." << std::endl;
+    throw;
+    }
+
+  /**************************
+    * Registered the processed images
+    */
+  if( this->GetOutDebug() )
+    {
+    std::cout << "Register the images ... " << std::endl;
+    }
+
+  try
+    {
+    this->InitializeRegistrator();
+    m_Preprocessor = NULL;
+    m_Parser = NULL;
+    m_Registrator->Execute();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "Error occured during registration" << std::endl;
+    throw;
+    }
+}
+
+}   // namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/ApplyField.h b/BRAINSCommonLib/ApplyField.h
new file mode 100755
index 00000000..7d4afb39
--- /dev/null
+++ b/BRAINSCommonLib/ApplyField.h
@@ -0,0 +1,63 @@
+/**
+  * \defgroup AF Apply Field
+  * \ingroup Reg
+  */
+#ifndef __ApplyField_h
+#define __ApplyField_h
+
+#include "itkObjectFactory.h"
+#include "itkObject.h"
+
+namespace itk
+{
+template 
+class ApplyField : public Object
+{
+public:
+  typedef ApplyField               Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  itkTypeMacro(MIMApplication, Object);
+
+  itkNewMacro(Self);
+
+  typedef TInputImage                         InputImageType;
+  typedef TOutputImage                        OutputImageType;
+  typedef typename OutputImageType::PixelType PixelType;
+  typedef typename InputImageType::Pointer    ImagePointer;
+
+  itkStaticConstMacro(ImageDimension, unsigned int, TInputImage::ImageDimension);
+
+  itkSetObjectMacro(InputImage, InputImageType);
+  itkGetObjectMacro(InputImage, InputImageType);
+  itkGetObjectMacro(OutputImage, OutputImageType);
+
+  /** Set/Get value to replace thresholded pixels. Pixels that lie *
+    *  within Lower and Upper (inclusive) will be replaced with this
+    *  value. The default is 1. */
+  itkSetMacro(DefaultPixelValue,  PixelType);
+  itkGetMacro(DefaultPixelValue,  PixelType);
+
+  itkSetObjectMacro(DeformationField, TDeformationField);
+
+  void Execute();
+
+  void ReleaseDataFlagOn();
+
+protected:
+  ApplyField();
+  virtual ~ApplyField();
+private:
+  typename InputImageType::Pointer m_InputImage;
+  typename OutputImageType::Pointer m_OutputImage;
+  typename TDeformationField::Pointer m_DeformationField;
+  PixelType m_DefaultPixelValue;
+};
+}
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "ApplyField.hxx"
+#endif
+#endif
diff --git a/BRAINSCommonLib/ApplyField.hxx b/BRAINSCommonLib/ApplyField.hxx
new file mode 100755
index 00000000..e84869b6
--- /dev/null
+++ b/BRAINSCommonLib/ApplyField.hxx
@@ -0,0 +1,62 @@
+#ifndef __ApplyField_hxx
+#define __ApplyField_hxx
+#include "ApplyField.h"
+#include "itkImage.h"
+#include "itkWarpImageFilter.h"
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkReinitializeLevelSetImageFilter.h"
+#include "itkIO.h"
+
+namespace itk
+{
+template 
+ApplyField::ApplyField() :
+  m_InputImage(0),
+  m_OutputImage(0),
+  m_DeformationField(0),
+  m_DefaultPixelValue(0)
+{
+}
+
+template 
+ApplyField::~ApplyField()
+{
+}
+
+template 
+void ApplyField::Execute()
+{
+  if( m_InputImage.IsNull() )
+    {
+    std::cout << "ERROR:  No Input image give.! " << std::endl;
+    }
+
+  typedef WarpImageFilter WarperType;
+  typename WarperType::Pointer warper = WarperType::New();
+  warper->SetInput(m_InputImage);
+  warper->SetDeformationField(m_DeformationField);
+  warper->SetOutputParametersFromImage(m_DeformationField);
+  warper->SetEdgePaddingValue(m_DefaultPixelValue);
+  warper->Update();
+  std::cout << "  Registration Applied" << std::endl;
+  m_OutputImage = warper->GetOutput();
+}
+
+template 
+void ApplyField::ReleaseDataFlagOn()
+{
+  // m_InputImage->DisconnectPipeline();
+  // m_DeformationField->DisconnectPipeline();
+}
+
+}
+#endif
diff --git a/BRAINSCommonLib/BRAINSCommonLib.h.in b/BRAINSCommonLib/BRAINSCommonLib.h.in
new file mode 100755
index 00000000..d11365a5
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSCommonLib.h.in
@@ -0,0 +1,13 @@
+/*
+ * Here is where system computed values get stored.
+ * These values should only change when the target compile platform changes.
+ */
+
+#if defined(WIN32) && !defined(BRAINSCOMMONLIB_STATIC)
+#pragma warning ( disable : 4275 )
+#endif
+
+#cmakedefine BUILD_SHARED_LIBS
+#ifndef BUILD_SHARED_LIBS
+#define BRAINSCOMMONLIB_STATIC
+#endif
diff --git a/BRAINSCommonLib/BRAINSCommonLibConfig.cmake.in b/BRAINSCommonLib/BRAINSCommonLibConfig.cmake.in
new file mode 100755
index 00000000..f7d4a091
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSCommonLibConfig.cmake.in
@@ -0,0 +1,7 @@
+# The BRAINSCommonLib source tree.
+set(BRAINSCommonLib_DATA_DIRS    "@BRAINSCommonLib_DATA_DIRS_CONFIG@")
+set(BRAINSCommonLib_INCLUDE_DIRS "@BRAINSCommonLib_INCLUDE_DIRS_CONFIG@")
+set(BRAINSCommonLib_LIBRARY_DIRS "@BRAINSCommonLib_LIBRARY_DIRS_CONFIG@")
+set(BRAINSCommonLib_USE_FILE     "@BRAINSCommonLib_USE_FILE_CONFIG@")
+set(BRAINSCommonLib_BUILDSCRIPTS_DIR  "@BRAINSCommonLib_INCLUDE_DIRS_CONFIG@/BuildScripts")
+set(ITK_DIR "@ITK_DIR_CONFIG@")
diff --git a/BRAINSCommonLib/BRAINSCommonLibInstallConfig.cmake.in b/BRAINSCommonLib/BRAINSCommonLibInstallConfig.cmake.in
new file mode 100644
index 00000000..e583d84c
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSCommonLibInstallConfig.cmake.in
@@ -0,0 +1,10 @@
+# BRAINSCommonLib could be installed anywhere, so set all paths based on where
+# this file was found (which should be the lib/BRAINSCommonLib directory of the
+# installation)
+get_filename_component(BRAINSCommonLib_CONFIG_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
+
+set(BRAINSCommonLib_INCLUDE_DIRS "${BRAINSCommonLib_CONFIG_DIR}/../../include/BRAINSCommonLib")
+set(BRAINSCommonLib_LIBRARY_DIRS "${BRAINSCommonLib_CONFIG_DIR}")
+set(BRAINSCommonLib_USE_FILE "${BRAINSCommonLib_CONFIG_DIR}/UseBRAINSCommonLib.cmake")
+set(ITK_DIR "@ITK_DIR@")
+
diff --git a/BRAINSCommonLib/BRAINSCommonLibLauncher.c.in b/BRAINSCommonLib/BRAINSCommonLibLauncher.c.in
new file mode 100644
index 00000000..e9d7b311
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSCommonLibLauncher.c.in
@@ -0,0 +1,30 @@
+#if defined(_WIN32)
+#if defined(CMAKE_INTDIR)
+#define itksys_SHARED_FORWARD_CONFIG_NAME CMAKE_INTDIR
+#define CONFIG_DIR_PRE CMAKE_INTDIR "/"
+#define CONFIG_DIR_POST "/" CMAKE_INTDIR
+#else
+#define CONFIG_DIR_PRE ""
+#define CONFIG_DIR_POST ""
+#endif
+#endif
+
+#define itksys_SHARED_FORWARD_DIR_BUILD "@BRAINSCommonLib_FORWARD_DIR_BUILD@"
+#define itksys_SHARED_FORWARD_PATH_BUILD @BRAINSCommonLib_FORWARD_PATH_BUILD@
+#define itksys_SHARED_FORWARD_PATH_INSTALL @BRAINSCommonLib_FORWARD_PATH_INSTALL@
+#if defined(_WIN32)
+#define itksys_SHARED_FORWARD_EXE_BUILD CONFIG_DIR_PRE "@BRAINSCommonLib_FORWARD_EXE@"
+#else
+#define itksys_SHARED_FORWARD_EXE_BUILD "@BRAINSCommonLib_FORWARD_DIR_BUILD@/@BRAINSCommonLib_FORWARD_EXE@"
+#endif
+#define itksys_SHARED_FORWARD_EXE_INSTALL "@BRAINSCommonLib_FORWARD_DIR_INSTALL@/@BRAINSCommonLib_FORWARD_EXE@"
+#define itksys_SHARED_FORWARD_OPTION_PRINT "--print"
+#define itksys_SHARED_FORWARD_OPTION_LDD "--ldd"
+
+#include 
+
+int main(int argc, char *argv[])
+{
+  return itksys_shared_forward_to_real(argc, argv);
+}
+
diff --git a/BRAINSCommonLib/BRAINSCommonLibWin32Header.h b/BRAINSCommonLib/BRAINSCommonLibWin32Header.h
new file mode 100755
index 00000000..24b857cb
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSCommonLibWin32Header.h
@@ -0,0 +1,22 @@
+// /  BRAINSCommonLibWin32Header - manage Windows system differences
+// /
+// / The BRAINSCommonLibWin32Header captures some system differences between
+// Unix
+// / and Windows operating systems.
+
+#ifndef __BRAINSCommonLibWin32Header_h
+#define __BRAINSCommonLibWin32Header_h
+
+#include 
+
+#if defined( WIN32 ) && !defined( BRAINSCommonLib_STATIC )
+#if defined( BRAINSCommonLib_EXPORTS )
+#define BRAINSCommonLib_EXPORT __declspec(dllexport)
+#else
+#define BRAINSCommonLib_EXPORT __declspec(dllimport)
+#endif
+#else
+#define BRAINSCommonLib_EXPORT
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/BRAINSFitBSpline.h b/BRAINSCommonLib/BRAINSFitBSpline.h
new file mode 100644
index 00000000..4e869822
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitBSpline.h
@@ -0,0 +1,205 @@
+#ifndef __BRAINSFitBSpline_h
+#define __BRAINSFitBSpline_h
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#if (ITK_VERSION_MAJOR < 4)
+#include "itkOptImageToImageMetric.h"
+#else
+#include "itkImageToImageMetric.h"
+#endif
+#include "genericRegistrationHelper.h"
+
+/**
+  * This class is the BSpline component of the BRAINSFit program developed at
+  *the University of Iowa.
+  * The master version of this file is always located from the nitric site.
+  * http://www.nitrc.org/projects/multimodereg/
+  */
+
+template 
+typename BSplineTransformType::Pointer
+DoBSpline(typename BSplineTransformType::Pointer InitializerBsplineTransform,
+          typename RegisterImageType::Pointer m_FixedVolume,
+          typename RegisterImageType::Pointer m_MovingVolume,
+          typename itk::ImageToImageMetric<
+            RegisterImageType, RegisterImageType>::Pointer CostMetricObject,
+          const double m_MaxBSplineDisplacement,
+          const float m_CostFunctionConvergenceFactor,
+          const float m_ProjectedGradientTolerance,
+          const bool m_DisplayDeformedImage,
+          const bool m_PromptUserAfterDisplay)
+{
+  /*
+    *  Begin straightline BSpline optimization, after
+    *GTRACT/Common/itkAnatomicalBSplineFilter.
+    */
+
+  typedef typename RegisterImageType::Pointer       RegisterImagePointer;
+  typedef typename RegisterImageType::ConstPointer  RegisterImageConstPointer;
+  typedef typename RegisterImageType::RegionType    RegisterImageRegionType;
+  typedef typename RegisterImageType::SizeType      RegisterImageSizeType;
+  typedef typename RegisterImageType::SpacingType   RegisterImageSpacingType;
+  typedef typename RegisterImageType::PointType     RegisterImagePointType;
+  typedef typename RegisterImageType::PixelType     RegisterImagePixelType;
+  typedef typename RegisterImageType::DirectionType RegisterImageDirectionType;
+  typedef typename RegisterImageType::IndexType     RegisterImageIndexType;
+
+  typedef typename BSplineTransformType::RegionType     TransformRegionType;
+  typedef typename TransformRegionType::SizeType        TransformSizeType;
+  typedef typename BSplineTransformType::SpacingType    TransformSpacingType;
+  typedef typename BSplineTransformType::OriginType     TransformOriginType;
+  typedef typename BSplineTransformType::DirectionType  TransformDirectionType;
+  typedef typename BSplineTransformType::ParametersType TransformParametersType;
+
+  typedef typename itk::LBFGSBOptimizer OptimizerType;
+
+  typedef typename itk::LinearInterpolateImageFunction<
+    RegisterImageType,
+    double>          InterpolatorType;
+
+  typedef typename itk::ImageRegistrationMethod<
+    RegisterImageType,
+    RegisterImageType>          RegistrationType;
+
+  typedef typename BSplineTransformType::Pointer     TransformTypePointer;
+  typedef typename OptimizerType::Pointer            OptimizerTypePointer;
+  typedef typename OptimizerType::ParametersType     OptimizerParameterType;
+  typedef typename OptimizerType::ScalesType         OptimizerScalesType;
+  typedef typename OptimizerType::BoundSelectionType OptimizerBoundSelectionType;
+  typedef typename OptimizerType::BoundValueType     OptimizerBoundValueType;
+
+  typedef typename InterpolatorType::Pointer InterpolatorTypePointer;
+  typedef typename RegistrationType::Pointer RegistrationTypePointer;
+
+  typedef typename itk::ResampleImageFilter<
+    RegisterImageType,
+    RegisterImageType>     ResampleFilterType;
+
+  // TODO:  Expose these to the command line for consistancy.
+  const int m_MaximumNumberOfIterations = 1500;
+
+  const int m_MaximumNumberOfEvaluations = 900;
+  const int m_MaximumNumberOfCorrections = 12;
+
+  OptimizerTypePointer    optimizer     = OptimizerType::New();
+  InterpolatorTypePointer interpolator  = InterpolatorType::New();
+  RegistrationTypePointer registration  = RegistrationType::New();
+
+  typename BSplineTransformType::Pointer m_OutputBSplineTransform = BSplineTransformType::New();
+  m_OutputBSplineTransform->SetIdentity();
+  m_OutputBSplineTransform->SetBulkTransform( InitializerBsplineTransform->GetBulkTransform() );
+  m_OutputBSplineTransform->SetFixedParameters( InitializerBsplineTransform->GetFixedParameters() );
+  m_OutputBSplineTransform->SetParametersByValue( InitializerBsplineTransform->GetParameters() );
+
+  /** Set up the Registration */
+  registration->SetMetric(CostMetricObject);
+  registration->SetOptimizer(optimizer);
+  registration->SetInterpolator(interpolator);
+  registration->SetTransform(m_OutputBSplineTransform);
+
+  /** Setup the Registration */
+  registration->SetFixedImage(m_FixedVolume);
+  registration->SetMovingImage(m_MovingVolume);
+
+  RegisterImageRegionType fixedImageRegion = m_FixedVolume->GetBufferedRegion();
+
+  registration->SetFixedImageRegion(fixedImageRegion);
+
+  registration->SetInitialTransformParameters( m_OutputBSplineTransform->GetParameters() );
+
+  OptimizerBoundSelectionType boundSelect( m_OutputBSplineTransform->GetNumberOfParameters() );
+  OptimizerBoundValueType     upperBound( m_OutputBSplineTransform->GetNumberOfParameters() );
+  OptimizerBoundValueType     lowerBound( m_OutputBSplineTransform->GetNumberOfParameters() );
+
+  /**
+    *
+    * Set the boundary condition for each variable, where
+    * select[i] = 0 if x[i] is unbounded,
+    *           = 1 if x[i] has only a lower bound,
+    *           = 2 if x[i] has both lower and upper bounds, and
+    *           = 3 if x[1] has only an upper bound
+    */
+  // TODO:  For control points outside the fixed image mask, it might be good to
+  // constrian
+  // the parameters to something different than those control points inside the
+  // fixed image mask.
+  if( vcl_abs(m_MaxBSplineDisplacement) < 1e-12 )
+    {
+    boundSelect.Fill(0);
+    }
+  else
+    {
+    boundSelect.Fill(2);
+    }
+  upperBound.Fill(m_MaxBSplineDisplacement);
+  lowerBound.Fill(-m_MaxBSplineDisplacement);
+  optimizer->SetBoundSelection(boundSelect);
+  optimizer->SetUpperBound(upperBound);
+  optimizer->SetLowerBound(lowerBound);
+
+  optimizer->SetCostFunctionConvergenceFactor(m_CostFunctionConvergenceFactor);
+  optimizer->SetProjectedGradientTolerance(m_ProjectedGradientTolerance);
+  optimizer->SetMaximumNumberOfIterations(m_MaximumNumberOfIterations);
+  optimizer->SetMaximumNumberOfEvaluations(m_MaximumNumberOfEvaluations);
+  optimizer->SetMaximumNumberOfCorrections(m_MaximumNumberOfCorrections);
+
+  // Create the Command observer and register it with the optimizer.
+  // TODO:  make this output optional.
+  //
+
+  const bool ObserveIterations = true;
+  if( ObserveIterations == true )
+    {
+    typedef BRAINSFit::CommandIterationUpdate
+    CommandIterationUpdateType;
+    typename CommandIterationUpdateType::Pointer observer =
+      CommandIterationUpdateType::New();
+    observer->SetDisplayDeformedImage(m_DisplayDeformedImage);
+    observer->SetPromptUserAfterDisplay(m_PromptUserAfterDisplay);
+    observer->SetPrintParameters(false);
+    observer->SetMovingImage(m_MovingVolume);
+    observer->SetFixedImage(m_FixedVolume);
+    observer->SetTransform(m_OutputBSplineTransform);
+    optimizer->AddObserver(itk::IterationEvent(), observer);
+    }
+
+  /* Now start the execute function */
+
+  // Add a time probe
+  itk::TimeProbesCollectorBase collector;
+
+  std::cout << std::endl << "Starting Registration" << std::endl;
+
+  try
+    {
+    collector.Start("Registration");
+    registration->StartRegistration();
+    collector.Stop("Registration");
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << "ExceptionObject caught !" << std::endl;
+    std::cerr << err << std::endl;
+    return NULL;
+    }
+
+  OptimizerType::ParametersType finalParameters =
+    registration->GetLastTransformParameters();
+
+  collector.Report();
+  std::cout << "Stop condition from optimizer." << optimizer->GetStopConditionDescription() << std::endl;
+
+  /* This call is required to copy the parameters */
+  m_OutputBSplineTransform->SetParametersByValue(finalParameters);
+  //  std::cout << "DELETEME:  " << finalParameters << std::endl;
+  return m_OutputBSplineTransform;
+}
+
+#endif // __BRAINSFitBSpline_H_
diff --git a/BRAINSCommonLib/BRAINSFitHelper.cxx b/BRAINSCommonLib/BRAINSFitHelper.cxx
new file mode 100644
index 00000000..783a90b3
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitHelper.cxx
@@ -0,0 +1,628 @@
+
+#include "BRAINSFitUtils.h"
+#include "BRAINSFitHelper.h"
+#include "BRAINSFitHelperTemplate.h"
+
+#include "genericRegistrationHelper.h"
+#include "itkNormalizedCorrelationImageToImageMetric.h"
+#include "itkMeanSquaresImageToImageMetric.h"
+#include "itkKullbackLeiblerCompareHistogramImageToImageMetric.h"
+#include "itkHistogramImageToImageMetric.h"
+#include "itkKappaStatisticImageToImageMetric.h"
+#include "itkMeanReciprocalSquareDifferenceImageToImageMetric.h"
+#include "itkMutualInformationHistogramImageToImageMetric.h"
+#include "itkGradientDifferenceImageToImageMetric.h"
+#include "itkCompareHistogramImageToImageMetric.h"
+#include "itkCorrelationCoefficientHistogramImageToImageMetric.h"
+#include "itkMatchCardinalityImageToImageMetric.h"
+#include "itkMeanSquaresHistogramImageToImageMetric.h"
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkNormalizedMutualInformationHistogramImageToImageMetric.h"
+
+#if ( ITK_VERSION_MAJOR < 4  ) // These are all defaults in ITKv4
+// Check that ITK was compiled with correct flags set:
+#ifndef ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
+#error \
+  "Results will not be correct if ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE is turned off"
+#endif
+#ifndef ITK_USE_ORIENTED_IMAGE_DIRECTION
+#error \
+  "Results will not be correct if ITK_USE_ORIENTED_IMAGE_DIRECTION is turned off"
+#endif
+#endif
+
+MaskImageType::ConstPointer ExtractConstPointerToImageMaskFromImageSpatialObject(
+  SpatialObjectType::ConstPointer inputSpatialObject)
+{
+  ImageMaskSpatialObjectType const * const temp =
+    dynamic_cast( inputSpatialObject.GetPointer() );
+
+  if( temp == NULL )
+    {
+    std::cout << "Invalid mask converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+    exit(-1);
+    }
+  ImageMaskSpatialObjectType::ConstPointer ImageMask( temp );
+  const MaskImageType::ConstPointer        tempOutputVolumeROI = ImageMask->GetImage();
+  return tempOutputVolumeROI;
+}
+
+namespace itk
+{
+
+BRAINSFitHelper::BRAINSFitHelper() :
+  m_FixedVolume(NULL),
+  m_MovingVolume(NULL),
+  m_PreprocessedMovingVolume(NULL),
+  m_FixedBinaryVolume(NULL),
+  m_MovingBinaryVolume(NULL),
+  m_OutputFixedVolumeROI(""),
+  m_OutputMovingVolumeROI(""),
+  m_PermitParameterVariation(0),
+  m_NumberOfSamples(500000),
+  m_NumberOfHistogramBins(50),
+  m_HistogramMatch(false),
+  m_RemoveIntensityOutliers(0.00),
+  m_NumberOfMatchPoints(10),
+  m_NumberOfIterations(1, 1500),
+  m_MaximumStepLength(0.2),
+  m_MinimumStepLength(1, 0.005),
+  m_RelaxationFactor(0.5),
+  m_TranslationScale(1000.0),
+  m_ReproportionScale(1.0),
+  m_SkewScale(1.0),
+  m_UseExplicitPDFDerivativesMode("AUTO"),
+  m_UseCachingOfBSplineWeightsMode("ON"),
+  m_BackgroundFillValue(0.0),
+  m_TransformType(1, "Rigid"),
+  m_InitializeTransformMode("Off"),
+  m_MaskInferiorCutOffFromCenter(1000),
+  m_SplineGridSize(3, 10),
+  m_CostFunctionConvergenceFactor(1e+9),
+  m_ProjectedGradientTolerance(1e-5),
+  m_MaxBSplineDisplacement(0.0),
+  m_ActualNumberOfIterations(0),
+  m_PermittedNumberOfIterations(0),
+  // m_AccumulatedNumberOfIterationsForAllLevels(0),
+  m_DebugLevel(0),
+  m_CurrentGenericTransform(NULL),
+  m_GenericTransformList(0),
+  m_DisplayDeformedImage(false),
+  m_PromptUserAfterDisplay(false),
+  m_FinalMetricValue(0.0),
+  m_ObserveIterations(true),
+  m_CostMetric("MMI"), // Default to Mattes Mutual Information Metric
+  m_Helper(NULL)
+{
+  m_SplineGridSize[0] = 14;
+  m_SplineGridSize[1] = 10;
+  m_SplineGridSize[2] = 12;
+}
+
+void
+BRAINSFitHelper::StartRegistration(void)
+{
+
+  //
+  // Do remove intensity outliers if requested
+  //
+  if(  m_RemoveIntensityOutliers > vcl_numeric_limits::epsilon() )
+    {
+    this->m_FixedVolume = ClampNoisyTailsOfImage(
+        m_RemoveIntensityOutliers, this->m_FixedVolume.GetPointer(), this->m_FixedBinaryVolume.GetPointer() );
+    this->m_PreprocessedMovingVolume = ClampNoisyTailsOfImage(
+        m_RemoveIntensityOutliers, this->m_MovingVolume.GetPointer(), this->m_MovingBinaryVolume.GetPointer() );
+      {
+      //
+      if( this->m_DebugLevel > 9 )
+        {
+          {
+          typedef itk::ImageFileWriter WriterType;
+          WriterType::Pointer writer = WriterType::New();
+          writer->UseCompressionOn();
+          writer->SetFileName("DEBUGNormalizedFixedVolume.nii.gz");
+          writer->SetInput(this->m_FixedVolume);
+          try
+            {
+            writer->Update();
+            }
+          catch( itk::ExceptionObject & err )
+            {
+            std::cout << "Exception Object caught: " << std::endl;
+            std::cout << err << std::endl;
+            throw;
+            }
+          }
+          {
+          typedef itk::ImageFileWriter WriterType;
+          WriterType::Pointer writer = WriterType::New();
+          writer->UseCompressionOn();
+          writer->SetFileName("DEBUGNormalizedMovingVolume.nii.gz");
+          writer->SetInput(this->m_PreprocessedMovingVolume);
+          try
+            {
+            writer->Update();
+            }
+          catch( itk::ExceptionObject & err )
+            {
+            std::cout << "Exception Object caught: " << std::endl;
+            std::cout << err << std::endl;
+            throw;
+            }
+          }
+        }
+      }
+    }
+  else
+    {
+    this->m_PreprocessedMovingVolume = this->m_MovingVolume;
+    }
+
+  // Do Histogram equalization on moving image if requested.
+  if( m_HistogramMatch )
+    {
+#if 0
+    std::cerr << " ********* ERROR ************"
+              << " Histogram Equalization Option for BRAINSFit does not work"
+              << " for now. Please do not use --histogramMatch"
+              << std::endl;
+    exit(-1);
+#else
+
+    typedef itk::OtsuHistogramMatchingImageFilter HistogramMatchingFilterType;
+    HistogramMatchingFilterType::Pointer histogramfilter = HistogramMatchingFilterType::New();
+
+    // TODO:  Regina:  Write various histogram matching specializations and
+    // compare them.
+    // histogramfilter->SetForegroundMode("Otsu"); // A simple Otsu threshold
+    // for each image .... BUT BE CAREFUL, need to do some quantile checking for
+    // degenerate images
+    // histogramfilter->SetForegroundMode("Simple"); // A simple average value
+    // of the image should be used
+    // histogramfilter->SetForegroundMode("Quantile"); // Only values between
+    // the 25th and 66th quantile should be used.
+    // histogramfilter->SetForegroundMode("Masks"); // Foreground is
+    // specifically defined by masks.
+
+    histogramfilter->SetReferenceImage(this->m_FixedVolume);
+    if( this->m_FixedBinaryVolume.IsNull() )
+      {
+      std::cout << "ERROR:  Histogram matching requires a fixed mask." << std::endl;
+      exit(-1);
+      }
+      {
+      histogramfilter->SetReferenceMask( m_FixedBinaryVolume.GetPointer() );
+      }
+    histogramfilter->SetInput(this->m_PreprocessedMovingVolume);
+    if( this->m_MovingBinaryVolume.IsNull() )
+      {
+      std::cout << "ERROR:  Histogram matching requires a moving mask." << std::endl;
+      exit(-1);
+      }
+      {
+      histogramfilter->SetSourceMask( m_MovingBinaryVolume.GetPointer() );
+      }
+
+    histogramfilter->SetNumberOfHistogramLevels(this->m_NumberOfHistogramBins);
+    histogramfilter->SetNumberOfMatchPoints(this->m_NumberOfMatchPoints);
+    histogramfilter->Update();
+    this->m_PreprocessedMovingVolume = histogramfilter->GetOutput();
+    if( this->m_DebugLevel > 5 )
+      {
+      typedef itk::ImageFileWriter WriterType;
+      WriterType::Pointer writer = WriterType::New();
+      writer->UseCompressionOn();
+      writer->SetFileName("DEBUGHISTOGRAMMATCHEDMOVING.nii.gz");
+      writer->SetInput(this->m_PreprocessedMovingVolume);
+      try
+        {
+        writer->Update();
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        std::cout << "Exception Object caught: " << std::endl;
+        std::cout << err << std::endl;
+        throw;
+        }
+      }
+#endif
+    }
+  else
+    {
+    this->m_PreprocessedMovingVolume = this->m_MovingVolume;
+    }
+
+  if( this->m_CostMetric == "MMI" )
+    {
+    typedef COMMON_MMI_METRIC_TYPE MetricType;
+    this->SetupRegistration();
+
+    MetricType::Pointer localCostMetric = this->GetCostMetric();
+    localCostMetric->SetNumberOfHistogramBins(this->m_NumberOfHistogramBins);
+    const bool UseCachingOfBSplineWeights = ( m_UseCachingOfBSplineWeightsMode == "ON" ) ? true : false;
+    localCostMetric->SetUseCachingOfBSplineWeights(UseCachingOfBSplineWeights);
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "MSE" )
+    {
+    typedef itk::MeanSquaresImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "NC" )
+    {
+    typedef itk::NormalizedCorrelationImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  // This requires additional machinery (training transform, etc) and hence
+  // isn't as easy to incorporate
+  // into the BRAINSFit framework.
+  /*else if(this->m_CostMetric == "KL")
+    {
+    typedef itk::KullbackLeiblerCompareHistogramImageToImageMetric MetricType;
+    this->SetupRegistration();
+this->RunRegistration();
+    }*/
+  else if( this->m_CostMetric == "KS" )
+    {
+    if( this->m_HistogramMatch )
+      {
+      itkExceptionMacro(<< "The KS cost metric is not compatible with histogram matching.");
+      }
+    // This metric only works with binary images that it knows the value of.
+    // It defaults to 255, so we threshold the inputs to 255.
+    typedef itk::BinaryThresholdImageFilter BinaryThresholdFixedVolumeType;
+    BinaryThresholdFixedVolumeType::Pointer binaryThresholdFixedVolume = BinaryThresholdFixedVolumeType::New();
+    binaryThresholdFixedVolume->SetInput(this->m_FixedVolume);
+    binaryThresholdFixedVolume->SetOutsideValue(0);
+    binaryThresholdFixedVolume->SetInsideValue(255);
+    binaryThresholdFixedVolume->SetLowerThreshold(1);
+    binaryThresholdFixedVolume->Update();
+    this->m_FixedVolume = binaryThresholdFixedVolume->GetOutput();
+
+    typedef itk::BinaryThresholdImageFilter BinaryThresholdMovingVolumeType;
+    BinaryThresholdMovingVolumeType::Pointer binaryThresholdMovingVolume = BinaryThresholdMovingVolumeType::New();
+    binaryThresholdMovingVolume->SetInput(this->m_MovingVolume);
+    binaryThresholdMovingVolume->SetOutsideValue(0);
+    binaryThresholdMovingVolume->SetInsideValue(255);
+    binaryThresholdMovingVolume->SetLowerThreshold(1);
+    binaryThresholdMovingVolume->Update();
+    this->m_PreprocessedMovingVolume = binaryThresholdMovingVolume->GetOutput();
+
+    typedef itk::KappaStatisticImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "MRSD" )
+    {
+    typedef itk::MeanReciprocalSquareDifferenceImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "MIH" )
+    {
+    typedef itk::MutualInformationHistogramImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "GD" )
+    {
+    typedef itk::GradientDifferenceImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "CCH" )
+    {
+    typedef itk::CorrelationCoefficientHistogramImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "MC" )
+    {
+    typedef itk::MatchCardinalityImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "MSEH" )
+    {
+    typedef itk::MeanSquaresHistogramImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else if( this->m_CostMetric == "NMIH" )
+    {
+    typedef itk::NormalizedMutualInformationHistogramImageToImageMetric MetricType;
+    this->SetupRegistration();
+    this->RunRegistration();
+    }
+  else
+    {
+    std::cout << "Metric \"" << this->m_CostMetric << "\" not valid." << std::endl;
+    }
+}
+
+void
+BRAINSFitHelper::PrintSelf(std::ostream & os, Indent indent) const
+{
+  // Superclass::PrintSelf(os,indent);
+  os << indent << "FixedVolume:\n"  <<   this->m_FixedVolume << std::endl;
+  os << indent << "MovingVolume:\n" <<   this->m_MovingVolume << std::endl;
+  os << indent << "PreprocessedMovingVolume:\n" <<   this->m_PreprocessedMovingVolume << std::endl;
+  if( this->m_FixedBinaryVolume.IsNotNull() )
+    {
+    os << indent << "FixedBinaryVolume:\n" << this->m_FixedBinaryVolume << std::endl;
+    }
+  else
+    {
+    os << indent << "FixedBinaryVolume: IS NULL" << std::endl;
+    }
+  if( this->m_MovingBinaryVolume.IsNotNull() )
+    {
+    os << indent << "MovingBinaryVolume:\n" << this->m_MovingBinaryVolume << std::endl;
+    }
+  else
+    {
+    os << indent << "MovingBinaryVolume: IS NULL" << std::endl;
+    }
+  os << indent << "NumberOfSamples:      " << this->m_NumberOfSamples << std::endl;
+
+  os << indent << "NumberOfIterations:    [";
+  for( unsigned int q = 0; q < this->m_NumberOfIterations.size(); ++q )
+    {
+    os << this->m_NumberOfIterations[q] << " ";
+    }
+  os << "]" << std::endl;
+  os << indent << "NumberOfHistogramBins:" << this->m_NumberOfHistogramBins << std::endl;
+  os << indent << "MaximumStepLength:    " << this->m_MaximumStepLength << std::endl;
+  os << indent << "MinimumStepLength:     [";
+  for( unsigned int q = 0; q < this->m_MinimumStepLength.size(); ++q )
+    {
+    os << this->m_MinimumStepLength[q] << " ";
+    }
+  os << "]" << std::endl;
+  os << indent << "TransformType:     [";
+  for( unsigned int q = 0; q < this->m_TransformType.size(); ++q )
+    {
+    os << this->m_TransformType[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  os << indent << "RelaxationFactor:    " << this->m_RelaxationFactor << std::endl;
+  os << indent << "TranslationScale:    " << this->m_TranslationScale << std::endl;
+  os << indent << "ReproportionScale:   " << this->m_ReproportionScale << std::endl;
+  os << indent << "SkewScale:           " << this->m_SkewScale << std::endl;
+  os << indent << "UseExplicitPDFDerivativesMode:  " << this->m_UseExplicitPDFDerivativesMode << std::endl;
+  os << indent << "UseCachingOfBSplineWeightsMode: " << this->m_UseCachingOfBSplineWeightsMode << std::endl;
+  os << indent << "BackgroundFillValue:            " << this->m_BackgroundFillValue << std::endl;
+  os << indent << "InitializeTransformMode:        " << this->m_InitializeTransformMode << std::endl;
+  os << indent << "MaskInferiorCutOffFromCenter:   " << this->m_MaskInferiorCutOffFromCenter << std::endl;
+  os << indent << "ActualNumberOfIterations:       " << this->m_ActualNumberOfIterations << std::endl;
+  os << indent << "PermittedNumberOfIterations:       " << this->m_PermittedNumberOfIterations << std::endl;
+  // os << indent << "AccumulatedNumberOfIterationsForAllLevels: " <<
+  // this->m_AccumulatedNumberOfIterationsForAllLevels << std::endl;
+
+  os << indent << "SplineGridSize:     [";
+  for( unsigned int q = 0; q < this->m_SplineGridSize.size(); ++q )
+    {
+    os << this->m_SplineGridSize[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  os << indent << "PermitParameterVariation:     [";
+  for( unsigned int q = 0; q < this->m_PermitParameterVariation.size(); ++q )
+    {
+    os << this->m_PermitParameterVariation[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  if( m_CurrentGenericTransform.IsNotNull() )
+    {
+    os << indent << "CurrentGenericTransform:\n" << this->m_CurrentGenericTransform << std::endl;
+    }
+  else
+    {
+    os << indent << "CurrentGenericTransform: IS NULL" << std::endl;
+    }
+  os << indent << "CostMetric:       " << this->m_CostMetric << std::endl;
+}
+
+void
+BRAINSFitHelper::PrintCommandLine(const bool dumpTempVolumes, const std::string suffix) const
+{
+  std::cout << "The equivalent command line to the current run would be:" << std::endl;
+
+  const std::string fixedVolumeString("DEBUGFixedVolume_" + suffix + ".nii.gz");
+  const std::string movingVolumeString("DEBUGMovingVolume_" + suffix + ".nii.gz");
+  const std::string fixedBinaryVolumeString("DEBUGFixedBinaryVolume_" + suffix + ".nii.gz");
+  const std::string movingBinaryVolumeString("DEBUGMovingBinaryVolume_" + suffix + ".nii.gz");
+
+  std::ostringstream oss;
+  oss << "BRAINSFit \\" << std::endl;
+  if( dumpTempVolumes == true )
+    {
+      {
+      typedef itk::ImageFileWriter WriterType;
+      WriterType::Pointer writer = WriterType::New();
+      writer->UseCompressionOn();
+      writer->SetFileName(fixedVolumeString);
+      writer->SetInput(this->m_FixedVolume);
+      try
+        {
+        writer->Update();
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        oss << "Exception Object caught: " << std::endl;
+        oss << err << std::endl;
+        throw;
+        }
+      }
+      {
+      typedef itk::ImageFileWriter WriterType;
+      WriterType::Pointer writer = WriterType::New();
+      writer->UseCompressionOn();
+      writer->SetFileName(movingVolumeString);
+      writer->SetInput(this->m_MovingVolume);
+      try
+        {
+        writer->Update();
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        oss << "Exception Object caught: " << std::endl;
+        oss << err << std::endl;
+        throw;
+        }
+      }
+    }
+  oss << "--costMetric " << this->m_CostMetric << " \\" << std::endl;
+  oss << "--fixedVolume "  <<  fixedVolumeString   << "  \\" << std::endl;
+  oss << "--movingVolume " <<  movingVolumeString  << "  \\" << std::endl;
+  if( this->m_HistogramMatch )
+    {
+    oss << "--histogramMatch " <<  "  \\" << std::endl;
+    }
+
+    {
+    if( this->m_FixedBinaryVolume.IsNotNull() )
+      {
+      oss << "--fixedBinaryVolume " << fixedBinaryVolumeString  << "  \\" << std::endl;
+        {
+          {
+          const MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+            ExtractConstPointerToImageMaskFromImageSpatialObject(m_FixedBinaryVolume.GetPointer() );
+          itkUtil::WriteConstImage(tempOutputFixedVolumeROI.GetPointer(), fixedBinaryVolumeString);
+          }
+        }
+      }
+    if( this->m_MovingBinaryVolume.IsNotNull() )
+      {
+      oss << "--movingBinaryVolume " << movingBinaryVolumeString  << "  \\" << std::endl;
+        {
+
+          {
+          const MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+            ExtractConstPointerToImageMaskFromImageSpatialObject(m_MovingBinaryVolume.GetPointer() );
+          itkUtil::WriteConstImage(tempOutputMovingVolumeROI.GetPointer(), movingBinaryVolumeString);
+          }
+        }
+      }
+    if( this->m_FixedBinaryVolume.IsNotNull()  || this->m_MovingBinaryVolume.IsNotNull() )
+      {
+      oss << "--maskProcessingMode ROI "   << "  \\" << std::endl;
+      }
+    }
+  oss << "--numberOfSamples " << this->m_NumberOfSamples  << "  \\" << std::endl;
+
+  oss << "--numberOfIterations ";
+  for( unsigned int q = 0; q < this->m_NumberOfIterations.size(); ++q )
+    {
+    oss << this->m_NumberOfIterations[q];
+    if( q < this->m_NumberOfIterations.size() - 1 )
+      {
+      oss << ",";
+      }
+    }
+  oss << " \\" << std::endl;
+  oss << "--numberOfHistogramBins " << this->m_NumberOfHistogramBins  << "  \\" << std::endl;
+  oss << "--maximumStepLength " << this->m_MaximumStepLength  << "  \\" << std::endl;
+  oss << "--minimumStepLength ";
+  for( unsigned int q = 0; q < this->m_MinimumStepLength.size(); ++q )
+    {
+    oss << this->m_MinimumStepLength[q];
+    if( q < this->m_MinimumStepLength.size() - 1 )
+      {
+      oss << ",";
+      }
+    }
+  oss << " \\" << std::endl;
+  oss << "--transformType ";
+  for( unsigned int q = 0; q < this->m_TransformType.size(); ++q )
+    {
+    oss << this->m_TransformType[q];
+    if( q < this->m_TransformType.size() - 1 )
+      {
+      oss << ",";
+      }
+    }
+  oss << " \\" << std::endl;
+
+  oss << "--relaxationFactor " << this->m_RelaxationFactor  << "  \\" << std::endl;
+  oss << "--translationScale " << this->m_TranslationScale  << "  \\" << std::endl;
+  oss << "--reproportionScale " << this->m_ReproportionScale  << "  \\" << std::endl;
+  oss << "--skewScale " << this->m_SkewScale  << "  \\" << std::endl;
+  oss << "--useExplicitPDFDerivativesMode " << this->m_UseExplicitPDFDerivativesMode  << "  \\" << std::endl;
+  oss << "--useCachingOfBSplineWeightsMode " << this->m_UseCachingOfBSplineWeightsMode  << "  \\" << std::endl;
+  oss << "--maxBSplineDisplacement " << this->m_MaxBSplineDisplacement << " \\" << std::endl;
+  oss << "--projectedGradientTolerance " << this->m_ProjectedGradientTolerance << " \\" << std::endl;
+  oss << "--costFunctionConvergenceFactor " << this->m_CostFunctionConvergenceFactor << " \\" << std::endl;
+  oss << "--backgroundFillValue " << this->m_BackgroundFillValue  << "  \\" << std::endl;
+  if( this->m_InitializeTransformMode == "useGeometryAlign" )
+    {
+    oss << "--useGeometryAlign \\" << std::endl;
+    }
+  else if( this->m_InitializeTransformMode == "useMomentsAlign" )
+    {
+    oss << "--useMomentsAlign \\" << std::endl;
+    }
+  else if( this->m_InitializeTransformMode == "useCenterOfHeadAlign" )
+    {
+    oss << "--useCenterOfHeadAlign \\" << std::endl;
+    }
+  oss << "--initializeTransformMode " << this->m_InitializeTransformMode  << "  \\" << std::endl;
+  oss << "--maskInferiorCutOffFromCenter " << this->m_MaskInferiorCutOffFromCenter  << "  \\" << std::endl;
+  oss << "--splineGridSize ";
+  for( unsigned int q = 0; q < this->m_SplineGridSize.size(); ++q )
+    {
+    oss << this->m_SplineGridSize[q];
+    if( q < this->m_SplineGridSize.size() - 1 )
+      {
+      oss << ",";
+      }
+    }
+  oss << " \\" << std::endl;
+
+  if( this->m_PermitParameterVariation.size() > 0 )
+    {
+    oss << "--permitParameterVariation ";
+    for( unsigned int q = 0; q < this->m_PermitParameterVariation.size(); ++q )
+      {
+      oss << this->m_PermitParameterVariation[q];
+      if( q < this->m_PermitParameterVariation.size() - 1 )
+        {
+        oss << ",";
+        }
+      }
+    oss << " \\" << std::endl;
+    }
+  if( m_CurrentGenericTransform.IsNotNull() )
+    {
+    const std::string initialTransformString("DEBUGInitialTransform_" + suffix + ".mat");
+    WriteBothTransformsToDisk(this->m_CurrentGenericTransform.GetPointer(), initialTransformString, "");
+    oss << "--initialTransform " << initialTransformString  << "  \\" << std::endl;
+    }
+    {
+    const std::string outputVolume("DEBUGOutputVolume_" + suffix + ".nii.gz");
+    oss << "--outputVolume " << outputVolume  << "  \\" << std::endl;
+    std::cout << oss.str() << std::endl;
+    }
+    {
+    const std::string outputTransform("DEBUGOutputTransform" + suffix + ".mat");
+    oss << "--outputTransform " << outputTransform  << "  \\" << std::endl;
+    std::cout << oss.str() << std::endl;
+    }
+  const std::string TesterScript("DEBUGScript" + suffix + ".sh");
+  std::ofstream     myScript;
+  myScript.open( TesterScript.c_str() );
+  myScript << oss.str() << std::endl;
+  myScript.close();
+}
+
+void
+BRAINSFitHelper::GenerateData()
+{
+  this->StartRegistration();
+}
+
+} // end namespace itk
diff --git a/BRAINSCommonLib/BRAINSFitHelper.h b/BRAINSCommonLib/BRAINSFitHelper.h
new file mode 100644
index 00000000..f76b09ed
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitHelper.h
@@ -0,0 +1,435 @@
+#ifndef  __BRAINSFitHelper_h
+#define  __BRAINSFitHelper_h
+
+/**
+  * \author Hans J. Johnson
+  *
+  * The intension of the BRIANSFitHelper is to provide a simple non-templated
+  * class that can be used in other programs in a way that is very similar to
+  * the command line version of the program from the SlicerExecutionModel
+  * version of the BRAINSFitPrimary program.
+  *
+  * Almost all the command line options are available in this version, but
+  * there is no need to read or write files to disk in order to use this class.
+  *
+  */
+#include 
+#include 
+#include 
+#include 
+#include "itkImageRandomNonRepeatingConstIteratorWithIndex.h"
+
+#include "BRAINSCommonLibWin32Header.h"
+
+// TODO:  This needs to be moved to the top, and header files moved to this
+// header where needed.
+#include "BRAINSFitHelperTemplate.h"
+#include "BRAINSFitBSpline.h"
+#include "BRAINSFitUtils.h"
+
+#include "itkIO.h"
+#include "GenericTransformImage.h"
+#include "itkFindCenterOfBrainFilter.h"
+#include "ReadMask.h"
+#include "BRAINSMacro.h"
+
+namespace itk
+{
+/** Method for verifying that the ordering of the transformTypes is consistent
+  * with converting routines. */
+BRAINSCommonLib_EXPORT extern void ValidateTransformRankOrdering(const std::vector & transformType);
+
+}
+
+namespace itk
+{
+
+class BRAINSCommonLib_EXPORT BRAINSFitHelper : public Object
+{
+public:
+  /** Standard class typedefs. */
+  typedef BRAINSFitHelper          Self;
+  typedef ProcessObject            Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  typedef float                         PixelType;
+  typedef itk::Image      FixedVolumeType;
+  typedef FixedVolumeType::ConstPointer FixedImageConstPointer;
+  typedef FixedVolumeType::Pointer      FixedImagePointer;
+
+  typedef itk::Image       MovingVolumeType;
+  typedef MovingVolumeType::ConstPointer MovingImageConstPointer;
+  typedef MovingVolumeType::Pointer      MovingImagePointer;
+
+  /** Constants for the image dimensions */
+  itkStaticConstMacro(FixedImageDimension, unsigned int, FixedVolumeType::ImageDimension);
+  itkStaticConstMacro(MovingImageDimension, unsigned int, MovingVolumeType::ImageDimension);
+
+  typedef SpatialObject  FixedBinaryVolumeType;
+  typedef SpatialObject MovingBinaryVolumeType;
+  typedef FixedBinaryVolumeType::Pointer                              FixedBinaryVolumePointer;
+  typedef MovingBinaryVolumeType::Pointer                             MovingBinaryVolumePointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(BRAINSFitHelper, ProcessObject);
+
+  /** Set/Get the Fixed image. */
+  itkSetObjectMacro(FixedVolume, FixedVolumeType);
+  itkGetConstObjectMacro(FixedVolume, FixedVolumeType);
+
+  /** Set/Get the Moving image. */
+  itkSetObjectMacro(MovingVolume, MovingVolumeType)
+  itkGetConstObjectMacro(MovingVolume, MovingVolumeType);
+
+  /** The preprocessedMoving volume SHOULD NOT BE SET, you can get it out of the
+    *  algorithm.*/
+  itkGetObjectMacro(PreprocessedMovingVolume, MovingVolumeType);
+
+  itkSetObjectMacro(FixedBinaryVolume, FixedBinaryVolumeType);
+  itkGetConstObjectMacro(FixedBinaryVolume, FixedBinaryVolumeType);
+  itkSetObjectMacro(MovingBinaryVolume, MovingBinaryVolumeType);
+  itkGetConstObjectMacro(MovingBinaryVolume, MovingBinaryVolumeType);
+
+  itkSetMacro(OutputFixedVolumeROI,  std::string);
+  itkGetConstMacro(OutputFixedVolumeROI,  std::string);
+  itkSetMacro(OutputMovingVolumeROI, std::string);
+  itkGetConstMacro(OutputMovingVolumeROI, std::string);
+
+  // TODO:  This should be converted to use the
+  //       interpolation mechanisms from GenericTransform
+  typedef enum
+    {
+    LINEAR_INTERP = 0,
+    WINDOWSINC_INTERP = 1,
+    } InterpolationType;
+
+  itkSetMacro(NumberOfSamples,                   unsigned int);
+  itkGetConstMacro(NumberOfSamples,              unsigned int);
+  itkSetMacro(NumberOfHistogramBins,             unsigned int);
+  itkGetConstMacro(NumberOfHistogramBins,        unsigned int);
+  itkSetMacro(NumberOfMatchPoints,               unsigned int);
+  itkGetConstMacro(NumberOfMatchPoints,          unsigned int);
+  VECTORitkSetMacro(NumberOfIterations,   std::vector /**/);
+  VECTORitkSetMacro(MinimumStepLength,    std::vector );
+  itkSetMacro(MaximumStepLength,             double);
+  itkGetConstMacro(MaximumStepLength,             double);
+  itkSetMacro(RelaxationFactor,              double);
+  itkGetConstMacro(RelaxationFactor,              double);
+  itkSetMacro(TranslationScale,              double);
+  itkGetConstMacro(TranslationScale,              double);
+  itkSetMacro(ReproportionScale,             double);
+  itkGetConstMacro(ReproportionScale,             double);
+  itkSetMacro(SkewScale,                     double);
+  itkGetConstMacro(SkewScale,                     double);
+  itkSetMacro(UseExplicitPDFDerivativesMode, std::string);
+  itkGetConstMacro(UseExplicitPDFDerivativesMode, std::string);
+  itkSetMacro(UseCachingOfBSplineWeightsMode, std::string);
+  itkGetConstMacro(UseCachingOfBSplineWeightsMode, std::string);
+  itkSetMacro(CostFunctionConvergenceFactor, double);
+  itkGetConstMacro(CostFunctionConvergenceFactor, double);
+  itkSetMacro(ProjectedGradientTolerance,    double);
+  itkGetConstMacro(ProjectedGradientTolerance,    double);
+  itkSetMacro(MaxBSplineDisplacement,        double);
+  itkGetConstMacro(MaxBSplineDisplacement,        double);
+  itkSetMacro(BackgroundFillValue,           double);
+  itkGetConstMacro(BackgroundFillValue,           double);
+  VECTORitkSetMacro(TransformType, std::vector );
+  itkSetMacro(InitializeTransformMode, std::string);
+  itkGetConstMacro(InitializeTransformMode, std::string);
+  itkSetMacro(MaskInferiorCutOffFromCenter, double);
+  itkGetConstMacro(MaskInferiorCutOffFromCenter, double);
+  itkSetMacro(CurrentGenericTransform,  GenericTransformType::Pointer);
+  itkGetConstMacro(CurrentGenericTransform,  GenericTransformType::Pointer);
+  VECTORitkSetMacro(SplineGridSize, std::vector       );
+
+  itkGetConstMacro(ActualNumberOfIterations,      unsigned int);
+  itkGetConstMacro(PermittedNumberOfIterations,   unsigned int);
+
+  itkGetConstMacro(FinalMetricValue,         double);
+  /** Set/Get the Debugging level for filter verboseness */
+  itkSetMacro(DebugLevel, unsigned int);
+  itkGetConstMacro(DebugLevel, unsigned int);
+  itkSetMacro(DisplayDeformedImage, bool);
+  itkGetConstMacro(DisplayDeformedImage, bool);
+  itkSetMacro(PromptUserAfterDisplay, bool);
+  itkGetConstMacro(PromptUserAfterDisplay, bool);
+  itkSetMacro(ObserveIterations,        bool);
+  itkGetConstMacro(ObserveIterations,        bool);
+
+  const std::vector * GetGenericTransformListPtr()
+  {
+    return &m_GenericTransformList;
+  }
+
+  /** Method to set the Permission to vary by level  */
+  void SetPermitParameterVariation(std::vector perms)
+  {
+    m_PermitParameterVariation.resize( perms.size() );
+    for( unsigned int i = 0; i < perms.size(); ++i )
+      {
+      m_PermitParameterVariation[i] = perms[i];
+      }
+  }
+
+  itkSetMacro(HistogramMatch, bool);
+  itkGetConstMacro(HistogramMatch, bool);
+
+  itkSetMacro(RemoveIntensityOutliers, float);
+  itkGetConstMacro(RemoveIntensityOutliers, float);
+
+  itkSetMacro(CostMetric, std::string);
+  itkGetConstMacro(CostMetric, std::string);
+
+  /** Method that initiates the registration. */
+  void StartRegistration(void);
+
+  void PrintCommandLine(const bool dumpTempVolumes, const std::string suffix) const;
+
+protected:
+  BRAINSFitHelper();
+  virtual ~BRAINSFitHelper()
+  {
+  }
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Method invoked by the pipeline in order to trigger the computation of
+    * the registration. */
+  void  GenerateData();
+
+private:
+
+  BRAINSFitHelper(const Self &); // purposely not implemented
+  void operator=(const Self &);  // purposely not implemented
+
+  template 
+  void SetupRegistration();
+
+  template 
+  void RunRegistration();
+
+  template 
+  typename TLocalCostMetric::Pointer GetCostMetric();
+
+  FixedImagePointer  m_FixedVolume;
+  MovingImagePointer m_MovingVolume;
+  MovingImagePointer m_PreprocessedMovingVolume;
+
+  FixedBinaryVolumePointer  m_FixedBinaryVolume;
+  MovingBinaryVolumePointer m_MovingBinaryVolume;
+  std::string               m_OutputFixedVolumeROI;
+  std::string               m_OutputMovingVolumeROI;
+  std::vector          m_PermitParameterVariation;
+
+  unsigned int m_NumberOfSamples;
+  unsigned int m_NumberOfHistogramBins;
+  bool         m_HistogramMatch;
+  float        m_RemoveIntensityOutliers;
+  unsigned int m_NumberOfMatchPoints;
+  // TODO:  Would be better to have unsigned int
+  std::vector         m_NumberOfIterations;
+  double                   m_MaximumStepLength;
+  std::vector      m_MinimumStepLength;
+  double                   m_RelaxationFactor;
+  double                   m_TranslationScale;
+  double                   m_ReproportionScale;
+  double                   m_SkewScale;
+  std::string              m_UseExplicitPDFDerivativesMode;
+  std::string              m_UseCachingOfBSplineWeightsMode;
+  double                   m_BackgroundFillValue;
+  std::vector m_TransformType;
+  std::string              m_InitializeTransformMode;
+  double                   m_MaskInferiorCutOffFromCenter;
+  std::vector         m_SplineGridSize;
+  double                   m_CostFunctionConvergenceFactor;
+  double                   m_ProjectedGradientTolerance;
+  double                   m_MaxBSplineDisplacement;
+  unsigned int             m_ActualNumberOfIterations;
+  unsigned int             m_PermittedNumberOfIterations;
+  // unsigned int             m_AccumulatedNumberOfIterationsForAllLevels;
+  unsigned int                               m_DebugLevel;
+  GenericTransformType::Pointer              m_CurrentGenericTransform;
+  std::vector m_GenericTransformList;
+  bool                                       m_DisplayDeformedImage;
+  bool                                       m_PromptUserAfterDisplay;
+  double                                     m_FinalMetricValue;
+  bool                                       m_ObserveIterations;
+  std::string                                m_CostMetric;
+  itk::Object::Pointer                       m_Helper;
+};  // end BRAINSFitHelper class
+
+template 
+void
+BRAINSFitHelper::SetupRegistration()
+{
+
+  typedef typename TLocalCostMetric::FixedImageType                              FixedImageType;
+  typedef typename TLocalCostMetric::MovingImageType                             MovingImageType;
+  typedef typename itk::BRAINSFitHelperTemplate HelperType;
+
+  typedef typename itk::LinearInterpolateImageFunction InterpolatorType;
+  typename InterpolatorType::Pointer localLinearInterpolator = InterpolatorType::New();
+  //
+  // set up cost metric
+  typename TLocalCostMetric::Pointer localCostMetric = TLocalCostMetric::New();
+  localCostMetric->ReinitializeSeed(76926294);
+  localCostMetric->SetInterpolator(localLinearInterpolator);
+  localCostMetric->SetFixedImage(this->m_FixedVolume);
+  localCostMetric->SetMovingImage(this->m_PreprocessedMovingVolume);
+
+  if( this->m_MovingBinaryVolume.IsNotNull() )
+    {
+    localCostMetric->SetMovingImageMask(this->m_MovingBinaryVolume);
+    }
+  if( this->m_FixedBinaryVolume.IsNotNull() )
+    {
+    localCostMetric->SetUseAllPixels(false);
+    // Convert to using list of samples that are desired.
+    // Do not set this if using explicit samples
+    // localCostMetric->SetFixedImageMask(this->m_FixedBinaryVolume);
+    typename TLocalCostMetric::FixedImageIndexContainer myListOfIndexLocations;
+    myListOfIndexLocations.reserve(this->m_NumberOfSamples);
+    itk::ImageRandomNonRepeatingConstIteratorWithIndex NRit( this->m_FixedVolume,
+                                                                             this->m_FixedVolume->GetBufferedRegion() );
+    NRit.SetNumberOfSamples(this->m_FixedVolume->GetBufferedRegion().GetNumberOfPixels() );
+    NRit.GoToBegin();
+
+    if( this->m_NumberOfSamples == 0 )
+      {
+      this->m_NumberOfSamples = this->m_FixedVolume->GetBufferedRegion().GetNumberOfPixels();
+      }
+    size_t currentCount = 0;
+    while( ( !NRit.IsAtEnd() ) && ( currentCount < this->m_NumberOfSamples ) )
+      {
+      typename FixedImageType::PointType testPoint;
+      this->m_FixedVolume->TransformIndexToPhysicalPoint(NRit.GetIndex(), testPoint);
+      if( this->m_FixedBinaryVolume->IsInside(testPoint) )
+        {
+        myListOfIndexLocations.push_back(NRit.GetIndex() );
+        ++currentCount;
+        }
+      ++NRit;
+      }
+
+    assert(currentCount != 0 );
+    this->m_NumberOfSamples = myListOfIndexLocations.size();
+    // Redundant with SetFixedImageIndexes
+    // localCostMetric->SetUseFixedImageIndexes(true);
+    // Redundant with SetFixedImageIndexes
+    // localCostMetric->SetNumberOfFixedImageSamples(this->m_NumberOfSamples);
+    // Redundant with SetNumberOfFixedImageSamples
+    // localCostMetric->SetNumberOfSpatialSamples(this->m_NumberOfSamples);
+    localCostMetric->SetFixedImageIndexes(myListOfIndexLocations);
+    }
+  else
+    {
+    localCostMetric->SetFixedImageRegion( this->m_FixedVolume->GetBufferedRegion() );
+    if( this->m_NumberOfSamples > 0 )
+      {
+      localCostMetric->SetNumberOfSpatialSamples(this->m_NumberOfSamples);
+      }
+    else
+      {
+      localCostMetric->SetUseAllPixels(true);
+      }
+    }
+
+  typename HelperType::Pointer
+  myHelper = BRAINSFitHelperTemplate::New();
+  myHelper->SetTransformType(this->m_TransformType);
+  myHelper->SetFixedVolume(this->m_FixedVolume);
+  myHelper->SetMovingVolume(this->m_PreprocessedMovingVolume);
+  myHelper->SetHistogramMatch(this->m_HistogramMatch);
+  myHelper->SetRemoveIntensityOutliers(this->m_RemoveIntensityOutliers);
+  myHelper->SetNumberOfMatchPoints(this->m_NumberOfMatchPoints);
+  myHelper->SetFixedBinaryVolume(this->m_FixedBinaryVolume);
+  myHelper->SetMovingBinaryVolume(this->m_MovingBinaryVolume);
+  myHelper->SetOutputFixedVolumeROI(this->m_OutputFixedVolumeROI);
+  myHelper->SetOutputMovingVolumeROI(this->m_OutputMovingVolumeROI);
+  myHelper->SetPermitParameterVariation(this->m_PermitParameterVariation);
+  myHelper->SetNumberOfSamples(this->m_NumberOfSamples);
+  myHelper->SetNumberOfHistogramBins(this->m_NumberOfHistogramBins);
+  myHelper->SetNumberOfIterations(this->m_NumberOfIterations);
+  myHelper->SetMaximumStepLength(this->m_MaximumStepLength);
+  myHelper->SetMinimumStepLength(this->m_MinimumStepLength);
+  myHelper->SetRelaxationFactor(this->m_RelaxationFactor);
+  myHelper->SetTranslationScale(this->m_TranslationScale);
+  myHelper->SetReproportionScale(this->m_ReproportionScale);
+  myHelper->SetSkewScale(this->m_SkewScale);
+  myHelper->SetBackgroundFillValue(this->m_BackgroundFillValue);
+  myHelper->SetInitializeTransformMode(this->m_InitializeTransformMode);
+  myHelper->SetUseExplicitPDFDerivativesMode(this->m_UseExplicitPDFDerivativesMode);
+  myHelper->SetMaskInferiorCutOffFromCenter(this->m_MaskInferiorCutOffFromCenter);
+  myHelper->SetCurrentGenericTransform(this->m_CurrentGenericTransform);
+  myHelper->SetSplineGridSize(this->m_SplineGridSize);
+  myHelper->SetCostFunctionConvergenceFactor(this->m_CostFunctionConvergenceFactor);
+  myHelper->SetProjectedGradientTolerance(this->m_ProjectedGradientTolerance);
+  myHelper->SetMaxBSplineDisplacement(this->m_MaxBSplineDisplacement);
+  myHelper->SetDisplayDeformedImage(this->m_DisplayDeformedImage);
+  myHelper->SetPromptUserAfterDisplay(this->m_PromptUserAfterDisplay);
+  myHelper->SetDebugLevel(this->m_DebugLevel);
+  myHelper->SetCostMetricObject(localCostMetric);
+  if( this->m_DebugLevel > 7 )
+    {
+    this->PrintCommandLine(true, "BF");
+    }
+  this->m_Helper = static_cast(myHelper.GetPointer() );
+}
+
+template 
+void
+BRAINSFitHelper::RunRegistration()
+{
+  typedef typename TLocalCostMetric::FixedImageType  FixedImageType;
+  typedef typename TLocalCostMetric::MovingImageType MovingImageType;
+  typedef typename itk::BRAINSFitHelperTemplate
+  HelperType;
+
+  const typename HelperType::Pointer myHelper( dynamic_cast(this->m_Helper.GetPointer() ) );
+  if( myHelper.IsNull() )
+    {
+    std::cout << "ERROR:  Invalid BRAINSFitHelper conversion" << __FILE__ << " " << __LINE__ << std::endl;
+    }
+
+  myHelper->StartRegistration();
+  this->m_CurrentGenericTransform = myHelper->GetCurrentGenericTransform();
+  this->m_ActualNumberOfIterations = myHelper->GetActualNumberOfIterations();
+  this->m_PermittedNumberOfIterations = myHelper->GetPermittedNumberOfIterations();
+  this->m_GenericTransformList.resize(myHelper->GetGenericTransformListPtr()->size() );
+  std::copy(myHelper->GetGenericTransformListPtr()->begin(),
+            myHelper->GetGenericTransformListPtr()->end(), this->m_GenericTransformList.begin() );
+
+}
+
+template 
+typename TLocalCostMetric::Pointer
+BRAINSFitHelper::GetCostMetric()
+{
+  typedef typename TLocalCostMetric::FixedImageType  FixedImageType;
+  typedef typename TLocalCostMetric::MovingImageType MovingImageType;
+  typedef typename itk::BRAINSFitHelperTemplate
+  HelperType;
+  typedef typename HelperType::MetricType GenericMetricType;
+
+  const typename HelperType::Pointer myHelper( dynamic_cast(this->m_Helper.GetPointer() ) );
+  if( myHelper.IsNull() )
+    {
+    std::cout << "ERROR:  Invalid BRAINSFitHelper conversion" << __FILE__ << " " << __LINE__ << std::endl;
+    }
+
+  const typename GenericMetricType::Pointer metric = myHelper->GetCostMetricObject();
+  typename TLocalCostMetric::Pointer rval = dynamic_cast(metric.GetPointer() );
+  if( rval.IsNull() )
+    {
+    std::cout << "ERROR:  Invalid CostMetric conversion" << __FILE__ << " " << __LINE__ << std::endl;
+    }
+  return rval;
+}
+
+}   // end namespace itk
+
+#endif  // __BRAINSFITHELPER__
diff --git a/BRAINSCommonLib/BRAINSFitHelperTemplate.h b/BRAINSCommonLib/BRAINSFitHelperTemplate.h
new file mode 100644
index 00000000..b6ecaf45
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitHelperTemplate.h
@@ -0,0 +1,271 @@
+#ifndef  __BRAINSFitHelperTemplate_h
+#define  __BRAINSFitHelperTemplate_h
+
+/**
+  * \author Hans J. Johnson
+  *
+  * The intension of the BRIANSFitHelperTemplate is to provide a
+  * class that can be used in other programs in a way that is very similar to
+  * the command line version of the program from the SlicerExecutionModel
+  * version of the BRAINSFitPrimary program.
+  *
+  * Almost all the command line options are available in this version, but
+  * there is no need to read or write files to disk in order to use this class.
+  */
+#include 
+#include 
+#include 
+#include 
+
+#include "itkIO.h"
+#include "itkVector.h"
+#include "itkMedianImageFilter.h"
+#include "itkHistogramMatchingImageFilter.h"
+
+#include "itkCenteredVersorTransformInitializer.h"
+#include "itkCenteredTransformInitializer.h"
+#include "itkVersorRigid3DTransformOptimizer.h"
+#include "itkVersorRigid3DTransformOptimizer.h"
+#include "itkVersorTransformOptimizer.h"
+#include "itkMultiThreader.h"
+#include "itkResampleImageFilter.h"
+#include "itkAffineTransform.h"
+#include "itkImageMaskSpatialObject.h"
+
+#include "itkFindCenterOfBrainFilter.h"
+
+// TODO:  This needs to be moved to the top, and header files moved to this
+// header where needed.
+#include "BRAINSFitBSpline.h"
+#include "BRAINSFitUtils.h"
+
+#include "ConvertToRigidAffine.h"
+#include "genericRegistrationHelper.h"
+#include "ReadMask.h"
+#include "BRAINSMacro.h"
+#include "GenericTransformImage.h"
+#include "BRAINSCommonLibWin32Header.h"
+
+typedef itk::SpatialObject<3>      SpatialObjectType;
+typedef SpatialObjectType::Pointer ImageMaskPointer;
+
+namespace itk
+{
+/** Method for verifying that the ordering of the transformTypes is consistent
+  * with converting routines. */
+BRAINSCommonLib_EXPORT extern void ValidateTransformRankOrdering(const std::vector & transformType);
+
+}
+
+namespace itk
+{
+
+template 
+class BRAINSCommonLib_EXPORT BRAINSFitHelperTemplate : public Object
+{
+public:
+  /** Standard class typedefs. */
+  typedef BRAINSFitHelperTemplate  Self;
+  typedef ProcessObject            Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  typedef typename FixedImageType::ConstPointer FixedImageConstPointer;
+  typedef typename FixedImageType::Pointer      FixedImagePointer;
+
+  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;
+  typedef typename MovingImageType::Pointer      MovingImagePointer;
+
+  typedef typename itk::ImageToImageMetric MetricType;
+
+  /** Constants for the image dimensions */
+  itkStaticConstMacro(FixedImageDimension, unsigned int, FixedImageType::ImageDimension);
+  itkStaticConstMacro(MovingImageDimension, unsigned int, MovingImageType::ImageDimension);
+
+  typedef SpatialObject  FixedBinaryVolumeType;
+  typedef SpatialObject MovingBinaryVolumeType;
+  typedef typename FixedBinaryVolumeType::Pointer                     FixedBinaryVolumePointer;
+  typedef typename MovingBinaryVolumeType::Pointer                    MovingBinaryVolumePointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(BRAINSFitHelperTemplate, ProcessObject);
+
+  /** Set/Get the Fixed image. */
+  itkSetObjectMacro(FixedVolume, FixedImageType);
+  itkGetConstObjectMacro(FixedVolume, FixedImageType);
+
+  /** Set/Get the Moving image. */
+  itkSetObjectMacro(MovingVolume, MovingImageType)
+  itkGetConstObjectMacro(MovingVolume, MovingImageType);
+
+  itkSetObjectMacro(FixedBinaryVolume, FixedBinaryVolumeType);
+  itkGetConstObjectMacro(FixedBinaryVolume, FixedBinaryVolumeType);
+  itkSetObjectMacro(MovingBinaryVolume, MovingBinaryVolumeType);
+  itkGetConstObjectMacro(MovingBinaryVolume, MovingBinaryVolumeType);
+
+  itkSetMacro(OutputFixedVolumeROI,  std::string);
+  itkGetConstMacro(OutputFixedVolumeROI,  std::string);
+  itkSetMacro(OutputMovingVolumeROI, std::string);
+  itkGetConstMacro(OutputMovingVolumeROI, std::string);
+
+  itkSetObjectMacro(CostMetricObject, MetricType);
+  itkGetObjectMacro(CostMetricObject, MetricType);
+
+  // TODO:  This should be converted to use the
+  //       interpolation mechanisms from GenericTransform
+  typedef enum
+    {
+    LINEAR_INTERP = 0,
+    WINDOWSINC_INTERP = 1,
+    } InterpolationType;
+
+  itkSetMacro(NumberOfSamples,        unsigned int);
+  itkGetConstMacro(NumberOfSamples,        unsigned int);
+  itkSetMacro(NumberOfHistogramBins,         unsigned int);
+  itkGetConstMacro(NumberOfHistogramBins,         unsigned int);
+  itkSetMacro(NumberOfMatchPoints,           unsigned int);
+  itkGetConstMacro(NumberOfMatchPoints,           unsigned int);
+  VECTORitkSetMacro(NumberOfIterations,   std::vector /**/);
+  VECTORitkSetMacro(MinimumStepLength, std::vector );
+  itkSetMacro(MaximumStepLength,             double);
+  itkGetConstMacro(MaximumStepLength,             double);
+  itkSetMacro(RelaxationFactor,              double);
+  itkGetConstMacro(RelaxationFactor,              double);
+  itkSetMacro(TranslationScale,              double);
+  itkGetConstMacro(TranslationScale,              double);
+  itkSetMacro(ReproportionScale,             double);
+  itkGetConstMacro(ReproportionScale,             double);
+  itkSetMacro(SkewScale,                     double);
+  itkGetConstMacro(SkewScale,                     double);
+  itkSetMacro(CostFunctionConvergenceFactor, double);
+  itkGetConstMacro(CostFunctionConvergenceFactor, double);
+  itkSetMacro(ProjectedGradientTolerance,    double);
+  itkGetConstMacro(ProjectedGradientTolerance,    double);
+  itkSetMacro(MaxBSplineDisplacement,        double);
+  itkGetConstMacro(MaxBSplineDisplacement,        double);
+  itkSetMacro(BackgroundFillValue,           double);
+  itkGetConstMacro(BackgroundFillValue,           double);
+  VECTORitkSetMacro(TransformType, std::vector );
+  itkSetMacro(InitializeTransformMode, std::string);
+  itkGetConstMacro(InitializeTransformMode, std::string);
+  itkSetMacro(UseExplicitPDFDerivativesMode, std::string);
+  itkGetConstMacro(UseExplicitPDFDerivativesMode, std::string);
+  itkSetMacro(MaskInferiorCutOffFromCenter, double);
+  itkGetConstMacro(MaskInferiorCutOffFromCenter, double);
+  itkSetMacro(CurrentGenericTransform,  GenericTransformType::Pointer);
+  itkGetConstMacro(CurrentGenericTransform,  GenericTransformType::Pointer);
+  VECTORitkSetMacro(SplineGridSize, std::vector       );
+
+  itkGetConstMacro(ActualNumberOfIterations,      unsigned int);
+  itkGetConstMacro(PermittedNumberOfIterations,   unsigned int);
+
+  itkGetConstMacro(FinalMetricValue,         double);
+  /** Set/Get the Debugging level for filter verboseness */
+  itkSetMacro(DebugLevel, unsigned int);
+  itkGetConstMacro(DebugLevel, unsigned int);
+  itkSetMacro(DisplayDeformedImage, bool);
+  itkGetConstMacro(DisplayDeformedImage, bool);
+  itkSetMacro(PromptUserAfterDisplay, bool);
+  itkGetConstMacro(PromptUserAfterDisplay, bool);
+  itkSetMacro(ObserveIterations,        bool);
+  itkGetConstMacro(ObserveIterations,        bool);
+
+  const std::vector * GetGenericTransformListPtr()
+  {
+    return &m_GenericTransformList;
+  }
+
+  /** Method to set the Permission to vary by level  */
+  void SetPermitParameterVariation(std::vector perms)
+  {
+    m_PermitParameterVariation.resize( perms.size() );
+    for( unsigned int i = 0; i < perms.size(); ++i )
+      {
+      m_PermitParameterVariation[i] = perms[i];
+      }
+  }
+
+  itkSetMacro(HistogramMatch, bool);
+  itkGetConstMacro(HistogramMatch, bool);
+
+  itkSetMacro(RemoveIntensityOutliers, bool);
+  itkGetConstMacro(RemoveIntensityOutliers, bool);
+  /** Method that initiates the registration. */
+  void StartRegistration(void);
+
+protected:
+  BRAINSFitHelperTemplate();
+  virtual ~BRAINSFitHelperTemplate()
+  {
+  }
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Method invoked by the pipeline in order to trigger the computation of
+    * the registration. */
+  void  GenerateData();
+
+  /** instantiate and call the Registration Helper */
+  template 
+  void FitCommonCode(int numberOfIterations,
+                     double minimumStepLength,
+                     typename TransformType::Pointer & initialITKTransform);
+private:
+
+  BRAINSFitHelperTemplate(const Self &); // purposely not implemented
+  void operator=(const Self &);          // purposely not implemented
+
+  FixedImagePointer  m_FixedVolume;
+  MovingImagePointer m_MovingVolume;
+
+  FixedBinaryVolumePointer  m_FixedBinaryVolume;
+  MovingBinaryVolumePointer m_MovingBinaryVolume;
+  std::string               m_OutputFixedVolumeROI;
+  std::string               m_OutputMovingVolumeROI;
+
+  unsigned int m_NumberOfSamples;
+  unsigned int m_NumberOfHistogramBins;
+  bool         m_HistogramMatch;
+  float        m_RemoveIntensityOutliers;
+  unsigned int m_NumberOfMatchPoints;
+
+  // TODO:  Would be better to have unsigned int
+  std::vector         m_NumberOfIterations;
+  double                   m_MaximumStepLength;
+  std::vector      m_MinimumStepLength;
+  double                   m_RelaxationFactor;
+  double                   m_TranslationScale;
+  double                   m_ReproportionScale;
+  double                   m_SkewScale;
+  double                   m_BackgroundFillValue;
+  std::vector m_TransformType;
+  std::string              m_InitializeTransformMode;
+  std::string              m_UseExplicitPDFDerivativesMode;
+  double                   m_MaskInferiorCutOffFromCenter;
+  std::vector         m_SplineGridSize;
+  double                   m_CostFunctionConvergenceFactor;
+  double                   m_ProjectedGradientTolerance;
+  double                   m_MaxBSplineDisplacement;
+  unsigned int             m_ActualNumberOfIterations;
+  unsigned int             m_PermittedNumberOfIterations;
+  // unsigned int             m_AccumulatedNumberOfIterationsForAllLevels;
+  unsigned int                               m_DebugLevel;
+  GenericTransformType::Pointer              m_CurrentGenericTransform;
+  std::vector m_GenericTransformList;
+  bool                                       m_DisplayDeformedImage;
+  bool                                       m_PromptUserAfterDisplay;
+  double                                     m_FinalMetricValue;
+  bool                                       m_ObserveIterations;
+  typename MetricType::Pointer                 m_CostMetricObject;
+  std::vector m_PermitParameterVariation;
+};  // end BRAINSFitHelperTemplate class
+}   // end namespace itk
+
+#include "BRAINSFitHelperTemplate.hxx"
+
+#endif  // __BRAINSFITHELPER__
diff --git a/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx b/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx
new file mode 100644
index 00000000..37ba96d2
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitHelperTemplate.hxx
@@ -0,0 +1,1824 @@
+#include "itkIO.h"
+#ifdef USE_DEBUG_IMAGE_VIEWER
+#include "DebugImageViewerClient.h"
+#endif
+
+#include "BRAINSFitUtils.h"
+#include "itkEuler3DTransform.h"
+#include "itkCheckerBoardImageFilter.h"
+#include "itkOtsuHistogramMatchingImageFilter.h"
+#include 
+#include "BRAINSFitHelperTemplate.h"
+
+#include "itkLabelObject.h"
+#include "itkStatisticsLabelObject.h"
+#include "itkLabelImageToStatisticsLabelMapFilter.h"
+
+namespace itk
+{
+inline
+void
+ValidateTransformRankOrdering(const std::vector & transformType)
+{
+  // Need to review transform types in the transform type vector to ensure that
+  // they are ordered appropriately
+  // for processing.  I.e. that they go from low dimensional to high
+  // dimensional, and throw an error if
+  // B-Spline is before Rigid, or any other non-sensical ordering of the
+  // transform types.
+  // Rigid=1, ScaleVersor3D=2, ScaleSkewVersor3D=3, Affine=4, and (BSpline or
+  // ROIBspline)=5
+  unsigned int CurrentTransformRank = 0;
+  for( unsigned int l = 0; l < transformType.size(); ++l )
+    {
+    if( transformType[l] == "Rigid" )
+      {
+      if( CurrentTransformRank <= 1 )
+        {
+        CurrentTransformRank = 1;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpine)" << std::endl;
+        exit(-1);
+        }
+      }
+    else if( transformType[l] == "ScaleVersor3D" )
+      {
+      if( CurrentTransformRank <= 2 )
+        {
+        CurrentTransformRank = 2;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpline)" << std::endl;
+        exit(-1);
+        }
+      }
+    else if( transformType[l] == "ScaleSkewVersor3D" )
+      {
+      if( CurrentTransformRank <= 3 )
+        {
+        CurrentTransformRank = 3;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpline)" << std::endl;
+        exit(-1);
+        }
+      }
+    else if( transformType[l] == "Affine" )
+      {
+      if( CurrentTransformRank <= 4 )
+        {
+        CurrentTransformRank = 4;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpline)" << std::endl;
+        exit(-1);
+        }
+      }
+    else if( transformType[l] == "BSpline" )
+      {
+      if( CurrentTransformRank <= 5 )
+        {
+        CurrentTransformRank = 5;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpline)" << std::endl;
+        exit(-1);
+        }
+      }
+    else if( transformType[l] == "ROIBSpline" )
+      {
+      if( CurrentTransformRank <= 5 )
+        {
+        CurrentTransformRank = 5;
+        }
+      else
+        {
+        std::cerr << "Ordering of transforms does not proceed from\n"
+                  << "smallest to largest.  Please review settings for transformType.\n"
+                  << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < (BSpline | ROIBSpline)" << std::endl;
+        exit(-1);
+        }
+      }
+
+    else
+      {
+      std::cerr << " ERROR:  Invalid transform type specified for element " << l << " of --transformType: "
+                << transformType[l] << std::endl;
+      std::cerr << "Ordering of transforms must proceed from\n"
+                << "smallest to largest.  Please review settings for transformType.\n"
+                << "Rigid < ScaleVersor3D < ScaleSkewVersor3D < Affine < BSpline" << std::endl;
+      exit(-1);
+      }
+    }
+}
+
+template 
+typename TransformType::Pointer DoCenteredInitialization(
+  typename FixedImageType::Pointer & orientedFixedVolume,
+  typename MovingImageType::Pointer & orientedMovingVolume,
+  ImageMaskPointer & fixedMask,         // NOTE:  This is both input and output
+                                        // variable,  the Mask is updated by
+                                        // this function
+  ImageMaskPointer & movingMask,        // NOTE:  This is both input and output
+                                        // variable,  the Mask is updated by
+                                        // this function
+  std::string & initializeTransformMode,
+  typename MetricType::Pointer & CostMetricObject)
+{
+  typename TransformType::Pointer initialITKTransform = TransformType::New();
+  initialITKTransform->SetIdentity();
+
+  if( initializeTransformMode == "useGeometryAlign" )
+    {
+    // useGeometryAlign assumes objects are center in field of view, with
+    // different
+    typedef itk::CenteredTransformInitializer OrdinaryInitializerType;
+    typename OrdinaryInitializerType::Pointer CenteredInitializer =
+      OrdinaryInitializerType::New();
+
+    CenteredInitializer->SetFixedImage(orientedFixedVolume);
+    CenteredInitializer->SetMovingImage(orientedMovingVolume);
+    CenteredInitializer->SetTransform(initialITKTransform);
+    CenteredInitializer->GeometryOn();                    // Use the image spce
+                                                          // center
+    CenteredInitializer->InitializeTransform();
+    }
+  else if( initializeTransformMode == "useCenterOfHeadAlign"
+           || initializeTransformMode == "useCenterOfROIAlign" )
+    {
+    typedef typename itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+    typedef itk::Image                                         MaskImageType;
+    typename MovingImageType::PointType movingCenter;
+    typename FixedImageType::PointType fixedCenter;
+
+    if( initializeTransformMode == "useCenterOfROIAlign" )
+      {
+      // calculate the centers of each ROI
+      typedef itk::StatisticsLabelObject LabelObjectType;
+      typedef itk::LabelMap               LabelMapType;
+      typedef itk::LabelImageToStatisticsLabelMapFilter
+      LabelStatisticsFilterType;
+      typedef LabelMapType::LabelObjectContainerType LabelObjectContainerType;
+
+      const typename MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+        ExtractConstPointerToImageMaskFromImageSpatialObject(fixedMask.GetPointer() );
+      const typename MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+        ExtractConstPointerToImageMaskFromImageSpatialObject(movingMask.GetPointer() );
+
+      LabelStatisticsFilterType::Pointer movingImageToLabel = LabelStatisticsFilterType::New();
+      movingImageToLabel->SetInput( tempOutputMovingVolumeROI.GetPointer() );
+      movingImageToLabel->SetFeatureImage( tempOutputMovingVolumeROI.GetPointer() );
+      movingImageToLabel->SetComputePerimeter(false);
+      movingImageToLabel->Update();
+
+      LabelStatisticsFilterType::Pointer fixedImageToLabel = LabelStatisticsFilterType::New();
+      fixedImageToLabel->SetInput( tempOutputFixedVolumeROI.GetPointer() );
+      fixedImageToLabel->SetFeatureImage( tempOutputFixedVolumeROI.GetPointer() );
+      fixedImageToLabel->SetComputePerimeter(false);
+      fixedImageToLabel->Update();
+
+      LabelObjectType *movingLabel = movingImageToLabel->GetOutput()->GetNthLabelObject(0);
+      LabelObjectType *fixedLabel = fixedImageToLabel->GetOutput()->GetNthLabelObject(0);
+
+      LabelObjectType::CentroidType movingCentroid = movingLabel->GetCentroid();
+      LabelObjectType::CentroidType fixedCentroid = fixedLabel->GetCentroid();
+
+      movingCenter[0] = movingCentroid[0];
+      movingCenter[1] = movingCentroid[1];
+      movingCenter[2] = movingCentroid[2];
+
+      fixedCenter[0] = fixedCentroid[0];
+      fixedCenter[1] = fixedCentroid[1];
+      fixedCenter[2] = fixedCentroid[2];
+
+      // calculate the translation (and rotation?)
+      // initialize the transform center using the fixed ROI center
+      }
+    else       // CenterOfHead
+      {        //     typename MovingImageType::PointType movingCenter =
+               // GetCenterOfBrain(orientedMovingVolume);
+               //     typename FixedImageType::PointType fixedCenter =
+               // GetCenterOfBrain(orientedFixedVolume);
+      typedef typename itk::FindCenterOfBrainFilter
+      MovingFindCenterFilter;
+      typename MovingFindCenterFilter::Pointer movingFindCenter =
+        MovingFindCenterFilter::New();
+      movingFindCenter->SetInput(orientedMovingVolume);
+      if( movingMask.IsNotNull() )
+        {
+        const typename MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(movingMask.GetPointer() );
+        movingFindCenter->SetImageMask( tempOutputMovingVolumeROI );
+        }
+      movingFindCenter->Update();
+      movingCenter = movingFindCenter->GetCenterOfBrain();
+        {
+        // convert mask image to mask
+        typedef typename itk::ImageMaskSpatialObject
+        ImageMaskSpatialObjectType;
+        typename ImageMaskSpatialObjectType::Pointer mask =
+          ImageMaskSpatialObjectType::New();
+        mask->SetImage( movingFindCenter->GetClippedImageMask() );
+
+        typename MaskImageType::Pointer ClippedMask = movingFindCenter->GetClippedImageMask();
+        // itkUtil::WriteImage( ClippedMask ,
+        // std::string("MOVING_MASK.nii.gz"));
+
+        mask->ComputeObjectToWorldTransform();
+        const typename SpatialObjectType::Pointer p = dynamic_cast( mask.GetPointer() );
+        if( p.IsNull() )
+          {
+          std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+          exit(-1);
+          }
+        movingMask = p;
+        }
+
+      typedef typename itk::FindCenterOfBrainFilter
+      FixedFindCenterFilter;
+      typename FixedFindCenterFilter::Pointer fixedFindCenter =
+        FixedFindCenterFilter::New();
+      fixedFindCenter->SetInput(orientedFixedVolume);
+      if( fixedMask.IsNotNull() )
+        {
+        const typename MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(fixedMask.GetPointer() );
+        fixedFindCenter->SetImageMask(tempOutputFixedVolumeROI);
+        }
+      fixedFindCenter->Update();
+      fixedCenter = fixedFindCenter->GetCenterOfBrain();
+
+        {
+        // convert mask image to mask
+        typedef typename itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+        typename ImageMaskSpatialObjectType::Pointer mask = ImageMaskSpatialObjectType::New();
+        mask->SetImage( fixedFindCenter->GetClippedImageMask() );
+
+        typename MaskImageType::Pointer ClippedMask = fixedFindCenter->GetClippedImageMask();
+
+        mask->ComputeObjectToWorldTransform();
+        const typename SpatialObjectType::Pointer p = dynamic_cast( mask.GetPointer() );
+        if( p.IsNull() )
+          {
+          std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+          exit(-1);
+          }
+        fixedMask = p;
+        }
+      }
+
+    const double movingHeadScaleGuessRatio = 1;
+    /*
+     *
+     *fixedFindCenter->GetHeadSizeEstimate()/movingFindCenter->GetHeadSizeEstimate();
+     */
+
+    typename TransformType::InputPointType rotationCenter;
+    typename TransformType::OutputVectorType translationVector;
+    itk::Vector scaleValue;
+    for( unsigned int i = 0; i < Dimension; ++i )
+      {
+      rotationCenter[i]    = fixedCenter[i];
+      translationVector[i] = movingCenter[i] - fixedCenter[i];
+      scaleValue[i] = movingHeadScaleGuessRatio;
+      }
+    typedef itk::Euler3DTransform EulerAngle3DTransformType;
+    typename EulerAngle3DTransformType::Pointer bestEulerAngles3D = EulerAngle3DTransformType::New();
+    bestEulerAngles3D->SetCenter(rotationCenter);
+    bestEulerAngles3D->SetTranslation(translationVector);
+
+    typedef itk::Euler3DTransform EulerAngle3DTransformType;
+    typename EulerAngle3DTransformType::Pointer currentEulerAngles3D = EulerAngle3DTransformType::New();
+    currentEulerAngles3D->SetCenter(rotationCenter);
+    currentEulerAngles3D->SetTranslation(translationVector);
+
+    CostMetricObject->SetTransform(currentEulerAngles3D);
+    CostMetricObject->Initialize();
+    double max_cc = 0.0;
+    // void QuickSampleParameterSpace(void)
+      {
+      currentEulerAngles3D->SetRotation(0, 0, 0);
+      // Initialize with current guess;
+      max_cc = CostMetricObject->GetValue( currentEulerAngles3D->GetParameters() );
+      const double HARange = 12.0;
+      const double PARange = 12.0;
+      // rough search in neighborhood.
+      const double one_degree = 1.0F * vnl_math::pi / 180.0F;
+      const double HAStepSize = 3.0 * one_degree;
+      const double PAStepSize = 3.0 * one_degree;
+      // Quick search just needs to get an approximate angle correct.
+        {
+        for( double HA = -HARange * one_degree; HA <= HARange * one_degree; HA += HAStepSize )
+          {
+          for( double PA = -PARange * one_degree; PA <= PARange * one_degree; PA += PAStepSize )
+            {
+            currentEulerAngles3D->SetRotation(PA, 0, HA);
+            const double current_cc = CostMetricObject->GetValue( currentEulerAngles3D->GetParameters() );
+            if( current_cc < max_cc )
+              {
+              max_cc = current_cc;
+              bestEulerAngles3D->SetFixedParameters( currentEulerAngles3D->GetFixedParameters() );
+              bestEulerAngles3D->SetParameters( currentEulerAngles3D->GetParameters() );
+              }
+            // #define DEBUGGING_PRINT_IMAGES
+#ifdef DEBUGGING_PRINT_IMAGES
+              {
+              std::cout << "quick search "
+                        << " HA= " << ( currentEulerAngles3D->GetParameters()[2] ) * 180.0 / vnl_math::pi
+                        << " PA= " << ( currentEulerAngles3D->GetParameters()[0] ) * 180.0 / vnl_math::pi
+                        << " cc="  <<  current_cc
+                        << std::endl;
+              }
+            if( 0 )
+              {
+              typedef itk::ResampleImageFilter ResampleFilterType;
+              typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+
+              resampler->SetTransform(currentEulerAngles3D);
+              resampler->SetInput(orientedMovingVolume);
+              // Remember:  the Data is Moving's, the shape is Fixed's.
+              resampler->SetOutputParametersFromImage(orientedFixedVolume);
+              resampler->Update();                  //  Explicit Update()
+                                                    // required
+              // here.
+              typename FixedImageType::Pointer ResampledImage = resampler->GetOutput();
+
+              typedef itk::CheckerBoardImageFilter Checkerfilter;
+              typename Checkerfilter::Pointer checker = Checkerfilter::New();
+              unsigned int array[3] = { 36, 36, 36 };
+
+              checker->SetInput1(orientedFixedVolume);
+              checker->SetInput2(ResampledImage);
+              checker->SetCheckerPattern(array);
+              try
+                {
+                checker->Update();
+                }
+              catch( itk::ExceptionObject & err )
+                {
+                std::cout << "Caught an ITK exception: " << std::endl;
+                std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+                }
+              char filename[300];
+              sprintf(filename, "%05.2f_%05.2f_%05.2f.nii.gz",
+                      ( currentEulerAngles3D->GetParameters()[2] ) * 180 / vnl_math::pi,
+                      ( currentEulerAngles3D->GetParameters()[0] ) * 180 / vnl_math::pi, current_cc);
+
+                {
+                typedef typename itk::ImageFileWriter WriterType;
+                typename WriterType::Pointer writer = WriterType::New();
+                writer->UseCompressionOn();
+                writer->SetFileName(filename);
+                writer->SetInput( checker->GetOutput() );
+                try
+                  {
+                  writer->Update();
+                  }
+                catch( itk::ExceptionObject & err )
+                  {
+                  std::cout << "Exception Object caught: " << std::endl;
+                  std::cout << err << std::endl;
+                  throw;
+                  }
+                }
+              }
+#endif
+            }
+          }
+        }
+      // DEBUGGING_PRINT_IMAGES INFORMATION
+#ifdef DEBUGGING_PRINT_IMAGES
+        {
+        std::cout << "FINAL: quick search "
+                  << " HA= " << ( bestEulerAngles3D->GetParameters()[2] ) * 180.0 / vnl_math::pi
+                  << " PA= " << ( bestEulerAngles3D->GetParameters()[0] ) * 180.0 / vnl_math::pi
+                  << " cc="  <<  max_cc
+                  << std::endl;
+        }
+#endif
+      }
+    typename VersorRigid3DTransformType::Pointer quickSetVersor = VersorRigid3DTransformType::New();
+    quickSetVersor->SetCenter( bestEulerAngles3D->GetCenter() );
+    quickSetVersor->SetTranslation( bestEulerAngles3D->GetTranslation() );
+      {
+      itk::Versor localRotation;
+      localRotation.Set( bestEulerAngles3D->GetRotationMatrix() );
+      quickSetVersor->SetRotation(localRotation);
+      }
+#ifdef DEBUGGING_PRINT_IMAGES
+      {
+      typedef itk::ResampleImageFilter ResampleFilterType;
+      typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+
+      resampler->SetTransform(quickSetVersor);
+      resampler->SetInput(orientedMovingVolume);
+      // Remember:  the Data is Moving's, the shape is Fixed's.
+      resampler->SetOutputParametersFromImage(orientedFixedVolume);
+      resampler->Update();                    //  Explicit Update() required
+                                              // here.
+      typename FixedImageType::Pointer ResampledImage = resampler->GetOutput();
+
+      typedef itk::CheckerBoardImageFilter Checkerfilter;
+      typename Checkerfilter::Pointer checker = Checkerfilter::New();
+      unsigned int array[3] = { 18, 18, 18 };
+
+      checker->SetInput1(orientedFixedVolume);
+      checker->SetInput2(ResampledImage);
+      checker->SetCheckerPattern(array);
+      try
+        {
+        checker->Update();
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        std::cout << "Caught an ITK exception: " << std::endl;
+        std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+        }
+      char filename[300];
+      sprintf(filename, "FINAL_%05.2f_%05.2f_%05.2f.nii.gz",
+              ( bestEulerAngles3D->GetParameters()[2] ) * 180 / vnl_math::pi,
+              ( bestEulerAngles3D->GetParameters()[0] ) * 180 / vnl_math::pi, max_cc);
+
+        {
+        typedef typename itk::ImageFileWriter WriterType;
+        typename WriterType::Pointer writer = WriterType::New();
+        wirter->UseCompressionOn();
+        writer->SetFileName(filename);
+        // writer->SetInput(checker->GetOutput());
+        writer->SetInput(ResampledImage);
+        try
+          {
+          writer->Update();
+          }
+        catch( itk::ExceptionObject & err )
+          {
+          std::cout << "Exception Object caught: " << std::endl;
+          std::cout << err << std::endl;
+          throw;
+          }
+        }
+      }
+#endif
+    AssignRigid::AssignConvertedTransform( initialITKTransform, quickSetVersor.GetPointer() );
+    }
+  else if( initializeTransformMode == "useMomentsAlign" )
+    {
+    // useMomentsAlign assumes that the structures being registered have same
+    // amount
+    // of mass approximately uniformly distributed.
+    typename SpecificInitializerType::Pointer CenteredInitializer =
+      SpecificInitializerType::New();
+
+    CenteredInitializer->SetFixedImage(orientedFixedVolume);
+    CenteredInitializer->SetMovingImage(orientedMovingVolume);
+    CenteredInitializer->SetTransform(initialITKTransform);
+    CenteredInitializer->MomentsOn();                    // Use intensity center
+                                                         // of
+    // mass
+
+    CenteredInitializer->InitializeTransform();
+    }
+  else                     // can't happen unless an unimplemented CLP option
+                           // was
+  // added:
+    {
+    std::cout << "FAILURE:  Improper mode for initializeTransformMode: "
+              << initializeTransformMode << std::endl;
+    exit(-1);
+    }
+  std::cout << "Initializing transform with "  << initializeTransformMode
+            << " to " << std::endl;
+  std::cout << initialITKTransform << std::endl;
+  std::cout << "===============================================" << std::endl;
+  return initialITKTransform;
+}
+
+template 
+BRAINSFitHelperTemplate::BRAINSFitHelperTemplate() :
+  m_FixedVolume(NULL),
+  m_MovingVolume(NULL),
+  m_FixedBinaryVolume(NULL),
+  m_MovingBinaryVolume(NULL),
+  m_OutputFixedVolumeROI(""),
+  m_OutputMovingVolumeROI(""),
+  m_NumberOfSamples(500000),
+  m_NumberOfHistogramBins(50),
+  m_HistogramMatch(false),
+  m_RemoveIntensityOutliers(0.00),
+  m_NumberOfMatchPoints(10),
+  m_NumberOfIterations(1, 1500),
+  m_MaximumStepLength(0.2),
+  m_MinimumStepLength(1, 0.005),
+  m_RelaxationFactor(0.5),
+  m_TranslationScale(1000.0),
+  m_ReproportionScale(1.0),
+  m_SkewScale(1.0),
+  m_BackgroundFillValue(0.0),
+  m_TransformType(1, "Rigid"),
+  m_InitializeTransformMode("Off"),
+  m_UseExplicitPDFDerivativesMode("Off"),
+  m_MaskInferiorCutOffFromCenter(1000),
+  m_SplineGridSize(3, 10),
+  m_CostFunctionConvergenceFactor(1e+9),
+  m_ProjectedGradientTolerance(1e-5),
+  m_MaxBSplineDisplacement(0.0),
+  m_ActualNumberOfIterations(0),
+  m_PermittedNumberOfIterations(0),
+  // m_AccumulatedNumberOfIterationsForAllLevels(0),
+  m_DebugLevel(0),
+  m_CurrentGenericTransform(NULL),
+  m_GenericTransformList(0),
+  m_DisplayDeformedImage(false),
+  m_PromptUserAfterDisplay(false),
+  m_FinalMetricValue(0.0),
+  m_ObserveIterations(true),
+  m_CostMetricObject(NULL),
+  m_PermitParameterVariation(0)
+{
+  m_SplineGridSize[0] = 14;
+  m_SplineGridSize[1] = 10;
+  m_SplineGridSize[2] = 12;
+}
+
+template 
+template 
+void
+BRAINSFitHelperTemplate::FitCommonCode(
+  int numberOfIterations,
+  double minimumStepLength,
+  typename TransformType::Pointer &
+  initialITKTransform)
+{
+  // FitCommonCode
+  typedef typename itk::MultiModal3DMutualRegistrationHelper
+   MultiModal3DMutualRegistrationHelperType;
+
+  typename MultiModal3DMutualRegistrationHelperType::Pointer
+  appMutualRegistration = MultiModal3DMutualRegistrationHelperType::New();
+
+  appMutualRegistration->SetNumberOfHistogramBins(m_NumberOfHistogramBins);
+
+  appMutualRegistration->SetNumberOfIterations( numberOfIterations);
+
+  // TODO:  What do the following two lines really accomplish
+  // debug parameter, suppressed from command line
+  const bool initialTransformPassThru(false);
+  appMutualRegistration->SetInitialTransformPassThruFlag( initialTransformPassThru );
+  appMutualRegistration->SetPermitParameterVariation( m_PermitParameterVariation );
+  appMutualRegistration->SetNumberOfSamples( m_NumberOfSamples );
+  appMutualRegistration->SetRelaxationFactor( m_RelaxationFactor );
+  appMutualRegistration->SetMaximumStepLength( m_MaximumStepLength );
+  appMutualRegistration->SetMinimumStepLength( minimumStepLength );
+  appMutualRegistration->SetTranslationScale( m_TranslationScale );
+  appMutualRegistration->SetReproportionScale( m_ReproportionScale );
+  appMutualRegistration->SetSkewScale( m_SkewScale );
+
+  appMutualRegistration->SetFixedImage(    m_FixedVolume    );
+  appMutualRegistration->SetMovingImage(   m_MovingVolume   );
+  appMutualRegistration->SetCostMetricObject( this->m_CostMetricObject );
+
+  appMutualRegistration->SetBackgroundFillValue(   m_BackgroundFillValue   );
+
+  appMutualRegistration->SetInitialTransform( initialITKTransform );
+  appMutualRegistration->SetDisplayDeformedImage(m_DisplayDeformedImage);
+  appMutualRegistration->SetPromptUserAfterDisplay(m_PromptUserAfterDisplay);
+  appMutualRegistration->SetObserveIterations(m_ObserveIterations);
+  /*
+   *  At this point appMutualRegistration should be all set to make
+   *  an itk pipeline class templated in TransformType etc.
+   *  with all its inputs in place;
+   */
+  // initialize the interconnects between components
+  appMutualRegistration->Initialize();
+
+  typename TransformType::Pointer finalTransform;
+  try
+    {
+    appMutualRegistration->Update();
+    finalTransform = appMutualRegistration->GetTransform();
+    this->m_FinalMetricValue = appMutualRegistration->GetFinalMetricValue();
+    this->m_ActualNumberOfIterations = appMutualRegistration->GetActualNumberOfIterations();
+    this->m_PermittedNumberOfIterations = numberOfIterations;
+    // this->m_AccumulatedNumberOfIterationsForAllLevels +=
+    // appMutualRegistration->GetActualNumberOfIterations();
+    }
+  catch( itk::ExceptionObject& err )
+    {
+    // pass exception to caller
+    std::cout << "ERROR OCCURED: " << err << std::endl;
+    exit(-1);
+    throw err;
+    }
+
+    {   // Put the transform on the CurrentTransformList
+        // Initialize next level of transformations with previous transform
+        // result
+    this->m_CurrentGenericTransform = finalTransform;
+    }
+}
+
+template 
+void
+BRAINSFitHelperTemplate::StartRegistration(void)
+{
+  typedef COMMON_MMI_METRIC_TYPE MattesMutualInformationMetricType;
+  unsigned currentTransformId = 0;
+
+  if( std::string(this->m_InitializeTransformMode) != "Off" )
+    {
+    m_GenericTransformList.resize(m_TransformType.size() + 1);
+    }
+  else
+    {
+    m_GenericTransformList.resize( m_TransformType.size() );
+    }
+
+  if( this->m_DebugLevel > 3 )
+    {
+    this->PrintSelf(std::cout, 3);
+    }
+  std::vector localMinimumStepLength( m_TransformType.size() );
+  if( m_MinimumStepLength.size() != m_TransformType.size() )
+    {
+    if( m_MinimumStepLength.size() != 1 )
+      {
+      std::cout << "ERROR:  Wrong number of parameters for MinimumStepLength."
+                << "It either needs to be 1 or the same size as TransformType."
+                << std::endl;
+      exit(-1);
+      }
+    for( unsigned int q = 0; q < m_TransformType.size(); ++q )
+      {
+      localMinimumStepLength[q] = m_MinimumStepLength[0];
+      }
+    }
+  else
+    {
+    localMinimumStepLength = m_MinimumStepLength;
+    }
+  std::vector localNumberOfIterations( m_TransformType.size() );
+  if( m_NumberOfIterations.size() != m_TransformType.size() )
+    {
+    if( m_NumberOfIterations.size() != 1 )
+      {
+      std::cout << "ERROR:  Wrong number of parameters for NumberOfIterations."
+                << " It either needs to be 1 or the same size as TransformType."
+                << std::endl;
+      exit(-1);
+      }
+    for( unsigned int q = 0; q < m_TransformType.size(); ++q )
+      {
+      localNumberOfIterations[q] = m_NumberOfIterations[0];
+      }
+    }
+  else
+    {
+    localNumberOfIterations = m_NumberOfIterations;
+    }
+  std::string localInitializeTransformMode(this->m_InitializeTransformMode);
+  for( unsigned int currentTransformIndex = 0;
+       currentTransformIndex < m_TransformType.size();
+       currentTransformIndex++ )
+    {
+    const std::string currentTransformType(m_TransformType[currentTransformIndex]);
+    std::cout << "TranformTypes: "
+              << currentTransformType << "(" << currentTransformIndex + 1 << " of " << m_TransformType.size() << ")."
+              << std::endl;
+    std::cout << std::flush << std::endl;
+    }
+
+  // Initialize Transforms
+  if( localInitializeTransformMode != "Off" )
+  // Use CenteredVersorTranformInitializer
+    {
+    typedef VersorRigid3DTransformType TransformType;
+    std::cout << "Initializing transform with " << localInitializeTransformMode << std::endl;
+    typedef itk::CenteredVersorTransformInitializer InitializerType;
+
+    TransformType::Pointer initialITKTransform =
+      DoCenteredInitialization(
+        m_FixedVolume,
+        m_MovingVolume,
+        m_FixedBinaryVolume,
+        m_MovingBinaryVolume,
+        localInitializeTransformMode, this->m_CostMetricObject);
+    m_CurrentGenericTransform = initialITKTransform.GetPointer();
+    localInitializeTransformMode = "Off";        // Now reset to Off once
+    // initialization is done.
+
+    // Now if necessary clip the images based on m_MaskInferiorCutOffFromCenter
+    DoCenteredTransformMaskClipping(
+      m_FixedBinaryVolume,
+      m_MovingBinaryVolume,
+      initialITKTransform,
+      m_MaskInferiorCutOffFromCenter);
+
+      {   // Write out some debugging information if requested
+      typedef itk::Image                               MaskImageType;
+      typedef itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+      if( ( !this->m_FixedBinaryVolume.IsNull() ) && ( m_OutputFixedVolumeROI != "" ) )
+        {
+        const MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(this->m_FixedBinaryVolume.GetPointer() );
+        itkUtil::WriteConstImage(tempOutputFixedVolumeROI, m_OutputFixedVolumeROI);
+        }
+      if( ( !this->m_MovingBinaryVolume.IsNull() ) && ( m_OutputMovingVolumeROI != "" ) )
+        {
+        const MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(this->m_MovingBinaryVolume.GetPointer() );
+        itkUtil::WriteConstImage(tempOutputMovingVolumeROI, m_OutputMovingVolumeROI);
+        }
+      }
+
+    m_GenericTransformList[currentTransformId++] = initialITKTransform;
+    }
+  for( unsigned int currentTransformIndex = 0;
+       currentTransformIndex < m_TransformType.size();
+       currentTransformIndex++ )
+    {
+    // m_AccumulatedNumberOfIterationsForAllLevels +=
+    // localNumberOfIterations[currentTransformIndex];
+    const std::string currentTransformType(m_TransformType[currentTransformIndex]);
+    std::cout << "\n\n\n=============================== "
+              << "Starting Transform Estimations for "
+              << currentTransformType << "(" << currentTransformIndex + 1
+              << " of " << m_TransformType.size() << ")."
+              << "==============================="
+              << std::endl;
+    std::cout << std::flush << std::endl;
+    //
+    // Break into cases on TransformType:
+    //
+    if( currentTransformType == "Rigid" )
+      {
+      //  Choose TransformType for the itk registration class template:
+      typedef VersorRigid3DTransformType           TransformType;
+      typedef itk::VersorRigid3DTransformOptimizer OptimizerType;
+      // const int NumberOfEstimatedParameter = 6;
+
+      //
+      // Process the initialITKTransform as VersorRigid3DTransform:
+      //
+      TransformType::Pointer initialITKTransform = TransformType::New();
+      initialITKTransform->SetIdentity();
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( ( transformFileType == "ScaleVersor3DTransform" )
+                   || ( transformFileType == "ScaleSkewVersor3DTransform" )
+                   || ( transformFileType == "AffineTransform" ) )
+            {
+            // CONVERTING TO RIGID TRANSFORM TYPE from other type:
+            std::cout << "WARNING:  Extracting Rigid component type from transform." << std::endl;
+            VersorRigid3DTransformType::Pointer tempInitializerITKTransform = ComputeRigidTransformFromGeneric(
+                m_CurrentGenericTransform.GetPointer() );
+            AssignRigid::AssignConvertedTransform( initialITKTransform, tempInitializerITKTransform.GetPointer() );
+            }
+          else
+            {
+            std::cout
+            <<
+            "Unsupported initial transform file -- TransformBase first transform typestring, "
+            << transformFileType
+            << " not equal to required type VersorRigid3DTransform"
+            << std::endl;
+            return;
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform" << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode == "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? true : false;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+
+      this->FitCommonCode
+        (localNumberOfIterations[currentTransformIndex],
+        localMinimumStepLength[currentTransformIndex],
+        initialITKTransform);
+      localInitializeTransformMode = "Off";   // Now turn of the initiallize
+                                              // code to off
+
+      }
+    else if( currentTransformType == "ScaleVersor3D" )
+      {
+      //  Choose TransformType for the itk registration class template:
+      typedef ScaleVersor3DTransformType    TransformType;
+      typedef itk::VersorTransformOptimizer OptimizerType;
+      // const int NumberOfEstimatedParameter = 9;
+
+      //
+      // Process the initialITKTransform as ScaleVersor3DTransform:
+      //
+      TransformType::Pointer initialITKTransform = TransformType::New();
+      initialITKTransform->SetIdentity();
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "ScaleVersor3DTransform" )
+            {
+            const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( ( transformFileType == "ScaleSkewVersor3DTransform" )
+                   || ( transformFileType == "AffineTransform" ) )
+            {
+            // CONVERTING TO RIGID TRANSFORM TYPE from other type:
+            // TODO: we should preserve the Scale components
+            std::cout << "WARNING:  Extracting Rigid component type from transform." << std::endl;
+            VersorRigid3DTransformType::Pointer tempInitializerITKTransform = ComputeRigidTransformFromGeneric(
+                m_CurrentGenericTransform.GetPointer() );
+            AssignRigid::AssignConvertedTransform( initialITKTransform, tempInitializerITKTransform.GetPointer() );
+            }
+          else              // || transformFileType ==
+                            // "ScaleSkewVersor3DTransform"
+          // ||
+          // transformFileType == "AffineTransform"
+            {
+            std::cout
+            <<
+            "Unsupported initial transform file -- TransformBase first transform typestring, "
+            << transformFileType
+            <<
+            " not equal to required type VersorRigid3DTransform OR ScaleVersor3DTransform"
+            << std::endl;
+            return;
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform"
+          << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode == "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? true : false;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+      // #include "FitCommonCode.tmpl"
+      this->FitCommonCode
+        (localNumberOfIterations[currentTransformIndex],
+        localMinimumStepLength[currentTransformIndex],
+        initialITKTransform);
+      localInitializeTransformMode = "Off";   // Now turn of the initiallize
+                                              // code to off
+      }
+    else if( currentTransformType == "ScaleSkewVersor3D" )
+      {
+      //  Choose TransformType for the itk registration class template:
+      typedef ScaleSkewVersor3DTransformType TransformType;
+      typedef itk::VersorTransformOptimizer  OptimizerType;
+      // const int NumberOfEstimatedParameter = 15;
+
+      //
+      // Process the initialITKTransform as ScaleSkewVersor3D:
+      //
+      TransformType::Pointer initialITKTransform = TransformType::New();
+      initialITKTransform->SetIdentity();
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "ScaleVersor3DTransform" )
+            {
+            const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "ScaleSkewVersor3DTransform" )
+            {
+            const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( ( transformFileType == "AffineTransform" ) )
+            {
+            // CONVERTING TO RIGID TRANSFORM TYPE from other type:
+            // TODO:  We should really preserve the Scale and Skew components
+            std::cout << "WARNING:  Extracting Rigid component type from transform." << std::endl;
+            VersorRigid3DTransformType::Pointer tempInitializerITKTransform = ComputeRigidTransformFromGeneric(
+                m_CurrentGenericTransform.GetPointer() );
+            AssignRigid::AssignConvertedTransform( initialITKTransform, tempInitializerITKTransform.GetPointer() );
+            }
+          else              // || transformFileType == "AffineTransform" ||
+          // transformFileType
+          // == "ScaleVersor3DTransform"
+            {
+            std::cout
+            <<
+            "Unsupported initial transform file -- TransformBase first transform typestring, "
+            << transformFileType
+            << " not equal to required type VersorRigid3DTransform "
+            << "OR ScaleVersor3DTransform OR ScaleSkewVersor3DTransform"
+            << std::endl;
+            return;
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform"
+          << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode == "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? true : false;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+      // #include "FitCommonCode.tmpl"
+      this->FitCommonCode
+        (localNumberOfIterations[currentTransformIndex],
+        localMinimumStepLength[currentTransformIndex],
+        initialITKTransform);
+      localInitializeTransformMode = "Off";   // Now turn of the initiallize
+                                              // code to off
+      }
+    else if( currentTransformType == "Affine" )
+      {
+      //  Choose TransformType for the itk registration class template:
+      typedef itk::AffineTransform  TransformType;
+      typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
+      // const int NumberOfEstimatedParameter = 12;
+
+      //
+      // Process the initialITKTransform
+      //
+      TransformType::Pointer initialITKTransform = TransformType::New();
+      initialITKTransform->SetIdentity();
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "ScaleVersor3DTransform" )
+            {
+            const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "ScaleSkewVersor3DTransform" )
+            {
+            const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else if( transformFileType == "AffineTransform" )
+            {
+            const AffineTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(initialITKTransform,
+                                                  tempInitializerITKTransform);
+            }
+          else              //  NO SUCH CASE!!
+            {
+            std::cout
+            <<
+            "Unsupported initial transform file -- TransformBase first transform typestring, "
+            << transformFileType
+            << " not equal to any recognized type VersorRigid3DTransform OR "
+            << "ScaleVersor3DTransform OR ScaleSkewVersor3DTransform OR AffineTransform"
+            << std::endl;
+            return;
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform"
+          << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode == "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? true : false;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+      // #include "FitCommonCode.tmpl"
+      this->FitCommonCode
+        (localNumberOfIterations[currentTransformIndex],
+        localMinimumStepLength[currentTransformIndex],
+        initialITKTransform);
+      localInitializeTransformMode = "Off";   // Now turn of the initiallize
+                                              // code to off
+      }
+    else if( currentTransformType == "BSpline" )
+      {
+      //
+      // Process the bulkAffineTransform for BSpline's BULK
+      //
+      AffineTransformType::Pointer bulkAffineTransform =
+        AffineTransformType::New();
+      bulkAffineTransform->SetIdentity();
+
+      typedef itk::Image RegisterImageType;
+
+      BSplineTransformType::Pointer outputBSplineTransform =
+        BSplineTransformType::New();
+      outputBSplineTransform->SetIdentity();
+
+      BSplineTransformType::Pointer initialBSplineTransform =
+        BSplineTransformType::New();
+      initialBSplineTransform->SetIdentity();
+
+        {
+        typedef BSplineTransformType::RegionType TransformRegionType;
+        typedef TransformRegionType::SizeType    TransformSizeType;
+        typedef itk::BSplineDeformableTransformInitializer
+         InitializerType;
+        InitializerType::Pointer transformInitializer = InitializerType::New();
+        transformInitializer->SetTransform(initialBSplineTransform);
+        transformInitializer->SetImage(m_FixedVolume);
+        TransformSizeType tempGridSize;
+        tempGridSize[0] = m_SplineGridSize[0];
+        tempGridSize[1] = m_SplineGridSize[1];
+        tempGridSize[2] = m_SplineGridSize[2];
+        transformInitializer->SetGridSizeInsideTheImage(tempGridSize);
+        transformInitializer->InitializeTransform();
+        }
+
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "ScaleVersor3DTransform" )
+            {
+            const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "ScaleSkewVersor3DTransform" )
+            {
+            const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "AffineTransform" )
+            {
+            const AffineTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "BSplineDeformableTransform" )
+            {
+            const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+
+            initialBSplineTransform->SetBulkTransform(
+              tempInitializerITKTransform->GetBulkTransform() );
+            BSplineTransformType::ParametersType tempFixedInitialParameters =
+              tempInitializerITKTransform->GetFixedParameters();
+            BSplineTransformType::ParametersType initialFixedParameters =
+              initialBSplineTransform->GetFixedParameters();
+
+            bool checkMatch = true;         // Assume true;
+            if( initialFixedParameters.GetSize() != tempFixedInitialParameters.GetSize() )
+              {
+              checkMatch = false;
+              std::cerr << "ERROR INITILIZATION FIXED PARAMETERS DO NOT MATCH: " << initialFixedParameters.GetSize()
+                        << " != " << tempFixedInitialParameters.GetSize() << std::endl;
+              }
+            if( checkMatch )             //  This ramus covers the hypothesis
+                                         // that
+            // the
+            // FixedParameters represent the grid locations of the spline nodes.
+              {
+              for( unsigned int i = 0; i < initialFixedParameters.GetSize(); ++i )
+                {
+                if( initialFixedParameters.GetElement(i) != tempFixedInitialParameters.GetElement(i) )
+                  {
+                  checkMatch = false;
+                  std::cerr << "ERROR FIXED PARAMETERS DO NOT MATCH: " << initialFixedParameters.GetElement(i)
+                            << " != " << tempFixedInitialParameters.GetElement(i) << std::endl;
+                  }
+                }
+              }
+            if( checkMatch )
+              {
+              BSplineTransformType::ParametersType tempInitialParameters =
+                tempInitializerITKTransform->GetParameters();
+              if( initialBSplineTransform->GetNumberOfParameters() ==
+                  tempInitialParameters.Size() )
+                {
+                initialBSplineTransform->SetFixedParameters(
+                  tempFixedInitialParameters);
+                initialBSplineTransform->SetParametersByValue(tempInitialParameters);
+                }
+              else
+                {
+                // Error, initializing from wrong size transform parameters;
+                //  Use its bulk transform only?
+                std::cerr
+                << "Trouble using the m_CurrentGenericTransform for initializing a BSPlineDeformableTransform:"
+                << std::endl;
+                std::cerr
+                <<
+                "The initializing BSplineDeformableTransform has a different"
+                << " number of Parameters, than what is required for the requested grid."
+                << std::endl;
+                std::cerr
+                << "BRAINSFit was only able to use the bulk transform that was before it."
+                << std::endl;
+                exit(-1);
+                }
+              }
+            else
+              {
+              std::cerr
+              << "ERROR:  initialization BSpline transform does not have the same "
+              << "parameter dimensions as the one currently specified."
+              << std::endl;
+              exit(-1);
+              }
+            }
+          else
+            {
+            std::cerr << "ERROR:  Invalid transform initializer type found:  " << transformFileType << std::endl;
+            exit(-1);
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform"
+          << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          // As recommended in documentation in
+          // itkMattesMutualInformationImageToImageMetric
+          // "UseExplicitPDFDerivatives = False ... This method is well suited
+          // for Transforms with a large number of parameters, such as,
+          // BSplineDeformableTransforms."
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode != "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? false : true;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+      outputBSplineTransform =
+        DoBSpline(
+          initialBSplineTransform,
+          m_FixedVolume, m_MovingVolume,
+          this->m_CostMetricObject.GetPointer(),
+          this->m_MaxBSplineDisplacement,
+          this->m_CostFunctionConvergenceFactor,
+          this->m_ProjectedGradientTolerance,
+          this->m_DisplayDeformedImage,
+          this->m_PromptUserAfterDisplay);
+      if( outputBSplineTransform.IsNull() )
+        {
+        std::cout
+        << "Error -- the BSpline fit has failed." << std::endl;
+        std::cout
+        << "Error -- the BSpline fit has failed." << std::endl;
+
+        m_ActualNumberOfIterations = 1;
+        m_PermittedNumberOfIterations = 1;
+        }
+      else
+        {
+        // Initialize next level of transformations with previous transform
+        // result
+        // TransformList.clear();
+        // TransformList.push_back(finalTransform);
+        m_CurrentGenericTransform = outputBSplineTransform;
+        // Now turn of the initiallize code to off
+        localInitializeTransformMode = "Off";
+          {
+          // HACK:  The BSpline optimizer does not return the correct iteration
+          // values.
+          m_ActualNumberOfIterations = 1;
+          m_PermittedNumberOfIterations = 3;
+          }
+        }
+      }
+    // AF: ROIBSpline use the bounding box of the input label to initialize
+    //     the BSpline grid, instead of using the whole image volume. This is
+    //     particularly useful when the region of interest is small wrt the
+    // image
+    else if( currentTransformType == "ROIBSpline" )
+      {
+      //
+      // Process the bulkAffineTransform for BSpline's BULK
+      //
+
+      AffineTransformType::Pointer bulkAffineTransform =
+        AffineTransformType::New();
+      bulkAffineTransform->SetIdentity();
+
+      typedef itk::Image RegisterImageType;
+
+      BSplineTransformType::Pointer outputBSplineTransform =
+        BSplineTransformType::New();
+      outputBSplineTransform->SetIdentity();
+
+      BSplineTransformType::Pointer initialBSplineTransform =
+        BSplineTransformType::New();
+      initialBSplineTransform->SetIdentity();
+
+        {
+        // typedef itk::Image< unsigned char, 3 >
+        //                               MaskImageType;
+        // typedef itk::ImageMaskSpatialObject< MaskImageType::ImageDimension >
+        // ImageMaskSpatialObjectType;
+
+        typedef BSplineTransformType::RegionType TransformRegionType;
+        typedef TransformRegionType::SizeType    TransformSizeType;
+        typedef itk::BSplineDeformableTransformInitializer
+         InitializerType;
+
+        const typename MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(m_FixedBinaryVolume.GetPointer() );
+        const typename MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+          ExtractConstPointerToImageMaskFromImageSpatialObject(m_MovingBinaryVolume.GetPointer() );
+
+        // typedef ImageMaskSpatialObjectType::ImageType
+        //                            MaskImageType;
+        typedef itk::ResampleImageFilter ResampleFilterType;
+        ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+        resampler->SetTransform(m_CurrentGenericTransform);
+        resampler->SetInput(  tempOutputMovingVolumeROI.GetPointer() );
+        resampler->SetOutputParametersFromImage( tempOutputFixedVolumeROI.GetPointer() );
+        resampler->Update();
+
+        typedef itk::AddImageFilter AddFilterType;
+        AddFilterType::Pointer adder = AddFilterType::New();
+        adder->SetInput1( tempOutputFixedVolumeROI.GetPointer() );
+        adder->SetInput2( resampler->GetOutput() );
+        adder->Update();
+
+        /*
+         * typedef itk::ImageFileWriter WriterType;
+         * WriterType::Pointer writer = WriterType::New();
+         * writer->SetFileName( "/tmp/jointMask.nrrd" );
+         * writer->SetInput( adder->GetOutput() );
+         * writer->Update();
+         */
+
+        ImageMaskSpatialObjectType::Pointer jointMask = ImageMaskSpatialObjectType::New();
+        jointMask->SetImage( adder->GetOutput() );
+        jointMask->ComputeObjectToWorldTransform();
+
+        typename FixedImageType::Pointer    roiImage = FixedImageType::New();
+        typename FixedImageType::RegionType roiRegion =
+          jointMask->GetAxisAlignedBoundingBoxRegion();
+        typename FixedImageType::SpacingType roiSpacing =
+          m_FixedVolume->GetSpacing();
+        /*
+         * std::cout << "Image size: " <<
+         *    m_FixedVolume->GetBufferedRegion().GetSize() << std::endl;
+         * std::cout << "ROI size: " << roiRegion.GetSize() << std::endl;
+         * std::cout << "ROI spacing: " << roiSpacing << std::endl;
+         * std::cout << "ROI index: " << roiRegion.GetIndex() << std::endl;
+         * std::cout << "ROI size in physical space: " <<
+         * roiRegion.GetSize()[0]*roiSpacing[0] << " " <<
+         * roiRegion.GetSize()[1]*roiSpacing[1] << " " <<
+         * roiRegion.GetSize()[2]*roiSpacing[2] << std::endl;
+         */
+
+        typename FixedImageType::PointType roiOriginPt;
+        typename FixedImageType::IndexType roiOriginIdx;
+        roiOriginIdx.Fill(0);
+        m_FixedVolume->TransformIndexToPhysicalPoint(roiRegion.GetIndex(), roiOriginPt);
+        roiRegion.SetIndex(roiOriginIdx);
+        roiImage->SetRegions(roiRegion);
+        roiImage->Allocate();
+        roiImage->FillBuffer(1.);
+        roiImage->SetSpacing(roiSpacing);
+        roiImage->SetOrigin(roiOriginPt);
+        roiImage->SetDirection( m_FixedVolume->GetDirection() );
+
+        /*
+         * std::cout << "ROI origin: " << roiOriginPt << std::endl;
+         * typedef itk::ImageFileWriter WriterType;
+         * WriterType::Pointer writer = WriterType::New();
+         * writer->SetFileName( "/tmp/bsplineroi.nrrd" );
+         * writer->SetInput( roiImage );
+         * writer->Update();
+         */
+
+        InitializerType::Pointer transformInitializer = InitializerType::New();
+        transformInitializer->SetTransform(initialBSplineTransform);
+        transformInitializer->SetImage(roiImage);
+        TransformSizeType tempGridSize;
+        tempGridSize[0] = m_SplineGridSize[0];
+        tempGridSize[1] = m_SplineGridSize[1];
+        tempGridSize[2] = m_SplineGridSize[2];
+        transformInitializer->SetGridSizeInsideTheImage(tempGridSize);
+        transformInitializer->InitializeTransform();
+        }
+
+      if( m_CurrentGenericTransform.IsNotNull() )
+        {
+        try
+          {
+          const std::string transformFileType = m_CurrentGenericTransform->GetNameOfClass();
+          if( transformFileType == "VersorRigid3DTransform" )
+            {
+            const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "ScaleVersor3DTransform" )
+            {
+            const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "ScaleSkewVersor3DTransform" )
+            {
+            const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "AffineTransform" )
+            {
+            const AffineTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+            AssignRigid::AssignConvertedTransform(bulkAffineTransform,
+                                                  tempInitializerITKTransform);
+            initialBSplineTransform->SetBulkTransform(bulkAffineTransform);
+            }
+          else if( transformFileType == "BSplineDeformableTransform" )
+            {
+            const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+              dynamic_cast( m_CurrentGenericTransform.GetPointer() );
+            if( tempInitializerITKTransform.IsNull() )
+              {
+              std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+              }
+
+            initialBSplineTransform->SetBulkTransform(
+              tempInitializerITKTransform->GetBulkTransform() );
+            BSplineTransformType::ParametersType tempFixedInitialParameters =
+              tempInitializerITKTransform->GetFixedParameters();
+            BSplineTransformType::ParametersType initialFixedParameters =
+              initialBSplineTransform->GetFixedParameters();
+
+            bool checkMatch = true;         // Assume true;
+            if( initialFixedParameters.GetSize() != tempFixedInitialParameters.GetSize() )
+              {
+              checkMatch = false;
+              std::cerr << "ERROR INITILIZATION FIXED PARAMETERS DO NOT MATCH: " << initialFixedParameters.GetSize()
+                        << " != " << tempFixedInitialParameters.GetSize() << std::endl;
+              }
+            if( checkMatch )             //  This ramus covers the hypothesis
+                                         // that
+            // the
+            // FixedParameters represent the grid locations of the spline nodes.
+              {
+              for( unsigned int i = 0; i < initialFixedParameters.GetSize(); ++i )
+                {
+                if( initialFixedParameters.GetElement(i) != tempFixedInitialParameters.GetElement(i) )
+                  {
+                  checkMatch = false;
+                  std::cerr << "ERROR FIXED PARAMETERS DO NOT MATCH: " << initialFixedParameters.GetElement(i)
+                            << " != " << tempFixedInitialParameters.GetElement(i) << std::endl;
+                  }
+                }
+              }
+            if( checkMatch )
+              {
+              BSplineTransformType::ParametersType tempInitialParameters =
+                tempInitializerITKTransform->GetParameters();
+              if( initialBSplineTransform->GetNumberOfParameters() ==
+                  tempInitialParameters.Size() )
+                {
+                initialBSplineTransform->SetFixedParameters(
+                  tempFixedInitialParameters);
+                initialBSplineTransform->SetParametersByValue(tempInitialParameters);
+                }
+              else
+                {
+                // Error, initializing from wrong size transform parameters;
+                //  Use its bulk transform only?
+                std::cerr
+                << "Trouble using the m_CurrentGenericTransform for initializing a BSPlineDeformableTransform:"
+                << std::endl;
+                std::cerr
+                <<
+                "The initializing BSplineDeformableTransform has a different"
+                << " number of Parameters, than what is required for the requested grid."
+                << std::endl;
+                std::cerr
+                << "BRAINSFit was only able to use the bulk transform that was before it."
+                << std::endl;
+                exit(-1);
+                }
+              }
+            else
+              {
+              std::cerr
+              << "ERROR:  initialization BSpline transform does not have the same "
+              << "parameter dimensions as the one currently specified."
+              << std::endl;
+              exit(-1);
+              }
+            }
+          else
+            {
+            std::cerr << "ERROR:  Invalid transform initializer type found:  " << transformFileType << std::endl;
+            exit(-1);
+            }
+          }
+        catch( itk::ExceptionObject & excp )
+          {
+          std::cout << "[FAILED]" << std::endl;
+          std::cerr
+          << "Error while reading the m_CurrentGenericTransform"
+          << std::endl;
+          std::cerr << excp << std::endl;
+          return;
+          }
+        }
+
+        {
+        // Special optimizations only for the MMI metric
+        // that need adjusting based on both the type of metric, and
+        // the "dimensionality" of the transform being adjusted.
+        typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+          dynamic_cast(this->m_CostMetricObject.GetPointer() );
+        if( test_MMICostMetric.IsNotNull() )
+          {
+          const bool UseExplicitPDFDerivatives =
+            ( m_UseExplicitPDFDerivativesMode != "ON" || m_UseExplicitPDFDerivativesMode == "AUTO" ) ? false : true;
+          test_MMICostMetric->SetUseExplicitPDFDerivatives(UseExplicitPDFDerivatives);
+          }
+        }
+      outputBSplineTransform =
+        DoBSpline(
+          initialBSplineTransform,
+          m_FixedVolume, m_MovingVolume,
+          this->m_CostMetricObject.GetPointer(),
+          this->m_MaxBSplineDisplacement,
+          this->m_CostFunctionConvergenceFactor,
+          this->m_ProjectedGradientTolerance,
+          this->m_DisplayDeformedImage,
+          this->m_PromptUserAfterDisplay);
+      if( outputBSplineTransform.IsNull() )
+        {
+        std::cout
+        << "Error -- the BSpline fit has failed." << std::endl;
+        std::cout
+        << "Error -- the BSpline fit has failed." << std::endl;
+
+        m_ActualNumberOfIterations = 1;
+        m_PermittedNumberOfIterations = 1;
+        }
+      else
+        {
+        // Initialize next level of transformations with previous transform
+        // result
+        // TransformList.clear();
+        // TransformList.push_back(finalTransform);
+        m_CurrentGenericTransform = outputBSplineTransform;
+        // Now turn of the initiallize code to off
+        localInitializeTransformMode = "Off";
+          {
+          // HACK:  The BSpline optimizer does not return the correct iteration
+          // values.
+          m_ActualNumberOfIterations = 1;
+          m_PermittedNumberOfIterations = 3;
+          }
+        }
+      }
+
+    else
+      {
+      std::cout
+      << "Error choosing what kind of transform to fit \""
+      << currentTransformType << "(" << currentTransformIndex + 1 << " of " << m_TransformType.size() << "). "
+      << std::endl;
+      std::cout << std::flush << std::endl;
+      exit(-1);
+      return;
+      }
+
+    if( currentTransformId > m_GenericTransformList.size() - 1 )
+      {
+      std::cerr << "Out of bounds access for transform vector!" << std::endl;
+      exit(-1);
+      return;
+      }
+    m_GenericTransformList[currentTransformId++] = m_CurrentGenericTransform;
+    }
+
+  return;
+}
+
+template 
+void
+BRAINSFitHelperTemplate::PrintSelf(std::ostream & os, Indent indent) const
+{
+  // Superclass::PrintSelf(os,indent);
+  os << indent << "FixedVolume:\n"  <<   this->m_FixedVolume << std::endl;
+  os << indent << "MovingVolume:\n" <<   this->m_MovingVolume << std::endl;
+  if( this->m_FixedBinaryVolume.IsNotNull() )
+    {
+    os << indent << "FixedBinaryVolume:\n" << this->m_FixedBinaryVolume << std::endl;
+    }
+  else
+    {
+    os << indent << "FixedBinaryVolume: IS NULL" << std::endl;
+    }
+  if( this->m_MovingBinaryVolume.IsNotNull() )
+    {
+    os << indent << "MovingBinaryVolume:\n" << this->m_MovingBinaryVolume << std::endl;
+    }
+  else
+    {
+    os << indent << "MovingBinaryVolume: IS NULL" << std::endl;
+    }
+  os << indent << "NumberOfSamples:      " << this->m_NumberOfSamples << std::endl;
+
+  os << indent << "NumberOfIterations:    [";
+  for( unsigned int q = 0; q < this->m_NumberOfIterations.size(); ++q )
+    {
+    os << this->m_NumberOfIterations[q] << " ";
+    }
+  os << "]" << std::endl;
+  os << indent << "NumberOfHistogramBins:" << this->m_NumberOfHistogramBins << std::endl;
+  os << indent << "MaximumStepLength:    " << this->m_MaximumStepLength << std::endl;
+  os << indent << "MinimumStepLength:     [";
+  for( unsigned int q = 0; q < this->m_MinimumStepLength.size(); ++q )
+    {
+    os << this->m_MinimumStepLength[q] << " ";
+    }
+  os << "]" << std::endl;
+  os << indent << "TransformType:     [";
+  for( unsigned int q = 0; q < this->m_TransformType.size(); ++q )
+    {
+    os << this->m_TransformType[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  os << indent << "RelaxationFactor:    " << this->m_RelaxationFactor << std::endl;
+  os << indent << "TranslationScale:    " << this->m_TranslationScale << std::endl;
+  os << indent << "ReproportionScale:   " << this->m_ReproportionScale << std::endl;
+  os << indent << "SkewScale:           " << this->m_SkewScale << std::endl;
+  os << indent << "BackgroundFillValue:            " << this->m_BackgroundFillValue << std::endl;
+  os << indent << "InitializeTransformMode:        " << this->m_InitializeTransformMode << std::endl;
+  os << indent << "MaskInferiorCutOffFromCenter:   " << this->m_MaskInferiorCutOffFromCenter << std::endl;
+  os << indent << "ActualNumberOfIterations:       " << this->m_ActualNumberOfIterations << std::endl;
+  os << indent << "PermittedNumberOfIterations:       " << this->m_PermittedNumberOfIterations << std::endl;
+  // os << indent << "AccumulatedNumberOfIterationsForAllLevels: " <<
+  // this->m_AccumulatedNumberOfIterationsForAllLevels << std::endl;
+
+  os << indent << "SplineGridSize:     [";
+  for( unsigned int q = 0; q < this->m_SplineGridSize.size(); ++q )
+    {
+    os << this->m_SplineGridSize[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  os << indent << "PermitParameterVariation:     [";
+  for( unsigned int q = 0; q < this->m_PermitParameterVariation.size(); ++q )
+    {
+    os << this->m_PermitParameterVariation[q] << " ";
+    }
+  os << "]" << std::endl;
+
+  if( m_CurrentGenericTransform.IsNotNull() )
+    {
+    os << indent << "CurrentGenericTransform:\n" << this->m_CurrentGenericTransform << std::endl;
+    }
+  else
+    {
+    os << indent << "CurrentGenericTransform: IS NULL" << std::endl;
+    }
+}
+
+template 
+void
+BRAINSFitHelperTemplate::GenerateData()
+{
+  this->StartRegistration();
+}
+
+} // end namespace itk
diff --git a/BRAINSCommonLib/BRAINSFitUtils.h b/BRAINSCommonLib/BRAINSFitUtils.h
new file mode 100644
index 00000000..8c46c0ac
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSFitUtils.h
@@ -0,0 +1,290 @@
+#ifndef __BRAINSFitUtils_h
+#define __BRAINSFitUtils_h
+
+#include "itkImageRegionIteratorWithIndex.h"
+#include "itkImageDuplicator.h"
+
+#include "itkScaleVersor3DTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkAffineTransform.h"
+#include "itkVersorRigid3DTransform.h"
+#include "itkBSplineDeformableTransform.h"
+#include "itkBRAINSROIAutoImageFilter.h"
+
+#include "vcl_algorithm.h"
+
+/**
+  * This file contains utility functions that are common to a few of the
+  *BRAINSFit Programs.
+  */
+
+static const unsigned int BFNSSpaceDimension = 3;
+static const unsigned int BFNSplineOrder = 3;
+typedef double CoordinateRepType;
+typedef itk::BSplineDeformableTransform<
+  CoordinateRepType,
+  BFNSSpaceDimension,
+  BFNSplineOrder>                                        BSplineTransformType;
+
+typedef itk::VersorRigid3DTransform              VersorRigid3DTransformType;
+typedef itk::ScaleVersor3DTransform              ScaleVersor3DTransformType;
+typedef itk::ScaleSkewVersor3DTransform          ScaleSkewVersor3DTransformType;
+typedef itk::AffineTransform AffineTransformType;
+
+typedef itk::SpatialObject<3>                                      SpatialObjectType;
+typedef SpatialObjectType::Pointer                                 ImageMaskPointer;
+typedef itk::Image                               MaskImageType;
+typedef itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+
+/**
+ * Boilerplate conversion to get a safe reference to the internal Image stored in a
+ * ImageMaskSpatialObjectType
+ */
+extern MaskImageType::ConstPointer ExtractConstPointerToImageMaskFromImageSpatialObject(
+  SpatialObjectType::ConstPointer inputSpatialObject);
+
+template 
+void DoCenteredTransformMaskClipping(
+  ImageMaskPointer & fixedMask,
+  ImageMaskPointer & movingMask,
+  typename TransformType::Pointer transform,
+  double maskInferiorCutOffFromCenter)
+{
+  if( fixedMask.IsNull()  ||  movingMask.IsNull() )
+    {
+    return;
+    }
+  if( maskInferiorCutOffFromCenter >= 1000.0 )
+    {
+    return;
+    }
+  std::cerr << "maskInferiorCutOffFromCenter is " << maskInferiorCutOffFromCenter << std::endl;
+
+  typedef itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+
+  typedef unsigned char                          PixelType;
+  typedef itk::Image MaskImageType;
+
+  typename TransformType::InputPointType rotationCenter = transform->GetCenter();
+  typename TransformType::OutputVectorType translationVector = transform->GetTranslation();
+
+  typename MaskImageType::PointType fixedCenter;
+  typename MaskImageType::PointType movingCenter;
+  for( unsigned int i = 0; i < VImageDimension; ++i )
+    {
+    fixedCenter[i]  = rotationCenter[i];
+    movingCenter[i] = translationVector[i] - rotationCenter[i];
+    }
+
+  typename MaskImageType::Pointer fixedMaskImage  = NULL;
+    {
+    const typename MaskImageType::ConstPointer tempOutputFixedVolumeROI =
+      ExtractConstPointerToImageMaskFromImageSpatialObject(fixedMask.GetPointer() );
+    typedef itk::ImageDuplicator DuplicatorType;
+    typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+    duplicator->SetInputImage(tempOutputFixedVolumeROI);
+    duplicator->Update();
+    fixedMaskImage = duplicator->GetOutput();
+    }
+  typename MaskImageType::Pointer movingMaskImage = NULL;
+    {
+    const typename MaskImageType::ConstPointer tempOutputMovingVolumeROI =
+      ExtractConstPointerToImageMaskFromImageSpatialObject(movingMask.GetPointer() );
+    typedef itk::ImageDuplicator DuplicatorType;
+    typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+    duplicator->SetInputImage(tempOutputMovingVolumeROI);
+    duplicator->Update();
+    movingMaskImage = duplicator->GetOutput();
+    }
+
+  typename MaskImageType::PointType fixedInferior  = fixedCenter;
+  typename MaskImageType::PointType movingInferior = movingCenter;
+
+  fixedInferior[2] -= maskInferiorCutOffFromCenter;   // negative because
+                                                      // Superior is large in
+                                                      // magnitude.
+  movingInferior[2] -= maskInferiorCutOffFromCenter;  // ITK works in an LPS
+                                                      // system.
+
+  //  Here we will set the appropriate parts of the f/m MaskImages to zeros....
+  typename MaskImageType::PixelType zero = 0;
+  typename MaskImageType::PointType location;
+  typedef itk::ImageRegionIteratorWithIndex MaskIteratorType;
+
+  MaskIteratorType fixedIter( fixedMaskImage, fixedMaskImage->GetLargestPossibleRegion() );
+  fixedIter.Begin();
+  while( !fixedIter.IsAtEnd() )
+    {
+    fixedMaskImage->TransformIndexToPhysicalPoint(fixedIter.GetIndex(), location);
+    if( location[2] < fixedInferior[2] )
+      {
+      fixedIter.Set(zero);
+      }
+    ++fixedIter;
+    }
+
+  MaskIteratorType movingIter( movingMaskImage, movingMaskImage->GetLargestPossibleRegion() );
+  movingIter.Begin();
+  while( !movingIter.IsAtEnd() )
+    {
+    movingMaskImage->TransformIndexToPhysicalPoint(movingIter.GetIndex(), location);
+    if( location[2] < movingInferior[2] )
+      {
+      movingIter.Set(zero);
+      }
+    ++movingIter;
+    }
+
+  typename ImageMaskSpatialObjectType::Pointer  fixedMaskSpatialObject = ImageMaskSpatialObjectType::New();
+  fixedMaskSpatialObject->SetImage(fixedMaskImage);
+  fixedMaskSpatialObject->ComputeObjectToWorldTransform();
+  fixedMask = fixedMaskSpatialObject.GetPointer();
+
+  typename ImageMaskSpatialObjectType::Pointer  movingMaskSpatialObject = ImageMaskSpatialObjectType::New();
+  movingMaskSpatialObject->SetImage(movingMaskImage);
+  movingMaskSpatialObject->ComputeObjectToWorldTransform();
+  movingMask = movingMaskSpatialObject.GetPointer();
+}
+
+/**
+ * The ComputeRobustMinMaxMean function will identify the 10th and 90th quantile
+ * an extropolate an expected min/max values (i.e the 0th, and 100th quantile) from
+ * that estimate.  The value returned for the true min/max values are
+ * the min(estimate 0thquantile, actualmin)/max(estimated 100thquantile, actualmax);
+ *
+ * This is a robust way to remove small numbers of high spike noise from artificially
+ * expanding the range of the image.  It helps to ensure that the middle 80% of the image
+ * occupies a sufficient part of the range computed.
+ *
+ */
+template 
+void ComputeRobustMinMaxMean(
+  const float Qalpha, // Remove 1% from computations by setting Qalpha=0.005
+  typename TInputImage::ConstPointer image,
+  typename TMaskImage::ConstPointer mask,
+  float & minValue, // TODO:  Make this into
+                    // itk::NumericTraits::RealType;
+  float & maxValue, // TODO:  Make this into
+                    // itk::NumericTraits::RealType;
+  float & meanValue // TODO:  Make this into
+                    // itk::NumericTraits::RealType;
+  )
+{
+  // This is a more stable way of determining the range of values that the image
+  // has.
+  // By eliminating possible "bright or dark" noise in the image.
+  minValue = vcl_numeric_limits::max();
+  maxValue = vcl_numeric_limits::min();
+  std::vector fixedList(image->GetBufferedRegion().GetNumberOfPixels() );
+    {
+    itk::ImageRegionConstIteratorWithIndex fi(image, image->GetBufferedRegion() );
+    while( !fi.IsAtEnd() )
+      {
+      typename TInputImage::PointType physicalPoint;
+      image->TransformIndexToPhysicalPoint(fi.GetIndex(), physicalPoint);
+
+      bool inCaluationRegion = true;
+      if( mask.IsNotNull() &&  ( !mask->IsInside(physicalPoint) ) )  // A null
+                                                                     // mask
+                                                                     // implies
+                                                                     // entire
+                                                                     // space is
+                                                                     // to be
+                                                                     // used.
+        {
+        inCaluationRegion = false;
+        }
+      if( inCaluationRegion )
+        {
+        const typename TInputImage::PixelType currValue = fi.Get();
+        minValue = vcl_min(minValue, currValue);
+        maxValue = vcl_max(maxValue, currValue);
+        fixedList.push_back(currValue);
+        }
+      ++fi;
+      }
+    }
+  std::sort(fixedList.begin(), fixedList.end() );
+
+  // Make sure that center 1/2 (25%-75%) of intensity values spans center 1/2 of
+  // histogram
+  // Compute extended line through these two Quantile points
+  const float LQx = Qalpha;
+  const float HQx = 1.0 - Qalpha;
+
+  const float fixedLQy = fixedList[static_cast(fixedList.size() * LQx)];
+  const float fixedHQy = fixedList[static_cast(fixedList.size() * HQx)];
+  const float fixedQSlope = (fixedHQy - fixedLQy) / (HQx - LQx);
+  const float fixedZeroQy = fixedLQy - fixedQSlope * LQx;
+  const float fixedOneQy = fixedQSlope * 1.0 + fixedZeroQy;
+
+  std::cout << " Quantile Fixed Points " << Qalpha << ": " << fixedLQy << " " << fixedHQy << " slope: "
+            << fixedQSlope <<  std::endl;
+  std::cout << " Quantile Range" << ": " << fixedZeroQy << " " << fixedOneQy << std::endl;
+  std::cout << "PreFix Range: " << minValue   << " " << maxValue << std::endl;
+
+  // Now set to the range of values based on linear extrapolation of the
+  // quantiles
+  minValue = vcl_max(fixedZeroQy, minValue);
+  maxValue = vcl_min(fixedOneQy, maxValue);
+  std::cout << "PostFix Range: " << minValue   << " " << maxValue << std::endl;
+
+    { // For all voxels in valid range, compute the mean.
+     // This assumes that other values are noise values, and that their values
+     // have no meaning.
+    float  sum = 0.0F;
+    size_t counter = 0;
+    for( typename std::vector::const_iterator it = fixedList.begin();
+         it != fixedList.end(); ++it )
+      {
+      const float value = static_cast(*it);
+      if( value <= maxValue && value >= minValue )
+        {
+        sum += value;
+        counter++;
+        }
+      }
+    meanValue = sum / static_cast(counter);
+    }
+}
+
+/**
+ *This function produces an image where the very high and low tails of the image are clamped
+ */
+template 
+typename TInputImage::Pointer ClampNoisyTailsOfImage(
+  const float m_RemoveIntensityOutliers,
+  typename TInputImage::ConstPointer InputImage,
+  typename TMaskSpatialObject::ConstPointer mask)
+{
+  typedef itk::ImageDuplicator DuplicatorType;
+  typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+  duplicator->SetInputImage(InputImage);
+  duplicator->Update();
+  typename TInputImage::Pointer image = duplicator->GetOutput();
+
+  float min;
+  float max;
+  float mean;
+  ComputeRobustMinMaxMean(
+    m_RemoveIntensityOutliers,
+    image.GetPointer(),
+    mask.GetPointer(), min, max, mean);
+  itk::ImageRegionIterator fi(image, image->GetBufferedRegion() );
+  while( !fi.IsAtEnd() )
+    {
+    if( fi.Value() > max )
+      {
+      fi.Set(max);
+      }
+    if( fi.Value() < min )
+      {
+      fi.Set(min);
+      }
+    ++fi;
+    }
+
+  return image;
+}
+
+#endif // __BRAINSFITUTILS_h
diff --git a/BRAINSCommonLib/BRAINSMacro.h b/BRAINSCommonLib/BRAINSMacro.h
new file mode 100644
index 00000000..22c0c288
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSMacro.h
@@ -0,0 +1,57 @@
+#ifndef __BRAINSMacro_h
+#define __BRAINSMacro_h
+
+/**
+  * This class encapulates all the functionality needed to run the BRAINSFit
+  *program without any command line options.
+  *
+  * It is a class that has all the functionality after the command line options
+  *are processed and the images pre-processed, and
+  * returns all binary versions of the objects for post-processing.
+  *
+  * NOTE:  This class is not templated!
+  */
+
+#if defined( ITK_LEAN_AND_MEAN ) || defined( __BORLANDC__ ) || defined( NDEBUG )
+#define VECTORitkDebugMacro(s, type, x)
+#else
+#define VECTORitkDebugMacro(s, type, x)                               \
+    {                                                                   \
+    if( this->GetDebug() && ::itk::Object::GetGlobalWarningDisplay() ) \
+      {                                                                 \
+      ::std::ostringstream itkmsg;                                      \
+      itkmsg << "Debug: In " __FILE__ ", line " << __LINE__ << "\n"     \
+             << this->GetNameOfClass() << " (" << this << "):" << s;    \
+      for( type::const_iterator it = x.begin(); it != x.end(); ++it )  \
+        {                                                               \
+        itkmsg << " "                                                   \
+               << *( it );                                              \
+        }                                                               \
+      itkmsg << "\n\n";                                                 \
+      ::itk::OutputWindowDisplayDebugText( itkmsg.str().c_str() );      \
+      }                                                                 \
+    }
+#endif
+/** Set built-in type.  Creates member Set"name"() (e.g., SetVisibility()); */
+#define VECTORitkSetMacro(name, type)                          \
+  virtual void Set##name(const type _arg)                   \
+    {                                                          \
+    VECTORitkDebugMacro("setting " #name " to ", type, _arg); \
+    type::const_iterator fromIt = _arg.begin();                \
+    type::const_iterator toIt = this->m_##name.begin();      \
+      {                                                        \
+      this->m_##name.resize( _arg.size() );                  \
+      this->m_##name = _arg;                                 \
+      this->Modified();                                        \
+      }                                                        \
+    }
+
+/** Get built-in type.  Creates member Get"name"() (e.g., GetVisibility()); */
+#define VECTORitkGetConstMacro(name, type)                                      \
+  virtual type Get##name()                                                   \
+    {                                                                           \
+    VECTORitkDebugMacro("returning " << #name " of ", type, this->m_##name); \
+    return this->m_##name;                                                    \
+    }
+
+#endif // __BRAINSMACRO_h
diff --git a/BRAINSCommonLib/BRAINSROIAutoUtils.h b/BRAINSCommonLib/BRAINSROIAutoUtils.h
new file mode 100644
index 00000000..5677f29c
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSROIAutoUtils.h
@@ -0,0 +1,3 @@
+#ifndef __BRAINSROIAutoUtils_h
+#define __BRAINSROIAutoUtils_h
+#endif // __BRAINSROIAutoUtils_h
diff --git a/BRAINSCommonLib/BRAINSThreadControl.h b/BRAINSCommonLib/BRAINSThreadControl.h
new file mode 100644
index 00000000..756a8c63
--- /dev/null
+++ b/BRAINSCommonLib/BRAINSThreadControl.h
@@ -0,0 +1,35 @@
+#ifndef BRAINSThreadControl_h
+#define BRAINSThreadControl_h
+
+#include 
+#include 
+#include "itkMultiThreader.h"
+
+namespace BRAINSUtils
+{
+inline
+void SetThreadCount(int desiredCount)
+{
+  int threadCount(-1);
+  if( desiredCount > 0 )  // NOTE: Default is -1, which then uses the
+  // ITK default.
+    {
+    threadCount = desiredCount;
+    }
+  else
+    {
+    std::string numThreads;
+    if(itksys::SystemTools::GetEnv("NSLOTS",numThreads))
+      {
+      std::istringstream s(numThreads,std::istringstream::in);
+      s >> threadCount;
+      }
+    }
+  if(threadCount > 0)
+    {
+    itk::MultiThreader::SetGlobalMaximumNumberOfThreads(threadCount);
+    }
+}
+}
+
+#endif // BRAINSThreadControl_h
diff --git a/BRAINSCommonLib/BuildScripts/BRAINSLogo.bmp b/BRAINSCommonLib/BuildScripts/BRAINSLogo.bmp
new file mode 100644
index 00000000..32d42cce
Binary files /dev/null and b/BRAINSCommonLib/BuildScripts/BRAINSLogo.bmp differ
diff --git a/BRAINSCommonLib/BuildScripts/BRAINSLogo.h b/BRAINSCommonLib/BuildScripts/BRAINSLogo.h
new file mode 100644
index 00000000..d9f06e58
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/BRAINSLogo.h
@@ -0,0 +1,48 @@
+/*
+ * Resource generated for file:
+ *    BRAINSIcon.png (zlib, base64) (image file)
+ */
+static const unsigned int  ModuleLogoWidth          = 40;
+static const unsigned int  ModuleLogoHeight         = 40;
+static const unsigned int  ModuleLogoPixelSize     = 4;
+static const unsigned long ModuleLogoLength         = 2572;
+static const unsigned long image_BRAINSIcon_decoded_length = 6400;
+
+static const unsigned char ModuleLogoImage[]
+  = "eNrtWHm0lVMU//V6hcjQJIXGV2nQ8FJJE9E8aNJE8yulQa/UIw00KLUiJEkRmQsLmZaMWb"
+    "FMKSLRi0SWtRQasLK33z7nfvd+972vW9JaslZ/7HXOPfcM+9t7/357n7PvU+jez6D7EiL7"
+    "js6YHLX9KPH2aI2xf9T2+z/YLxhL1v9YGEv4IZBjaMx+/7YxIXs2Qvb4Niz5x7gXJdU8ic"
+    "87xH5mK+oR7V+2mkv5lvKNE9FtbMOSy7HceD+QxFhCJF8/mJebZ+222Hm5qfGx813okCug"
+    "3dpAB3aDDusNyRkOzbkaOmEYdEY29I6pkPk3QudPgt4+GXob+wtvgiy6GTo+y8+NiVzPtS"
+    "YTh0Hm5kAXz4DY/Nsm+7UmC6ZA5kyEjhkIvXOq15O+c77Ma78/voA2qQ8F/htJT4d+shpq"
+    "esT8nISPPzdDRvd3c8WkQIG4aNBPS4gGfRuPrdGCaZBC6ZBSxSCN6kAuqOW+Wc6vBjm5SG"
+    "JeeK/gDPtvYHf6m3G1f1N+fOh26Ir5Sd8kEd8ZOVbhbGitKtBeHejnIdBbJ0IanA8tVwY6"
+    "iGdedhG0bTOns55ZInq/woWgryynj7/2WMjrX/0eetXl/0y/M06Ddm0N6d4W2rop1M6vUR"
+    "napRWk8rnQhrWh1StD6laHNqUdB/fw82pm0IZ59ksvCH1xmcfM3gh8bFkDrXDO4et3cSNo"
+    "387Q0f0gGeWgxahrJep0VknaqDh9XBzaogG0znmQDhdDW14IadccOrwPMdiavxtDTy+afM"
+    "awXtTvO8ivGxJ8E9jvwXmHH8s3XkO9GKvm15LFoFXKU69S0D4dvY9pP+1wCbQiv7dJpuMC"
+    "bXYB1OKxPqUh7TyXuO3ZPnlf8/0Hz1DHXdADX3odAzvu+hhi/gjwEZKksT6dIIwp00kql4"
+    "PUZuzXyIC0agLNHgy5KNPtI0N7Qq4dAKVPrZWRV0HoW2lcDzplFKR/VxeXcl6lBGZsf/pB"
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+    "T98xDWY1KbMViPHLJ4JuTdVW6dZLGGG0ROzB4EWbUQMm5w/jPC5xqn6k8ev2Y/4+21T/h8"
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+    "i4C2r+X9ZT352OS5PqoVQ5JRhjrnMYat/C28zw2r2NxwprE8lhrXpdls8fxtvpacm1mfVt"
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+    "nenuXvLkQujqpdA1xMg7TzJfr4GsXOj1s3uz4db4ZM8h3q9icejv9rw3We2qP1DIi65lTU"
+    "ZOD0RCfZvj7hBu3c7Qmh1sv/P5M/5GYW8L3GvJLe6ubnc3F19H+n6Vtx98Yxhb9l8Q24e7"
+    "n/GZYSL+37H0fvVZ/I0oeKc62Nrj77vH33ePv+8eZOxv/VXNiA==";
diff --git a/BRAINSCommonLib/BuildScripts/BRAINSLogo.ico b/BRAINSCommonLib/BuildScripts/BRAINSLogo.ico
new file mode 100644
index 00000000..eaeeea6e
Binary files /dev/null and b/BRAINSCommonLib/BuildScripts/BRAINSLogo.ico differ
diff --git a/BRAINSCommonLib/BuildScripts/BRAINSLogo.png b/BRAINSCommonLib/BuildScripts/BRAINSLogo.png
new file mode 100644
index 00000000..821ada74
Binary files /dev/null and b/BRAINSCommonLib/BuildScripts/BRAINSLogo.png differ
diff --git a/BRAINSCommonLib/BuildScripts/BRAINSSEMCommandLineWrarpperTester.cxx b/BRAINSCommonLib/BuildScripts/BRAINSSEMCommandLineWrarpperTester.cxx
new file mode 100644
index 00000000..52cd75f6
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/BRAINSSEMCommandLineWrarpperTester.cxx
@@ -0,0 +1,36 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $HeadURL$
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even 
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+// This file is intended to be compiled and linked against a shared
+// library CLP to prevent the need to compile twice.
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int main(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
diff --git a/BRAINSCommonLib/BuildScripts/CMakeBRAINS3BuildMacros.cmake b/BRAINSCommonLib/BuildScripts/CMakeBRAINS3BuildMacros.cmake
new file mode 100644
index 00000000..d31e1501
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/CMakeBRAINS3BuildMacros.cmake
@@ -0,0 +1,171 @@
+#-----------------------------------------------------------------------------
+# See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details
+# #-----------------------------------------------------------------------------
+if(POLICY CMP0016)
+  cmake_policy(SET CMP0016 NEW)
+endif()
+if(POLICY CMP0017)
+  cmake_policy(SET CMP0017 OLD)
+endif()
+
+include(ExternalProject)
+
+if(INTEGRATE_WITH_SLICER)
+  set(BRAINS_BUILD OFF CACHE INTERNAL "Set BRAINS_BUILD to off for slicer builds" FORCE )
+else()
+  set(BRAINS_BUILD ON CACHE INTERNAL "Set BRAINS_BUILD to on for non-slicer builds" FORCE )
+endif()
+
+#
+
+#-----------------------------------------------------------------------------
+# Build the optional DEBUGIMAGEVIEWER
+if(NOT SETOPTIONALDEBUGIMAGEVIEWER)
+macro(SETOPTIONALDEBUGIMAGEVIEWER)
+if(BRAINS_BUILD)
+  option(USE_DEBUG_IMAGE_VIEWER "Use the DEBUG_IMAGE_VIEWER for debugging" ON)
+else(BRAINS_BUILD)
+  option(USE_DEBUG_IMAGE_VIEWER "Use the DEBUG_IMAGE_VIEWER for debugging" OFF)
+endif(BRAINS_BUILD)
+
+mark_as_advanced(USE_DEBUG_IMAGE_VIEWER)
+set(OPTIONAL_DEBUG_LINK_LIBRARIES) ## Set it to empty as the default
+if( USE_DEBUG_IMAGE_VIEWER )
+   if(NOT KWWidgets_SOURCE_DIR)
+     find_package(KWWidgets REQUIRED)
+     include(${KWWidgets_USE_FILE})
+   endif(NOT KWWidgets_SOURCE_DIR)
+   add_definitions(-DUSE_DEBUG_IMAGE_VIEWER)
+   find_path(DEBUG_IMAGE_VIEWER_INCLUDE_DIR DebugImageViewerClient.h ${CMAKE_INSTALL_PREFIX}/include)
+   include_directories(${DEBUG_IMAGE_VIEWER_INCLUDE_DIR})
+   set(OPTIONAL_DEBUG_LINK_LIBRARIES ${KWWidgets_LIBRARIES})
+endif( USE_DEBUG_IMAGE_VIEWER )
+endmacro(SETOPTIONALDEBUGIMAGEVIEWER)
+endif(NOT SETOPTIONALDEBUGIMAGEVIEWER)
+
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+## A macro to create executables for Slicer or BRAINS3
+if(NOT CONFIGUREBRAINSORSLICERPROPERTIES)
+  macro(CONFIGUREBRAINSORSLICERPROPERTIES PROGNAME PROGCLI PROGSOURCES LIBSOURCES ENTRYPOINTNAME EXTRA_LIBS)
+
+  find_package(SlicerExecutionModel NO_MODULE REQUIRED GenerateCLP)
+  include(${GenerateCLP_USE_FILE})
+
+  get_filename_component(TMP_FILENAME ${PROGCLI} NAME_WE)
+  set(PROGCLI_HEADER "${CMAKE_CURRENT_BINARY_DIR}/${TMP_FILENAME}CLP.h")
+
+  set(CLP_SOURCES ${PROGSOURCES} ${LIBSOURCES})
+  set(CLP_PRIMARY_SOURCES ${LIBSOURCES})
+  if(EXISTS  ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h)
+    GENERATECLP(CLP_SOURCES ${PROGCLI} ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h)
+  else()
+    GENERATECLP(CLP_SOURCES ${PROGCLI} )
+  endif()
+
+  add_executable( ${PROGNAME} ${CLP_SOURCES} ${PROGCLI_HEADER})
+
+  if(WIN32)
+    set(BRAINS_ITK_LIBS "")
+  else(WIN32)
+    if(ITK_VERSION_MAJOR LESS "4")
+      set(BRAINS_ITK_LIBS ITKAlgorithms ITKIO ITKBasicFilters)
+    else()
+      set(BRAINS_ITK_LIBS ${ITK_LIBRARIES})
+    endif()
+  endif(WIN32)
+  target_link_libraries (${PROGNAME} BRAINSCommonLib ${BRAINS_ITK_LIBS} ${OPTIONAL_DEBUG_LINK_LIBRARIES} ${EXTRA_LIBS} )
+
+  if (INTEGRATE_WITH_SLICER)
+    #if(NOT slicer3_set_plugins_output_path)
+    #  include(${Slicer_SOURCE_DIR}/CMake/Slicer3PluginsMacros.cmake)
+    #endif()
+    ### If building as part of the INTEGRATE_WITH_SLICER, then only build the shared object, and not the command line program.
+
+    message(STATUS "Building ${PROGNAME} for Slicer4 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+    add_library(${PROGNAME}Lib SHARED ${CLP_PRIMARY_SOURCES} ${PROGCLI_HEADER})
+    set_target_properties (${PROGNAME}Lib PROPERTIES COMPILE_FLAGS "-D${ENTRYPOINTNAME}=ModuleEntryPoint")
+    target_link_libraries (${PROGNAME}Lib BRAINSCommonLib ${BRAINS_ITK_LIBS} ${OPTIONAL_DEBUG_LINK_LIBRARIES} ${EXTRA_LIBS} )
+
+    # install each target in the production area (where it would appear in an
+    # installation) and install each target in the developer area (for running
+    # from a build)
+    set(TARGETS ${PROGNAME}Lib ${PROGNAME})
+    #slicer3_set_plugins_output_path(${PROGNAME}Lib)
+    #slicer3_set_plugins_output_path(${PROGNAME})
+    #slicer3_install_plugins(${TARGETS})
+    install(TARGETS ${PROGNAME}
+            RUNTIME DESTINATION bin
+            LIBRARY DESTINATION lib
+            ARCHIVE DESTINATION lib
+            COMPONENT Development
+            )
+
+  else (INTEGRATE_WITH_SLICER)
+  endif (INTEGRATE_WITH_SLICER)
+    ### If building outside of Slicer3, then only build the command line executable.
+    install(TARGETS ${PROGNAME}
+      RUNTIME DESTINATION bin
+      LIBRARY DESTINATION lib
+      ARCHIVE DESTINATION lib
+      COMPONENT Development)
+
+endmacro(CONFIGUREBRAINSORSLICERPROPERTIES PROGNAME PROGCLI PROGSOURCES LIBSOURCES)
+endif(NOT CONFIGUREBRAINSORSLICERPROPERTIES)
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------
+## A macro to create CLP dependant libraries for Slicer or BRAINS3
+if(NOT CONFIGUREBRAINSORSLICERLIBRARY)
+macro(CONFIGUREBRAINSORSLICERLIBRARY LIBNAME LIBCLI LIBSOURCES EXTRA_LIBS)
+
+  set(CLP_SOURCES ${LIBSOURCES})
+  if("x${LIBCLI}" MATCHES "x")
+    ## Nothing to do if there is no CLI component
+  else()
+    find_package(SlicerExecutionModel NO_MODULE REQUIRED GenerateCLP)
+    include(${GenerateCLP_USE_FILE})
+
+    get_filename_component(TMP_FILENAME ${LIBCLI} NAME_WE)
+    set(LIBCLI_HEADER "${CMAKE_CURRENT_BINARY_DIR}/${TMP_FILENAME}CLP.h")
+
+    if(EXISTS  ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h)
+      GENERATECLP(CLP_SOURCES ${LIBCLI} ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h)
+    else()
+      GENERATECLP(CLP_SOURCES ${LIBCLI} )
+    endif()
+  endif()
+
+  add_library( ${LIBNAME} ${CLP_SOURCES} ${LIBCLI_HEADER})
+  target_link_libraries (${LIBNAME} BRAINSCommonLib ${ITK_LIBRARIES} ${OPTIONAL_DEBUG_LINK_LIBRARIES} ${EXTRA_LIBS} )
+
+  ##HACK:  if (INTEGRATE_WITH_SLICER)
+    #if(NOT slicer3_set_plugins_output_path)
+    #  include(${Slicer_SOURCE_DIR}/CMake/Slicer3PluginsMacros.cmake)
+    #endif()
+    ### If building as part of the INTEGRATE_WITH_SLICER, then only build the shared object, and not the command line program.
+    # install each target in the production area (where it would appear in an
+    # installation) and install each target in the developer area (for running
+    # from a build)
+    #slicer3_set_plugins_output_path(${LIBNAME})
+    #set(TARGETS ${LIBNAME})
+    #slicer3_install_plugins(${TARGETS})
+  ##HACK:  else (INTEGRATE_WITH_SLICER)
+    install(TARGETS ${LIBNAME}
+      RUNTIME DESTINATION bin
+      LIBRARY DESTINATION lib
+      ARCHIVE DESTINATION lib
+      COMPONENT Development)
+  ##HACK:  endif (INTEGRATE_WITH_SLICER)
+
+endmacro(CONFIGUREBRAINSORSLICERLIBRARY LIBNAME LIBCLI LIBSOURCES)
+endif(NOT CONFIGUREBRAINSORSLICERLIBRARY)
diff --git a/BRAINSCommonLib/BuildScripts/CMakeBuildMacros.cmake b/BRAINSCommonLib/BuildScripts/CMakeBuildMacros.cmake
new file mode 100644
index 00000000..83cf720f
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/CMakeBuildMacros.cmake
@@ -0,0 +1,44 @@
+#  This file contains common Macros that are useful for controlling
+#  hierarchial build where common components may be included in more
+#  than one subdirectory, but we only want a single copy of it built.
+
+
+###############################################################################
+###############################################################################
+## A simple macro to set variables ONLY if it has not been set
+## This is needed when stand-alone packages are combined into
+## a larger package, and the desired behavior is that all the
+## binary results end up in the combined directory.
+if(NOT SETIFEMPTY)
+macro(SETIFEMPTY)
+  set(KEY ${ARGV0})
+  set(VALUE ${ARGV1})
+  if(NOT ${KEY})
+    set(${ARGV})
+  endif(NOT ${KEY})
+endmacro(SETIFEMPTY KEY VALUE)
+endif(NOT SETIFEMPTY)
+
+###############################################################################
+###############################################################################
+## MakeTestDriverFromSEMTool
+## For tools made with the slicer execution model,
+## This macro will build a test driver that adds the
+## --compare
+## --compareIntensityTolerance
+## --compareRadiusTolerance
+## --compareNumberOfPixelsTolerance
+## to the SEM tools.
+macro(MakeTestDriverFromSEMTool SEMToolName SEMToolTestSourceName)
+  set(SEMToolLibName        ${SEMToolName}Lib)
+
+  set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "#include \"itkTestDriverBeforeTest.inc\"")
+  set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "#include \"itkTestDriverAfterTest.inc\"")
+  create_test_sourcelist(${SEMToolName}   ${SEMToolName}TestDriver.cxx ${SEMToolTestSourceName}
+     EXTRA_INCLUDE itkTestDriverIncludeRequiredIOFactories.h
+     FUNCTION  ProcessArgumentsAndRegisterRequiredFactories
+     )
+  add_executable(${SEMToolName}TestDriver ${SEMToolName}TestDriver.cxx ${SEMToolTestSourceName})
+  target_link_libraries(${SEMToolName}TestDriver ${SEMToolLibName} ${ITKTestKernel_LIBRARIES})
+endmacro(MakeTestDriverFromSEMTool SEMToolName)
+
diff --git a/BRAINSCommonLib/BuildScripts/CMakeCommonExternalDefinitions.cmake b/BRAINSCommonLib/BuildScripts/CMakeCommonExternalDefinitions.cmake
new file mode 100644
index 00000000..1eb3ad49
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/CMakeCommonExternalDefinitions.cmake
@@ -0,0 +1,427 @@
+
+#-----------------------------------------------------------------------------
+## The FORCE_BUILD_CHECK macro adds a forecebuild step that will cause the
+## external project build process to be checked for updates each time
+## a dependent project is built.  It MUST be called AFTER the ExternalProject_Add
+## step for the project that you want to force building on.
+macro(FORCE_BUILD_CHECK  proj)
+    ExternalProject_Add_Step(${proj} forcebuild
+      COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_CURRENT_BUILD_DIR}/${proj}-prefix/src/${proj}-stamp/${proj}-build
+      DEPENDEES configure
+      DEPENDERS build
+      ALWAYS 1
+    )
+endmacro()
+
+#-----------------------------------------------------------------------------
+## empty until ITK is brought into here as an ExternalProject
+macro(PACKAGE_NEEDS_ITK LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck ITK)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_ITK)
+    find_package(ITK REQUIRED)
+    include(${ITK_USE_FILE})
+    set(ITK_DEPEND "") ## Set the external depandancy for ITK
+  else()
+    set(proj Insight)
+    ExternalProject_Add(${proj}
+    #GIT_REPOSITORY "http://itk.org/ITK.git"
+    GIT_REPOSITORY "git://github.com/hjmjohnson/ITK.git"
+    # This tag fixes two items:  #1) ImageDuplicator for vector images, #2) respect metric->NumberOfThreads
+    #GIT_TAG "0219c81682779b7cc51166578b5e3af5a1b887d1"
+    GIT_TAG "ITKv3ForBRAINS20110416"
+      UPDATE_COMMAND ""
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DBUILD_TESTING:BOOL=OFF
+        -DITK_USE_REVIEW:BOOL=ON
+        -DITK_USE_REVIEW_STATISTICS:BOOL=ON
+        -DITK_USE_TRANSFORM_IO_FACTORIES:BOOL=ON
+        -DITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON
+        -DITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE:BOOL=ON
+        -DITK_USE_OPTIMIZED_REGISTRATION_METHODS:BOOL=ON
+        -DITK_USE_PORTABLE_ROUND:BOOL=ON
+        -DITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=ON
+        -DITK_USE_TRANSFORM_IO_FACTORIES:BOOL=ON
+        -DITK_LEGACY_REMOVE:BOOL=ON
+        INSTALL_COMMAND ""
+        #    INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    FORCE_BUILD_CHECK(${proj})
+    set(ITK_DIR ${CMAKE_CURRENT_BINARY_DIR}/Insight-build)
+    set (ITK_DEPEND ${proj}) ## Set the internal dependancy for ITK
+  endif()
+endmacro()
+
+#-----------------------------------------------------------------------------
+# Get and build VTK
+#
+macro(PACKAGE_NEEDS_VTKWITHQT LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck VTK)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_VTK)
+    find_package(VTK 5.6 REQUIRED)
+    include(${VTK_USE_FILE})
+    set(VTK_DEPEND "") ## Set the external depandancy for ITK
+  else()
+    set(proj vtk-5-6)
+    set(vtk_tag -r VTK-5-6)
+    set(vtk_module VTK)
+
+    set(vtk_WRAP_TCL OFF)
+    set(vtk_WRAP_PYTHON OFF)
+
+    find_package(Qt4 REQUIRED)
+    if(QT_USE_FILE)
+      include(${QT_USE_FILE})
+    endif(QT_USE_FILE)
+    set(QT_ARGS
+        -DDESIRED_QT_VERSION:STRING=4
+        -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE}
+      )
+
+    set(vtk_QT_ARGS)
+    set(vtk_QT_ARGS
+        ${QT_ARGS}
+        -DVTK_USE_GUISUPPORT:BOOL=ON
+        -DVTK_USE_QVTK:BOOL=ON
+        -DVTK_USE_QT:BOOL=ON
+    )
+    if(APPLE)
+      # Qt 4.6 binary libs are built with empty OBJCXX_FLAGS for mac Cocoa
+      set(vtk_QT_ARGS
+        ${vtk_QT_ARGS}
+        -DVTK_USE_CARBON:BOOL=OFF
+        -DVTK_USE_COCOA:BOOL=ON
+        -DVTK_REQUIRED_OBJCXX_FLAGS:STRING=
+        )
+    endif(APPLE)
+
+    ExternalProject_Add(${proj}
+      GIT_REPOSITORY "git://vtk.org/VTK.git"
+      GIT_TAG "v5.6.1"
+      # CVS_REPOSITORY ":pserver:anonymous:vtk@public.kitware.com:/cvsroot/VTK"
+      # CVS_MODULE "${vtk_module}"
+      # CVS_TAG ${vtk_tag}
+      UPDATE_COMMAND ""
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DVTK_USE_PARALLEL:BOOL=ON
+        -DVTK_DEBUG_LEAKS:BOOL=OFF
+        -DVTK_WRAP_TCL:BOOL=${vtk_WRAP_TCL}
+        -DVTK_WRAP_PYTHON:BOOL=${vtk_WRAP_PYTHON}
+        ${vtk_QT_ARGS}
+      INSTALL_COMMAND ""
+      #  INSTALL_DIR "${CMAKE_INSTALL_PREFIX}"
+    )
+    FORCE_BUILD_CHECK(${proj})
+
+    set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
+    set(VTK_DEPEND ${proj})
+    message(STATUS "Setting VTK_DIR to -DVTK_DIR:PATH=${VTK_DIR}")
+    set(VTK_CMAKE
+       -DVTK_DIR:PATH=${VTK_DIR}
+        ${QT_ARGS}
+    )
+  endif()
+endmacro()
+
+macro(PACKAGE_NEEDS_VTK_NOGUI LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck VTK)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_VTK)
+    find_package(VTK 5.6 REQUIRED)
+    include(${VTK_USE_FILE})
+    set(VTK_DEPEND "") ## Set the external depandancy for ITK
+  else()
+    set(proj vtk-5-6)
+    set(vtk_tag -r VTK-5-6)
+    set(vtk_module VTK)
+
+    set(vtk_WRAP_TCL OFF)
+    set(vtk_WRAP_PYTHON OFF)
+
+    set(vtk_GUI_ARGS
+        -DVTK_USE_GUISUPPORT:BOOL=OFF
+        -DVTK_USE_QVTK:BOOL=OFF
+        -DVTK_USE_QT:BOOL=OFF
+        -DVTK_USE_X:BOOL=OFF
+        -DVTK_USE_CARBON:BOOL=OFF
+        -DVTK_USE_COCOA:BOOL=OFF
+        -DVTK_USE_RENDERING:BOOL=OFF
+    )
+    if(APPLE)
+      # Qt 4.6 binary libs are built with empty OBJCXX_FLAGS for mac Cocoa
+      set(vtk_GUI_ARGS
+        ${vtk_GUI_ARGS}
+        -DVTK_REQUIRED_OBJCXX_FLAGS:STRING=
+        )
+    endif(APPLE)
+
+    ExternalProject_Add(${proj}
+      CVS_REPOSITORY ":pserver:anonymous:vtk@public.kitware.com:/cvsroot/VTK"
+      CVS_MODULE "${vtk_module}"
+      CVS_TAG ${vtk_tag}
+      UPDATE_COMMAND ""
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DVTK_USE_PARALLEL:BOOL=ON
+        -DVTK_DEBUG_LEAKS:BOOL=OFF
+        -DVTK_WRAP_TCL:BOOL=${vtk_WRAP_TCL}
+        -DVTK_WRAP_PYTHON:BOOL=${vtk_WRAP_PYTHON}
+        ${vtk_GUI_ARGS}
+      INSTALL_COMMAND ""
+      #  INSTALL_DIR "${CMAKE_INSTALL_PREFIX}"
+    )
+    FORCE_BUILD_CHECK(${proj})
+
+    set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
+    set(VTK_DEPEND ${proj})
+    message(STATUS "Setting VTK_DIR to -DVTK_DIR:PATH=${VTK_DIR}")
+    set(VTK_CMAKE
+       -DVTK_DIR:PATH=${VTK_DIR}
+    )
+  endif()
+endmacro()
+
+macro(PACKAGE_NEEDS_VTK_NOGUI LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck VTK)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_VTK)
+    find_package(VTK 5.6 REQUIRED)
+    include(${VTK_USE_FILE})
+    set(VTK_DEPEND "") ## Set the external depandancy for ITK
+  else()
+    set(proj vtk-5-6)
+    set(vtk_tag -r VTK-5-6)
+    set(vtk_module VTK)
+
+    set(vtk_WRAP_TCL OFF)
+    set(vtk_WRAP_PYTHON OFF)
+
+    set(vtk_GUI_ARGS
+        -DVTK_USE_GUISUPPORT:BOOL=OFF
+        -DVTK_USE_QVTK:BOOL=OFF
+        -DVTK_USE_QT:BOOL=OFF
+        -DVTK_USE_X:BOOL=OFF
+        -DVTK_USE_CARBON:BOOL=OFF
+        -DVTK_USE_COCOA:BOOL=OFF
+        -DVTK_USE_RENDERING:BOOL=OFF
+    )
+    if(APPLE)
+      # Qt 4.6 binary libs are built with empty OBJCXX_FLAGS for mac Cocoa
+      set(vtk_GUI_ARGS
+        ${vtk_GUI_ARGS}
+        -DVTK_REQUIRED_OBJCXX_FLAGS:STRING=
+        )
+    endif(APPLE)
+
+    ExternalProject_Add(${proj}
+      CVS_REPOSITORY ":pserver:anonymous:vtk@public.kitware.com:/cvsroot/VTK"
+      CVS_MODULE "${vtk_module}"
+      CVS_TAG ${vtk_tag}
+      UPDATE_COMMAND ""
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DVTK_USE_PARALLEL:BOOL=ON
+        -DVTK_DEBUG_LEAKS:BOOL=OFF
+        -DVTK_WRAP_TCL:BOOL=${vtk_WRAP_TCL}
+        -DVTK_WRAP_PYTHON:BOOL=${vtk_WRAP_PYTHON}
+        ${vtk_GUI_ARGS}
+      INSTALL_COMMAND ""
+      #  INSTALL_DIR "${CMAKE_INSTALL_PREFIX}"
+    )
+    FORCE_BUILD_CHECK(${proj})
+
+    set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
+    set(VTK_DEPEND ${proj})
+    message(STATUS "Setting VTK_DIR to -DVTK_DIR:PATH=${VTK_DIR}")
+    set(VTK_CMAKE
+       -DVTK_DIR:PATH=${VTK_DIR}
+    )
+  endif()
+endmacro()
+
+macro(PACKAGE_NEEDS_VTK_WITHR LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck VTK)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_VTK)
+    find_package(VTK 5.7 REQUIRED)
+    include(${VTK_USE_FILE})
+    set(VTK_DEPEND "") ## Set the external depandancy for ITK
+  else()
+    set(proj vtk-head)
+
+    set(vtk_WRAP_TCL OFF)
+    set(vtk_WRAP_PYTHON OFF)
+
+    set(vtk_GUI_ARGS
+        -DVTK_USE_GUISUPPORT:BOOL=OFF
+        -DVTK_USE_QVTK:BOOL=OFF
+        -DVTK_USE_QT:BOOL=OFF
+        -DVTK_USE_X:BOOL=OFF
+        -DVTK_USE_CARBON:BOOL=OFF
+        -DVTK_USE_COCOA:BOOL=OFF
+        -DVTK_USE_RENDERING:BOOL=OFF
+    )
+    if(APPLE)
+      # Qt 4.6 binary libs are built with empty OBJCXX_FLAGS for mac Cocoa
+      set(vtk_GUI_ARGS
+        ${vtk_GUI_ARGS}
+        -DVTK_REQUIRED_OBJCXX_FLAGS:STRING=
+        )
+    endif(APPLE)
+
+    ExternalProject_Add(${proj}
+      GIT_REPOSITORY "git://vtk.org/VTK.git"
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      DEPENDS ${R_DEPEND}
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DVTK_USE_PARALLEL:BOOL=OFF
+        -DVTK_DEBUG_LEAKS:BOOL=OFF
+        -DVTK_WRAP_TCL:BOOL=${vtk_WRAP_TCL}
+        -DVTK_WRAP_PYTHON:BOOL=${vtk_WRAP_PYTHON}
+        -DVTK_USE_GNU_R:BOOL=ON
+        -DR_COMMAND:FILEPATH=${R_DIR}/bin/R
+        -DR_INCLUDE_DIR:PATH=${R_DIR}/include
+        -DR_LIBRARY_BASE=${R_DIR}/lib
+        -DR_LIBRARY_BLAS:FILEPATH=${R_DIR}/lib/libRblas${CMAKE_SHARED_LIBRARY_SUFFIX}
+        -DR_LIBRARY_LAPACK:FILEPATH=${R_DIR}/lib/libRlapack${CMAKE_SHARED_LIBRARY_SUFFIX}
+        #-DVTK_R_HOME:PATH=${CMAKE_CURRENT_BINARY_DIR}/R-build
+        ${vtk_GUI_ARGS}
+      INSTALL_COMMAND ""
+      #  INSTALL_DIR "${CMAKE_INSTALL_PREFIX}"
+    )
+    FORCE_BUILD_CHECK(${proj})
+
+    set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
+    set(VTK_DEPEND ${proj})
+    message(STATUS "Setting VTK_DIR to -DVTK_DIR:PATH=${VTK_DIR}")
+    set(VTK_CMAKE
+       -DVTK_DIR:PATH=${VTK_DIR}
+    )
+  endif()
+endmacro()
+#-----------------------------------------------------------------------------
+# Get and build SlicerExecutionModel
+##  Build the SlicerExecutionModel Once, and let all derived project use the same version
+macro(PACKAGE_NEEDS_SlicerExecutionModel LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck SlicerExecutionModel)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_SlicerExecutionModel)
+    find_package(SlicerExecutionModel NO_MODULE REQUIRED GenerateCLP)
+    include(${GenerateCLP_USE_FILE})
+    set(GenerateCLP_DEPEND "")
+    set(SlicerExecutionModel_DEPEND "")
+  else()
+    #### ALWAYS BUILD WITH STATIC LIBS
+    set(proj SlicerExecutionModel)
+    ExternalProject_Add(${proj}
+      SVN_REPOSITORY "http://svn.slicer.org/Slicer3/trunk/Libs/SlicerExecutionModel"
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      DEPENDS ${ITK_DEPEND}
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DITK_DIR:PATH=${ITK_DIR}
+        INSTALL_COMMAND ""
+        # INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    FORCE_BUILD_CHECK(${proj})
+    set(GenerateCLP_DIR ${CMAKE_CURRENT_BINARY_DIR}/SlicerExecutionModel-build/GenerateCLP)
+    set(GenerateCLP_DEPEND "${proj}")
+    set(SlicerExecutionModel_DEPEND "${proj}")
+  endif()
+endmacro()
+
+#-----------------------------------------------------------------------------
+# Get and build BRAINSCommonLib
+macro(PACKAGE_NEEDS_BRAINSCommonLib LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck BRAINSCommonLib)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_BRAINSCommonLib)
+    find_package(BRAINSCommonLib NO_MODULE REQUIRED)
+    include(${BRAINSCommonLib_USE_FILE})
+    set(BRAINSCommonLib_DEPEND "")
+  else()
+    set(proj BRAINSCommonLib)
+    ExternalProject_Add(${proj}
+      SVN_REPOSITORY "http://www.nitrc.org/svn/brains/BRAINSCommonLib/trunk"
+      SVN_USERNAME "slicerbot"
+      SVN_PASSWORD "slicer"
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      DEPENDS ${ITK_DEPEND}
+      CMAKE_GENERATOR ${gen}
+      CMAKE_ARGS
+        ${LOCAL_CMAKE_BUILD_OPTIONS}
+        -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+        -DITK_DIR:PATH=${ITK_DIR}
+        INSTALL_COMMAND ""
+        # INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    FORCE_BUILD_CHECK(${proj})
+    set(BRAINSCommonLib_DIR ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLib-build)
+    set(BRAINSCommonLib_DEPEND "${proj}")
+  endif()
+endmacro()
+
+#-----------------------------------------------------------------------------
+# Get and build R statistical library
+macro(PACKAGE_NEEDS_RSTATS LOCAL_CMAKE_BUILD_OPTIONS gen)
+  set(packageToCheck R)
+  option(OPT_USE_SYSTEM_${packageToCheck} "Use the system's ${packageToCheck} library." OFF)
+  #  mark_as_advanced(OPT_USE_SYSTEM_${packageToCheck})
+  if(OPT_USE_SYSTEM_R)
+    find_package(R NO_MODULE REQUIRED)
+    include(${R_USE_FILE})
+    set(R_DEPEND "")
+  else()
+    set(proj R)
+    ExternalProject_Add(${proj}
+      URL "http://streaming.stat.iastate.edu/CRAN/src/base/R-2/R-2.12.0.tar.gz"
+      SOURCE_DIR ${proj}
+      BINARY_DIR ${proj}-build
+      DEPENDS ""
+      CONFIGURE_COMMAND ${CMAKE_CURRENT_BINARY_DIR}/R/configure --prefix=${CMAKE_CURRENT_BINARY_DIR} --enable-BLAS-shlib
+      #CMAKE_ARGS
+      #  ${LOCAL_CMAKE_BUILD_OPTIONS}
+      #  -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+      #  -DITK_DIR:PATH=${ITK_DIR}
+      #  INSTALL_COMMAND ""
+        # INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}
+    )
+    FORCE_BUILD_CHECK(${proj})
+    set(R_DIR ${CMAKE_CURRENT_BINARY_DIR}/R-build)
+    set(R_DEPEND "${proj}")
+  endif()
+endmacro()
diff --git a/BRAINSCommonLib/BuildScripts/CMakeLists.txt b/BRAINSCommonLib/BuildScripts/CMakeLists.txt
new file mode 100644
index 00000000..749da416
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/CMakeLists.txt
@@ -0,0 +1,12 @@
+### This is just the absolute minimum script necessary
+### to define a separate project that contains all the
+### goodie scripts needed to support the biulding
+### the BRAINS* tools
+
+project(BRAINSBuildScripts)
+cmake_minimum_required(VERSION 2.8)
+
+message(STATUS "CMAKE_INSTALL_PREFIX = ${CMAKE_INSTALL_PREFIX}")
+
+install( FILES License.txt DESTINATION ${CMAKE_INSTALL_PREFIX} )
+
diff --git a/BRAINSCommonLib/BuildScripts/ExternalData.cmake b/BRAINSCommonLib/BuildScripts/ExternalData.cmake
new file mode 100644
index 00000000..7056c0e3
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/ExternalData.cmake
@@ -0,0 +1,657 @@
+# - Manage data files stored outside source tree
+# Use this module to unambiguously reference data files stored outside the
+# source tree and fetch them at build time from arbitrary local and remote
+# content-addressed locations.  Functions provided by this module recognize
+# arguments with the syntax "DATA{}" as references to external data,
+# replace them with full paths to local copies of those data, and create build
+# rules to fetch and update the local copies.
+#
+# The DATA{} syntax is literal and the  is a full or relative path
+# within the source tree.  The source tree must contain either a real data
+# file at  or a "content link" at  containing a hash of the
+# real file using a hash algorithm corresponding to .  For example, the
+# argument "DATA{img.png}" may be satisfied by either a real "img.png" file in
+# the current source directory or a "img.png.md5" file containing its MD5 sum.
+#
+# The 'ExternalData_Expand_Arguments' function evaluates DATA{} references
+# in its arguments and constructs a new list of arguments:
+#  ExternalData_Expand_Arguments(
+#       # Name of data management target
+#       # Output variable
+#    [args...]  # Input arguments, DATA{} allowed
+#    )
+# It replaces each DATA{} reference argument with the full path of a real
+# data file on disk that will exist after the  builds.
+#
+# The 'ExternalData_Add_Test' function wraps around the CMake add_test()
+# command but supports DATA{} reference arguments:
+#  ExternalData_Add_Test(
+#       # Name of data management target
+#    ...        # Arguments of add_test(), DATA{} allowed
+#    )
+# It passes its arguments through ExternalData_Expand_Arguments and then
+# invokes add_test() using the results.
+#
+# The 'ExternalData_Add_Target' function creates a custom target to manage
+# local instances of data files stored externally:
+#  ExternalData_Add_Target(
+#       # Name of data management target
+#    )
+# It creates custom commands in the target as necessary to make data files
+# available for each DATA{} reference previously evaluated by other functions
+# provided by this module.  A list of URL templates must be provided in the
+# variable ExternalData_URL_TEMPLATES using the placeholders "%(algo)" and
+# "%(hash)" in each template.  Data fetch rules try each URL template in order
+# by substituting the hash algorithm name for "%(algo)" and the hash value for
+# "%(hash)".
+#
+# The following hash algorithms are supported:
+#    %(algo)          Description
+#    -------     -----     -----------
+#    MD5         .md5      Message-Digest Algorithm 5, RFC 1321
+# Note that the hashes are used only for unique data identification and
+# download verification.  This is not security software.
+#
+# Example usage:
+#   include(ExternalData)
+#   set(ExternalData_URL_TEMPLATES "file:///local/%(algo)/%(hash)"
+#                                  "http://data.org/%(algo)/%(hash)")
+#   ExternalData_Add_Test(MyData
+#     NAME MyTest
+#     COMMAND MyExe DATA{MyInput.png}
+#     )
+#   ExternalData_Add_Target(MyData)
+# When test "MyTest" runs the "DATA{MyInput.png}" argument will be replaced by
+# the full path to a real instance of the data file "MyInput.png" on disk.  If
+# the source tree contains a content link such as "MyInput.png.md5" then the
+# "MyData" target creates a real "MyInput.png" in the build tree.
+#
+# The DATA{} syntax can automatically recognize and fetch a file series.  If
+# the source tree contains a group of files or content links named like a
+# series then a DATA{} reference to one member adds rules to fetch all of
+# them.  Although all members of a series are fetched, only the file
+# originally named by the DATA{} argument is substituted for it.  Two
+# variables configure recognition of a series from DATA{}.  First,
+# ExternalData_SERIES_PARSE is a regex of the form "^(...)(...)(...)$" to
+# parse , , and  parts from .  Second,
+# ExternalData_SERIES_MATCH is a regex matching the  part of series
+# members named .  Note that the  of a series
+# does not include a hash-algorithm extension.  Both series configuration
+# variables have default values that work well for common cases.
+#
+# The DATA{} syntax can alternatively match files associated with the named
+# file and contained in the same directory.  Associated files may be specified
+# by options using the syntax DATA{,,,...}.  Each option may
+# specify one file by name or specify a regular expression to match file names
+# using the syntax REGEX:.  For example, the arguments
+#   DATA{MyData/MyInput.mhd,MyInput.img}             # File pair
+#   DATA{MyData/MyFrames00.png,MyFrames[0-9]+\\.png} # Series
+# will pass MyInput.mha and MyFrames00.png on the command line but ensure
+# that the associated files are present next to them.
+#
+# The variable ExternalData_LINK_CONTENT may be set to the name of a supported
+# hash algorithm to enable automatic conversion of real data files referenced
+# by the DATA{} syntax into content links.  For each such  a content
+# link named "" is created.  The original file is renamed to the
+# form ".ExternalData__" to stage it for future transmission to
+# one of the locations in the list of URL templates (by means outside the
+# scope of this module).  The data fetch rule created for the content link
+# will use the staged object if it cannot be found using any URL template.
+#
+# The variable ExternalData_SOURCE_ROOT may be set to the highest source
+# directory containing any path named by a DATA{} reference.  The default is
+# CMAKE_SOURCE_DIR.  ExternalData_SOURCE_ROOT and CMAKE_SOURCE_DIR must refer
+# to directories within a single source distribution (e.g. they come together
+# in one tarball).
+#
+# Variables ExternalData_TIMEOUT_INACTIVITY and ExternalData_TIMEOUT_ABSOLUTE
+# set the download inactivity and absolute timeouts, in seconds.  The defaults
+# are 60 seconds and 300 seconds, respectively.  Set either timeout to 0
+# seconds to disable enforcement.  The inactivity timeout is enforced only
+# with CMake >= 2.8.5.
+
+#=============================================================================
+# Copyright 2010-2011 Kitware, Inc.
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#
+# * Redistributions of source code must retain the above copyright
+#   notice, this list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright
+#   notice, this list of conditions and the following disclaimer in the
+#   documentation and/or other materials provided with the distribution.
+#
+# * Neither the names of Kitware, Inc., the Insight Software Consortium,
+#   nor the names of their contributors may be used to endorse or promote
+#   products derived from this software without specific prior written
+#   permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#=============================================================================
+
+function(ExternalData_add_test target)
+  ExternalData_expand_arguments("${target}" testArgs ${ARGN})
+  add_test(${testArgs})
+endfunction()
+
+function(ExternalData_add_target target)
+  if(NOT ExternalData_URL_TEMPLATES)
+    message(FATAL_ERROR "ExternalData_URL_TEMPLATES is not set!")
+  endif()
+  set(config ${CMAKE_CURRENT_BINARY_DIR}/${target}_config.cmake)
+  configure_file(${_ExternalData_SELF_DIR}/ExternalData_config.cmake.in ${config} @ONLY)
+
+  set(files "")
+
+  # Set "_ExternalData_FILE_${file}" for each output file to avoid duplicate
+  # rules.  Use local data first to prefer real files over content links.
+
+  # Custom commands to copy or link local data.
+  get_property(data_local GLOBAL PROPERTY _ExternalData_${target}_LOCAL)
+  foreach(entry IN LISTS data_local)
+    string(REPLACE "|" ";" tuple "${entry}")
+    list(GET tuple 0 file)
+    list(GET tuple 1 name)
+    if(NOT DEFINED "_ExternalData_FILE_${file}")
+      set("_ExternalData_FILE_${file}" 1)
+      add_custom_command(
+        COMMENT "Generating ${file}"
+        OUTPUT "${file}"
+        COMMAND ${CMAKE_COMMAND} -Drelative_top=${CMAKE_BINARY_DIR}
+                                 -Dfile=${file} -Dname=${name}
+                                 -DExternalData_ACTION=local
+                                 -DExternalData_CONFIG=${config}
+                                 -P ${_ExternalData_SELF}
+        DEPENDS "${name}"
+        )
+      list(APPEND files "${file}")
+    endif()
+  endforeach()
+
+  # Custom commands to fetch remote data.
+  get_property(data_fetch GLOBAL PROPERTY _ExternalData_${target}_FETCH)
+  foreach(entry IN LISTS data_fetch)
+    string(REPLACE "|" ";" tuple "${entry}")
+    list(GET tuple 0 file)
+    list(GET tuple 1 name)
+    list(GET tuple 2 ext)
+    if(NOT DEFINED "_ExternalData_FILE_${file}")
+      set("_ExternalData_FILE_${file}" 1)
+      add_custom_command(
+        # Users care about the data file, so hide the hash/timestamp file.
+        COMMENT "Generating ${file}"
+        # The hash/timestamp file is the output from the build perspective.
+        # List the real file as a second output in case it is a broken link.
+        # The files must be listed in this order so CMake can hide from the
+        # make tool that a symlink target may not be newer than the input.
+        OUTPUT "${file}${ext}" "${file}"
+        # Run the data fetch/update script.
+        COMMAND ${CMAKE_COMMAND} -DExternalData_OBJECT_DIR=${CMAKE_BINARY_DIR}/ExternalData/Objects
+                                 -Drelative_top=${CMAKE_BINARY_DIR}
+                                 -Dfile=${file} -Dname=${name} -Dext=${ext}
+                                 -DExternalData_ACTION=fetch
+                                 -DExternalData_CONFIG=${config}
+                                 -P ${_ExternalData_SELF}
+        # Update whenever the object hash changes.
+        DEPENDS "${name}${ext}"
+        )
+      list(APPEND files "${file}${ext}")
+    endif()
+  endforeach()
+
+  # Custom target to drive all update commands.
+  add_custom_target(${target} ALL DEPENDS ${files})
+endfunction()
+
+function(ExternalData_expand_arguments target outArgsVar)
+  # Replace DATA{} references with real arguments.
+  set(data_regex "^xDATA{([^{}\r\n]*)}$")
+  set(outArgs "")
+  foreach(arg IN LISTS ARGN)
+    if("x${arg}" MATCHES "${data_regex}")
+      string(REGEX REPLACE "${data_regex}" "\\1" data "x${arg}")
+      _ExternalData_arg("${target}" "${arg}" "${data}" file)
+      list(APPEND outArgs "${file}")
+    else()
+      list(APPEND outArgs "${arg}")
+    endif()
+  endforeach()
+  set("${outArgsVar}" "${outArgs}" PARENT_SCOPE)
+endfunction()
+
+#-----------------------------------------------------------------------------
+# Private helper interface
+
+set(_ExternalData_SELF "${CMAKE_CURRENT_LIST_FILE}")
+get_filename_component(_ExternalData_SELF_DIR "${_ExternalData_SELF}" PATH)
+
+function(_ExternalData_compute_hash var_hash algo file)
+  if("${algo}" STREQUAL "MD5")
+    # TODO: Errors
+    execute_process(COMMAND "${CMAKE_COMMAND}" -E md5sum "${file}"
+      OUTPUT_VARIABLE output)
+    string(SUBSTRING "${output}" 0 32 hash)
+    set("${var_hash}" "${hash}" PARENT_SCOPE)
+  else()
+    # TODO: Other hashes.
+    message(FATAL_ERROR "Hash algorithm ${algo} unimplemented.")
+  endif()
+endfunction()
+
+function(_ExternalData_exact_regex regex_var string)
+  string(REGEX REPLACE "([][+.*()^])" "\\\\\\1" regex "${string}")
+  set("${regex_var}" "${regex}" PARENT_SCOPE)
+endfunction()
+
+function(_ExternalData_atomic_write file content)
+  string(RANDOM LENGTH 6 random)
+  set(tmp "${file}.tmp${random}")
+  file(WRITE "${tmp}" "${content}")
+  file(RENAME "${tmp}" "${file}")
+endfunction()
+
+function(_ExternalData_link_content name var_ext)
+  if("${ExternalData_LINK_CONTENT}" MATCHES "^(MD5)$")
+    set(algo "${ExternalData_LINK_CONTENT}")
+  else()
+    message(FATAL_ERROR
+      "Unknown hash algorithm specified by ExternalData_LINK_CONTENT:\n"
+      "  ${ExternalData_LINK_CONTENT}")
+  endif()
+  _ExternalData_compute_hash(hash "${algo}" "${name}")
+  get_filename_component(dir "${name}" PATH)
+  set(staged "${dir}/.ExternalData_${algo}_${hash}")
+  set(ext ".md5")
+  _ExternalData_atomic_write("${name}${ext}" "${hash}\n")
+  file(RENAME "${name}" "${staged}")
+  set("${var_ext}" "${ext}" PARENT_SCOPE)
+
+  file(RELATIVE_PATH relname "${ExternalData_SOURCE_ROOT}" "${name}${ext}")
+  message(STATUS "Linked ${relname} to ExternalData ${algo}/${hash}")
+endfunction()
+
+function(_ExternalData_arg target arg options var_file)
+  # Separate data path from the options.
+  string(REPLACE "," ";" options "${options}")
+  list(GET options 0 data)
+  list(REMOVE_AT options 0)
+
+  # Convert to full path.
+  if(IS_ABSOLUTE "${data}")
+    set(absdata "${data}")
+  else()
+    # TODO: If ${data} does not start in "./" or "../" then use search path?
+    get_filename_component(absdata "${CMAKE_CURRENT_SOURCE_DIR}/${data}" ABSOLUTE)
+  endif()
+
+  # Convert to relative path under the source tree.
+  if(NOT ExternalData_SOURCE_ROOT)
+    set(ExternalData_SOURCE_ROOT "${CMAKE_SOURCE_DIR}")
+  endif()
+  set(top_src "${ExternalData_SOURCE_ROOT}")
+  file(RELATIVE_PATH reldata "${top_src}" "${absdata}")
+  if(IS_ABSOLUTE "${reldata}" OR "${reldata}" MATCHES "^\\.\\./")
+    message(FATAL_ERROR "Data file referenced by argument\n"
+      "  ${arg}\n"
+      "does not lie under the top-level source directory\n"
+      "  ${top_src}\n")
+  endif()
+  set(top_bin "${CMAKE_BINARY_DIR}/ExternalData") # TODO: .../${target} ?
+
+  set(external "") # Entries external to the source tree.
+  set(internal "") # Entries internal to the source tree.
+  set(have_original 0)
+
+  # Process options.
+  set(associated_files "")
+  set(associated_regex "")
+  foreach(opt ${options})
+    if("x${opt}" MATCHES "^xREGEX:[^:/]+$")
+      # Regular expression to match associated files.
+      string(REGEX REPLACE "^REGEX:" "" regex "${opt}")
+      list(APPEND associated_regex "${regex}")
+    elseif("x${opt}" MATCHES "^[^][:/*?]+$")
+      # Specific associated file.
+      list(APPEND associated_files "${opt}")
+    else()
+      message(FATAL_ERROR "Unknown option \"${opt}\" in argument\n"
+        "  ${arg}\n")
+    endif()
+  endforeach()
+
+  if(associated_files OR associated_regex)
+    # Load the named data file and listed/matching associated files.
+    _ExternalData_arg_single()
+    _ExternalData_arg_associated()
+  elseif("${reldata}" MATCHES "(^|/)[^/.]+$")
+    # Files with no extension cannot be a series.
+    _ExternalData_arg_single()
+  else()
+    # Match a whole file series by default.
+    _ExternalData_arg_series()
+  endif()
+
+  if(NOT have_original)
+    message(FATAL_ERROR "Data file referenced by argument\n"
+      "  ${arg}\n"
+      "corresponds to source tree path\n"
+      "  ${reldata}\n"
+      "that does not exist (with or without an extension)!")
+  endif()
+
+  if(external)
+    # Make the series available in the build tree.
+    set_property(GLOBAL APPEND PROPERTY
+      _ExternalData_${target}_FETCH "${external}")
+    set_property(GLOBAL APPEND PROPERTY
+      _ExternalData_${target}_LOCAL "${internal}")
+    set("${var_file}" "${top_bin}/${reldata}" PARENT_SCOPE)
+  else()
+    # The whole series is in the source tree.
+    set("${var_file}" "${top_src}/${reldata}" PARENT_SCOPE)
+  endif()
+endfunction()
+
+macro(_ExternalData_arg_associated)
+  # Associated files lie in the same directory.
+  get_filename_component(reldir "${reldata}" PATH)
+  if(reldir)
+    set(reldir "${reldir}/")
+  endif()
+  _ExternalData_exact_regex(reldir_regex "${reldir}")
+
+  # Find files named explicitly.
+  foreach(file ${associated_files})
+    _ExternalData_exact_regex(file_regex "${file}")
+    _ExternalData_arg_find_files("${reldir}${file}" "${reldir_regex}${file_regex}")
+  endforeach()
+
+  # Find files matching the given regular expressions.
+  set(all "")
+  set(sep "")
+  foreach(regex ${associated_regex})
+    set(all "${all}${sep}${reldir_regex}${regex}")
+    set(sep "|")
+  endforeach()
+  _ExternalData_arg_find_files("${reldir}" "${all}")
+endmacro()
+
+macro(_ExternalData_arg_single)
+  # Match only the named data by itself.
+  _ExternalData_exact_regex(data_regex "${reldata}")
+  _ExternalData_arg_find_files("${reldata}" "${data_regex}")
+endmacro()
+
+macro(_ExternalData_arg_series)
+  # Configure series parsing and matching.
+  if(ExternalData_SERIES_PARSE)
+    if(NOT "${ExternalData_SERIES_PARSE}" MATCHES
+        "^\\^\\([^()]*\\)\\([^()]*\\)\\([^()]*\\)\\$$")
+      message(FATAL_ERROR
+        "ExternalData_SERIES_PARSE is set to\n"
+        "  ${ExternalData_SERIES_PARSE}\n"
+        "which is not of the form\n"
+        "  ^(...)(...)(...)$\n")
+    endif()
+    set(series_parse "${ExternalData_SERIES_PARSE}")
+  else()
+    set(series_parse "^(.*)()(\\.[^./]*)$")
+  endif()
+  if(ExternalData_SERIES_MATCH)
+    set(series_match "${ExternalData_SERIES_MATCH}")
+  else()
+    set(series_match "[_.]?[0-9]*")
+  endif()
+
+  # Parse the base, number, and extension components of the series.
+  string(REGEX REPLACE "${series_parse}" "\\1;\\2;\\3" tuple "${reldata}")
+  list(LENGTH tuple len)
+  if(NOT "${len}" EQUAL 3)
+    message(FATAL_ERROR "Data file referenced by argument\n"
+      "  ${arg}\n"
+      "corresponds to path\n"
+      "  ${reldata}\n"
+      "that does not match regular expression\n"
+      "  ${series_parse}")
+  endif()
+  list(GET tuple 0 relbase)
+  list(GET tuple 2 ext)
+
+  # Glob files that might match the series.
+  # Then match match base, number, and extension.
+  _ExternalData_exact_regex(series_base "${relbase}")
+  _ExternalData_exact_regex(series_ext "${ext}")
+  _ExternalData_arg_find_files("${relbase}*${ext}"
+    "${series_base}${series_match}${series_ext}")
+endmacro()
+
+function(_ExternalData_arg_find_files pattern regex)
+  file(GLOB globbed RELATIVE "${top_src}" "${top_src}/${pattern}*")
+  foreach(entry IN LISTS globbed)
+    string(REGEX REPLACE "^(${regex})(\\.md5|)$" "\\1;\\2" tuple "${entry}")
+    list(LENGTH tuple len)
+    if("${len}" EQUAL 2)
+      list(GET tuple 0 relname)
+      list(GET tuple 1 alg)
+      set(name "${top_src}/${relname}")
+      set(file "${top_bin}/${relname}")
+      if(alg)
+        list(APPEND external "${file}|${name}|${alg}")
+      elseif(ExternalData_LINK_CONTENT)
+        _ExternalData_link_content("${name}" alg)
+        list(APPEND external "${file}|${name}|${alg}")
+      else()
+        list(APPEND internal "${file}|${name}")
+      endif()
+      if("${relname}" STREQUAL "${reldata}")
+        set(have_original 1)
+      endif()
+    endif()
+  endforeach()
+  set(external "${external}" PARENT_SCOPE)
+  set(internal "${internal}" PARENT_SCOPE)
+  set(have_original "${have_original}" PARENT_SCOPE)
+endfunction()
+
+#-----------------------------------------------------------------------------
+# Private script mode interface
+
+if(CMAKE_GENERATOR OR NOT ExternalData_ACTION)
+  return()
+endif()
+
+if(ExternalData_CONFIG)
+  include(${ExternalData_CONFIG})
+endif()
+if(NOT ExternalData_URL_TEMPLATES)
+  message(FATAL_ERROR "No ExternalData_URL_TEMPLATES set!")
+endif()
+
+function(_ExternalData_link_or_copy src dst)
+  # Create a temporary file first.
+  get_filename_component(dst_dir "${dst}" PATH)
+  file(MAKE_DIRECTORY "${dst_dir}")
+  string(RANDOM LENGTH 6 random)
+  set(tmp "${dst}.tmp${random}")
+  if(UNIX)
+    # Create a symbolic link.
+    set(tgt "${src}")
+    if(relative_top)
+      # Use relative path if files are close enough.
+      file(RELATIVE_PATH relsrc "${relative_top}" "${src}")
+      file(RELATIVE_PATH relfile "${relative_top}" "${dst}")
+      if(NOT IS_ABSOLUTE "${relsrc}" AND NOT "${relsrc}" MATCHES "^\\.\\./" AND
+          NOT IS_ABSOLUTE "${reldst}" AND NOT "${reldst}" MATCHES "^\\.\\./")
+        file(RELATIVE_PATH tgt "${dst_dir}" "${src}")
+      endif()
+    endif()
+    execute_process(COMMAND "${CMAKE_COMMAND}" -E create_symlink "${tgt}" "${tmp}" RESULT_VARIABLE result)
+  else()
+    # Create a copy.
+    execute_process(COMMAND "${CMAKE_COMMAND}" -E copy "${src}" "${tmp}" RESULT_VARIABLE result)
+  endif()
+  if(result)
+    file(REMOVE "${tmp}")
+    message(FATAL_ERROR "Failed to create\n  ${tmp}\nfrom\n  ${obj}")
+  endif()
+
+  # Atomically create/replace the real destination.
+  file(RENAME "${tmp}" "${dst}")
+endfunction()
+
+function(_ExternalData_download_file url file err_var msg_var)
+  set(retry 3)
+  while(retry)
+    math(EXPR retry "${retry} - 1")
+    if("${CMAKE_VERSION}" VERSION_GREATER 2.8.4.20110602)
+      if(ExternalData_TIMEOUT_INACTIVITY)
+        set(inactivity_timeout INACTIVITY_TIMEOUT ${ExternalData_TIMEOUT_INACTIVITY})
+      elseif(NOT "${ExternalData_TIMEOUT_INACTIVITY}" EQUAL 0)
+        set(inactivity_timeout INACTIVITY_TIMEOUT 60)
+      else()
+        set(inactivity_timeout "")
+      endif()
+    else()
+      set(inactivity_timeout "")
+    endif()
+    if(ExternalData_TIMEOUT_ABSOLUTE)
+      set(absolute_timeout TIMEOUT ${ExternalData_TIMEOUT_ABSOLUTE})
+    elseif(NOT "${ExternalData_TIMEOUT_ABSOLUTE}" EQUAL 0)
+      set(absolute_timeout TIMEOUT 300)
+    else()
+      set(absolute_timeout "")
+    endif()
+    file(DOWNLOAD "${url}" "${file}" STATUS status ${inactivity_timeout} ${absolute_timeout} SHOW_PROGRESS)
+    list(GET status 0 err)
+    list(GET status 1 msg)
+    if(NOT err OR NOT "${msg}" MATCHES "partial|timeout")
+      break()
+    elseif(retry)
+      message(STATUS "[download terminated: ${msg}, retries left: ${retry}]")
+    endif()
+  endwhile()
+  set("${err_var}" "${err}" PARENT_SCOPE)
+  set("${msg_var}" "${msg}" PARENT_SCOPE)
+endfunction()
+
+function(_ExternalData_download_object name hash algo var_obj)
+  set(obj "${ExternalData_OBJECT_DIR}/${algo}/${hash}")
+  if(EXISTS "${obj}")
+    message(STATUS "Found object: \"${obj}\"")
+    set("${var_obj}" "${obj}" PARENT_SCOPE)
+    return()
+  endif()
+
+  string(RANDOM LENGTH 6 random)
+  set(tmp "${obj}.tmp${random}")
+  set(found 0)
+  set(tried "")
+  foreach(url_template IN LISTS ExternalData_URL_TEMPLATES)
+    string(REPLACE "%(hash)" "${hash}" url_tmp "${url_template}")
+    string(REPLACE "%(algo)" "${algo}" url "${url_tmp}")
+    message(STATUS "Fetching \"${url}\"")
+    _ExternalData_download_file("${url}" "${tmp}" err errMsg)
+    set(tried "${tried}\n  ${url}")
+    if(err)
+      set(tried "${tried} (${errMsg})")
+    else()
+      # Verify downloaded object.
+      _ExternalData_compute_hash(dl_hash "${algo}" "${tmp}")
+      if("${dl_hash}" STREQUAL "${hash}")
+        set(found 1)
+        break()
+      else()
+        set(tried "${tried} (wrong hash ${algo}=${dl_hash})")
+      endif()
+    endif()
+    file(REMOVE "${tmp}")
+  endforeach()
+
+  get_filename_component(dir "${name}" PATH)
+  set(staged "${dir}/.ExternalData_${algo}_${hash}")
+
+  if(found)
+    file(RENAME "${tmp}" "${obj}")
+    message(STATUS "Downloaded object: \"${obj}\"")
+  elseif(EXISTS "${staged}")
+    set(obj "${staged}")
+    message(STATUS "Staged object: \"${obj}\"")
+  else()
+    message(FATAL_ERROR "Object ${algo}=${hash} not found at:${tried}")
+  endif()
+
+  set("${var_obj}" "${obj}" PARENT_SCOPE)
+endfunction()
+
+if("${ExternalData_ACTION}" STREQUAL "fetch")
+  foreach(v ExternalData_OBJECT_DIR file name ext)
+    if(NOT DEFINED "${v}")
+      message(FATAL_ERROR "No \"-D${v}=\" value provided!")
+    endif()
+  endforeach()
+
+  file(READ "${name}${ext}" hash)
+  string(STRIP "${hash}" hash)
+
+  if("${ext}" STREQUAL ".md5")
+    set(algo "MD5")
+  else()
+    message(FATAL_ERROR "Unknown hash algorithm extension \"${ext}\"")
+  endif()
+
+  _ExternalData_download_object("${name}" "${hash}" "${algo}" obj)
+
+  # Check if file already corresponds to the object.
+  set(file_up_to_date 0)
+  if(EXISTS "${file}" AND EXISTS "${file}${ext}")
+    file(READ "${file}${ext}" f_hash)
+    string(STRIP "${f_hash}" f_hash)
+    if("${f_hash}" STREQUAL "${hash}")
+      #message(STATUS "File already corresponds to object")
+      set(file_up_to_date 1)
+    endif()
+  endif()
+
+  if(file_up_to_date)
+    # Touch the file to convince the build system it is up to date.
+    execute_process(COMMAND "${CMAKE_COMMAND}" -E touch "${file}")
+  else()
+    _ExternalData_link_or_copy("${obj}" "${file}")
+  endif()
+
+  # Atomically update the hash/timestamp file to record the object referenced.
+  _ExternalData_atomic_write("${file}${ext}" "${hash}\n")
+elseif("${ExternalData_ACTION}" STREQUAL "local")
+  foreach(v file name)
+    if(NOT DEFINED "${v}")
+      message(FATAL_ERROR "No \"-D${v}=\" value provided!")
+    endif()
+  endforeach()
+  _ExternalData_link_or_copy("${name}" "${file}")
+elseif("${ExternalData_ACTION}" STREQUAL "store")
+  foreach(v dir file)
+    if(NOT DEFINED "${v}")
+      message(FATAL_ERROR "No \"-D${v}=\" value provided!")
+    endif()
+  endforeach()
+  if(NOT DEFINED algo)
+    set(algo "MD5")
+  endif()
+  _ExternalData_compute_hash(hash "${algo}" "${file}")
+else()
+  message(FATAL_ERROR "Unknnown ExternalData_ACTION=[${ExternalData_ACTION}]")
+endif()
diff --git a/BRAINSCommonLib/BuildScripts/ExternalData_config.cmake.in b/BRAINSCommonLib/BuildScripts/ExternalData_config.cmake.in
new file mode 100644
index 00000000..dcd9af91
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/ExternalData_config.cmake.in
@@ -0,0 +1,3 @@
+set(ExternalData_URL_TEMPLATES "@ExternalData_URL_TEMPLATES@")
+set(ExternalData_TIMEOUT_INACTIVITY "@ExternalData_TIMEOUT_INACTIVITY@")
+set(ExternalData_TIMEOUT_ABSOLUTE "@ExternalData_TIMEOUT_ABSOLUTE@")
diff --git a/BRAINSCommonLib/BuildScripts/IJMacros.txt b/BRAINSCommonLib/BuildScripts/IJMacros.txt
new file mode 100644
index 00000000..0221a602
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/IJMacros.txt
@@ -0,0 +1,73 @@
+#Macro to find a package and load it
+#(you shouldn't need to modify this code)
+MACRO(LOADPACKAGE Package)
+  SET(Included FALSE)
+  IF(EXISTS "/home/tester/XMLTestParser.py")
+    #If we're in the test environment, check and see if we're being asked for
+    #a specific version of some package.  If so, we'll provide a direct path
+    #instead of counting on CMake to choose the right version.
+    IF(${Package} MATCHES "^ITK.*2[.]2[.]1$")
+      SET(ITK_DIR "/home/tester/ITK2.2.1/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindITK.cmake")
+      INCLUDE(${ITK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(${Package} MATCHES "^ITK.*2[.]2[.]1$")
+    IF(NOT Included AND ${Package} MATCHES "^ITK.*1[.]8[.]1$")
+      SET(ITK_DIR "/home/tester/ITK1.8.1/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindITK.cmake")
+      INCLUDE(${ITK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^ITK.*1[.]8[.]1$")
+    IF(NOT Included AND ${Package} MATCHES "^VTK.*4[.]4$")
+      SET(VTK_DIR "/home/tester/VTK4.4/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindVTK.cmake")
+      INCLUDE(${VTK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK.*4[.]4$")
+    IF(NOT Included AND ${Package} MATCHES "^VTK.*5[.]0$")
+      SET(VTK_DIR "/home/tester/VTK5.0/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindVTK.cmake")
+      INCLUDE(${VTK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK.*5[.]0$")
+    #If we get this far and we still haven't found a match, set it up so the
+    #next block of code has a chance at finding the package.
+    IF(NOT Included AND ${Package} MATCHES "^VTK")
+      SET(Package "VTK")
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK")
+    IF(NOT Included AND ${Package} MATCHES "^ITK")
+      SET(Package "ITK")
+    ENDIF(NOT Included AND ${Package} MATCHES "^ITK")
+  ENDIF(EXISTS "/home/tester/XMLTestParser.py")
+  
+  #no point in executing the code below if we already found the package we're
+  #looking for.
+  IF(NOT Included)
+    FIND_PACKAGE(${Package})
+    IF(${Package}_FOUND)
+      #most packages define a Package_INCLUDE_DIR variable, so we'll check for
+      #that first
+      IF(${Package}_INCLUDE_DIR)
+  INCLUDE(${${Package}_INCLUDE_DIR})
+  SET(Included TRUE)
+      ELSE(${Package}_INCLUDE_DIR)
+  #VTK and ITK prefer to define a Package_USE_FILE, so we need to look for
+  #that too
+  IF(${Package}_USE_FILE)
+    INCLUDE(${${Package}_USE_FILE})
+    SET(Included TRUE)
+  ENDIF(${Package}_USE_FILE)
+      ENDIF(${Package}_INCLUDE_DIR)
+      #then there's some other pesky packages that don't like to define standard
+      #variables at all.  If you're trying to include one of those you might have
+      #to do a little bit of investigating on your own.
+      IF(NOT Included)
+  MESSAGE(FATAL_ERROR "${Package} was found, but couldn't be included.\n
+    Try including it manually out of the FOREACH in the CMakeLists file.\n
+    Look at Find${Package}.cmake in the CMake module directory for clues
+    on what you're supposed to include.  Good luck.")
+      ENDIF(NOT Included)
+    ENDIF(${Package}_FOUND)
+  ENDIF(NOT Included)
+ENDMACRO(LOADPACKAGE)
+
diff --git a/BRAINSCommonLib/BuildScripts/InitialCache-Linux64.cmake b/BRAINSCommonLib/BuildScripts/InitialCache-Linux64.cmake
new file mode 100644
index 00000000..b416f3cc
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/InitialCache-Linux64.cmake
@@ -0,0 +1,30 @@
+## These setting are for building Linux versions of the software
+## The compiler flags are set to allow 64 bit building against the
+## Qt libraries, and have been confirmed to work on
+## compute22.psychiatry.uiowa.edu
+## (Red Hat Enterprise Linux WS release 4 (Nahant Update 8))
+
+
+set (CMAKE_CXX_COMPILER "/usr/bin/g++" CACHE STRING "The g++ compiler")
+set (CMAKE_C_COMPILER "/usr/bin/gcc" CACHE STRING "The gcc compiler")
+set (ARCH "Linux-64" CACHE STRING "")
+set (ABI "Release" CACHE STRING "")
+set (MAKECOMMAND "make -j8" CACHE STRING "" )
+set (CMAKE_MAKE_PROGRAM "/usr/bin/make" CACHE FILEPATH "" )
+set (CVSCOMMAND "/usr/bin/cvs" CACHE FILEPATH "" )
+set (CVS_UPDATE_OPTIONS "-d -A -P -C" CACHE STRING "" )
+set (BUILDNAME "${ARCH}-${ABI}" CACHE STRING "" )
+set (SITE "uiowa" CACHE STRING "" )
+set (CMAKE_SKIP_RPATH "ON" CACHE BOOL "" )
+set (CMAKE_BUILD_TYPE "${ABI}" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O2 -msse -mmmx -msse2 -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_DEBUG "-UNDEBUG -g -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS "-UNDEBUG -g -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_RELEASE "-pipe -DNDEBUG -O2 -msse -mmmx -msse2 -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_DEBUG "-UNDEBUG -g -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS "-UNDEBUG -g -m64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (COVERAGE_COMMAND "/usr/bin/gcov" CACHE FILEPATH "" )
+set (DART_TESTING_TIMEOUT "600" CACHE STRING "" )
+set (MEMORYCHECK_COMMAND "/usr/bin/valgrind" CACHE PATH "" )
+set (MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --quiet --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=100 --verbose --demangle=yes --suppressions=${CTEST_SOURCE_DIRECTORY}/CMake/InsightValgrind.supp" CACHE STRING "" )
+
diff --git a/BRAINSCommonLib/BuildScripts/InitialCache-MacOSX_PROFILE.cmake b/BRAINSCommonLib/BuildScripts/InitialCache-MacOSX_PROFILE.cmake
new file mode 100644
index 00000000..3c221dcd
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/InitialCache-MacOSX_PROFILE.cmake
@@ -0,0 +1,37 @@
+## These setting are for building Macintosh versions of the software
+## The compiler flags are set to allow 64 bit building against the
+## Qt libraries, and have been confirmed to work on 10.6.3 version of
+## MacOSX
+
+## -arch arch
+## Compile for the specified target architecture arch. The allowable values are i386, x86_64, ppc
+## and ppc64. Multiple options work, and direct the compiler to produce "universal" binaries
+## including object code for each architecture specified with -arch. This option only works if
+## assembler and libraries are available for each architecture specified. (APPLE ONLY)
+
+
+
+set (CMAKE_CXX_COMPILER "/usr/bin/g++-4.2" CACHE STRING "The g++ compiler")
+set (CMAKE_C_COMPILER "/usr/bin/gcc-4.2" CACHE STRING "The gcc compiler")
+set (ARCH "Mac64" CACHE STRING "")
+set (ABI "Debug" CACHE STRING "")
+set (MAKECOMMAND "make -j8" CACHE STRING "" )
+set (CMAKE_MAKE_PROGRAM "/usr/bin/make" CACHE FILEPATH "" )
+set (CVSCOMMAND "/usr/bin/cvs" CACHE FILEPATH "" )
+set (CVS_UPDATE_OPTIONS "-d -A -P -C" CACHE STRING "" )
+set (BUILDNAME "${ARCH}-${ABI}" CACHE STRING "" )
+set (SITE "uiowa" CACHE STRING "" )
+set (CMAKE_SKIP_RPATH "ON" CACHE BOOL "" )
+set (CMAKE_BUILD_TYPE "${ABI}" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O2 -msse -mmmx -msse2 -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_DEBUG "-fprofile-arcs -ftest-coverage -pg -UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_RELEASE "-pipe -DNDEBUG -O2 -msse -mmmx -msse2 -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_DEBUG "-fprofile-arcs -ftest-coverage -pg -UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_EXE_LINKER_FLAGS_DEBUG "-fprofile-arcs" CACHE STRING "" )
+set (COVERAGE_COMMAND "/usr/bin/gcov" CACHE FILEPATH "" )
+set (DART_TESTING_TIMEOUT "600" CACHE STRING "" )
+set (MEMORYCHECK_COMMAND "/usr/bin/valgrind" CACHE PATH "" )
+set (MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --quiet --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=100 --verbose --demangle=yes --suppressions=${CTEST_SOURCE_DIRECTORY}/CMake/InsightValgrind.supp" CACHE STRING "" )
+
diff --git a/BRAINSCommonLib/BuildScripts/InitialCache-OSX64.cmake b/BRAINSCommonLib/BuildScripts/InitialCache-OSX64.cmake
new file mode 100644
index 00000000..d7c6f367
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/InitialCache-OSX64.cmake
@@ -0,0 +1,36 @@
+## These setting are for building Macintosh versions of the software
+## The compiler flags are set to allow 64 bit building against the
+## Qt libraries, and have been confirmed to work on 10.6.3 version of
+## MacOSX
+
+## -arch arch
+## Compile for the specified target architecture arch. The allowable values are i386, x86_64, ppc
+## and ppc64. Multiple options work, and direct the compiler to produce "universal" binaries
+## including object code for each architecture specified with -arch. This option only works if
+## assembler and libraries are available for each architecture specified. (APPLE ONLY)
+
+
+
+set (CMAKE_CXX_COMPILER "/usr/bin/g++-4.2" CACHE STRING "The g++ compiler")
+set (CMAKE_C_COMPILER "/usr/bin/gcc-4.2" CACHE STRING "The gcc compiler")
+set (ARCH "Mac64" CACHE STRING "")
+set (ABI "Release" CACHE STRING "")
+set (MAKECOMMAND "make -j8" CACHE STRING "" )
+set (CMAKE_MAKE_PROGRAM "/usr/bin/make" CACHE FILEPATH "" )
+set (CVSCOMMAND "/usr/bin/cvs" CACHE FILEPATH "" )
+set (CVS_UPDATE_OPTIONS "-d -A -P -C" CACHE STRING "" )
+set (BUILDNAME "${ARCH}-${ABI}" CACHE STRING "" )
+set (SITE "uiowa" CACHE STRING "" )
+set (CMAKE_SKIP_RPATH "ON" CACHE BOOL "" )
+set (CMAKE_BUILD_TYPE "${ABI}" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O2 -msse -mmmx -msse2 -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS_DEBUG "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_CXX_FLAGS "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_RELEASE "-pipe -DNDEBUG -O2 -msse -mmmx -msse2 -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS_DEBUG "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (CMAKE_C_FLAGS "-UNDEBUG -g -m64 -arch x86_64 -Wall -W -Wshadow -Wcast-qual -Wwrite-strings" CACHE STRING "" )
+set (COVERAGE_COMMAND "/usr/bin/gcov" CACHE FILEPATH "" )
+set (DART_TESTING_TIMEOUT "600" CACHE STRING "" )
+set (MEMORYCHECK_COMMAND "/usr/bin/valgrind" CACHE PATH "" )
+set (MEMORYCHECK_COMMAND_OPTIONS "--trace-children=yes --quiet --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=100 --verbose --demangle=yes --suppressions=${CTEST_SOURCE_DIRECTORY}/CMake/InsightValgrind.supp" CACHE STRING "" )
+
diff --git a/BRAINSCommonLib/BuildScripts/License.txt b/BRAINSCommonLib/BuildScripts/License.txt
new file mode 100644
index 00000000..a189dbeb
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/License.txt
@@ -0,0 +1,9 @@
+Copyright (c) 1992-2010 University of Iowa. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+• Neither the name of the University of Iowa nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+• This software designed to be used only for research purposes. Clinical applications are not recommended, and this software has NOT been evaluated by the United States FDA for any clinical use.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
diff --git a/BRAINSCommonLib/BuildScripts/LocalExternalProjectDefinitionPreCMake2_8_4.cmake b/BRAINSCommonLib/BuildScripts/LocalExternalProjectDefinitionPreCMake2_8_4.cmake
new file mode 100644
index 00000000..2744b137
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/LocalExternalProjectDefinitionPreCMake2_8_4.cmake
@@ -0,0 +1,968 @@
+# - Create custom targets to build projects in external trees
+# The 'ExternalProject_Add' function creates a custom target to drive
+# download, update/patch, configure, build, install and test steps of an
+# external project:
+#  ExternalProject_Add(    # Name for custom target
+#    [DEPENDS projects...]       # Targets on which the project depends
+#    [PREFIX dir]                # Root dir for entire project
+#    [LIST_SEPARATOR sep]        # Sep to be replaced by ; in cmd lines
+#    [TMP_DIR dir]               # Directory to store temporary files
+#    [STAMP_DIR dir]             # Directory to store step timestamps
+#   #--Download step--------------
+#    [DOWNLOAD_DIR dir]          # Directory to store downloaded files
+#    [DOWNLOAD_COMMAND cmd...]   # Command to download source tree
+#    [CVS_REPOSITORY cvsroot]    # CVSROOT of CVS repository
+#    [CVS_MODULE mod]            # Module to checkout from CVS repo
+#    [CVS_TAG tag]               # Tag to checkout from CVS repo
+#    [SVN_REPOSITORY url]        # URL of Subversion repo
+#    [SVN_REVISION rev]          # Revision to checkout from Subversion repo
+#    [URL /.../src.tgz]          # Full path or URL of source
+#   #--Update/Patch step----------
+#    [UPDATE_COMMAND cmd...]     # Source work-tree update command
+#    [PATCH_COMMAND cmd...]      # Command to patch downloaded source
+#   #--Configure step-------------
+#    [SOURCE_DIR dir]            # Source dir to be used for build
+#    [CONFIGURE_COMMAND cmd...]  # Build tree configuration command
+#    [CMAKE_COMMAND /.../cmake]  # Specify alternative cmake executable
+#    [CMAKE_GENERATOR gen]       # Specify generator for native build
+#    [CMAKE_ARGS args...]        # Arguments to CMake command line
+#   #--Build step-----------------
+#    [BINARY_DIR dir]            # Specify build dir location
+#    [BUILD_COMMAND cmd...]      # Command to drive the native build
+#    [BUILD_IN_SOURCE 1]         # Use source dir for build dir
+#   #--Install step---------------
+#    [INSTALL_DIR dir]           # Installation prefix
+#    [INSTALL_COMMAND cmd...]    # Command to drive install after build
+#   #--Test step---------------
+#    [TEST_BEFORE_INSTALL 1]     # Add test step executed before install step
+#    [TEST_AFTER_INSTALL 1]      # Add test step executed after install step
+#    [TEST_COMMAND cmd...]       # Command to drive test
+#    )
+# The *_DIR options specify directories for the project, with default
+# directories computed as follows.
+# If the PREFIX option is given to ExternalProject_Add() or the EP_PREFIX
+# directory property is set, then an external project is built and installed
+# under the specified prefix:
+#   TMP_DIR      = /tmp
+#   STAMP_DIR    = /src/-stamp
+#   DOWNLOAD_DIR = /src
+#   SOURCE_DIR   = /src/
+#   BINARY_DIR   = /src/-build
+#   INSTALL_DIR  = 
+# Otherwise, if the EP_BASE directory property is set then components
+# of an external project are stored under the specified base:
+#   TMP_DIR      = /tmp/
+#   STAMP_DIR    = /Stamp/
+#   DOWNLOAD_DIR = /Download/
+#   SOURCE_DIR   = /Source/
+#   BINARY_DIR   = /Build/
+#   INSTALL_DIR  = /Install/
+# If no PREFIX, EP_PREFIX, or EP_BASE is specified then the default
+# is to set PREFIX to "-prefix".
+# Relative paths are interpreted with respect to the build directory
+# corresponding to the source directory in which ExternalProject_Add is
+# invoked.
+#
+# If SOURCE_DIR is explicitly set to an existing directory the project
+# will be built from it.
+# Otherwise a download step must be specified using one of the
+# DOWNLOAD_COMMAND, CVS_*, SVN_*, or URL options.
+# The URL option may refer locally to a directory or source tarball,
+# or refer to a remote tarball (e.g. http://.../src.tgz).
+#
+# The 'ExternalProject_Add_Step' function adds a custom step to an external
+# project:
+#  ExternalProject_Add_Step(  # Names of project and custom step
+#    [COMMAND cmd...]        # Command line invoked by this step
+#    [COMMENT "text..."]     # Text printed when step executes
+#    [DEPENDEES steps...]    # Steps on which this step depends
+#    [DEPENDERS steps...]    # Steps that depend on this step
+#    [DEPENDS files...]      # Files on which this step depends
+#    [ALWAYS 1]              # No stamp file, step always runs
+#    [WORKING_DIRECTORY dir] # Working directory for command
+#    )
+# The command line, comment, and working directory of every standard
+# and custom step is processed to replace tokens
+# ,
+# ,
+# ,
+# and 
+# with corresponding property values.
+#
+# The 'ExternalProject_Get_Property' function retrieves external project
+# target properties:
+#  ExternalProject_Get_Property( [prop1 [prop2 [...]]])
+# It stores property values in variables of the same name.
+# Property names correspond to the keyword argument names of
+# 'ExternalProject_Add'.
+
+#=============================================================================
+# Copyright 2008-2009 Kitware, Inc.
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distributed this file outside of CMake, substitute the full
+#  License text for the above reference.)
+
+# Pre-compute a regex to match documented keywords for each command.
+file(STRINGS "${CMAKE_CURRENT_LIST_FILE}" lines LIMIT_COUNT 100
+     REGEX "^#  (  \\[[A-Z_]+ [^]]*\\] +#.*$|[A-Za-z_]+\\()")
+foreach(line IN LISTS lines)
+  if("${line}" MATCHES "^#  [A-Za-z_]+\\(")
+    if(_ep_func)
+      set(_ep_keywords_${_ep_func} "${_ep_keywords_${_ep_func}})$")
+    endif()
+    string(REGEX REPLACE "^#  ([A-Za-z_]+)\\(.*" "\\1" _ep_func "${line}")
+    #message("function [${_ep_func}]")
+    set(_ep_keywords_${_ep_func} "^(")
+    set(_ep_keyword_sep)
+  else()
+    string(REGEX REPLACE "^#    \\[([A-Z_]+) .*" "\\1" _ep_key "${line}")
+    #message("  keyword [${_ep_key}]")
+    set(_ep_keywords_${_ep_func}
+      "${_ep_keywords_${_ep_func}}${_ep_keyword_sep}${_ep_key}")
+    set(_ep_keyword_sep "|")
+  endif()
+endforeach()
+if(_ep_func)
+  set(_ep_keywords_${_ep_func} "${_ep_keywords_${_ep_func}})$")
+endif()
+
+
+function(_ep_parse_arguments f name ns args)
+  # Transfer the arguments to this function into target properties for the
+  # new custom target we just added so that we can set up all the build steps
+  # correctly based on target properties.
+  #
+  # We loop through ARGN and consider the namespace starting with an
+  # upper-case letter followed by at least two more upper-case letters
+  # or underscores to be keywords.
+  set(key)
+
+  foreach(arg IN LISTS args)
+    set(is_value 1)
+
+    if(arg MATCHES "^[A-Z][A-Z_][A-Z_]+$" AND
+        NOT ((arg STREQUAL "${key}") AND (key STREQUAL "COMMAND")) AND
+        NOT arg MATCHES "^(TRUE|FALSE)$")
+      if(_ep_keywords_${f} AND arg MATCHES "${_ep_keywords_${f}}")
+        set(is_value 0)
+      else()
+        if(NOT (key STREQUAL "COMMAND")
+          AND NOT (key STREQUAL "CVS_MODULE")
+          AND NOT (key STREQUAL "DEPENDS")
+          )
+          message(AUTHOR_WARNING "unknown ${f} keyword: ${arg}")
+        endif()
+      endif()
+    endif()
+
+    if(is_value)
+      if(key)
+        # Value
+        if(NOT arg STREQUAL "")
+          set_property(TARGET ${name} APPEND PROPERTY ${ns}${key} "${arg}")
+        else()
+          get_property(have_key TARGET ${name} PROPERTY ${ns}${key} SET)
+          if(have_key)
+            get_property(value TARGET ${name} PROPERTY ${ns}${key})
+            set_property(TARGET ${name} PROPERTY ${ns}${key} "${value};${arg}")
+          else()
+            set_property(TARGET ${name} PROPERTY ${ns}${key} "${arg}")
+          endif()
+        endif()
+      else()
+        # Missing Keyword
+        message(AUTHOR_WARNING "value '${arg}' with no previous keyword in ${f}")
+      endif()
+    else()
+      set(key "${arg}")
+    endif()
+  endforeach()
+endfunction(_ep_parse_arguments)
+
+
+define_property(DIRECTORY PROPERTY "EP_BASE" INHERITED
+  BRIEF_DOCS "Base directory for External Project storage."
+  FULL_DOCS
+  "See documentation of the ExternalProject_Add() function in the "
+  "ExternalProject module."
+  )
+
+define_property(DIRECTORY PROPERTY "EP_PREFIX" INHERITED
+  BRIEF_DOCS "Top prefix for External Project storage."
+  FULL_DOCS
+  "See documentation of the ExternalProject_Add() function in the "
+  "ExternalProject module."
+  )
+
+
+function(_ep_write_downloadfile_script script_filename remote local timeout)
+  if(NOT timeout)
+    set(timeout 30)
+  endif()
+
+  file(WRITE ${script_filename}
+"message(STATUS \"downloading...
+     src='${remote}'
+     dst='${local}'\")
+
+file(DOWNLOAD
+  \"${remote}\"
+  \"${local}\"
+  TIMEOUT ${timeout}
+  STATUS status
+  LOG log)
+
+list(GET status 0 status_code)
+list(GET status 1 status_string)
+
+if(NOT status_code EQUAL 0)
+  message(FATAL_ERROR \"error: downloading '${remote}' failed
+  status_code: \${status_code}
+  status_string: \${status_string}
+  log: \${log}
+\")
+endif()
+
+message(STATUS \"downloading... done\")
+"
+)
+
+endfunction(_ep_write_downloadfile_script)
+
+
+function(_ep_write_extractfile_script script_filename filename tmp directory)
+  set(args "")
+
+  if(filename MATCHES ".tar$")
+    set(args xf)
+  endif()
+
+  if(filename MATCHES ".tgz$")
+    set(args xfz)
+  endif()
+
+  if(filename MATCHES ".tar.gz$")
+    set(args xfz)
+  endif()
+
+  if(args STREQUAL "")
+    message(SEND_ERROR "error: do not know how to extract '${filename}' -- known types are .tar, .tgz and .tar.gz")
+    return()
+  endif()
+
+  file(WRITE ${script_filename}
+"# Make file names absolute:
+#
+get_filename_component(filename \"${filename}\" ABSOLUTE)
+get_filename_component(tmp \"${tmp}\" ABSOLUTE)
+get_filename_component(directory \"${directory}\" ABSOLUTE)
+
+message(STATUS \"extracting...
+     src='\${filename}'
+     dst='\${directory}'\")
+
+# Prepare a space for extracting:
+#
+set(i 1)
+while(EXISTS \"\${tmp}/extract\${i}\")
+  math(EXPR i \"\${i} + 1\")
+endwhile()
+set(ut_dir \"\${tmp}/extract\${i}\")
+file(MAKE_DIRECTORY \"\${ut_dir}\")
+
+# Extract it:
+#
+message(STATUS \"extracting... [tar ${args}]\")
+execute_process(COMMAND \${CMAKE_COMMAND} -E tar ${args} \${filename}
+  WORKING_DIRECTORY \${ut_dir}
+  RESULT_VARIABLE rv)
+
+if(NOT rv EQUAL 0)
+  message(STATUS \"extracting... [error clean up]\")
+  file(REMOVE_RECURSE \"\${ut_dir}\")
+  message(FATAL_ERROR \"error: extract of '\${filename}' failed\")
+endif()
+
+# Analyze what came out of the tar file:
+#
+message(STATUS \"extracting... [analysis]\")
+file(GLOB contents \"\${ut_dir}/*\")
+list(LENGTH contents n)
+if(NOT n EQUAL 1 OR NOT IS_DIRECTORY \"\${contents}\")
+  set(contents \"\${ut_dir}\")
+endif()
+
+# Copy \"the one\" directory to the final directory:
+#
+message(STATUS \"extracting... [copy]\")
+file(COPY \"\${contents}/\" DESTINATION \${directory})
+
+# Clean up:
+#
+message(STATUS \"extracting... [clean up]\")
+file(REMOVE_RECURSE \"\${ut_dir}\")
+
+message(STATUS \"extracting... done\")
+"
+)
+
+endfunction(_ep_write_extractfile_script)
+
+
+function(_ep_set_directories name)
+  get_property(prefix TARGET ${name} PROPERTY _EP_PREFIX)
+  if(NOT prefix)
+    get_property(prefix DIRECTORY PROPERTY EP_PREFIX)
+    if(NOT prefix)
+      get_property(base DIRECTORY PROPERTY EP_BASE)
+      if(NOT base)
+        set(prefix "${name}-prefix")
+      endif()
+    endif()
+  endif()
+  if(prefix)
+    set(tmp_default "${prefix}/tmp")
+    set(download_default "${prefix}/src")
+    set(source_default "${prefix}/src/${name}")
+    set(binary_default "${prefix}/src/${name}-build")
+    set(stamp_default "${prefix}/src/${name}-stamp")
+    set(install_default "${prefix}")
+  else() # assert(base)
+    set(tmp_default "${base}/tmp/${name}")
+    set(download_default "${base}/Download/${name}")
+    set(source_default "${base}/Source/${name}")
+    set(binary_default "${base}/Build/${name}")
+    set(stamp_default "${base}/Stamp/${name}")
+    set(install_default "${base}/Install/${name}")
+  endif()
+  get_property(build_in_source TARGET ${name} PROPERTY _EP_BUILD_IN_SOURCE)
+  if(build_in_source)
+    get_property(have_binary_dir TARGET ${name} PROPERTY _EP_BINARY_DIR SET)
+    if(have_binary_dir)
+      message(FATAL_ERROR
+        "External project ${name} has both BINARY_DIR and BUILD_IN_SOURCE!")
+    endif()
+  endif()
+  set(top "${CMAKE_CURRENT_BINARY_DIR}")
+  set(places stamp download source binary install tmp)
+  foreach(var ${places})
+    string(TOUPPER "${var}" VAR)
+    get_property(${var}_dir TARGET ${name} PROPERTY _EP_${VAR}_DIR)
+    if(NOT ${var}_dir)
+      set(${var}_dir "${${var}_default}")
+    endif()
+    if(NOT IS_ABSOLUTE "${${var}_dir}")
+      get_filename_component(${var}_dir "${top}/${${var}_dir}" ABSOLUTE)
+    endif()
+    set_property(TARGET ${name} PROPERTY _EP_${VAR}_DIR "${${var}_dir}")
+  endforeach()
+  if(build_in_source)
+    get_property(source_dir TARGET ${name} PROPERTY _EP_SOURCE_DIR)
+    set_property(TARGET ${name} PROPERTY _EP_BINARY_DIR "${source_dir}")
+  endif()
+
+  # Make the directories at CMake configure time *and* add a custom command
+  # to make them at build time. They need to exist at makefile generation
+  # time for Borland make and wmake so that CMake may generate makefiles
+  # with "cd C:\short\paths\with\no\spaces" commands in them.
+  #
+  # Additionally, the add_custom_command is still used in case somebody
+  # removes one of the necessary directories and tries to rebuild without
+  # re-running cmake.
+  foreach(var ${places})
+    string(TOUPPER "${var}" VAR)
+    get_property(dir TARGET ${name} PROPERTY _EP_${VAR}_DIR)
+    file(MAKE_DIRECTORY "${dir}")
+    if(NOT EXISTS "${dir}")
+      message(FATAL_ERROR "dir '${dir}' does not exist after file(MAKE_DIRECTORY)")
+    endif()
+  endforeach()
+endfunction(_ep_set_directories)
+
+
+function(ExternalProject_Get_Property name)
+  foreach(var ${ARGN})
+    string(TOUPPER "${var}" VAR)
+    get_property(${var} TARGET ${name} PROPERTY _EP_${VAR})
+    if(NOT ${var})
+      message(FATAL_ERROR "External project \"${name}\" has no ${var}")
+    endif()
+    set(${var} "${${var}}" PARENT_SCOPE)
+  endforeach()
+endfunction(ExternalProject_Get_Property)
+
+
+function(_ep_get_configure_command_id name cfg_cmd_id_var)
+  get_target_property(cmd ${name} _EP_CONFIGURE_COMMAND)
+
+  if(cmd STREQUAL "")
+    # Explicit empty string means no configure step for this project
+    set(${cfg_cmd_id_var} "none" PARENT_SCOPE)
+  else()
+    if(NOT cmd)
+      # Default is "use cmake":
+      set(${cfg_cmd_id_var} "cmake" PARENT_SCOPE)
+    else()
+      # Otherwise we have to analyze the value:
+      if(cmd MATCHES "^[^;]*/configure")
+        set(${cfg_cmd_id_var} "configure" PARENT_SCOPE)
+      elseif(cmd MATCHES "^[^;]*/cmake" AND NOT cmd MATCHES ";-[PE];")
+        set(${cfg_cmd_id_var} "cmake" PARENT_SCOPE)
+      elseif(cmd MATCHES "config")
+        set(${cfg_cmd_id_var} "configure" PARENT_SCOPE)
+      else()
+        set(${cfg_cmd_id_var} "unknown:${cmd}" PARENT_SCOPE)
+      endif()
+    endif()
+  endif()
+endfunction(_ep_get_configure_command_id)
+
+
+function(_ep_get_build_command name step cmd_var)
+  set(cmd "${${cmd_var}}")
+  if(NOT cmd)
+    set(args)
+    _ep_get_configure_command_id(${name} cfg_cmd_id)
+    if(cfg_cmd_id STREQUAL "cmake")
+      # CMake project.  Select build command based on generator.
+      get_target_property(cmake_generator ${name} _EP_CMAKE_GENERATOR)
+      if("${cmake_generator}" MATCHES "Make" AND
+          "${cmake_generator}" STREQUAL "${CMAKE_GENERATOR}")
+        # The project uses the same Makefile generator.  Use recursive make.
+        set(cmd "$(MAKE)")
+        if(step STREQUAL "INSTALL")
+          set(args install)
+        endif()
+        if(step STREQUAL "TEST")
+          set(args test)
+        endif()
+      else()
+        # Drive the project with "cmake --build".
+        get_target_property(cmake_command ${name} _EP_CMAKE_COMMAND)
+        if(cmake_command)
+          set(cmd "${cmake_command}")
+        else()
+          set(cmd "${CMAKE_COMMAND}")
+        endif()
+        set(args --build ${binary_dir} --config ${CMAKE_CFG_INTDIR})
+        if(step STREQUAL "INSTALL")
+          list(APPEND args --target install)
+        endif()
+        # But for "TEST" drive the project with corresponding "ctest".
+        if(step STREQUAL "TEST")
+          string(REGEX REPLACE "^(.*/)cmake([^/]*)$" "\\1ctest\\2" cmd "${cmd}")
+          set(args "")
+        endif()
+      endif()
+    else() # if(cfg_cmd_id STREQUAL "configure")
+      # Non-CMake project.  Guess "make" and "make install" and "make test".
+      set(cmd "make")
+      if(step STREQUAL "INSTALL")
+        set(args install)
+      endif()
+      if(step STREQUAL "TEST")
+        set(args test)
+      endif()
+    endif()
+
+    # Use user-specified arguments instead of default arguments, if any.
+    get_property(have_args TARGET ${name} PROPERTY _EP_${step}_ARGS SET)
+    if(have_args)
+      get_target_property(args ${name} _EP_${step}_ARGS)
+    endif()
+
+    list(APPEND cmd ${args})
+  endif()
+
+  set(${cmd_var} "${cmd}" PARENT_SCOPE)
+endfunction(_ep_get_build_command)
+
+
+# This module used to use "/${CMAKE_CFG_INTDIR}" directly and produced
+# makefiles with "/./" in paths for custom command dependencies. Which
+# resulted in problems with parallel make -j invocations.
+#
+# This function was added so that the suffix (search below for ${cfgdir}) is
+# only set to "/${CMAKE_CFG_INTDIR}" when ${CMAKE_CFG_INTDIR} is not going to
+# be "." (multi-configuration build systems like Visual Studio and Xcode...)
+#
+function(_ep_get_configuration_subdir_suffix suffix_var)
+  set(suffix "")
+  if(CMAKE_CONFIGURATION_TYPES)
+    set(suffix "/${CMAKE_CFG_INTDIR}")
+  endif()
+  set(${suffix_var} "${suffix}" PARENT_SCOPE)
+endfunction(_ep_get_configuration_subdir_suffix)
+
+
+function(ExternalProject_Add_Step name step)
+  set(cmf_dir ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles)
+  ExternalProject_Get_Property(${name} stamp_dir)
+
+  _ep_get_configuration_subdir_suffix(cfgdir)
+
+  add_custom_command(APPEND
+    OUTPUT ${cmf_dir}${cfgdir}/${name}-complete
+    DEPENDS ${stamp_dir}${cfgdir}/${name}-${step}
+    )
+  _ep_parse_arguments(ExternalProject_Add_Step
+                       ${name} _EP_${step}_ "${ARGN}")
+
+  # Steps depending on this step.
+  get_property(dependers TARGET ${name} PROPERTY _EP_${step}_DEPENDERS)
+  foreach(depender IN LISTS dependers)
+    add_custom_command(APPEND
+      OUTPUT ${stamp_dir}${cfgdir}/${name}-${depender}
+      DEPENDS ${stamp_dir}${cfgdir}/${name}-${step}
+      )
+  endforeach()
+
+  # Dependencies on files.
+  get_property(depends TARGET ${name} PROPERTY _EP_${step}_DEPENDS)
+
+  # Dependencies on steps.
+  get_property(dependees TARGET ${name} PROPERTY _EP_${step}_DEPENDEES)
+  foreach(dependee IN LISTS dependees)
+    list(APPEND depends ${stamp_dir}${cfgdir}/${name}-${dependee})
+  endforeach()
+
+  # The command to run.
+  get_property(command TARGET ${name} PROPERTY _EP_${step}_COMMAND)
+  if(command)
+    set(comment "Performing ${step} step for '${name}'")
+  else()
+    set(comment "No ${step} step for '${name}'")
+  endif()
+  get_property(work_dir TARGET ${name} PROPERTY _EP_${step}_WORKING_DIRECTORY)
+
+  # Replace list separators.
+  get_property(sep TARGET ${name} PROPERTY _EP_LIST_SEPARATOR)
+  if(sep AND command)
+    string(REPLACE "${sep}" "\\;" command "${command}")
+  endif()
+
+  # Replace location tags.
+  foreach(var comment command work_dir)
+    if(${var})
+      foreach(dir SOURCE_DIR BINARY_DIR INSTALL_DIR TMP_DIR)
+        get_property(val TARGET ${name} PROPERTY _EP_${dir})
+        string(REPLACE "<${dir}>" "${val}" ${var} "${${var}}")
+      endforeach()
+    endif()
+  endforeach()
+
+  # Custom comment?
+  get_property(comment_set TARGET ${name} PROPERTY _EP_${step}_COMMENT SET)
+  if(comment_set)
+    get_property(comment TARGET ${name} PROPERTY _EP_${step}_COMMENT)
+  endif()
+
+  # Run every time?
+  get_property(always TARGET ${name} PROPERTY _EP_${step}_ALWAYS)
+  if(always)
+    set_property(SOURCE ${stamp_dir}${cfgdir}/${name}-${step} PROPERTY SYMBOLIC 1)
+    set(touch)
+  else()
+    set(touch ${CMAKE_COMMAND} -E touch ${stamp_dir}${cfgdir}/${name}-${step})
+  endif()
+
+  add_custom_command(
+    OUTPUT ${stamp_dir}${cfgdir}/${name}-${step}
+    COMMENT ${comment}
+    COMMAND ${command}
+    COMMAND ${touch}
+    DEPENDS ${depends}
+    WORKING_DIRECTORY ${work_dir}
+    VERBATIM
+    )
+endfunction(ExternalProject_Add_Step)
+
+
+function(_ep_add_mkdir_command name)
+  ExternalProject_Get_Property(${name}
+    source_dir binary_dir install_dir stamp_dir download_dir tmp_dir)
+
+  _ep_get_configuration_subdir_suffix(cfgdir)
+
+  ExternalProject_Add_Step(${name} mkdir
+    COMMENT "Creating directories for '${name}'"
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${source_dir}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${binary_dir}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${install_dir}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${tmp_dir}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${stamp_dir}${cfgdir}
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${download_dir}
+    )
+endfunction(_ep_add_mkdir_command)
+
+
+function(_ep_add_download_command name)
+  ExternalProject_Get_Property(${name} source_dir stamp_dir download_dir tmp_dir)
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_DOWNLOAD_COMMAND SET)
+  get_property(cmd TARGET ${name} PROPERTY _EP_DOWNLOAD_COMMAND)
+  get_property(cvs_repository TARGET ${name} PROPERTY _EP_CVS_REPOSITORY)
+  get_property(svn_repository TARGET ${name} PROPERTY _EP_SVN_REPOSITORY)
+  get_property(url TARGET ${name} PROPERTY _EP_URL)
+
+  # TODO: Perhaps file:// should be copied to download dir before extraction.
+  string(REGEX REPLACE "^file://" "" url "${url}")
+
+  set(depends)
+  set(comment)
+  set(work_dir)
+
+  #  message(WARNING "${name}  source_dir: ${source_dir} download_dir: ${download_dir} tmp_dir: ${tmp_dir} ")
+  #  message(WARNING "${name}  CMD_SET: ${cmd_set} CMD: ${cmd} CVS: ${cvs_repository} SVN: ${svn_repository} URL: ${url} ")
+  if(cmd_set)
+    set(work_dir ${download_dir})
+  elseif(cvs_repository)
+    find_package(CVS)
+    if(NOT CVS_EXECUTABLE)
+      message(FATAL_ERROR "error: could not find cvs for checkout of ${name}")
+    endif()
+
+    get_target_property(cvs_module ${name} _EP_CVS_MODULE)
+    if(NOT cvs_module)
+      message(FATAL_ERROR "error: no CVS_MODULE")
+    endif()
+
+    get_property(cvs_tag TARGET ${name} PROPERTY _EP_CVS_TAG)
+
+    set(repository ${cvs_repository})
+    set(module ${cvs_module})
+    set(tag ${cvs_tag})
+    configure_file(
+      "${CMAKE_ROOT}/Modules/RepositoryInfo.txt.in"
+      "${stamp_dir}/${name}-cvsinfo.txt"
+      @ONLY
+      )
+
+    get_filename_component(src_name "${source_dir}" NAME)
+    get_filename_component(work_dir "${source_dir}" PATH)
+    set(comment "Performing download step (CVS checkout) for '${name}'")
+    set(cmd ${CVS_EXECUTABLE} -d ${cvs_repository} -q co ${cvs_tag} -d ${src_name} ${cvs_module})
+    list(APPEND depends ${stamp_dir}/${name}-cvsinfo.txt)
+  elseif(svn_repository)
+    find_package(Subversion)
+    if(NOT Subversion_SVN_EXECUTABLE)
+      message(FATAL_ERROR "error: could not find svn for checkout of ${name}")
+    endif()
+
+    get_property(svn_revision TARGET ${name} PROPERTY _EP_SVN_REVISION)
+
+    set(repository ${svn_repository})
+    set(module)
+    set(tag ${svn_revision})
+    configure_file(
+      "${CMAKE_ROOT}/Modules/RepositoryInfo.txt.in"
+      "${stamp_dir}/${name}-svninfo.txt"
+      @ONLY
+      )
+
+    get_filename_component(src_name "${source_dir}" NAME)
+    get_filename_component(work_dir "${source_dir}" PATH)
+    set(comment "Performing download step (SVN checkout) for '${name}'")
+    set(cmd ${Subversion_SVN_EXECUTABLE} co ${svn_repository} ${svn_revision} ${src_name})
+    list(APPEND depends ${stamp_dir}/${name}-svninfo.txt)
+  elseif(url)
+    get_filename_component(work_dir "${source_dir}" PATH)
+    set(repository "external project URL")
+    set(module "${url}")
+    set(tag "")
+    configure_file(
+      "${CMAKE_ROOT}/Modules/RepositoryInfo.txt.in"
+      "${stamp_dir}/${name}-urlinfo.txt"
+      @ONLY
+      )
+    list(APPEND depends ${stamp_dir}/${name}-urlinfo.txt)
+    if(IS_DIRECTORY "${url}")
+      get_filename_component(abs_url_dir "${url}" ABSOLUTE)
+      get_filename_component(abs_source_dir "${source_dir}" ABSOLUTE)
+      set(comment "Performing download step (DIR copy) for '${name}'")
+      if ( "${abs_source_dir}" MATCHES "${abs_url_dir}" )
+        #message(WARNING "${abs_source_dir} MATCHES ${abs_url_dir}" )
+        set(cmd ${CMAKE_COMMAND} -E echo "${abs_source_dir} MATCHES ${abs_url_dir}" )
+      else()
+        message(FATAL_ERROR "Trying to remove the ${abs_source_dir} ${abs_source_dir} MATCHES ${abs_url_dir}")
+        set(cmd   ${CMAKE_COMMAND} -E remove_directory ${abs_source_dir}
+          COMMAND ${CMAKE_COMMAND} -E copy_directory ${abs_url_dir} ${abs_source_dir})
+      endif()
+      # TODO: Support other archive formats.
+      file(WRITE "${stamp_dir}/donothing-${name}.cmake" "### DO NOTHING")
+      list(APPEND cmd ${CMAKE_COMMAND} -P ${stamp_dir}/donothing-${name}.cmake)
+    else()
+      if("${url}" MATCHES "^[a-z]+://")
+        # TODO: Should download and extraction be different steps?
+        string(REGEX MATCH "[^/]*$" fname "${url}")
+        if(NOT "${fname}" MATCHES "\\.(tar|tgz|tar\\.gz)$")
+          message(FATAL_ERROR "Could not extract tarball filename from url:\n  ${url}")
+        endif()
+        set(file ${download_dir}/${fname})
+        _ep_write_downloadfile_script("${stamp_dir}/download-${name}.cmake" "${url}" "${file}" "")
+        set(cmd ${CMAKE_COMMAND} -P ${stamp_dir}/download-${name}.cmake
+          COMMAND)
+        set(comment "Performing download step (download and extract) for '${name}'")
+      else()
+        set(file "${url}")
+        set(comment "Performing download step (extract) for '${name}'")
+      endif()
+      # TODO: Support other archive formats.
+      _ep_write_extractfile_script("${stamp_dir}/extract-${name}.cmake" "${file}" "${tmp_dir}" "${source_dir}")
+      list(APPEND cmd ${CMAKE_COMMAND} -P ${stamp_dir}/extract-${name}.cmake)
+    endif()
+  else()
+    if(EXISTS ${source_dir}/CMakeLists.txt)
+       message(WARNING "WARNING: no download info for '${name}' -- using SOURCE_DIR set as ${source_dir}")
+    else()
+       message(SEND_ERROR "error: no download info for '${name}' -- please specify existing SOURCE_DIR or one of URL, CVS_REPOSITORY and CVS_MODULE, SVN_REPOSITORY or DOWNLOAD_COMMAND")
+    endif()
+  endif()
+
+  ExternalProject_Add_Step(${name} download
+    COMMENT ${comment}
+    COMMAND ${cmd}
+    WORKING_DIRECTORY ${work_dir}
+    DEPENDS ${depends}
+    DEPENDEES mkdir
+    )
+endfunction(_ep_add_download_command)
+
+
+function(_ep_add_update_command name)
+  ExternalProject_Get_Property(${name} source_dir)
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_UPDATE_COMMAND SET)
+  get_property(cmd TARGET ${name} PROPERTY _EP_UPDATE_COMMAND)
+  get_property(cvs_repository TARGET ${name} PROPERTY _EP_CVS_REPOSITORY)
+  get_property(svn_repository TARGET ${name} PROPERTY _EP_SVN_REPOSITORY)
+
+  set(work_dir)
+  set(comment)
+  set(always)
+
+  if(cmd_set)
+    set(work_dir ${source_dir})
+  elseif(cvs_repository)
+    if(NOT CVS_EXECUTABLE)
+      message(FATAL_ERROR "error: could not find cvs for update of ${name}")
+    endif()
+    set(work_dir ${source_dir})
+    set(comment "Performing update step (CVS update) for '${name}'")
+    get_property(cvs_tag TARGET ${name} PROPERTY _EP_CVS_TAG)
+    set(cmd ${CVS_EXECUTABLE} -d ${cvs_repository} -q up -dP ${cvs_tag})
+    set(always 1)
+  elseif(svn_repository)
+    if(NOT Subversion_SVN_EXECUTABLE)
+      message(FATAL_ERROR "error: could not find svn for update of ${name}")
+    endif()
+    set(work_dir ${source_dir})
+    set(comment "Performing update step (SVN update) for '${name}'")
+    get_property(svn_revision TARGET ${name} PROPERTY _EP_SVN_REVISION)
+    set(cmd ${Subversion_SVN_EXECUTABLE} up ${svn_revision})
+    set(always 1)
+  endif()
+
+  ExternalProject_Add_Step(${name} update
+    COMMENT ${comment}
+    COMMAND ${cmd}
+    ALWAYS ${always}
+    WORKING_DIRECTORY ${work_dir}
+    DEPENDEES download
+    )
+endfunction(_ep_add_update_command)
+
+
+function(_ep_add_patch_command name)
+  ExternalProject_Get_Property(${name} source_dir)
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_PATCH_COMMAND SET)
+  get_property(cmd TARGET ${name} PROPERTY _EP_PATCH_COMMAND)
+
+  set(work_dir)
+
+  if(cmd_set)
+    set(work_dir ${source_dir})
+  endif()
+
+  ExternalProject_Add_Step(${name} patch
+    COMMAND ${cmd}
+    WORKING_DIRECTORY ${work_dir}
+    DEPENDEES download
+    )
+endfunction(_ep_add_patch_command)
+
+
+# TODO: Make sure external projects use the proper compiler
+function(_ep_add_configure_command name)
+  ExternalProject_Get_Property(${name} source_dir binary_dir)
+
+  _ep_get_configuration_subdir_suffix(cfgdir)
+
+  # Depend on other external projects (file-level).
+  set(file_deps)
+  get_property(deps TARGET ${name} PROPERTY _EP_DEPENDS)
+  foreach(dep IN LISTS deps)
+    get_property(dep_stamp_dir TARGET ${dep} PROPERTY _EP_STAMP_DIR)
+    list(APPEND file_deps ${dep_stamp_dir}${cfgdir}/${dep}-done)
+  endforeach()
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_CONFIGURE_COMMAND SET)
+  if(cmd_set)
+    get_property(cmd TARGET ${name} PROPERTY _EP_CONFIGURE_COMMAND)
+  else()
+    get_target_property(cmake_command ${name} _EP_CMAKE_COMMAND)
+    if(cmake_command)
+      set(cmd "${cmake_command}")
+    else()
+      set(cmd "${CMAKE_COMMAND}")
+    endif()
+
+    get_property(cmake_args TARGET ${name} PROPERTY _EP_CMAKE_ARGS)
+    list(APPEND cmd ${cmake_args})
+
+    get_target_property(cmake_generator ${name} _EP_CMAKE_GENERATOR)
+    if(cmake_generator)
+      list(APPEND cmd "-G${cmake_generator}" "${source_dir}")
+    else()
+      list(APPEND cmd "-G${CMAKE_GENERATOR}" "${source_dir}")
+    endif()
+  endif()
+
+  ExternalProject_Add_Step(${name} configure
+    COMMAND ${cmd}
+    WORKING_DIRECTORY ${binary_dir}
+    DEPENDEES update patch
+    DEPENDS ${file_deps}
+    )
+endfunction(_ep_add_configure_command)
+
+
+function(_ep_add_build_command name)
+  ExternalProject_Get_Property(${name} binary_dir)
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_BUILD_COMMAND SET)
+  if(cmd_set)
+    get_property(cmd TARGET ${name} PROPERTY _EP_BUILD_COMMAND)
+  else()
+    _ep_get_build_command(${name} BUILD cmd)
+  endif()
+
+  ExternalProject_Add_Step(${name} build
+    COMMAND ${cmd}
+    WORKING_DIRECTORY ${binary_dir}
+    DEPENDEES configure
+    )
+endfunction(_ep_add_build_command)
+
+
+function(_ep_add_install_command name)
+  ExternalProject_Get_Property(${name} binary_dir)
+
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_INSTALL_COMMAND SET)
+  if(cmd_set)
+    get_property(cmd TARGET ${name} PROPERTY _EP_INSTALL_COMMAND)
+  else()
+    _ep_get_build_command(${name} INSTALL cmd)
+  endif()
+
+  ExternalProject_Add_Step(${name} install
+    COMMAND ${cmd}
+    WORKING_DIRECTORY ${binary_dir}
+    DEPENDEES build
+    )
+endfunction(_ep_add_install_command)
+
+
+function(_ep_add_test_command name)
+  ExternalProject_Get_Property(${name} binary_dir)
+
+  get_property(before TARGET ${name} PROPERTY _EP_TEST_BEFORE_INSTALL)
+  get_property(after TARGET ${name} PROPERTY _EP_TEST_AFTER_INSTALL)
+  get_property(cmd_set TARGET ${name} PROPERTY _EP_TEST_COMMAND SET)
+
+  # Only actually add the test step if one of the test related properties is
+  # explicitly set. (i.e. the test step is omitted unless requested...)
+  #
+  if(cmd_set OR before OR after)
+    if(cmd_set)
+      get_property(cmd TARGET ${name} PROPERTY _EP_TEST_COMMAND)
+    else()
+      _ep_get_build_command(${name} TEST cmd)
+    endif()
+
+    if(before)
+      set(dep_args DEPENDEES build DEPENDERS install)
+    else()
+      set(dep_args DEPENDEES install)
+    endif()
+
+    ExternalProject_Add_Step(${name} test
+      COMMAND ${cmd}
+      WORKING_DIRECTORY ${binary_dir}
+      ${dep_args}
+      )
+  endif()
+endfunction(_ep_add_test_command)
+
+
+function(ExternalProject_Add name)
+  _ep_get_configuration_subdir_suffix(cfgdir)
+
+  # Add a custom target for the external project.
+  set(cmf_dir ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles)
+  add_custom_target(${name} ALL DEPENDS ${cmf_dir}${cfgdir}/${name}-complete)
+  set_property(TARGET ${name} PROPERTY _EP_IS_EXTERNAL_PROJECT 1)
+  _ep_parse_arguments(ExternalProject_Add ${name} _EP_ "${ARGN}")
+  _ep_set_directories(${name})
+  ExternalProject_Get_Property(${name} stamp_dir)
+
+  # The 'complete' step depends on all other steps and creates a
+  # 'done' mark.  A dependent external project's 'configure' step
+  # depends on the 'done' mark so that it rebuilds when this project
+  # rebuilds.  It is important that 'done' is not the output of any
+  # custom command so that CMake does not propagate build rules to
+  # other external project targets.
+  add_custom_command(
+    OUTPUT ${cmf_dir}${cfgdir}/${name}-complete
+    COMMENT "Completed '${name}'"
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${cmf_dir}${cfgdir}
+    COMMAND ${CMAKE_COMMAND} -E touch ${cmf_dir}${cfgdir}/${name}-complete
+    COMMAND ${CMAKE_COMMAND} -E touch ${stamp_dir}${cfgdir}/${name}-done
+    DEPENDS ${stamp_dir}${cfgdir}/${name}-install
+    VERBATIM
+    )
+
+
+  # Depend on other external projects (target-level).
+  get_property(deps TARGET ${name} PROPERTY _EP_DEPENDS)
+  foreach(arg IN LISTS deps)
+    add_dependencies(${name} ${arg})
+  endforeach()
+
+  # Set up custom build steps based on the target properties.
+  # Each step depends on the previous one.
+  #
+  # The target depends on the output of the final step.
+  # (Already set up above in the DEPENDS of the add_custom_target command.)
+  #
+  _ep_add_mkdir_command(${name})
+  _ep_add_download_command(${name})
+  _ep_add_update_command(${name})
+  _ep_add_patch_command(${name})
+  _ep_add_configure_command(${name})
+  _ep_add_build_command(${name})
+  _ep_add_install_command(${name})
+
+  # Test is special in that it might depend on build, or it might depend
+  # on install.
+  #
+  _ep_add_test_command(${name})
+endfunction(ExternalProject_Add)
diff --git a/BRAINSCommonLib/BuildScripts/MIDAS.cmake b/BRAINSCommonLib/BuildScripts/MIDAS.cmake
new file mode 100644
index 00000000..bd552e4e
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/MIDAS.cmake
@@ -0,0 +1,162 @@
+# - Configure a project for downloading test data from a MIDAS server
+# Include this module in the top CMakeLists.txt file of a project to
+# enable downloading test data from MIDAS. Requires CTest module.
+#   project(MyProject)
+#   ...
+#   include(CTest)
+#   include(MIDAS)
+#
+# To use this module, set the following variable in your script:
+#   MIDAS_REST_URL - URL of the MIDAS server's REST API
+# Other optional variables:
+#   MIDAS_DATA_DIR         - Where to place downloaded files
+#                          - Defaults to PROJECT_BINARY_DIR/MIDAS_Data
+#   MIDAS_KEY_DIR          - Where the key files are located
+#                          - Defaults to PROJECT_SOURCE_DIR/MIDAS_Keys
+#   MIDAS_DOWNLOAD_TIMEOUT - Timeout for download stage (default 0)
+#
+# Then call the following macro:
+#  midas_add_test(  [args...])
+#   testName: Name of the test
+#   program: The executable to be run after the download is complete
+#   args: Optional args to the program.  If an arg is of the form
+#         MIDAS{foo.ext.md5}, the actual file foo.ext will be
+#         substituted for it at test time once the file is downloaded,
+#         assuming the keyfile foo.ext.md5 exists in MIDAS_KEY_DIR.
+#
+# EXAMPLE:
+#  midas_add_test(someTest php MIDAS{test.php.md5})
+#   is analogous to
+#  add_test(someTest php test.php)
+#   if the file test.php had already existed on disk.
+#
+# NOTES:
+# * The MIDAS{} substitution method can also be passed a relative path
+#   from the MIDAS_KEY_DIR to the key file, so that you can place key files
+#   in subdirectories under MIDAS_KEY_DIR. Ex: MIDAS{test1/input/foo.png.md5}
+#
+#=============================================================================
+# Copyright 2010 Kitware, Inc.
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+
+function(midas_add_test)
+  # Determine the test name.
+  list(GET ARGN 0 firstArg)
+  if(firstArg STREQUAL "NAME")
+    list(GET ARGN 1 testName)
+  else(firstArg STREQUAL "NAME")
+    list(GET ARGN 0 testName)
+  endif(firstArg STREQUAL "NAME")
+
+  if(NOT DEFINED MIDAS_REST_URL)
+    message(FATAL_ERROR "You must set MIDAS_REST_URL to the URL of the MIDAS REST API.")
+  endif(NOT DEFINED MIDAS_REST_URL)
+
+  if(NOT DEFINED MIDAS_KEY_DIR)
+    set(MIDAS_KEY_DIR "${PROJECT_SOURCE_DIR}/MIDAS_Keys")
+  endif(NOT DEFINED MIDAS_KEY_DIR)
+
+  if(NOT DEFINED MIDAS_DATA_DIR)
+    set(MIDAS_DATA_DIR "${PROJECT_BINARY_DIR}/MIDAS_Data")
+  endif(NOT DEFINED MIDAS_DATA_DIR)
+  file(MAKE_DIRECTORY "${MIDAS_DATA_DIR}/MIDAS_FetchScripts")
+  file(MAKE_DIRECTORY "${MIDAS_DATA_DIR}/MIDAS_Hashes")
+
+  if(NOT DEFINED MIDAS_DOWNLOAD_TIMEOUT)
+    set(MIDAS_DOWNLOAD_TIMEOUT_STR "")
+  else(NOT DEFINED MIDAS_DOWNLOAD_TIMEOUT)
+    set(MIDAS_DOWNLOAD_TIMEOUT_STR "TIMEOUT ${MIDAS_DOWNLOAD_TIMEOUT}")
+  endif(NOT DEFINED MIDAS_DOWNLOAD_TIMEOUT)
+
+  set(downloadScripts "")
+
+  # Substitute the downloaded file argument(s)
+  foreach(arg ${ARGN})
+    if(arg MATCHES "MIDAS[a-zA-Z_]*{[^}]*}")
+      string(REGEX MATCH "MIDAS[a-zA-Z_]*{([^}]*)}" toReplace "${arg}")
+      string(REGEX MATCH "^MIDAS[a-zA-Z_]*" keyword "${toReplace}")
+      string(REGEX REPLACE "MIDAS[a-zA-Z_]*{([^}]*)}" "\\1" keyFile "${toReplace}")
+      # Split up the checksum extension from the real filename
+      string(REGEX MATCH "\\.[^\\.]*$" hash_alg "${keyFile}")
+      string(REGEX REPLACE "\\.[^\\.]*$" "" base_file "${keyFile}")
+      string(REPLACE "." "" hash_alg "${hash_alg}")
+      string(TOUPPER "${hash_alg}" hash_alg)
+      get_filename_component(base_filepath "${base_file}" PATH)
+      get_filename_component(base_filename "${base_file}" NAME)
+      get_filename_component(base_fileext  "${base_file}" EXT)
+
+      # Resolve file location
+      if(NOT EXISTS "${MIDAS_KEY_DIR}/${keyFile}")
+        message(FATAL_ERROR "MIDAS key file ${MIDAS_KEY_DIR}/${keyFile} does not exist.")
+      endif(NOT EXISTS "${MIDAS_KEY_DIR}/${keyFile}")
+
+      # Obtain the checksum
+      file(READ "${MIDAS_KEY_DIR}/${keyFile}" checksum)
+
+      # Write the test script file for downloading
+      file(WRITE "${MIDAS_DATA_DIR}/MIDAS_FetchScripts/fetch_${checksum}_${base_filename}.cmake"
+  "message(STATUS \"Data is here: ${MIDAS_REST_URL}/midas.bitstream.by.hash?hash=${checksum}&algorithm=${hash_alg}\")
+if(NOT EXISTS \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${checksum}\")
+  file(DOWNLOAD ${MIDAS_REST_URL}/midas.bitstream.by.hash?hash=${checksum}&algorithm=${hash_alg} \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\" ${MIDAS_DOWNLOAD_TIMEOUT_STR} STATUS status)
+  list(GET status 0 exitCode)
+  list(GET status 1 errMsg)
+  if(NOT exitCode EQUAL 0)
+    file(REMOVE \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\")
+    message(FATAL_ERROR \"Error downloading ${checksum}: \${errMsg}\")
+  endif(NOT exitCode EQUAL 0)
+
+  execute_process(COMMAND \"${CMAKE_COMMAND}\" -E md5sum \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\" OUTPUT_VARIABLE output)
+  string(SUBSTRING \${output} 0 32 computedChecksum)
+
+  if(NOT computedChecksum STREQUAL ${checksum})
+    file(READ \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\" serverResponse)
+    file(REMOVE \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\")
+    message(FATAL_ERROR \"Error: Computed checksum (\${computedChecksum}) did not match expected (${checksum}). Server response: \${serverResponse}\")
+  else(NOT computedChecksum STREQUAL ${checksum})
+    file(RENAME \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${testName}_${checksum}\" \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${checksum}\")
+  endif(NOT computedChecksum STREQUAL ${checksum})
+endif(NOT EXISTS \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${checksum}\")
+
+# Add a symbolic link so we can use the human-readable filename in the command line
+file(MAKE_DIRECTORY \"${MIDAS_DATA_DIR}/${base_filepath}\")
+file(REMOVE \"${MIDAS_DATA_DIR}/${base_file}\")
+
+if(WIN32)
+  # windows does not support symlinks, so we must duplicate the file for now
+  configure_file(\"${MIDAS_DATA_DIR}/MIDAS_Hashes/${checksum}\" \"${MIDAS_DATA_DIR}/${testName}_${base_file}\" COPYONLY)
+  file(RENAME \"${MIDAS_DATA_DIR}/${testName}_${base_file}\" \"${MIDAS_DATA_DIR}/${base_file}\")
+else(WIN32)
+  execute_process(COMMAND \"${CMAKE_COMMAND}\" -E create_symlink \"${MIDAS_DATA_DIR}/MIDAS_Hashes/${checksum}\" \"${MIDAS_DATA_DIR}/${base_file}\")
+endif(WIN32)
+")
+
+      list(APPEND downloadScripts "${MIDAS_DATA_DIR}/MIDAS_FetchScripts/fetch_${checksum}_${base_filename}.cmake")
+      if(NOT keyword STREQUAL "MIDAS_FETCH_ONLY")
+        string(REGEX REPLACE ${toReplace} "${MIDAS_DATA_DIR}/${base_file}" newArg "${arg}")
+        list(APPEND testArgs ${newArg})
+      endif(NOT keyword STREQUAL "MIDAS_FETCH_ONLY")
+    else(arg MATCHES "MIDAS[a-zA-Z_]*{[^}]*}")
+      list(APPEND testArgs ${arg})
+    endif(arg MATCHES "MIDAS[a-zA-Z_]*{[^}]*}")
+  endforeach(arg)
+
+  file(WRITE "${MIDAS_DATA_DIR}/MIDAS_FetchScripts/${testName}_fetchData.cmake"
+       "#This is an auto generated file -- do not edit\n\n")
+  list(REMOVE_DUPLICATES downloadScripts)
+  foreach(downloadScript ${downloadScripts})
+    file(APPEND "${MIDAS_DATA_DIR}/MIDAS_FetchScripts/${testName}_fetchData.cmake" "include(\"${downloadScript}\")\n")
+  endforeach(downloadScript)
+
+  add_test(${testName}_fetchData "${CMAKE_COMMAND}" -P "${MIDAS_DATA_DIR}/MIDAS_FetchScripts/${testName}_fetchData.cmake")
+  set_tests_properties(${testName}_fetchData PROPERTIES FAIL_REGULAR_EXPRESSION "(Error downloading)|(Error: Computed checksum)")
+  # Finally, create the test
+  add_test(${testArgs})
+  set_tests_properties(${testName} PROPERTIES DEPENDS ${testName}_fetchData)
+endfunction(midas_add_test)
diff --git a/BRAINSCommonLib/BuildScripts/Module_Dummy.in b/BRAINSCommonLib/BuildScripts/Module_Dummy.in
new file mode 100755
index 00000000..30996725
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/Module_Dummy.in
@@ -0,0 +1,17 @@
+#!/usr/bin/tclsh
+catch {set script [info script]}
+catch {set script [file normalize $script]}
+catch {set execdir [file dirname [file dirname $script ]]}
+set env(@OS_VARNAME_FOR_LIBRARY_PATH@) [ exec $execdir/brains3_setup.sh @OS_VARNAME_FOR_LIBRARY_PATH@ ]
+set command "$execdir/@BGCbin_name@ $argv"
+set fp [ open "| $command |& cat" "r"]
+while { ![eof $fp ] } {
+    gets $fp line
+    puts $line
+}
+if { [catch "close $fp" res] } {
+    exit [ lindex $errorCode 2 ]
+} else {
+    exit 0
+}
+
diff --git a/BRAINSCommonLib/BuildScripts/PreventInSourceBuilds.cmake b/BRAINSCommonLib/BuildScripts/PreventInSourceBuilds.cmake
new file mode 100644
index 00000000..bfae464c
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/PreventInSourceBuilds.cmake
@@ -0,0 +1,55 @@
+#
+# This function will prevent in-source builds
+function(AssureOutOfSourceBuilds project_name)
+  # make sure the user doesn't play dirty with symlinks
+  get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
+  get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
+
+  # disallow in-source builds
+  if("${srcdir}" STREQUAL "${bindir}")
+    message("###########################################################################")
+    message("# ${project_name} should not be configured & built in the ${project_name} source directory")
+    message("# You must run cmake in a build directory.")
+    message("# For example:")
+    message("#")
+    message("#     mkdir ${project_name}-Sandbox ; cd ${project_name}-sandbox")
+    message("#")
+    message("# Check out source code in ${project_name}-sandbox")
+    message("#")
+    message("#     mkdir ${project_name}-build")
+    message("#")
+    message("# this will create the following directory structure")
+    message("#")
+    message("# ${project_name}-Sandbox")
+    message("#  +--${project_name}")
+    message("#  +--${project_name}-build")
+    message("#")
+    message("# Then you can proceed to configure and build")
+    message("# by using the following commands")
+    message("#")
+    message("#     cd ${project_name}-build")
+    message("#     cmake ../${project_name} # or ccmake, or cmake-gui")
+    message("#     make")
+    message("#")
+    message("# NOTE: Given that you already tried to make an in-source build")
+    message("#       CMake have already created several files & directories")
+    message("#       in your source tree.")
+    message("#")
+    message("# The following command will show you all files not part of ${project_name}")
+    message("#       cd ${project_name}-Sandbox/${project_name}")
+    message("#       svn status | grep '[^?]' | awk '{print \$2}'")
+    message("#")
+    message("# WARNING: if you have added files to ${project_name} but not used svn add")
+    message("# to add them to SVN's version control, this command will display them")
+    message("# along with the files CMake created during configuration.  You will need")
+    message("# to either save them outside the ${project_name} source tree, or run svn add")
+    message("# to let SVN know they are legitimate source files.")
+    message("# Once you've verified that all unknown files are the result of CMake")
+    message("# configuration, you can run this command to clean them up")
+    message("#       svn status | grep '[^?]' | awk '{print \$2}' | xargs rm -fr")
+    message("###########################################################################")
+    message(FATAL_ERROR "Quitting configuration")
+  endif()
+endfunction()
+
+AssureOutOfSourceBuilds(${CMAKE_PROJECT_NAME})
diff --git a/BRAINSCommonLib/BuildScripts/SEMCommanLineSharedLibraryWrapper.cxx b/BRAINSCommonLib/BuildScripts/SEMCommanLineSharedLibraryWrapper.cxx
new file mode 100644
index 00000000..8db2f22e
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/SEMCommanLineSharedLibraryWrapper.cxx
@@ -0,0 +1,40 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $HeadURL$
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even 
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+// This file is intended to be compiled and linked against a shared
+// library CLP to prevent the need to compile twice.
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef __BORLANDC__
+#define ITK_LEAN_AND_MEAN
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int main(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
diff --git a/BRAINSCommonLib/BuildScripts/SEMMacroBuildCLI.cmake b/BRAINSCommonLib/BuildScripts/SEMMacroBuildCLI.cmake
new file mode 100644
index 00000000..5c979d78
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/SEMMacroBuildCLI.cmake
@@ -0,0 +1,165 @@
+
+#
+# Depends on:
+#  CMakeParseArguments.cmake from Cmake 2.8.4 or greater
+#
+include(CMakeParseArguments)
+
+macro(SEMMacroBuildCLI)
+  set(options EXECUTABLE_ONLY NO_INSTALL VERBOSE)
+  set(oneValueArgs  NAME LOGO_HEADER CLI_XML_FILE CLI_SHARED_LIBRARY_WRAPPER_CXX
+                    RUNTIME_OUTPUT_DIRECTORY
+                    LIBRARY_OUTPUT_DIRECTORY
+                    ARCHIVE_OUTPUT_DIRECTORY
+                    INSTALL_RUNTIME_DESTINATION
+                    INSTALL_LIBRARY_DESTINATION
+                    INSTALL_ARCHIVE_DESTINATION
+  )
+  set(multiValueArgs ADDITIONAL_SRCS TARGET_LIBRARIES LINK_DIRECTORIES INCLUDE_DIRECTORIES)
+  CMAKE_PARSE_ARGUMENTS(LOCAL_SEM
+    "${options}"
+    "${oneValueArgs}"
+    "${multiValueArgs}"
+    ${ARGN}
+    )
+
+
+  message(STATUS "Configuring SEM CLI module: ${LOCAL_SEM_NAME}")
+  # --------------------------------------------------------------------------
+  # Print information helpful for debugging checks
+  # --------------------------------------------------------------------------
+  if(LOCAL_SEM_VERBOSE)
+    list(APPEND ALL_OPTIONS ${options} ${oneValueArgs} ${multiValueArgs})
+    foreach(curr_opt ${ALL_OPTIONS})
+      message(STATUS "STATUS: ${curr_opt} = ${LOCAL_SEM_${curr_opt}}")
+    endforeach()
+  endif()
+  if(LOCAL_SEM_INSTALL_UNPARSED_ARGUMENTS)
+    message(STATUS "WARNING:  Unparsed arguments given [${LOCAL_SEM_INSTALL_UNPARSED_ARGUMENTS}]")
+  endif()
+  # --------------------------------------------------------------------------
+  # Sanity checks
+  # --------------------------------------------------------------------------
+  if(NOT DEFINED LOCAL_SEM_NAME)
+    message(FATAL_ERROR "error: NAME is mandatory: [${LOCAL_SEM_NAME}]")
+  endif()
+
+  if(DEFINED LOCAL_SEM_LOGO_HEADER AND NOT EXISTS ${LOCAL_SEM_LOGO_HEADER})
+    message(WARNING "warning: Specified LOGO_HEADER [${LOCAL_SEM_LOGO_HEADER}] doesn't exist")
+    set(LOCAL_SEM_LOGO_HEADER)
+  endif()
+
+  foreach(v LOCAL_SEM_CLI_SHARED_LIBRARY_WRAPPER_CXX)
+    if(NOT EXISTS "${${v}}")
+      message(FATAL_ERROR "error: Variable ${v} point to an non-existing file or directory !")
+    endif()
+  endforeach()
+
+  if(DEFINED LOCAL_SEM_CLI_XML_FILE)
+    set(cli_xml_file ${LOCAL_SEM_CLI_XML_FILE})
+    if(NOT EXISTS ${cli_xml_file})
+      message(STATUS "WARNING: Requested Xml file [${cli_xml_file}] doesn't exist !")
+    endif()
+  else()
+    set(cli_xml_file ${CMAKE_CURRENT_SOURCE_DIR}/${LOCAL_SEM_NAME}.xml)
+    if(NOT EXISTS ${cli_xml_file})
+      set(cli_xml_file ${CMAKE_CURRENT_BINARY_DIR}/${LOCAL_SEM_NAME}.xml)
+      if(NOT EXISTS ${cli_xml_file})
+        message(STATUS "WARNING: Default SOURECE_DIR Xml file [${cli_xml_file}] doesn't exist !")
+        message(STATUS "WARNING: Default BINARY_DIR Xml file [${cli_xml_file}] doesn't exist !")
+      endif()
+    endif()
+  endif()
+  if(NOT EXISTS ${cli_xml_file})
+      message(FATAL_ERROR "Xml file [${cli_xml_file}] doesn't exist !")
+  endif()
+
+  set(CLP ${LOCAL_SEM_NAME})
+
+  # SlicerExecutionModel
+  find_package(SlicerExecutionModel REQUIRED GenerateCLP)
+  include(${GenerateCLP_USE_FILE})
+
+  set(${CLP}_SOURCE ${CLP}.cxx ${LOCAL_SEM_ADDITIONAL_SRCS})
+  generateclp(${CLP}_SOURCE ${cli_xml_file} ${LOCAL_SEM_LOGO_HEADER})
+
+  if(DEFINED LOCAL_SEM_LINK_DIRECTORIES)
+    link_directories(${LOCAL_SEM_LINK_DIRECTORIES})
+  endif()
+
+  if(DEFINED LOCAL_SEM_INCLUDE_DIRECTORIES)
+    include_directories(${LOCAL_SEM_INCLUDE_DIRECTORIES})
+  endif()
+
+  set(cli_targets)
+
+  if(NOT LOCAL_SEM_EXECUTABLE_ONLY)
+
+    add_library(${CLP}Lib SHARED ${${CLP}_SOURCE})
+    set_target_properties(${CLP}Lib PROPERTIES COMPILE_FLAGS "-Dmain=ModuleEntryPoint")
+    if(DEFINED LOCAL_SEM_TARGET_LIBRARIES)
+      target_link_libraries(${CLP}Lib ${LOCAL_SEM_TARGET_LIBRARIES})
+    endif()
+
+    add_executable(${CLP} ${LOCAL_SEM_CLI_SHARED_LIBRARY_WRAPPER_CXX})
+    target_link_libraries(${CLP} ${CLP}Lib)
+
+    set(cli_targets ${CLP} ${CLP}Lib)
+
+  else()
+
+    add_executable(${CLP} ${${CLP}_SOURCE})
+    if(DEFINED LOCAL_SEM_TARGET_LIBRARIES)
+      target_link_libraries(${CLP} ${LOCAL_SEM_TARGET_LIBRARIES})
+    endif()
+
+    set(cli_targets ${CLP})
+
+  endif()
+
+  # Set labels associated with the target.
+  set_target_properties(${cli_targets} PROPERTIES LABELS ${CLP})
+
+  if(NOT DEFINED LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY)
+    set(LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+    message(STATUS "WARNING:  Setting default RUNTIME_OUTPUT_DIRECTORY to ${LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY}")
+  endif()
+  if(NOT DEFINED LOCAL_SEM_LIBRARY_OUTPUT_DIRECTORY)
+    set(LOCAL_SEM_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+    message(STATUS "WARNING:  Setting default LIBRARY_OUTPUT_DIRECTORY to ${LOCAL_SEM_LIBRARY_OUTPUT_DIRECTORY}")
+  endif()
+  if(NOT DEFINED LOCAL_SEM_ARCHIVE_OUTPUT_DIRECTORY)
+    set(LOCAL_SEM_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+    message(STATUS "WARNING:  Setting default ARCHIVE_OUTPUT_DIRECTORY to ${LOCAL_SEM_ARCHIVE_OUTPUT_DIRECTORY}")
+  endif()
+  if(NOT DEFINED LOCAL_SEM_INSTALL_RUNTIME_DESTINATION)
+    set(LOCAL_SEM_INSTALL_RUNTIME_DESTINATION ${CMAKE_BINARY_DIR}/bin)
+    message(STATUS "WARNING:  Setting default INSTALL_RUNTIME_DESTINATION to ${LOCAL_SEM_INSTALL_RUNTIME_DESTINATION}")
+  endif()
+  if(NOT DEFINED LOCAL_SEM_INSTALL_LIBRARY_DESTINATION)
+    set(LOCAL_SEM_INSTALL_LIBRARY_DESTINATION ${CMAKE_BINARY_DIR}/lib)
+    message(STATUS "WARNING:  Setting default INSTALL_LIBRARY_DESTINATION to ${LOCAL_SEM_INSTALL_LIBRARY_DESTINATION}")
+  endif()
+  if(NOT DEFINED LOCAL_SEM_INSTALL_ARCHIVE_DESTINATION)
+    set(LOCAL_SEM_INSTALL_ARCHIVE_DESTINATION ${CMAKE_BINARY_DIR}/lib)
+    message(STATUS "WARNING:  Setting default INSTALL_ARCHIVE_DESTINATION to ${LOCAL_SEM_INSTALL_ARCHIVE_DESTINATION}")
+  endif()
+
+  set_target_properties(${cli_targets} PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY "${LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY}"
+    LIBRARY_OUTPUT_DIRECTORY "${LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY}"
+    ARCHIVE_OUTPUT_DIRECTORY "${LOCAL_SEM_RUNTIME_OUTPUT_DIRECTORY}"
+    )
+
+  if(NOT LOCAL_SEM_NO_INSTALL)
+    # Install each target in the production area (where it would appear in an installation)
+    # and install each target in the developer area (for running from a build)
+    install(TARGETS ${cli_targets}
+      RUNTIME DESTINATION ${LOCAL_SEM_INSTALL_RUNTIME_DESTINATION} COMPONENT RuntimeLibraries
+      LIBRARY DESTINATION ${LOCAL_SEM_INSTALL_LIBRARY_DESTINATION} COMPONENT RuntimeLibraries
+      ARCHIVE DESTINATION ${LOCAL_SEM_INSTALL_ARCHIVE_DESTINATION} COMPONENT RuntimeLibraries
+      )
+  endif()
+
+
+endmacro()
diff --git a/BRAINSCommonLib/BuildScripts/SEMToolTestName.cxx.in b/BRAINSCommonLib/BuildScripts/SEMToolTestName.cxx.in
new file mode 100644
index 00000000..3581378c
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/SEMToolTestName.cxx.in
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int @SEMToolTestName@(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSCommonLib/BuildScripts/ValgrindSuppression.supp b/BRAINSCommonLib/BuildScripts/ValgrindSuppression.supp
new file mode 100644
index 00000000..035f77ed
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/ValgrindSuppression.supp
@@ -0,0 +1,2278 @@
+##----------------------------------------------------------------------#r
+
+# Errors to suppress by default in BRAINS2
+
+# Format of this file is:
+# {
+#     name_of_suppression
+#     tool_name:supp_kind
+#     (optional extra info for some suppression types)
+#     caller0 name, or /name/of/so/file.so
+#     caller1 name, or ditto
+#     (optionally: caller2 name)
+#     (optionally: caller3 name)
+#  }
+#
+# For Memcheck, the supp_kinds are:
+#
+#     Param Value1 Value2 Value4 Value8 Value16
+#     Free Addr1 Addr2 Addr4 Addr8 Addr16
+#     Cond (previously known as Value0)
+#
+# and the optional extra info is:
+#     if Param: name of system call param
+#     if Free: name of free-ing fn)
+
+##----------------------------------------------------------------------##
+
+{
+   glib-Cond-0
+   Memcheck:Free
+   obj:*libglib-1.2.so.0.0.10
+}
+
+{
+   Some Error from the itk::MultiThreader::DispatchSingleMethodThread
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_allocate_tls
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader26DispatchSingleMethodThreadEPNS0_16ThreadInfoStructE
+}
+{
+  Some Error from the itk::MultiThreader::SingleMethodExecute
+  Memcheck:Leak
+  fun:calloc
+  obj:/lib/ld-2.3.?.so
+  fun:_dl_allocate_tls
+  fun:allocate_stack
+  fun:pthread_create@@GLIBC_2.1
+  fun:_ZN3itk13MultiThreader26DispatchSingleMethodThreadEPNS0_16ThreadInfoStructE
+}
+{
+  Error2
+  Memcheck:Free
+  fun:calloc
+  obj:*/ld-2.3.?.so
+  fun:_dl_allocate_tls
+  fun:allocate_stack
+  fun:pthread_create@@GLIBC_2.1
+  fun:_ZN3itk13MultiThreader19SingleMethodExecuteEv
+  fun:_ZN3itk11ImageSourceINS_5ImageIfLj3EEEE12GenerateDataEv
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_allocate_tls
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader11SpawnThreadEPFPvS1_ES1_
+}
+
+{
+  lib/ld conditional jump errors
+  Memcheck:Cond
+  obj:*/ld-2.3.?.so
+  obj:*/ld-2.3.?.so
+  obj:*/ld-2.3.?.so
+}
+{
+  CrazyTclError1
+  Memcheck:Leak
+  fun:calloc
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:TclpAlloc
+  fun:Tcl_Alloc
+  fun:Tcl_MutexLock
+  fun:TclInitObjSubsystem
+  fun:TclInitSubsystems
+  fun:Tcl_FindExecutable
+  fun:Tcl_Main
+}
+{
+  CrazyTclError2
+  Memcheck:Leak
+  fun:calloc
+  obj:/lib/ld-2.3.?.so
+  fun:_dl_allocate_tls
+  fun:allocate_stack
+  fun:pthread_create@@GLIBC_2.1
+  fun:TclpThreadCreate
+  fun:Tcl_InitNotifier
+  fun:TclInitNotifier
+  fun:TclInitSubsystems
+  fun:Tcl_FindExecutable
+  fun:Tcl_Main
+  fun:main
+}
+
+{
+  CrazyTclError3
+  Memcheck:Leak
+  fun:realloc
+  fun:TclpRealloc
+  fun:Tcl_Realloc
+  fun:Tcl_SetObjLength
+  obj:/usr/lib/libtcl8.4.so.0
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:Tcl_FSEvalFile
+  fun:Tcl_Main
+}
+
+{
+  CrazyTclError4
+  Memcheck:Leak
+  fun:malloc
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:TclpAlloc
+  fun:Tcl_Alloc
+  obj:/usr/lib/libtcl8.4.so.0
+  obj:/usr/lib/libtcl8.4.so.0
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:Tcl_GetsObj
+  fun:Tcl_Gets
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:Tcl_SetSystemEncoding
+  fun:TclpSetInitialEncodings
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:Tcl_FindExecutable
+  fun:Tcl_Main
+}
+
+{
+  CrazyTclError5
+  Memcheck:Leak
+  fun:malloc
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:TclpAlloc
+  fun:Tcl_Alloc
+  fun:Tcl_MutexLock
+  fun:TclInitObjSubsystem
+  fun:TclInitSubsystems
+  fun:Tcl_FindExecutable
+  fun:Tcl_Main
+}
+
+{
+  CrazyTclError6
+  Memcheck:Leak
+  fun:malloc
+  fun:TclThreadAllocObj
+  fun:Tcl_NewObj
+  fun:TclpInitLibraryPath
+  obj:/usr/lib/libtcl8.4.so.0
+  fun:Tcl_FindExecutable
+  fun:Tcl_Main
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc
+   fun:_Z63itkGreyLevelCooccurrenceMatrixTextureCoefficientsCalculatorTestiPPc
+   fun:main
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/ld-2.3.?.so
+   fun:_dl_allocate_tls
+   fun:allocate_stack
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader19SingleMethodExecuteEv
+   fun:_ZN3itk11ImageSourceINS_5ImageIdLj6EEEE12GenerateDataEv
+   fun:_ZN3itk13ProcessObject16UpdateOutputDataEPNS_10DataObjectE
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc
+   fun:_ZN3itk12OutputWindow11DisplayTextEPKc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:__cxa_throw
+}
+{
+   ostream stuff
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc
+}
+{
+   ostream stuff
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZNSolsEm
+   fun:_ZNSolsEj
+}
+{
+   basic_ostream From cumulative gaussian optimizer
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc
+}
+{
+   ostream stuff
+   Memcheck:Value4
+   obj:/usr/lib/libstdc++.so.6.0.3
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE13_M_insert_intImEES3_S3_RSt8ios_basecT_
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE6do_putES3_RSt8ios_basecm
+   fun:_ZNSolsEm
+}
+{
+   ostream stuff
+   Memcheck:Value8
+   fun:vfprintf
+   fun:vsnprintf
+   fun:snprintf
+   obj:/usr/lib/libstdc++.so.6.0.3
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE15_M_insert_floatIdEES3_S3_RSt8ios_baseccT_
+}
+{
+   itkThreadLoggerTest 1
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/ld-2.3.?.so
+   fun:_dl_allocate_tls
+   fun:allocate_stack
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader11SpawnThreadEPFPvS1_ES1_
+   fun:_ZN3itk12ThreadLoggerC1Ev
+   fun:_ZN3itk12ThreadLogger3NewEv
+   fun:_Z19itkThreadLoggerTestiPPc
+   fun:main
+}
+{
+   itkThreadLoggerTest 1
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_allocate_tls
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader11SpawnThreadEPFPvS1_ES1_
+   fun:_ZN3itk12ThreadLoggerC1Ev
+   fun:_ZN3itk12ThreadLogger3NewEv
+}
+{
+   itkCommonPrintTest
+   Memcheck:Cond
+   obj:/usr/lib/libstdc++.so.6.0.3
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE13_M_insert_intImEES3_S3_RSt8ios_basecT_
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE6do_putES3_RSt8ios_basecPKv
+   fun:_ZNSolsEPKv
+   fun:_ZNK3itk21KLMSegmentationBorder9PrintSelfERSoNS_6IndentE
+   fun:_ZNK3itk11LightObject5PrintERSoNS_6IndentE
+   fun:_ZNK3itk12SmartPointerINS_21KLMSegmentationBorderEE5PrintERSo
+   fun:_ZN3itklsINS_21KLMSegmentationBorderEEERSoS2_NS_12SmartPointerIT_EE
+   fun:_Z18itkCommonPrintTestiPPc
+   fun:main
+}
+{
+   itkCommonPrintTest
+   Memcheck:Value4
+   obj:/usr/lib/libstdc++.so.6.0.3
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE13_M_insert_intImEES3_S3_RSt8ios_basecT_
+   fun:_ZNKSt7num_putIcSt19ostreambuf_iteratorIcSt11char_traitsIcEEE6do_putES3_RSt8ios_basecPKv
+   fun:_ZNSolsEPKv
+   fun:_ZNK3itk21KLMSegmentationBorder9PrintSelfERSoNS_6IndentE
+   fun:_ZNK3itk11LightObject5PrintERSoNS_6IndentE
+   fun:_ZNK3itk12SmartPointerINS_21KLMSegmentationBorderEE5PrintERSo
+   fun:_ZN3itklsINS_21KLMSegmentationBorderEEERSoS2_NS_12SmartPointerIT_EE
+   fun:_Z18itkCommonPrintTestiPPc
+   fun:main
+}
+{
+   Below block is after changes to Multithreader, Aug 05
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/ld-2.3.?.so
+   fun:_dl_allocate_tls
+   fun:allocate_stack
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader26DispatchSingleMethodThreadEPNS0_16ThreadInfoStructE
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/ld-2.3.?.so
+   fun:_dl_allocate_tls
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader26DispatchSingleMethodThreadEPNS0_16ThreadInfoStructE
+   fun:_ZN3itk13MultiThreader19SingleMethodExecuteEv
+   fun:_ZN3itk11ImageSourceINS_5ImageIfLj2EEEE12GenerateDataEv
+   fun:_ZN3itk13ProcessObject16UpdateOutputDataEPNS_10DataObjectE
+   fun:_ZN3itk10DataObject16UpdateOutputDataEv
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/ld-2.3.?.so
+   fun:_dl_allocate_tls
+   fun:pthread_create@@GLIBC_2.1
+   fun:_ZN3itk13MultiThreader26DispatchSingleMethodThreadEPNS0_16ThreadInfoStructE
+   fun:_ZN3itk13MultiThreader19SingleMethodExecuteEv
+}
+{
+   Exception allocation
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:__cxa_allocate_exception
+}
+{
+   Exception allocation
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:__cxa_allocate_exception
+}
+{
+  index(strchr.S)
+  Memcheck:Cond
+  fun:index
+}
+{
+  /lib/libz
+  Memcheck:Cond
+  obj:*/libz.so.1.2.3
+}
+{
+   
+   Memcheck:Param
+   write(buf)
+   fun:__write_nocancel
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_X11TransWrite
+   obj:/usr/X11R6/lib/libX11.so.6.2
+}
+{
+   
+   Memcheck:Free
+   fun:free
+   fun:__GI__dl_deallocate_tls
+   fun:vgArch_thread_exit
+   fun:thread_exit_wrapper
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__cxa_get_globals
+   fun:_ZSt18uncaught_exceptionv
+   fun:_ZNSo6sentryD1Ev
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:XextCreateExtension
+   fun:__glXInitialize
+   fun:glXGetConfig
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dlerror_run
+   fun:dlsym
+   fun:__errno_location
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:OpenDriver
+   fun:__glXRegisterExtensions
+   fun:__glXNewIndirectAPI
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_internal
+   fun:openaux
+   fun:_dl_catch_error_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps_internal
+   fun:dl_open_worker
+   fun:_dl_catch_error_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__glXstrdup
+   fun:OpenDriver
+   fun:__glXRegisterExtensions
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_internal
+   fun:dl_open_worker
+   fun:_dl_catch_error_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:dl_open_worker
+   fun:_dl_catch_error_internal
+   fun:__GI__dl_open
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_check_map_versions_internal
+   fun:dl_open_worker
+   fun:_dl_catch_error_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__glXNewIndirectAPI
+   fun:glXMakeCurrent
+   fun:_ZN22vtkXOpenGLRenderWindow11MakeCurrentEv
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__fgl_glapi_add_entrypoint
+   fun:__driRegisterExtensions
+   fun:__glXRegisterExtensions
+}
+{
+   
+   Memcheck:Cond
+   obj:/lib/ld-2.3.6.so
+   obj:/lib/ld-2.3.6.so
+   obj:/lib/ld-2.3.6.so
+   obj:/lib/ld-2.3.6.so
+   obj:/lib/ld-2.3.6.so
+   obj:/lib/ld-2.3.6.so
+}
+# This is a list of valgrind warnings to
+# suppress by default with all VXL programs.
+# They consist of occasions where valgrind is being too strict,
+# of where errors and deep in the OS, and we can maybe assume
+# that they don't cause any problems.
+# For Glibcpp (version>=3) set environment variable
+# GLIBCPP_FORCE_NEW=yes to avoid lots of incorrect leak warnings
+
+# Author: Ian Scott.
+
+# Format of this file is:
+# {
+#     name_of_suppression
+#     skin_name:supp_kind
+#     (optional extra info for some suppression types)
+#     caller0 name, or /name/of/so/file.so
+#     caller1 name, or ditto
+#     (optionally: caller2 name)
+#     (optionally: caller3 name)
+#  }
+#
+# For Memcheck, the supp_kinds are:
+#
+#     Param Value1 Value2 Value4 Value8
+#     Free Addr1 Addr2 Addr4 Addr8 Leak
+#     Cond (previously known as Value0)
+#
+# and the optional extra info is:
+#     if Param: name of system call param
+#     if Free: name of free-ing fn)
+
+{
+   malloc/__newlocale(Leak)
+   Addrcheck,Memcheck:Leak
+   fun:malloc
+   fun:__newlocale
+   fun:_ZNSt6locale5facet18_S_create_c_localeERP15__locale_structPKcS2_
+}
+{
+   malloc/realloc/argz_append(Leak)
+   Addrcheck,Memcheck:Leak
+   fun:malloc
+   fun:realloc
+   fun:__argz_append
+}
+{
+   my_malloc/specifics/pthread(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:my_malloc
+   fun:get_or_allocate_specifics_ptr
+   fun:__pthread_key_create
+}
+
+# A leak found in every call to putenv
+# Space must be allocated for the new environment
+# variable. It shouldn't accumulate over time
+{
+   vpl_putenv/known(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:malloc
+   fun:__strdup
+   fun:_Z10vpl_putenvPKc
+}
+
+
+# Lots of leaks found in vul/tests/test_url.cxx
+# when calling vul_http_exists
+# I assume they are correctly managed in libc and
+# do not accumulate over time.
+{
+   gethostbyname/libc/1(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps
+   fun:dl_open_worker
+}
+{
+   gethostbyname/libc/2(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object
+   fun:openaux
+}
+{
+   gethostbyname/libc/3(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:malloc
+   fun:__res_nsend
+   fun:__res_nquery
+}
+{
+   gethostbyname/libc/4(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:calloc
+   fun:_dl_check_map_versions
+   fun:dl_open_worker
+}
+{
+   gethostbyname/libc/5(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:calloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+}
+{
+   gethostbyname/libc/6(Leak)
+   AddrCheck,Memcheck:Leak
+   fun:malloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+}
+
+# Lots of uninitialised memory reads found in triangle.c
+# The uninitialised value is loaded, but then discarded.
+# Unfortunately valgrind treats loading into a floating-point
+# register as a final use, and so triggers the error.
+{
+   v3p/netlib/triangulate/1(Uninitialised_value)
+   Memcheck:Value8
+   fun:fast_expansion_sum_zeroelim
+   fun:incircleadapt
+   fun:incircle
+   fun:mergehulls
+}
+{
+   v3p/netlib/triangulate/2(Uninitialised_value)
+   Memcheck:Value8
+   fun:fast_expansion_sum_zeroelim
+   fun:incircleadapt
+   fun:incircle
+   fun:triangulatepolygon
+}
+{
+   v3p/netlib/triangulate/3(Uninitialised_value)
+   Memcheck:Value8
+   fun:fast_expansion_sum_zeroelim
+   fun:incircleadapt
+   fun:incircle
+   fun:insertsite
+}
+{
+   
+   Memcheck:Addr1
+   fun:strcmp
+   fun:_dl_map_object_internal
+}
+{
+   
+   Memcheck:Cond
+   fun:_dl_relocate_object_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+}
+{
+   
+   Memcheck:Cond
+   fun:_dl_relocate_object_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+}
+{
+   
+   Memcheck:Cond
+   fun:__stpcpy
+   obj:/lib/libc-2.3.3.so
+   fun:__sysconf
+}
+{
+   
+   Memcheck:Cond
+   fun:__stpcpy
+   obj:/lib/libc-2.3.3.so
+   fun:setlocale
+   fun:TclpSetInitialEncodings
+}
+{
+   
+   Memcheck:Cond
+   fun:__stpcpy
+   fun:setlocale
+   fun:TclpSetInitialEncodings
+}
+{
+   
+   Memcheck:Cond
+   fun:__stpcpy
+   obj:/lib/libc-2.3.3.so
+   fun:__pthread_once
+}
+{
+   
+   Memcheck:Cond
+   fun:__stpcpy
+   obj:/lib/libc-2.3.3.so
+   fun:__nss_hosts_lookup
+   fun:gethostbyname_r
+   fun:gethostbyname
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_X11TransConnect
+   fun:_X11TransConnectDisplay
+   fun:XOpenDisplay
+   fun:TkpOpenDisplay
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XlcDefaultMapModifiers
+   fun:XSetLocaleModifiers
+   obj:/usr/lib/libtk8.4.so
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XrmDefaultInitParseInfo
+   fun:_XrmInitParseInfo
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XrmGetFileDatabase
+   fun:_XInitKeysymDB
+   fun:XStringToKeysym
+   fun:TkStringToKeysym
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/X11/locale/lib/common/ximcp.so.2
+   fun:_XimOpenIM
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XOpenIM
+   obj:/usr/lib/libtk8.4.so
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XlcResolveLocaleName
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XlcCreateLocaleDataBase
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:XauFileName
+   fun:XauGetBestAuthByAddr
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_X11TransConnectDisplay
+   fun:XOpenDisplay
+   fun:TkpOpenDisplay
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XrmInternalStringToQuark
+   fun:XrmStringToQuark
+   fun:_XlcGetCharSet
+   fun:_XlcAddCT
+   fun:_XlcInitCTInfo
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XlcAddCT
+   fun:_XlcInitCTInfo
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   obj:/usr/lib/libtk8.4.so
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:__strdup
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Addr4
+   obj:/lib/libc-2.3.3.so
+   obj:/lib/libc-2.3.3.so
+   obj:/lib/libc-2.3.3.so
+   obj:/lib/libc-2.3.3.so
+   obj:/lib/libc-2.3.3.so
+   fun:__libc_freeres
+   fun:vgPlain___libc_freeres_wrapper
+   fun:exit
+   fun:Tcl_Exit
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcCreateLC
+   fun:_XlcDefaultLoader
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_check_map_versions_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+}
+{
+   
+   Memcheck:Overlap
+   fun:memcpy
+   obj:/usr/X11R6/lib/libXt.so.6.0
+   fun:_XtGetResources
+   obj:/usr/X11R6/lib/libXt.so.6.0
+   fun:_XtAppCreateShell
+   fun:XtVaAppCreateShell
+}
+{
+   
+   Memcheck:Cond
+   fun:strlen
+   obj:/lib/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XrmInitParseInfo
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XrmGetStringDatabase
+   obj:/usr/X11R6/lib/libXt.so.6.0
+   obj:/usr/X11R6/lib/libXt.so.6.0
+   fun:_XtDisplayInitialize
+   fun:XtDisplayInitialize
+   fun:_ZN29vtkXRenderWindowTclInteractor10InitializeEv
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:XShmCreateImage
+   fun:alloc_shm_back_buffer
+   fun:xmesa_alloc_back_buffer
+   fun:xmesa_resize_buffers
+   fun:_mesa_ResizeBuffersMESA
+   fun:_mesa_set_viewport
+   fun:_mesa_Viewport
+   fun:glViewport
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:XCreateImage
+   fun:initialize_visual_and_buffer
+   fun:XMesaCreateWindowBuffer2
+   fun:Fake_glXMakeContextCurrent
+   fun:Fake_glXMakeCurrent
+   fun:glXMakeCurrent
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XNoticeCreateBitmap
+   fun:XCreatePixmap
+   fun:XCreateBitmapFromData
+   fun:GetBitmap
+   fun:Tk_GetBitmap
+   fun:TkButtonWorldChanged
+   fun:ConfigureButton
+   fun:ButtonCreate
+   fun:Tk_ButtonObjCmd
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:TclObjInterpProc
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:Tcl_EvalObjEx
+   fun:NamespaceEvalCmd
+   fun:Tcl_NamespaceObjCmd
+   fun:TclEvalObjvInternal
+   fun:Tcl_EvalEx
+   fun:Tcl_Eval
+   fun:Tcl_GlobalEval
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:strdup
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_check_map_versions_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:XCreateGC
+   fun:initialize_visual_and_buffer
+   fun:XMesaCreateWindowBuffer2
+   fun:Fake_glXMakeContextCurrent
+   fun:Fake_glXMakeCurrent
+   fun:glXMakeCurrent
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:XGetVisualInfo
+   fun:get_visual
+   fun:choose_x_visual
+   fun:choose_visual
+   fun:Fake_glXChooseVisual
+   fun:glXChooseVisual
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_mesa_malloc
+   fun:_mesa_new_buffer_object
+   fun:_mesa_init_buffer_objects
+   fun:init_attrib_groups
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Cond
+   fun:strchr
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XlcDynamicLoad
+   fun:_XOpenLC
+   fun:_XlcCurrentLC
+   fun:XSetLocaleModifiers
+   fun:OpenIM
+   fun:TkpOpenDisplay
+   fun:GetScreen
+   fun:CreateTopLevelWindow
+   fun:TkCreateMainWindow
+   fun:CreateFrame
+   fun:TkCreateFrame
+   fun:Initialize
+   fun:Tk_Init
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:_mesa_alloc_program
+   fun:alloc_shared_state
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_mesa_malloc
+   fun:alloc_vertex_store
+   fun:_tnl_NewList
+   fun:_mesa_NewList
+   fun:glNewList
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_mesa_malloc
+   fun:XMesaCreateVisual
+   fun:save_glx_visual
+   fun:choose_visual
+   fun:Fake_glXChooseVisual
+   fun:glXChooseVisual
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:XMesaCreateVisual
+   fun:save_glx_visual
+   fun:choose_visual
+   fun:Fake_glXChooseVisual
+   fun:glXChooseVisual
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:_mesa_NewHashTable
+   fun:_mesa_init_occlude
+   fun:init_attrib_groups
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_mesa_malloc
+   fun:_mesa_strdup
+   fun:_mesa_init_program
+   fun:init_attrib_groups
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:_mesa_NewHashTable
+   fun:_mesa_init_depth
+   fun:init_attrib_groups
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_mesa_calloc
+   fun:_mesa_new_texture_object
+   fun:alloc_shared_state
+   fun:_mesa_initialize_context
+   fun:XMesaCreateContext
+   fun:Fake_glXCreateContext
+   fun:glXCreateContext
+}
+
+{
+   
+   Memcheck:Param
+   write(buf)
+   fun:write
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_X11TransWrite
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XReply
+   fun:XSync
+}
+
+{
+   
+   Memcheck:Cond
+   fun:_playback_copy_to_current
+   fun:_tnl_playback_vertex_list
+   fun:execute_list
+   fun:_mesa_CallList
+   fun:glCallList
+}
+
+{
+   
+   Memcheck:Addr4
+   obj:/lib/tls/libc-2.3.3.so
+   obj:/lib/tls/libc-2.3.3.so
+   obj:/lib/tls/libc-2.3.3.so
+   obj:/lib/tls/libc-2.3.3.so
+   obj:/lib/tls/libc-2.3.3.so
+   fun:__libc_freeres
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:get_dispatch
+   fun:glXChooseVisual
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libXcursor.so.1.0
+   fun:XcursorTryShapeCursor
+   fun:_XTryShapeCursor
+   fun:XCreateGlyphCursor
+   fun:TkGetCursorByName
+}
+
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   obj:/lib/libdl-2.3.3.so
+   fun:dlsym
+   fun:fcntl
+   fun:TclpOpenFileChannel
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:open_path
+   fun:_dl_map_object_internal
+   obj:/lib/tls/libc-2.3.3.so
+   fun:_dl_catch_error_internal
+   fun:_dl_open
+   obj:/lib/libdl-2.3.3.so
+   fun:_dl_catch_error_internal
+   obj:/lib/libdl-2.3.3.so
+   fun:dlopen
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:_XNoticeCreateBitmap
+   fun:XCreatePixmap
+   fun:XCreateBitmapFromData
+   obj:/usr/lib/libtk8.4.so
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XQueryFont
+   obj:/usr/X11R6/lib/libXcursor.so.1.0
+   fun:XcursorTryShapeCursor
+   fun:_XTryShapeCursor
+   fun:XCreateGlyphCursor
+   fun:TkGetCursorByName
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XQueryFont
+   obj:/usr/X11R6/lib/libXcursor.so.1.0
+   fun:XcursorTryShapeCursor
+   fun:_XTryShapeCursor
+   fun:XCreateGlyphCursor
+   fun:TkGetCursorByName
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/X11R6/lib/libX11.so.6.2
+   fun:XQueryFont
+   obj:/usr/X11R6/lib/libXcursor.so.1.0
+   fun:XcursorTryShapeCursor
+   fun:_XTryShapeCursor
+   fun:XCreateGlyphCursor
+   fun:TkGetCursorByName
+}
+
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_mesa_malloc
+   fun:alloc_vertex_store
+   fun:_save_compile_vertex_list
+   fun:_save_wrap_buffers
+   fun:_save_wrap_filled_vertex
+   fun:save_attrib_0_3
+   fun:_save_Vertex3fv
+   fun:glVertex3fv
+}
+{
+   
+   Memcheck:Cond
+   fun:_dl_relocate_object
+   fun:dl_main
+   fun:_dl_sysdep_start
+   fun:_dl_start
+   obj:/lib/ld-2.3.5.so
+}
+{
+   
+   Memcheck:Cond
+   fun:_dl_relocate_object
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+}
+{
+   
+   Memcheck:Cond
+   fun:PyObject_Free
+}
+{
+   
+   Memcheck:Cond
+   fun:PyObject_Realloc
+}
+{
+   
+   Memcheck:Value4
+   fun:PyObject_Free
+}
+{
+   
+   Memcheck:Value4
+   fun:PyObject_Realloc
+}
+{
+   
+   Memcheck:Addr4
+   fun:PyObject_Free
+}
+{
+   
+   Memcheck:Addr4
+   fun:PyObject_Realloc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:strdup
+   fun:Py_InitializeEx
+   fun:Py_Initialize
+   fun:Py_Main
+   fun:main
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:PyList_New
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_map_object_deps
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:expand_dynamic_string_token
+   fun:_dl_map_object
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:realloc
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:PyThread_allocate_lock
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:PyObject_Malloc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:PyMem_Malloc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:PyStructSequence_InitType
+   fun:initposix
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_check_map_versions
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:calloc
+   fun:_dl_new_object
+   fun:_dl_map_object_from_fd
+   fun:_dl_map_object
+   fun:dl_open_worker
+   fun:_dl_catch_error
+   fun:_dl_open
+   fun:dlopen_doit
+   fun:_dl_catch_error
+   fun:_dlerror_run
+   fun:dlopen@@GLIBC_2.1
+   fun:_PyImport_GetDynLoadFunc
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   obj:/usr/lib/libpython2.4.so.1.0
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   fun:PyObject_Realloc
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:TclpAlloc
+   fun:Tcl_Alloc
+   fun:TclCreateExecEnv
+   fun:Tcl_CreateInterp
+   fun:Tcl_Main
+   fun:main
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   fun:TclpRealloc
+   fun:Tcl_AttemptRealloc
+   fun:Tcl_AttemptSetObjLength
+   fun:AppendUtfToUtfRep
+   fun:TclpNativeJoinPath
+   fun:Tcl_FSJoinPath
+   fun:TclFileDirname
+   fun:Tcl_FileObjCmd
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:Tcl_EvalObjEx
+   fun:Tcl_NamespaceObjCmd
+   fun:TclEvalObjvInternal
+   fun:Tcl_EvalEx
+   fun:Tcl_FSEvalFile
+   fun:Tcl_SourceObjCmd
+   fun:TclEvalObjvInternal
+   fun:Tcl_EvalObjv
+   fun:Tcl_EvalObjEx
+   fun:Tcl_UplevelObjCmd
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   fun:TclpRealloc
+   fun:Tcl_Realloc
+   fun:Tcl_SetObjLength
+   fun:TclpNativeJoinPath
+   fun:Tcl_FSJoinPath
+   fun:Tcl_FSJoinToPath
+   fun:SetFsPathFromAny
+   fun:Tcl_ConvertToType
+   fun:Tcl_FSConvertToPathType
+   fun:Tcl_FSGetNormalizedPath
+   fun:Tcl_FSOpenFileChannel
+   fun:Tcl_OpenObjCmd
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:TclObjInterpProc
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:Tcl_EvalObjEx
+   fun:Tcl_ForeachObjCmd
+   fun:TclEvalObjvInternal
+   fun:Tcl_EvalEx
+}
+{
+   
+   Memcheck:Leak
+   fun:realloc
+   fun:TclpRealloc
+   fun:Tcl_Realloc
+   fun:Tcl_SetObjLength
+   fun:TclpNativeJoinPath
+   fun:Tcl_FSJoinPath
+   fun:Tcl_FSJoinToPath
+   fun:SetFsPathFromAny
+   fun:Tcl_ConvertToType
+   fun:Tcl_FSConvertToPathType
+   fun:FSGetPathType
+   fun:Tcl_FSSplitPath
+   fun:TclFSNormalizeAbsolutePath
+   fun:Tcl_FSGetNormalizedPath
+   fun:Tcl_FSOpenFileChannel
+   fun:Tcl_OpenObjCmd
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:TclObjInterpProc
+   fun:TclEvalObjvInternal
+   fun:TclExecuteByteCode
+   fun:TclCompEvalObj
+   fun:Tcl_EvalObjEx
+   fun:Tcl_ForeachObjCmd
+   fun:TclEvalObjvInternal
+   fun:Tcl_EvalEx
+   fun:Tcl_FSEvalFile
+}
+{
+   
+   Memcheck:Leak
+   fun:malloc
+   fun:TclpAlloc
+   fun:Tcl_Alloc
+   fun:TclAllocateFreeObjects
+   fun:Tcl_NewObj
+   fun:TclpInitLibraryPath
+   fun:TclFindEncodings
+   fun:Tcl_FindExecutable
+   fun:Tcl_Main
+   fun:main
+}
+{
+   
+   Memcheck:Leak
+   fun:_Znwj
+   fun:_ZN9__gnu_cxx6__poolILb1EE13_M_initializeEPFvPvE
+   obj:/usr/lib/libstdc++.so.6.0.5
+   obj:/usr/lib/libstdc++.so.6.0.5
+   fun:_ZNSs4_Rep9_S_createEjjRKSaIcE
+   obj:/usr/lib/libstdc++.so.6.0.5
+   fun:_ZNSsC1EPKcRKSaIcE
+   fun:_ZN5cmsys11SystemTools18AddTranslationPathEPKcS2_
+   fun:_ZN5cmsys11SystemTools15ClassInitializeEv
+   fun:_Z41__static_initialization_and_destruction_0ii
+   obj:/home/barre/build/CMake-CMake-2-2-cvs-release/bin/ctest
+   obj:/home/barre/build/CMake-CMake-2-2-cvs-release/bin/ctest
+   fun:__libc_csu_init
+   fun:__libc_start_main
+}
+{
+   
+   Memcheck:Leak
+   fun:_Znwj
+   fun:_ZN9__gnu_cxx6__poolILb1EE16_M_reserve_blockEjj
+   obj:/usr/lib/libstdc++.so.6.0.5
+   fun:_ZNSs4_Rep9_S_createEjjRKSaIcE
+   obj:/usr/lib/libstdc++.so.6.0.5
+   fun:_ZNSsC1EPKcRKSaIcE
+   fun:_ZN5cmsys11SystemTools18AddTranslationPathEPKcS2_
+   fun:_ZN5cmsys11SystemTools15ClassInitializeEv
+   fun:_Z41__static_initialization_and_destruction_0ii
+   obj:/home/barre/build/CMake-CMake-2-2-cvs-release/bin/ctest
+   obj:/home/barre/build/CMake-CMake-2-2-cvs-release/bin/ctest
+   fun:__libc_csu_init
+   fun:__libc_start_main
+}
+{
+   VectorFFTTest1
+   Memcheck:Cond
+   fun:_Z3Cmpdd
+   fun:_Z3CmpRKSt7complexIfES2_
+   fun:main
+}
+{
+   VectorFFTTest2
+   Memcheck:Cond
+   fun:_Z3Cmpdd
+   fun:main
+}
+{
+   vfprintf1
+   Memcheck:Value4
+   fun:_itoa_word
+   fun:vfprintf
+}
+{
+   vfprintf3
+   Memcheck:Cond
+   fun:__mpn_extract_double
+   fun:__printf_fp
+   fun:vfprintf
+}
+{
+   vfprintf4
+   Memcheck:Cond
+   fun:vfprintf
+}
+{
+   b2AffineWrite
+   Memcheck:Param
+   write(buf)
+   fun:__write_nocancel
+   fun:_IO_do_write@@GLIBC_2.1
+   fun:_IO_file_close_it@@GLIBC_2.1
+   fun:fclose@@GLIBC_2.1
+   fun:_ZN17B2AffineTransformIN3itk5ImageIfLj3EEEE5WriteERKSsS5_S5_
+}
+# Suppress valgrind warnings for zlib
+#
+#----- Forwarded Message
+#From: rick reynolds 
+#Date: Wed, 13 Jun 2007 11:32:08 -0400
+#To: , , ,
+#
+#Subject: nifti updates
+#So I've been playing with the nifti code a bit.  I'll list the
+#updates in a separate email, just for clarity.  Hopefully the
+#Valgrind warnings are basically gone now.  The only one that
+#should remain is the one containing these lines:
+#
+#----------------------------------------------------------------------
+#==31427== Conditional jump or move depends on uninitialised value(s)
+#==31427==    by 0x3A1DA045CA: deflate (in /usr/lib64/libz.so.1.2.1.2)
+#==31427==    by 0x3A1DA03AE4: gzclose (in /usr/lib64/libz.so.1.2.1.2)
+#==31427==    by 0x4175C5: nifti_image_write_hdr_img2 (nifti1_io.c:5181)
+#----------------------------------------------------------------------
+#
+#We cannot fix this.  It is due to intentional performance code
+#in the zlib library, and is addressed by the zlib FAQ.  See
+#question #36 at http://www.zlib.net/zlib_faq.html, if you are
+#interested.
+{
+    LibZ1
+    Memcheck:Cond
+    obj:/*/libz.*
+}
+#################
+#Bash Suppressions
+{
+   bash21
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash20
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash19
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash18
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash17
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash16
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash15
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash14
+   Memcheck:Leak
+   fun:realloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:print_simple_command
+   fun:execute_command_internal
+   fun:execute_command
+   obj:/bin/bash
+   fun:execute_command_internal
+   fun:parse_and_execute
+}
+{
+   bash13
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash12
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash11
+   Memcheck:Leak
+   fun:realloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:print_simple_command
+   fun:execute_command_internal
+   fun:execute_command
+   obj:/bin/bash
+   fun:execute_command_internal
+   fun:parse_and_execute
+}
+{
+   bash10
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash09
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash08
+   Memcheck:Leak
+   fun:realloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:print_simple_command
+   fun:execute_command_internal
+   fun:execute_command
+   obj:/bin/bash
+   fun:execute_command_internal
+   fun:parse_and_execute
+}
+{
+   bash07
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash06
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash05
+   Memcheck:Leak
+   fun:realloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:print_simple_command
+   fun:execute_command_internal
+   fun:execute_command
+   obj:/bin/bash
+   fun:execute_command_internal
+   fun:parse_and_execute
+}
+{
+   bash04
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+{
+   bash03
+   Memcheck:Leak
+   fun:malloc
+   fun:xrealloc
+   obj:/bin/bash
+   fun:yyparse
+   fun:parse_command
+   fun:parse_and_execute
+   obj:/bin/bash
+   fun:maybe_execute_file
+   obj:/bin/bash
+   fun:main
+}
+{
+   bash02
+   Memcheck:Leak
+   fun:realloc
+   fun:xrealloc
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   obj:/bin/bash
+   fun:print_simple_command
+   fun:execute_command_internal
+   fun:execute_command
+   obj:/bin/bash
+   fun:execute_command_internal
+   fun:parse_and_execute
+}
+{
+   bash01
+   Memcheck:Leak
+   fun:malloc
+   fun:xmalloc
+   fun:set_default_locale
+   fun:main
+}
+
+{
+   getpwduid suppression for GLIBC_2.2.5
+   Memcheck:Param
+   socketcall.sendto(msg)
+   fun:send
+   fun:get_mapping
+   fun:__nscd_get_map_ref
+   fun:nscd_getpw_r
+   fun:__nscd_getpwuid_r
+   fun:getpwuid_r@@GLIBC_2.2.5
+   fun:getpwuid
+}
+
diff --git a/BRAINSCommonLib/BuildScripts/brains.kws.xml b/BRAINSCommonLib/BuildScripts/brains.kws.xml
new file mode 100644
index 00000000..a95c2916
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/brains.kws.xml
@@ -0,0 +1,19 @@
+
+
+120
+0,1,2
+[A-Z]
+m_[A-Z]
+0
+1
+1
+3
+/**, *, */,true
+SPACE,2,true,true
+itk
+[NameOfClass],itk
+__[NameOfClass]_[Extension]
+2
+
+1,1
+
diff --git a/BRAINSCommonLib/BuildScripts/brains.uncrustify.cfg b/BRAINSCommonLib/BuildScripts/brains.uncrustify.cfg
new file mode 100644
index 00000000..2c5184cd
--- /dev/null
+++ b/BRAINSCommonLib/BuildScripts/brains.uncrustify.cfg
@@ -0,0 +1,2126 @@
+###This is the configuration file that seems to meet the ITK
+###standard for formatting according to the ITK style guide.
+###need to verify that it will pass the KWStyle mechanisms.
+#Uncrustify 0.51+svn
+
+#
+#General options
+#
+
+#The type of line endings
+newlines                                 = auto     #auto / lf / crlf / cr
+
+#The original size of tabs in the input
+  input_tab_size                           = 2        #number
+
+#The size of tabs in the output (only used if align_with_tabs=true)
+    output_tab_size                          = 2        #number
+
+#The ascii value of the string escape char, usually 92 (\) or 94 (^). (Pawn)
+      string_escape_char                       = 92       #number
+
+#Alternate string escape char for Pawn. Only works right before the quote char.
+        string_escape_char2                      = 0        #number
+
+#
+#Indenting
+#
+
+#The number of columns to indent per level.
+#Usually 2, 3, 4, or 8.
+          indent_columns                           = 2        #number
+
+#How to use tabs when indenting code
+#0 =spaces only
+#1 =indent with tabs, align with spaces
+#2 =indent and align with tabs
+            indent_with_tabs                         = 0        #number
+
+#Whether to indent strings broken by '\' so that they line up
+              indent_align_string                      = true    #false / true
+
+#The number of spaces to indent multi-line XML strings.
+#Requires indent_align_string=True
+                indent_xml_string                        = 0        #number
+
+#Spaces to indent '{' from level
+                  indent_brace                             = 0        #number
+
+#Whether braces are indented to the body level
+                    indent_braces                            = true    #false / true
+
+#Disabled indenting function braces if indent_braces is true
+                      indent_braces_no_func                    = true    #false / true
+
+#Disabled indenting struct braces if indent_braces is true
+                        indent_braces_no_struct                  = true    #false / true
+
+#Disabled indenting class braces if indent_braces is true
+                          indent_braces_no_class                   = true    #false / true
+
+#Indent based on the size of the brace parent, ie 'if' => 3 spaces, 'for' => 4 spaces, etc.
+                            indent_brace_parent                      = false    #false / true
+
+#Whether the 'namespace' body is indented
+                              indent_namespace                         = false    #false / true
+
+#The number of spaces to indent a namespace block
+                                indent_namespace_level                   = 0
+
+#If the body of the namespace is longer than this number, it won't be indented.
+#Requires indent_namespace=true. Default=0 (no limit)
+                                  indent_namespace_limit                   = 3
+
+#Whether the 'extern "C"' body is indented
+                                    indent_extern                            = false    #false / true
+
+##Would like class body brace to not be indented.
+#Whether the 'class' body is indented
+                                      indent_class                             = true    #false / true
+
+#Whether to indent the stuff after a leading class colon
+                                        indent_class_colon                       = false    #false / true
+
+#False =treat 'else\nif' as 'else if' for indenting purposes
+#True =indent the 'if' one level
+                                          indent_else_if                           = true    #false / true
+
+#Amount to indent variable declarations after a open brace. neg=relative, pos=absolute
+                                            indent_var_def_blk                       = 0        #number
+
+#True :  indent continued function call parameters one indent level
+#False : align parameters under the open paren
+                                              indent_func_call_param                   = false    #false / true
+
+#Same as indent_func_call_param, but for function defs
+                                                indent_func_def_param                    = false    #false / true
+
+#Same as indent_func_call_param, but for function protos
+                                                  indent_func_proto_param                  = false    #false / true
+
+#Same as indent_func_call_param, but for class declarations
+                                                    indent_func_class_param                  = false    #false / true
+
+#Same as indent_func_call_param, but for class variable constructors
+                                                      indent_func_ctor_var_param               = false    #false
+                                                        / true
+
+#Same as indent_func_call_param, but for templates
+                                                        indent_template_param                    = false    #false
+                                                          / true
+
+#Double the indent for indent_func_xxx_param options
+                                                          indent_func_param_double                 = false    #false
+                                                            / true
+
+#Indentation column for standalone 'const' function decl/proto qualifier
+                                                            indent_func_const                        =
+                                                              0        #number
+
+#Indentation column for standalone 'throw' function decl/proto qualifier
+                                                              indent_func_throw                        =
+                                                                0        #number
+
+#The number of spaces to indent a continued '->' or '.'
+#Usually set to 0, 1, or indent_columns.
+                                                                indent_member                            =
+                                                                  2        #number
+
+#Spaces to indent single line (' // ') comments on lines before code
+                                                                  indent_sing_line_comments                =
+                                                                    0        #number
+
+#If set, will indent trailing single line (' // ') comments relative
+#to the code instead of trying to keep the same absolute column
+                                                                    indent_relative_single_line_comments     =
+                                                                      false    #false / true
+
+#Spaces to indent 'case' from 'switch'
+#Usually 0 or indent_columns.
+                                                                      indent_switch_case                       =
+                                                                        2        #number
+
+#Spaces to shift the 'case' line, without affecting any other lines
+#Usually 0.
+                                                                        indent_case_shift                        =
+                                                                          0        #number
+
+#Spaces to indent '{' from 'case'.
+#By default, the brace will appear under the 'c' in case.
+#Usually set to 0 or indent_columns.
+                                                                          indent_case_brace                        =
+                                                                            2        #number
+
+#Whether to indent comments found in first column
+                                                                            indent_col1_comment                      =
+                                                                              true    #false / true
+
+#How to indent goto labels
+#> 0 : absolute column where 1 is the leftmost column
+#<= 0 : subtract from brace indent
+                                                                              indent_label
+                                                                                = 1        #number
+
+#Same as indent_label, but for access specifiers that are followed by a colon
+                                                                                  indent_access_spec
+                                                                                    = 1        #number
+
+#Indent the code after an access specifier by one level.
+#If set, this option forces 'indent_access_spec=0'
+                                                                                      indent_access_spec_body
+                                                                                        = false    #false / true
+
+#If \
+                                                                                          an open paren is followed by a newline, indent the next line so that it lines up after the open paren (not recommended)
+                                                                                          indent_paren_nl
+                                                                                            = false    #false / true
+
+#Controls the indent of a close paren after a newline.
+#0 : Indent to body level
+#1 : Align under the open paren
+#2 : Indent to the brace level
+                                                                                              indent_paren_close
+                                                                                                = 0        #number
+
+#Controls the indent of a comma when inside a paren.If TRUE, aligns under the open paren
+                                                                                                  indent_comma_paren
+                                                                                                    = false    #false
+                                                                                                      / true
+
+#Controls the indent of a BOOL operator when inside a paren.If TRUE, aligns under the open paren
+                                                                                                      indent_bool_paren
+                                                                                                        = false    #
+                                                                                                          false / true
+
+#If \
+                                                                                                          an open square is followed by a newline, indent the next line so that it lines up after the open square (not recommended)
+                                                                                                          indent_square_nl
+                                                                                                            = false
+                                                                                                              #false
+                                                                                                              / true
+
+#Don 't change the relative indent of ESQL/C 'EXEC SQL' bodies
+                                                                                                              indent_preserve_sql
+                                                                                                                = false
+                                                                                                                  #
+                                                                                                                  false / true
+
+#Align continued statements at the '='. Default=True
+#If FALSE or the '=' is followed by a newline, the next line is indent one tab.
+                                                                                                                  indent_align_assign
+                                                                                                                    =
+                                                                                                                      true
+                                                                                                                      #false / true
+
+#
+#Spacing options
+#
+
+#Add or remove space around arithmetic operator '+', '-', '/', '*', etc
+                                                                                                                      sp_arith
+                                                                                                                        =
+                                                                                                                          add
+                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space around assignment operator '=', '+=', etc
+                                                                                                                          sp_assign
+                                                                                                                            =
+                                                                                                                              add
+                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before assignment operator '=', '+=', etc. Overrides sp_assign.
+                                                                                                                              sp_before_assign
+                                                                                                                                =
+                                                                                                                                  add
+                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space after assignment operator '=', '+=', etc. Overrides sp_assign.
+                                                                                                                                  sp_after_assign
+                                                                                                                                    =
+                                                                                                                                      add
+                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space around assignment '=' in enum
+                                                                                                                                      sp_enum_assign
+                                                                                                                                        =
+                                                                                                                                          add
+                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space before assignment '=' in enum. Overrides sp_enum_assign.
+                                                                                                                                          sp_enum_before_assign
+                                                                                                                                            =
+                                                                                                                                              add
+                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space after assignment '=' in enum. Overrides sp_enum_assign.
+                                                                                                                                              sp_enum_after_assign
+                                                                                                                                                =
+                                                                                                                                                  add
+                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space around boolean operators '&&' and '||'
+                                                                                                                                                  sp_bool
+                                                                                                                                                    =
+                                                                                                                                                      add
+                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space around compare operator '<', '>', '==', etc
+                                                                                                                                                      sp_compare
+                                                                                                                                                        =
+                                                                                                                                                          add
+                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space inside '(' and ')'
+                                                                                                                                                          sp_inside_paren
+                                                                                                                                                            =
+                                                                                                                                                              add
+                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space between nested parens
+                                                                                                                                                              sp_paren_paren
+                                                                                                                                                                =
+                                                                                                                                                                  ignore
+                                                                                                                                                                  #ignore / add / remove / force
+
+#Whether to balance spaces inside nested parens
+                                                                                                                                                                  sp_balance_nested_parens
+                                                                                                                                                                    =
+                                                                                                                                                                      true
+                                                                                                                                                                      #false / true
+
+#Add or remove space between ')' and '{'
+                                                                                                                                                                      sp_paren_brace
+                                                                                                                                                                        =
+                                                                                                                                                                          add
+                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space before pointer star '*'
+                                                                                                                                                                          sp_before_ptr_star
+                                                                                                                                                                            =
+                                                                                                                                                                              add
+                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before pointer star '*' that isn't followed by a variable name
+#If set to 'ignore', sp_before_ptr_star is used instead.
+                                                                                                                                                                              sp_before_unnamed_ptr_star
+                                                                                                                                                                                =
+                                                                                                                                                                                  add
+                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between pointer stars '*'
+                                                                                                                                                                                  sp_between_ptr_star
+                                                                                                                                                                                    =
+                                                                                                                                                                                      remove
+                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after pointer star '*', if followed by a word.
+                                                                                                                                                                                      sp_after_ptr_star
+                                                                                                                                                                                        =
+                                                                                                                                                                                          remove
+                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space after a pointer star '*', if followed by a func proto/def.
+                                                                                                                                                                                          sp_after_ptr_star_func
+                                                                                                                                                                                            =
+                                                                                                                                                                                              remove
+                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before a pointer star '*', if followed by a func proto/def.
+                                                                                                                                                                                              sp_before_ptr_star_func
+                                                                                                                                                                                                =
+                                                                                                                                                                                                  add
+                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before a reference sign '&'
+                                                                                                                                                                                                  sp_before_byref
+                                                                                                                                                                                                    =
+                                                                                                                                                                                                      add
+                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before a reference sign '&' that isn't followed by a variable name
+#If set to 'ignore', sp_before_byref is used instead.
+                                                                                                                                                                                                      sp_before_unnamed_byref
+                                                                                                                                                                                                        =
+                                                                                                                                                                                                          add
+                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space after reference sign '&', if followed by a word.
+                                                                                                                                                                                                          sp_after_byref
+                                                                                                                                                                                                            =
+                                                                                                                                                                                                              remove
+                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space after a reference sign '&', if followed by a func proto/def.
+                                                                                                                                                                                                              sp_after_byref_func
+                                                                                                                                                                                                                =
+                                                                                                                                                                                                                  remove
+                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before a reference sign '&', if followed by a func proto/def.
+                                                                                                                                                                                                                  sp_before_byref_func
+                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between type and word
+                                                                                                                                                                                                                      sp_after_type
+                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                          force
+                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space in 'template <' vs 'template<'.
+#If set to ignore, sp_before_angle is used.
+                                                                                                                                                                                                                          sp_template_angle
+                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                              add
+                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before '<>'
+                                                                                                                                                                                                                              sp_before_angle
+                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                  remove
+                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space inside '<' and '>'
+                                                                                                                                                                                                                                  sp_inside_angle
+                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after '<>'
+                                                                                                                                                                                                                                      sp_after_angle
+                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                          add
+                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space between '<>' and '(' as found in 'new List();'
+                                                                                                                                                                                                                                          sp_angle_paren
+                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                              remove
+                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space between '<>' and a word as in 'List m;'
+                                                                                                                                                                                                                                              sp_angle_word
+                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                  add
+                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before '(' of 'if', 'for', 'switch', and 'while'
+                                                                                                                                                                                                                                                  sp_before_sparen
+                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space inside if-condition '(' and ')'
+                                                                                                                                                                                                                                                      sp_inside_sparen
+                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                          add
+                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space before if-condition ')'. Overrides sp_inside_sparen.
+                                                                                                                                                                                                                                                          sp_inside_sparen_close
+                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                              add
+                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space after ')' of 'if', 'for', 'switch', and 'while'
+                                                                                                                                                                                                                                                              sp_after_sparen
+                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                  ignore
+                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between ')' and '{' of 'if', 'for', 'switch', and 'while'
+                                                                                                                                                                                                                                                                  sp_sparen_brace
+                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'invariant' and '(' in the D language.
+                                                                                                                                                                                                                                                                      sp_invariant_paren
+                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                          ignore
+                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space after the ')' in 'invariant (C) c' in the D language.
+                                                                                                                                                                                                                                                                          sp_after_invariant_paren
+                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                              ignore
+                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before empty statement ';' on 'if', 'for' and 'while'
+                                                                                                                                                                                                                                                                              sp_special_semi
+                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                  remove
+                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before ';'
+                                                                                                                                                                                                                                                                                  sp_before_semi
+                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before ';' in non-empty 'for' statements
+                                                                                                                                                                                                                                                                                      sp_before_semi_for
+                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                          remove
+                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space before a semicolon of an empty part of a for statment.
+                                                                                                                                                                                                                                                                                          sp_before_semi_for_empty
+                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                              remove
+                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space after the final semicolon of an empty part of a for statment: for ( ; ;  ).
+                                                                                                                                                                                                                                                                                              sp_after_semi_for_empty
+                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                  add
+                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before '[' (except '[]')
+                                                                                                                                                                                                                                                                                                  sp_before_square
+                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before '[]'
+                                                                                                                                                                                                                                                                                                      sp_before_squares
+                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                          remove
+                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space inside '[' and ']'
+                                                                                                                                                                                                                                                                                                          sp_inside_square
+                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                              remove
+                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space after ','
+                                                                                                                                                                                                                                                                                                              sp_after_comma
+                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                  add
+                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space before ','
+                                                                                                                                                                                                                                                                                                                  sp_before_comma
+                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after class ':'
+                                                                                                                                                                                                                                                                                                                      sp_after_class_colon
+                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                          add
+                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space before class ':'
+                                                                                                                                                                                                                                                                                                                          sp_before_class_colon
+                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                              add
+                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space before case ':'
+                                                                                                                                                                                                                                                                                                                              sp_before_case_colon
+                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                  remove
+                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between 'operator' and operator sign
+                                                                                                                                                                                                                                                                                                                                  sp_after_operator
+                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between the operator symbol and the open paren, as in 'operator ++('
+                                                                                                                                                                                                                                                                                                                                      sp_after_operator_sym
+                                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                                          remove
+                                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space after C/D cast, ie 'cast(int)a' vs 'cast(int) a' or '(int)a' vs '(int) a'
+                                                                                                                                                                                                                                                                                                                                          sp_after_cast
+                                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                                              remove
+                                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove spaces inside cast parens
+                                                                                                                                                                                                                                                                                                                                              sp_inside_paren_cast
+                                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                                  remove
+                                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between the type and open paren in a C++ cast, ie 'int(exp)' vs 'int (exp)'
+                                                                                                                                                                                                                                                                                                                                                  sp_cpp_cast_paren
+                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'sizeof' and '('
+                                                                                                                                                                                                                                                                                                                                                      sp_sizeof_paren
+                                                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                                                          remove
+                                                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space after the tag keyword (Pawn)
+                                                                                                                                                                                                                                                                                                                                                          sp_after_tag
+                                                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                                                              remove
+                                                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space inside enum '{' and '}'
+                                                                                                                                                                                                                                                                                                                                                              sp_inside_braces_enum
+                                                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                                                  ignore
+                                                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space inside struct/union '{' and '}'
+                                                                                                                                                                                                                                                                                                                                                                  sp_inside_braces_struct
+                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space inside '{' and '}'
+                                                                                                                                                                                                                                                                                                                                                                      sp_inside_braces
+                                                                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                                                                          ignore
+                                                                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space inside '{}'
+                                                                                                                                                                                                                                                                                                                                                                          sp_inside_braces_empty
+                                                                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                                                                              ignore
+                                                                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space between return type and function name
+#A minimum of 1 is forced except for pointer return types.
+                                                                                                                                                                                                                                                                                                                                                                              sp_type_func
+                                                                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                                                                  ignore
+                                                                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between function name and '(' on function declaration
+                                                                                                                                                                                                                                                                                                                                                                                  sp_func_proto_paren
+                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between function name and '(' on function definition
+                                                                                                                                                                                                                                                                                                                                                                                      sp_func_def_paren
+                                                                                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                                                                                          ignore
+                                                                                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space inside empty function '()'
+                                                                                                                                                                                                                                                                                                                                                                                          sp_inside_fparens
+                                                                                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                                                                                              ignore
+                                                                                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space inside function '(' and ')'
+                                                                                                                                                                                                                                                                                                                                                                                              sp_inside_fparen
+                                                                                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                                                                                  ignore
+                                                                                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between ']' and '(' when part of a function call.
+                                                                                                                                                                                                                                                                                                                                                                                                  sp_square_fparen
+                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between ')' and '{' of function
+                                                                                                                                                                                                                                                                                                                                                                                                      sp_fparen_brace
+                                                                                                                                                                                                                                                                                                                                                                                                        =
+                                                                                                                                                                                                                                                                                                                                                                                                          ignore
+                                                                                                                                                                                                                                                                                                                                                                                                          #ignore / add / remove / force
+
+#Add or remove space between function name and '(' on function calls
+                                                                                                                                                                                                                                                                                                                                                                                                          sp_func_call_paren
+                                                                                                                                                                                                                                                                                                                                                                                                            =
+                                                                                                                                                                                                                                                                                                                                                                                                              ignore
+                                                                                                                                                                                                                                                                                                                                                                                                              #ignore / add / remove / force
+
+#Add or remove space between the user function name and '(' on function calls
+#You need to set a keyword to be a user function, like this: 'set func_call_user _' in the config file.
+                                                                                                                                                                                                                                                                                                                                                                                                              sp_func_call_user_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                =
+                                                                                                                                                                                                                                                                                                                                                                                                                  ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                  #ignore / add / remove / force
+
+#Add or remove space between a constructor/destructor and the open paren
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_func_class_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'return' and '('
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_return_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between '__attribute__' and '('
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_attribute_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'defined' and '(' in '#if defined (FOO)'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_defined_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'throw' and '(' in 'throw (something)'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_throw_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between macro and value
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_macro
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between macro function ')' and value
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_macro_func
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'else' and '{' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_else_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between '}' and 'else' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_brace_else
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between '}' and the name of a typedef on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_brace_typedef
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'catch' and '{' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_catch_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between '}' and 'catch' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_brace_catch
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'finally' and '{' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_finally_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between '}' and 'finally' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_brace_finally
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between 'try' and '{' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_try_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space between get/set and '{' if on the same line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_getset_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before the '::' operator
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_before_dc
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the '::' operator
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_after_dc
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove around the D named array initializer ':' operator
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_d_array_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the '!' (not) operator.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_not
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the '~' (invert) operator.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_inv
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the '&' (address-of) operator.
+#This does not affect the spacing after a '&' that is part of a type.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_addr
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space around the '.' or '->' operators
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_member
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the '*' (dereference) operator.
+#This does not affect the spacing after a '*' that is part of a type.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_deref
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after '+' or '-', as in 'x = -5' or 'y = +7'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_sign
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before or after '++' and '--', as in '(--x)' or 'y++;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_incdec
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before a backslash-newline at the end of a line
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_before_nl_cont
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the scope '+' or '-', as in '-(void) foo;' or '+(int) bar;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_after_oc_scope
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the colon in message specs
+#'-(int) f:(int) x;' vs '-(int) f: (int) x;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_after_oc_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before the colon in message specs
+#'-(int) f: (int) x;' vs '-(int) f : (int) x;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_before_oc_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the colon in message specs
+#'[object setValue:1];' vs '[object setValue: 1];'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_after_send_oc_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space before the colon in message specs
+#'[object setValue:1];' vs '[object setValue :1];'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_before_send_oc_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space after the (type) in message specs
+#'-(int) f: (int) x;' vs '-(int) f: (int)x;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_after_oc_type
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space around the ':' in 'b ? t : f'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_cond_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove space around the '?' in 'b ? t : f'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_cond_question
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Fix the spacing between 'case' and the label. Only 'ignore' and 'force' make sense here.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_case_label
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Control the space around the D '..' operator.
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_range
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Control the space after the opening of a C++ comment ' // A' vs '//A'
+                                                                                                                                                                                                                                                                                                                                                                                                                  sp_cmt_cpp_start
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#
+#Code alignment (not left column spaces/tabs)
+#
+
+#Whether to keep non-indenting tabs
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_keep_tabs
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to use tabs for alinging
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_with_tabs
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to bump out to the next tab when aligning
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_on_tabstop
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to left-align numbers
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_number_left
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Align variable definitions in prototypes and functions
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_func_params
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Align parameters in single-line functions that have the same name.
+#The function names must already be aligned with each other.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_same_func_call_params
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The span for aligning variable definitions (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#How to align the star in variable definitions.
+#0 =Part of the type     'void *   foo;'
+#1 =Part of the variable 'void     *foo;'
+#2 =Dangling             'void    *foo;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_star_style
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#How to align the '&' in variable definitions.
+#0 =Part of the type
+#1 =Part of the variable
+#2 =Dangling
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_amp_style
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The threshold for aligning variable definitions (0=no limit)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_thresh
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The gap for aligning variable definitions
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to align the colon in struct bit fields
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to align inline struct/enum/union variable definitions
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_def_inline
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The span for aligning on '=' in assignments (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_assign_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The threshold for aligning on '=' in assignments (0=no limit)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_assign_thresh
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning on '=' in enums (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_enum_equ_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The threshold for aligning on '=' in enums (0=no limit)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_enum_equ_thresh
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning struct/union (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_struct_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The threshold for aligning struct/union member definitions (0=no limit)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_struct_thresh
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The gap for aligning struct/union member definitions
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_var_struct_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning struct initializer values (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_struct_init_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The minimum space between the type and the synonym of a typedef
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_typedef_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning single-line typedefs (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_typedef_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#How to align typedef'd functions with other typedefs
+#0 : Don't mix them at all
+#1 : align the open paren with the types
+#2 : align the function type name with the other type names
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_typedef_func
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Controls the positioning of the '*' in typedefs. Just try it.
+#0 : Align on typdef type, ignore '*'
+#1 : The '*' is part of type name: typedef int  *pint;
+#2 : The '*' is part of the type, but dangling: typedef int *pint;
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_typedef_star_style
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Controls the positioning of the '&' in typedefs. Just try it.
+#0 : Align on typdef type, ignore '&'
+#1 : The '&' is part of type name: typedef int  &pint;
+#2 : The '&' is part of the type, but dangling: typedef int &pint;
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_typedef_amp_style
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning comments that end lines (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_right_cmt_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#If aligning comments, mix with comments after '}' and #endif with less than 3 spaces before the comment
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_right_cmt_mix
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If a trailing comment is more than this number of columns away from the text it follows,
+#it will qualify for being aligned.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_right_cmt_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning function prototypes (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_func_proto_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Minimum gap between the return type and the function name.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_func_proto_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Align function protos on the 'operator' keyword instead of what follows
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_on_operator
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to mix aligning prototype and variable declarations.
+#If true, align_var_def_XXX options are used instead of align_func_proto_XXX options.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_mix_var_proto
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Align single-line functions with function prototypes, uses align_func_proto_span
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_single_line_func
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Aligning the open brace of single-line functions.
+#Requires align_single_line_func=true, uses align_func_proto_span
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_single_line_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Gap for align_single_line_brace.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_single_line_brace_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning ObjC msg spec (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_oc_msg_spec_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to align macros wrapped with a backslash and a newline.
+#This will not work right if the macro contains a multi-line comment.
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_nl_cont
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The minimum space between label and value of a preprocessor define
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_pp_define_gap
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The span for aligning on '#define' bodies (0=don't align)
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_pp_define_span
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Align lines that start with '<<' with previous '<<'. Default=true
+                                                                                                                                                                                                                                                                                                                                                                                                                  align_left_shift
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Newline adding and removing options
+#
+
+#Whether to collapse empty blocks between '{' and '}'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_collapse_empty_body
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line braced assignments - 'foo_t f = { 1, 2 };'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_assign_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line braced statements inside a class xx { } body
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_class_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line enums: 'enum foo { BAR = 15 };'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_enum_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line get or set functions
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_getset_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line function definitions - 'int foo() { return 0; }'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Don 't split one-line if/else statements - 'if(a) b++;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_if_leave_one_liners
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add or remove newlines at the start of the file
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_start_of_file
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#The number of newlines at the start of the file (only used if nl_start_of_file is 'add' or 'force'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_start_of_file_min
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Add or remove newline at the end of the file
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_end_of_file
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      force
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#The number of newlines at the end of the file (only used if nl_end_of_file is 'add' or 'force')
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_end_of_file_min
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Add or remove newline between '=' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_assign_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between '=' and '[' (D only)
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_assign_square
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after '= [' (D only). Will also affect the newline before the ']'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_square_assign
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#The number of newlines after a block of variable definitions
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_var_def_blk
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Add or remove newline between a function call's ')' and '{', as in:
+#list_for_each (item, &list) { }
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_fcall_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'enum' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_enum_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'struct and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_struct_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'union' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_union_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'if' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_if_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between '}' and 'else'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_brace_else
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'else if' and '{'
+#If set to ignore, nl_if_brace is used instead
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_elseif_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'else' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_else_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'else' and 'if'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_else_if
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between '}' and 'finally'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_brace_finally
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'finally' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_finally_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'try' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_try_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between get/set and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_getset_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'for' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_for_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'catch' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_catch_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between '}' and 'catch'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_brace_catch
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'while' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_while_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'do' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_do_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between '}' and 'while' of 'do' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_brace_while
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      remove
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'switch' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_switch_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add a newline between ')' and '{' if the ')' is on a different line than the if/for/etc.
+#Overrides nl_for_brace, nl_if_brace, nl_switch_brace, nl_while_switch, and nl_catch_brace.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_multi_line_cond
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Force a newline in a define after the macro name for multi-line defines.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_multi_line_define
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline before 'case' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_case
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add or remove newline between ')' and 'throw'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_throw
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to put a newline after 'case' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_case
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Newline between namespace and {
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_namespace_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'template<>' and whatever follows.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_template_class
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between 'class' and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_class_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after each ',' in the constructor member initialization
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_class_init_args
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between return type and function name in definition
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_type_name
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between function scope and name in a definition
+#Controls the newline after '::' in 'void A::f() { }'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_scope_name
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between return type and function name in a prototype
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_proto_type_name
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between a function name and the opening '('
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_paren
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after '(' in a function declaration
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_decl_start
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after each ',' in a function declaration
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_decl_args
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline before the ')' in a function declaration
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_func_decl_end
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline between function signature and '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_fdef_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to put a newline after 'return' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_return
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add or remove a newline between the return keyword and return expression.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_return_expr
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to put a newline after semicolons, except in 'for' statements
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_semicolon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline after brace open.
+#This also adds a newline before the matching brace close.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_brace_open
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If nl_after_brace_open and nl_after_brace_open_cmt are true, a newline is
+#placed between the open brace and a trailing single-line comment.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_brace_open_cmt
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline after a virtual brace open.
+#These occur in un-braced if/while/do/for statement bodies.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_vbrace_open
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline after a brace close.
+#Does not apply if followed by a necessary ';'.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_brace_close
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline after a virtual brace close.
+#Would add a newline before return in: 'if (foo) a++; return;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_vbrace_close
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to alter newlines in '#define' macros
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_define_macro
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to not put blanks after '#ifxx', '#elxx', or before '#endif'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_squeeze_ifdef
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add or remove newline before 'if'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_if
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after 'if'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_if
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline before 'for'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_for
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after 'for'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_for
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline before 'while'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_while
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after 'while'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_while
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline before 'switch'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_switch
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after 'switch'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_switch
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline before 'do'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_do
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove newline after 'do'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_do
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to double-space commented-entries in struct/enum
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_ds_struct_enum_cmt
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to double-space before the close brace of a struct/union/enum
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_ds_struct_enum_close_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add or remove a newline around a class colon.
+#Related to pos_class_colon, nl_class_init_args, and pos_comma.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_class_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Change simple unbraced if statements into a one-liner
+#'if(b)\n i++;' => 'if(b) i++;'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_create_if_one_liner
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Change simple unbraced for statements into a one-liner
+#'for (i=0;i<5;i++)\n foo(i);' => 'for (i=0;i<5;i++) foo(i);'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_create_for_one_liner
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Change simple unbraced while statements into a one-liner
+#'while (i<5)\n foo(i++);' => 'while (i<5) foo(i++);'
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_create_while_one_liner
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Positioning options
+#
+
+#The position of arithmetic operators in wrapped expressions
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_arith
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      lead
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#The position of assignment in wrapped expressions
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_assign
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      lead
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#The position of boolean operators in wrapped expressions
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_bool
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      lead
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#The position of the comma in wrapped expressions
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_comma
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      trail
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#The position of the comma in the constructor initialization list
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_class_comma
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      trail
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#The position of colons between constructor and member initialization
+                                                                                                                                                                                                                                                                                                                                                                                                                  pos_class_colon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      trail
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / lead / trail
+
+#
+#Line Splitting options
+#
+
+#Try to limit code width to N number of columns
+                                                                                                                                                                                                                                                                                                                                                                                                                  code_width
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      120
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to fully split long 'for' statements at semi-colons
+                                                                                                                                                                                                                                                                                                                                                                                                                  ls_for_split_full
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to fully split long function protos/calls at commas
+                                                                                                                                                                                                                                                                                                                                                                                                                  ls_func_split_full
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Blank line options
+#
+
+#The maximum consecutive newlines
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_max
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after a function prototype, if followed by another function prototype
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_func_proto
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after a function prototype, if not followed by another function prototype
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_func_proto_group
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after '}' of a multi-line function body
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_func_body
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after '}' of a single line function body
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_func_body_one_liner
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The minimum number of newlines before a multi-line comment.
+#Doesn 't apply if after a brace open or another multi-line comment.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_block_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The minimum number of newlines before a single-line C comment.
+#Doesn 't apply if after a brace open or other single-line C comments.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_c_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The minimum number of newlines before a CPP comment.
+#Doesn 't apply if after a brace open or other CPP comments.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_cpp_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to force a newline after a mulit-line comment.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_multiline_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The number of newlines before a 'private:', 'public:', 'protected:', 'signals:', or 'slots:' label.
+#Will not change the newline count if after a brace open.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_before_access_spec
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      1
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after a 'private:', 'public:', 'protected:', 'signals:', or 'slots:' label.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_access_spec
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines between a function def and the function comment.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_comment_func_def
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines after a try-catch-finally block that isn't followed by a brace close.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_after_try_catch_finally
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines before and after a property, indexer or event decl.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_around_cs_property
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of newlines between the get/set/add/remove handlers in C#.
+#0 = No change.
+                                                                                                                                                                                                                                                                                                                                                                                                                  nl_between_get_set
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to remove blank lines after '{'
+                                                                                                                                                                                                                                                                                                                                                                                                                  eat_blanks_after_open_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to remove blank lines before '}'
+                                                                                                                                                                                                                                                                                                                                                                                                                  eat_blanks_before_close_brace
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Code modifying options (non-whitespace)
+#
+
+#Add or remove braces on single-line 'do' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_do
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove braces on single-line 'for' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_for
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove braces on single-line function defintions. (Pawn)
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_function
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove braces on single-line 'if' statement. Will not remove the braces if they contain an 'else'.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_if
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Don 't remove braces around statements that span N newlines
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_nl
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Add or remove braces on single-line 'while' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_brace_while
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      add
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Add or remove unnecessary paren on 'return' statement
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_paren_on_return
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to change optional semicolons to real semicolons
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_pawn_semicolon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Add parens on 'while' and 'if' statement around bools
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_full_paren_if_bool
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to remove superfluous semicolons
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_remove_extra_semicolon
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If a function body exceeds the specified number of newlines and doesn't have a comment after
+#the close brace, a comment will be added.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_add_long_function_closebrace_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#If a switch body exceeds the specified number of newlines and doesn't have a comment after
+#the close brace, a comment will be added.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_add_long_switch_closebrace_comment
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#If TRUE, will sort consecutive single-line 'import' statements [Java, D]
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_sort_import
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If TRUE, will sort consecutive single-line 'using' statements [C#]
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_sort_using
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If TRUE, will sort consecutive single-line '#include' statements [C/C++] and '#import' statements [Obj-C]
+#This is generally a bad idea, as it may break your code.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_sort_include
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If TRUE, it will move a 'break' that appears after a fully braced 'case' before the close brace.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_move_case_break
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If TRUE, it will remove a void 'return;' that appears as the last statement in a function.
+                                                                                                                                                                                                                                                                                                                                                                                                                  mod_remove_empty_return
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Comment modifications
+#
+
+#Try to wrap comments at cmt_width columns
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_width
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      80
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#If false, disable all multi-line comment changes, including cmt_width and leading chars.
+#Default is true.
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_indent_multi
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to group c-comments that look like they are in a block
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_c_group
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put an empty '/*' on the first line of the combined c-comment
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_c_nl_start
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline before the closing '*/' of the combined c-comment
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_c_nl_end
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to group cpp-comments that look like they are in a block
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_cpp_group
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put an empty '/*' on the first line of the combined cpp-comment
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_cpp_nl_start
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a newline before the closing '*/' of the combined cpp-comment
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_cpp_nl_end
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to change cpp-comments into c-comments
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_cpp_to_c
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to put a star on subsequent comment lines
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_star_cont
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The number of spaces to insert at the start of subsequent comment lines
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_sp_before_star_cont
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The number of spaces to insert after the star on subsequent comment lines
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_sp_after_star_cont
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#For multi-line comments with a '*' lead, remove leading spaces if the first and last lines of
+#the comment are the same length. Default=True
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_multi_check_last
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      true
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#The filename that contains text to insert at the head of a file if the file doesn't start with a C/C++ comment.
+#Will substitue $(filename) with the current file's name.
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_insert_file_header
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ""
+                                                                                                                                                                                                                                                                                                                                                                                                                      #string
+
+#The filename that contains text to insert at the end of a file if the file doesn't end with a C/C++ comment.
+#Will substitue $(filename) with the current file's name.
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_insert_file_footer
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ""
+                                                                                                                                                                                                                                                                                                                                                                                                                      #string
+
+#The \
+                                                                                                                                                                                                                                                                                                                                                                                                                  filename that contains text to insert before a function implementation if the function isn't preceeded with a C/C++ comment.
+#Will substitue $(function) with the function name and $(javaparam) with the javadoc @param and @return stuff.
+#Will also substitute $(fclass) with the class name: void CFoo::Bar() { ... }
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_insert_func_header
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ""
+                                                                                                                                                                                                                                                                                                                                                                                                                      #string
+
+#The filename that contains text to insert before a class if the class isn't preceeded with a C/C++ comment.
+#Will substitue $(class) with the class name.
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_insert_class_header
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ""
+                                                                                                                                                                                                                                                                                                                                                                                                                      #string
+
+#If a preprocessor is encountered when stepping backwards from a function name, then
+#this option decides whether the comment should be inserted.
+#Affects cmt_insert_func_header and cmt_insert_class_header.
+                                                                                                                                                                                                                                                                                                                                                                                                                  cmt_insert_before_preproc
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#
+#Preprocessor options
+#
+
+#Control indent of preprocessors inside #if blocks at brace level 0
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_indent
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Whether to indent #if/#else/#endif at the brace level (true) or from column 1 (false)
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_indent_at_level
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If pp_indent_at_level=false, specifies the number of columns to indent per level. Default=1.
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_indent_count
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Add or remove space after #based on pp_level of #if blocks
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_space
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      ignore
+                                                                                                                                                                                                                                                                                                                                                                                                                      #ignore / add / remove / force
+
+#Sets the number of spaces added with pp_space
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_space_count
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#The indent for #region and #endregion in C#and '#pragma region' in C/C++
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_indent_region
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      0
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Whether to indent the code between #region and #endregion
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_region_indent_code
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#If pp_indent_at_level=true, sets the indent for #if, #else, and #endif when not at file-level
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_indent_if
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      2
+                                                                                                                                                                                                                                                                                                                                                                                                                      #number
+
+#Control whether to indent the code between #if, #else and #endif when not at file-level
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_if_indent_code
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#Whether to indent '#define' at the brace level (true) or from column 1 (false)
+                                                                                                                                                                                                                                                                                                                                                                                                                  pp_define_at_level
+                                                                                                                                                                                                                                                                                                                                                                                                                    =
+                                                                                                                                                                                                                                                                                                                                                                                                                      false
+                                                                                                                                                                                                                                                                                                                                                                                                                      #false / true
+
+#You can force a token to be a type with the 'type' option.
+#Example :
+#type myfoo1 myfoo2
+#
+#You can create custom macro-based indentation using macro-open,
+#macro -else and macro-close.
+#Example :
+#macro -open  BEGIN_TEMPLATE_MESSAGE_MAP
+#macro -open  BEGIN_MESSAGE_MAP
+#macro -close END_MESSAGE_MAP
+#
+#You can assign any keyword to any type with the set option.
+#set func_call_user _ N_
+
diff --git a/BRAINSCommonLib/CMakeLists.txt b/BRAINSCommonLib/CMakeLists.txt
new file mode 100644
index 00000000..6dc4430b
--- /dev/null
+++ b/BRAINSCommonLib/CMakeLists.txt
@@ -0,0 +1,114 @@
+project(BRAINSCommonLibProject)
+set(LOCAL_PROJECT_NAME BRAINSCommonLib)
+cmake_minimum_required(VERSION 2.8)
+cmake_policy(VERSION 2.8)
+
+enable_testing()
+include(Dart)
+include(CPack)
+
+include(GenerateBRAINSCommonLibConfig.cmake)
+include(BuildScripts/CMakeBRAINS3BuildMacros.cmake)
+if(NOT SETIFEMPTY)
+macro(SETIFEMPTY)
+  set(KEY ${ARGV0})
+  set(VALUE ${ARGV1})
+  if(NOT ${KEY})
+    set(${ARGV})
+  endif(NOT ${KEY})
+endmacro(SETIFEMPTY KEY VALUE)
+endif(NOT SETIFEMPTY)
+
+###
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_BINARY_DIR}/bin)
+link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+###
+if(NOT ITK_FOUND)
+    find_package(ITK REQUIRED)
+    include(${ITK_USE_FILE})
+    message("ITK_INCLUDE_DIRS=${ITK_INCLUDE_DIRS}")
+endif(NOT ITK_FOUND)
+
+#-----------------------------------------------------------------------------
+# Output directories.
+#
+
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/BRAINSCommonLib.h.in
+  ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLib.h
+  )
+
+include_directories(
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  ${CMAKE_CURRENT_BINARY_DIR}
+  )
+
+set(BRAINSCommonLib_SRCS GenericTransformImage.cxx BRAINSFitHelper.cxx Slicer3LandmarkIO.cxx)
+
+## Always build BRAINSCommonLib as static
+add_library(BRAINSCommonLib STATIC ${BRAINSCommonLib_SRCS})
+target_link_libraries(BRAINSCommonLib ${ITK_LIBRARIES} )
+
+install(TARGETS BRAINSCommonLib
+  RUNTIME DESTINATION bin                 COMPONENT Development
+  LIBRARY DESTINATION lib/BRAINSCommonLib COMPONENT Development
+  ARCHIVE DESTINATION lib/BRAINSCommonLib COMPONENT Development
+    )
+
+file(GLOB __files1 "${CMAKE_CURRENT_SOURCE_DIR}/*.h")
+file(GLOB __files2 "${CMAKE_CURRENT_SOURCE_DIR}/*.hxx")
+install(FILES ${__files1} ${__files2} ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLib.h DESTINATION include/BRAINSCommonLib COMPONENT Development)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/BRAINSCommonLibInstallConfig.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLibInstallConfig.cmake
+               @ONLY)
+
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLibInstallConfig.cmake DESTINATION lib/BRAINSCommonLib COMPONENT Development RENAME BRAINSCommonLibConfig.cmake)
+
+set(BRAINSCommonLib_BUILDSCRIPTS_DIR_CONFIG ${CMAKE_INSTALL_PREFIX}/include/BRAINSCommonLib/BuildScripts)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/UseBRAINSCommonLib.cmake.in
+               ${CMAKE_CURRENT_BINARY_DIR}/UseBRAINSCommonLib.cmake @ONLY)
+
+# install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/UseBRAINSCommonLib.cmake.in
+#         DESTINATION lib/BRAINSCommonLib
+#         COMPONENT Development
+#         RENAME UseBRAINSCommonLib.cmake)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/UseBRAINSCommonLib.cmake
+  DESTINATION lib/BRAINSCommonLib
+  COMPONENT Development)
+
+#=======================================================================
+# Install the common build scripts for BRAINS tools in a common location
+#=======================================================================
+file(GLOB BRAINSBUILD_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "BuildScripts/*")
+foreach(BUILDFILE ${BRAINSBUILD_FILES})
+  #message(STATUS "${BUILDFILE} ${CMAKE_CURRENT_BINARY_DIR}/${BUILDFILE}")
+  configure_file(${BUILDFILE} ${CMAKE_CURRENT_BINARY_DIR}/${BUILDFILE} @ONLY)
+endforeach()
+install(FILES ${BRAINSBUILD_FILES} DESTINATION include/BRAINSCommonLib/BuildScripts COMPONENT Development)
+
+#=======================================================================
+# Install the common build scripts for BRAINS tools in a common location
+#=======================================================================
+file(GLOB_RECURSE BRAINSTEST_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}/TestData" "*.md5")
+set(TESTFILES_TO_INSTALL "")
+foreach(TESTFILE ${BRAINSTEST_FILES})
+  #message(STATUS "### ${TESTFILE} ${CMAKE_CURRENT_BINARY_DIR}/TestData/${TESTFILE}")
+  configure_file("TestData/${TESTFILE}" ${CMAKE_CURRENT_BINARY_DIR}/TestData/${TESTFILE} @ONLY)
+  list(APPEND TESTFILES_TO_INSTALL "TestData/${TESTFILE}")
+endforeach()
+install(FILES ${TESTFILES_TO_INSTALL} DESTINATION include/BRAINSCommonLib/TestData COMPONENT Development)
+
+#CONFIGUREBRAINSORSLICERLIBRARY( BRAINSCommonLib "" ${BRAINSCommonLib_SRCS} "")
+
+##HACK NEED BETTER TESTS add_directory( TestLargestForegroundFilledMaskImageFilter )
+##HACK NEED BETTER TESTS add_directory( Test_FindCenterOfBrainFilter )
+if(BUILD_TESTING)
+  add_subdirectory(TestSuite)
+endif(BUILD_TESTING)
+
diff --git a/BRAINSCommonLib/CTestConfig.cmake b/BRAINSCommonLib/CTestConfig.cmake
new file mode 100644
index 00000000..0102da05
--- /dev/null
+++ b/BRAINSCommonLib/CTestConfig.cmake
@@ -0,0 +1,13 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   enable_testing()
+##   include(CTest)
+set(CTEST_PROJECT_NAME "BRAINSCommonLib")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=BRAINSCommonLib")
+set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/BRAINSCommonLib/CleanBrainLabelMap.h b/BRAINSCommonLib/CleanBrainLabelMap.h
new file mode 100644
index 00000000..1de18849
--- /dev/null
+++ b/BRAINSCommonLib/CleanBrainLabelMap.h
@@ -0,0 +1,71 @@
+#ifndef CleanBrainLabelMap_h
+#include "itkImage.h"
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkFlatStructuringElement.h"
+#include "itkBinaryErodeImageFilter.h"
+#include "itkBinaryDilateImageFilter.h"
+#include "itkBinaryBallStructuringElement.h"
+#include "itkRelabelComponentImageFilter.h"
+#include "itkAndImageFilter.h"
+#include "itkVotingBinaryHoleFillingImageFilter.h"
+
+template 
+typename TOutputImage::Pointer
+CleanBrainLabelMap(const TInputImage *inputImage)
+{
+  typedef typename
+  itk::BinaryThresholdImageFilter BinaryThresholdFilterType;
+
+  typename BinaryThresholdFilterType::Pointer binaryThresholdFilter =
+    BinaryThresholdFilterType::New();
+  binaryThresholdFilter->SetLowerThreshold(1);
+  binaryThresholdFilter->SetUpperThreshold(255);
+  binaryThresholdFilter->SetInput(inputImage);
+  binaryThresholdFilter->Update();
+  typename TInputImage::Pointer emsBrainMask(binaryThresholdFilter->GetOutput() );
+
+  typedef typename itk::FlatStructuringElement KernelType;
+  typename KernelType::RadiusType erodeRadius = { { 2, 2, 2 } };
+  KernelType erodeKernel = KernelType::Ball(erodeRadius);
+
+  typedef typename itk::BinaryErodeImageFilter BinaryErodeFilterType;
+  typename BinaryErodeFilterType::Pointer erodeFilter = BinaryErodeFilterType::New();
+
+  erodeFilter->SetInput(emsBrainMask);
+  erodeFilter->SetKernel(erodeKernel);
+
+  typedef typename itk::RelabelComponentImageFilter
+  RelabelComponentFilterType;
+  typename RelabelComponentFilterType::Pointer relabelFilter =
+    RelabelComponentFilterType::New();
+  relabelFilter->SetInput(erodeFilter->GetOutput() );
+  relabelFilter->SetMinimumObjectSize(30000);
+
+  typename KernelType::RadiusType dilateRadius = { { 4, 4, 4 } };
+  KernelType dilateKernel = KernelType::Ball(dilateRadius);
+
+  typedef typename itk::BinaryDilateImageFilter BinaryDilateFilterType;
+  typename BinaryDilateFilterType::Pointer dilateFilter = BinaryDilateFilterType::New();
+
+  dilateFilter->SetKernel(dilateKernel);
+  dilateFilter->SetInput(relabelFilter->GetOutput() );
+
+  typedef typename itk::AndImageFilter AndFilterType;
+  typename AndFilterType::Pointer andFilter = AndFilterType::New();
+  andFilter->SetInput1(emsBrainMask);
+  andFilter->SetInput2(dilateFilter->GetOutput() );
+
+  typename TInputImage::SizeType holeFillingRadius = { { 3, 3, 3 } };
+
+  typedef typename itk::VotingBinaryHoleFillingImageFilter HoleFillingFilterType;
+  typename HoleFillingFilterType::Pointer holeFillingFilter =
+    HoleFillingFilterType::New();
+  holeFillingFilter->SetInput(andFilter->GetOutput() );
+  holeFillingFilter->SetRadius(holeFillingRadius);
+  holeFillingFilter->SetForegroundValue(1);
+  holeFillingFilter->SetBackgroundValue(0);
+  holeFillingFilter->Update();
+  return holeFillingFilter->GetOutput();
+}
+
+#endif // CleanBrainLabelMap_h
diff --git a/BRAINSCommonLib/ConvertToRigidAffine.h b/BRAINSCommonLib/ConvertToRigidAffine.h
new file mode 100644
index 00000000..b25941d3
--- /dev/null
+++ b/BRAINSCommonLib/ConvertToRigidAffine.h
@@ -0,0 +1,492 @@
+#ifndef __ConvertToRigidAffine_h
+#define __ConvertToRigidAffine_h
+#include 
+#include 
+#include 
+#include 
+#include "itkScaleVersor3DTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkMacro.h"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+// TODO:  Need to make return types an input template type.
+namespace AssignRigid
+{
+typedef itk::AffineTransform AffineTransformType;
+typedef AffineTransformType::Pointer    AffineTransformPointer;
+
+typedef vnl_matrix_fixed VnlTransformMatrixType44;
+
+typedef itk::Matrix Matrix3D;
+typedef  itk::Versor      VersorType;
+
+typedef AffineTransformType::MatrixType       MatrixType;
+typedef AffineTransformType::InputPointType   PointType;
+typedef AffineTransformType::OutputVectorType VectorType;
+
+typedef itk::VersorRigid3DTransform
+VersorRigid3DTransformType;
+typedef VersorRigid3DTransformType::Pointer
+VersorRigid3DTransformPointer;
+typedef VersorRigid3DTransformType::ParametersType
+VersorRigid3DParametersType;
+
+typedef itk::ScaleVersor3DTransform
+ScaleVersor3DTransformType;
+typedef ScaleVersor3DTransformType::Pointer ScaleVersor3DTransformPointer;
+typedef ScaleVersor3DTransformType::ParametersType
+ScaleVersor3DParametersType;
+
+typedef itk::ScaleSkewVersor3DTransform
+ScaleSkewVersor3DTransformType;
+typedef ScaleSkewVersor3DTransformType::Pointer
+ScaleSkewVersor3DTransformPointer;
+typedef ScaleSkewVersor3DTransformType::ParametersType
+ScaleSkewVersor3DParametersType;
+
+/**
+  * AffineTransformPointer  :=  AffineTransformPointer
+  */
+inline void
+AssignConvertedTransform(AffineTransformPointer & result,
+                         const AffineTransformType::ConstPointer affine)
+{
+  if( result.IsNotNull() )
+    {
+    result->SetParameters( affine->GetParameters() );
+    result->SetFixedParameters( affine->GetFixedParameters() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, while assigning AffineTransformPointer := AffineTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * AffineTransformPointer  :=  VnlTransformMatrixType44
+  */
+inline void
+AssignConvertedTransform(AffineTransformPointer & result,
+                         const VnlTransformMatrixType44 & matrix)
+{
+  if( result.IsNotNull() )
+    {
+    MatrixType rotator;         // can't do = conversion.
+    rotator.operator=( matrix.extract(3, 3, 0, 0) );
+
+    VectorType offset;
+    for( unsigned int i = 0; i < 3; ++i )
+      {
+      offset[i] = matrix.get(i, 3);
+      }
+    itk::Point ZeroCenter;
+    ZeroCenter.Fill(0.0);
+    result->SetIdentity();
+    result->SetCenter(ZeroCenter);         // Assume that rotation is about 0.0
+    result->SetMatrix(rotator);
+    result->SetOffset(offset);          // It is offset in this case, and not
+    // Translation.
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, while assigning AffineTransformPointer := VnlTransformMatrixType44."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * VnlTransformMatrixType44  :=  AffineTransformPointer
+  */
+inline void
+AssignConvertedTransform(VnlTransformMatrixType44 & result,
+                         const AffineTransformType::ConstPointer affine)
+{
+  if( affine.IsNotNull() )
+    {
+    MatrixType rotator = affine->GetMatrix();
+    VectorType offset = affine->GetOffset();          // This needs to be offst
+                                                      // in
+    // this case, and not
+    // Translation.
+    result.update(rotator.GetVnlMatrix(), 0, 0);
+    for( unsigned int i = 0; i < 3; ++i )
+      {
+      result.put(i, 3, offset[i]);
+      result.put(3, i, 0.0);
+      }
+    result.put(3, 3, 1.0);
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, while assigning VnlTransformMatrixType44 := AffineTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * AffineTransformPointer  :=  ScaleSkewVersor3DTransformPointer
+  */
+inline void
+AssignConvertedTransform(AffineTransformPointer & result,
+                         const ScaleSkewVersor3DTransformType::ConstPointer scale)
+{
+  if( result.IsNotNull() && scale.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( scale->GetCenter() );
+    result->SetMatrix( scale->GetMatrix() );
+    result->SetTranslation( scale->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning AffineTransformPointer := ScaleSkewVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * ScaleSkewVersor3DTransformPointer  :=  ScaleSkewVersor3DTransformPointer
+  */
+inline void
+AssignConvertedTransform(ScaleSkewVersor3DTransformPointer & result,
+                         const ScaleSkewVersor3DTransformType::ConstPointer scale)
+{
+  if( result.IsNotNull() && scale.IsNotNull() )
+    {
+    result->SetParameters( scale->GetParameters() );
+    result->SetFixedParameters( scale->GetFixedParameters() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning AffineTransformPointer := ScaleSkewVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * AffineTransformPointer  :=  ScaleVersor3DTransformPointer
+  */
+
+inline void
+AssignConvertedTransform(AffineTransformPointer & result,
+                         const ScaleVersor3DTransformType::ConstPointer scale)
+{
+  if( result.IsNotNull() && scale.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( scale->GetCenter() );
+    result->SetMatrix( scale->GetMatrix() );       // NOTE:  This matrix has
+                                                   // both
+    // rotation ans scale components.
+    result->SetTranslation( scale->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning AffineTransformPointer := ScaleVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * ScaleVersor3DTransformPointer  :=  ScaleVersor3DTransformPointer
+  */
+
+inline void
+AssignConvertedTransform(ScaleVersor3DTransformPointer & result,
+                         const ScaleVersor3DTransformType::ConstPointer scale)
+{
+  if( result.IsNotNull() && scale.IsNotNull() )
+    {
+    result->SetParameters( scale->GetParameters() );
+    result->SetFixedParameters( scale->GetFixedParameters() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning ScaleVersor3DTransform := ScaleVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * AffineTransformPointer  :=  VersorRigid3DTransformPointer
+  */
+inline void
+AssignConvertedTransform(AffineTransformPointer & result,
+                         const VersorRigid3DTransformType::ConstPointer versorTransform)
+{
+  if( result.IsNotNull() && versorTransform.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( versorTransform->GetCenter() );
+    result->SetMatrix( versorTransform->GetMatrix() );        // We MUST
+                                                              // SetMatrix
+    // before the
+    // SetOffset -- not
+    // after!
+    result->SetTranslation( versorTransform->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning AffineTransformPointer := VersorRigid3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * *VersorRigid3DTransformPointer  :=  VersorRigid3DTransformPointer
+  */
+
+inline void AssignConvertedTransform(
+  VersorRigid3DTransformPointer & result,
+  const VersorRigid3DTransformType::ConstPointer versorRigid)
+{
+  if( result.IsNotNull() && versorRigid.IsNotNull() )
+    {
+    result->SetParameters( versorRigid->GetParameters() );
+    result->SetFixedParameters( versorRigid->GetFixedParameters() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning VersorRigid3DTransformPointer := VersorRigid3DTTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * ScaleSkewVersor3DTransformPointer  :=  ScaleVersor3DTransformPointer
+  */
+inline void AssignConvertedTransform(
+  ScaleSkewVersor3DTransformPointer & result,
+  const ScaleVersor3DTransformType::ConstPointer scale)
+{
+  if( result.IsNotNull() && scale.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( scale->GetCenter() );
+    result->SetRotation( scale->GetVersor() );
+    result->SetScale( scale->GetScale() );
+    result->SetTranslation( scale->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning ScaleSkewVersor3DTransformPointer := ScaleVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * ScaleSkewVersor3DTransformPointer  :=  VersorRigid3DTransformPointer
+  */
+inline void AssignConvertedTransform(
+  ScaleSkewVersor3DTransformPointer & result,
+  const VersorRigid3DTransformType::ConstPointer versorRigid)
+{
+  if( result.IsNotNull() && versorRigid.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( versorRigid->GetCenter() );
+    result->SetRotation( versorRigid->GetVersor() );
+    result->SetTranslation( versorRigid->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning ScaleSkewVersor3DTransformPointer := VersorRigid3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * ScaleVersor3DTransformPointer  :=  VersorRigid3DTransformPointer
+  */
+inline void AssignConvertedTransform(
+  ScaleVersor3DTransformPointer & result,
+  const VersorRigid3DTransformType::ConstPointer versorRigid)
+{
+  if( result.IsNotNull() && versorRigid.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( versorRigid->GetCenter() );
+    result->SetRotation( versorRigid->GetVersor() );
+    result->SetTranslation( versorRigid->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning ScaleVersor3DTransformPointer := VersorRigid3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+inline void ExtractVersorRigid3DTransform(
+  VersorRigid3DTransformPointer & result,
+  const ScaleVersor3DTransformType::ConstPointer scaleVersorRigid)
+{
+  if( result.IsNotNull() && scaleVersorRigid.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( scaleVersorRigid->GetCenter() );
+    result->SetRotation( scaleVersorRigid->GetVersor() );
+    result->SetTranslation( scaleVersorRigid->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning VersorRigid3DTransformPointer := ScaleVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+inline void ExtractVersorRigid3DTransform(
+  VersorRigid3DTransformPointer & result,
+  const ScaleSkewVersor3DTransformType::ConstPointer scaleSkewVersorRigid)
+{
+  if( result.IsNotNull() && scaleSkewVersorRigid.IsNotNull() )
+    {
+    result->SetIdentity();
+    result->SetCenter( scaleSkewVersorRigid->GetCenter() );
+    result->SetRotation( scaleSkewVersorRigid->GetVersor() );
+    result->SetTranslation( scaleSkewVersorRigid->GetTranslation() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning VersorRigid3DTransformPointer := ScaleSkewVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+inline void ExtractVersorRigid3DTransform(
+  VersorRigid3DTransformPointer & result,
+  const VersorRigid3DTransformType::ConstPointer versorRigid)
+{
+  if( result.IsNotNull() && versorRigid.IsNotNull() )
+    {
+    result->SetParameters( versorRigid->GetParameters() );
+    result->SetFixedParameters( versorRigid->GetFixedParameters() );
+    }
+  else
+    {
+    std::cout
+    <<
+    "Error missing Pointer data, assigning VersorRigid3DTransformPointer := ScaleVersor3DTransformPointer."
+    << std::endl;
+    throw;
+    }
+}
+
+/**
+  * VersorRigid3DTransformPointer  :=  AffineTransformPointer
+  */
+
+/**
+  * Utility function in which we claim the singular-value decomposition (svd)
+  * gives the orthogonalization of a matrix in its U component.  However we
+  * must clip out the null subspace, if any.
+  */
+inline Matrix3D
+orthogonalize(const Matrix3D rotator)
+{
+  vnl_svd decomposition(
+    rotator.GetVnlMatrix(),
+    -1E-6);
+  vnl_diag_matrix::singval_t> Winverse( decomposition.Winverse() );
+
+  vnl_matrix W(3, 3);
+  W.fill( double(0) );
+  for( unsigned int i = 0; i < 3; ++i )
+    {
+    if( decomposition.Winverse() (i, i) != 0.0 )
+      {
+      W(i, i) = 1.0;
+      }
+    }
+
+  vnl_matrix result(
+    decomposition.U() * W * decomposition.V().conjugate_transpose() );
+
+  //    std::cout << " svd Orthonormalized Rotation: " << std::endl
+  //      << result << std::endl;
+  Matrix3D Orthog;
+  Orthog.operator=(result);
+
+  return Orthog;
+}
+
+inline void
+ExtractVersorRigid3DTransform(VersorRigid3DTransformPointer & result,
+                              const AffineTransformType::ConstPointer affine)
+{
+  if( result.IsNotNull() && affine.IsNotNull() )
+    {
+    Matrix3D   NonOrthog = affine->GetMatrix();
+    Matrix3D   Orthog( orthogonalize(NonOrthog) );
+    MatrixType rotator;
+    rotator.operator=(Orthog);
+
+    VersorType versor;
+    versor.Set(rotator);          //    --> controversial!  Is rotator
+                                  // orthogonal as
+    // required?
+    // versor.Normalize();
+
+    result->SetIdentity();
+    result->SetCenter( affine->GetCenter() );
+    result->SetRotation(versor);
+    result->SetTranslation( affine->GetTranslation() );
+    }
+  else
+    {
+    std::cout << "Error missing Pointer data, assigning "
+              << "VersorRigid3DTransformPointer := AffineTransformPointer."
+              << std::endl;
+    throw;
+    }
+}
+
+}
+#endif  // __RigidAffine_h
diff --git a/BRAINSCommonLib/CreateField.h b/BRAINSCommonLib/CreateField.h
new file mode 100644
index 00000000..5dcebabc
--- /dev/null
+++ b/BRAINSCommonLib/CreateField.h
@@ -0,0 +1,134 @@
+/**
+  * \defgroup CF Create Field
+  * \ingroup Reg
+  */
+#ifndef __CreateField_h
+#define __CreateField_h
+
+#include "itkObjectFactory.h"
+#include "itkObject.h"
+#include "itkFixedArray.h"
+#include "itkArray.h"
+#include "itkVector.h"
+#include "itkImage.h"
+#include "itkMultiResolutionPDEDeformableRegistration.h"
+#include "itkRecursiveMultiResolutionPyramidImageFilter.h"
+
+namespace itk
+{
+template 
+class CreateField : public Object
+{
+public:
+  typedef CreateField              Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  itkTypeMacro(MIMApplication, Object);
+
+  itkNewMacro(Self);
+
+  itkSetStringMacro(Image1Filename);
+  itkGetStringMacro(Image1Filename);
+  itkSetStringMacro(Image2Filename);
+  itkGetStringMacro(Image2Filename);
+  itkSetStringMacro(ParameterFilename);
+
+  typedef TImage                      ImageType;
+  typedef typename ImageType::Pointer ImagePointer;
+  itkStaticConstMacro(ImageDimension, unsigned int, TImage::ImageDimension);
+  typedef Array IterationsArrayType;
+  itkGetObjectMacro(ImageOne, ImageType);
+  itkGetObjectMacro(ImageTwo, ImageType);
+  itkSetObjectMacro(ImageOne, ImageType);
+  itkSetObjectMacro(ImageTwo, ImageType);
+  itkSetMacro(NumberOfHistogramLevels, unsigned long);
+  itkGetMacro(NumberOfHistogramLevels, unsigned long);
+
+  itkGetMacro(NumberOfMatchPoints, unsigned long);
+  itkSetMacro(NumberOfMatchPoints, unsigned long);
+
+  itkGetMacro(NumberOfLevels, unsigned short);
+  typedef FixedArray ShrinkFactorsType;
+  itkGetMacro(Image1ShrinkFactors, ShrinkFactorsType);
+  itkSetMacro(Image1ShrinkFactors, ShrinkFactorsType);
+  itkGetMacro(Image2ShrinkFactors, ShrinkFactorsType);
+  itkSetMacro(Image2ShrinkFactors, ShrinkFactorsType);
+  itkGetConstReferenceMacro(NumberOfIterations, IterationsArrayType);
+
+  typedef TImage                             InputImageType;
+  typedef typename InputImageType::PixelType InputPixelType;
+  typedef T2Image                            OutputImageType;
+  itkGetObjectMacro(FixedImage, OutputImageType);
+  itkGetObjectMacro(MovingImage, OutputImageType);
+  itkGetMacro(FixedImageMinimum, InputPixelType);
+  itkGetMacro(MovingImageMinimum, InputPixelType);
+
+  typedef TImage
+  FixedImageType;
+  typedef T2Image
+  MovingImageType;
+  typedef Vector FieldPixelType;
+  typedef Image TDeformationField;
+  typedef RecursiveMultiResolutionPyramidImageFilter                         FixedImagePyramidType;
+  typedef RecursiveMultiResolutionPyramidImageFilter                        MovingImagePyramidType;
+  typedef MultiResolutionPDEDeformableRegistration     RegistrationType;
+
+  typedef Array
+  UnsignedIntArray;
+  itkSetClampMacro( NumberOfLevels, unsigned short, 1,
+                    NumericTraits::max() );
+  itkSetMacro(NumberOfIterations, UnsignedIntArray);
+  itkGetObjectMacro(DeformationField, TDeformationField);
+  void StartNewLevel();
+
+  void Execute();
+
+  void ReleaseDataFlagOn();
+
+protected:
+  CreateField();
+  virtual ~CreateField();
+private:
+  typename ImageType::Pointer m_ImageOne;
+  typename ImageType::Pointer m_ImageTwo;
+  std::string m_Image1Filename;
+  std::string m_Image2Filename;
+  std::string m_ParameterFilename;
+
+  unsigned long     m_NumberOfHistogramLevels;
+  unsigned long     m_NumberOfMatchPoints;
+  unsigned short    m_NumberOfLevels;
+  ShrinkFactorsType m_Image1ShrinkFactors;
+  ShrinkFactorsType m_Image2ShrinkFactors;
+  UnsignedIntArray  m_NumberOfIterations;
+
+  InputPixelType m_FixedImageMinimum;
+  InputPixelType m_MovingImageMinimum;
+
+  typename OutputImageType::Pointer m_FixedImage;
+  typename OutputImageType::Pointer m_MovingImage;
+  typename FixedImagePyramidType::Pointer m_FixedImagePyramid;
+  typename MovingImagePyramidType::Pointer m_MovingImagePyramid;
+  typename TDeformationField::Pointer m_DeformationField;
+  unsigned long m_Tag;
+  typename RegistrationType::Pointer m_Registration;
+
+  typedef typename OutputImageType::Pointer OutputImagePointer;
+  void NormalizeImage(InputImageType *input, OutputImagePointer & output, InputPixelType & min);
+
+};
+}
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "CreateField.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/CreateField.hxx b/BRAINSCommonLib/CreateField.hxx
new file mode 100644
index 00000000..d99c5e5c
--- /dev/null
+++ b/BRAINSCommonLib/CreateField.hxx
@@ -0,0 +1,328 @@
+#ifndef __CreateField_hxx
+#define __CreateField_hxx
+#include "CreateField.h"
+#include "itkIOCommon.h"
+#include "itkVectorIndexSelectionCastImageFilter.h"
+#include "itkIO.h"
+#include 
+
+namespace itk
+{
+template 
+CreateField::CreateField()
+{
+  // MUST GRAB IMAGE 1 AND 2, Parameter Map and Warped Image Name
+  m_Image1Filename = "";
+  m_Image2Filename = "";
+  m_ParameterFilename = "";
+
+  m_ImageOne = NULL;
+  m_ImageTwo = NULL;
+
+  m_NumberOfHistogramLevels = 1024;
+  m_NumberOfMatchPoints = 7;
+
+  m_NumberOfLevels = 1;
+  m_Image1ShrinkFactors.Fill(1);
+  m_Image2ShrinkFactors.Fill(1);
+
+  m_NumberOfIterations = IterationsArrayType(1);
+  m_NumberOfIterations.Fill(10);
+
+  m_FixedImage  = NULL;
+  m_MovingImage = NULL;
+
+  m_NumberOfHistogramLevels = 256;
+  m_NumberOfMatchPoints = 1;
+
+  m_FixedImageMinimum = 0;
+  m_MovingImageMinimum = 0;
+
+  m_DeformationField = NULL;
+
+  m_FixedImagePyramid  = FixedImagePyramidType::New();
+  m_FixedImagePyramid->UseShrinkImageFilterOff();
+  m_MovingImagePyramid = MovingImagePyramidType::New();
+  m_MovingImagePyramid->UseShrinkImageFilterOff();
+  m_Registration       = RegistrationType::New();
+
+  m_Registration->SetFixedImagePyramid(m_FixedImagePyramid);
+  m_Registration->SetMovingImagePyramid(m_MovingImagePyramid);
+
+  typedef SimpleMemberCommand CommandType;
+  typename CommandType::Pointer command = CommandType::New();
+  command->SetCallbackFunction(this, &Self::StartNewLevel);
+
+  m_Tag = m_Registration->AddObserver(IterationEvent(), command);
+}
+
+template 
+CreateField::~CreateField()
+{
+  m_Registration->RemoveObserver(m_Tag);
+}
+
+template 
+void CreateField::Execute()
+{
+  try
+    {
+    std::cout << "  Reading Input Images and Parameters" << std::endl;
+    m_ImageOne = itkUtil::ReadImage(m_Image1Filename);
+    m_ImageTwo = itkUtil::ReadImage(m_Image2Filename);
+
+    FILE *paramFile;
+    paramFile = fopen(m_ParameterFilename.c_str(), "r");
+    if( !paramFile )
+      {
+      itkExceptionMacro(<< "  Could not open parameter file. ");
+      }
+
+    unsigned int uNumber;
+
+    if( fscanf(paramFile, "%d", &uNumber) != 1 )
+      {
+      itkExceptionMacro(<< "  Could not find the number of histogram levels.");
+      }
+    m_NumberOfMatchPoints = uNumber;
+
+    if( fscanf(paramFile, "%d", &uNumber) != 1 )
+      {
+      itkExceptionMacro(<< "Could not find the number of match points.");
+      }
+    m_NumberOfHistogramLevels = uNumber;
+
+    if( fscanf(paramFile, "%d", &uNumber) != 1 )
+      {
+      itkExceptionMacro(<< "Could not find the number of levels.");
+      }
+    m_NumberOfLevels = uNumber;
+
+      {
+      itk::Array temp(m_NumberOfLevels);
+
+      temp.Fill(0);
+      m_NumberOfIterations = temp;
+      }
+    for( unsigned int j = 0; j < m_NumberOfLevels; ++j )
+      {
+      if( fscanf(paramFile, "%d", &uNumber) != 1 )
+        {
+        itkExceptionMacro(<< "Could not find number of iterations per level. ");
+        }
+      m_NumberOfIterations[j] = uNumber;
+      }
+    for( unsigned int j = 0; j < ImageDimension; ++j )
+      {
+      if( fscanf(paramFile, "%d", &uNumber) != 1 )
+        {
+        itkExceptionMacro(<< "Could not find atlas starting shrink factor. ");
+        }
+      m_Image1ShrinkFactors[j] = uNumber;
+      }
+    for( unsigned int j = 0; j < ImageDimension; ++j )
+      {
+      if( fscanf(paramFile, "%d", &uNumber) != 1 )
+        {
+        itkExceptionMacro(
+          << "  Could not find subject starting shrink factor. ");
+        }
+      m_Image2ShrinkFactors[j] = uNumber;
+      }
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "  Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "  Error occurred during input parsing." << std::endl;
+    throw;
+    }
+
+  std::cout << "  Preprocessing the images" << std::endl;
+  try
+    {
+    this->NormalizeImage(m_ImageTwo, m_FixedImage, m_FixedImageMinimum);
+    this->NormalizeImage(m_ImageOne, m_MovingImage, m_MovingImageMinimum);
+
+    typedef HistogramMatchingImageFilter FilterType;
+    typename FilterType::Pointer filter = FilterType::New();
+
+    filter->SetInput(m_MovingImage);
+    filter->SetReferenceImage(m_FixedImage);
+    filter->SetNumberOfHistogramLevels(m_NumberOfHistogramLevels);
+    filter->SetNumberOfMatchPoints(m_NumberOfMatchPoints);
+    filter->ThresholdAtMeanIntensityOn();
+    filter->Update();
+
+    m_MovingImage = filter->GetOutput();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "  Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "  Error occured during preprocessing." << std::endl;
+    throw;
+    }
+
+  std::cout << "  Registering the images" << std::endl;
+
+  try
+    {
+    m_FixedImage->SetMetaDataDictionary( m_ImageTwo->GetMetaDataDictionary() );
+    m_MovingImage->SetMetaDataDictionary( m_ImageOne->GetMetaDataDictionary() );
+    if( ( m_FixedImage->GetDirection() != m_MovingImage->GetDirection() )
+        // TODO:  Remove dependance on RIP from
+          ( itk::SpatialOrientationAdapter().FromDirectionCosines( m_FixedImage->GetDirection() )
+          != itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIP )
+        )
+      {
+      std::cout
+      << "Image Directions are not the same or are not in RIP orientation "
+      << std::endl
+      << m_FixedImage->GetDirection()
+      << "=============" << std::endl
+      << m_MovingImage->GetDirection()
+      << std::endl;
+      }
+    // m_ImageOne->DisconnectPipeline();
+    m_ImageOne = NULL;
+    // m_ImageTwo->DisconnectPipeline();
+    m_ImageTwo = NULL;
+
+    m_FixedImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+    m_FixedImagePyramid->SetStartingShrinkFactors(
+      m_Image2ShrinkFactors.GetDataPointer() );
+
+    m_MovingImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+    m_MovingImagePyramid->SetStartingShrinkFactors(
+      m_Image1ShrinkFactors.GetDataPointer() );
+
+    m_Registration->SetFixedImage(m_FixedImage);
+    m_Registration->SetMovingImage(m_MovingImage);
+    m_Registration->SetNumberOfLevels(m_NumberOfLevels);
+    m_Registration->SetNumberOfIterations( m_NumberOfIterations.data_block() );
+    try
+      {
+      m_Registration->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "  Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::cout << errno << " " << __FILE__ << " " << __LINE__ << std::endl;
+      std::cout << "  Caught a non-ITK exception " << __FILE__ << " "
+                << __LINE__ << std::endl;
+      }
+
+    try
+      {
+      m_Registration->ReleaseDataFlagOn();
+      m_DeformationField = m_Registration->GetOutput();
+      // m_DeformationField->DisconnectPipeline();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "  Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::cout << "  Caught a non-ITK exception " << __FILE__ << " "
+                << __LINE__ << std::endl;
+      throw;
+      }
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "  Caught an ITK exception: " << std::endl;
+    std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+    throw err;
+    }
+  catch( ... )
+    {
+    std::cout << "  Error occured during registration" << std::endl;
+    throw;
+    }
+}
+
+template 
+void CreateField::ReleaseDataFlagOn()
+{
+  // m_FixedImage->DisconnectPipeline();
+  m_FixedImage = NULL;
+  // m_MovingImage->DisconnectPipeline();
+  m_MovingImage = NULL;
+}
+
+template 
+void CreateField::NormalizeImage(InputImageType *input,
+                                          OutputImagePointer & output,
+                                          InputPixelType & min)
+{
+  typedef MinimumMaximumImageFilter MinMaxFilterType;
+  typename MinMaxFilterType::Pointer minMaxFilter = MinMaxFilterType::New();
+
+  minMaxFilter->SetInput(input);
+  minMaxFilter->Update();
+
+  min = minMaxFilter->GetMinimum();
+  double shift = -1.0 * static_cast( min );
+  double scale = static_cast( minMaxFilter->GetMaximum() );
+  scale += shift;
+  scale = 1.0 / scale;
+
+  typedef ShiftScaleImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+
+  filter->SetInput(input);
+  filter->SetShift(shift);
+  filter->SetScale(scale);
+  filter->Update();
+
+  output = filter->GetOutput();
+}
+
+template 
+void FFCreateNewImageFromTemplate(
+  typename OutputImageType::Pointer & PointerToOutputImage,
+  const typename InputImageType::Pointer & PreInitializedImage)
+{
+  PointerToOutputImage = OutputImageType::New();
+  PointerToOutputImage->SetRegions(
+    PreInitializedImage->GetLargestPossibleRegion() );
+  PointerToOutputImage->CopyInformation(PreInitializedImage);
+  PointerToOutputImage->Allocate();
+  PointerToOutputImage->FillBuffer(0);
+  CHECK_CORONAL( PointerToOutputImage->GetDirection() );
+}
+
+template 
+void CreateField::StartNewLevel()
+{
+  std::cout << "  Starting level " << m_Registration->GetCurrentLevel()
+            << std::endl;
+}
+
+}
+#endif
diff --git a/BRAINSCommonLib/CrossOverAffineSystem.h b/BRAINSCommonLib/CrossOverAffineSystem.h
new file mode 100644
index 00000000..603f64d1
--- /dev/null
+++ b/BRAINSCommonLib/CrossOverAffineSystem.h
@@ -0,0 +1,135 @@
+#ifndef __CrossOverAffineSystem_h
+#define __CrossOverAffineSystem_h
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "itkScaleVersor3DTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkMacro.h"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+/*
+  *  The "Coordinate System" problem is closely related to generation
+  *  of reliable choices for an affine transform.  AffineTransforms need
+  *  to be generated in terms of a graphical vector space to map from,
+  *  and a possibly different graphical vector space to map to.
+  *
+  *
+  */
+
+template 
+class ITK_EXPORT CrossOverAffineSystem : public itk::LightProcessObject
+{
+public:
+  /** Standard class typedefs. */
+  typedef CrossOverAffineSystem         Self;
+  typedef itk::LightProcessObject       Superclass;
+  typedef itk::SmartPointer       Pointer;
+  typedef itk::SmartPointer ConstPointer;
+
+  /** New method for creating an object using a factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(CrossOverAffineSystem, itk::LightProcessObject);
+
+  /** Dimension of the domain space. */
+  itkStaticConstMacro(SpaceDimension,  unsigned int, NDimensions);
+  itkStaticConstMacro(AffineDimension, unsigned int, NDimensions + 1);
+
+  /** Type of the scalar representing coordinate and vector elements. */
+  typedef  TCoordinateType ScalarType;
+
+  typedef vnl_matrix_fixed VnlTransformMatrixType44;
+  // typedef vnl_matrix_fixed
+  //  VnlTransformMatrixType33;
+
+  /** Affine conversion type for this class */
+  typedef itk::AffineTransform                                         AffineTransformType;
+  typedef typename AffineTransformType::Pointer          AffineTransformPointer;
+  typedef typename AffineTransformType::MatrixType       MatrixType;
+  typedef typename AffineTransformType::InputPointType   PointType;
+  typedef typename AffineTransformType::OutputVectorType VectorType;
+  typedef typename VectorType::ValueType                 ValueType;
+
+  /** Quaternion conversion types for this class */
+  typedef itk::VersorTransform        VersorTransformType;
+  typedef typename VersorTransformType::Pointer        VersorTransformPointer;
+  typedef typename VersorTransformType::ParametersType VersorParametersType;
+
+  typedef itk::VersorRigid3DTransform
+  VersorRigid3DTransformType;
+  typedef typename VersorRigid3DTransformType::Pointer
+  VersorRigid3DTransformPointer;
+  typedef typename VersorRigid3DTransformType::ParametersType
+  VersorRigid3DParametersType;
+
+  typedef itk::ScaleVersor3DTransform
+  ScaleVersor3DTransformType;
+  typedef typename ScaleVersor3DTransformType::Pointer
+  ScaleVersor3DTransformPointer;
+  typedef typename ScaleVersor3DTransformType::ParametersType
+  ScaleVersor3DParametersType;
+
+  typedef itk::ScaleSkewVersor3DTransform
+  ScaleSkewVersor3DTransformType;
+  typedef typename ScaleSkewVersor3DTransformType::Pointer
+  ScaleSkewVersor3DTransformPointer;
+  typedef typename ScaleSkewVersor3DTransformType::ParametersType
+  ScaleSkewVersor3DParametersType;
+
+  /** Get the four coordinated AffineTransform conversions. */
+  itkGetMacro(InhaleEncodeConversion, AffineTransformPointer);
+  itkGetMacro(InhaleDecodeConversion, AffineTransformPointer);
+  itkGetMacro(ExhaleEncodeConversion, AffineTransformPointer);
+  itkGetMacro(ExhaleDecodeConversion, AffineTransformPointer);
+
+  /** Generate the four coordinated AffineTransform conversions. */
+  void EncloseInScaling(const VectorType & EncodeScale, const VectorType & DecodeScale);
+
+  void EncloseInTranslation(const VectorType & EncodeShift, const VectorType & DecodeShift);
+
+  void EncloseInCentering(const PointType & EncodeCenter, const PointType & DecodeCenter);
+
+  void EncloseInAffineTransforms(AffineTransformPointer EncodeAffineTransform,
+                                 AffineTransformPointer DecodeAffineTransform);
+
+protected:
+
+  /** Set the four coordinated AffineTransform conversions. */
+  itkSetMacro(InhaleEncodeConversion, AffineTransformPointer);
+  itkSetMacro(InhaleDecodeConversion, AffineTransformPointer);
+  itkSetMacro(ExhaleEncodeConversion, AffineTransformPointer);
+  itkSetMacro(ExhaleDecodeConversion, AffineTransformPointer);
+
+  CrossOverAffineSystem();
+  virtual ~CrossOverAffineSystem();
+
+  mutable AffineTransformPointer m_InhaleEncodeConversion;
+  mutable AffineTransformPointer m_InhaleDecodeConversion;
+  mutable AffineTransformPointer m_ExhaleEncodeConversion;
+  mutable AffineTransformPointer m_ExhaleDecodeConversion;
+private:
+  CrossOverAffineSystem(const Self &); // purposely not implemented
+  void operator=(const Self &);        // purposely not implemented
+
+};
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "CrossOverAffineSystem.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/CrossOverAffineSystem.hxx b/BRAINSCommonLib/CrossOverAffineSystem.hxx
new file mode 100644
index 00000000..38a1838a
--- /dev/null
+++ b/BRAINSCommonLib/CrossOverAffineSystem.hxx
@@ -0,0 +1,193 @@
+#ifndef __CrossOverAffineSystem_hxx
+#define __CrossOverAffineSystem_hxx
+
+#include "itkNumericTraits.h"
+#include "CrossOverAffineSystem.h"
+
+/**
+  * Constructor
+  */
+template 
+CrossOverAffineSystem
+::CrossOverAffineSystem() :
+  m_InhaleEncodeConversion(),
+  m_InhaleDecodeConversion(),
+  m_ExhaleEncodeConversion(),
+  m_ExhaleDecodeConversion()
+{
+  m_InhaleEncodeConversion = AffineTransformType::New();
+  m_InhaleDecodeConversion = AffineTransformType::New();
+  m_ExhaleEncodeConversion = AffineTransformType::New();
+  m_ExhaleDecodeConversion = AffineTransformType::New();
+
+  m_InhaleEncodeConversion->SetIdentity();
+  m_InhaleDecodeConversion->SetIdentity();
+  m_ExhaleEncodeConversion->SetIdentity();
+  m_ExhaleDecodeConversion->SetIdentity();
+}
+
+/**
+  * Destructor
+  */
+template 
+CrossOverAffineSystem::
+~CrossOverAffineSystem()
+{
+  return;
+}
+
+/**
+  * Utility function not provided in general vector implementations.
+  */
+template 
+typename CrossOverAffineSystem::VectorType
+Reciprocal(const typename CrossOverAffineSystem::VectorType & Scale)
+{
+  typedef typename CrossOverAffineSystem::VectorType VectorType;
+  VectorType ReciprocalScale(Scale);
+  for( unsigned int i = 0; i < NDimensions; ++i )
+    {
+    ReciprocalScale[i] = 1.0 / ReciprocalScale[i];
+    }
+  return ReciprocalScale;
+}
+
+// #define VERBOSE_PRINTING 1
+
+/**
+  * Build up the Inhale and Exhale transform enclosures by wrapping as follows:
+  * (ResliceScaleReciprocal * InhaleEncode) * T * (InhaleDecode * StandardScale)
+  * (ResliceScale * ExhaleEncode) * T * (ExhaleDecode * StandardScaleReciprocal)
+  * So in EstablishCrossOverSystemForAir16() in TransformAdaptor.hxx,
+  * the two arguments are to be given from the 'inhale' point of view.
+  */
+template 
+void
+CrossOverAffineSystem::EncloseInScaling(const VectorType & EncodeScale,
+                                                                      const VectorType & DecodeScale)
+{
+#ifdef VERBOSE_PRINTING
+  std::cout << "Encode Scale: " << EncodeScale << std::endl;
+  std::cout << "Decode Scale: " << DecodeScale << std::endl;
+#endif
+
+  const bool EncodeApplyUpstream = false;
+  const bool DecodeApplyUpstream = true;
+
+  m_InhaleEncodeConversion->Scale(EncodeScale,
+                                  EncodeApplyUpstream);
+  m_InhaleDecodeConversion->Scale(DecodeScale,
+                                  DecodeApplyUpstream);
+
+  VectorType ReciprocalEncodeScale( Reciprocal(
+                                      EncodeScale) );
+
+  VectorType ReciprocalDecodeScale( Reciprocal(
+                                      DecodeScale) );
+
+  m_ExhaleEncodeConversion->Scale(ReciprocalEncodeScale,
+                                  EncodeApplyUpstream);
+  m_ExhaleDecodeConversion->Scale(ReciprocalDecodeScale,
+                                  EncodeApplyUpstream);
+}
+
+/**
+  * Build up the Inhale and Exhale transform enclosures by wrapping as follows:
+  * (-ResliceShift * InhaleEncode) * T * (InhaleDecode * StandardShift)
+  * (ResliceShift * ExhaleEncode) * T * (ExhaleDecode * -StandardShift)
+  * So in EstablishCrossOverSystemForAir16() in TransformAdaptor.hxx,
+  * the two arguments are to be given from the 'inhale' point of view.
+  */
+template 
+void
+CrossOverAffineSystem::EncloseInTranslation(const VectorType & EncodeShift,
+                                                                          const VectorType & DecodeShift)
+{
+#ifdef VERBOSE_PRINTING
+  std::cout << "Encode Shift: " << EncodeShift << std::endl;
+  std::cout << "Decode Shift: " << DecodeShift << std::endl;
+#endif
+
+  const bool EncodeApplyUpstream = false;
+  const bool DecodeApplyUpstream = true;
+
+  m_InhaleEncodeConversion->Translate(EncodeShift,
+                                      EncodeApplyUpstream);
+  m_InhaleDecodeConversion->Translate(DecodeShift,
+                                      DecodeApplyUpstream);
+
+  m_ExhaleEncodeConversion->Translate(-EncodeShift,
+                                      EncodeApplyUpstream);
+  m_ExhaleDecodeConversion->Translate(-DecodeShift,
+                                      DecodeApplyUpstream);
+#ifdef VERBOSE_PRINTING
+  std::cout << " -- InhaleEncoder Shift: "
+            << m_InhaleEncodeConversion->GetOffset() << std::endl;
+  std::cout << " -- InhaleDecoder Shift: "
+            << m_InhaleDecodeConversion->GetOffset() << std::endl;
+  std::cout << " -- ExhaleEncoder Shift: "
+            << m_ExhaleEncodeConversion->GetOffset() << std::endl;
+  std::cout << " -- ExhaleDecoder Shift: "
+            << m_ExhaleDecodeConversion->GetOffset() << std::endl;
+#endif
+}
+
+template 
+void
+CrossOverAffineSystem::EncloseInCentering(const PointType & EncodeCenter,
+                                                                        const PointType & DecodeCenter)
+{
+#ifdef VERBOSE_PRINTING
+  std::cout << "Encode Center: " << EncodeCenter << std::endl;
+  std::cout << "Decode center: " << DecodeCenter << std::endl;
+#endif
+
+  m_InhaleEncodeConversion->SetCenter(EncodeCenter);
+  m_InhaleDecodeConversion->SetCenter(DecodeCenter);
+
+  m_ExhaleEncodeConversion->SetCenter(EncodeCenter);
+  m_ExhaleDecodeConversion->SetCenter(DecodeCenter);
+#ifdef VERBOSE_PRINTING
+  std::cout << " -- InhaleEncoder Shift: "
+            << m_InhaleEncodeConversion->GetOffset() << std::endl;
+  std::cout << " -- InhaleDecoder Shift: "
+            << m_InhaleDecodeConversion->GetOffset() << std::endl;
+  std::cout << " -- ExhaleEncoder Shift: "
+            << m_ExhaleEncodeConversion->GetOffset() << std::endl;
+  std::cout << " -- ExhaleDecoder Shift: "
+            << m_ExhaleDecodeConversion->GetOffset() << std::endl;
+#endif
+}
+
+/**
+  * Build up the Inhale and Exhale transform enclosures by wrapping in
+  * two entire transforms in like fashion to the more useful routines above.
+  * The two arguments are to be given from the 'inhale' point of view.
+  */
+template 
+void
+CrossOverAffineSystem::EncloseInAffineTransforms(AffineTransformPointer Encode,
+                                                                               AffineTransformPointer Decode)
+{
+  const bool EncodeApplyUpstream = false;
+  const bool DecodeApplyUpstream = true;
+
+  m_InhaleEncodeConversion->Compose(Encode,
+                                    EncodeApplyUpstream);
+  m_InhaleDecodeConversion->Compose(Decode,
+                                    DecodeApplyUpstream);
+
+  AffineTransformPointer EncodeInverse = AffineTransformType::New();
+  AffineTransformPointer DecodeInverse = AffineTransformType::New();
+  Encode->GetInverse(EncodeInverse);
+  Decode->GetInverse(DecodeInverse);
+
+  m_ExhaleEncodeConversion->Compose(EncodeInverse,
+                                    EncodeApplyUpstream);
+  m_ExhaleDecodeConversion->Compose(DecodeInverse,
+                                    DecodeApplyUpstream);
+}
+
+#endif
diff --git a/BRAINSCommonLib/DemonsPreprocessor.h b/BRAINSCommonLib/DemonsPreprocessor.h
new file mode 100644
index 00000000..999088c4
--- /dev/null
+++ b/BRAINSCommonLib/DemonsPreprocessor.h
@@ -0,0 +1,201 @@
+#ifndef __DemonsPreprocessor_h
+#define __DemonsPreprocessor_h
+
+#include "itkObject.h"
+
+namespace itk
+{
+/** \class DemonsPreprocessor
+  *
+  * This component pre-processes the moving and fixed image before
+  * registration.
+  * If the fixed image dimensions are different from the moving image it will
+  *    * resample the moving image to match the fixed image dimensions.
+  * Histogram matching is done to solve the intensity mismatch problem.
+  *
+  * The preprocessor also called the skull-stripping filter itkBOBF
+  * if an atlas and subject whole brain masks are specified.
+  *
+  * The preprocessing is activatived by method Execute().
+  *
+  * Inputs:
+  *    - pointer to original fixed image
+  *    - pointer original moving image
+  *    - number of histogram levels
+  *    - number of match points
+  *
+  * Outputs:
+  *    - pointer to processed fixed image
+  *    - pointer to processed moving image
+  *    - the minimum value of original fixed image
+  *    - the minimum value of original moving image
+  *
+  */
+template 
+class ITK_EXPORT DemonsPreprocessor : public Object
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef DemonsPreprocessor       Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(DemonsPreprocessor, Object);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Input Image Type. */
+  typedef TInputImage InputImageType;
+  /** Output Image Type. */
+  typedef TOutputImage OutputImageType;
+
+  /** Input image pixel type. */
+  typedef typename InputImageType::PixelType  InputPixelType;
+  typedef typename OutputImageType::PixelType PixelType;
+  typedef typename OutputImageType::IndexType IndexType;
+  typedef typename OutputImageType::SizeType  SizeType;
+
+  /** Image dimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int, TInputImage::ImageDimension);
+
+  /** Set the input fixed image. */
+  itkSetObjectMacro(InputFixedImage, InputImageType);
+
+  /** Set the input moving image. */
+  itkSetObjectMacro(InputMovingImage, InputImageType);
+
+  /** Deformation field value type. */
+  typedef float FieldValueType;
+
+  /** Deformation field pixel type. */
+  typedef Vector FieldPixelType;
+
+  /** Deformation field type. */
+  typedef Image TDeformationField;
+
+  /** Set the initial Deformation Field. */
+  itkSetObjectMacro(InitialDeformationField, TDeformationField);
+  itkGetObjectMacro(InitialDeformationField, TDeformationField);
+
+  /** Set the number of histogram levels to use. */
+  itkSetMacro(NumberOfHistogramLevels, unsigned long);
+
+  /** Set the number of match points to use. */
+  itkSetMacro(NumberOfMatchPoints, unsigned long);
+
+  /** Method to execute the preprocessing. */
+  virtual void Execute();
+
+  /** Get the output fixed image. */
+  itkGetObjectMacro(OutputFixedImage, OutputImageType);
+
+  /** Get the output moving image. */
+  itkGetObjectMacro(OutputMovingImage, OutputImageType);
+
+  /** Get the output moving image. */
+  itkGetObjectMacro(UnNormalizedMovingImage, OutputImageType);
+
+  /** Get the output moving image. */
+  itkGetObjectMacro(UnNormalizedFixedImage, OutputImageType);
+
+  /** Get minimum value of original fixed image. */
+  itkGetMacro(FixedImageMinimum, InputPixelType);
+
+  /** Get minimum value of original moving image. */
+  itkGetMacro(MovingImageMinimum, InputPixelType);
+
+  /* BOBF macros
+    * Set Target Mask filename */
+  itkSetStringMacro(FixedBinaryVolume);
+  itkGetStringMacro(FixedBinaryVolume);
+
+  /** Set Template Mask filename */
+  itkSetStringMacro(MovingBinaryVolume);
+  itkGetStringMacro(MovingBinaryVolume);
+
+  /** Set/Get the lower threshold. The default is 0. */
+  itkSetMacro(Lower, PixelType);
+  itkGetMacro(Lower, PixelType);
+
+  /** Set/Get the upper threshold. The default is 70 */
+  itkSetMacro(Upper, PixelType);
+  itkGetMacro(Upper, PixelType);
+
+  itkSetMacro(DefaultPixelValue,  PixelType);
+  itkGetMacro(DefaultPixelValue,  PixelType);
+
+  itkSetMacro(MedianFilterSize,  SizeType);
+  itkGetMacro(MedianFilterSize,  SizeType);
+
+  /** Set the radius of the neighborhood used for a mask. */
+  itkSetMacro(Radius, SizeType);
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Radius, SizeType);
+
+  /** Set the Seed of the neighborhood used for a mask. */
+  itkSetMacro(Seed, IndexType);
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Seed, IndexType);
+
+  /**Set Debug mode*/
+  itkSetMacro(OutDebug, bool);
+  itkGetConstMacro(OutDebug, bool);
+
+  /**Set histogram matching*/
+  itkSetMacro(UseHistogramMatching, bool);
+  itkGetConstMacro(UseHistogramMatching, bool);
+protected:
+  DemonsPreprocessor();
+  ~DemonsPreprocessor()
+  {
+  }
+private:
+  DemonsPreprocessor(const Self &);      // purposely not implemented
+  void operator=(const Self &);          // purposely not implemented
+
+  typename InputImageType::Pointer m_InputFixedImage;
+  typename InputImageType::Pointer m_InputMovingImage;
+  typename OutputImageType::Pointer m_OutputFixedImage;
+  typename OutputImageType::Pointer m_OutputMovingImage;
+  typename OutputImageType::Pointer m_UnNormalizedMovingImage;
+  typename OutputImageType::Pointer m_UnNormalizedFixedImage;
+  typename TDeformationField::Pointer m_InitialDeformationField;
+
+  unsigned long m_NumberOfHistogramLevels;
+  unsigned long m_NumberOfMatchPoints;
+
+  InputPixelType m_FixedImageMinimum;
+  InputPixelType m_MovingImageMinimum;
+
+  std::string m_FixedBinaryVolume;
+  std::string m_MovingBinaryVolume;
+  IndexType   m_Seed;
+  PixelType   m_Lower;
+  PixelType   m_Upper;
+  PixelType   m_DefaultPixelValue;
+  SizeType    m_Radius;
+  bool        m_OutDebug;
+  SizeType    m_MedianFilterSize;
+  typedef typename OutputImageType::Pointer OutputImagePointer;
+  typedef typename InputImageType::Pointer  InputImagePointer;
+
+  bool m_UseHistogramMatching;
+
+  /*MakeBOBF function takes in a brain image and a whole brain mask and strips
+    * the skull of the image.*/
+  OutputImagePointer MakeBOBFImage(OutputImagePointer input, std::string MaskName);
+
+};
+}   // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "DemonsPreprocessor.hxx"
+#endif
+
+#endif // _DemonsPreprocessor_h
diff --git a/BRAINSCommonLib/DemonsPreprocessor.hxx b/BRAINSCommonLib/DemonsPreprocessor.hxx
new file mode 100644
index 00000000..ad5a71b0
--- /dev/null
+++ b/BRAINSCommonLib/DemonsPreprocessor.hxx
@@ -0,0 +1,234 @@
+#ifndef __DemonsPreprocessor_hxx
+#define __DemonsPreprocessor_hxx
+
+#include "DemonsPreprocessor.h"
+#include "itkMinimumMaximumImageFilter.h"
+#include "itkShiftScaleImageFilter.h"
+#include "itkHistogramMatchingImageFilter.h"
+#include "itkBOBFFilter.h"
+#include "itkAffineTransform.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkIO.h"
+#include "itkMedianImageFilter.h"
+
+#include "itkMultiResolutionPDEDeformableRegistration.h"
+#include "itkDiffeomorphicDemonsRegistrationFilter.h"
+#include "itkWarpImageFilter.h"
+
+namespace itk
+{
+template 
+DemonsPreprocessor
+::DemonsPreprocessor()
+{
+  m_UseHistogramMatching = 0;
+  m_NumberOfHistogramLevels = 256;
+  m_NumberOfMatchPoints = 1;
+
+  m_FixedImageMinimum =  NumericTraits::NonpositiveMin();
+  m_MovingImageMinimum = NumericTraits::NonpositiveMin();
+
+  m_FixedBinaryVolume = "none";
+  m_MovingBinaryVolume = "none";
+  //    m_Seed =  NumericTraits::Zero;
+  for( unsigned i = 0; i < TInputImage::ImageDimension; ++i )
+    {
+    m_Seed[i] = 0;
+    m_MedianFilterSize[i] = 0;
+    }
+  m_Lower = NumericTraits::NonpositiveMin();
+  m_Upper = NumericTraits::max();
+
+  m_DefaultPixelValue = NumericTraits::One;
+  m_Radius.Fill(1);
+  m_OutDebug = false;
+}
+
+template 
+void
+DemonsPreprocessor
+::Execute()
+{
+  if( m_MedianFilterSize[0] > 0  ||  m_MedianFilterSize[1] > 0
+      ||  m_MedianFilterSize[2] > 0 )
+    {
+    typedef typename itk::MedianImageFilter MedianImageFilterType;
+    typename MedianImageFilterType::Pointer medianFilter =
+      MedianImageFilterType::New();
+    medianFilter->SetRadius(m_MedianFilterSize);
+    medianFilter->SetInput(m_InputFixedImage);
+    medianFilter->Update();
+    m_InputFixedImage = medianFilter->GetOutput();
+    //
+    // reinitialize
+    medianFilter = MedianImageFilterType::New();
+    medianFilter->SetRadius(m_MedianFilterSize);
+    medianFilter->SetInput(m_InputMovingImage);
+    medianFilter->Update();
+    m_InputMovingImage = medianFilter->GetOutput();
+    }
+    { // Create UnNormalized...Images
+      {
+      this->m_UnNormalizedFixedImage =
+        itkUtil::PreserveCast(
+          this->m_InputFixedImage);
+      }
+      {
+      m_UnNormalizedMovingImage =
+        itkUtil::PreserveCast(
+          this->m_InputMovingImage);
+      }
+    }
+
+  //  m_OutputFixedImage =
+  // itkUtil::CopyImage(m_UnNormalizedFixedImage);
+
+  m_OutputMovingImage = itkUtil::CopyImage(
+      m_UnNormalizedMovingImage);
+
+  if( this->GetUseHistogramMatching() )
+    {
+    typedef HistogramMatchingImageFilter HistogramMatchingFilterType;
+    typename HistogramMatchingFilterType::Pointer histogramfilter =
+      HistogramMatchingFilterType::New();
+    if( this->GetOutDebug() )
+      {
+      std::cout << "Performing Histogram Matching \n";
+      }
+    if( ( vcl_numeric_limits::max()
+          - vcl_numeric_limits::min() ) <
+        m_NumberOfHistogramLevels )
+      {
+      std::cout << "The intensity of range is less than Histogram levels!!"
+                << std::endl;
+      }
+    histogramfilter->SetInput(m_UnNormalizedMovingImage);
+    histogramfilter->SetReferenceImage(m_UnNormalizedFixedImage);
+
+    histogramfilter->SetNumberOfHistogramLevels(m_NumberOfHistogramLevels);
+    histogramfilter->SetNumberOfMatchPoints(m_NumberOfMatchPoints);
+    histogramfilter->ThresholdAtMeanIntensityOn();
+    histogramfilter->Update();
+    //      m_OutputFixedImage  = histogramfilter->GetOutput();
+    m_OutputMovingImage  = histogramfilter->GetOutput();
+    // +DANGER: ALIASING:  m_OutputMovingImage EQ m_UnNormalizedMovingImage by
+    // design.
+    // Create a copy just to be safe.  This s probably a waste of memory.
+    // m_OutputMovingImage =
+    // itkUtil::CopyImage(m_UnNormalizedMovingImage);
+    }
+
+  //  m_OutputMovingImage =
+  // itkUtil::CopyImage(m_UnNormalizedMovingImage);
+
+  m_OutputFixedImage = itkUtil::CopyImage(
+      m_UnNormalizedFixedImage);
+
+  if( this->GetOutDebug() )
+    {
+    std::cout << "Writing Histogram equalized image" << std::endl;
+    itkUtil::WriteImage(m_OutputFixedImage,
+                                      "HistogramModifiedFixedImage.nii.gz");
+    std::cout << "Writing UnormalizedMovingImage equalized image" << std::endl;
+    itkUtil::WriteImage(m_UnNormalizedMovingImage,
+                                      "HistogramReferenceMovingImage.nii.gz");
+    }
+  // Make BOBF Images if specified
+  if( this->m_FixedBinaryVolume != std::string("none") )
+    {
+    if( this->GetOutDebug() )
+      {
+      std::cout << "Making BOBF \n";
+      std::cout << "PRE Fixed Origin" << m_OutputFixedImage->GetOrigin()
+                << std::endl;
+      }
+    m_OutputFixedImage = this->MakeBOBFImage(m_OutputFixedImage,
+                                             m_FixedBinaryVolume);
+    if( this->GetOutDebug() )
+      {
+      std::cout << "Fixed Origin" << m_OutputFixedImage->GetOrigin()
+                << std::endl;
+      std::cout << "PRE Moving Origin" << m_OutputMovingImage->GetOrigin()
+                << std::endl;
+      }
+    m_OutputMovingImage = this->MakeBOBFImage(m_OutputMovingImage,
+                                              m_MovingBinaryVolume);
+    if( this->GetOutDebug() )
+      {
+      std::cout << "Moving Origin" << m_OutputMovingImage->GetOrigin()
+                << std::endl;
+      std::cout << "Writing Brain Only Background Filled Moving image"
+                << std::endl;
+      itkUtil::WriteImage(m_OutputMovingImage,
+                                        "BOBF_Moving.nii.gz");
+      itkUtil::WriteImage(m_OutputFixedImage, "BOBF_Fixed.nii.gz");
+      }
+    }
+  m_InputMovingImage = NULL;
+  m_InputFixedImage = NULL;
+}
+
+/*This function takes in a brain image and a whole brain mask and strips the
+  * skull of the image. It uses the BOBF filter to perform the skull
+  * stripping.*/
+
+template 
+typename DemonsPreprocessor::OutputImagePointer
+DemonsPreprocessor
+::MakeBOBFImage(OutputImagePointer input, std::string MaskName)
+{
+  OutputImagePointer Mask = itkUtil::ReadImage(MaskName);
+
+  if( ( m_UnNormalizedFixedImage->GetLargestPossibleRegion().GetSize() !=
+        Mask->GetLargestPossibleRegion().GetSize() )
+      || ( m_UnNormalizedFixedImage->GetSpacing() != Mask->GetSpacing() ) )
+    {
+    if( this->GetOutDebug() )
+      {
+      std::cout << "Writing Resampled Output image" << std::endl;
+      itkUtil::WriteImage(Mask, "Resampled.mask");
+      }
+    }
+
+  typedef BOBFFilter BOBFFilterType;
+  typename BOBFFilterType::Pointer BOBFfilter = BOBFFilterType::New();
+  if( this->GetOutDebug() )
+    {
+    std::cout
+    <<
+    "Making Brain only Background filled image with the following parameters. "
+    << std::endl;
+    std::cout << "Lower Threshold:  " << m_Lower << std::endl;
+    std::cout << "Upper Threshold:  " << m_Upper << std::endl;
+    std::cout << "Neighborhood:  " << m_Radius << std::endl;
+    std::cout << "Background fill Value:  " << m_DefaultPixelValue << std::endl;
+    std::cout << "Seed :  " << m_Seed  << std::endl;
+    }
+
+  BOBFfilter->SetLower(m_Lower);
+  BOBFfilter->SetUpper(m_Upper);
+  BOBFfilter->SetRadius(m_Radius);
+  BOBFfilter->SetReplaceValue(m_DefaultPixelValue);
+  BOBFfilter->SetSeed(m_Seed);
+  BOBFfilter->SetInputImage(input);
+  BOBFfilter->SetInputMask(Mask);
+  try
+    {
+    BOBFfilter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+
+  OutputImagePointer output = BOBFfilter->GetOutput();
+  return output;
+}
+
+}   // namespace itk
+
+#endif // _DemonsPreprocessor_hxx
diff --git a/BRAINSCommonLib/DemonsRegistrator.h b/BRAINSCommonLib/DemonsRegistrator.h
new file mode 100644
index 00000000..34ff8b56
--- /dev/null
+++ b/BRAINSCommonLib/DemonsRegistrator.h
@@ -0,0 +1,279 @@
+#ifndef __DemonsRegistrator_h
+#define __DemonsRegistrator_h
+
+#include "itkObject.h"
+#include "itkVector.h"
+#include "itkImage.h"
+#include "itkMultiResolutionPDEDeformableRegistration.h"
+#include "itkMultiResolutionLogDomainDeformableRegistration.h"
+#include "itkRecursiveMultiResolutionPyramidImageFilter.h"
+#include "itkLogDomainDeformableRegistrationFilter.h"
+
+#include "itkArray.h"
+
+namespace itk
+{
+/** \class DemonsRegistrator
+  *
+  * This component computes the transform to register a
+  * moving image onto a fixed image.
+  *
+  * In particular, it uses the deformable demons registration
+  * algorithm.
+  *
+  * The registration is done using a multiresolution strategy.
+  * At each resolution level, the downsampled images are obtained
+  * using a RecursiveMultiResolutionPyramidImageFilter.
+  *
+  * \warning This class requires both images to be 3D.
+  * It can write out the deformation field and the checker board image
+  * of the fixed and output image.
+  *
+  * The registration process is activated by method Execute().
+  *
+  * Inputs:
+  *   - pointer to fixed image
+  *   - pointer to moving image
+  *   - number of resolution levels
+  *   - number of optimization iterations at each level
+  *   - the initial rigid (quaternion) transform parameters
+  *   - the coarest level shrink factors for the fixed image
+  *   - the coarest level shrink factors for the moving image
+  *
+  * Outputs:
+  *   - output deformation field
+  *   - output image
+  *   - Checkerboard image
+  *   - x,y,z components of displacement fields.
+  */
+template <
+  class TRealImage,
+  class TOutputImage,
+  class TFieldValue = ITK_TYPENAME TRealImage::PixelType
+  >
+class DemonsRegistrator : public Object
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef DemonsRegistrator        Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(DemonsRegistrator, Object);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Fixed Image Type. */
+  typedef TRealImage RealImageType;
+
+  /** Moving Image Type. */
+  typedef typename TOutputImage::PixelType PixelType;
+
+  /** Image dimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int, TRealImage::ImageDimension);
+
+  /** Type to hold the number of checker boxes per dimension */
+  typedef FixedArray::ImageDimension>  PatternArrayType;
+
+  /** Set Checker pattern */
+  itkSetMacro(CheckerBoardPattern, PatternArrayType);
+  itkGetConstReferenceMacro(CheckerBoardPattern, PatternArrayType);
+
+  /** Deformation field value type. */
+  typedef TFieldValue FieldValueType;
+
+  /** Deformation field pixel type. */
+  typedef Vector FieldPixelType;
+
+  /** Deformation field type. */
+  typedef Image TDeformationField;
+
+  /** Fixed Image Pyramid Type. */
+  typedef RecursiveMultiResolutionPyramidImageFilter<
+    RealImageType,
+    RealImageType>    FixedImagePyramidType;
+
+  /** Moving Image Pyramid Type. */
+  typedef RecursiveMultiResolutionPyramidImageFilter<
+    RealImageType,
+    RealImageType>   MovingImagePyramidType;
+
+  /** Registration Method. */
+  typedef MultiResolutionPDEDeformableRegistration<
+    RealImageType,
+    RealImageType,
+    TDeformationField, float>    RegistrationType;
+
+  typedef MultiResolutionLogDomainDeformableRegistration<
+    RealImageType,
+    RealImageType,
+    TDeformationField, float>    LDRegistrationType;
+
+  /** UnsignedIntArray type. */
+  typedef Array UnsignedIntArray;
+
+  /** ShrinkFactorsArray type. */
+  typedef FixedArray ShrinkFactorsArray;
+
+  /** Set the intial deformation field */
+  itkSetObjectMacro(InitialDeformationField, TDeformationField);
+
+  /** Set the fixed image. */
+  itkSetObjectMacro(FixedImage, RealImageType);
+
+  /** Set the moving image. */
+  itkSetObjectMacro(MovingImage, RealImageType);
+
+  /** Set the Unnormalized moving image. */
+  itkSetObjectMacro(UnNormalizedMovingImage, RealImageType);
+
+  /** Set the Unnormalized moving image. */
+  itkSetObjectMacro(UnNormalizedFixedImage, RealImageType);
+
+  /** Set the number of resolution levels. */
+  itkSetClampMacro( NumberOfLevels, unsigned short, 1,
+                    NumericTraits::max() );
+
+  /** Set the number of iterations per level. */
+  itkSetMacro(NumberOfIterations, UnsignedIntArray);
+
+  /** Set the fixed and moving image shrink factors. */
+  itkSetMacro(FixedImageShrinkFactors, ShrinkFactorsArray);
+  itkSetMacro(MovingImageShrinkFactors, ShrinkFactorsArray);
+
+  /** Set Displacementname */
+  itkSetStringMacro(DisplacementBaseName);
+  itkGetStringMacro(DisplacementBaseName);
+
+  /** Set WarpedImageName */
+  itkSetStringMacro(WarpedImageName);
+  itkGetStringMacro(WarpedImageName);
+
+  /** Set CheckerBoard ImageName */
+  itkSetStringMacro(CheckerBoardFilename);
+  itkGetStringMacro(CheckerBoardFilename);
+
+  /** Set Deformation field output file Name */
+  itkSetStringMacro(DeformationFieldOutputName);
+  itkGetStringMacro(DeformationFieldOutputName);
+
+  /**Set histogram matching */
+  itkSetMacro(UseHistogramMatching, bool);
+  itkGetConstMacro(UseHistogramMatching, bool);
+
+  /** Method to execute the registration. */
+  virtual void Execute();
+
+  /** Get the deformation field. */
+  itkGetObjectMacro(DeformationField, TDeformationField);
+
+  /** Initialize registration at the start of new level. */
+  void StartNewLevel();
+
+  /** Output Normalized Image.*/
+  itkSetStringMacro(OutNormalized);
+  itkGetStringMacro(OutNormalized);
+
+  /** Set Debug mode */
+  itkSetMacro(OutDebug, bool);
+  itkGetConstMacro(OutDebug,  bool);
+
+  itkSetStringMacro(FixedLandmarkFilename);
+  itkGetStringMacro(FixedLandmarkFilename);
+  itkSetStringMacro(MovingLandmarkFilename);
+  itkGetStringMacro(MovingLandmarkFilename);
+
+  itkSetMacro(DefaultPixelValue, typename RealImageType::PixelType);
+  itkGetMacro(DefaultPixelValue, typename RealImageType::PixelType);
+
+  /** Get the interpolation Mode. */
+  itkGetMacro(InterpolationMode, std::string);
+  itkSetMacro(InterpolationMode, std::string);
+
+  typedef itk::PDEDeformableRegistrationFilter BaseRegistrationFilterType;
+  void SetRegistrationFilter(BaseRegistrationFilterType *filter)
+  {
+    this->m_Registration->SetRegistrationFilter(filter);
+  }
+
+  typedef itk::LogDomainDeformableRegistrationFilter
+  LDDRegistrationFilterType;
+  void SetLDDRegistrationFilter(
+    LDDRegistrationFilterType *filter)
+  {
+    this->m_LDRegistration->SetRegistrationFilter(filter);
+  }
+
+  RegistrationType * GetRegistrationType(void)
+  {
+    return m_Registration;
+  }
+
+  void SetUseLogDomain(bool bl)
+  {
+    this->m_UseLogDomain = bl;
+  }
+
+  bool GetUseLogDomain()
+  {
+    return this->m_UseLogDomain;
+  }
+
+protected:
+  DemonsRegistrator();
+  ~DemonsRegistrator();
+private:
+  DemonsRegistrator(const Self &);                // purposely not implemented
+  void operator=(const Self &);                   // purposely not implemented
+
+  void WriteDisplacementComponents();
+
+  typename TDeformationField::Pointer m_InitialDeformationField;
+  typename RealImageType::Pointer m_FixedImage;
+  typename RealImageType::Pointer m_MovingImage;
+  typename RealImageType::Pointer m_UnNormalizedMovingImage;
+  typename RealImageType::Pointer m_UnNormalizedFixedImage;
+  typename FixedImagePyramidType::Pointer m_FixedImagePyramid;
+  typename MovingImagePyramidType::Pointer m_MovingImagePyramid;
+  typename RegistrationType::Pointer m_Registration;
+  typename LDRegistrationType::Pointer m_LDRegistration;
+  typename RealImageType::PixelType m_DefaultPixelValue;
+
+  unsigned short   m_NumberOfLevels;
+  UnsignedIntArray m_NumberOfIterations;
+
+  ShrinkFactorsArray m_MovingImageShrinkFactors;
+  ShrinkFactorsArray m_FixedImageShrinkFactors;
+
+  typename TDeformationField::Pointer m_DeformationField;
+  std::string      m_FixedLandmarkFilename;
+  std::string      m_MovingLandmarkFilename;
+  unsigned long    m_Tag;
+  std::string      m_DisplacementBaseName;
+  std::string      m_WarpedImageName;
+  std::string      m_CheckerBoardFilename;
+  std::string      m_DeformationFieldOutputName;
+  PatternArrayType m_CheckerBoardPattern;
+  std::string      m_OutNormalized;
+  bool             m_OutDebug;
+  bool             m_UseHistogramMatching;
+  bool             m_UseLogDomain;
+  std::string      m_InterpolationMode;
+};
+}   // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "DemonsRegistrator.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/DemonsRegistrator.hxx b/BRAINSCommonLib/DemonsRegistrator.hxx
new file mode 100644
index 00000000..f2bae3a4
--- /dev/null
+++ b/BRAINSCommonLib/DemonsRegistrator.hxx
@@ -0,0 +1,479 @@
+#ifndef __DemonsRegistrator_hxx
+#define __DemonsRegistrator_hxx
+
+#include 
+#include 
+#include "DemonsRegistrator.h"
+#include "itkCommand.h"
+#include "ApplyField.h"
+#include "itkStatisticsImageFilter.h"
+#include "itkMetaImageIO.h"
+#include "itkMetaDataObject.h"
+#include "itkIOCommon.h"
+#include "itkVectorIndexSelectionCastImageFilter.h"
+#include "vector"
+#include "itkCheckerBoardImageFilter.h"
+#include "itkIO.h"
+
+#include "itkMultiResolutionPDEDeformableRegistration.h"
+#include "itkDiffeomorphicDemonsRegistrationFilter.h"
+#include "itkWarpImageFilter.h"
+#include "itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.h"
+#include "GenericTransformImage.h"
+
+namespace itk
+{
+/*This function writes the displacement fields of the Deformation.*/
+template 
+void DemonsRegistrator::WriteDisplacementComponents()
+{
+  m_DefaultPixelValue = NumericTraits::One;
+
+  // we use the vector index selection filter to break the deformation field
+  // into x,y,z components.
+  typedef itk::Image                  ComponentImageType;
+  typedef itk::VectorIndexSelectionCastImageFilter ComponentFilterType;
+
+  std::string CurrentComponentFilename;
+  try
+    {
+    char ext[3][14] = { "_xdisp.nii.gz", "_ydisp.nii.gz", "_zdisp.nii.gz" };
+
+    typename ComponentFilterType::Pointer myComponentFilter =
+      ComponentFilterType::New();
+    myComponentFilter->SetInput(m_DeformationField);
+    for( unsigned int extiter = 0; extiter < 3; ++extiter )
+      {
+      CurrentComponentFilename = m_DisplacementBaseName + ext[extiter];
+      if( this->GetOutDebug() )
+        {
+        std::cout << "Writing Transform Image: "
+                  << CurrentComponentFilename << std::endl;
+        }
+
+      myComponentFilter->SetIndex(extiter);
+
+      typename ComponentImageType::Pointer DisplacementComponentImagePtr =
+        myComponentFilter->GetOutput();
+
+      itkUtil::WriteImage(DisplacementComponentImagePtr,
+                                              CurrentComponentFilename);
+      }
+    }
+  catch( itk::ExceptionObject & e )
+    {
+    std::cerr << "exception in file Displacement File Writer("
+              << CurrentComponentFilename << ")" << std::endl;
+    std::cerr << e.GetDescription() << std::endl;
+    std::cerr << e.GetLocation() << std::endl;
+    exit(-1);
+    }
+}
+
+/*Constructor to initialize the parameters.*/
+template <
+  class TRealImage,
+  class TOutputImage,
+  class TFieldValue>
+DemonsRegistrator::DemonsRegistrator()
+{
+  // Images need to be set from the outside
+  m_FixedImage = NULL;
+  m_MovingImage = NULL;
+  m_DeformationField = NULL;
+
+  m_Registration = RegistrationType::New();
+  m_LDRegistration = LDRegistrationType::New();
+
+  // Set up internal registrator with default components
+  m_FixedImagePyramid = FixedImagePyramidType::New();
+  m_FixedImagePyramid->UseShrinkImageFilterOff();
+  m_MovingImagePyramid = MovingImagePyramidType::New();
+  m_MovingImagePyramid->UseShrinkImageFilterOff();
+
+  m_DefaultPixelValue =  NumericTraits::Zero;
+
+  // Default parameters
+  m_NumberOfLevels = 1;
+
+  m_FixedImageShrinkFactors.Fill(1);
+  m_MovingImageShrinkFactors.Fill(1);
+
+  m_NumberOfIterations = UnsignedIntArray(1);
+  m_NumberOfIterations.Fill(10);
+  m_WarpedImageName = "none";
+  m_DisplacementBaseName = "none";
+  m_CheckerBoardFilename = "none";
+  m_DeformationFieldOutputName = "none";
+  m_CheckerBoardPattern.Fill(4);
+  m_OutNormalized  = "OFF";
+
+  m_UseHistogramMatching = false;
+  m_OutDebug = false;
+  m_UseLogDomain = false;
+
+  m_InitialDeformationField = NULL;
+  m_InterpolationMode = "Linear";
+}
+
+template <
+  class TRealImage,
+  class TOutputImage,
+  class TFieldValue>
+DemonsRegistrator::~DemonsRegistrator()
+{
+  if( !m_UseLogDomain )
+    {
+    if( m_Tag )
+      {
+      m_Registration->RemoveObserver(m_Tag);
+      }
+    }
+  else
+    {
+    if( m_Tag )
+      {
+      m_LDRegistration->RemoveObserver(m_Tag);
+      }
+    }
+}
+
+/*Perform the registration of preprocessed images.*/
+template <
+  typename TRealImage,
+  class TOutputImage,
+  class TFieldValue>
+void DemonsRegistrator::Execute()
+{
+#if 1
+  // Setup the image pyramids
+  m_FixedImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+  m_FixedImagePyramid->SetStartingShrinkFactors(
+    m_FixedImageShrinkFactors.GetDataPointer() );
+
+  m_MovingImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+  m_MovingImagePyramid->
+  SetStartingShrinkFactors( m_MovingImageShrinkFactors.GetDataPointer() );
+#endif
+  // Setup the registrator
+
+  if( !this->GetUseLogDomain() )
+    {
+    m_Registration->SetFixedImagePyramid(m_FixedImagePyramid);
+    m_Registration->SetMovingImagePyramid(m_MovingImagePyramid);
+
+    // Setup an registration observer
+    typedef SimpleMemberCommand CommandType;
+    typename CommandType::Pointer command = CommandType::New();
+    command->SetCallbackFunction(this, &Self::StartNewLevel);
+
+    m_Tag = m_Registration->AddObserver(IterationEvent(), command);
+
+    typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction<
+      TDeformationField, double> FieldInterpolatorType;
+
+    typename FieldInterpolatorType::Pointer VectorInterpolator =
+      FieldInterpolatorType::New();
+
+    m_Registration->GetFieldExpander()->SetInterpolator(VectorInterpolator);
+
+    m_Registration->SetFixedImage(m_FixedImage);
+    m_Registration->SetMovingImage(m_MovingImage);
+    m_Registration->SetNumberOfLevels(m_NumberOfLevels);
+    m_Registration->SetNumberOfIterations( m_NumberOfIterations.
+                                           data_block() );
+
+    // Setup the initial deformation field
+    if( this->m_InitialDeformationField.IsNotNull() )
+      {
+      m_Registration->SetInitialDeformationField(this->m_InitialDeformationField);
+      }
+    if( this->m_FixedLandmarkFilename != ""
+        && this->m_MovingLandmarkFilename != "" )
+      {
+      std::cerr
+      << "Registering Landmarks as an initializer is not yet implemented"
+      << std::endl;
+      exit(-1);
+      }
+    // Perform the registration.
+    try
+      {
+      m_Registration->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::
+      cout << "Caught a non-ITK exception " << __FILE__ << " " << __LINE__
+           << std::endl;
+      }
+    if( this->GetOutDebug() )
+      {
+      std::cout
+      <<
+      "Moving image shrink factors used in each level of MultiResolution Schedule\n"
+      << m_MovingImagePyramid->GetSchedule() << std::endl;
+      std::cout
+      <<
+      "Fixed image shrink factors used in each level of MultiResolution Schedule\n"
+      << m_FixedImagePyramid->GetSchedule() << std::endl;
+      }
+    try
+      {
+      m_DeformationField = m_Registration->GetOutput();
+      if( m_DeformationField->GetDirection() != m_FixedImage->GetDirection() )
+        {
+        std::cout << "ERROR Directions don't match\n"
+                  << m_DeformationField->GetDirection()
+                  << "\n"
+                  << m_FixedImage->GetDirection()
+                  << std::endl;
+        exit(-1);
+        }
+      if( m_Tag )
+        {
+        m_Registration->RemoveObserver(m_Tag);
+        m_Tag = 0;
+        }
+      m_Registration = NULL;
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::
+      cout << "Caught a non-ITK exception " << __FILE__ << " " << __LINE__
+           << std::endl;
+      }
+    }
+
+  if( this->GetUseLogDomain() )
+    {
+    std::cout << "LogDomain!" << std::endl;
+    //  m_LDRegistration->SetFixedImagePyramid (m_FixedImagePyramid);
+    //  m_LDRegistration->SetMovingImagePyramid (m_MovingImagePyramid);
+
+    // Setup an registration observer
+    typedef SimpleMemberCommand CommandType;
+    typename CommandType::Pointer command = CommandType::New();
+    command->SetCallbackFunction(this, &Self::StartNewLevel);
+
+    m_Tag = m_LDRegistration->AddObserver(IterationEvent(), command);
+
+    typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction<
+      TDeformationField, double> FieldInterpolatorType;
+
+    typename FieldInterpolatorType::Pointer VectorInterpolator =
+      FieldInterpolatorType::New();
+
+    m_LDRegistration->GetFieldExpander()->SetInterpolator(VectorInterpolator);
+
+    m_LDRegistration->SetFixedImage(m_FixedImage);
+    m_LDRegistration->SetMovingImage(m_MovingImage);
+    m_LDRegistration->SetNumberOfLevels(m_NumberOfLevels);
+    m_LDRegistration->SetNumberOfIterations( m_NumberOfIterations.data_block() );
+
+#if 1
+    if( this->m_InitialDeformationField.IsNotNull() )
+      {
+      m_LDRegistration->SetArbitraryInitialVelocityField(this->m_InitialDeformationField);
+      }
+#endif
+
+    try
+      {
+      m_LDRegistration->UpdateLargestPossibleRegion();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::
+      cout << "Caught a non-ITK exception " << __FILE__ << " " << __LINE__
+           << std::endl;
+      }
+    if( this->GetOutDebug() )
+      {
+      std::cout
+      << "Moving image shrink factors used in each level of MultiResolution Schedule\n"
+      << m_MovingImagePyramid->GetSchedule() << std::endl;
+      std::cout
+      << "Fixed image shrink factors used in each level of MultiResolution Schedule\n"
+      << m_FixedImagePyramid->GetSchedule() << std::endl;
+      }
+    try
+      {
+      m_DeformationField = m_LDRegistration->GetDeformationField();
+      if( m_DeformationField->GetDirection() != m_FixedImage->GetDirection() )
+        {
+        std::cout << "ERROR Directions don't match\n"
+                  << m_DeformationField->GetDirection()
+                  << "\n"
+                  << m_FixedImage->GetDirection()
+                  << std::endl;
+        exit(-1);
+        }
+      if( m_Tag )
+        {
+        m_LDRegistration->RemoveObserver(m_Tag);
+        m_Tag = 0;
+        }
+      m_Registration = NULL;
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::
+      cout << "Caught a non-ITK exception " << __FILE__ << " " << __LINE__
+           << std::endl;
+      }
+    }
+
+  // Write the output deformation fields if specified by the user.
+  if( this->m_DeformationFieldOutputName != std::string("none")
+      && this->m_DeformationFieldOutputName != std::string("") )
+    {
+    itkUtil::WriteImage(m_DeformationField,
+                                           this->m_DeformationFieldOutputName);
+    if( this->GetOutDebug() )
+      {
+      std::cout << "---Deformation field has been written "
+                << this->m_DeformationFieldOutputName << "--" << std::endl;
+      }
+    }
+
+  //  Write out the displacement fields specified by the user.
+  if( this->m_DisplacementBaseName != std::string("none") )
+    {
+    this->WriteDisplacementComponents();
+    }
+
+  if( this->m_WarpedImageName != std::string("none") || this->m_CheckerBoardFilename != std::string("none") )
+    {
+    /*Warp the image with the generated deformation field.*/
+    typename RealImageType::Pointer DeformedMovingImagePtr(0);
+
+      {
+      typename RealImageType::Pointer sourceMovingImage = NULL;
+      if( this->GetUseHistogramMatching() == true )
+        {
+        sourceMovingImage = m_MovingImage;
+        }
+      else
+        {
+        sourceMovingImage = m_UnNormalizedMovingImage;
+        }
+      DeformedMovingImagePtr = TransformWarp(
+          sourceMovingImage,
+          m_FixedImage.GetPointer(),
+          0,
+          GetInterpolatorFromString(this->m_InterpolationMode),
+          m_DeformationField);
+      }
+
+    if( this->GetOutDebug() )
+      {
+      std::cout << "-----Direction of output warped image\n"
+                << DeformedMovingImagePtr->GetDirection()
+                << "\n-----Direction of deformation field\n"
+                << this->m_DeformationField->GetDirection() << std::endl;
+      }
+
+    /*Write the output image.*/
+
+    if( this->m_WarpedImageName != std::string("") && this->m_WarpedImageName != std::string("none") )
+      {
+      typename TOutputImage::Pointer CastImageSptr =
+        itkUtil::PreserveCast(
+          DeformedMovingImagePtr);
+      itkUtil::WriteImage(CastImageSptr,
+                                        this->m_WarpedImageName);
+
+      if( this->GetOutDebug() )
+        {
+        std::cout << "---Deformed Image has been written" <<  this->m_WarpedImageName << std::endl;
+        }
+      }
+    /*Write the checkerboard image of the fixed image and the output image.*/
+    if( this->m_CheckerBoardFilename != std::string("") && this->m_CheckerBoardFilename != std::string("none") )
+      {
+      typedef itk::CheckerBoardImageFilter Checkerfilter;
+      typename Checkerfilter::Pointer checker = Checkerfilter::New();
+      if( this->GetUseHistogramMatching() == true )
+        {
+        checker->SetInput1(m_FixedImage);
+        }
+      else
+        {
+        checker->SetInput1(m_UnNormalizedFixedImage);
+        }
+      checker->SetInput2(DeformedMovingImagePtr);
+      checker->SetCheckerPattern( this->GetCheckerBoardPattern() );
+      try
+        {
+        checker->Update();
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        std::cout << "Caught an ITK exception: " << std::endl;
+        std::cout << err << " " << __FILE__ << " " << __LINE__ << std::
+        endl;
+        throw err;
+        }
+      typename RealImageType::Pointer CheckerImagePtr = checker->GetOutput();
+      itkUtil::WriteImage(CheckerImagePtr,
+                                         this->m_CheckerBoardFilename);
+      if( this->GetOutDebug() )
+        {
+        std::cout << "---Checker Board Image has been written" << std::endl;
+        }
+      }
+    }
+}
+
+// Print out the present registration level.
+template <
+  class TRealImage,
+  class TOutputImage,
+  class TFieldValue>
+void DemonsRegistrator::StartNewLevel()
+{
+  if( this->GetOutDebug() )
+    {
+    if( !this->GetUseLogDomain() )
+      {
+      std::cout << "--- Starting level " << m_Registration->GetCurrentLevel() << std::endl;
+      }
+    else
+      {
+      std::cout << "--- Starting level " << m_LDRegistration->GetCurrentLevel() << std::endl;
+      }
+    }
+}
+
+} // namespace itk
+#endif
diff --git a/BRAINSCommonLib/GenerateBRAINSCommonLibConfig.cmake b/BRAINSCommonLib/GenerateBRAINSCommonLibConfig.cmake
new file mode 100644
index 00000000..3b2d2a29
--- /dev/null
+++ b/BRAINSCommonLib/GenerateBRAINSCommonLibConfig.cmake
@@ -0,0 +1,27 @@
+# Generate the BRAINSCommonLibConfig.cmake file in the build tree and configure
+# one the installation tree.
+
+# Settings specific to build trees
+#
+#
+set(BRAINSCommonLib_USE_FILE_CONFIG ${CMAKE_CURRENT_BINARY_DIR}/UseBRAINSCommonLib.cmake)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/UseBRAINSCommonLib.cmake.in
+  ${BRAINSCommonLib_USE_FILE_CONFIG}
+  @ONLY)
+
+set(BRAINSCommonLib_DATA_DIRS_CONFIG ${CMAKE_CURRENT_BINARY_DIR}/TestData)
+set(BRAINSCommonLib_INCLUDE_DIRS_CONFIG ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
+set(BRAINSCommonLib_LIBRARY_DIRS_CONFIG ${CMAKE_CURRENT_BINARY_DIR})
+set(ITK_DIR_CONFIG ${ITK_DIR})
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/BRAINSCommonLibConfig.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLibConfig.cmake @ONLY)
+
+# Settings specific for installation trees
+#
+#
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/UseBRAINSCommonLib.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/UseBRAINSCommonLib.cmake_install
+  @ONLY)
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/BRAINSCommonLibInstallConfig.cmake.in
+  ${CMAKE_CURRENT_BINARY_DIR}/BRAINSCommonLibConfig.cmake_install @ONLY)
diff --git a/BRAINSCommonLib/GenericTransformImage.cxx b/BRAINSCommonLib/GenericTransformImage.cxx
new file mode 100644
index 00000000..72233d9a
--- /dev/null
+++ b/BRAINSCommonLib/GenericTransformImage.cxx
@@ -0,0 +1,562 @@
+#include 
+#include "GenericTransformImage.h"
+
+#include "itkAffineTransform.h"
+#include "itkBSplineDeformableTransform.h"
+#include "itkCenteredAffineTransform.h"
+#include "itkCenteredEuler3DTransform.h"
+#include "itkCenteredRigid2DTransform.h"
+#include "itkCenteredSimilarity2DTransform.h"
+#include "itkEuler2DTransform.h"
+#include "itkEuler3DTransform.h"
+#include "itkFixedCenterOfRotationAffineTransform.h"
+#include "itkIdentityTransform.h"
+#include "itkQuaternionRigidTransform.h"
+#include "itkRigid2DTransform.h"
+#include "itkRigid3DPerspectiveTransform.h"
+#include "itkRigid3DTransform.h"
+#include "itkScalableAffineTransform.h"
+#include "itkScaleLogarithmicTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkScaleTransform.h"
+#include "itkScaleVersor3DTransform.h"
+#include "itkSimilarity2DTransform.h"
+#include "itkTranslationTransform.h"
+#include "itkVersorRigid3DTransform.h"
+#include "itkVersorTransform.h"
+#include "itkThinPlateR2LogRSplineKernelTransform.h"
+#include "itkThinPlateSplineKernelTransform.h"
+#include "itkTransformFactory.h"
+#include 
+
+// #include "itkSimilarity2DTransfor3DPerspectiveTransform.h"
+
+namespace itk
+{
+VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
+  const GenericTransformType::ConstPointer genericTransformToWrite)
+{
+  typedef VersorRigid3DTransformType VersorRigidTransformType;
+  VersorRigidTransformType::Pointer versorRigid = VersorRigidTransformType::New();
+  versorRigid->SetIdentity();
+  // //////////////////////////////////////////////////////////////////////////
+  // ConvertTransforms
+  //
+  if( genericTransformToWrite.IsNotNull() )
+    {
+    try
+      {
+      const std::string transformFileType = genericTransformToWrite->GetNameOfClass();
+      if( transformFileType == "VersorRigid3DTransform" )
+        {
+        const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+          dynamic_cast( genericTransformToWrite.GetPointer() );
+        if( tempInitializerITKTransform.IsNull() )
+          {
+          std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+          }
+        AssignRigid::ExtractVersorRigid3DTransform(versorRigid, tempInitializerITKTransform);
+        }
+      else if( transformFileType == "ScaleVersor3DTransform" )
+        {
+        const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+          dynamic_cast( genericTransformToWrite.GetPointer() );
+        if( tempInitializerITKTransform.IsNull() )
+          {
+          std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+          }
+        AssignRigid::ExtractVersorRigid3DTransform(versorRigid, tempInitializerITKTransform);
+        }
+      else if( transformFileType == "ScaleSkewVersor3DTransform" )
+        {
+        const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+          dynamic_cast( genericTransformToWrite.GetPointer() );
+        if( tempInitializerITKTransform.IsNull() )
+          {
+          std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+          }
+        AssignRigid::ExtractVersorRigid3DTransform(versorRigid, tempInitializerITKTransform);
+        }
+      else if( transformFileType == "AffineTransform" )
+        {
+        const AffineTransformType::ConstPointer tempInitializerITKTransform =
+          dynamic_cast( genericTransformToWrite.GetPointer() );
+        if( tempInitializerITKTransform.IsNull() )
+          {
+          std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+          }
+        AssignRigid::ExtractVersorRigid3DTransform(versorRigid, tempInitializerITKTransform);
+        }
+      /*
+        * else if(transformFileType == "BSplineDeformableTransform")
+        * {
+        * BSplineTransformType::Pointer tempInitializerITKTransform
+        * = dynamic_cast(
+        *    genericTransformToWrite.GetPointer() );
+                if ( tempInitializerITKTransform.IsNull() )
+                  {
+                  std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+                  }
+        * //AssignRigid::ExtractVersorRigid3DTransform(versorRigid,
+        *    tempInitializerITKTransform->GetBulkTransform());
+        * versorRigid=NULL; //NOT: Perhaps it makes sense to extract the rigid
+        *    part of the bulk transform.  But that is pretty obscure case.
+        * return NULL;
+        * }
+        */
+      else      //  NO SUCH CASE!!
+        {
+        std::cout
+        << "Unsupported initial transform file -- TransformBase first transform typestring, "
+        << transformFileType
+        << " not equal to any recognized type VersorRigid3DTransform OR "
+        << " ScaleVersor3DTransform OR ScaleSkewVersor3DTransform OR AffineTransform"
+        << std::endl;
+        return NULL;
+        }
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+      std::cout << "[FAILED]" << std::endl;
+      std::cerr
+      << "Error while converting the genericTransformToWrite to Rigid"
+      << std::endl;
+      std::cerr << excp << std::endl;
+      return NULL;
+      }
+    }
+  return versorRigid;
+}
+
+int WriteBothTransformsToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+                              const std::string & outputTransform,
+                              const std::string & strippedOutputTransform)
+{
+  // //////////////////////////////////////////////////////////////////////////
+  // Write out tranfoms.
+  //
+  if( genericTransformToWrite.IsNull() )
+    {
+    return 0;
+    }
+  try
+    {
+    const std::string transformFileType = genericTransformToWrite->GetNameOfClass();
+    if( transformFileType == "VersorRigid3DTransform" )
+      {
+      if( outputTransform.size() > 0 )  // Write out the transform
+        {
+        itk::WriteTransformToDisk(genericTransformToWrite, outputTransform);
+        }
+      }
+    else if( transformFileType == "ScaleVersor3DTransform" )
+      {
+      if( outputTransform.size() > 0 )  // Write out the transform
+        {
+        itk::WriteTransformToDisk(genericTransformToWrite, outputTransform);
+        }
+      }
+    else if( transformFileType == "ScaleSkewVersor3DTransform" )
+      {
+      if( outputTransform.size() > 0 )  // Write out the transform
+        {
+        itk::WriteTransformToDisk(genericTransformToWrite, outputTransform);
+        }
+      }
+    else if( transformFileType == "AffineTransform" )
+      {
+      if( outputTransform.size() > 0 )  // Write out the transform
+        {
+        itk::WriteTransformToDisk(genericTransformToWrite, outputTransform);
+        }
+      }
+    else if( transformFileType == "BSplineDeformableTransform" )
+      {
+      const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( genericTransformToWrite.GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      if( strippedOutputTransform.size() > 0 )
+        {
+        std::cout << "ERROR:  The rigid component of a BSpline transform is not supported." << std::endl;
+        }
+      if( outputTransform.size() > 0 )
+        {
+        itk::WriteTransformToDisk(genericTransformToWrite, outputTransform);
+        }
+      }
+    else      //  NO SUCH CASE!!
+      {
+      std::cout << "Unsupported initial transform file -- TransformBase first transform typestring, "
+                << transformFileType
+                <<
+      " not equal to any recognized type VersorRigid3DTransform OR ScaleVersor3DTransform OR ScaleSkewVersor3DTransform OR AffineTransform"
+                << std::endl;
+      return -1;
+      }
+    // Should just write out the rigid transform here.
+    if( strippedOutputTransform.size() > 0  )
+      {
+      typedef VersorRigid3DTransformType VersorRigidTransformType;
+      VersorRigidTransformType::Pointer versorRigid = itk::ComputeRigidTransformFromGeneric(genericTransformToWrite);
+      if( versorRigid.IsNotNull() )
+        {
+        itk::WriteTransformToDisk(versorRigid.GetPointer(), strippedOutputTransform);
+        }
+      }
+    }
+  catch( itk::ExceptionObject & excp )
+    {
+    std::cout << "[FAILED]" << std::endl;
+    std::cerr << "Error while writing the genericTransformToWrite"
+              << std::endl;
+    std::cerr << excp << std::endl;
+    exit(-1);
+    }
+  return 0;
+}
+
+int WriteStrippedRigidTransformToDisk(const GenericTransformType::ConstPointer genericTransformToWrite,
+                                      const std::string & strippedOutputTransform)
+{
+  return WriteBothTransformsToDisk(genericTransformToWrite, std::string(""), strippedOutputTransform);
+}
+
+GenericTransformType::Pointer ReadTransformFromDisk(const std::string & initialTransform)
+{
+  GenericTransformType::Pointer genericTransform = NULL;
+  //
+  //
+  // read in the initial ITKTransform
+  //
+  //
+  TransformReaderType::Pointer      transformListReader =  TransformReaderType::New();
+  TransformListType                 currentTransformList;
+  TransformListType::const_iterator currentTransformListIterator;
+
+  if( initialTransform.size() > 0 )
+    {
+    std::cout
+    << "Read ITK transform from text file: "
+    << initialTransform << std::endl;
+
+    transformListReader->SetFileName( initialTransform.c_str() );
+    try
+      {
+      transformListReader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cerr << "ExceptionObject caught !" << std::endl;
+      std::cerr << err << std::endl;
+      exit(-1);
+      }
+    currentTransformList = *( transformListReader->GetTransformList() );
+    if( currentTransformList.size() == 0 )
+      {
+      std::cout << "Number of currentTransformList = " << currentTransformList.size() << std::endl;
+      std::cout << "FATAL ERROR: Failed to read transform" << initialTransform << std::endl;
+      exit(-1);
+      }
+    }
+  if( currentTransformList.size() == 1 )  // Most simple transform types
+    {
+    // NOTE:  The dynamic casting here circumvents the standard smart pointer
+    // behavior.  It is important that
+    // by making a new copy and transfering the parameters it is more safe.  Now
+    // we only need to ensure
+    // that currentTransformList.begin() smart pointer is stable (i.e. not
+    // deleted) while the variable
+    // temp has a reference to it's internal structure.
+    const std::string transformFileType = ( *( currentTransformList.begin() ) )->GetNameOfClass();
+    if( transformFileType == "VersorRigid3DTransform" )
+      {
+      const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( ( *( currentTransformList.begin() ) ).GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      VersorRigid3DTransformType::Pointer tempCopy = VersorRigid3DTransformType::New();
+      AssignRigid::AssignConvertedTransform(tempCopy,
+                                            tempInitializerITKTransform);
+      genericTransform = tempCopy.GetPointer();
+      }
+    else if( transformFileType == "ScaleVersor3DTransform" )
+      {
+      const ScaleVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( ( *( currentTransformList.begin() ) ).GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      ScaleVersor3DTransformType::Pointer tempCopy = ScaleVersor3DTransformType::New();
+      AssignRigid::AssignConvertedTransform(tempCopy,
+                                            tempInitializerITKTransform);
+      genericTransform = tempCopy.GetPointer();
+      }
+    else if( transformFileType == "ScaleSkewVersor3DTransform" )
+      {
+      const ScaleSkewVersor3DTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( ( *( currentTransformList.begin() ) ).GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      ScaleSkewVersor3DTransformType::Pointer tempCopy = ScaleSkewVersor3DTransformType::New();
+      AssignRigid::AssignConvertedTransform(tempCopy,
+                                            tempInitializerITKTransform);
+      genericTransform = tempCopy.GetPointer();
+      }
+    else if( transformFileType == "AffineTransform" )
+      {
+      const AffineTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( ( *( currentTransformList.begin() ) ).GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      AffineTransformType::Pointer tempCopy = AffineTransformType::New();
+      AssignRigid::AssignConvertedTransform(tempCopy,
+                                            tempInitializerITKTransform);
+      genericTransform = tempCopy.GetPointer();
+      }
+    else if( transformFileType == "ThinPlateR2LogRSplineKernelTransform" )
+      {
+      const ThinPlateSpline3DTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( ( *( currentTransformList.begin() ) ).GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      ThinPlateSpline3DTransformType::Pointer tempCopy = ThinPlateSpline3DTransformType::New();
+      tempCopy->SetFixedParameters( tempInitializerITKTransform->GetFixedParameters() );
+      tempCopy->SetParametersByValue( tempInitializerITKTransform->GetParameters() );
+      tempCopy->ComputeWMatrix();
+      genericTransform = tempCopy.GetPointer();
+      }
+    }
+  else if( currentTransformList.size() == 2 )  // A special case for
+                                               // BSplineTransforms
+  // To recombine the bulk and the bSpline transforms.
+    {
+    // transformListReader->GetTransformList();
+    TransformListType::const_iterator initializeTransformsListIterator =
+      currentTransformList.begin();
+
+    const GenericTransformType::ConstPointer FirstTransform = dynamic_cast
+      ( ( *( initializeTransformsListIterator ) ).GetPointer() );
+    if( FirstTransform.IsNull() )
+      {
+      std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+      }
+    const std::string FirstTransformFileType = FirstTransform->GetNameOfClass();
+
+    ++initializeTransformsListIterator; // Increment to next iterator
+
+    const GenericTransformType::ConstPointer SecondTransform = dynamic_cast
+      ( ( *( initializeTransformsListIterator ) ).GetPointer() );
+    if( SecondTransform.IsNull() )
+      {
+      std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+      }
+    const std::string SecondTransformFileType = SecondTransform->GetNameOfClass();
+
+    BSplineTransformType::Pointer outputBSplineTransform =
+      BSplineTransformType::New();
+    outputBSplineTransform->SetIdentity();
+
+    // Now get the BSpline information
+    if( FirstTransformFileType == "BSplineDeformableTransform" )
+      {
+      const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast
+        ( FirstTransform.GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      outputBSplineTransform->SetFixedParameters( tempInitializerITKTransform->GetFixedParameters() );
+      outputBSplineTransform->SetParametersByValue( tempInitializerITKTransform->GetParameters() );
+      outputBSplineTransform->SetBulkTransform(SecondTransform);
+      }
+    else if( SecondTransformFileType == "BSplineDeformableTransform" )
+      {
+      const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast
+        ( SecondTransform.GetPointer() );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+      outputBSplineTransform->SetFixedParameters( tempInitializerITKTransform->GetFixedParameters() );
+      outputBSplineTransform->SetParametersByValue( tempInitializerITKTransform->GetParameters() );
+      outputBSplineTransform->SetBulkTransform(FirstTransform);
+      }
+    else
+      {
+      std::cout << "[FAILED]" << std::endl;
+      std::cerr
+      << "Error using the currentTransformList has two elements, but neither of them are a BSplineDeformableTransform/"
+      << std::endl;
+      std::cerr
+      << "There should not be more than two transforms in the transform list."
+      << std::endl;
+      return NULL;
+      }
+    genericTransform = outputBSplineTransform.GetPointer();
+    }
+  else if( currentTransformList.size() > 2 )
+    {
+    // Error, too many transforms on transform list.
+    std::cout << "[FAILED]" << std::endl;
+    std::cerr
+    << "Error using the currentTransformList for initializing a BSPlineDeformableTransform:"
+    << std::endl;
+    std::cerr
+    << "There should not be more than two transforms in the transform list."
+    << std::endl;
+    return NULL;
+    }
+  return genericTransform;
+}
+
+void WriteTransformToDisk(GenericTransformType const *const MyTransform, const std::string & TransformFilename)
+{
+  /*
+    *  Convert the transform to the appropriate assumptions and write it out as
+    *requested.
+    */
+    {
+    typedef itk::TransformFileWriter TransformWriterType;
+    TransformWriterType::Pointer transformWriter =  TransformWriterType::New();
+    transformWriter->SetFileName( TransformFilename.c_str() );
+
+    const std::string transformFileType = MyTransform->GetNameOfClass();
+    if( transformFileType == "BSplineDeformableTransform" )
+      {
+      const BSplineTransformType::ConstPointer tempInitializerITKTransform =
+        dynamic_cast( MyTransform );
+      if( tempInitializerITKTransform.IsNull() )
+        {
+        std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+        }
+
+      // NOTE: Order was reversed in order to get BSpline first, then Bulk
+      // transform in order to
+      // try to appease Slicer3.
+      transformWriter->AddTransform(tempInitializerITKTransform);
+      // Bulk transform is assumed to be second in Slicer3.
+      transformWriter->AddTransform( tempInitializerITKTransform->GetBulkTransform() );
+      }
+    else
+      {
+      transformWriter->AddTransform(MyTransform);
+      }
+    try
+      {
+      transformWriter->Update();
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+      std::cout << "[FAILED]" << std::endl;
+      std::cerr << "Error while writing transform file: "
+                << TransformFilename << std::endl;
+      std::cerr << excp << std::endl;
+      return;
+      }
+    // Test if the file exists.
+    if( !itksys::SystemTools::FileExists( TransformFilename.c_str() ) )
+      {
+      itk::ExceptionObject e(__FILE__, __LINE__, "Failed to write file", "WriteTransformToDisk");
+      std::ostringstream   msg;
+      msg << "The file was not successfully created. "
+          << std::endl << "Filename = " << TransformFilename
+          << std::endl;
+      e.SetDescription( msg.str().c_str() );
+      throw e;
+      exit(-1);
+      return;
+      }
+    }
+}
+
+//HACK:  This can now be removed!
+// Adding a single new transform require registering all the transform types.
+void AddExtraTransformRegister(void)
+{
+  // This is needed in order to read and write ScaleVersor3D TransformTypes.
+  // Hopefully in ITK-3-19 this will become part of the non-review transform
+  // types.
+  itk::TransformFactory >::RegisterDefaultTransforms();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+  itk::TransformFactory >::RegisterTransform();
+}
+
+} // end namespace itk
diff --git a/BRAINSCommonLib/GenericTransformImage.h b/BRAINSCommonLib/GenericTransformImage.h
new file mode 100644
index 00000000..1fbe8f73
--- /dev/null
+++ b/BRAINSCommonLib/GenericTransformImage.h
@@ -0,0 +1,209 @@
+#ifndef _GenericTransformImage_H_
+#define _GenericTransformImage_H_
+
+#include "BRAINSCommonLibWin32Header.h"
+
+#include 
+#include "itkImage.h"
+#include "itkCastImageFilter.h"
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkWarpImageFilter.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunction.h"
+#include "itkWindowedSincInterpolateImageFunction.h"
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkSignedMaurerDistanceMapImageFilter.h"
+#include "itkStatisticsImageFilter.h"
+#include "itkScaleVersor3DTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkAffineTransform.h"
+#include 
+#include 
+#include "itkVersorRigid3DTransform.h"
+#include "ConvertToRigidAffine.h"
+#include "itkResampleImageFilter.h"
+#include "itkImageDuplicator.h"
+#include "Imgmath.h"
+
+#include "itkTransformFactory.h"
+#include "itkTransformFileReader.h"
+#include "itkTransformFileWriter.h"
+//
+// TODO:  The next two should be hidden in the cxx files again.
+typedef itk::TransformFileReader                    TransformReaderType;
+typedef itk::TransformFileReader::TransformListType TransformListType;
+
+// TODO:  This should really be taken as a typedef from the BSpline class.
+// TODO:  These should be hidden in the BRAINSFit namespace.
+typedef itk::Transform GenericTransformType;
+
+namespace GenericTransformImageNS
+{
+static const unsigned int SpaceDimension = 3;
+static const unsigned int SplineOrder = 3;
+}
+
+typedef double CoordinateRepType;
+typedef itk::BSplineDeformableTransform<
+  CoordinateRepType,
+  GenericTransformImageNS::SpaceDimension,
+  GenericTransformImageNS::SplineOrder> BSplineTransformType;
+
+typedef itk::AffineTransform                      AffineTransformType;
+typedef itk::VersorRigid3DTransform                  VersorRigid3DTransformType;
+typedef itk::ScaleVersor3DTransform                  ScaleVersor3DTransformType;
+typedef itk::ScaleSkewVersor3DTransform              ScaleSkewVersor3DTransformType;
+typedef itk::ThinPlateR2LogRSplineKernelTransform ThinPlateSpline3DTransformType;
+
+namespace itk
+{
+/**
+  * \author Hans J. Johnson
+  * \brief A utility function to write ITK compliant transforms to disk in a way
+  *that is compliant with the ReadTransformFromDisk
+  * \param genericTransformToWrite A pointer to baseclass
+  *itk::Transform that is
+  * polymorphically cast to a real class like (i.e. itk::VersorRigid,
+  *itk::Affine, itk::BSpline, or similar)
+  * \param outputTransform the filename of the output transform.
+  * \code
+  * //To convert from non-const smart pointers ploymorphically to the smart
+  *ConstPointer up the class tree, use the GetPointer
+  * AffineTransformType::Pointer myAffine=AffineTransformType::New(); //NOTE:
+  * This is not a const smart pointer
+  * WriteTransformToDisk(myAffine.GetPointer(), "myAffineFile.mat");
+  * \endcode
+  */
+BRAINSCommonLib_EXPORT extern void WriteTransformToDisk(GenericTransformType const *const genericTransformToWrite,
+                                                        const std::string & outputTransform);
+
+/**
+  * \author Hans J. Johnson
+  * \brief A utility function to read ITK compliant transforms to disk in a way
+  *that is compliant with the WriteTransformFromDisk
+  * \param outputTransform the filename of the output transform.
+  * \return A pointer to baseclass itk::Transform that is
+  * polymorphically convertable to a real class like (i.e. itk::VersorRigid,
+  *itk::Affine, itk::BSpline, or similar)
+  * \code
+  * //To convert from non-const smart pointers ploymorphically to the smart
+  *ConstPointer up the class tree, use the GetPointer
+  * GenericTransformType::Pointer
+  *myGenericTransform=ReadTransformFromDisk(myAffine.GetPointer(),
+  *"myAffineFile.mat");
+  *
+  * VersorRigid3DTransformType::Pointer myVersorRigid3D=NULL;
+  * {
+  * const std::string transformFileType = myGenericTransform->GetNameOfClass();
+  * if ( transformFileType == "VersorRigid3DTransform" )
+  *   {
+  *   myVersorRigid3D->SetParameters( versorRigid->GetParameters() );
+  *   myVersorRigid3D->SetFixedParameters( versorRigid->GetFixedParameters() );
+  *   }
+  *   NOTE: It is more safe to copy parameters into the concrete class rather
+  *than attempting to dynamically
+  *   cast the base classes.  The reason is that the smart pointer management
+  *becomes very unweildy and
+  *   is hard to keep straight between the pointer that may delete the base
+  *class, and the pointer that
+  *   is the derived class.
+  * }
+  * \endcode
+  */
+BRAINSCommonLib_EXPORT extern GenericTransformType::Pointer ReadTransformFromDisk(const std::string & initialTransform);
+
+/**
+  * \author Hans J. Johnson
+  * \brief A utility function to write ITK compliant transforms to disk in a way
+  *that is compliant with the ReadTransformFromDisk
+  * \param genericTransformToWrite A pointer to baseclass
+  *itk::Transform that is
+  * polymorphically cast to a real class like (i.e. itk::VersorRigid,
+  *itk::Affine, itk::BSpline, or similar)
+  * \param outputTransform the filename of the output transform.
+  * \code
+  * //To convert from non-const smart pointers ploymorphically to the smart
+  *ConstPointer up the class tree, use the GetPointer
+  * AffineTransformType::Pointer myAffine=AffineTransformType::New(); //NOTE:
+  * This is not a const smart pointer
+  * WriteTransformToDisk(myAffine.GetPointer(), "myAffineFile.mat");
+  * \endcode
+  */
+BRAINSCommonLib_EXPORT extern VersorRigid3DTransformType::Pointer ComputeRigidTransformFromGeneric(
+  const GenericTransformType::ConstPointer genericTransformToWrite);
+
+/**
+  * \author Hans J. Johnson
+  * \brief Special purpose convenience function -- should not have a public
+  *interface.
+  */
+BRAINSCommonLib_EXPORT extern int WriteBothTransformsToDisk(
+  const GenericTransformType::ConstPointer genericTransformToWrite, const std::string & outputTransform,
+  const std::string & strippedOutputTransform);
+
+/**
+  * \author Hans J. Johnson
+  * \brief Special purpose convenience function -- should not have a public
+  *interface.
+  */
+BRAINSCommonLib_EXPORT extern int WriteStrippedRigidTransformToDisk(
+  const GenericTransformType::ConstPointer genericTransformToWrite, const std::string & strippedOutputTransform);
+
+BRAINSCommonLib_EXPORT extern void AddExtraTransformRegister(void);
+
+}
+
+/**
+  * \author Hans J. Johnson
+  * \brief A class to transform images
+  */
+template 
+typename OutputImageType::Pointer
+TransformResample(
+  InputImageType const *const inputImage,
+  const itk::ImageBase * const ReferenceImage,
+  typename InputImageType::PixelType defaultValue,
+  typename itk::InterpolateImageFunction::RealType>
+  ::Pointer interp,
+  typename GenericTransformType::Pointer transform);
+
+/**
+  * \author Hans J. Johnson
+  * \brief A class to transform images
+  */
+template 
+typename OutputImageType::Pointer
+TransformWarp(
+  InputImageType const *const inputImage,
+  const itk::ImageBase *ReferenceImage,
+  typename InputImageType::PixelType defaultValue,
+  typename itk::InterpolateImageFunction::RealType>
+  ::Pointer interp,
+  typename DeformationImageType::Pointer deformationField);
+
+/**
+  * \author Hans J. Johnson
+  * \brief A class to transform images.  Only one of genericTransform or
+  *DeformationField can be non-null.
+  */
+template 
+typename OutputImageType::Pointer GenericTransformImage(
+  InputImageType const *const OperandImage,
+  const itk::ImageBase *ReferenceImage,
+  typename DeformationImageType::Pointer DeformationField,
+  typename GenericTransformType::Pointer genericTransform,
+  typename InputImageType::PixelType suggestedDefaultValue, // NOTE:  This is
+                                                            // ignored in the
+                                                            // case of binary
+                                                            // image!
+  const std::string interpolationMode,
+  const bool binaryFlag);
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "GenericTransformImage.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/GenericTransformImage.hxx b/BRAINSCommonLib/GenericTransformImage.hxx
new file mode 100644
index 00000000..6562d589
--- /dev/null
+++ b/BRAINSCommonLib/GenericTransformImage.hxx
@@ -0,0 +1,324 @@
+#ifndef _GenericTransformImage_hxx_
+#define _GenericTransformImage_hxx_
+
+#include 
+#include "GenericTransformImage.h"
+#include "itkResampleInPlaceImageFilter.h"
+
+template 
+typename OutputImageType::Pointer
+TransformResample(
+  InputImageType const *const inputImage,
+  const itk::ImageBase * const ReferenceImage,
+  typename InputImageType::PixelType defaultValue,
+  typename itk::InterpolateImageFunction::RealType>
+  ::Pointer interp,
+  typename GenericTransformType::Pointer transform)
+{
+  typedef typename itk::ResampleImageFilter ResampleImageFilter;
+  typename ResampleImageFilter::Pointer resample = ResampleImageFilter::New();
+  resample->SetInput(inputImage);
+  resample->SetTransform(transform);
+  resample->SetInterpolator(interp);
+
+  if( ReferenceImage != NULL )
+    {
+    resample->SetOutputParametersFromImage(ReferenceImage);
+    }
+  else
+    {
+    std::cout << "Alert:  missing Reference Volume information default image size set to inputImage" << std::endl;
+    resample->SetOutputParametersFromImage(inputImage);
+    }
+  resample->SetDefaultPixelValue(defaultValue);
+  resample->Update();
+  typename OutputImageType::Pointer returnval = resample->GetOutput();
+  // returnval->DisconnectPipeline();
+  return returnval;
+}
+
+template 
+typename OutputImageType::Pointer
+TransformWarp(
+  InputImageType const *const inputImage,
+  const itk::ImageBase *ReferenceImage,
+  typename InputImageType::PixelType defaultValue,
+  typename itk::InterpolateImageFunction::RealType>
+  ::Pointer interp,
+  typename DeformationImageType::Pointer deformationField)
+{
+  typedef typename itk::WarpImageFilter WarpImageFilter;
+  typename WarpImageFilter::Pointer warp = WarpImageFilter::New();
+  warp->SetInput(inputImage);
+  warp->SetDeformationField(deformationField);
+  warp->SetInterpolator(interp);
+
+  if( ReferenceImage != NULL )
+    {
+    warp->SetOutputParametersFromImage(ReferenceImage);
+    }
+  else
+    {
+    std::cout << "Alert:  missing Reference Volume information default image size set to deformationField" << std::endl;
+    warp->SetOutputParametersFromImage(deformationField);
+    }
+  warp->SetEdgePaddingValue(defaultValue);
+  warp->Update();
+  typename OutputImageType::Pointer returnval = warp->GetOutput();
+  // returnval->DisconnectPipeline();
+  return returnval;
+}
+
+template 
+typename itk::InterpolateImageFunction::RealType>::
+Pointer
+GetInterpolatorFromString(const std::string interpolationMode)
+{
+  typedef typename itk::NumericTraits::RealType TInterpolatorPrecisionType;
+  if( interpolationMode == "NearestNeighbor" )
+    {
+    typedef typename itk::NearestNeighborInterpolateImageFunction
+    InterpolatorType;
+    return ( InterpolatorType::New() ).GetPointer();
+    }
+  else if( interpolationMode == "Linear" )
+    {
+    typedef typename itk::LinearInterpolateImageFunction
+    InterpolatorType;
+    return ( InterpolatorType::New() ).GetPointer();
+    }
+  else if( interpolationMode == "BSpline" )
+    {
+    typedef typename itk::BSplineInterpolateImageFunction
+    InterpolatorType;
+    return ( InterpolatorType::New() ).GetPointer();
+    }
+  else if( interpolationMode == "WindowedSinc" )
+    {
+    typedef typename itk::ConstantBoundaryCondition
+    BoundaryConditionType;
+    static const unsigned int WindowedSincHammingWindowRadius = 5;
+    typedef typename itk::Function::HammingWindowFunction<
+      WindowedSincHammingWindowRadius, TInterpolatorPrecisionType, TInterpolatorPrecisionType> WindowFunctionType;
+    typedef typename itk::WindowedSincInterpolateImageFunction<
+      InputImageType,
+      WindowedSincHammingWindowRadius,
+      WindowFunctionType,
+      BoundaryConditionType,
+      TInterpolatorPrecisionType>   InterpolatorType;
+    return ( InterpolatorType::New() ).GetPointer();
+    }
+  else
+    {
+    std::cout << "Error: Invalid interpolation mode specified -" << interpolationMode << "- " << std::endl;
+    std::cout << "\tValid modes: NearestNeighbor, Linear, BSpline, WindowedSinc" << std::endl;
+    }
+  return NULL;
+}
+
+template 
+typename OutputImageType::Pointer GenericTransformImage(
+  InputImageType const *const OperandImage,
+  const itk::ImageBase *ReferenceImage,
+  typename DeformationImageType::Pointer DeformationField,
+  typename GenericTransformType::Pointer genericTransform,
+  typename InputImageType::PixelType suggestedDefaultValue, // NOTE:  This is
+                                                            // ignored in the
+                                                            // case of binary
+                                                            // image!
+  const std::string interpolationMode,
+  const bool binaryFlag)
+{
+  // FIRST will need to convert binary image to signed distance in case
+  // binaryFlag is true.
+
+  typename InputImageType::ConstPointer PrincipalOperandImage;
+
+  // Splice in a case for dealing with binary images,
+  // where signed distance maps are warped and thresholds created.
+  if( binaryFlag )
+    {
+    if( interpolationMode == "NearestNeighbor" )
+      {
+      std::cout << "WARNING:  Using NearestNeighbor and SignedDistance" << std::endl
+                << "          for binary images is an unlikely combination." << std::endl
+                << "          you probably want Linear interpolationMode for" << std::endl
+                << "          the signed distance map implied by your choice" << std::endl
+                << "          of pixelType binary." << std::endl;
+      }
+    /* We make the values inside the structures positive and outside negative
+      * using
+      *  BinaryThresholdImageFilter. As the lower and upper threshold values are
+      *     0 only values of 0 in the image are filled with 0.0 and other
+      *     values are  1.0
+      */
+
+    typedef itk::BinaryThresholdImageFilter FloatThresholdFilterType;
+    typename FloatThresholdFilterType::Pointer initialFilter =
+      FloatThresholdFilterType::New();
+    initialFilter->SetInput(OperandImage);
+      {
+      const typename FloatThresholdFilterType::OutputPixelType outsideValue = 1.0;
+      const typename FloatThresholdFilterType::OutputPixelType insideValue  = 0.0;
+      initialFilter->SetOutsideValue(outsideValue);
+      initialFilter->SetInsideValue(insideValue);
+      const typename FloatThresholdFilterType::InputPixelType lowerThreshold = 0;
+      const typename FloatThresholdFilterType::InputPixelType upperThreshold = 0;
+      initialFilter->SetLowerThreshold(lowerThreshold);
+      initialFilter->SetUpperThreshold(upperThreshold);
+      }
+    initialFilter->Update();
+      {
+      typedef itk::SignedMaurerDistanceMapImageFilter DistanceFilterType;
+      typename DistanceFilterType::Pointer DistanceFilter = DistanceFilterType::New();
+      DistanceFilter->SetInput( initialFilter->GetOutput() );
+      // DistanceFilter->SetNarrowBandwidth( m_BandWidth );
+      DistanceFilter->SetInsideIsPositive(true);
+      DistanceFilter->SetUseImageSpacing(true);
+      DistanceFilter->SetSquaredDistance(false);
+
+      DistanceFilter->Update();
+      PrincipalOperandImage = DistanceFilter->GetOutput();
+      // PrincipalOperandImage->DisconnectPipeline();
+      }
+    // Using suggestedDefaultValue based on the size of the image so that
+    // intensity values
+    // are kept to a reasonable range.  (A costlier way calculates the image
+    // min.)
+    const typename InputImageType::SizeType size = PrincipalOperandImage->GetLargestPossibleRegion().GetSize();
+    const typename InputImageType::SpacingType spacing = PrincipalOperandImage->GetSpacing();
+    double diagonalLength = 0;
+    for( int s = 0; s < InputImageType::ImageDimension; ++s )
+      {
+      diagonalLength += size[s] * spacing[s];
+      }
+    // Consider the 3D diagonal value, to guarantee that the background
+    // filler is unlikely to add shapes to the thresholded signed
+    // distance image. This is an easy enough proof of a lower bound on
+    // the image min, since it works even if the mask is a single voxel in
+    // the image field corner. suggestedDefaultValue=
+    // vcl_sqrt( diagonalLength );
+    // In most cases, a heuristic fraction of the diagonal value is an
+    // even better lower bound: if the midpoint of the image is inside the
+    // mask, 1/2 is a lower bound as well, and the background is unlikely
+    // to drive the upper limit of the intensity range when we visualize
+    // the intermediate image for debugging.
+
+    suggestedDefaultValue = -vcl_sqrt(diagonalLength) * 0.5;
+    }
+  else // other than if (pixelType == "binary")
+    {
+    PrincipalOperandImage = OperandImage;
+    }
+
+  // RESAMPLE with the appropriate transform and interpolator:
+  // One name for the intermediate resampled float image.
+  typename InputImageType::Pointer TransformedImage;
+
+  if( DeformationField.IsNull() )  // (useTransform)
+    {
+    // std::cout<< " Deformation Field is Null... " << std::endl;
+    if( genericTransform.IsNotNull() )
+      {
+      if( interpolationMode == "ResampleInPlace" )
+        {
+        typedef itk::ResampleInPlaceImageFilter ResampleIPFilterType;
+        typedef typename ResampleIPFilterType::Pointer                           ResampleIPFilterPointer;
+
+        const VersorRigid3DTransformType::ConstPointer tempInitializerITKTransform =
+          dynamic_cast( genericTransform.GetPointer() );
+        if( tempInitializerITKTransform.IsNull() )
+          {
+          std::cout << "Error in type conversion" << __FILE__ << __LINE__ << std::endl;
+          std::cout << "ResampleInPlace is only allowed with rigid transform type." << std::endl;
+          }
+
+        ResampleIPFilterPointer resampleIPFilter = ResampleIPFilterType::New();
+        resampleIPFilter->SetInputImage( PrincipalOperandImage.GetPointer() );
+        resampleIPFilter->SetRigidTransform( tempInitializerITKTransform.GetPointer() );
+        resampleIPFilter->Update();
+        TransformedImage = resampleIPFilter->GetOutput();
+        }
+      else
+        {
+        TransformedImage = TransformResample(
+            PrincipalOperandImage,
+            ReferenceImage,
+            suggestedDefaultValue,
+            GetInterpolatorFromString(interpolationMode),
+            genericTransform);
+        }
+      }
+    }
+
+  else if( DeformationField.IsNotNull() )
+    {
+    //  std::cout<< "Deformation Field is given, so applied to the image..." <<
+    // std::endl;
+    TransformedImage = TransformWarp(
+        PrincipalOperandImage,
+        ReferenceImage,
+        suggestedDefaultValue,
+        GetInterpolatorFromString(interpolationMode),
+        DeformationField);
+    }
+
+  // FINALLY will need to convert signed distance to binary image in case
+  // binaryFlag is true.
+
+  typename InputImageType::Pointer FinalTransformedImage;
+
+  if( binaryFlag )
+    {
+    // A special case for dealing with binary images
+    // where signed distance maps are warped and thresholds created
+    typedef short int                                                                    MaskPixelType;
+    typedef typename itk::Image MaskImageType;
+
+    // Now Threshold and write out image
+    typedef typename itk::BinaryThresholdImageFilter BinaryThresholdFilterType;
+    typename BinaryThresholdFilterType::Pointer finalFilter =
+      BinaryThresholdFilterType::New();
+    finalFilter->SetInput(TransformedImage);
+
+    const typename BinaryThresholdFilterType::OutputPixelType outsideValue = 0;
+    const typename BinaryThresholdFilterType::OutputPixelType insideValue  = 1;
+    finalFilter->SetOutsideValue(outsideValue);
+    finalFilter->SetInsideValue(insideValue);
+    // Signed distance boundary voxels are defined as being included in the
+    // structure,  therefore the desired distance threshold is in the middle
+    // of the enclosing (negative) voxel ribbon around threshold 0.
+    const typename InputImageType::SpacingType Spacing = ReferenceImage->GetSpacing();
+    const typename BinaryThresholdFilterType::InputPixelType lowerThreshold =
+      -0.5 * 0.333333333333 * ( Spacing[0] + Spacing[1] + Spacing[2] );
+    //  std::cerr << "Lower Threshold == " << lowerThreshold << std::endl;
+
+    const typename BinaryThresholdFilterType::InputPixelType upperThreshold =
+      vcl_numeric_limits::max();
+    finalFilter->SetLowerThreshold(lowerThreshold);
+    finalFilter->SetUpperThreshold(upperThreshold);
+
+    finalFilter->Update();
+
+    typedef typename itk::CastImageFilter CastImageFilter;
+    typename CastImageFilter::Pointer castFilter = CastImageFilter::New();
+    castFilter->SetInput( finalFilter->GetOutput() );
+    castFilter->Update();
+
+    FinalTransformedImage = castFilter->GetOutput();
+    }
+  else
+    {
+    FinalTransformedImage = TransformedImage;
+    }
+
+  return FinalTransformedImage;
+}
+
+#endif
diff --git a/BRAINSCommonLib/Imgmath.h b/BRAINSCommonLib/Imgmath.h
new file mode 100644
index 00000000..0187daa5
--- /dev/null
+++ b/BRAINSCommonLib/Imgmath.h
@@ -0,0 +1,337 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+
+#ifndef __Imgmath_h
+#define __Imgmath_h
+
+/* This file contains the functions to perform pixel by pixel mathematical
+  * operations on 2 images. All the functions are performed by using ITK
+  * filters. */
+
+#include "itkImage.h"
+#include "itkSquaredDifferenceImageFilter.h"
+#include "itkImageRegionIterator.h"
+#include "itkSquaredDifferenceImageFilter.h"
+#include "itkAddImageFilter.h"
+#include "itkSubtractImageFilter.h"
+#include "itkDivideImageFilter.h"
+#include "itkMultiplyImageFilter.h"
+#include "itkMinimumImageFilter.h"
+#include "itkMaximumImageFilter.h"
+// TODO:  add these correctly so we get multi-threading.
+#include "itkInvertIntensityImageFilter.h"
+#include "itkAddConstantToImageFilter.h"
+#include "itkDivideByConstantImageFilter.h"
+#include "itkMultiplyByConstantImageFilter.h"
+#include "itkSqrtImageFilter.h"
+#include "itkExpImageFilter.h"
+#include "itkExpNegativeImageFilter.h"
+#include "itkLogImageFilter.h"
+#include 
+
+/* Iadd adds 2 images at every pixel location and outputs the resulting image.*/
+template 
+typename ImageType::Pointer Iadd(const typename ImageType::Pointer input1,
+                                 typename ImageType::Pointer input2)
+{
+  typedef itk::AddImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Isub subtracts 2 images at every pixel location and outputs the resulting
+  * image.*/
+template 
+typename ImageType::Pointer Isub(const typename ImageType::Pointer input1,
+                                 const typename ImageType::Pointer input2)
+{
+  typedef itk::SubtractImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Imul multiplies 2 images at every pixel location and outputs the resulting
+  * image.*/
+template 
+typename ImageType::Pointer Imul(const typename ImageType::Pointer input1,
+                                 const typename ImageType::Pointer input2)
+{
+  typedef itk::MultiplyImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Idiv divides 2 images at every pixel location and outputs the resulting
+  * image.*/
+template 
+typename ImageType::Pointer Idiv(const typename ImageType::Pointer input1,
+                                 const typename ImageType::Pointer input2)
+{
+  typedef itk::DivideImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Imax does the numerical generalization of OR on 2 (non-negative) images at
+  * every pixel location
+  * and outputs the resulting image.*/
+template 
+typename ImageType::Pointer Imax(const typename ImageType::Pointer input1,
+                                 const typename ImageType::Pointer input2)
+{
+  typedef itk::MaximumImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Imin does the numerical generalization of AND on 2 (non-negative) images at
+  * every pixel location
+  * and outputs the resulting image.*/
+template 
+typename ImageType::Pointer Imin(const typename ImageType::Pointer input1,
+                                 const typename ImageType::Pointer input2)
+{
+  typedef itk::MinimumImageFilter FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    exit(-1);
+    }
+  typename ImageType::Pointer image = filter->GetOutput();
+  return image;
+}
+
+/* Iavg takes an image and the number of images as inputs , divides each pixel
+  location of the image by the number of images outputs the resulting image.*/
+
+template 
+typename ImageType::Pointer Iavg(typename ImageType::Pointer input1, int nimgs)
+{
+  typename ImageType::Pointer image = ImageType::New();
+  image->SetRegions( input1->GetLargestPossibleRegion() );
+  image->CopyInformation(input1);
+  image->Allocate();
+  typedef typename itk::ImageRegionIterator ConstIteratorType;
+  ConstIteratorType in1( input1, input1->GetLargestPossibleRegion() );
+  ConstIteratorType out( image, image->GetLargestPossibleRegion() );
+  for( in1.GoToBegin(), out.GoToBegin(); !in1.IsAtEnd(); ++in1, ++out )
+    {
+    out.Set(in1.Get() / nimgs);
+    }
+
+  return image;
+}
+
+template 
+typename ImageType::Pointer IMask(typename ImageType::Pointer input1,
+                                  typename ImageType::Pointer mask)
+{
+  typename ImageType::Pointer image = ImageType::New();
+  image->SetRegions( input1->GetLargestPossibleRegion() );
+  image->CopyInformation(input1);
+  image->Allocate();
+  typedef typename itk::ImageRegionIterator RegionIteratorType;
+  RegionIteratorType in1( input1, input1->GetLargestPossibleRegion() );
+  RegionIteratorType in2( mask, mask->GetLargestPossibleRegion() );
+  RegionIteratorType out( image, image->GetLargestPossibleRegion() );
+  for( in1.GoToBegin(), out.GoToBegin(), in2.GoToBegin();
+       !in1.IsAtEnd();
+       ++in1, ++in2, ++out )
+    {
+    const typename ImageType::PixelType temp = in1.Get();
+    out.Set( ( in2.Get() > 0 ) ? temp : 0 );
+    }
+  return image;
+}
+
+template 
+typename ImageType::Pointer ImageAddConstant(
+  const typename ImageType::Pointer input,
+  const double shiftvalue)
+{
+  // TODO:  This should be a UnaryImageFunctor operation to get multi-threading.
+  typename ImageType::Pointer outImage = ImageType::New();
+  outImage->SetRegions( input->GetLargestPossibleRegion() );
+  outImage->CopyInformation(input);
+  outImage->Allocate();
+  typedef typename itk::ImageRegionIterator RegionIteratorType;
+  RegionIteratorType in( input, input->GetLargestPossibleRegion() );
+  RegionIteratorType out( outImage, outImage->GetLargestPossibleRegion() );
+  out.GoToBegin();
+  for( in.GoToBegin(); !in.IsAtEnd(); ++in )
+    {
+    out.Set( static_cast( ( in.Get()
+                                                           + shiftvalue ) ) );
+    ++out;
+    }
+  return outImage;
+}
+
+template 
+typename ImageType::Pointer ImageMultiplyConstant(
+  const typename ImageType::Pointer input,
+  const double scalevalue)
+{
+  typedef typename itk::MultiplyByConstantImageFilter
+  MultByConstFilterType;
+  typedef typename MultByConstFilterType::Pointer MultByConstFilterPointer;
+  MultByConstFilterPointer filt = MultByConstFilterType::New();
+  filt->SetInput(input);
+  filt->SetConstant(scalevalue);
+  filt->Update();
+  return filt->GetOutput();
+}
+
+/* ImageComplementConstant does the numerical generalization of NOT on one
+  * (non-negative) image
+  * at every pixel location and outputs the resulting image.  For finding the
+  *binary mask image Not,
+  * referencevalue should be 1;  however there is no defaulting to 1 here. */
+template 
+typename ImageType::Pointer ImageComplementConstant(
+  const typename ImageType::Pointer input,
+  const double referencevalue)
+{
+  // TODO:  This should be a UnaryImageFunctor operation to get multi-threading.
+  typename ImageType::Pointer outImage = ImageType::New();
+  outImage->SetRegions( input->GetLargestPossibleRegion() );
+  outImage->CopyInformation(input);
+  outImage->Allocate();
+  typedef typename itk::ImageRegionIterator RegionIteratorType;
+  RegionIteratorType in( input, input->GetLargestPossibleRegion() );
+  RegionIteratorType out( outImage, outImage->GetLargestPossibleRegion() );
+  out.GoToBegin();
+  for( in.GoToBegin(); !in.IsAtEnd(); ++in )
+    {
+    out.Set( static_cast( ( referencevalue
+                                                           - in.Get() ) ) );
+    ++out;
+    }
+  return outImage;
+}
+
+template 
+typename ImageType::Pointer ImageDivideConstant(
+  typename ImageType::Pointer input,
+  const double denominator)
+{
+  typename ImageType::Pointer DivImage = ImageMultiplyConstant(input,
+                                                                          1.0 / denominator);
+  return DivImage;
+}
+
+template 
+void ImageSqrtValue(typename ImageType::Pointer Output,
+                    const typename ImageType::Pointer Input)
+{
+  typename ImageType::Pointer image = ImageType::New();
+  image->SetRegions( Input->GetLargestPossibleRegion() );
+  image->CopyInformation(Input);
+  image->Allocate();
+  typedef typename itk::ImageRegionIterator RegionIteratorType;
+  RegionIteratorType in( Input, Input->GetLargestPossibleRegion() );
+  RegionIteratorType out( image, image->GetLargestPossibleRegion() );
+  for( in.GoToBegin(), out.GoToBegin(); !in.IsAtEnd(); ++in, ++out )
+    {
+    out.Set( static_cast( in.Get() ) );
+    }
+
+  Output = image;
+  return;
+}
+
+template 
+typename ImageType::Pointer
+ImageSqrtValue(const typename ImageType::Pointer input)
+{
+  typename ImageType::Pointer rval;
+  ImageSqrtValue(rval, input);
+  return rval;
+}
+
+#endif
diff --git a/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.h b/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.h
new file mode 100644
index 00000000..b37f1f29
--- /dev/null
+++ b/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.h
@@ -0,0 +1,155 @@
+/*=========================================================================
+ *
+ *  Copyright Insight Software Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+#ifndef __LOCAL_itkDifferenceImageFilter_h
+#define __LOCAL_itkDifferenceImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkNumericTraits.h"
+#include "itkArray.h"
+
+namespace itk
+{
+/** \class LOCAL_DifferenceImageFilter
+ * \brief Implements comparison between two images.
+ *
+ * This filter is used by the testing system to compute the difference between
+ * a valid image and an image produced by the test. The comparison value is
+ * computed by visiting all the pixels in the baseline images and comparing
+ * their values with the pixel values in the neighborhood of the homologous
+ * pixel in the other image.
+ *
+ * \ingroup IntensityImageFilters   MultiThreaded
+ * \ingroup ITKTestKernel
+ */
+template< class TInputImage, class TOutputImage >
+class ITK_EXPORT LOCAL_DifferenceImageFilter:
+  public ImageToImageFilter< TInputImage, TOutputImage >
+{
+public:
+  /** Standard class typedefs. */
+  typedef LOCAL_DifferenceImageFilter                           Self;
+  typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
+  typedef SmartPointer< Self >                            Pointer;
+  typedef SmartPointer< const Self >                      ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(LOCAL_DifferenceImageFilter, ImageToImageFilter);
+
+  /** Some convenient typedefs. */
+  typedef TInputImage                                         InputImageType;
+  typedef TOutputImage                                        OutputImageType;
+  typedef typename OutputImageType::PixelType                 OutputPixelType;
+  typedef typename OutputImageType::RegionType                OutputImageRegionType;
+  typedef typename NumericTraits< OutputPixelType >::RealType RealType;
+  typedef typename NumericTraits< RealType >::AccumulateType  AccumulateType;
+
+  /** Set the valid image input.  This will be input 0.  */
+  virtual void SetValidInput(const InputImageType *validImage);
+
+  /** Set the test image input.  This will be input 1.  */
+  virtual void SetTestInput(const InputImageType *testImage);
+
+  /** Set/Get the maximum distance away to look for a matching pixel.
+      Default is 0. */
+  itkSetMacro(ToleranceRadius, int);
+  itkGetConstMacro(ToleranceRadius, int);
+
+  /** Set/Get the minimum threshold for pixels to be different.
+      Default is 0. */
+  itkSetMacro(DifferenceThreshold, OutputPixelType);
+  itkGetConstMacro(DifferenceThreshold, OutputPixelType);
+
+  /** Set/Get ignore boundary pixels.  Useful when resampling may have
+   *    introduced difference pixel values along the image edge
+   *    Default = false */
+  itkSetMacro(IgnoreBoundaryPixels, bool);
+  itkGetConstMacro(IgnoreBoundaryPixels, bool);
+
+  /** Get parameters of the difference image after execution.  */
+  itkGetConstMacro(MeanDifference, RealType);
+  itkGetConstMacro(TotalDifference, AccumulateType);
+  itkGetConstMacro(NumberOfPixelsWithDifferences, SizeValueType);
+protected:
+  LOCAL_DifferenceImageFilter();
+  virtual ~LOCAL_DifferenceImageFilter() {}
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** LOCAL_DifferenceImageFilter can be implemented as a multithreaded
+   * filter.  Therefore, this implementation provides a
+   * ThreadedGenerateData() routine which is called for each
+   * processing thread. The output image data is allocated
+   * automatically by the superclass prior to calling
+   * ThreadedGenerateData().  ThreadedGenerateData can only write to
+   * the portion of the output image specified by the parameter
+   * "outputRegionForThread"
+   *
+   * \sa ImageToImageFilter::ThreadedGenerateData(),
+   *     ImageToImageFilter::GenerateData()  */
+  void ThreadedGenerateData(const OutputImageRegionType & threadRegion,
+                            ThreadIdType threadId);
+
+  void BeforeThreadedGenerateData();
+
+  void AfterThreadedGenerateData();
+
+  OutputPixelType m_DifferenceThreshold;
+
+  RealType m_MeanDifference;
+
+  AccumulateType m_TotalDifference;
+
+  SizeValueType m_NumberOfPixelsWithDifferences;
+
+  int m_ToleranceRadius;
+
+  Array< AccumulateType >    m_ThreadDifferenceSum;
+  Array< SizeValueType >     m_ThreadNumberOfPixels;
+
+private:
+  LOCAL_DifferenceImageFilter(const Self &); //purposely not implemented
+  void operator=(const Self &);        //purposely not implemented
+
+  bool m_IgnoreBoundaryPixels;
+};
+} // end namespace itk
+
+// Define instantiation macro for this template.
+#define ITK_TEMPLATE_LOCAL_DifferenceImageFilter(_, EXPORT, TypeX, TypeY)     \
+  namespace itk                                                         \
+  {                                                                     \
+  _( 2 ( class EXPORT LOCAL_DifferenceImageFilter< ITK_TEMPLATE_2 TypeX > ) ) \
+  namespace Templates                                                   \
+  {                                                                     \
+  typedef LOCAL_DifferenceImageFilter< ITK_TEMPLATE_2 TypeX >                 \
+  LOCAL_DifferenceImageFilter##TypeY;                                       \
+  }                                                                     \
+  }
+
+#if ITK_TEMPLATE_EXPLICIT
+#include "Templates/LOCAL_itkDifferenceImageFilter+-.h"
+#endif
+
+#if ITK_TEMPLATE_TXX
+#include "LOCAL_itkDifferenceImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.hxx b/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.hxx
new file mode 100644
index 00000000..151d50c9
--- /dev/null
+++ b/BRAINSCommonLib/LOCAL_itkDifferenceImageFilter.hxx
@@ -0,0 +1,271 @@
+/*=========================================================================
+ *
+ *  Copyright Insight Software Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+#ifndef __itkDifferenceImageFilter_hxx
+#define __itkDifferenceImageFilter_hxx
+
+#include "LOCAL_itkDifferenceImageFilter.h"
+
+#include "itkConstNeighborhoodIterator.h"
+#include "itkImageRegionIterator.h"
+#include "itkNeighborhoodAlgorithm.h"
+#include "itkProgressReporter.h"
+
+namespace itk
+{
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::LOCAL_DifferenceImageFilter()
+{
+  // We require two inputs to execute.
+  this->SetNumberOfRequiredInputs(2);
+
+  // Set the default DifferenceThreshold.
+  m_DifferenceThreshold = NumericTraits< OutputPixelType >::Zero;
+
+  // Set the default ToleranceRadius.
+  m_ToleranceRadius = 0;
+
+  // Initialize statistics about difference image.
+  m_MeanDifference = NumericTraits< RealType >::Zero;
+  m_TotalDifference = NumericTraits< AccumulateType >::Zero;
+  m_NumberOfPixelsWithDifferences = 0;
+  m_IgnoreBoundaryPixels = false;
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  this->Superclass::PrintSelf(os, indent);
+  os << indent << "ToleranceRadius: " << m_ToleranceRadius << "\n";
+  os << indent << "DifferenceThreshold: " << m_DifferenceThreshold << "\n";
+  os << indent << "MeanDifference: " << m_MeanDifference << "\n";
+  os << indent << "TotalDifference: " << m_TotalDifference << "\n";
+  os << indent << "NumberOfPixelsWithDifferences: "
+     << m_NumberOfPixelsWithDifferences << "\n";
+  os << indent << "IgnoreBoundaryPixels: "
+     << m_IgnoreBoundaryPixels << "\n";
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::SetValidInput(const InputImageType *validImage)
+{
+  // The valid image should be input 0.
+  this->SetInput(0, validImage);
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::SetTestInput(const InputImageType *testImage)
+{
+  // The test image should be input 1.
+  this->SetInput(1, testImage);
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::BeforeThreadedGenerateData()
+{
+  ThreadIdType numberOfThreads = this->GetNumberOfThreads();
+
+  // Initialize statistics about difference image.
+  m_MeanDifference = NumericTraits< RealType >::Zero;
+  m_TotalDifference = NumericTraits< AccumulateType >::Zero;
+  m_NumberOfPixelsWithDifferences = 0;
+
+  // Resize the thread temporaries
+  m_ThreadDifferenceSum.SetSize(numberOfThreads);
+  m_ThreadNumberOfPixels.SetSize(numberOfThreads);
+
+  // Initialize the temporaries
+  m_ThreadDifferenceSum.Fill(NumericTraits< AccumulateType >::Zero);
+  m_ThreadNumberOfPixels.Fill(0);
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::ThreadedGenerateData(const OutputImageRegionType & threadRegion, ThreadIdType threadId)
+{
+  typedef ConstNeighborhoodIterator< InputImageType >                           SmartIterator;
+  typedef ImageRegionConstIterator< InputImageType >                            InputIterator;
+  typedef ImageRegionIterator< OutputImageType >                                OutputIterator;
+  typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType > FacesCalculator;
+  typedef typename FacesCalculator::RadiusType                                  RadiusType;
+  typedef typename FacesCalculator::FaceListType                                FaceListType;
+  typedef typename FaceListType::iterator                                       FaceListIterator;
+  typedef typename InputImageType::PixelType                                    InputPixelType;
+
+  // Prepare standard boundary condition.
+  ZeroFluxNeumannBoundaryCondition< InputImageType > nbc;
+
+  // Get a pointer to each image.
+  const InputImageType *validImage = this->GetInput(0);
+  const InputImageType *testImage = this->GetInput(1);
+  OutputImageType *     outputPtr = this->GetOutput();
+
+  if( validImage->GetBufferedRegion() != testImage->GetBufferedRegion() )
+    {
+    itkExceptionMacro( << "Input images have different Buffered Resions." )
+    }
+
+  // Create a radius of pixels.
+  RadiusType radius;
+  const unsigned int minVoxelsNeeded = m_ToleranceRadius*2+1;
+  const typename TInputImage::SizeType imageSize = validImage->GetBufferedRegion().GetSize();
+  for( unsigned int d=0; d < TInputImage::ImageDimension; ++d )
+    {
+    if( minVoxelsNeeded < imageSize[d] )
+      {
+      radius[d] = m_ToleranceRadius;
+      }
+    else
+      {
+        radius[d] = ( (imageSize[d]-1)/2 );
+      }
+    }
+
+  // Find the data-set boundary faces.
+  FacesCalculator boundaryCalculator;
+  FaceListType    faceList = boundaryCalculator(testImage, threadRegion, radius);
+
+  // Support progress methods/callbacks.
+  ProgressReporter progress( this, threadId, threadRegion.GetNumberOfPixels() );
+
+  // Process the internal face and each of the boundary faces.
+  for ( FaceListIterator face = faceList.begin(); face != faceList.end(); ++face )
+    {
+    SmartIterator  test(radius, testImage, *face); // Iterate over test image.
+    InputIterator  valid(validImage, *face);       // Iterate over valid image.
+    OutputIterator out(outputPtr, *face);          // Iterate over output image.
+    if ( !test.GetNeedToUseBoundaryCondition() || !m_IgnoreBoundaryPixels )
+      {
+      test.OverrideBoundaryCondition(&nbc);
+
+      for ( valid.GoToBegin(), test.GoToBegin(), out.GoToBegin();
+            !valid.IsAtEnd();
+            ++valid, ++test, ++out )
+        {
+        // Get the current valid pixel.
+        InputPixelType t = valid.Get();
+
+        //  Assume a good match - so test center pixel first, for speed
+        RealType difference = static_cast< RealType >( t ) - test.GetCenterPixel();
+        if ( NumericTraits< RealType >::IsNegative(difference) )
+          {
+          difference = -difference;
+          }
+        OutputPixelType minimumDifference = static_cast< OutputPixelType >( difference );
+
+        // If center pixel isn't good enough, then test the neighborhood
+        if ( minimumDifference > m_DifferenceThreshold )
+          {
+          unsigned int neighborhoodSize = test.Size();
+          // Find the closest-valued pixel in the neighborhood of the test
+          // image.
+          for ( unsigned int i = 0; i < neighborhoodSize; ++i )
+            {
+            // Use the RealType for the difference to make sure we get the
+            // sign.
+            RealType differenceReal = static_cast< RealType >( t ) - test.GetPixel(i);
+            if ( NumericTraits< RealType >::IsNegative(differenceReal) )
+              {
+              differenceReal = -differenceReal;
+              }
+            OutputPixelType d = static_cast< OutputPixelType >( differenceReal );
+            if ( d < minimumDifference )
+              {
+              minimumDifference = d;
+              if ( minimumDifference <= m_DifferenceThreshold )
+                {
+                break;
+                }
+              }
+            }
+          }
+
+        // Check if difference is above threshold.
+        if ( minimumDifference > m_DifferenceThreshold )
+          {
+          // Store the minimum difference value in the output image.
+          out.Set(minimumDifference);
+
+          // Update difference image statistics.
+          m_ThreadDifferenceSum[threadId] += minimumDifference;
+          m_ThreadNumberOfPixels[threadId]++;
+          }
+        else
+          {
+          // Difference is below threshold.
+          out.Set(NumericTraits< OutputPixelType >::Zero);
+          }
+
+        // Update progress.
+        progress.CompletedPixel();
+        }
+      }
+    else
+      {
+      for ( out.GoToBegin(); !out.IsAtEnd(); ++out )
+        {
+        out.Set(NumericTraits< OutputPixelType >::Zero);
+        progress.CompletedPixel();
+        }
+      }
+    }
+}
+
+//----------------------------------------------------------------------------
+template< class TInputImage, class TOutputImage >
+void
+LOCAL_DifferenceImageFilter< TInputImage, TOutputImage >
+::AfterThreadedGenerateData()
+{
+  // Set statistics about difference image.
+  ThreadIdType numberOfThreads = this->GetNumberOfThreads();
+
+  for ( ThreadIdType i = 0; i < numberOfThreads; ++i )
+    {
+    m_TotalDifference += m_ThreadDifferenceSum[i];
+    m_NumberOfPixelsWithDifferences += m_ThreadNumberOfPixels[i];
+    }
+
+  // Get the total number of pixels processed in the region.
+  // This is different from the m_TotalNumberOfPixels which
+  // is the number of pixels that actually have differences
+  // above the intensity threshold.
+  OutputImageRegionType region = this->GetOutput()->GetRequestedRegion();
+  AccumulateType        numberOfPixels = region.GetNumberOfPixels();
+
+  // Calculate the mean difference.
+  m_MeanDifference = m_TotalDifference / numberOfPixels;
+}
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/PrettyPrintTable.h b/BRAINSCommonLib/PrettyPrintTable.h
new file mode 100644
index 00000000..265d739e
--- /dev/null
+++ b/BRAINSCommonLib/PrettyPrintTable.h
@@ -0,0 +1,157 @@
+#ifndef __PrettyPrintTable_h
+#define __PrettyPrintTable_h
+#include 
+#include 
+#include 
+#include 
+
+#if defined( _WIN32 ) || defined( _WIN64 )
+// Windows uses a different function name for this behavior.
+#define SNPRINTF_FUNC _snprintf
+#else
+#define SNPRINTF_FUNC snprintf
+#endif
+/**
+  * \class PrettyPrintTable
+  * \author Kent Williams
+  * Simple class to print out column-aligned tables
+  */
+class PrettyPrintTable
+{
+public:
+private:
+  typedef std::vector rowType;
+  typedef std::vector     tableType;
+
+  tableType    m_Table;
+  unsigned int m_Pad;
+  bool         m_rightJustify;
+public:
+  PrettyPrintTable() : m_Pad(1),
+    m_rightJustify(false)
+  {
+  }
+
+  void setTablePad(unsigned int pad)
+  {
+    this->m_Pad = pad;
+  }
+
+  void leftJustify(void)
+  {
+    m_rightJustify = false;
+  }
+
+  void rightJustify(void)
+  {
+    m_rightJustify = true;
+  }
+
+  void add(const unsigned int row, const unsigned int column, const char *const s)
+  {
+    // Make sure the table has enough rows.
+    if( m_Table.size() <= row )
+      { // Add empty rows
+      m_Table.resize(row + 1);
+      }
+    // For each row, make sure that it now has enough columns.
+    for( unsigned int q = 0; q < m_Table.size(); ++q )
+      {
+      if( m_Table[q].size() <= column )
+        {
+        m_Table[q].resize( column + 1, std::string("") );
+        }
+      }
+    m_Table[row][column] = s;
+  }
+
+  void add(const unsigned int row, const unsigned int column, const std::string & s)
+  {
+    add( row, column, s.c_str() );
+  }
+
+  void add(const unsigned int row, const unsigned int column, const int x, const char *printf_format = 0)
+  {
+    const char *format(printf_format == 0 ? "%d" : printf_format);
+    char        buf[4096];
+
+    SNPRINTF_FUNC(buf, 4096, format, x);
+    this->add(row, column, buf);
+  }
+
+  void add(const unsigned int row, const unsigned int column, const unsigned int x, const char *printf_format = 0)
+  {
+    const char *format(printf_format == 0 ? "%d" : printf_format);
+    char        buf[4096];
+
+    SNPRINTF_FUNC(buf, 4096, format, x);
+    this->add(row, column, buf);
+  }
+
+  void add(const unsigned int row, const unsigned int column, const double x, const char *printf_format = 0)
+  {
+    const char *format(printf_format == 0 ? "%lf" : printf_format);
+    char        buf[4096];
+
+    SNPRINTF_FUNC(buf, 4096, format, x);
+    this->add(row, column, buf);
+  }
+
+  void Print(std::ostream & output)
+  {
+    typedef std::vector ColWidthsType;
+    ColWidthsType colWidths(m_Table[0].size(), 0);
+    // find largest columns
+    for( unsigned i = 0; i < m_Table.size(); ++i )
+      {
+      for( unsigned j = 0; j < m_Table[i].size(); ++j )
+        {
+        if( colWidths[j] < m_Table[i][j].size() )
+          {
+          colWidths[j] = m_Table[i][j].size();
+          }
+        }
+      }
+    for( unsigned i = 0; i < m_Table.size(); ++i )
+      {
+      for( unsigned j = 0; j < m_Table[i].size(); ++j )
+        {
+        // if right justify, output leading blanks
+        if( m_rightJustify )
+          {
+          int count = colWidths[j]
+            - m_Table[i][j].size();
+          while( count-- )
+            {
+            output << " ";
+            }
+          }
+        unsigned int k(0);
+        for( k = 0; k < m_Table[i][j].size(); ++k )
+          {
+          output << m_Table[i][j][k];
+          }
+        unsigned int limit;
+        // if right justify, just output pad
+        if( m_rightJustify )
+          {
+          limit = this->m_Pad;
+          k = 0;
+          }
+        else
+          {
+          // print column fill + pad
+          limit = colWidths[j] + this->m_Pad;
+          }
+        for( ; k < limit; ++k )
+          {
+          output << " ";
+          }
+        }
+      output << std::endl;
+      }
+  }
+
+};
+
+#endif // PrettyPrintTable_h
diff --git a/BRAINSCommonLib/ReadMask.h b/BRAINSCommonLib/ReadMask.h
new file mode 100644
index 00000000..07b6377d
--- /dev/null
+++ b/BRAINSCommonLib/ReadMask.h
@@ -0,0 +1,37 @@
+#ifndef __ReadMask_h
+#define __ReadMask_h
+
+#include "itkIO.h"
+#include "itkImageMaskSpatialObject.h"
+
+template 
+typename MaskType::Pointer
+ReadImageMask(const std::string & filename,
+              typename itk::ImageBase * /*referenceImage*/)
+{
+  typedef unsigned char                                  MaskPixelType;
+  typedef typename itk::Image MaskImageType;
+  typename MaskImageType::Pointer OrientedMaskImage = NULL;
+
+  OrientedMaskImage = itkUtil::ReadImage(filename);
+  // TODO:  May want to check that physical spaces overlap?
+
+  // convert mask image to mask
+  typedef typename itk::ImageMaskSpatialObject
+  ImageMaskSpatialObjectType;
+  typename ImageMaskSpatialObjectType::Pointer mask =
+    ImageMaskSpatialObjectType::New();
+  mask->SetImage(OrientedMaskImage);
+  //
+  mask->ComputeObjectToWorldTransform();
+  // return pointer to mask
+  typename MaskType::Pointer p = dynamic_cast( mask.GetPointer() );
+  if( p.IsNull() )
+    {
+    std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+    exit(-1);
+    }
+  return p;
+}
+
+#endif // LoadMask_h
diff --git a/BRAINSCommonLib/SimpleXMLParserBase.h b/BRAINSCommonLib/SimpleXMLParserBase.h
new file mode 100644
index 00000000..83614290
--- /dev/null
+++ b/BRAINSCommonLib/SimpleXMLParserBase.h
@@ -0,0 +1,138 @@
+#ifndef __SimpleXMLParserBase_h
+#define __SimpleXMLParserBase_h
+//
+// standard includes
+#include 
+#include 
+#include 
+#include 
+//
+// xerces_c includes
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+XERCES_CPP_NAMESPACE_USE
+
+/**
+  * \class SimpleXMLParserBase
+  * contains the common code
+  * needed to Read and Write an XML file.
+  * Any actual interpretation is delegated to subclass
+  */
+class SimpleXMLParserBase
+{
+public:
+  typedef XercesDOMParser ParserType;
+  SimpleXMLParserBase() : m_Parser(0)
+  {
+  }
+
+  void Read(const std::string & filename)
+  {
+    try
+      {
+      XMLPlatformUtils::Initialize();
+      }
+    catch( const XMLException & toCatch )
+      {
+      std::cerr << "Can't Initialize XMLPlatformUtils" << std::endl;
+      throw;
+      }
+    //  Create our parser, then attach an error handler to the parser.
+    //  The parser will call back to methods of the ErrorHandler if it
+    //  discovers errors during the course of parsing the XML document.
+    //
+    this->m_Parser = new ParserType;
+    this->m_Parser->setValidationScheme(ParserType::Val_Auto);
+    this->m_Parser->setDoNamespaces(false);
+    this->m_Parser->setDoSchema(false);
+    this->m_Parser->setValidationSchemaFullChecking(false);
+    this->m_Parser->setCreateEntityReferenceNodes(false);
+    //
+    //  Parse the XML file, catching any XML exceptions that might propogate
+    //  out of it.
+    //
+    bool errorsOccurred = false;
+    try
+      {
+      this->m_Parser->parse( filename.c_str() );
+      }
+    catch( const OutOfMemoryException & )
+      {
+      std::cerr << "OutOfMemoryException" << std::endl;
+      errorsOccurred = true;
+      }
+    catch( const XMLException & e )
+      {
+      std::cerr << "An error occurred during parsing\n   Message: "
+                << e.getMessage() << std::endl;
+      errorsOccurred = true;
+      }
+
+    catch( const DOMException & e )
+      {
+      const unsigned int maxChars = 2047;
+      XMLCh              errText[maxChars + 1];
+
+      std::cerr << "\nDOM Error during parsing: '" << filename << "'\n"
+                << "DOMException code is:  " << e.code << std::endl;
+
+      if( DOMImplementation::loadDOMExceptionMsg(e.code, errText, maxChars) )
+        {
+        std::cerr << "Message is: " << errText << std::endl;
+        }
+
+      errorsOccurred = true;
+      }
+    catch( ... )
+      {
+      std::cerr << "An error occurred during parsing\n " << std::endl;
+      errorsOccurred = true;
+      }
+    if( errorsOccurred )
+      {
+      throw;
+      }
+  }
+
+  void Write(const std::string & filename)
+  {
+    if( m_Parser == 0 )
+      {
+      throw;
+      }
+    // get a serializer, an instance of DOMWriter
+    XMLCh tempStr[100];
+    XMLString::transcode("LS", tempStr, 99);
+    DOMImplementation *impl =
+      DOMImplementationRegistry::getDOMImplementation(tempStr);
+    DOMWriter *theSerializer =
+      ( (DOMImplementationLS *)impl )->createDOMWriter();
+
+    XMLFormatTarget *formatTarget = new LocalFileFormatTarget( filename.c_str() );
+    theSerializer->writeNode
+      ( formatTarget,
+      *static_cast( this->m_Parser->getDocument() ) );
+    delete theSerializer;
+  }
+
+  ParserType * Parser()
+  {
+    return m_Parser;
+  }
+
+protected:
+  ParserType *m_Parser;
+};
+
+#endif // SimpleXMLParserBase_h
diff --git a/BRAINSCommonLib/Slicer3LandmarkIO.cxx b/BRAINSCommonLib/Slicer3LandmarkIO.cxx
new file mode 100644
index 00000000..651952a9
--- /dev/null
+++ b/BRAINSCommonLib/Slicer3LandmarkIO.cxx
@@ -0,0 +1,99 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "Slicer3LandmarkIO.h"
+
+extern void
+WriteITKtoSlicer3Lmk( const std::string landmarksFilename,
+                      const LandmarksMapType & landmarks )
+{
+  const std::string fullPathLandmarksFileName = itksys::SystemTools::CollapseFullPath( landmarksFilename.c_str() );
+
+  std::stringstream lmkPointStream;
+
+  unsigned int numNamedLandmarks = 0;
+  for( LandmarksMapType::const_iterator it = landmarks.begin(); it != landmarks.end(); ++it )
+    {
+    if( ( it->first ).compare("") != 0 )
+      {
+      // NOTE: Slicer3 use RAS coordinate system to represent landmarks
+      // but ITK landmarks are in LPS, so we need to negate the first two
+      // component of the landmark points.
+      lmkPointStream <<     it->first       << ","
+                     << -( it->second[0] ) << ","
+                     << -( it->second[1] ) << ","
+                     << +( it->second[2] )
+                     << ",1,1\n"; // Note the last two columns are
+                                  // ,visible,editable
+      ++numNamedLandmarks;
+      }
+    }
+
+  std::stringstream lmksStream;
+  // Write the .fcvs header information.
+  lmksStream << "#Fiducial List file " << fullPathLandmarksFileName << std::endl;
+  lmksStream << "#numPoints = " << numNamedLandmarks << "\n";
+  lmksStream << "#symbolScale = 5" << std::endl;
+  lmksStream << "#visibility = 1" << std::endl;
+  lmksStream << "#textScale = 4.5" << std::endl;
+  lmksStream << "#color = 0.4,1,1" << std::endl;
+  lmksStream << "#selectedColor = 1,0.5,0.5" << std::endl;
+  lmksStream << "#label,x,y,z,sel,vis" << std::endl;
+  lmksStream << lmkPointStream.str();
+
+  // Now write file to disk
+  std::ofstream myfile;
+  myfile.open( fullPathLandmarksFileName.c_str() );
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Error: Can't write Slicer3 landmark file "
+              << fullPathLandmarksFileName << std::endl;
+    std::cerr.flush();
+    return;
+    }
+  myfile << lmksStream.str();
+  myfile.close();
+}
+
+extern LandmarksMapType
+ReadSlicer3toITKLmk( const std::string & landmarksFilename )
+{
+  LandmarksMapType landmarks;
+  std::string      landmarksFilenameTmp = itksys::SystemTools::CollapseFullPath( landmarksFilename.c_str() );
+  std::ifstream    myfile( landmarksFilenameTmp.c_str() );
+
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Error: Failed to load landmarks file!" << std::endl;
+    std::cerr.flush();
+    return landmarks; // return empty landmarks
+    }
+  std::string line;
+  while( getline( myfile, line ) )
+    {
+    if( line.compare( 0, 1, "#" ) != 0 )  // Skip lines starting with a #
+      {
+      size_t            pos1 = line.find( ',', 0 );
+      const std::string name = line.substr( 0, pos1 );
+      PointType         labelPos;
+      for( unsigned int i = 0; i < 3; ++i )
+        {
+        const size_t pos2 = line.find( ',', pos1 + 1 );
+        labelPos[i] = atof( line.substr(pos1 + 1, pos2 - pos1 - 1 ).c_str() );
+        if( i < 2 )  // Negate first two components for RAS -> LPS
+          {
+          labelPos[i] *= -1;
+          }
+        pos1 = pos2;
+        }
+      landmarks[name] = labelPos;
+      }
+    }
+
+  myfile.close();
+  return landmarks;
+}
+
diff --git a/BRAINSCommonLib/Slicer3LandmarkIO.h b/BRAINSCommonLib/Slicer3LandmarkIO.h
new file mode 100644
index 00000000..37d5e886
--- /dev/null
+++ b/BRAINSCommonLib/Slicer3LandmarkIO.h
@@ -0,0 +1,46 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __Slicer3LandmarkIO__h
+#define __Slicer3LandmarkIO__h
+
+#include "itkPoint.h"
+#include 
+
+#include 
+#include 
+#include 
+
+/*
+ * This IO utility program transforms between ITK landmarks (in LPS coordinate
+ * system) to Slicer3 landmarks (in RAS coordinate system).
+ */
+
+typedef itk::Point            PointType;
+typedef std::map LandmarksMapType;
+
+/*
+ * Write ITK landmarks to a Slicer3 landmark list file (.fcsv)
+ * Input:
+ * landmarksFilename  - the filename of the output Slicer landmark list file
+ * landmarks          - a map of landmarks (itkPoints) to be written into file
+ *
+ * Output:
+ * NONE
+ */
+extern void WriteITKtoSlicer3Lmk( const std::string landmarksFilename, const LandmarksMapType & landmarks );
+
+/*
+ * Read Slicer3 landmark list file (.fcsv) into a map of ITK points
+ * Input:
+ * landmarksFilename  - the filename of the input Slicer landmark list file
+ *
+ * Output:
+ * landmarks          - a map of itkPoints to save the landmarks in ITK
+ */
+extern LandmarksMapType ReadSlicer3toITKLmk( const std::string & landmarksFilename );
+
+#endif
diff --git a/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5 b/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5
new file mode 100644
index 00000000..65b24026
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5
@@ -0,0 +1 @@
+c34916939b720607bb5e288c14cf8b65
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5 b/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5
new file mode 100644
index 00000000..320f6c3b
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5
@@ -0,0 +1 @@
+37a7b73290fc6811bd54239861fb24b1
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5 b/BRAINSCommonLib/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5
new file mode 100644
index 00000000..52b695fd
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5
@@ -0,0 +1 @@
+dda9fde8ee4fa034a6a56f4cc22f2f55
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/AtlasBrain_SignedDistance.nii.gz.md5 b/BRAINSCommonLib/TestData/AtlasBrain_SignedDistance.nii.gz.md5
new file mode 100644
index 00000000..1738bce2
--- /dev/null
+++ b/BRAINSCommonLib/TestData/AtlasBrain_SignedDistance.nii.gz.md5
@@ -0,0 +1 @@
+fbbd51cf6e360a5325d55434c61e4e3e
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5
new file mode 100644
index 00000000..cc7b9bd4
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5
@@ -0,0 +1 @@
+e19a0452f8b647d05300906abb470fab
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5
new file mode 100644
index 00000000..49ce602f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5
@@ -0,0 +1 @@
+3273a81d72e662100363dd182c54b47e
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5
new file mode 100644
index 00000000..7c8dad23
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5
@@ -0,0 +1 @@
+19e4481a52fe3dc64c37e92fff751aac
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..8c04c046
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+5f96a6bb32258268ec6023e635cd92b9
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b8a5c384
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+9b6ab30aa97e6f2331a78fcec5b041b5
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5
new file mode 100644
index 00000000..62b2c5c8
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+2be56a4f3a852777fde1b49bd237ecf5
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..fb10ac56
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+05c6c173327d8351a0e5a62cc174ef91
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..5944f422
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+50070308caef3b2cac1a415d655673c9
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..53a730e8
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+723874386daa4e702ed360d796aa29c2
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
new file mode 100644
index 00000000..1de5149d
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
@@ -0,0 +1 @@
+138d28d14b99e2fcab20b7d69b9aa353
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..937e25f3
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+03483aa7c3fb11844b96cab1ab8bb045
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7a92baca
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..abf6af46
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5
new file mode 100644
index 00000000..0d936fea
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..14f9cbea
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5
new file mode 100644
index 00000000..ac55549b
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b80a5609
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5
new file mode 100644
index 00000000..dc63b0ae
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_KSAffineRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_KSAffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_KSAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_MCAffineRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_MCAffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_MCAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..637dd9c5
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7ce7c62d
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..20234367
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..920ec378
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7884f71b
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidMedianRotationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidMedianRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..f92343c1
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidMedianRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..4a46ef3e
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..a88e0267
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b6ac08a2
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5
new file mode 100644
index 00000000..4b69b994
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5
new file mode 100644
index 00000000..0eeda98f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..bbd9895e
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5
new file mode 100644
index 00000000..4fc26e4f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..79d9fc84
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5
new file mode 100644
index 00000000..ced2d09f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit.result.nii.gz.md5
new file mode 100644
index 00000000..7bbe0339
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..6fc55e47
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..8f115bc7
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5
new file mode 100644
index 00000000..def26bcf
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..949b2b34
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5
new file mode 100644
index 00000000..171861bb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5
new file mode 100644
index 00000000..74f21521
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b60c7efc
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..ad3104c9
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5
new file mode 100644
index 00000000..f0b25961
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleNoMasks.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7184f50c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_ScaleVersorScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/BRAINSFitTest_rotation.input.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSFitTest_rotation.input.nii.gz.md5
new file mode 100644
index 00000000..ba10ab7d
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSFitTest_rotation.input.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/BRAINSROIAutoTest_GenerateBrainMask.result.nii.gz.md5 b/BRAINSCommonLib/TestData/BRAINSROIAutoTest_GenerateBrainMask.result.nii.gz.md5
new file mode 100644
index 00000000..582134f8
--- /dev/null
+++ b/BRAINSCommonLib/TestData/BRAINSROIAutoTest_GenerateBrainMask.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
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new file mode 100644
index 00000000..3018cfc6
--- /dev/null
+++ b/BRAINSCommonLib/TestData/FCOB-aftergridcomp.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/FCOB-clipped.nii.gz.md5 b/BRAINSCommonLib/TestData/FCOB-clipped.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSCommonLib/TestData/FCOB-clipped.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/FCOB-grid.nii.gz.md5 b/BRAINSCommonLib/TestData/FCOB-grid.nii.gz.md5
new file mode 100644
index 00000000..616fbf0f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/FCOB-grid.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/FCOB-trimmed.nii.gz.md5 b/BRAINSCommonLib/TestData/FCOB-trimmed.nii.gz.md5
new file mode 100644
index 00000000..689b176e
--- /dev/null
+++ b/BRAINSCommonLib/TestData/FCOB-trimmed.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/InitialDeformationField.nii.gz.md5 b/BRAINSCommonLib/TestData/InitialDeformationField.nii.gz.md5
new file mode 100644
index 00000000..dfb194fa
--- /dev/null
+++ b/BRAINSCommonLib/TestData/InitialDeformationField.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5
new file mode 100644
index 00000000..582e8ca5
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5
new file mode 100644
index 00000000..9ac3c221
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5
new file mode 100644
index 00000000..817f8c74
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasks.mat.md5
new file mode 100644
index 00000000..817f8c74
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.mat.md5
new file mode 100644
index 00000000..817f8c74
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorRotationNoMasks.mat.md5
new file mode 100644
index 00000000..be827eed
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorScaleNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorScaleNoMasks.mat.md5
new file mode 100644
index 00000000..df82465c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleSkewVersorScaleNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorRotationNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorRotationNoMasks.mat.md5
new file mode 100644
index 00000000..fb74c9be
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorScaleNoMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorScaleNoMasks.mat.md5
new file mode 100644
index 00000000..9b22646f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_0.05_BRAINSFitTest_ScaleVersorScaleNoMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
new file mode 100644
index 00000000..153d125f
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.mat.md5
new file mode 100644
index 00000000..62bea250
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.mat.md5 b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.mat.md5
new file mode 100644
index 00000000..a169a5df
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/OutDefField.nii.gz.md5 b/BRAINSCommonLib/TestData/OutDefField.nii.gz.md5
new file mode 100644
index 00000000..2a5e180c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/OutDefField.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/OutDefField_orientedImage.nii.gz.md5 b/BRAINSCommonLib/TestData/OutDefField_orientedImage.nii.gz.md5
new file mode 100644
index 00000000..12d74b1c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/OutDefField_orientedImage.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T1.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T1.nii.gz.md5
new file mode 100644
index 00000000..0dd6c58d
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T1.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2.nii.gz.md5
new file mode 100644
index 00000000..9e430424
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2_mask.nii.gz.md5
new file mode 100644
index 00000000..8b6b5598
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_T2_mask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_brain_cut_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_brain_cut_mask.nii.gz.md5
new file mode 100644
index 00000000..27f78807
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_A_small/SUBJ_A_small_brain_cut_mask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T1.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T1.nii.gz.md5
new file mode 100644
index 00000000..3cbb7d83
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T1.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2.nii.gz.md5
new file mode 100644
index 00000000..2886927a
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2_mask.nii.gz.md5
new file mode 100644
index 00000000..57ea45c9
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_T2_mask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_brain_cut_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_brain_cut_mask.nii.gz.md5
new file mode 100644
index 00000000..f272e84d
--- /dev/null
+++ b/BRAINSCommonLib/TestData/SUBJ_B_small/SUBJ_B_small_brain_cut_mask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/TEST_AnisotropicData_output.nii.gz.md5 b/BRAINSCommonLib/TestData/TEST_AnisotropicData_output.nii.gz.md5
new file mode 100644
index 00000000..941eb533
--- /dev/null
+++ b/BRAINSCommonLib/TestData/TEST_AnisotropicData_output.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/TEST_output.nii.gz.md5 b/BRAINSCommonLib/TestData/TEST_output.nii.gz.md5
new file mode 100644
index 00000000..a87bd438
--- /dev/null
+++ b/BRAINSCommonLib/TestData/TEST_output.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/Unoriented_RawBrain_SignedDistance.nii.gz.md5 b/BRAINSCommonLib/TestData/Unoriented_RawBrain_SignedDistance.nii.gz.md5
new file mode 100644
index 00000000..7366427a
--- /dev/null
+++ b/BRAINSCommonLib/TestData/Unoriented_RawBrain_SignedDistance.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest5.result.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest5.result.nii.gz.md5
new file mode 100644
index 00000000..4e669639
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest5.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest6.result.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest6.result.nii.gz.md5
new file mode 100644
index 00000000..73e24256
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest6.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest7.result.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest7.result.nii.gz.md5
new file mode 100644
index 00000000..dba5c21c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateBRAINSResampleTest7.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateInitialTransform_Test.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateInitialTransform_Test.nii.gz.md5
new file mode 100644
index 00000000..fa06e4c1
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateInitialTransform_Test.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateOrientedImagesTest5.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateOrientedImagesTest5.nii.gz.md5
new file mode 100644
index 00000000..ea38c6a8
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateOrientedImagesTest5.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest6.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest6.nii.gz.md5
new file mode 100644
index 00000000..cba6cc11
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest6.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest7.nii.gz.md5 b/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest7.nii.gz.md5
new file mode 100644
index 00000000..f5c923f9
--- /dev/null
+++ b/BRAINSCommonLib/TestData/ValidateVectorOrientedImagesTest7.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/applyWarp1.nii.gz.md5 b/BRAINSCommonLib/TestData/applyWarp1.nii.gz.md5
new file mode 100644
index 00000000..5bf9d941
--- /dev/null
+++ b/BRAINSCommonLib/TestData/applyWarp1.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/applyWarp2.nii.gz.md5 b/BRAINSCommonLib/TestData/applyWarp2.nii.gz.md5
new file mode 100644
index 00000000..ee50b0a4
--- /dev/null
+++ b/BRAINSCommonLib/TestData/applyWarp2.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/applyWarp_BSpline.mat.md5 b/BRAINSCommonLib/TestData/applyWarp_BSpline.mat.md5
new file mode 100644
index 00000000..9a1a8b64
--- /dev/null
+++ b/BRAINSCommonLib/TestData/applyWarp_BSpline.mat.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons1.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons1.nii.gz.md5
new file mode 100644
index 00000000..5b635a42
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons1.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons2.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons2.nii.gz.md5
new file mode 100644
index 00000000..3bae0763
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons2.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons3.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons3.nii.gz.md5
new file mode 100644
index 00000000..80215a79
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons3.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons4.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons4.nii.gz.md5
new file mode 100644
index 00000000..8741afbe
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons4.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons5.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons5.nii.gz.md5
new file mode 100644
index 00000000..5897d4b2
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons5.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemonsWithMask.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemonsWithMask.nii.gz.md5
new file mode 100644
index 00000000..2cfa1c13
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemonsWithMask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/diffeomorphicDemons_AutoMask.nii.gz.md5 b/BRAINSCommonLib/TestData/diffeomorphicDemons_AutoMask.nii.gz.md5
new file mode 100644
index 00000000..6f036d77
--- /dev/null
+++ b/BRAINSCommonLib/TestData/diffeomorphicDemons_AutoMask.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/fastSymmetricForcesDemons.nii.gz.md5 b/BRAINSCommonLib/TestData/fastSymmetricForcesDemons.nii.gz.md5
new file mode 100644
index 00000000..5b56b978
--- /dev/null
+++ b/BRAINSCommonLib/TestData/fastSymmetricForcesDemons.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/geom.b2.test.nii.gz.md5 b/BRAINSCommonLib/TestData/geom.b2.test.nii.gz.md5
new file mode 100644
index 00000000..421704cb
--- /dev/null
+++ b/BRAINSCommonLib/TestData/geom.b2.test.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/logDemons.nii.gz.md5 b/BRAINSCommonLib/TestData/logDemons.nii.gz.md5
new file mode 100644
index 00000000..dd739387
--- /dev/null
+++ b/BRAINSCommonLib/TestData/logDemons.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/mouseFixed.nii.gz.md5 b/BRAINSCommonLib/TestData/mouseFixed.nii.gz.md5
new file mode 100644
index 00000000..ba6729e9
--- /dev/null
+++ b/BRAINSCommonLib/TestData/mouseFixed.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/mouseMoving.nii.gz.md5 b/BRAINSCommonLib/TestData/mouseMoving.nii.gz.md5
new file mode 100644
index 00000000..79f96eca
--- /dev/null
+++ b/BRAINSCommonLib/TestData/mouseMoving.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/orientedImagesDemons_test.nii.gz.md5 b/BRAINSCommonLib/TestData/orientedImagesDemons_test.nii.gz.md5
new file mode 100644
index 00000000..1a579f98
--- /dev/null
+++ b/BRAINSCommonLib/TestData/orientedImagesDemons_test.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.b2.test.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.b2.test.nii.gz.md5
new file mode 100644
index 00000000..8e998b7b
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.b2.test.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.geom.test.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.geom.test.nii.gz.md5
new file mode 100644
index 00000000..bc92cc24
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.geom.test.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.rescale.rigid.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.rescale.rigid.nii.gz.md5
new file mode 100644
index 00000000..34ec7923
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.rescale.rigid.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.rescale.test.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.rescale.test.nii.gz.md5
new file mode 100644
index 00000000..1696efe4
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.rescale.test.nii.gz.md5
@@ -0,0 +1 @@
+3705b9d451b1eb52eb7c15d4d5650dd3
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.test.mask.md5 b/BRAINSCommonLib/TestData/rotation.test.mask.md5
new file mode 100644
index 00000000..76739b82
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.test.mask.md5
@@ -0,0 +1 @@
+dd929140569763fdc31692061edd5595
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.test.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.test.nii.gz.md5
new file mode 100644
index 00000000..060ecdef
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.test.nii.gz.md5
@@ -0,0 +1 @@
+e4891faada07461571c27c477e6d736d
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotation.test_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/rotation.test_mask.nii.gz.md5
new file mode 100644
index 00000000..f3c10f78
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotation.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+989827131b94b75a201a7c4a946ca95b
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/rotationUShort.rescale.rigid.nii.gz.md5 b/BRAINSCommonLib/TestData/rotationUShort.rescale.rigid.nii.gz.md5
new file mode 100644
index 00000000..bc4abdab
--- /dev/null
+++ b/BRAINSCommonLib/TestData/rotationUShort.rescale.rigid.nii.gz.md5
@@ -0,0 +1 @@
+6eebd8c70081692ec757fed104333db3
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/scale.test.mask.md5 b/BRAINSCommonLib/TestData/scale.test.mask.md5
new file mode 100644
index 00000000..cf52ccf4
--- /dev/null
+++ b/BRAINSCommonLib/TestData/scale.test.mask.md5
@@ -0,0 +1 @@
+da905ca3300899a672840bd7cc0261b4
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/scale.test.nii.gz.md5 b/BRAINSCommonLib/TestData/scale.test.nii.gz.md5
new file mode 100644
index 00000000..7da1d1ea
--- /dev/null
+++ b/BRAINSCommonLib/TestData/scale.test.nii.gz.md5
@@ -0,0 +1 @@
+1fa2661a07130796300f23b66d7b5149
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/scale.test_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/scale.test_mask.nii.gz.md5
new file mode 100644
index 00000000..7bea3b70
--- /dev/null
+++ b/BRAINSCommonLib/TestData/scale.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+5c57ed69a6dfbab1875ec00879aa6fe2
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/standard.nii.gz.md5 b/BRAINSCommonLib/TestData/standard.nii.gz.md5
new file mode 100644
index 00000000..06497ce7
--- /dev/null
+++ b/BRAINSCommonLib/TestData/standard.nii.gz.md5
@@ -0,0 +1 @@
+871ffb8f546e670f8cf2c53924728ae5
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/symmetricLogDemons1.nii.gz.md5 b/BRAINSCommonLib/TestData/symmetricLogDemons1.nii.gz.md5
new file mode 100644
index 00000000..9269895c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/symmetricLogDemons1.nii.gz.md5
@@ -0,0 +1 @@
+753676d3bccf159980e4d8888f71047a
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/symmetricLogDemons2.nii.gz.md5 b/BRAINSCommonLib/TestData/symmetricLogDemons2.nii.gz.md5
new file mode 100644
index 00000000..162f858c
--- /dev/null
+++ b/BRAINSCommonLib/TestData/symmetricLogDemons2.nii.gz.md5
@@ -0,0 +1 @@
+9106e002e822398d1f9ee8a445b00c4e
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/test.mask.md5 b/BRAINSCommonLib/TestData/test.mask.md5
new file mode 100644
index 00000000..670c239b
--- /dev/null
+++ b/BRAINSCommonLib/TestData/test.mask.md5
@@ -0,0 +1 @@
+befa5b791b4d8c63c667b3bcab1783ae
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/test.nii.gz.md5 b/BRAINSCommonLib/TestData/test.nii.gz.md5
new file mode 100644
index 00000000..dac50682
--- /dev/null
+++ b/BRAINSCommonLib/TestData/test.nii.gz.md5
@@ -0,0 +1 @@
+70518dc3306838ebf1a6b187d61a28e9
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/test2.nii.gz.md5 b/BRAINSCommonLib/TestData/test2.nii.gz.md5
new file mode 100644
index 00000000..f4204447
--- /dev/null
+++ b/BRAINSCommonLib/TestData/test2.nii.gz.md5
@@ -0,0 +1 @@
+fb295d462eba7b231de4dd31dbc7ae3a
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/testMask.nii.gz.md5 b/BRAINSCommonLib/TestData/testMask.nii.gz.md5
new file mode 100644
index 00000000..086eb819
--- /dev/null
+++ b/BRAINSCommonLib/TestData/testMask.nii.gz.md5
@@ -0,0 +1 @@
+9e82cbc341ff59b2b2fb38d071ba6ba9
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/test_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/test_mask.nii.gz.md5
new file mode 100644
index 00000000..d3c10773
--- /dev/null
+++ b/BRAINSCommonLib/TestData/test_mask.nii.gz.md5
@@ -0,0 +1 @@
+5baf8e5fbcc414f3f4e84afd3de2f18a
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/thirionDemons.nii.gz.md5 b/BRAINSCommonLib/TestData/thirionDemons.nii.gz.md5
new file mode 100644
index 00000000..a313626a
--- /dev/null
+++ b/BRAINSCommonLib/TestData/thirionDemons.nii.gz.md5
@@ -0,0 +1 @@
+63ad8f465b46ce9e654fce1d6a2d294a
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/translation.rescale.test.nii.gz.md5 b/BRAINSCommonLib/TestData/translation.rescale.test.nii.gz.md5
new file mode 100644
index 00000000..af6ca9e1
--- /dev/null
+++ b/BRAINSCommonLib/TestData/translation.rescale.test.nii.gz.md5
@@ -0,0 +1 @@
+cba09d76112bb66e183b6abcd5b7ec00
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/translation.test.mask.md5 b/BRAINSCommonLib/TestData/translation.test.mask.md5
new file mode 100644
index 00000000..08e33e62
--- /dev/null
+++ b/BRAINSCommonLib/TestData/translation.test.mask.md5
@@ -0,0 +1 @@
+327b2c70900870ed68627c80af2426f5
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/translation.test.nii.gz.md5 b/BRAINSCommonLib/TestData/translation.test.nii.gz.md5
new file mode 100644
index 00000000..b99f87d5
--- /dev/null
+++ b/BRAINSCommonLib/TestData/translation.test.nii.gz.md5
@@ -0,0 +1 @@
+0acc2a5a1f20ed373c49103e189ba549
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestData/translation.test_mask.nii.gz.md5 b/BRAINSCommonLib/TestData/translation.test_mask.nii.gz.md5
new file mode 100644
index 00000000..bfb95dd9
--- /dev/null
+++ b/BRAINSCommonLib/TestData/translation.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+bf6514195fffb4c61cc1f1894b24f59e
\ No newline at end of file
diff --git a/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/CMakeLists.txt b/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/CMakeLists.txt
new file mode 100644
index 00000000..02cba9bb
--- /dev/null
+++ b/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/CMakeLists.txt
@@ -0,0 +1,7 @@
+##The start of a test program for this filter.
+## HACK-- This still needs to be finalized, and tests written.
+
+set(TestName TestLargestForegroundFilledMaskImageFilter)
+
+add_executable(${TestName} ${TestName}.cxx)
+target_link_libraries(${TestName})${ITK_LIBRARIES}
diff --git a/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/TestLargestForegroundFilledMaskImageFilter.cxx b/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/TestLargestForegroundFilledMaskImageFilter.cxx
new file mode 100644
index 00000000..76e24c09
--- /dev/null
+++ b/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/TestLargestForegroundFilledMaskImageFilter.cxx
@@ -0,0 +1,27 @@
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include "itkIO.h"
+#include 
+
+int
+main(int argc, char * *argv)
+{
+  if( argc < 3 )
+    {
+    std::cerr << "TestLargestForegrounFilledMaskImageFilter  "
+              << std::endl;
+    exit(1);
+    }
+  typedef itk::Image ImageType;
+  typedef itk::LargestForegroundFilledMaskImageFilter
+  FilterType;
+  std::string         inputname(argv[1]);
+  std::string         outputname(argv[2]);
+  ImageType::Pointer  image = itkUtil::ReadImage(inputname);
+  FilterType::Pointer filter = FilterType::New();
+  filter->SetInput(image);
+  filter->Update();
+  ImageType::Pointer outputImage = filter->GetOutput();
+  itkUtil::WriteImage(outputImage, outputname);
+  return 0;
+}
+
diff --git a/BRAINSCommonLib/TestSuite/BRAINSCleanMask.cxx b/BRAINSCommonLib/TestSuite/BRAINSCleanMask.cxx
new file mode 100644
index 00000000..322b6822
--- /dev/null
+++ b/BRAINSCommonLib/TestSuite/BRAINSCleanMask.cxx
@@ -0,0 +1,19 @@
+#include "CleanBrainLabelMap.h"
+#include "itkIO.h"
+
+int main(int argc, char * *argv)
+{
+  if( argc < 3 )
+    {
+    std::cerr << "Usage: BRAINSCleanMask inputLabelMap outputLabelMap" << std::endl;
+    return 1;
+    }
+  typedef itk::Image ImageType;
+
+  std::string inputName(argv[1]), outputName(argv[2]);
+
+  ImageType::Pointer input = itkUtil::ReadImage(inputName);
+  ImageType::Pointer output = CleanBrainLabelMap(input);
+  itkUtil::WriteImage(output, outputName);
+}
+
diff --git a/BRAINSCommonLib/TestSuite/CMakeLists.txt b/BRAINSCommonLib/TestSuite/CMakeLists.txt
new file mode 100644
index 00000000..bb6de8ed
--- /dev/null
+++ b/BRAINSCommonLib/TestSuite/CMakeLists.txt
@@ -0,0 +1,24 @@
+
+
+#configure_file(${BRAINSCommonLibProject_SOURCE_DIR}/CTestCustom.ctest ${BRAINSCommonLibProject_BINARY_DIR}/CTestCustom.ctest COPYONLY)
+
+add_executable(PrettyPrintTableTest PrettyPrintTableTest.cxx)
+set_target_properties(PrettyPrintTableTest
+  PROPERTIES RUNTIME_OUTPUT_DIRECTORY
+  ${BRAINSCommonLibProject_BINARY_DIR})
+
+add_test(NAME PrettyPrintTableTest COMMAND ${LAUNCH_EXE} $)
+
+add_executable(BRAINSCleanMask BRAINSCleanMask.cxx)
+target_link_libraries(BRAINSCleanMask ${ITK_LIBRARIES})
+
+## HACK: TODO: Make this test do something meaningful.
+#add_executable( itkResampleInPlaceImageFilterTest itkBasicFiltersTests.cxx )
+#target_link_libraries( itkResampleInPlaceImageFilterTest ITKIO ITKBasicFilters )
+#add_test( itkResampleInPlaceImageFilterTest itkResampleInPlaceImageFilterTest
+#    itkResampleInPlaceImageFilterTest
+#    ${ITK_DATA_ROOT}/Input/itkResampleInPlaceImageFilterTest.nii.gz
+#    ${ITK_DATA_ROOT}/Baseline/Review/itkResampleInPlaceImageFilterTest.nii.gz
+#    ${CMAKE_CURRENT_BINARY_DIR}/test_image.nii.gz
+#)
+
diff --git a/BRAINSCommonLib/TestSuite/PrettyPrintTableTest.cxx b/BRAINSCommonLib/TestSuite/PrettyPrintTableTest.cxx
new file mode 100644
index 00000000..3cf02e0a
--- /dev/null
+++ b/BRAINSCommonLib/TestSuite/PrettyPrintTableTest.cxx
@@ -0,0 +1,47 @@
+#include 
+#include "PrettyPrintTable.h"
+
+int main(int, char * *)
+{
+  PrettyPrintTable p;
+
+  p.setTablePad(5);
+  p.add(0, 0, "String");
+
+  p.add(0, 1, "SecondColumn");
+
+  p.add(0, 2, "4C");
+
+  p.add(0, 3, "5C");
+
+  p.add(1, 0, "Integers");
+
+  p.add(1, 1, 1, "%d"); // Similar to %d
+
+  p.add(1, 2, 2, "%d");
+
+  p.add(1, 3, 3, "%d");
+
+  p.add(1, 0, "ZeroPadInt");
+
+  p.add(1, 1, 1, "%02d"); // Similar to %02d in printf
+
+  p.add(1, 2, 2, "%02d");
+
+  p.add(1, 3, 3, "%02d");
+
+  p.add(2, 0, "FloatingPoint");
+
+  p.add(2, 1, 1.0F, "%+5.2f"); // Similar to %5.2f in printf
+
+  p.add(2, 2, 2.0F, "%+5.2f");
+
+  p.add(2, 3, 3.0F, "%+5.2f");
+
+  p.Print(std::cout);
+
+  p.rightJustify();
+
+  p.Print(std::cout);
+}
+
diff --git a/BRAINSCommonLib/TestSuite/itkResampleInPlaceImageFilterTest.cxx b/BRAINSCommonLib/TestSuite/itkResampleInPlaceImageFilterTest.cxx
new file mode 100644
index 00000000..0efd5cb0
--- /dev/null
+++ b/BRAINSCommonLib/TestSuite/itkResampleInPlaceImageFilterTest.cxx
@@ -0,0 +1,160 @@
+/* =========================================================================
+ *
+ *  Copyright Insight Software Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+/* =========================================================================
+ *  Created by Wei Lu on 10/14/10.
+ *  Copyright 2010 The University of Iowa
+ *=========================================================================*/
+
+#include "itkResampleInPlaceImageFilter.h"
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkVersorRigid3DTransform.h"
+#include "itkImageRegionConstIterator.h"
+
+#include 
+
+// return true if it fails the validation
+inline bool Validate( double input, double desired, double tolerance )
+{
+  return abs( input - desired ) > tolerance * abs( desired );
+}
+
+int itkResampleInPlaceImageFilterTest( int argc, char * argv[] )
+{
+  // Simple parameter check
+  if( argc < 3 )
+    {
+    std::cerr << "Wrong arguments!" << std::endl;
+    std::cerr << "Usage: ./" << argv[0] << " inputImage baselineImage outputImage" << std::endl;
+    exit( -1 );
+    }
+
+  bool   result = false; // test result default = no failure
+  double tol = 1.e-3;    // tolerance
+
+  // Image, filter, transform typedef
+  const unsigned int LocalImageDimension = 3;
+  typedef short PixelType;
+
+  typedef itk::Image ImageType;
+  typedef ImageType::Pointer                         ImagePointer;
+  typedef ImageType::PointType                       ImagePointType;
+  typedef ImageType::DirectionType                   ImageDirectionType;
+  typedef ImageType::SpacingType                     ImageSpacingType;
+
+  typedef itk::ImageRegionConstIterator ImageConstIterator;
+  typedef itk::ImageFileReader          ReaderType;
+  typedef itk::VersorRigid3DTransform      TransformType;
+
+  typedef itk::ResampleInPlaceImageFilter FilterType;
+
+  // Read in input test image
+  ImagePointer inputImage;
+    {
+    ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName( argv[1] );
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cerr << " Error while reading image file(s) with ITK:\n "
+                << err << std::endl;
+      }
+    inputImage = reader->GetOutput();
+    }
+
+  // Set up transforms
+  itk::Vector rotationAxis;
+  rotationAxis.Fill( 0. );
+  rotationAxis[0] = 1.;
+  double                 rotationAngle = .5; // in rad
+  itk::Vector translation;
+  translation.Fill( 0. );
+  translation[1] = 300.; // in mm along P-axis
+  TransformType::Pointer transform = TransformType::New();
+  transform->SetIdentity();
+  transform->SetRotation( rotationAxis, rotationAngle );
+  transform->Translate( translation, true );
+
+  // Set up the resample filter
+  FilterType::Pointer filter = FilterType::New();
+  filter->SetInputImage( inputImage );
+  filter->SetRigidTransform( transform );
+  filter->Update();
+  ImagePointer outputImage = filter->GetOutput();
+
+  // Get image info
+  ImagePointType     origin = outputImage->GetOrigin();
+  ImageDirectionType direction = outputImage->GetDirection();
+  ImageSpacingType   spacing = outputImage->GetSpacing();
+
+  // Read in baseline image
+  ImagePointer baselineImage;
+    {
+    ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName( argv[2] );
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cerr << " Error while reading image file(s) with ITK:\n "
+                << err << std::endl;
+      }
+    baselineImage = reader->GetOutput();
+    }
+  ImagePointType     origin_d = baselineImage->GetOrigin();
+  ImageDirectionType direction_d = baselineImage->GetDirection();
+  ImageSpacingType   spacing_d = baselineImage->GetSpacing();
+  // Image info validation
+  for( unsigned int i = 0; i < LocalImageDimension; ++i )
+    {
+    result = ( result || Validate( origin[i], origin_d[i], tol ) );
+    result = ( result || Validate( spacing[i], spacing_d[i], tol ) );
+    for( unsigned int j = 0; j < LocalImageDimension; ++j )
+      {
+      result = ( result || Validate( direction(i, j), direction_d(i, j), tol ) );
+      }
+    }
+
+  // Voxel contents validation
+  ImageConstIterator it1( outputImage, outputImage->GetRequestedRegion() );
+  ImageConstIterator it2( baselineImage, baselineImage->GetRequestedRegion() );
+  it1.GoToBegin();
+  it2.GoToBegin();
+  while( !it1.IsAtEnd() )
+    {
+    result = ( result || Validate( it1.Get(), it2.Get(), tol ) );
+    ++it1;
+    ++it2;
+    }
+
+  typedef itk::ImageFileWriter WriterType;
+  WriterType::Pointer writer = WriterType::New();
+  writer->SetFileName( argv[3] );
+  writer->SetInput( outputImage );
+  writer->Update();
+
+  return result;
+}
+
diff --git a/BRAINSCommonLib/Test_FindCenterOfBrainFilter/CMakeLists.txt b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/CMakeLists.txt
new file mode 100644
index 00000000..8cc9db58
--- /dev/null
+++ b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/CMakeLists.txt
@@ -0,0 +1,46 @@
+#
+# This is rather a problem: FindCenterOfBrainFilter is included in more than one
+# NITRC based BRAINS Project, which means that BRAINSFit_SOURCE_DIR is not always
+# defined.
+#
+# In practice, this is only a problem if programs other than BRAINSFit actually
+# add FindCenterOfBrainFilter as a subdirectory, rather than just using it for the
+# include files.
+#
+# But if a build fails because someone added it to a non-brainsfit application, I
+# hope they look at this file and read this comment, and CUT THAT BUSINESS RIGHT OUT.
+# Unless this is a subdirectory of BRAINSFit, there's NO USE adding it as a subdirectory
+# in the CMakeLists.txt.  It will just end in tears.
+#
+include_directories(${BRAINSFit_SOURCE_DIR}/BRAINSFit_Common)
+include_directories(${BRAINSFit_SOURCE_DIR}/LargestForegroundFilledMaskImageFilter)
+include_directories(${BRAINSFit_SOURCE_DIR}/FindCenterOfBrainFilter)
+
+enable_testing()
+include(Dart)
+
+set(FindCenterOfBrain_SRC
+FindCenterOfBrainCLP.cxx)
+
+generateclp(FindCenterOfBrain_SRC FindCenterOfBrain.xml)
+
+add_executable(FindCenterOfBrain ${FindCenterOfBrain_SRC})
+target_link_libraries(FindCenterOfBrain
+  ITKAlgorithms
+  ITKStatistics
+  ITKIO
+  ITKBasicFilters
+  ITKCommon
+  ITKNumerics)
+
+add_executable(ImageCompare ImageCompare.cxx)
+target_link_libraries(ImageCompare  ITKIO ITKNumerics ITKStatistics)
+
+set(FINDCENTER_PROG ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/FindCenterOfBrain)
+
+add_test(RudimentaryFindCenterOfBrainTest tclsh ${CMAKE_CURRENT_SOURCE_DIR}}/TestData/FindCenterOfBrainFilter/Test/TestFCOB.tcl
+  ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
+  ${BRAINSFit_SOURCE_DIR}/TestData
+  ${BRAINSFit_BINARY_DIR}/Testing
+  ${BRAINSFit_SOURCE_DIR}/TestData/ANON0006_20_T1_dbg_splayed.nii.gz
+)
diff --git a/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrain.xml b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrain.xml
new file mode 100644
index 00000000..1100a2ab
--- /dev/null
+++ b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrain.xml
@@ -0,0 +1,143 @@
+
+
+  Utility
+  FindCenterOfBrain
+  Finds the center point of a brain
+  
+  https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt 
+  Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu
+  Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3);  Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard)  
+  3.0.0
+  
+    
+    
+      InputVolume
+      --inputVolume
+      
+      The image in which to find the center.
+      input
+      
+    
+    
+      ImageMask
+      --imageMask
+      
+      
+      input
+      
+    
+    
+      ClippedImageMask
+      --clippedImageMask
+      
+      
+      output
+      
+    
+  
+  
+  
+    
+    
+      Maximize
+      --maximize
+      
+      
+      true
+    
+    
+      Axis
+      --axis
+      
+      
+      2
+    
+    
+      OtsuPercentileThreshold
+      --otsuPercentileThreshold
+      
+      
+      0.001
+    
+    
+      ClosingSize
+      --closingSize
+      
+      
+      7
+    
+    
+      HeadSizeLimit
+      --headSizeLimit
+      
+      
+      1000
+    
+
+    
+      HeadSizeEstimate
+      --headSizeEstimate
+      
+      
+      0
+    
+    
+      BackgroundValue
+      --backgroundValue
+      
+      
+      0
+    
+  
+  
+    
+    
+      GenerateDebugImages
+      --generateDebugImages
+      
+      
+      false
+    
+    
+      DebugDistanceImage
+      --debugDistanceImage
+      
+      
+      output
+      
+    
+    
+      DebugGridImage
+      --debugGridImage
+      
+      
+      output
+      
+    
+    
+      DebugAfterGridComputationsForegroundImage
+      --debugAfterGridComputationsForegroundImage
+      
+      
+      output
+      
+    
+    
+      DebugClippedImageMask
+      --debugClippedImageMask
+      
+      
+      output
+      
+    
+    
+      DebugTrimmedImage
+      --debugTrimmedImage
+      
+      
+      output
+      
+    
+    
+  
+
diff --git a/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrainCLP.cxx b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrainCLP.cxx
new file mode 100644
index 00000000..3f1c4fb8
--- /dev/null
+++ b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/FindCenterOfBrainCLP.cxx
@@ -0,0 +1,125 @@
+/*  KENT  -- This CLP Wrapped test program needs to exercise
+ *  the itkFindCenterOfBrainCLP.h class.
+ *
+ * As part of this testing, please move as many of the hard-coded
+ * debuggging images out of the txx files, and make it so that this
+ * test program will create those images from the command line.
+ *
+ * You will have to make some more member variables of the class for
+ * some of the intermediate images like "AfterGridComputationsForeground.nii.gz"
+ * so that the class can expose them to the test program.
+ *
+ * Please also write an ADD_TEST section to the CMakeLists.txt file that will execute this test program.
+ */
+#include "itkFindCenterOfBrainFilter.h"
+#include "itkIO.h"
+#include 
+
+int main(int argc, char * *argv)
+{
+  PARSE_ARGS;
+  if( InputVolume == "" )
+    {
+    std::cerr << "FindCenterOfBrain: missing input image name" << std::endl;
+    exit(1);
+    }
+  typedef itk::Image            ImageType;
+  typedef itk::FindCenterOfBrainFilter FindCenterFilterType;
+  typedef FindCenterFilterType::MaskImageType     MaskImageType;
+
+  ImageType::Pointer inputImage = itkUtil::ReadImage(InputVolume);
+  if( inputImage.IsNull() )
+    {
+    std::cerr << "FindCenterOfBrain: Can't read input image "
+              << InputVolume << std::endl;
+    exit(2);
+    }
+
+  FindCenterFilterType::Pointer filter = FindCenterFilterType::New();
+  filter->SetInput(inputImage);
+
+  MaskImageType::Pointer imageMask;
+  if( ImageMask != "" )
+    {
+    imageMask = itkUtil::ReadImage(ImageMask);
+    if( imageMask.IsNull() )
+      {
+      std::cerr << "FindCenterOfBrain: Can't read mask "
+                << ImageMask << std::endl;
+      exit(3);
+      }
+    filter->SetImageMask(imageMask);
+    }
+  filter->SetMaximize(Maximize);
+  filter->SetAxis(Axis);
+  filter->SetOtsuPercentileThreshold(OtsuPercentileThreshold);
+  filter->SetClosingSize(ClosingSize);
+  filter->SetHeadSizeLimit(HeadSizeLimit);
+  filter->SetHeadSizeEstimate(HeadSizeEstimate);
+  filter->SetBackgroundValue(BackgroundValue);
+  filter->SetGenerateDebugImages(GenerateDebugImages);
+  try
+    {
+    filter->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << "ExceptionObject caught !" << std::endl;
+    std::cerr << err << std::endl;
+    exit(4);
+    }
+  FindCenterFilterType::PointType center =
+    filter->GetCenterOfBrain();
+  std::cout << "Center Of Brain:"
+            << " " << center[0]
+            << " " << center[1]
+            << " " << center[2]
+            << std::endl;
+  if( ClippedImageMask != "" )
+    {
+    MaskImageType::Pointer clippedMask =
+      filter->GetClippedImageMask();
+    itkUtil::WriteImage(clippedMask,
+                                       ClippedImageMask);
+    }
+  if( !GenerateDebugImages )
+    {
+    exit(0);
+    }
+  if( DebugDistanceImage != "" )
+    {
+    FindCenterFilterType::DistanceImagePointer distImage =
+      filter->GetDebugDistanceImage();
+    itkUtil::WriteImage(distImage,
+                                                                 DebugDistanceImage);
+    }
+  if( DebugGridImage != "" )
+    {
+    FindCenterFilterType::InputImagePointer gridImage =
+      filter->GetDebugGridImage();
+    itkUtil::WriteImage(gridImage, DebugGridImage);
+    }
+  if( DebugAfterGridComputationsForegroundImage != "" )
+    {
+    MaskImageType::Pointer afterImage =
+      filter->GetDebugAfterGridComputationsForegroundImage();
+    itkUtil::WriteImage(afterImage,
+                                       DebugAfterGridComputationsForegroundImage);
+    }
+  if( DebugClippedImageMask != "" )
+    {
+    MaskImageType::Pointer clippedMask =
+      filter->GetDebugClippedImageMask();
+    itkUtil::WriteImage(clippedMask,
+                                       DebugClippedImageMask);
+    }
+  if( DebugTrimmedImage != "" )
+    {
+    ImageType::Pointer trimmedImage =
+      filter->GetDebugTrimmedImage();
+    itkUtil::WriteImage(trimmedImage,
+                                   DebugTrimmedImage);
+    }
+  exit(0);
+}
+
diff --git a/BRAINSCommonLib/Test_FindCenterOfBrainFilter/ImageCompare.cxx b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/ImageCompare.cxx
new file mode 100644
index 00000000..a2d95cfd
--- /dev/null
+++ b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/ImageCompare.cxx
@@ -0,0 +1,264 @@
+#include "itkWin32Header.h"
+#include 
+#include 
+#include "itkNumericTraits.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkExtractImageFilter.h"
+#include "itkDifferenceImageFilter.h"
+
+using namespace std;
+
+#define ITK_TEST_DIMENSION_MAX 6
+
+int RegressionTestImage(const char *, const char *, int, bool);
+
+int main(int argc, char * *argv)
+{
+  if( argc < 3 )
+    {
+    cerr << "Usage:" << endl;
+    cerr << "testImage, baselineImage1, [baselineImage2, baselineImage3, ...]" << endl;
+    cerr << "Note that if you supply more than one baselineImage, this test will pass if any" << endl;
+    cerr << "of them match the testImage" << endl;
+    return -1;
+    }
+  int bestBaselineStatus = 2001;
+  int bestBaseline = 2;
+  try
+    {
+    if( argc == 3 )
+      {
+      bestBaselineStatus = RegressionTestImage(argv[1], argv[2], 0, false);
+      }
+    else
+      {
+      int currentStatus = 2001;
+      for( int i = 2; i < argc; i++ )
+        {
+        currentStatus = RegressionTestImage(argv[1], argv[i], 0, false);
+        if( currentStatus < bestBaselineStatus )
+          {
+          bestBaselineStatus = currentStatus;
+          bestBaseline = i;
+          }
+        if( bestBaselineStatus == 0 )
+          {
+          break;
+          }
+        }
+      }
+    // generate images of our closest match
+    if( bestBaselineStatus == 0 )
+      {
+      RegressionTestImage(argv[1], argv[bestBaseline], 1, false);
+      }
+    else
+      {
+      RegressionTestImage(argv[1], argv[bestBaseline], 1, true);
+      }
+    }
+  catch( const itk::ExceptionObject & e )
+    {
+    std::cerr << "ITK test driver caught an ITK exception:\n";
+    std::cerr << e.GetFile() << ":" << e.GetLine() << ":\n"
+              << e.GetDescription() << "\n";
+    bestBaselineStatus = -1;
+    }
+  catch( const std::exception & e )
+    {
+    std::cerr << "ITK test driver caught an exception:\n";
+    std::cerr << e.what() << "\n";
+    bestBaselineStatus = -1;
+    }
+  catch( ... )
+    {
+    std::cerr << "ITK test driver caught an unknown exception!!!\n";
+    bestBaselineStatus = -1;
+    }
+  cout << bestBaselineStatus << endl;
+  return bestBaselineStatus;
+}
+
+// Regression Testing Code
+int RegressionTestImage(const char *testImageFilename, const char *baselineImageFilename,
+                        int reportErrors, bool differences)
+{
+  // Use the factory mechanism to read the test and baseline files and convert
+  // them to double
+  typedef itk::Image        ImageType;
+  typedef itk::Image OutputType;
+  typedef itk::Image                      DiffOutputType;
+  typedef itk::ImageFileReader                   ReaderType;
+
+  // Read the baseline file
+  ReaderType::Pointer baselineReader = ReaderType::New();
+  baselineReader->SetFileName(baselineImageFilename);
+  try
+    {
+    baselineReader->UpdateLargestPossibleRegion();
+    }
+  catch( itk::ExceptionObject & e )
+    {
+    std::cerr << "Exception detected while reading " << baselineImageFilename << " : "  << e.GetDescription();
+    return 1000;
+    }
+
+  // Read the file generated by the test
+  ReaderType::Pointer testReader = ReaderType::New();
+  testReader->SetFileName(testImageFilename);
+  try
+    {
+    testReader->UpdateLargestPossibleRegion();
+    }
+  catch( itk::ExceptionObject & e )
+    {
+    std::cerr << "Exception detected while reading " << testImageFilename << " : "  << e.GetDescription() << std::endl;
+    return 1000;
+    }
+
+  // The sizes of the baseline and test image must match
+  ImageType::SizeType baselineSize;
+  baselineSize = baselineReader->GetOutput()->GetLargestPossibleRegion().GetSize();
+  ImageType::SizeType testSize;
+  testSize = testReader->GetOutput()->GetLargestPossibleRegion().GetSize();
+
+  if( baselineSize != testSize )
+    {
+    std::cerr << "The size of the Baseline image and Test image do not match!" << std::endl;
+    std::cerr << "Baseline image: " << baselineImageFilename
+              << " has size " << baselineSize << std::endl;
+    std::cerr << "Test image:     " << testImageFilename
+              << " has size " << testSize << std::endl;
+    return 1;
+    }
+
+  // Now compare the two images
+  typedef itk::DifferenceImageFilter DiffType;
+  DiffType::Pointer diff = DiffType::New();
+  diff->SetValidInput( baselineReader->GetOutput() );
+  diff->SetTestInput( testReader->GetOutput() );
+  diff->SetDifferenceThreshold(2.0);
+  diff->UpdateLargestPossibleRegion();
+
+  double status = diff->GetTotalDifference();
+
+  if( reportErrors )
+    {
+    typedef itk::RescaleIntensityImageFilter RescaleType;
+    typedef itk::ExtractImageFilter     ExtractType;
+    typedef itk::ImageFileWriter                    WriterType;
+    typedef itk::ImageRegion                RegionType;
+    OutputType::IndexType index; index.Fill(0);
+    OutputType::SizeType  size; size.Fill(0);
+
+    RescaleType::Pointer rescale = RescaleType::New();
+    rescale->SetOutputMinimum( itk::NumericTraits::NonpositiveMin() );
+    rescale->SetOutputMaximum( itk::NumericTraits::max() );
+    rescale->SetInput( diff->GetOutput() );
+    rescale->UpdateLargestPossibleRegion();
+
+    RegionType region;
+    region.SetIndex(index);
+
+    size = rescale->GetOutput()->GetLargestPossibleRegion().GetSize();
+    for( unsigned int i = 2; i < ITK_TEST_DIMENSION_MAX; i++ )
+      {
+      size[i] = 0;
+      }
+    region.SetSize(size);
+
+    ExtractType::Pointer extract = ExtractType::New();
+    extract->SetInput( rescale->GetOutput() );
+    extract->SetExtractionRegion(region);
+
+    WriterType::Pointer writer = WriterType::New();
+    writer->SetInput( extract->GetOutput() );
+    if( differences )
+      {
+      // if there are discrepencies, create an diff image
+      std::cout << "";
+      std::cout << status;
+      std::cout <<  "" << std::endl;
+
+      ::std::ostringstream diffName;
+      diffName << testImageFilename << ".diff.png";
+      try
+        {
+        rescale->SetInput( diff->GetOutput() );
+        rescale->Update();
+        }
+      catch( ... )
+        {
+        std::cerr << "Error during rescale of " << diffName.str() << std::endl;
+        }
+      writer->SetFileName( diffName.str().c_str() );
+      try
+        {
+        writer->Update();
+        }
+      catch( ... )
+        {
+        std::cerr << "Error during write of " << diffName.str() << std::endl;
+        }
+
+      std::cout << "";
+      std::cout << diffName.str();
+      std::cout << "" << std::endl;
+      }
+    ::std::ostringstream baseName;
+    baseName << testImageFilename << ".base.png";
+    try
+      {
+      rescale->SetInput( baselineReader->GetOutput() );
+      rescale->Update();
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during rescale of " << baseName.str() << std::endl;
+      }
+    try
+      {
+      writer->SetFileName( baseName.str().c_str() );
+      writer->Update();
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during write of " << baseName.str() << std::endl;
+      }
+
+    std::cout << "";
+    std::cout << baseName.str();
+    std::cout << "" << std::endl;
+
+    ::std::ostringstream testName;
+    testName << testImageFilename << ".test.png";
+    try
+      {
+      rescale->SetInput( testReader->GetOutput() );
+      rescale->Update();
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during rescale of " << testName.str()
+                << std::endl;
+      }
+    try
+      {
+      writer->SetFileName( testName.str().c_str() );
+      writer->Update();
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during write of " << testName.str() << std::endl;
+      }
+
+    std::cout << "";
+    std::cout << testName.str();
+    std::cout << "" << std::endl;
+    }
+  return ( status != 0 ) ? 1 : 0;
+}
+
diff --git a/BRAINSCommonLib/Test_FindCenterOfBrainFilter/TestFCOB.tcl b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/TestFCOB.tcl
new file mode 100644
index 00000000..1df5c4ed
--- /dev/null
+++ b/BRAINSCommonLib/Test_FindCenterOfBrainFilter/TestFCOB.tcl
@@ -0,0 +1,91 @@
+#!/bin/sh
+#exec tclsh "$0" "$@"
+puts "# of arguments $argc ; commandline = $argv"
+if { $argc != 4 } {
+    puts "TestFCOB.tcl progdir baselinedatadir outputdatadir imagefile"
+    exit 1
+}
+
+proc compare { a b } {
+    set diff [ expr { abs( [ expr { $a - $b } ] ) } ]
+    if { $diff > 0.0001 } {
+        return 0
+    } else {
+        return 1
+    }
+    
+}
+
+# test program for FindCenterOfBrain
+set progdir [lindex $argv 0]
+set baselinedata [lindex $argv 1]
+set outputdata [lindex $argv 2]
+set imagefile [lindex $argv 3]
+
+set command "$progdir/FindCenterOfBrain --inputVolume $imagefile"
+set command "$command --generateDebugImages"
+set command "$command --debugTrimmedImage $outputdata/trimmed.nii.gz"
+set command "$command --debugClippedImageMask $outputdata/clipped.nii.gz"
+set command "$command --debugAfterGridComputationsForegroundImage $outputdata/aftergridcomp.nii.gz"
+set command "$command --debugGridImage $outputdata/grid.nii.gz"
+set command "$command --debugDistanceImage $outputdata/distance.nii.gz"
+
+puts "running $command"
+
+set fcob [open "| $command " ]
+
+while { [gets $fcob line] >= 0 } {
+    puts "Line = $line"
+    if { [ string match "*Center Of Brain*" $line ] } {
+        puts "CENTER OF BRAIN SEEN Line = $line"
+        set start [ string first : $line  ]
+        set start [ expr $start + 2 ]
+        set center [ string range $line $start end ]
+        puts "CENTER OF BRAIN : $center"
+        set listlength [ llength $center ]
+        puts "LENGTH: $listlength"
+        set x [lindex $center 0 ]
+        puts "x = $x"
+        set y [lindex $center 1 ]
+        puts "y = $y"
+        set z [lindex $center 2 ]
+        puts "z = $z"
+        if { [ compare $x 97.7757 ] && [ compare $y -89.2801 ] && [ compare $z -98.4934 ] } {
+            puts "consistent computation of center of brain"
+            break
+        } else {
+            exit 1
+        }
+    }
+}
+
+# test intermediate files
+set names [ list trimmed grid clipped aftergridcomp ]
+for { set i 0 } { $i < [llength $names] } { incr i } {
+
+    set current [ lindex $names $i ]
+
+    set compare_result \
+        [ catch { exec ImageCompare $baselinedata/FCOB-$current.nii.gz \
+                      $outputdata/$current.nii.gz } result ]
+    puts $result
+    if { $compare_result != 0 } {
+        puts  "$baselinedata/FCOB-$current.nii.gz and $outputdata/$current.nii.gz differ"
+        exit $compare_result
+    } else {
+        puts "$baselinedata/FCOB-$current.nii.gz and $outputdata/$current.nii.gz match"
+    }
+    
+}
+exit 0
+
+# set compare_result \
+# [ catch { exec ImageCompare $baselinedata/FCOB-trimmed.nii.gz \
+#               $outputdata/trimmed.nii.gz } result ]
+# puts $result
+# if { $compare_result != 0 } {
+#     puts 
+#     exit $compare_result
+# } else {
+#     puts "$baselinedata/FCOB-trimmed.nii.gz and $outputdata/trimmed.nii.gz differ match"
+# }
diff --git a/BRAINSCommonLib/ThirionRegistration.h b/BRAINSCommonLib/ThirionRegistration.h
new file mode 100644
index 00000000..6f978b53
--- /dev/null
+++ b/BRAINSCommonLib/ThirionRegistration.h
@@ -0,0 +1,276 @@
+#ifndef __ThirionRegistration_h
+#define __ThirionRegistration_h
+
+#include 
+#include "DemonsPreprocessor.h"
+#include "DemonsRegistrator.h"
+#include "ValidationInputParser.h"
+#include "ApplicationBase.h"
+#include "itkCheckerBoardImageFilter.h"
+namespace itk
+{
+/*This file defines Thirion registration class which initializes the input
+  * parser, preprocessor and the registrator. */
+
+template 
+class ThirionRegistration : public ApplicationBase<
+    ValidationInputParser,
+    DemonsPreprocessor,
+    DemonsRegistrator
+    >
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef ThirionRegistration Self;
+  typedef ApplicationBase,
+                          DemonsPreprocessor,
+                          DemonsRegistrator >
+  Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Deformation field pixel type. */
+  typedef float                     FieldValueType;
+  typedef Vector FieldPixelType;
+  typedef Image  TDeformationField;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ThirionRegistration, ApplicationBase);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Image types. */
+  typedef TImage     ImageType;
+  typedef TRealImage RealImageType;
+
+  /** Image dimension. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TImage::ImageDimension);
+
+  /** Type to hold the number of checker boxes per dimension */
+  typedef FixedArray::ImageDimension> PatternArrayType;
+
+  typedef typename ImageType::PixelType PixelType;
+  typedef typename ImageType::IndexType IndexType;
+  typedef typename ImageType::SizeType  SizeType;
+
+  /** ShrinkFactors type. */
+  typedef FixedArray::ImageDimension> ShrinkFactorsType;
+
+  /** IterationArray type. */
+  typedef Array IterationsArrayType;
+
+  /** Set the atlas patient ID. */
+  itkSetStringMacro(TheMovingImageFilename);
+  itkGetStringMacro(TheMovingImageFilename);
+
+  /** Set the subject patient ID. */
+  itkSetStringMacro(TheFixedImageFilename);
+  itkGetStringMacro(TheFixedImageFilename);
+
+  /** Set the initial Displacement Field one of 3 ways. */
+  itkSetStringMacro(InitialDeformationFieldFilename);
+  itkGetStringMacro(InitialDeformationFieldFilename);
+
+  itkSetStringMacro(InitialCoefficientFilename);
+  itkGetStringMacro(InitialCoefficientFilename);
+
+  itkSetStringMacro(InitialTransformFilename);
+  itkGetStringMacro(InitialTransformFilename);
+
+  /** Set Displacementname */
+  itkSetStringMacro(DisplacementBaseName);
+  itkGetStringMacro(DisplacementBaseName);
+  /** Set WarpedImageName */
+  itkSetStringMacro(WarpedImageName);
+  itkGetStringMacro(WarpedImageName);
+
+  /** Set input parameter file */
+  // itkSetStringMacro (ParameterFilename);
+
+  /** Set output transformation filename. */
+  itkSetStringMacro(OutputFilename);
+
+  /** Set checker board Image filename */
+  itkSetStringMacro(CheckerBoardFilename);
+  itkGetStringMacro(CheckerBoardFilename);
+
+  /** Set Deformation field output filename */
+  itkSetStringMacro(DeformationFieldOutputName);
+  itkGetStringMacro(DeformationFieldOutputName);
+
+  /** Set Checker pattern */
+  itkSetMacro(CheckerBoardPattern, PatternArrayType);
+  itkGetConstReferenceMacro(CheckerBoardPattern, PatternArrayType);
+
+  /** Set append output file boolean. */
+  itkSetMacro(AppendOutputFile, bool);
+  itkGetMacro(AppendOutputFile, bool);
+  itkBooleanMacro(AppendOutputFile);
+
+  /* BOBF macros
+    * Set Target Mask filename */
+  itkSetStringMacro(BOBFTargetMask);
+  itkGetStringMacro(BOBFTargetMask);
+
+  /** Set Template Mask filename */
+  itkSetStringMacro(BOBFTemplateMask);
+  itkGetStringMacro(BOBFTemplateMask);
+
+  /** Force Centered Image. */
+  itkSetMacro(ForceCoronalZeroOrigin, bool);
+  itkGetConstMacro(ForceCoronalZeroOrigin, bool);
+
+  /** Output Normalized Image. */
+  itkSetStringMacro(OutNormalized);
+  itkGetStringMacro(OutNormalized);
+
+  /** Set/Get the lower threshold. The default is 0. */
+  itkSetMacro(Lower, PixelType);
+  itkGetMacro(Lower, PixelType);
+
+  /** Set/Get the upper threshold. The default is 70 */
+  itkSetMacro(Upper, PixelType);
+  itkGetMacro(Upper, PixelType);
+
+  /** Set/Get value to replace thresholded pixels. Pixels that lie *
+    *  within Lower and Upper (inclusive) will be replaced with this
+    *  value. The default is 1. */
+  itkSetMacro(DefaultPixelValue, PixelType);
+  itkGetMacro(DefaultPixelValue, PixelType);
+
+  /** Set the radius of the neighborhood used for a mask. */
+  itkSetMacro(Radius, SizeType);
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Radius, SizeType);
+
+  /** Set the Seed of the neighborhood used for a mask. */
+  itkSetMacro(Seed, IndexType);
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Seed, IndexType);
+
+  itkSetMacro(MedianFilterSize,  SizeType);
+  itkGetMacro(MedianFilterSize,  SizeType);
+
+  /** Set the initial deformation field to prime registration */
+  //    itkSetObjectMacro(InitialDeformationField,TDeformationField);
+  /** Set the Input Landmark Filename*/
+  itkSetStringMacro(FixedLandmarkFilename);
+  itkGetStringMacro(FixedLandmarkFilename);
+  itkSetStringMacro(MovingLandmarkFilename);
+  itkGetStringMacro(MovingLandmarkFilename);
+
+  /** Set histogram matching*/
+  itkSetMacro(UseHistogramMatching, bool);
+  itkGetConstMacro(UseHistogramMatching, bool);
+
+  /** Get the number of histogram bins. */
+  itkGetConstMacro(NumberOfHistogramLevels, unsigned long);
+  itkSetMacro(NumberOfHistogramLevels, unsigned long);
+
+  /** Get the number of match points. */
+  itkGetConstMacro(NumberOfMatchPoints, unsigned long);
+  itkSetMacro(NumberOfMatchPoints, unsigned long);
+
+  /** Get the number of levels. */
+  itkGetMacro(NumberOfLevels, unsigned short);
+  itkSetMacro(NumberOfLevels, unsigned short);
+
+  /** Get the atlas image starting shrink factors. */
+  itkGetConstReferenceMacro(TheMovingImageShrinkFactors, ShrinkFactorsType);
+  void SetTheMovingImageShrinkFactors(const ShrinkFactorsType & shrinkfactors)
+  {
+    this->m_TheMovingImageShrinkFactors = shrinkfactors;
+  }
+
+  /** Get the subject image starting shrink factors. */
+  itkGetConstReferenceMacro(TheFixedImageShrinkFactors, ShrinkFactorsType);
+  void SetTheFixedImageShrinkFactors(const ShrinkFactorsType & shrinkfactors)
+  {
+    this->m_TheFixedImageShrinkFactors = shrinkfactors;
+  }
+
+  /** Get the number of iterations at each level. */
+  itkGetConstReferenceMacro(NumberOfIterations, IterationsArrayType);
+  void SetNumberOfIterations(const IterationsArrayType & iterations)
+  {
+    m_NumberOfIterations = iterations;
+  }
+
+  typedef itk::PDEDeformableRegistrationFilter BaseRegistrationFilterType;
+  void SetRegistrationFilter(
+    typename BaseRegistrationFilterType::Pointer filter)
+  {
+    this->m_Registrator->SetRegistrationFilter(filter);
+  }
+
+protected:
+
+  ThirionRegistration();
+  virtual ~ThirionRegistration()
+  {
+  }
+
+  /** Initialize the input parser. */
+  virtual void InitializeParser();
+
+  /** Initialize the preprocessor */
+  virtual void InitializePreprocessor();
+
+  /** Initialize the registrator  */
+  virtual void InitializeRegistrator();
+
+private:
+
+  std::string m_TheMovingImageFilename;
+  std::string m_TheFixedImageFilename;
+  std::string m_InitialDeformationFieldFilename;
+  std::string m_InitialCoefficientFilename;
+  std::string m_InitialTransformFilename;
+  std::string m_DisplacementBaseName;
+  std::string m_WarpedImageName;
+
+  // std::string m_ParameterFilename;
+  bool m_ForceCoronalZeroOrigin;
+  bool m_UseHistogramMatching;
+
+  std::string m_OutNormalized;
+  //    std::string m_OutDebug;
+  std::string      m_OutputFilename;
+  std::string      m_CheckerBoardFilename;
+  std::string      m_DeformationFieldOutputName;
+  bool             m_AppendOutputFile;
+  PatternArrayType m_CheckerBoardPattern;
+  std::string      m_BOBFTargetMask;
+  std::string      m_BOBFTemplateMask;
+  IndexType        m_Seed;
+  PixelType        m_Lower;
+  PixelType        m_Upper;
+  PixelType        m_DefaultPixelValue;
+  SizeType         m_Radius; // for BOBF filter.
+  SizeType         m_MedianFilterSize;
+  std::string      m_FixedLandmarkFilename;
+  std::string      m_MovingLandmarkFilename;
+  // typename TDeformationField::Pointer m_InitialDeformationField;
+  unsigned long       m_NumberOfHistogramLevels;
+  unsigned long       m_NumberOfMatchPoints;
+  unsigned short      m_NumberOfLevels;
+  ShrinkFactorsType   m_TheMovingImageShrinkFactors;
+  ShrinkFactorsType   m_TheFixedImageShrinkFactors;
+  IterationsArrayType m_NumberOfIterations;
+};
+}          // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "ThirionRegistration.hxx"
+#endif
+#endif
diff --git a/BRAINSCommonLib/ThirionRegistration.hxx b/BRAINSCommonLib/ThirionRegistration.hxx
new file mode 100644
index 00000000..ecc08fa4
--- /dev/null
+++ b/BRAINSCommonLib/ThirionRegistration.hxx
@@ -0,0 +1,160 @@
+#ifndef __ThirionRegistration_hxx
+#define __ThirionRegistration_hxx
+
+#include "ThirionRegistration.h"
+
+namespace itk
+{
+template 
+ThirionRegistration
+::ThirionRegistration()
+{
+  m_TheMovingImageFilename = "";
+  m_TheFixedImageFilename = "";
+
+  // m_ParameterFilename = "";
+  m_OutputFilename = "";
+  m_AppendOutputFile = true;
+  m_WarpedImageName = "none";
+  m_CheckerBoardFilename = "none";
+  m_DeformationFieldOutputName = "none";
+  m_DisplacementBaseName = "none";
+  m_CheckerBoardPattern.Fill(4);
+  m_Lower = NumericTraits::NonpositiveMin();
+  m_Upper = NumericTraits::max();
+  m_DefaultPixelValue = NumericTraits::Zero;
+  m_Radius.Fill(1);
+  m_BOBFTargetMask = "none";
+  m_BOBFTemplateMask = "none";
+  m_ForceCoronalZeroOrigin = false;
+  m_OutNormalized = "OFF";
+  m_UseHistogramMatching = false;
+  //    m_OutDebug = false;
+  m_NumberOfHistogramLevels = 256;
+  m_NumberOfMatchPoints = 2;
+  m_NumberOfLevels = 4;   // if that fixes it, I'm going to do something else
+  m_NumberOfIterations = IterationsArrayType(m_NumberOfLevels);
+  m_NumberOfIterations[0] = 2000;
+  m_NumberOfIterations[1] = 500;
+  m_NumberOfIterations[2] = 250;
+  m_NumberOfIterations[3] = 100;
+  for( unsigned i = 0; i < ImageType::ImageDimension; ++i )
+    {
+    m_TheMovingImageShrinkFactors[i] = 4;   // 16;
+    m_TheFixedImageShrinkFactors[i] = 4;    // 16;
+    m_Seed[i] = 0;
+    m_MedianFilterSize[i] = 0;
+    }
+}
+
+/*This method initializes the input parser which reads in the moving image,
+  * fixed image and parameter file.*/
+
+template 
+void
+ThirionRegistration
+::InitializeParser()
+{
+  this->m_Parser->SetTheMovingImageFilename(
+    this->m_TheMovingImageFilename.c_str() );
+
+  this->m_Parser->SetTheFixedImageFilename( this->m_TheFixedImageFilename.c_str() );
+  this->m_Parser->SetForceCoronalZeroOrigin( this->GetForceCoronalZeroOrigin() );
+
+  this->m_Parser->SetInitialDeformationFieldFilename(
+    this->m_InitialDeformationFieldFilename.c_str() );
+  this->m_Parser->SetInitialCoefficientFilename(
+    this->m_InitialCoefficientFilename.c_str() );
+  this->m_Parser->SetInitialTransformFilename(
+    this->m_InitialTransformFilename.c_str() );
+  //            this->m_Parser->SetParameterFilename(
+  // this->m_ParameterFilename.c_str() );
+  this->m_Parser->SetNumberOfHistogramLevels( this->GetNumberOfHistogramLevels() );
+  this->m_Parser->SetNumberOfMatchPoints( this->GetNumberOfMatchPoints() );
+  this->m_Parser->SetNumberOfLevels( this->GetNumberOfLevels() );
+  this->m_Parser->SetTheMovingImageShrinkFactors(
+    this->GetTheMovingImageShrinkFactors() );
+  this->m_Parser->SetTheFixedImageShrinkFactors(
+    this->GetTheFixedImageShrinkFactors() );
+  this->m_Parser->SetNumberOfIterations( this->GetNumberOfIterations() );
+  this->m_Parser->SetOutDebug( this->GetOutDebug() );
+}
+
+/*This method initializes the preprocessor which processes the moving and fixed
+  * images before registration. The image files which are read in using the
+  *    parser are given to the preprocessor.*/
+
+template 
+void
+ThirionRegistration
+::InitializePreprocessor()
+{
+  this->m_Preprocessor->SetInputFixedImage( this->m_Parser->GetTheFixedImage() );
+  this->m_Preprocessor->SetInputMovingImage( this->m_Parser->GetTheMovingImage() );
+  this->m_Preprocessor->SetInitialDeformationField(
+    this->m_Parser->GetInitialDeformationField() );
+  this->m_Preprocessor->SetUseHistogramMatching( this->GetUseHistogramMatching() );
+  this->m_Preprocessor->SetNumberOfHistogramLevels(
+    this->m_Parser->GetNumberOfHistogramLevels() );
+  this->m_Preprocessor->SetNumberOfMatchPoints(
+    this->m_Parser->GetNumberOfMatchPoints() );
+  this->m_Preprocessor->SetBOBFTargetMask( this->GetBOBFTargetMask() );
+  this->m_Preprocessor->SetBOBFTemplateMask( this->GetBOBFTemplateMask() );
+  this->m_Preprocessor->SetLower( this->GetLower() );
+  this->m_Preprocessor->SetUpper( this->GetUpper() );
+  this->m_Preprocessor->SetRadius( this->GetRadius() );
+  this->m_Preprocessor->SetDefaultPixelValue( this->GetDefaultPixelValue() );
+  this->m_Preprocessor->SetSeed( this->GetSeed() );
+  this->m_Preprocessor->SetOutDebug( this->GetOutDebug() );
+  this->m_Preprocessor->SetMedianFilterSize( this->GetMedianFilterSize() );
+  this->m_Preprocessor->SetInitialDeformationField(
+    this->m_Parser->GetInitialDeformationField() );
+}
+
+/*This method initializes the registration process. The preprocessed output
+  * files are passed to the registrator.*/
+
+template 
+void
+ThirionRegistration
+::InitializeRegistrator()
+{
+  this->m_Registrator->SetDisplacementBaseName( this->GetDisplacementBaseName() );
+  this->m_Registrator->SetWarpedImageName( this->GetWarpedImageName() );
+  this->m_Registrator->SetCheckerBoardFilename( this->GetCheckerBoardFilename() );
+  this->m_Registrator->SetDeformationFieldOutputName(
+    this->GetDeformationFieldOutputName() );
+  this->m_Registrator->SetCheckerBoardPattern( this->GetCheckerBoardPattern() );
+  this->m_Registrator->SetFixedImage( this->m_Preprocessor->GetOutputFixedImage() );
+  this->m_Registrator->SetMovingImage(
+    this->m_Preprocessor->GetOutputMovingImage() );
+  this->m_Registrator->SetUnNormalizedMovingImage(
+    this->m_Preprocessor->GetUnNormalizedMovingImage() );
+  this->m_Registrator->SetUnNormalizedFixedImage(
+    this->m_Preprocessor->GetUnNormalizedFixedImage() );
+  this->m_Registrator->SetInitialDeformationField(
+    this->m_Parser->GetInitialDeformationField() );
+  this->m_Registrator->SetDefaultPixelValue(
+    this->m_Preprocessor->GetDefaultPixelValue() );
+  this->m_Registrator->SetUseHistogramMatching( this->GetUseHistogramMatching() );
+  this->m_Registrator->SetNumberOfLevels( this->m_Parser->GetNumberOfLevels() );
+  this->m_Registrator->SetNumberOfIterations(
+    this->m_Parser->GetNumberOfIterations() );
+  this->m_Registrator->SetInterpolationMode( this->GetInterpolationMode() );
+
+  this->m_Registrator->SetFixedImageShrinkFactors(
+    this->m_Parser->GetTheFixedImageShrinkFactors() );
+  this->m_Registrator->SetMovingImageShrinkFactors(
+    this->m_Parser->GetTheMovingImageShrinkFactors() );
+
+  this->m_Registrator->SetOutNormalized( this->GetOutNormalized() );
+  this->m_Registrator->SetOutDebug( this->GetOutDebug() );
+  this->m_Registrator->SetDeformationFieldOutputName(
+    this->m_DeformationFieldOutputName);
+  this->m_Registrator->SetFixedLandmarkFilename(this->m_FixedLandmarkFilename);
+  this->m_Registrator->SetMovingLandmarkFilename(this->m_MovingLandmarkFilename);
+}
+
+}   // namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/TransformAdaptor.h b/BRAINSCommonLib/TransformAdaptor.h
new file mode 100644
index 00000000..e5c44d90
--- /dev/null
+++ b/BRAINSCommonLib/TransformAdaptor.h
@@ -0,0 +1,161 @@
+#ifndef __TransformAdaptor_h
+#define __TransformAdaptor_h
+
+#include "CrossOverAffineSystem.h"
+
+namespace itk
+{
+/** \class TransformAdaptor
+  *
+  * This component converts transform formats required for
+  * input and output for use in registration.
+  *
+  * The preprocessing is activatived by method ExecuteInput().
+  *
+  * The postprocessing is activatived by method ExecuteOutput().
+  *
+  * Inputs:
+  *    - pointer to original fixed image
+  *    - pointer original moving image
+  *
+  * Outputs:
+  *    - pointer to transform representing the pre-transform
+  *    - pointer to transform representing the post-transform
+  *
+  * After registration, the overall transform is obtained by
+  * composing pre-transform, the registration transform and
+  * the post-transform.
+  *
+  */
+template 
+class ITK_EXPORT TransformAdaptor : public LightProcessObject
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef TransformAdaptor         Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(TransformAdaptor, Object);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Input Image Type. */
+  typedef TInputImage                       InputImageType;
+  typedef typename InputImageType::Pointer  InputImagePointer;
+  typedef typename InputImageType::SizeType InputImageSizeType;
+
+  /** Image dimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int, TInputImage::ImageDimension);
+
+  /** Type of the scalar representing coordinate and vector elements. */
+  typedef  TCoordinateType
+  ScalarType;
+
+  typedef vnl_matrix_fixed VnlTransformMatrixType44;
+
+  /** Affine transform type. */
+  typedef AffineTransform AffineTransformType;
+  typedef typename AffineTransformType::Pointer
+  AffineTransformPointer;
+  typedef typename AffineTransformType::MatrixType
+  MatrixType;
+  typedef typename AffineTransformType::InputPointType
+  PointType;
+  typedef typename AffineTransformType::OutputVectorType
+  VectorType;
+  typedef typename VectorType::ValueType
+  ValueType;
+
+  /** CrossOverAffineSystem type. */
+  typedef CrossOverAffineSystem CrossOverAffineSystemType;
+  typedef typename CrossOverAffineSystemType::Pointer
+  CrossOverAffineSystemPointer;
+
+  /** Set the input fixed image. */
+  iplSetMacro(FixedImage, InputImagePointer);
+  iplGetMacro(FixedImage, InputImagePointer);
+
+  /** Set the input moving image. */
+  iplSetMacro(MovingImage, InputImagePointer);
+  iplGetMacro(MovingImage, InputImagePointer);
+
+  /** Methods to execute the transform processing. */
+  void ExecuteInput();
+
+  void ExecuteOutput();
+
+  /** Methods to define and perform Air16 AffineTransform conversion. */
+  void EstablishCrossOverSystemForAir16(void);
+
+  void EstablishCrossOverSystemForB2xfrm(void);
+
+  void ConvertInputAffineToITKAffine(void);
+
+  void ConvertITKAffineToOutputAffine(void);
+
+  iplSetMacro(CenterMovingAffineTransform, AffineTransformPointer);
+  iplGetMacro(CenterMovingAffineTransform, AffineTransformPointer);
+  iplSetMacro(DeCenterMovingAffineTransform, AffineTransformPointer);
+  iplGetMacro(DeCenterMovingAffineTransform, AffineTransformPointer);
+  iplSetMacro(CenterFixedAffineTransform, AffineTransformPointer);
+  iplGetMacro(CenterFixedAffineTransform, AffineTransformPointer);
+  iplSetMacro(DeCenterFixedAffineTransform, AffineTransformPointer);
+  iplGetMacro(DeCenterFixedAffineTransform, AffineTransformPointer);
+
+  iplGetMacro(InputAffineTransformFilename, std::string);
+  iplSetMacro(InputAffineTransformFilename, std::string);
+  iplGetMacro(OutputAffineTransformFilename, std::string);
+  iplSetMacro(OutputAffineTransformFilename, std::string);
+
+  iplSetMacro(InputAffineTransform, AffineTransformPointer);
+  iplGetMacro(InputAffineTransform, AffineTransformPointer);
+  iplSetMacro(ITKAffineTransform, AffineTransformPointer);
+  iplGetMacro(ITKAffineTransform, AffineTransformPointer);
+  iplSetMacro(OutputAffineTransform, AffineTransformPointer);
+  iplGetMacro(OutputAffineTransform, AffineTransformPointer);
+
+  iplSetMacro(CrossOverAffineSystem, CrossOverAffineSystemPointer);
+  iplGetMacro(CrossOverAffineSystem, CrossOverAffineSystemPointer);
+protected:
+  TransformAdaptor();
+  ~TransformAdaptor()
+  {
+  }
+private:
+  TransformAdaptor(const Self &);               // purposely not implemented
+  void operator=(const Self &);                 // purposely not implemented
+
+  InputImagePointer m_FixedImage;
+  InputImagePointer m_MovingImage;
+
+  AffineTransformPointer m_CenterFixedAffineTransform;
+  AffineTransformPointer m_CenterMovingAffineTransform;
+
+  AffineTransformPointer m_DeCenterFixedAffineTransform;
+  AffineTransformPointer m_DeCenterMovingAffineTransform;
+
+  std::string m_InputAffineTransformFilename;
+  std::string m_OutputAffineTransformFilename;
+
+  AffineTransformPointer m_ITKAffineTransform;
+  AffineTransformPointer m_InputAffineTransform;
+  AffineTransformPointer m_OutputAffineTransform;
+
+  CrossOverAffineSystemPointer m_CrossOverAffineSystem;
+};
+}   // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "TransformAdaptor.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/TransformAdaptor.hxx b/BRAINSCommonLib/TransformAdaptor.hxx
new file mode 100644
index 00000000..b1b69d63
--- /dev/null
+++ b/BRAINSCommonLib/TransformAdaptor.hxx
@@ -0,0 +1,373 @@
+#ifndef __TransformAdaptor_hxx
+#define __TransformAdaptor_hxx
+
+#include "TransformAdaptor.h"
+
+namespace itk
+{
+template 
+TransformAdaptor
+::TransformAdaptor()
+{
+  m_FixedImage   = NULL;
+  m_MovingImage  = NULL;
+
+  m_CenterMovingAffineTransform = AffineTransformType::New();
+  m_CenterFixedAffineTransform = AffineTransformType::New();
+
+  m_DeCenterMovingAffineTransform = AffineTransformType::New();
+  m_DeCenterFixedAffineTransform = AffineTransformType::New();
+
+  m_InputAffineTransform = AffineTransformType::New();
+  m_ITKAffineTransform = AffineTransformType::New();
+  m_OutputAffineTransform = AffineTransformType::New();
+}
+
+template 
+void
+TransformAdaptor
+::ExecuteInput()
+{
+  if( GetInputAffineTransformFilename().size() != 0 )
+    {
+    std::cout << "Initial Transform :" << GetInputAffineTransformFilename()
+              << std::endl;
+    // Only read if InputAffineTransformFilename was set.
+
+    if( GetInputAffineTransformFilename().find(".air16") != std::string::npos )
+      {
+      SetInputAffineTransform(
+        ReadAir16File( GetInputAffineTransformFilename().c_str() ) );
+      EstablishCrossOverSystemForAir16();
+      ConvertInputAffineToITKAffine();
+      }
+    else if( GetInputAffineTransformFilename().find(".xfrm") !=
+             std::string::npos )
+      {
+      SetInputAffineTransform(
+        ReadB2AffineFile( GetInputAffineTransformFilename().c_str() ) );
+      EstablishCrossOverSystemForB2xfrm();
+      ConvertInputAffineToITKAffine();
+      }
+    else
+      {
+      itkExceptionMacro( << "Unsupported transform file type, "
+                         << GetInputAffineTransformFilename() );
+      }
+    }
+  else   // No InputAffineTransformFilename given by user:
+    {
+    std::cout << "Initial Transform Not Provided." << std::endl;
+    // Compose the preprocess and initialization transforms
+    // Get into centered space.
+    // This must agree with decoding the 'overall transform', below.
+
+    GetITKAffineTransform()->SetIdentity();
+    // const bool ApplyUpstream = false;
+    // GetITKAffineTransform()->Compose( GetDeCenterFixedAffineTransform(),
+    //                                   ApplyUpstream );
+    // GetITKAffineTransform()->Compose( GetCenterMovingAffineTransform(),
+    //                                   ApplyUpstream );
+    }
+}
+
+template 
+void
+TransformAdaptor
+::ExecuteOutput()
+{
+  /***************************
+    * Compute overall transform in the output side of the transform adaptor
+    */
+
+  std::cout << "Overall transform matrix: " << std::endl;
+  std::cout << GetITKAffineTransform()->GetMatrix() << std::endl;
+  std::cout << "Overall transform offset: " << std::endl;
+  std::cout << GetITKAffineTransform()->GetOffset() << std::endl;
+
+  if( GetOutputAffineTransformFilename().size() != 0 )
+    {
+    // Only write if OutputAffineTransformFilename was set.
+
+    if( GetOutputAffineTransformFilename().find(".air16") != std::string::npos )
+      {
+      EstablishCrossOverSystemForAir16();
+      ConvertITKAffineToOutputAffine();
+      }
+    else if( GetOutputAffineTransformFilename().find(".xfrm") !=
+             std::string::npos )
+      {
+      EstablishCrossOverSystemForB2xfrm();
+      ConvertITKAffineToOutputAffine();
+      }
+    else
+      {
+      itkExceptionMacro( << "Unsupported transform file type, "
+                         << GetInputAffineTransformFilename() );
+      }
+    }
+}
+
+template 
+void
+TransformAdaptor
+::EstablishCrossOverSystemForAir16(void)
+{
+  /*
+    *  IMPORTANT:  In the new design, conversion is accomplished by enclosing
+    *the
+    *              alien transform in an encoding-decoding pair of
+    *AffineTransforms.
+    *
+    *  All the paired EncloseIn operators are expressed in their Inhale sense.
+    */
+
+  m_CrossOverAffineSystem = CrossOverAffineSystemType::New();   // established
+                                                                // the 4
+                                                                // identity
+                                                                // Affines.
+
+    { /*  This is code for flipping axes, specific to Air16 files.
+        */
+    VectorType Flip(1.0);
+
+    const int flipIndex = 1;  // A Flip in Y gets the rotation components of
+    // Air16 evidently right.
+    Flip[flipIndex] = -1.0;
+
+    GetCrossOverAffineSystem()->EncloseInScaling(Flip, Flip);
+    }
+
+  if( false )   // Turning this off ...
+    {
+    /*  address voxel floor corners on the outside, address voxel centers on the
+      * inside.
+      */
+    VectorType const MovingImageSpacing( GetMovingImage()->GetSpacing() );
+
+    VectorType const FixedImageSpacing( GetFixedImage()->GetSpacing() );
+
+    ValueType const down(-0.5);
+
+    VectorType const HalfFixedVoxelDown( FixedImageSpacing.operator *(down) );
+
+    ValueType const up(0.5);
+
+    VectorType const HalfMovingVoxelUp( MovingImageSpacing.operator*(up) );
+
+    GetCrossOverAffineSystem()->EncloseInTranslation(HalfMovingVoxelUp,
+                                                     HalfFixedVoxelDown);
+    }
+
+    { /*  addressing voxels on the outside, addressing millimeters on the
+        * inside.
+        */
+    VectorType const FixedImageScaleReciprocal(
+      Reciprocal( GetFixedImage()->GetSpacing() ) );
+
+    VectorType const MovingImageScale( GetMovingImage()->GetSpacing() );
+
+    GetCrossOverAffineSystem()->EncloseInScaling(FixedImageScaleReciprocal,
+                                                 MovingImageScale);
+    }
+
+  if( false )   // Turning this alternative off ...
+    {
+    /*  uncentered on the outside (like the b2 standard, RIP), centered on the
+      * inside.
+      */
+    VectorType const MovingImageCenter(
+      GetCenterMovingAffineTransform()->GetOffset() );
+
+    VectorType const FixedImageCenter(
+      GetCenterFixedAffineTransform()->GetOffset() );
+
+    GetCrossOverAffineSystem()->EncloseInTranslation(FixedImageCenter,
+                                                     -MovingImageCenter);
+    }
+  if( false )   // Turning this off made the output image pass through
+                // correctly;
+    {
+    VectorType const MovingImageCenter(
+      GetCenterMovingAffineTransform()->GetOffset() );
+
+    VectorType const FixedImageCenter(
+      GetCenterFixedAffineTransform()->GetOffset() );
+
+    /*  uncentered on the outside (like the b2 standard, RIP), centered on the
+      * inside.
+      */
+    //  GetCrossOverAffineSystem()->EncloseInTranslation(FixedImageCenter,
+    // -MovingImageCenter);
+
+    PointType MovingCenter;
+    PointType FixedCenter;
+    for( unsigned int i = 0; i < NDimensions; ++i )
+      {
+      MovingCenter[i] = MovingImageCenter[i];
+      FixedCenter[i] = FixedImageCenter[i];
+      }
+
+    GetCrossOverAffineSystem()->EncloseInCentering(FixedCenter, MovingCenter);
+    }
+}
+
+template 
+void
+TransformAdaptor
+::EstablishCrossOverSystemForB2xfrm(void)
+{
+  /*
+    *  IMPORTANT:  In the new design, conversion is accomplished by enclosing
+    *the
+    *              alien transform in an encoding-decoding pair of
+    *AffineTransforms.
+    *
+    *  All the paired EncloseIn operators are expressed in their Inhale sense.
+    */
+
+  m_CrossOverAffineSystem = CrossOverAffineSystemType::New();   // established
+                                                                // the 4
+                                                                // identity
+                                                                // Affines.
+
+  if( false )   // Turning this off ...
+    {
+    /*  address voxel floor corners on the outside, address voxel centers on the
+      * inside.
+      */
+    VectorType const MovingImageSpacing( GetMovingImage()->GetSpacing() );
+
+    VectorType const FixedImageSpacing( GetFixedImage()->GetSpacing() );
+
+    ValueType const down(-0.5);
+
+    VectorType const HalfFixedVoxelDown( FixedImageSpacing.operator *(down) );
+
+    ValueType const up(0.5);
+
+    VectorType const HalfMovingVoxelUp( MovingImageSpacing.operator*(up) );
+
+    GetCrossOverAffineSystem()->EncloseInTranslation(HalfMovingVoxelUp,
+                                                     HalfFixedVoxelDown);
+    }
+
+    { /*  addressing voxels on the outside, addressing millimeters on the
+        * inside.
+        */
+    VectorType const FixedImageScaleReciprocal(
+      Reciprocal( GetFixedImage()->GetSpacing() ) );
+
+    VectorType const MovingImageScale( GetMovingImage()->GetSpacing() );
+
+    GetCrossOverAffineSystem()->EncloseInScaling(FixedImageScaleReciprocal,
+                                                 MovingImageScale);
+    }
+
+  if( false )   // Turning this off made the output image pass through
+                // correctly;
+    {
+    VectorType const MovingImageCenter(
+      GetCenterMovingAffineTransform()->GetOffset() );
+
+    VectorType const FixedImageCenter(
+      GetCenterFixedAffineTransform()->GetOffset() );
+
+    /*  uncentered on the outside (like the b2 standard, RIP), centered on the
+      * inside.
+      */
+    //  GetCrossOverAffineSystem()->EncloseInTranslation(FixedImageCenter,
+    // -MovingImageCenter);
+
+    PointType MovingCenter;
+    PointType FixedCenter;
+    for( unsigned int i = 0; i < NDimensions; ++i )
+      {
+      MovingCenter[i] = MovingImageCenter[i];
+      FixedCenter[i] = FixedImageCenter[i];
+      }
+
+    GetCrossOverAffineSystem()->EncloseInCentering(FixedCenter, MovingCenter);
+    }
+}
+
+/*
+  *  So much for conversion transform initialization.
+  *  The affine convention converters below are general to
+  *  any affine representation.  Just initialize the conversion
+  *  logic with the appropriate EstablishCrossOverSystem call.
+  *
+  *  TODO:  Add other conventions besides b2/xfrm, Air16:  matlab/spm, nifti.
+  */
+
+template 
+void
+TransformAdaptor
+::ConvertInputAffineToITKAffine(void)
+{
+#ifndef NDEBUG
+  std::cout << "Inhaling Shift: " << GetInputAffineTransform()->GetOffset()
+            << std::endl;
+#endif
+
+  GetITKAffineTransform()->SetIdentity();
+  const bool ApplyUpstream = false;
+
+  GetITKAffineTransform()->Compose(
+    GetCrossOverAffineSystem()->GetInhaleEncodeConversion(),
+    ApplyUpstream);
+  GetITKAffineTransform()->Compose(GetInputAffineTransform(),
+                                   ApplyUpstream);
+  GetITKAffineTransform()->Compose(
+    GetCrossOverAffineSystem()->GetInhaleDecodeConversion(),
+    ApplyUpstream);
+#ifndef NDEBUG
+  std::cout << std::endl
+            << " <]-- Inhaled Shift: "
+            << GetITKAffineTransform()->GetOffset() << std::endl;
+  std::cout << " <]-- Inhaled Rotation: " << std::endl
+            << GetITKAffineTransform()->GetMatrix() << std::endl;
+#endif
+}
+
+template 
+void
+TransformAdaptor
+::ConvertITKAffineToOutputAffine(void)
+{
+  GetOutputAffineTransform()->SetIdentity();
+  const bool ApplyUpstream = false;
+
+#ifndef NDEBUG
+  std::cout << "Exhaling Shift: " << GetITKAffineTransform()->GetOffset()
+            << std::endl;
+#endif
+
+  GetOutputAffineTransform()->Compose(
+    GetCrossOverAffineSystem()->GetExhaleEncodeConversion(),
+    ApplyUpstream);
+  GetOutputAffineTransform()->Compose(GetITKAffineTransform(),
+                                      ApplyUpstream);
+  GetOutputAffineTransform()->Compose(
+    GetCrossOverAffineSystem()->GetExhaleDecodeConversion(),
+    ApplyUpstream);
+
+#ifndef NDEBUG
+  std::cout << std::endl
+            << " <]-- Exhaled Shift: "
+            << GetOutputAffineTransform()->GetOffset() << std::endl;
+  std::cout << " <]-- Exhaled Rotation: " << std::endl
+            << GetOutputAffineTransform()->GetMatrix() << std::endl;
+#endif
+}
+
+}   // namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/TransformToDeformationField.h b/BRAINSCommonLib/TransformToDeformationField.h
new file mode 100644
index 00000000..c155d3bb
--- /dev/null
+++ b/BRAINSCommonLib/TransformToDeformationField.h
@@ -0,0 +1,88 @@
+#ifndef __TransformToDeformationField_h
+#define __TransformToDeformationField_h
+#include "itkIO.h"
+#include "CrossOverAffineSystem.h"
+// #include "itkImageRegionIteratorWithIndex.h"
+#include 
+
+/**
+  * Go from any subclass of Transform, to the corresponding deformation field
+  */
+template 
+DeformationFieldPointerType
+TransformToDeformationField
+  (itk::ImageBase *templateImage,
+  TransformPointerType xfrm)
+{
+#if 1
+  typedef typename DeformationFieldPointerType::ObjectType OutputType;
+  typedef typename itk::TransformToDeformationFieldSource
+  TodefType;
+  typename TodefType::Pointer todef( TodefType::New() );
+  todef->SetOutputParametersFromImage(templateImage);
+  todef->SetTransform(xfrm);
+  try
+    {
+    todef->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    throw err; // pass the buck up.
+    }
+  // copy image
+  // itk::ImageRegionIterator
+  //   from(todef->GetOutput(),todef->GetOutput()->GetLargestPossibleRegion()),
+  //   to(deformation,deformation->GetLargestPossibleRegion());
+  // for(from.GoToBegin(),to.GoToBegin();
+  //     from != from.End() && to != to.End(); ++from,++to)
+  //   {
+  //   to.Value() = from.Value();
+  //   }
+  return todef->GetOutput();
+#else
+  typedef typename TransformPointerType::ObjectType TransformType;
+  typedef typename DeformationFieldPointerType::ObjectType
+  TDeformationField;
+  typedef typename TDeformationField::PixelType
+  DeformationPixelType;
+
+  typedef itk::ImageRegionIteratorWithIndex IteratorType;
+  IteratorType it( deformation, deformation->GetBufferedRegion() );
+  it.GoToBegin();
+  while( !it.IsAtEnd() )
+    {
+    typename TDeformationField::IndexType CurrentIndex = it.GetIndex();
+    typename itk::Point IndexPhysicalLocation;
+    deformation->TransformIndexToPhysicalPoint(CurrentIndex,
+                                               IndexPhysicalLocation);
+    // Need to copy because the types may not be the same.
+    typename TransformType::InputPointType TransformIndexPhysicalLocation;
+    for( unsigned int curr_dim = 0;
+         curr_dim < DeformationPixelType::Dimension;
+         curr_dim++ )
+      {
+      TransformIndexPhysicalLocation[curr_dim] =
+        IndexPhysicalLocation[curr_dim];
+      }
+
+    const typename TransformType::OutputPointType TransformedPhysicalLocation =
+      xfrm->TransformPoint(TransformIndexPhysicalLocation);
+
+    DeformationPixelType DisplacementInPhysicalSpace;
+    for( unsigned int curr_dim = 0;
+         curr_dim < DeformationPixelType::Dimension;
+         curr_dim++ )
+      {
+      DisplacementInPhysicalSpace[curr_dim] =
+        static_cast(
+          TransformedPhysicalLocation[curr_dim] - IndexPhysicalLocation[curr_dim] );
+      }
+    it.Set(DisplacementInPhysicalSpace);
+    ++it;
+    }
+
+#endif
+}
+
+#endif // TransformToDeformationField_h
diff --git a/BRAINSCommonLib/UseBRAINSCommonLib.cmake.in b/BRAINSCommonLib/UseBRAINSCommonLib.cmake.in
new file mode 100644
index 00000000..43756b57
--- /dev/null
+++ b/BRAINSCommonLib/UseBRAINSCommonLib.cmake.in
@@ -0,0 +1,18 @@
+find_package(ITK REQUIRED)
+if(ITK_FOUND)
+  include(${ITK_USE_FILE})
+else(ITK_FOUND)
+  message(FATAL_ERROR "Cannot build without ITK. Please set ITK_DIR.")
+endif(ITK_FOUND)
+set(BRAINSCommonLib_DATA_DIRS @BRAINSCommonLib_DATA_DIRS_CONFIG@)
+include_directories(${BRAINSCommonLib_INCLUDE_DIRS})
+link_directories(${BRAINSCommonLib_LIBRARY_DIRS})
+
+# The BRAINSCommonLib source tree.
+set(BRAINSCommonLib_DATA_DIRS    "@BRAINSCommonLib_DATA_DIRS_CONFIG@")
+set(BRAINSCommonLib_INCLUDE_DIRS "@BRAINSCommonLib_INCLUDE_DIRS_CONFIG@")
+set(BRAINSCommonLib_LIBRARY_DIRS "@BRAINSCommonLib_LIBRARY_DIRS_CONFIG@")
+set(BRAINSCommonLib_USE_FILE     "@BRAINSCommonLib_USE_FILE_CONFIG@")
+set(BRAINSCommonLib_BUILDSCRIPTS_DIR  "@BRAINSCommonLib_BUILDSCRIPTS_DIR_CONFIG@")
+set(ITK_DIR "@ITK_DIR_CONFIG@")
+
diff --git a/BRAINSCommonLib/ValidationInputParser.h b/BRAINSCommonLib/ValidationInputParser.h
new file mode 100644
index 00000000..48347110
--- /dev/null
+++ b/BRAINSCommonLib/ValidationInputParser.h
@@ -0,0 +1,210 @@
+#ifndef __ValidationInputParser_h
+#define __ValidationInputParser_h
+
+#include 
+#include "itkObjectFactory.h"
+#include "itkObject.h"
+#include "itkFixedArray.h"
+#include "itkArray.h"
+
+#include "itkVersorRigid3DTransform.h"
+#include "itkScaleVersor3DTransform.h"
+#include "itkScaleSkewVersor3DTransform.h"
+#include "itkAffineTransform.h"
+#include 
+
+namespace itk
+{
+// 6 Parameters
+typedef itk::VersorRigid3DTransform VersorRigid3DTransformType;
+// 9 Parameters
+typedef itk::ScaleVersor3DTransform ScaleVersor3DTransformType;
+// 15 Parameters
+typedef itk::ScaleSkewVersor3DTransform ScaleSkewVersor3DTransformType;
+// 12 Parameters
+typedef itk::AffineTransform AffineTransformType;
+/** \class ValidationInputParser
+  *
+  * This component parse an input parameter file for a simple
+  * atlas based segmentation application.
+  *
+  * This class is activated by method Execute().
+  *
+  * Inputs:
+  *  - altas image name
+  *  - subject image name
+  *  - the  parameter filename
+  *
+  *
+  * Outputs:
+  *  - pointer to the subject (fixed) image
+  *  - pointer to the atlas (moving) image
+  *  - the number of histogram levels to use
+  *  - the number of histogram match points to use
+  *  - the number of levels
+  *  - the number of iterations at each level
+  *  - the fixed image starting shrink factors
+  *  - the moving image starting shrink factors
+  *
+  */
+
+template 
+class ITK_EXPORT ValidationInputParser : public Object
+{
+public:
+
+  /** Standard class typedefs. */
+  typedef ValidationInputParser    Self;
+  typedef Object                   Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ValidationInputParser, Object);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Image Type. */
+  typedef TImage                      ImageType;
+  typedef typename ImageType::Pointer ImagePointer;
+
+  /** Image dimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int, TImage::ImageDimension);
+  itkStaticConstMacro(SplineOrder, unsigned int, 3);
+
+  /** Transform Types. */
+  typedef VersorRigid3DTransform                                  VersorRigid3DTransformType;
+  typedef ScaleSkewVersor3DTransform                              ScaleSkewVersor3DTransformType;
+  typedef AffineTransform AffineTransformType;
+
+  typedef double CoordinateRepType;
+  typedef typename itk::BSplineDeformableTransform<
+    CoordinateRepType,
+    itkGetStaticConstMacro(ImageDimension),
+    itkGetStaticConstMacro(SplineOrder)> BSplineTransformType;
+
+  /** Deformation field value type. */
+  typedef float FieldValueType;
+
+  /** Deformation field pixel type. */
+  typedef Vector FieldPixelType;
+
+  /** Deformation field type. */
+  typedef Image TDeformationField;
+
+  /** ShrinkFactors type. */
+  typedef FixedArray ShrinkFactorsType;
+
+  /** IterationArray type. */
+  typedef Array IterationsArrayType;
+
+  /** Set the atlas patient. */
+  itkSetStringMacro(TheMovingImageFilename);
+
+  /** Set the subject patient. */
+  itkSetStringMacro(TheFixedImageFilename);
+
+  /** Set the initial Displacement Field one of 3 ways. */
+  itkSetStringMacro(InitialDeformationFieldFilename);
+  itkSetStringMacro(InitialCoefficientFilename);
+  itkSetStringMacro(InitialTransformFilename);
+
+  /** Set input parameter file name. */
+  //            itkSetStringMacro( ParameterFilename );
+
+  /** Parse the input file. */
+  void Execute();
+
+  /** Get pointer to the atlas image. */
+  itkGetObjectMacro(TheMovingImage, ImageType);
+
+  /** Get pointer to the subject image. */
+  itkGetObjectMacro(TheFixedImage, ImageType);
+
+  /**force Centered Image.*/
+  itkSetMacro(ForceCoronalZeroOrigin, bool);
+  itkGetConstMacro(ForceCoronalZeroOrigin, bool);
+
+  /** Get pointer to the subject image. */
+  itkGetObjectMacro(InitialDeformationField, TDeformationField);
+
+  /** Get the number of histogram bins. */
+  itkGetConstMacro(NumberOfHistogramLevels, unsigned long);
+  itkSetMacro(NumberOfHistogramLevels, unsigned long);
+
+  /** Get the number of match points. */
+  itkGetConstMacro(NumberOfMatchPoints, unsigned long);
+  itkSetMacro(NumberOfMatchPoints, unsigned long);
+
+  /** Get the number of levels. */
+  itkGetMacro(NumberOfLevels, unsigned short);
+  itkSetMacro(NumberOfLevels, unsigned short);
+
+  /**Set Debug mode*/
+  itkSetMacro(OutDebug, bool);
+  itkGetConstMacro(OutDebug, bool);
+
+  /** Get the atlas image starting shrink factors. */
+  itkGetConstReferenceMacro(TheMovingImageShrinkFactors, ShrinkFactorsType);
+  void SetTheMovingImageShrinkFactors(const ShrinkFactorsType & shrinkfactors)
+  {
+    this->m_TheMovingImageShrinkFactors = shrinkfactors;
+  }
+
+  /** Get the subject image starting shrink factors. */
+  itkGetConstReferenceMacro(TheFixedImageShrinkFactors, ShrinkFactorsType);
+  void SetTheFixedImageShrinkFactors(const ShrinkFactorsType & shrinkfactors)
+  {
+    this->m_TheFixedImageShrinkFactors = shrinkfactors;
+  }
+
+  /** Get the number of iterations at each level. */
+  itkGetConstReferenceMacro(NumberOfIterations, IterationsArrayType);
+  void SetNumberOfIterations(const IterationsArrayType & iterations)
+  {
+    m_NumberOfIterations = iterations;
+  }
+
+protected:
+  ValidationInputParser();
+  ~ValidationInputParser()
+  {
+  }
+private:
+  ValidationInputParser(const Self &);      // purposely not implemented
+  void operator=(const Self &);             // purposely not implemented
+
+  std::string m_TheMovingImageFilename;
+  std::string m_TheFixedImageFilename;
+  std::string m_InitialDeformationFieldFilename;
+  std::string m_InitialCoefficientFilename;
+  std::string m_InitialTransformFilename;
+  std::string m_ParameterFilename;
+
+  typename ImageType::Pointer m_TheMovingImage;
+  typename ImageType::Pointer m_TheFixedImage;
+
+  bool m_ForceCoronalZeroOrigin;
+  //  bool                          m_HistogramMatching;
+  bool m_OutDebug;
+
+  typename TDeformationField::Pointer m_InitialDeformationField;
+
+  unsigned long       m_NumberOfHistogramLevels;
+  unsigned long       m_NumberOfMatchPoints;
+  unsigned short      m_NumberOfLevels;
+  ShrinkFactorsType   m_TheMovingImageShrinkFactors;
+  ShrinkFactorsType   m_TheFixedImageShrinkFactors;
+  IterationsArrayType m_NumberOfIterations;
+};
+}   // namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "ValidationInputParser.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/ValidationInputParser.hxx b/BRAINSCommonLib/ValidationInputParser.hxx
new file mode 100644
index 00000000..bee63c30
--- /dev/null
+++ b/BRAINSCommonLib/ValidationInputParser.hxx
@@ -0,0 +1,207 @@
+#ifndef __ValidationInputParser_hxx
+#define __ValidationInputParser_hxx
+
+#include "ValidationInputParser.h"
+#include "itkMetaDataObject.h"
+#include "itkNumericTraits.h"
+#include "vnl/vnl_math.h"
+#include "itkImage.h"
+#include "itkAffineTransform.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkIO.h"
+#include "itkTransformToDeformationFieldSource.h"
+#include "itkTransform.h"
+#include "itkAffineTransform.h"
+#include "itkScaleVersor3DTransform.h"
+#include "ConvertToRigidAffine.h"
+
+// The following was just copied out of iccdefWarpImage.cc.  Sorry.
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkSpatialOrientation.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkBSplineInterpolateImageFunction.h"
+#include 
+#include 
+#include "itkImageRegionIterator.h"
+#include "TransformToDeformationField.h"
+#include 
+// #include 
+// #include "Jacobian.h"
+#include 
+
+#ifdef __USE_BRAINS2_INTEGRATION
+#include "iccdefdeformation/Deformation.h"
+#include "iccdefdeformation/Utils.h"
+#include "b2Affine_rw.h"
+#include "iccdefdeformation/HarmonicArrayIO.h"
+#endif
+
+namespace itk
+{
+template 
+ValidationInputParser
+::ValidationInputParser()
+{
+  m_TheMovingImageFilename = "";
+  m_TheFixedImageFilename = "";
+
+  m_ParameterFilename = "";
+
+  m_TheMovingImage = NULL;
+  m_TheFixedImage = NULL;
+
+  m_NumberOfHistogramLevels = 1024;
+  m_NumberOfMatchPoints = 7;
+
+  m_NumberOfLevels = 1;
+  m_TheMovingImageShrinkFactors.Fill(1);
+  m_TheFixedImageShrinkFactors.Fill(1);
+
+  m_NumberOfIterations = IterationsArrayType(1);
+  m_NumberOfIterations.Fill(10);
+
+  m_OutDebug = false;
+  m_ForceCoronalZeroOrigin = false;
+}
+
+template 
+void
+ValidationInputParser
+::Execute()
+{
+  /*************************
+    * Read in the images
+    */
+  if( this->m_ForceCoronalZeroOrigin == true )
+    {
+    std::cout << "---Forcing Brains2 Orientation not yet implemented"
+              << std::endl;
+    exit(-1);
+    }
+  else
+    {
+    m_TheFixedImage = itkUtil::ReadImage(m_TheFixedImageFilename);
+    m_TheMovingImage = itkUtil::ReadImage(m_TheMovingImageFilename);
+    }
+  // TODO:  Need to ensure that the fixed and moving images have the same
+  // orientations.
+
+  // TODO:  Need to figure out how to read in the initial deformation field.
+  // std::cerr << "About to check for deformation field file " <<
+  // m_InitialDeformationFieldFilename << std::endl;
+  // std::cerr << "About to check for transform file " <<
+  // m_InitialTransformFilename << std::endl;
+  // std::cerr << "About to check for Coefficient file" <<
+  // m_InitialCoefficientFilename << std::endl;
+  if( m_InitialDeformationFieldFilename != "" )
+    {
+    typedef   itk::ImageFileReader FieldReaderType;
+    typename FieldReaderType::Pointer fieldReader = FieldReaderType::New();
+    fieldReader->SetFileName( m_InitialDeformationFieldFilename.c_str() );
+    try
+      {
+      fieldReader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cerr << "Caught an ITK exception: " << std::endl;
+      throw err;
+      }
+    if( this->GetOutDebug() )
+      {
+      std::cout << "\nReading Deformation fields.\n";
+      }
+    m_InitialDeformationField = fieldReader->GetOutput();
+    //  typename ImageType::DirectionType DeformationOrientation;
+    //  DeformationOrientation=deformationField->GetDirection();
+    }
+  else if( m_InitialTransformFilename != "" )
+    {
+#if 1
+    // TODO: Zhao,  please implement the following, and test that it works
+    // within
+    //      the regression test suite.
+
+    // VBRAINSDemonWarpPrimary.cxx
+    // Review reading of transform files from BRAINSFit code for
+    // reading Versor/Euler/Affine file from
+    // Apparently when you register one transform, you need to register all your
+    // transforms.
+    //
+    AddExtraTransformRegister();
+
+    //  #######Now use TransformToDeformationFieldSource
+    typedef itk::TransformToDeformationFieldSource
+    DeformationFieldGeneratorType;
+    typedef typename DeformationFieldGeneratorType::TransformType TransformType;
+    // Only a templated base class.
+
+    typename TransformType::Pointer trsf = ReadTransformFromDisk(m_InitialTransformFilename);
+
+    typename DeformationFieldGeneratorType::Pointer defGenerator = DeformationFieldGeneratorType::New();
+    defGenerator->SetOutputSpacing( this->GetTheFixedImage()->GetSpacing() );
+    defGenerator->SetOutputOrigin( this->GetTheFixedImage()->GetOrigin() );
+    defGenerator->SetOutputDirection( this->GetTheFixedImage()->GetDirection() );
+    defGenerator->SetOutputSize( this->GetTheFixedImage()->GetLargestPossibleRegion().GetSize() );
+    defGenerator->SetOutputIndex( this->GetTheFixedImage()->GetLargestPossibleRegion().GetIndex() );
+    defGenerator->SetTransform(trsf);
+    try
+      {
+      defGenerator->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cerr << "ExceptionObject caught !" << std::endl;
+      std::cerr << err << std::endl;
+      exit(-1);
+      }
+    m_InitialDeformationField = defGenerator->GetOutput();
+    // itkUtil::WriteImage(m_InitialDeformationField,
+    // "initialDeformationfield.nii.gz");
+#endif
+    }
+  else if( m_InitialCoefficientFilename != "" )
+    {
+#ifdef __USE_BRAINS2_INTEGRATION
+    DeformationFieldFFTType::Pointer mu;        // mu1, mu2, mu3;
+    std::string                      CoeffNameInput(
+      m_InitialCoefficientFilename.c_str() );
+
+      {
+      if( this->GetOutDebug() )
+        {
+        std::cout << "Reading: " << CoeffNameInput << std::endl;
+        }
+      HarmonicReadAll3D(mu, CoeffNameInput);
+      }
+    if( this->GetOutDebug() )
+      {
+      std::cout << "\nCreating Deformation fields from Coefficient files\n";
+      }
+    m_InitialDeformationField = CreateITKDisplacementFieldFromCoeffs(mu);
+#else
+    std::cout << "ERROR:  InitialCoefficientFilename not supported yet" << std::endl;
+    exit(-1);
+#endif
+    }
+
+  // Print out the parameters.
+  if( this->GetOutDebug() )
+    {
+    std::cout << "NumberOfHistogramLevels : " << m_NumberOfHistogramLevels
+              << std::endl;
+    std::cout << "NumberOfMatchPoints : " << m_NumberOfMatchPoints << std::endl;
+    std::cout << "NumberOfLevels : " << m_NumberOfLevels << std::endl;
+    std::cout << "NumberOfIterations : " << m_NumberOfIterations << std::endl;
+    std::cout << "TheMovingImageShrinkFactors : "
+              << m_TheMovingImageShrinkFactors << std::endl;
+    std::cout << "TheFixedImageShrinkFactors : "
+              << m_TheFixedImageShrinkFactors << std::endl;
+    }
+}
+
+} // namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/genericRegistrationHelper.h b/BRAINSCommonLib/genericRegistrationHelper.h
new file mode 100644
index 00000000..103a9e30
--- /dev/null
+++ b/BRAINSCommonLib/genericRegistrationHelper.h
@@ -0,0 +1,428 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __genericRegistrationHelper_h
+#define __genericRegistrationHelper_h
+#if defined( _MSC_VER )
+#pragma warning ( disable : 4786 )
+#endif
+
+#if (ITK_VERSION_MAJOR < 4)
+#include "itkOptImageToImageMetric.h"
+#include "itkOptMattesMutualInformationImageToImageMetric.h"
+#else
+#include "itkImageToImageMetric.h"
+#include "itkMattesMutualInformationImageToImageMetric.h"
+#endif
+#define COMMON_MMI_METRIC_TYPE itk::MattesMutualInformationImageToImageMetric
+
+#include "itkImageRegistrationMethod.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkImage.h"
+#include "itkDataObjectDecorator.h"
+
+#include "itkCenteredTransformInitializer.h"
+
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkShiftScaleImageFilter.h"
+#include 
+#include 
+#include 
+#include 
+
+#include "itkMultiThreader.h"
+#include "itkResampleImageFilter.h"
+#ifdef USE_DEBUG_IMAGE_VIEWER
+#include "DebugImageViewerClient.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "Imgmath.h"
+#endif
+
+#include "itkIO.h"
+
+#include 
+
+enum
+  {
+  Dimension = 3,
+  MaxInputDimension = 4
+  };
+
+//  The following section of code implements a Command observer
+//  that will monitor the evolution of the registration process.
+//
+#include "itkCommand.h"
+
+namespace BRAINSFit
+{
+template 
+class CommandIterationUpdate : public itk::Command
+{
+public:
+  typedef  CommandIterationUpdate Self;
+  typedef  itk::Command           Superclass;
+  typedef itk::SmartPointer Pointer;
+  itkNewMacro(Self);
+  typedef          TOptimizer  OptimizerType;
+  typedef const OptimizerType *OptimizerPointer;
+  void SetDisplayDeformedImage(bool x)
+  {
+    m_DisplayDeformedImage = x;
+#if USE_DEBUG_IMAGE_VIEWER
+    m_DebugImageDisplaySender.SetEnabled(x);
+#endif
+  }
+
+  void SetPromptUserAfterDisplay(bool x)
+  {
+    m_PromptUserAfterDisplay = x;
+#if USE_DEBUG_IMAGE_VIEWER
+    m_DebugImageDisplaySender.SetPromptUser(x);
+#endif
+  }
+
+  void SetPrintParameters(bool x)
+  {
+    m_PrintParameters = x;
+  }
+
+  void SetFixedImage(typename TImage::Pointer fixed)
+  {
+    m_FixedImage = fixed;
+  }
+
+  void SetMovingImage(typename TImage::Pointer moving)
+  {
+    m_MovingImage = moving;
+  }
+
+  void SetTransform(typename TTransform::Pointer & xfrm)
+  {
+    m_Transform = xfrm;
+  }
+
+  void Execute(itk::Object *caller, const itk::EventObject & event)
+  {
+    Execute( (const itk::Object *)caller, event );
+  }
+
+  typename TImage::Pointer Transform(typename TTransform::Pointer & xfrm)
+  {
+    //      std::cerr << "Moving Volume (in observer): " << this->m_MovingImage
+    // << std::endl;
+    typedef typename itk::LinearInterpolateImageFunction InterpolatorType;
+    typename InterpolatorType::Pointer interp = InterpolatorType::New();
+    typedef typename itk::ResampleImageFilter ResampleImageFilter;
+    typename ResampleImageFilter::Pointer resample = ResampleImageFilter::New();
+    resample->SetInput(m_MovingImage);
+    resample->SetTransform(xfrm);
+    resample->SetInterpolator(interp);
+    resample->SetOutputParametersFromImage(m_FixedImage);
+    resample->SetOutputDirection( m_FixedImage->GetDirection() );
+    resample->SetDefaultPixelValue(0);
+    resample->Update();
+    typename TImage::Pointer rval = resample->GetOutput();
+    // rval->DisconnectPipeline();
+    return rval;
+  }
+
+  void Execute(const itk::Object *object, const itk::EventObject & event)
+  {
+    OptimizerPointer optimizer = dynamic_cast( object );
+
+    if( optimizer == NULL )
+      {
+      std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+      exit(-1);
+      }
+    if( !itk::IterationEvent().CheckEvent(&event) )
+      {
+      return;
+      }
+
+    typename OptimizerType::ParametersType parms =
+      optimizer->GetCurrentPosition();
+    int  psize = parms.GetNumberOfElements();
+    bool parmsNonEmpty = false;
+    for( int i = 0; i < psize; ++i )
+      {
+      if( parms[i] != 0.0 )
+        {
+        parmsNonEmpty = true;
+        break;
+        }
+      }
+
+    if( m_PrintParameters )
+      {
+      std::cout << std::setw(  4 ) << std::setfill( ' ' ) << optimizer->GetCurrentIteration() << "   ";
+      std::cout << std::setw( 10 ) << std::setfill( ' ' ) << optimizer->GetValue() << "   ";
+      if( parmsNonEmpty )
+        {
+        std::cout << parms;
+        }
+      std::cout << std::endl;
+      }
+
+#ifdef USE_DEBUG_IMAGE_VIEWER
+    if( m_DisplayDeformedImage )
+      {
+      if( parmsNonEmpty )
+        {
+        m_Transform->SetParametersByValue(parms);
+        }
+      // else, if it is a vnl optimizer wrapper, i.e., the BSpline optimizer,
+      // the only hint you get
+      // is in the transform object used by the optimizer, so don't erase it,
+      // use it.
+      typename TImage::Pointer transformResult =
+        this->Transform(m_Transform);
+      //      std::cerr << "Moving Volume (after transform): " <<
+      // transformResult << std::endl;
+      m_DebugImageDisplaySender.SendImage(transformResult, 1);
+      typename TImage::Pointer diff = Isub(m_FixedImage, transformResult);
+
+      m_DebugImageDisplaySender.SendImage(diff, 2);
+      }
+#endif
+  }
+
+  typedef typename COMMON_MMI_METRIC_TYPE MattesMutualInformationMetricType;
+  void SetMetricObject(typename MattesMutualInformationMetricType::Pointer metric_Object)
+  {
+    // NOTE:  Returns NULL if not MattesMutualInformationImageToImageMetric
+    this->m_CostMetricObject = dynamic_cast(metric_Object.GetPointer() );
+    // NO NEED FOR CHECKING IF DYNAMIC CAST WORKED, invalid cast is OK with a
+    // NULL return
+  }
+
+protected:
+  CommandIterationUpdate() : m_DisplayDeformedImage(false),
+    m_PromptUserAfterDisplay(false),
+    m_PrintParameters(true),
+    m_MovingImage(NULL),
+    m_FixedImage(NULL),
+    m_Transform(NULL),
+    m_CostMetricObject(NULL)
+  {
+  }
+private:
+  bool m_DisplayDeformedImage;
+  bool m_PromptUserAfterDisplay;
+  bool m_PrintParameters;
+
+  typename TImage::Pointer m_MovingImage;
+  typename TImage::Pointer m_FixedImage;
+  typename TTransform::Pointer m_Transform;
+
+  typename MattesMutualInformationMetricType::Pointer m_CostMetricObject;
+
+#ifdef USE_DEBUG_IMAGE_VIEWER
+  DebugImageViewerClient m_DebugImageDisplaySender;
+#endif
+};
+} // end namespace BRAINSFit
+
+namespace itk
+{
+// TODO:  Remove default MetricType here, and force a choice
+template 
+class ITK_EXPORT MultiModal3DMutualRegistrationHelper : public ProcessObject
+{
+public:
+  /** Standard class typedefs. */
+  typedef MultiModal3DMutualRegistrationHelper Self;
+  typedef ProcessObject                        Superclass;
+  typedef SmartPointer                   Pointer;
+  typedef SmartPointer             ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(MultiModal3DMutualRegistrationHelper, ProcessObject);
+
+  typedef          TFixedImage                  FixedImageType;
+  typedef typename FixedImageType::ConstPointer FixedImageConstPointer;
+  typedef typename FixedImageType::Pointer      FixedImagePointer;
+
+  typedef          TMovingImage                  MovingImageType;
+  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;
+  typedef typename MovingImageType::Pointer      MovingImagePointer;
+
+  typedef          TTransformType         TransformType;
+  typedef typename TransformType::Pointer TransformPointer;
+
+  /** Type for the output: Using Decorator pattern for enabling
+    *  the Transform to be passed in the data pipeline */
+  typedef DataObjectDecorator    TransformOutputType;
+  typedef typename TransformOutputType::Pointer TransformOutputPointer;
+  typedef typename TransformOutputType::ConstPointer
+  TransformOutputConstPointer;
+
+  typedef          TOptimizer                    OptimizerType;
+  typedef const OptimizerType *                  OptimizerPointer;
+  typedef typename OptimizerType::ScalesType     OptimizerScalesType;
+  typedef typename OptimizerType::ParametersType OptimizerParametersType;
+
+  typedef typename MetricType::FixedImageMaskType  FixedBinaryVolumeType;
+  typedef typename FixedBinaryVolumeType::Pointer  FixedBinaryVolumePointer;
+  typedef typename MetricType::MovingImageMaskType MovingBinaryVolumeType;
+  typedef typename MovingBinaryVolumeType::Pointer MovingBinaryVolumePointer;
+
+  typedef LinearInterpolateImageFunction<
+    MovingImageType,
+    double>    InterpolatorType;
+
+  typedef ImageRegistrationMethod RegistrationType;
+  typedef typename RegistrationType::Pointer                       RegistrationPointer;
+
+  typedef itk::CenteredTransformInitializer<
+    TransformType,
+    FixedImageType,
+    MovingImageType>    TransformInitializerType;
+
+  typedef itk::ResampleImageFilter<
+    MovingImageType,
+    FixedImageType>     ResampleFilterType;
+
+  /** Initialize by setting the interconnects between the components. */
+  virtual void Initialize(void); // throw ( ExceptionObject );
+
+  /** Method that initiates the registration. */
+  void StartRegistration(void);
+
+  /** Set/Get the Fixed image. */
+  void SetFixedImage(FixedImagePointer fixedImage);
+
+  itkGetConstObjectMacro(FixedImage, FixedImageType);
+
+  /** Set/Get the Moving image. */
+  void SetMovingImage(MovingImagePointer movingImage);
+
+  itkGetConstObjectMacro(MovingImage, MovingImageType);
+
+  /** Set/Get the InitialTransfrom. */
+  void SetInitialTransform(typename TransformType::Pointer initialTransform);
+  itkGetConstObjectMacro(InitialTransform, TransformType);
+
+  /** Set/Get the Transfrom. */
+  itkSetObjectMacro(Transform, TransformType);
+  typename TransformType::Pointer GetTransform(void);
+
+  // itkSetMacro( PermitParameterVariation, std::vector      );
+
+  itkSetObjectMacro(CostMetricObject, MetricType);
+  itkGetObjectMacro(CostMetricObject, MetricType);
+
+  itkSetMacro(NumberOfSamples,               unsigned int);
+  itkSetMacro(NumberOfHistogramBins,         unsigned int);
+  itkSetMacro(NumberOfIterations,            unsigned int);
+  itkSetMacro(RelaxationFactor,              double);
+  itkSetMacro(MaximumStepLength,             double);
+  itkSetMacro(MinimumStepLength,             double);
+  itkSetMacro(TranslationScale,              double);
+  itkSetMacro(ReproportionScale,             double);
+  itkSetMacro(SkewScale,                     double);
+  itkSetMacro(InitialTransformPassThruFlag,  bool);
+  itkSetMacro(BackgroundFillValue,           double);
+  itkSetMacro(DisplayDeformedImage,          bool);
+  itkSetMacro(PromptUserAfterDisplay,        bool);
+  itkGetConstMacro(FinalMetricValue,         double);
+  itkGetConstMacro(ActualNumberOfIterations, unsigned int);
+  itkSetMacro(ObserveIterations,        bool);
+  itkGetConstMacro(ObserveIterations,        bool);
+  /** Returns the transform resulting from the registration process  */
+  const TransformOutputType * GetOutput() const;
+
+  /** Make a DataObject of the correct type to be used as the specified
+    * output. */
+  virtual DataObjectPointer MakeOutput(unsigned int idx);
+
+  /** Method to return the latest modified time of this object or
+    * any of its cached ivars */
+  unsigned long GetMTime() const;
+
+  /** Method to set the Permission to vary by level  */
+  void SetPermitParameterVariation(std::vector perms)
+  {
+    m_PermitParameterVariation.resize( perms.size() );
+    for( unsigned int i = 0; i < perms.size(); ++i )
+      {
+      m_PermitParameterVariation[i] = perms[i];
+      }
+  }
+
+protected:
+  MultiModal3DMutualRegistrationHelper();
+  virtual ~MultiModal3DMutualRegistrationHelper()
+  {
+  }
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Method invoked by the pipeline in order to trigger the computation of
+    * the registration. */
+  void  GenerateData();
+
+private:
+  MultiModal3DMutualRegistrationHelper(const Self &);             // purposely
+                                                                  // not
+  // implemented
+  void operator=(const Self &);                                   // purposely
+
+  // not
+
+  // implemented
+
+  // FixedImageConstPointer           m_FixedImage;
+  // MovingImageConstPointer          m_MovingImage;
+
+  FixedImagePointer  m_FixedImage;
+  MovingImagePointer m_MovingImage;
+  TransformPointer   m_InitialTransform;
+  TransformPointer   m_Transform;
+  //
+  // make sure parameters persist until after they're used by the transform
+
+  RegistrationPointer m_Registration;
+
+  std::vector m_PermitParameterVariation;
+  typename MetricType::Pointer  m_CostMetricObject;
+
+  unsigned int m_NumberOfSamples;
+  unsigned int m_NumberOfHistogramBins;
+  unsigned int m_NumberOfIterations;
+  double       m_RelaxationFactor;
+  double       m_MaximumStepLength;
+  double       m_MinimumStepLength;
+  double       m_TranslationScale;
+  double       m_ReproportionScale;
+  double       m_SkewScale;
+  bool         m_InitialTransformPassThruFlag;
+  double       m_BackgroundFillValue;
+  unsigned int m_ActualNumberOfIterations;
+  bool         m_DisplayDeformedImage;
+  bool         m_PromptUserAfterDisplay;
+  double       m_FinalMetricValue;
+  bool         m_ObserveIterations;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "genericRegistrationHelper.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/genericRegistrationHelper.hxx b/BRAINSCommonLib/genericRegistrationHelper.hxx
new file mode 100644
index 00000000..8e1a9b30
--- /dev/null
+++ b/BRAINSCommonLib/genericRegistrationHelper.hxx
@@ -0,0 +1,650 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *  Date:      $Date: 2007-08-02 14:58:12 -0500 (Thu, 02 Aug 2007) $
+ *  Version:   $Revision: 10282 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __genericRegistrationHelper_hxx
+#define __genericRegistrationHelper_hxx
+
+#include "genericRegistrationHelper.h"
+
+#include "itkVersor.h"
+#include "itkMatrix.h"
+#include "ConvertToRigidAffine.h"
+
+#include "itkWindowedSincInterpolateImageFunction.h"
+
+namespace itk
+{
+
+template 
+void MakeDebugJointHistogram(const std::string debugOutputDirectory, const typename JointPDFType::Pointer myHistogram,
+                             const int globalIteration,
+                             const int currentIteration)
+{
+  std::stringstream fn("");
+
+  fn << debugOutputDirectory << "/DEBUGHistogram_"
+     << std::setw( 4 ) << std::setfill( '0' ) << globalIteration
+     << "_"
+     << std::setw( 4 ) << std::setfill( '0' ) << currentIteration
+     << ".png";
+  // typename JOINTPDFType::ConstPointer =
+  // typedef itk::CastImageFilter
+  // > CasterType;
+  typedef itk::RescaleIntensityImageFilter > CasterType;
+  // typedef itk::ShiftScaleImageFilter > CasterType;
+  typename CasterType::Pointer myCaster = CasterType::New();
+  myCaster->SetInput(myHistogram);
+  // myCaster->SetShift(0);
+  // myCaster->SetScale(255);
+  myCaster->Update();
+  itkUtil::WriteImage >( myCaster->GetOutput(), fn.str() );
+  std::cout << "Writing jointPDF: " << fn.str() << std::endl;
+}
+
+/*
+  * Constructor
+  */
+template 
+MultiModal3DMutualRegistrationHelper
+::MultiModal3DMutualRegistrationHelper() :
+  m_FixedImage(0),                         // has to be provided by the user.
+  m_MovingImage(0),                        // has to be provided by the user.
+  m_InitialTransform(0),                   // has to be provided by the user.
+  m_Transform(0),                          // has to be provided by
+                                           // this->Initialize().
+  m_Registration(0),                       // has to be provided by
+                                           // this->Initialize().
+  m_PermitParameterVariation(0),
+  m_NumberOfSamples(100000),
+  m_NumberOfHistogramBins(200),
+  m_NumberOfIterations(0),
+  m_RelaxationFactor(0.5),
+  m_MaximumStepLength(0.2000),
+  m_MinimumStepLength(0.0001),
+  m_TranslationScale(1000.0),
+  m_ReproportionScale(25.0),
+  m_SkewScale(25.0),
+  m_InitialTransformPassThruFlag(false),
+  m_BackgroundFillValue(0.0),
+  m_DisplayDeformedImage(false),
+  m_PromptUserAfterDisplay(false),
+  m_FinalMetricValue(0),
+  m_ObserveIterations(true)
+{
+  this->SetNumberOfRequiredOutputs(1);    // for the Transform
+
+  TransformOutputPointer transformDecorator =
+    static_cast( this->MakeOutput(0).GetPointer() );
+
+  this->ProcessObject::SetNthOutput( 0, transformDecorator.GetPointer() );
+
+  this->SetTransform( TransformType::New() );
+  this->m_Transform->SetIdentity();
+  this->m_CostMetricObject = NULL;
+}
+
+/*
+  * Initialize by setting the interconnects between components.
+  */
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::Initialize(void) // throw ( ExceptionObject )
+{
+  if( !m_FixedImage )
+    {
+    itkExceptionMacro(<< "FixedImage is not present");
+    }
+
+  if( !m_MovingImage )
+    {
+    itkExceptionMacro(<< "MovingImage is not present");
+    }
+
+  //
+  // Connect the transform to the Decorator.
+  //
+  TransformOutputType *transformOutput =
+    static_cast( this->ProcessObject::GetOutput(0) );
+
+  transformOutput->Set( m_Transform.GetPointer() );
+
+  typename OptimizerType::Pointer optimizer      = OptimizerType::New();
+  typename InterpolatorType::Pointer interpolator   = InterpolatorType::New();
+
+  optimizer->SetMaximize(false);   // Mutual Information metrics are to be
+                                   // minimized.
+
+  m_Registration = RegistrationType::New();
+
+    {
+    // Special BUG work around for MMI metric
+    // that does not work in multi-threaded mode
+    typedef COMMON_MMI_METRIC_TYPE MattesMutualInformationMetricType;
+    typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+      dynamic_cast(this->m_CostMetricObject.GetPointer() );
+    if( test_MMICostMetric.IsNotNull() )
+      {
+      this->m_CostMetricObject->SetNumberOfThreads(1);
+      this->m_Registration->SetNumberOfThreads(1);
+      }
+    }
+  m_Registration->SetMetric(this->m_CostMetricObject);
+  m_Registration->SetOptimizer(optimizer);
+  m_Registration->SetInterpolator(interpolator);
+
+  m_Registration->SetTransform(m_Transform);
+  m_Registration->SetFixedImage(m_FixedImage);
+  m_Registration->SetMovingImage(m_MovingImage);
+
+  m_Registration->SetFixedImageRegion( m_FixedImage->GetLargestPossibleRegion() );
+
+  std::vector localPermissionToVary( m_Transform->GetNumberOfParameters() );
+
+    {
+    unsigned int i = 0;
+    while( i < m_Transform->GetNumberOfParameters() )
+      {
+      if( i < m_PermitParameterVariation.size() )
+        {
+        localPermissionToVary[i] = m_PermitParameterVariation[i];
+        }
+      else
+        {
+        localPermissionToVary[i] = 1;
+        }
+      ++i;
+      }
+    }
+  // Decode localPermissionToVary from its initial segment,
+  // PermitParameterVariation.
+  if( ( m_PermitParameterVariation.size() != m_Transform->GetNumberOfParameters() )
+      && ( m_PermitParameterVariation.size() != 0 ) )
+    {
+    std::cout
+    << "WARNING:  The permit parameters SHOULD match the number of parameters used for this registration type."
+    << std::endl;
+    std::cout << "WARNING:  Padding with 1's for the unspecified parameters" << std::endl;
+    std::cout << "m_PermitParameterVariation " << m_PermitParameterVariation.size() << " != "
+              << m_Transform->GetNumberOfParameters() << std::endl;
+    std::cout << "\nUSING: [ ";
+    for( unsigned int i = 0; i < localPermissionToVary.size(); ++i )
+      {
+      std::cout << localPermissionToVary[i] << " ";
+      }
+    std::cout << " ]" << std::endl;
+    }
+
+  if( m_InitialTransform )
+    {
+    // TODO: There should be no need to convert here, just assign m_Transform
+    // from m_InitialTransform.
+    //      They should be the same type!
+      {
+      const typename TTransformType::ConstPointer tempInitializerITKTransform = m_InitialTransform.GetPointer();
+      // NOTE By calling AssignConvertedTransform, it also copies the values
+      AssignRigid::AssignConvertedTransform(m_Transform, tempInitializerITKTransform);
+      }
+
+    // No need to step on parameters that may not vary; they will remain
+    // identical with
+    // values from InitialTransform which defaults correctly to SetIdentity().
+    }
+  else      // Won't happen under BRAINSFitPrimary.
+    {
+    std::cout
+    << "FAILURE:  InitialTransform must be set in MultiModal3DMutualRegistrationHelper before Initialize is called."
+    << std::endl;
+    exit(-1);
+    //  m_Transform would be SetIdentity() if this case continued.
+    }
+
+  //  We now pass the parameters of the current transform as the initial
+  //  parameters to be used when the registration process starts.
+  m_Registration->SetInitialTransformParameters( m_Transform->GetParameters() );
+
+  const double translationScale  = 1.0 / m_TranslationScale;
+  const double reproportionScale = 1.0 / m_ReproportionScale;
+  const double skewScale         = 1.0 / m_SkewScale;
+
+  OptimizerScalesType optimizerScales( m_Transform->GetNumberOfParameters() );
+
+  if( m_Transform->GetNumberOfParameters() == 15 )     //  ScaleSkew
+    {
+    for( unsigned int i = 0; i < m_Transform->GetNumberOfParameters(); ++i )
+      {
+      optimizerScales[i] = 1.0;
+      }
+    for( unsigned int i = 3; i < 6; ++i )
+      {
+      optimizerScales[i] = translationScale;
+      }
+    for( unsigned int i = 6; i < 9; ++i )
+      {
+      optimizerScales[i] = reproportionScale;
+      }
+    for( unsigned int i = 9; i < 15; ++i )
+      {
+      optimizerScales[i] = skewScale;
+      }
+    }
+  else if( m_Transform->GetNumberOfParameters() == 12 )     //  Affine
+    {
+    for( unsigned int i = 0; i < 9; ++i )
+      {
+      optimizerScales[i] = 1.0;
+      }
+    for( unsigned int i = 9; i < 12; ++i )
+      {
+      optimizerScales[i] = translationScale;
+      }
+    }
+  else if( m_Transform->GetNumberOfParameters() == 9 )    // ScaleVersorRigid3D
+    {
+    for( unsigned int i = 0; i < 3; ++i )
+      {
+      optimizerScales[i] = 1.0;
+      }
+    for( unsigned int i = 3; i < 6; ++i )
+      {
+      optimizerScales[i] = translationScale;
+      }
+    for( unsigned int i = 6; i < 9; ++i )
+      {
+      optimizerScales[i] = reproportionScale;
+      }
+    }
+  else if( m_Transform->GetNumberOfParameters() == 6 )     //  VersorRigid3D
+    {
+    for( unsigned int i = 0; i < 3; ++i )
+      {
+      optimizerScales[i] = 1.0;
+      }
+    for( unsigned int i = 3; i < 6; ++i )
+      {
+      optimizerScales[i] = translationScale;
+      }
+    }
+  else     // most likely (m_Transform->GetNumberOfParameters() == 3): uniform
+           // parameter scaling, whether
+           // just rotating OR just translating.
+    {
+    for( unsigned int i = 0; i < m_Transform->GetNumberOfParameters(); ++i )
+      {
+      optimizerScales[i] = 1.0;
+      }
+    }
+  // Step on parameters that may not vary; they also must be identical with
+  // SetIdentity().
+  for( unsigned int i = 0; i < m_Transform->GetNumberOfParameters(); ++i )
+    {
+    if( localPermissionToVary[i] == 0 )
+      {
+      // Make huge to greatly penilize any motion
+      optimizerScales[i] = 0.5 * vcl_numeric_limits::max();
+      }
+    }
+
+  std::cout << "Initializer, optimizerScales: " << optimizerScales << "."
+            << std::endl;
+  optimizer->SetScales(optimizerScales);
+
+  optimizer->SetRelaxationFactor(m_RelaxationFactor);
+  optimizer->SetMaximumStepLength(m_MaximumStepLength);
+  optimizer->SetMinimumStepLength(m_MinimumStepLength);
+  optimizer->SetNumberOfIterations(m_NumberOfIterations);
+
+#if 0
+  // if (globalVerbose)
+  if( 0 )
+    {
+    std::cout << "Initializer, RelaxationFactor: " << m_RelaxationFactor
+              << "." << std::endl;
+    std::cout << "Initializer, MaximumStepLength: " << m_MaximumStepLength
+              << "." << std::endl;
+    std::cout << "Initializer, MinimumStepLength: " << m_MinimumStepLength
+              << "." << std::endl;
+    std::cout << "Initializer, NumberOfIterations: " << m_NumberOfIterations
+              << "." << std::endl;
+    std::cout << "Registration, Transform : " << m_Transform << "."
+              << std::endl;
+    std::cout << "Registration, FixedImage : " << m_FixedImage << "."
+              << std::endl;
+    std::cout << "Registration, MovingImage : " << m_MovingImage << "."
+              << std::endl;
+    }
+#endif
+
+  // Create the Command observer and register it with the optimizer.
+  // TODO:  make this output optional.
+  //
+  if( this->m_ObserveIterations == true )
+    {
+    typedef BRAINSFit::CommandIterationUpdate
+    CommandIterationUpdateType;
+    typename CommandIterationUpdateType::Pointer observer =
+      CommandIterationUpdateType::New();
+    observer->SetDisplayDeformedImage(m_DisplayDeformedImage);
+    observer->SetPromptUserAfterDisplay(m_PromptUserAfterDisplay);
+    observer->SetPrintParameters(true);
+    observer->SetMovingImage(m_MovingImage);
+    observer->SetFixedImage(m_FixedImage);
+    observer->SetTransform(m_Transform);
+
+    typedef COMMON_MMI_METRIC_TYPE MattesMutualInformationMetricType;
+    typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+      dynamic_cast(this->m_CostMetricObject.GetPointer() );
+    if( test_MMICostMetric.IsNotNull() )
+      {
+      observer->SetMetricObject(test_MMICostMetric);
+      }
+    optimizer->AddObserver(itk::IterationEvent(), observer);
+    // std::cout << "Observer Configured" << std::endl;
+    }
+  else
+    {
+    // std::cout << "Skipping Observer Configuration" << std::endl;
+    }
+  std::cout << std::flush;
+}
+
+/*
+  * Starts the Registration Process
+  */
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::StartRegistration(void)
+{
+  if( !m_InitialTransformPassThruFlag )
+    {
+    bool               successful = false;
+    const unsigned int diff = this->m_NumberOfSamples / 10;
+    while( !successful )
+      {
+      try
+        {
+        m_Registration->StartRegistration();
+        successful = true;
+        }
+      catch( itk::ExceptionObject & err )
+        {
+        // Attempt to auto-recover i too many samples were requested.
+        // std::cerr << "ExceptionObject caught !" << std::endl;
+        // std::cerr << err << std::endl;
+        // Pass exception to caller
+        //        throw err;
+        //
+        // lower the number of samples you request
+        typename MetricType::Pointer autoResetNumberOfSamplesMetric =
+          dynamic_cast( this->m_Registration->GetMetric() );
+        if( autoResetNumberOfSamplesMetric.IsNull() )
+          {
+          std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+          throw err;
+          }
+        unsigned int localNumberOfSamples = autoResetNumberOfSamplesMetric->GetNumberOfSpatialSamples();
+        if( diff > localNumberOfSamples )
+          {
+          // we are done.  This can not be recovered from.
+          throw err;
+          }
+        localNumberOfSamples -= diff;
+        autoResetNumberOfSamplesMetric->SetNumberOfSpatialSamples(localNumberOfSamples);
+        }
+      }
+
+    OptimizerParametersType finalParameters( m_Transform->GetNumberOfParameters() );
+
+    finalParameters = m_Registration->GetLastTransformParameters();
+
+    OptimizerPointer optimizer =
+      dynamic_cast( m_Registration->GetOptimizer() );
+    if( optimizer == NULL )
+      {
+      std::cout << "ERROR::" << __FILE__ << " " << __LINE__ << std::endl;
+      exit(-1);
+      }
+    std::cout << "Stop condition from optimizer." << optimizer->GetStopConditionDescription() << std::endl;
+    m_FinalMetricValue = optimizer->GetValue();
+    m_ActualNumberOfIterations = optimizer->GetCurrentIteration();
+    m_Transform->SetParametersByValue(finalParameters);
+
+    //
+    // GenerateHistogram
+    // TODO: KENT:  BRAINSFit tools need to define a common output directory for
+    // all debug images to be written.
+    //             by default the it should be the same as the outputImage, and
+    // if that does not exists, then it
+    //             should default to the same directory as the outputTransform,
+    // or it should be specified by the
+    //             user on the command line.
+    //             The following function should only be called when BRAINSFit
+    // command line tool is called with
+    //             --debugLevel 7 or greater, and it should write the 3D
+    // JointPDF image to the debugOutputDirectory
+    //             location.
+    const std::string debugOutputDirectory("");
+    if( debugOutputDirectory != "" )
+      {
+      // Special BUG work around for MMI metric
+      // that does not work in multi-threaded mode
+      typedef COMMON_MMI_METRIC_TYPE MattesMutualInformationMetricType;
+      static int TransformIterationCounter = 10000;
+      typename MattesMutualInformationMetricType::Pointer test_MMICostMetric =
+        dynamic_cast(this->m_CostMetricObject.GetPointer() );
+      if( test_MMICostMetric.IsNotNull() )
+        {
+        typedef itk::Image JointPDFType;
+        const JointPDFType::Pointer myHistogram = test_MMICostMetric->GetJointPDF();
+        MakeDebugJointHistogram(debugOutputDirectory, myHistogram, TransformIterationCounter,
+                                              optimizer->GetCurrentIteration() );
+        TransformIterationCounter += 10000;
+        }
+      }
+    }
+
+  typename TransformType::MatrixType matrix = m_Transform->GetMatrix();
+  typename TransformType::OffsetType offset = m_Transform->GetOffset();
+
+  std::cout << std::endl << "Matrix = " << std::endl << matrix << std::endl;
+  std::cout << "Offset = " << offset << std::endl << std::endl;
+
+}
+
+/**
+  *
+  */
+template 
+unsigned long
+MultiModal3DMutualRegistrationHelper
+::GetMTime() const
+{
+  unsigned long mtime = Superclass::GetMTime();
+  unsigned long m;
+
+  // Some of the following should be removed once ivars are put in the
+  // input and output lists
+
+  if( m_Transform )
+    {
+    m = m_Transform->GetMTime();
+    mtime = ( m > mtime ? m : mtime );
+    }
+
+  if( m_Registration )
+    {
+    m = m_Registration->GetMTime();
+    mtime = ( m > mtime ? m : mtime );
+    }
+
+  if( m_InitialTransform )
+    {
+    m = m_InitialTransform->GetMTime();
+    mtime = ( m > mtime ? m : mtime );
+    }
+
+  if( m_FixedImage )
+    {
+    m = m_FixedImage->GetMTime();
+    mtime = ( m > mtime ? m : mtime );
+    }
+
+  if( m_MovingImage )
+    {
+    m = m_MovingImage->GetMTime();
+    mtime = ( m > mtime ? m : mtime );
+    }
+
+  return mtime;
+}
+
+/*
+  * Generate Data
+  */
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::GenerateData()
+{
+  this->StartRegistration();
+}
+
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::SetFixedImage(FixedImagePointer fixedImage)
+{
+  itkDebugMacro("setting Fixed Image to " << fixedImage);
+
+  if( this->m_FixedImage.GetPointer() != fixedImage )
+    {
+    this->m_FixedImage = fixedImage;
+    this->ProcessObject::SetNthInput(0, this->m_FixedImage);
+    this->Modified();
+    }
+}
+
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::SetMovingImage(MovingImagePointer movingImage)
+{
+  itkDebugMacro("setting Moving Image to " << movingImage);
+
+  if( this->m_MovingImage.GetPointer() != movingImage )
+    {
+    this->m_MovingImage = movingImage;
+    this->ProcessObject::SetNthInput(1, this->m_MovingImage);
+    this->Modified();
+    }
+}
+
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::SetInitialTransform(typename TransformType::Pointer initialTransform)
+{
+  itkDebugMacro("setting Initial Transform to " << initialTransform);
+  if( this->m_InitialTransform.GetPointer() != initialTransform )
+    {
+    this->m_InitialTransform = initialTransform;
+    this->Modified();
+    }
+}
+
+template 
+typename MultiModal3DMutualRegistrationHelper::TransformType::Pointer
+MultiModal3DMutualRegistrationHelper
+::GetTransform(void)
+{
+  this->Update();
+  return m_Transform;
+}
+
+/*
+  *  Get Output
+  */
+template 
+const typename MultiModal3DMutualRegistrationHelper::TransformOutputType
+* MultiModal3DMutualRegistrationHelper
+::GetOutput() const
+  {
+  return static_cast(
+           this->ProcessObject::GetOutput(0) );
+  }
+
+template 
+DataObject::Pointer
+MultiModal3DMutualRegistrationHelper
+::MakeOutput(unsigned int output)
+{
+  switch( output )
+    {
+    case 0:
+      return static_cast( TransformOutputType::New().GetPointer() );
+      break;
+    default:
+      itkExceptionMacro(
+        "MakeOutput request for an output number larger than the expected number of outputs");
+      return 0;
+    }
+}
+
+/*
+  * PrintSelf
+  */
+template 
+void
+MultiModal3DMutualRegistrationHelper
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+  os << indent << "Transform: " << m_Transform.GetPointer() << std::endl;
+  os << indent << "Fixed Image: " << m_FixedImage.GetPointer() << std::endl;
+  os << indent << "Moving Image: " << m_MovingImage.GetPointer() << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/iplProg_Common.vpj b/BRAINSCommonLib/iplProg_Common.vpj
new file mode 100644
index 00000000..82eb202a
--- /dev/null
+++ b/BRAINSCommonLib/iplProg_Common.vpj
@@ -0,0 +1,173 @@
+
+
+  
+    
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+    
+  
+  
+    
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+      
+        
+      
+    
+  
+  
+    
+      
+    
+  
+  
+    
+      
+      
+      
+    
+    
+      
+      
+    
+    
+    
+    
+    
+  
+
diff --git a/BRAINSCommonLib/itkBOBFFilter.h b/BRAINSCommonLib/itkBOBFFilter.h
new file mode 100644
index 00000000..a3a38c80
--- /dev/null
+++ b/BRAINSCommonLib/itkBOBFFilter.h
@@ -0,0 +1,121 @@
+#ifndef __itkBOBFFilter_h
+#define __itkBOBFFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkFixedArray.h"
+
+namespace itk
+{
+/** \class BOBFilter
+  */
+template 
+class ITK_EXPORT BOBFFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef BOBFFilter                                    Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(BOBFFilter, ImageToImageFilter);
+
+  /** ImageDimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+
+  /** Typedef to describe the output image region type. */
+  typedef typename TOutputImage::RegionType OutputImageRegionType;
+
+  /** Inherited typedefs. */
+  typedef typename Superclass::InputImageType         InputImageType;
+  typedef typename Superclass::InputImagePointer      InputImagePointer;
+  typedef typename Superclass::InputImageConstPointer InputImageConstPointer;
+  typedef typename Superclass::OutputImageType        OutputImageType;
+  typedef typename Superclass::OutputImagePointer     OutputImagePointer;
+
+  /** Pixel related typedefs. */
+  typedef typename InputImageType::PixelType  InputPixelType;
+  typedef typename OutputImageType::PixelType OutputPixelType;
+  typedef typename InputImageType::IndexType  IndexType;
+  typedef typename InputImageType::SizeType   InputSizeType;
+
+  /** Set/Get the Input image. */
+  void SetInputImage(const InputImageType *source)
+  {
+    this->SetInput(source);
+  }
+
+  const InputImageType * GetInputImage(void)
+  {
+    return this->GetInput();
+  }
+
+  /** Set the input mask */
+  void SetInputMask(const InputImageType *image);
+
+  /** Get the input mask */
+  const InputImageType * GetInputMask(void);
+
+  /** Set seed point. */
+
+  /** Set/Get the lower threshold. The default is 0. */
+  itkSetMacro(Lower, InputPixelType);
+  itkGetMacro(Lower, InputPixelType);
+
+  /** Set/Get the upper threshold. The default is the largest possible
+    *  value for the InputPixelType. */
+  itkSetMacro(Upper, InputPixelType);
+  itkGetMacro(Upper, InputPixelType);
+
+  /** Set/Get value to replace thresholded pixels. Pixels that lie *
+    *  within Lower and Upper (inclusive) will be replaced with this
+    *  value. The default is 1. */
+  itkSetMacro(ReplaceValue, OutputPixelType);
+  itkGetMacro(ReplaceValue, OutputPixelType);
+
+  /** Set the radius of the neighborhood used for a mask. */
+  itkSetMacro(Radius, InputSizeType);
+
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Radius, InputSizeType);
+
+  /** Set the Seed of the neighborhood used for a mask. */
+  itkSetMacro(Seed, IndexType);
+
+  /** Get the radius of the neighborhood used to compute the median */
+  itkGetConstReferenceMacro(Seed, IndexType);
+
+  /** Method to execute the Filter */
+  void GenerateData();
+
+protected:
+  BOBFFilter();
+  ~BOBFFilter()
+  {
+  }
+private:
+  BOBFFilter(const Self &);      // purposely not implemented
+  void operator=(const Self &);  // purposely not implemented
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  // std::vector m_Seeds;
+  IndexType       m_Seed;
+  InputPixelType  m_Lower;
+  InputPixelType  m_Upper;
+  OutputPixelType m_ReplaceValue;
+  InputSizeType   m_Radius;
+};
+}   // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBOBFFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkBOBFFilter.hxx b/BRAINSCommonLib/itkBOBFFilter.hxx
new file mode 100644
index 00000000..d6391bfb
--- /dev/null
+++ b/BRAINSCommonLib/itkBOBFFilter.hxx
@@ -0,0 +1,103 @@
+#ifndef __itkBOBFFilter_hxx
+#define __itkBOBFFilter_hxx
+
+#include "itkBOBFFilter.h"
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkNumericTraits.h"
+#include 
+#include "itkNeighborhoodConnectedImageFilter.h"
+
+namespace itk
+{
+/*
+  *
+  */
+template 
+BOBFFilter
+::BOBFFilter()
+{
+  this->SetNumberOfRequiredInputs(2);
+  m_Seed.Fill(0);
+  m_Lower = NumericTraits::NonpositiveMin();
+  m_Upper = NumericTraits::max();
+  m_ReplaceValue = NumericTraits::One;
+  m_Radius.Fill(1);
+}
+
+/*
+  *
+  */
+template 
+void
+BOBFFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  // os << indent << "UpperGradient: ";
+  // os << m_UpperGradient << std::endl;
+}
+
+/*
+  *
+  */
+template 
+void
+BOBFFilter::SetInputMask(
+  const typename BOBFFilter
+  ::InputImageType *image)
+{
+  this->SetNthInput( 1, const_cast( image ) );
+}
+
+template 
+const typename BOBFFilter
+::InputImageType
+* BOBFFilter
+::GetInputMask()
+  {
+  return static_cast
+         ( this->ProcessObject::GetInput(1) );
+  }
+
+template 
+void BOBFFilter::GenerateData()
+{
+  OutputImagePointer     OutputPtr = this->GetOutput();
+  InputImageConstPointer InputImage  = this->GetInputImage();
+  InputImageConstPointer InputMask  = this->GetInputMask();
+
+  /*Allocate the output*/
+  OutputPtr->SetRequestedRegion( InputImage->GetRequestedRegion() );
+  OutputPtr->SetBufferedRegion( InputImage->GetBufferedRegion() );
+  OutputPtr->SetLargestPossibleRegion( InputImage->GetLargestPossibleRegion() );
+  OutputPtr->CopyInformation(InputImage);
+  OutputPtr->Allocate();
+
+  typedef ImageRegionConstIterator InputIterator;
+  typedef ImageRegionIterator     OutputIterator;
+
+  OutputIterator outItr( OutputPtr, OutputPtr->GetLargestPossibleRegion() );
+
+  InputIterator ImgItr( InputImage, InputImage->GetLargestPossibleRegion() );
+
+  InputIterator MskItr( InputMask, InputMask->GetLargestPossibleRegion() );
+  for( ImgItr.GoToBegin(), MskItr.GoToBegin(), outItr.GoToBegin();
+       !ImgItr.IsAtEnd();
+       ++ImgItr, ++MskItr, ++outItr )
+    {
+    if( MskItr.Get() == 0 )
+      {
+      outItr.Set(m_ReplaceValue);
+      }
+    else
+      {
+      outItr.Set( ImgItr.Get() );
+      }
+    }
+}
+
+}   // end namespace itk
+
+#endif // _itkBOBFFilter_hxx
diff --git a/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.h b/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.h
new file mode 100644
index 00000000..e6c15ad6
--- /dev/null
+++ b/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.h
@@ -0,0 +1,179 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkBRAINSROIAutoImageFilter.h,v $
+ *  Language:  C++
+ *  Date:      $Date: 2008-10-16 19:33:40 $
+ *  Version:   $Revision: 1.7 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkBRAINSROIAutoImageFilter_h
+#define __itkBRAINSROIAutoImageFilter_h
+
+// First make sure that the configuration is available.
+// This line can be removed once the optimized versions
+// gets integrated into the main directories.
+#include "itkConfigure.h"
+#include "itkImageToImageFilter.h"
+#include "itkImage.h"
+
+#include "itkImageMaskSpatialObject.h"
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include "itkCastImageFilter.h"
+
+typedef itk::SpatialObject<3>      SpatialObjectType;
+typedef SpatialObjectType::Pointer ImageMaskPointer;
+
+namespace itk
+{
+/** \class BRAINSROIAutoImageFilter
+  * \brief This is a class to help with identifying common tissue
+  * Regions in an image.
+  *
+  * \sa Image
+  * \sa Neighborhood
+  *
+  * \ingroup IntensityImageFilters
+  */
+template 
+class ITK_EXPORT BRAINSROIAutoImageFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Extract dimension from input and output image. */
+  itkStaticConstMacro(InputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+
+  /** Convenient typedefs for simplifying declarations. */
+  typedef TInputImage  InputImageType;
+  typedef TOutputImage OutputImageType;
+
+  /** Standard class typedefs. */
+  typedef BRAINSROIAutoImageFilter                            Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                                  Pointer;
+  typedef SmartPointer                            ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(BRAINSROIAutoImageFilter, ImageToImageFilter);
+
+  /** Image typedef support. */
+  typedef typename InputImageType::PixelType  InputPixelType;
+  typedef typename OutputImageType::PixelType OutputPixelType;
+
+  typedef typename InputImageType::RegionType  InputImageRegionType;
+  typedef typename OutputImageType::RegionType OutputImageRegionType;
+
+  typedef typename InputImageType::SizeType InputSizeType;
+
+  typedef itk::Image                            UCHARIMAGE;
+  typedef itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+
+  /** */
+  itkSetMacro(OtsuPercentileThreshold, double);
+  itkGetConstMacro(OtsuPercentileThreshold, double);
+  /** */
+  itkSetMacro(ThresholdCorrectionFactor, double);
+  itkGetConstMacro(ThresholdCorrectionFactor, double);
+  /** The closing size in mm, this is rounded up to the next closest number of
+    * voxel by taking Spacing into account */
+  itkSetMacro(ClosingSize, double);
+  itkGetConstMacro(ClosingSize, double);
+  /** The dilation size in mm, this is rounded up to the next closest number of
+    * voxel by taking Spacing into account */
+  itkSetMacro(DilateSize, double);
+  itkGetConstMacro(DilateSize, double);
+
+  // NOTE:  This will generate a new spatial object each time it is called, and
+  // not return the previous spatial object
+  ImageMaskPointer GetSpatialObjectROI(void)
+  {
+    if( m_ResultMaskPointer.IsNull() )  // This is a cheap way to only create
+                                        // the mask once, note that this is made
+                                        // null when GenerateData is called.
+      {
+      typedef itk::CastImageFilter CastImageFilter;
+      typename CastImageFilter::Pointer castFilter = CastImageFilter::New();
+      castFilter->SetInput( this->GetOutput() );
+      castFilter->Update();
+
+      // convert mask image to mask
+      typename ImageMaskSpatialObjectType::Pointer mask = ImageMaskSpatialObjectType::New();
+      mask->SetImage( castFilter->GetOutput() );
+      mask->ComputeObjectToWorldTransform();
+      m_ResultMaskPointer = dynamic_cast( mask.GetPointer() );
+      if( m_ResultMaskPointer.IsNull() )
+        {
+        std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+        exit(-1);
+        }
+      }
+    return m_ResultMaskPointer;
+  }
+
+  typename UCHARIMAGE::ConstPointer GetBinaryImageROI()
+  {
+    ImageMaskPointer tmp = this->GetSpatialObjectROI();
+
+    typename UCHARIMAGE::ConstPointer rval;
+    if( tmp.IsNotNull() )
+      {
+      const typename itk::ImageMaskSpatialObject<3>::ConstPointer imso =
+        dynamic_cast *>(tmp.GetPointer() );
+      if( imso.IsNull() )
+        {
+        std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+        exit(-1);
+        }
+      if( imso.IsNotNull() )
+        {
+        rval = imso->GetImage();
+        }
+      }
+    return rval;
+  }
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( SameDimensionCheck,
+                   ( Concept::SameDimension ) );
+  /** End concept checking */
+#endif
+protected:
+  BRAINSROIAutoImageFilter();
+  virtual ~BRAINSROIAutoImageFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  void GenerateData();
+
+private:
+  BRAINSROIAutoImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);           // purposely not implemented
+
+  double           m_OtsuPercentileThreshold;
+  double           m_ThresholdCorrectionFactor;
+  double           m_ClosingSize;
+  double           m_DilateSize;
+  ImageMaskPointer m_ResultMaskPointer;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBRAINSROIAutoImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.hxx b/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.hxx
new file mode 100644
index 00000000..ac45781f
--- /dev/null
+++ b/BRAINSCommonLib/itkBRAINSROIAutoImageFilter.hxx
@@ -0,0 +1,84 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkBRAINSROIAutoImageFilter.hxx,v $
+ *  Language:  C++
+ *  Date:      $Date: 2008-10-16 16:45:09 $
+ *  Version:   $Revision: 1.13 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *    This software is distributed WITHOUT ANY WARRANTY; without even
+ *    the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *    PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkBRAINSROIAutoImageFilter_hxx
+#define __itkBRAINSROIAutoImageFilter_hxx
+#include "itkBRAINSROIAutoImageFilter.h"
+
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkNumericTraits.h"
+#include "itkProgressAccumulator.h"
+
+namespace itk
+{
+template 
+BRAINSROIAutoImageFilter
+::BRAINSROIAutoImageFilter()
+{
+  // this filter requires two input images
+  this->SetNumberOfRequiredInputs(1);
+  m_OtsuPercentileThreshold = 0.01;
+  m_ClosingSize = 9.0;
+  m_ThresholdCorrectionFactor = 1.0;
+  m_DilateSize = 0.0;
+  m_ResultMaskPointer = NULL;
+}
+
+template 
+void
+BRAINSROIAutoImageFilter
+::GenerateData()
+{
+  m_ResultMaskPointer = NULL; // Need to make this null during every re-run of
+                              // the data.
+  // Create a process accumulator for tracking the progress of this minipipeline
+  ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+  progress->SetMiniPipelineFilter(this);
+
+  typedef itk::LargestForegroundFilledMaskImageFilter LFFMaskFilterType;
+  typename LFFMaskFilterType::Pointer LFF = LFFMaskFilterType::New();
+  // Register the filter with the with progress accumulator using
+  // equal weight proportion
+  progress->RegisterInternalFilter(LFF, 1.0f);
+  LFF->SetInput( this->GetInput() );
+  LFF->SetOtsuPercentileThreshold(m_OtsuPercentileThreshold);
+  LFF->SetClosingSize(m_ClosingSize);
+  LFF->SetDilateSize(m_DilateSize);
+  LFF->SetThresholdCorrectionFactor(m_ThresholdCorrectionFactor);
+  LFF->Update();
+  this->GraftOutput( LFF->GetOutput() );
+}
+
+template 
+void
+BRAINSROIAutoImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "OtsuPercentileThreshold: "
+     << m_OtsuPercentileThreshold << std::endl;
+  os << indent << "ThresholdCorrectionFactor: "
+     << m_ThresholdCorrectionFactor << std::endl;
+  os << indent << "ClosingSize: "
+     << m_ClosingSize << std::endl;
+  os << indent << "DilateSize: "
+     << m_DilateSize << std::endl;
+}
+
+} // end namespace itk
+#endif
diff --git a/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.h b/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.h
new file mode 100644
index 00000000..be4343a7
--- /dev/null
+++ b/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.h
@@ -0,0 +1,91 @@
+#ifndef __itkComputeHistogramQuantileThresholds_h
+#define __itkComputeHistogramQuantileThresholds_h
+
+#include 
+#include 
+
+namespace itk
+{
+/**
+  * \class ComputeHistogramQuantileThresholds
+  * \author Hans J. Johnson
+  *
+  * This filter just computes Histogram Quantile Thresholds.  It does not apply
+  *the thresholds.
+  *
+  */
+template 
+class ITK_EXPORT ComputeHistogramQuantileThresholds :
+  public Object
+{
+public:
+  /** Extract dimension from input and output image. */
+  itkStaticConstMacro(InputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+
+  /** Convenient typedefs for simplifying declarations. */
+  typedef TInputImage                           InputImageType;
+  typedef typename InputImageType::ConstPointer InputImagePointer;
+  typedef typename InputImageType::RegionType   InputImageRegionType;
+  typedef typename InputImageType::PixelType    InputPixelType;
+
+  typedef ComputeHistogramQuantileThresholds Self;
+  typedef Object                             Superclass;
+  typedef SmartPointer                 Pointer;
+  typedef typename TMaskImage::PixelType     MaskPixelType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ComputeHistogramQuantileThresholds, Object);
+
+  /** set Quantile Threshold */
+  itkSetMacro(QuantileLowerThreshold, double);
+  itkGetConstMacro(QuantileLowerThreshold, double);
+  itkSetMacro(QuantileUpperThreshold, double);
+  itkGetConstMacro(QuantileUpperThreshold, double);
+
+  itkGetConstMacro(LowerIntensityThresholdValue, typename InputImageType::PixelType);
+  itkGetConstMacro(UpperIntensityThresholdValue, typename InputImageType::PixelType);
+  itkGetConstMacro(NumberOfValidHistogramsEntries, unsigned int);
+
+  itkGetConstObjectMacro(Image, InputImageType);
+  itkSetConstObjectMacro(Image, InputImageType);
+
+  itkSetMacro(ImageMin, typename TInputImage::PixelType);
+  itkGetConstMacro(ImageMin, typename TInputImage::PixelType);
+  itkSetMacro(ImageMax, typename TInputImage::PixelType);
+  itkGetConstMacro(ImageMax, typename TInputImage::PixelType);
+
+  itkGetConstObjectMacro(BinaryPortionImage, TMaskImage);
+  itkSetObjectMacro(BinaryPortionImage, TMaskImage);
+
+  void Calculate();
+
+protected:
+  ComputeHistogramQuantileThresholds();
+  ~ComputeHistogramQuantileThresholds();
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+  InputImagePointer m_Image;
+  typename TMaskImage::Pointer m_BinaryPortionImage;
+  void ImageMinMax(InputPixelType & min, InputPixelType & max);
+
+  double m_QuantileLowerThreshold;
+  double m_QuantileUpperThreshold;
+  typename TInputImage::PixelType m_ImageMin;
+  typename TInputImage::PixelType m_ImageMax;
+
+  typename InputImageType::PixelType m_LowerIntensityThresholdValue;
+  typename InputImageType::PixelType m_UpperIntensityThresholdValue;
+  unsigned int m_NumberOfValidHistogramsEntries;
+};
+} // end namespace itk
+
+#if ITK_TEMPLATE_TXX
+#include "itkComputeHistogramQuantileThresholds.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.hxx b/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.hxx
new file mode 100644
index 00000000..e2a31a57
--- /dev/null
+++ b/BRAINSCommonLib/itkComputeHistogramQuantileThresholds.hxx
@@ -0,0 +1,159 @@
+#ifndef __itkComputeHistogramQuantileThresholds_hxx
+#define __itkComputeHistogramQuantileThresholds_hxx
+#include "itkComputeHistogramQuantileThresholds.h"
+
+// #include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include "itkScalarImagePortionToHistogramGenerator.h"
+
+namespace itk
+{
+template 
+ComputeHistogramQuantileThresholds
+::ComputeHistogramQuantileThresholds() :
+  m_QuantileLowerThreshold(0.0),
+  m_QuantileUpperThreshold(1.0)
+{
+}
+
+template 
+ComputeHistogramQuantileThresholds
+::~ComputeHistogramQuantileThresholds()
+{
+}
+
+template 
+void
+ComputeHistogramQuantileThresholds
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << "QuantileLowerThreshold "
+     << m_QuantileLowerThreshold << " "
+     << "QuantileUpperThreshold "
+     << m_QuantileUpperThreshold << std::endl;
+}
+
+template 
+void
+ComputeHistogramQuantileThresholds
+::ImageMinMax(typename TInputImage::PixelType & ImageMin,
+              typename TInputImage::PixelType & ImageMax)
+{
+  typename MinimumMaximumImageFilter::Pointer minmaxFilter =
+    MinimumMaximumImageFilter::New();
+  minmaxFilter->SetInput( this->GetImage() );
+  minmaxFilter->Update();
+  ImageMax = minmaxFilter->GetMaximum();
+  ImageMin = minmaxFilter->GetMinimum();
+}
+
+/**
+  *
+  * @author hjohnson (8/12/2008)
+  *
+  * @param m_LowerIntensityThresholdValue  The intensity value where
+  *"HistogramQuantileLowerThreshold" voxels
+  *              are below this threshold
+  * @param m_UpperIntensityThresholdValue  The intensity value where
+  *"HistogramQuantileUpperThreshold" voxels
+  *              are above this threshold
+  * @param m_NumberOfValidHistogramsEntries  The number of non-zero histogram
+  *bins
+  */
+template 
+void
+ComputeHistogramQuantileThresholds
+::Calculate()
+{
+  this->ImageMinMax(this->m_ImageMin, this->m_ImageMax);
+
+  typedef Statistics::ScalarImagePortionToHistogramGenerator
+  HistogramGeneratorType;
+  typename HistogramGeneratorType::Pointer histogramGenerator =
+    HistogramGeneratorType::New();
+  histogramGenerator->SetInput( this->GetImage() );
+  if( m_BinaryPortionImage.IsNotNull() )
+    {
+    histogramGenerator->SetBinaryPortionImage(m_BinaryPortionImage);
+    }
+
+  int NumberOfBins = static_cast( m_ImageMax - m_ImageMin + 1 );
+  histogramGenerator->SetNumberOfBins(NumberOfBins);
+  histogramGenerator->SetMarginalScale(1.0);
+  histogramGenerator->SetHistogramMin(m_ImageMin);
+  histogramGenerator->SetHistogramMax(m_ImageMax);
+
+  histogramGenerator->Compute();
+  typedef typename HistogramGeneratorType::HistogramType HistogramType;
+  HistogramType *histogram = const_cast( histogramGenerator->GetOutput() );
+  //  If the number of non-zero bins is <= 2, then it is a binary image, and
+  // Otsu won't do:
+  //
+  m_NumberOfValidHistogramsEntries = 0;
+    {
+    typename HistogramType::Iterator histIt = histogram->Begin();
+    bool saw_lowest = false;
+    while( histIt != histogram->End() )
+      {
+      // walking a 1-dimensional histogram from low to high:
+      const double measurement(histIt.GetMeasurementVector()[0]);
+
+      if( histIt.GetFrequency() != 0 )
+        {
+        ++m_NumberOfValidHistogramsEntries;
+        m_UpperIntensityThresholdValue = static_cast( measurement + 0.5 );
+        // rounding by chopping
+        if( !saw_lowest )
+          {
+          m_LowerIntensityThresholdValue = static_cast( measurement + 0.5 );
+          // rounding by chopping
+          saw_lowest = true;
+          }
+        }
+      ++histIt;
+      }
+
+    if( m_NumberOfValidHistogramsEntries <= 2 )  // then it is a binary image:
+      {
+      std::cout
+      << "Image handled with only two catgegories; effectively, binary thresholding."
+      << std::endl;
+      }
+    else
+      {
+      m_LowerIntensityThresholdValue =
+        static_cast
+        ( histogram->Quantile(0, this->m_QuantileLowerThreshold) );
+      m_UpperIntensityThresholdValue =
+        static_cast
+        ( histogram->Quantile(0, this->m_QuantileUpperThreshold) );
+      std::cout
+      << m_NumberOfValidHistogramsEntries
+      << " ValidHistogramsEntries,  "
+      << histogram->GetTotalFrequency()
+      << " TotalFrequency"
+      << std::endl;
+      std::cout
+      << m_QuantileLowerThreshold
+      << " ---> "
+      << static_cast( m_LowerIntensityThresholdValue )
+      << std::endl;
+      std::cout
+      << m_QuantileUpperThreshold
+      << " ---> "
+      << static_cast( m_UpperIntensityThresholdValue )
+      << std::endl;
+      }
+    }
+  return;
+}
+
+}
+#endif // __itkComputeHistogramQuantileThresholds_hxx
diff --git a/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.h b/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.h
new file mode 100644
index 00000000..5d56cb28
--- /dev/null
+++ b/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.h
@@ -0,0 +1,332 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    itkDiffusionTensor3DReconstructionWithMaskImageFilter.h
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkDiffusionTensor3DReconstructionWithMaskImageFilter_h
+#define __itkDiffusionTensor3DReconstructionWithMaskImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkDiffusionTensor3D.h"
+#include "vnl/vnl_matrix.h"
+#include "vnl/vnl_vector_fixed.h"
+#include "vnl/vnl_matrix_fixed.h"
+#include "vnl/algo/vnl_svd.h"
+#include "itkVectorContainer.h"
+#include "itkVectorImage.h"
+
+namespace itk
+{
+
+#if ITK_VERSION_MAJOR < 4 && ! defined (ITKv3_THREAD_ID_TYPE_DEFINED)
+#define ITKv3_THREAD_ID_TYPE_DEFINED 1
+  typedef int ThreadIdType ;
+#endif
+
+/** \class DiffusionTensor3DReconstructionWithMaskImageFilter
+ * \brief This class takes as input one or more reference image (acquired in the
+ * absence of diffusion sensitizing gradients) and 'n' diffusion
+ * weighted images and their gradient directions and computes an image of
+ * tensors. (with DiffusionTensor3D as the pixel type). Once that is done, you
+ * can apply filters on this tensor image to compute FA, ADC, RGB weighted
+ * maps etc.
+ *
+ * \par Inputs and Usage
+ * There are two ways to use this class. When you have one reference image and \c n
+ * gradient images, you would use the class as
+ * \code
+ *       filter->SetReferenceImage( image0 );
+ *       filter->AddGradientImage( direction1, image1 );
+ *       filter->AddGradientImage( direction2, image2 );
+ *   ...
+ * \endcode
+ *
+ * \par
+ * When you have the 'n' gradient and one or more reference images in a single
+ * multi-component image (VectorImage), you can specify the images simply as
+ * \code
+ *       filter->SetGradientImage( directionsContainer, vectorImage );
+ * \endcode
+ * Note that this method is used to specify both the reference and gradient images.
+ * This is convenient when the DWI images are read in using the
+ * NRRD
+ * format. Like the Nrrd format, the reference images are those components of the
+ * vectorImage whose gradient direction is (0,0,0). If more than one reference image
+ * is present, they are averaged prior to applying the Stejskal-Tanner equations.
+ *
+ * \par Outputs
+ * The output image is an image of Tensors:
+ * \code
+ *       Image< DiffusionTensor3D< TTensorPixelType >, 3 >
+ * \endcode
+ *
+ * \par Parameters
+ * \li Threshold -  Threshold on the reference image data. The output tensor will
+ * be a null tensor for pixels in the reference image that have a value less
+ * than this.
+ * \li BValue - See the documentation of SetBValue().
+ * \li At least 6 gradient images must be specified for the filter to be able
+ * to run.
+ *
+ *
+ * \par Template parameters
+ * The class is templated over the pixel type of the reference and gradient
+ * images (expected to be scalar data types) and the internal representation
+ * of the DiffusionTensor3D pixel (double, float etc).
+ *
+ * \par References:
+ * \li[1]
+ * C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis,
+ * "Processing and visualization for Diffusion tensor MRI", Medical image
+ * Analysis, 2002, pp 93-108.
+ * \li[2]
+ * A Dual Tensor Basis Solution to the Stejskal-Tanner Equations for DT-MRI
+ *
+ * \par WARNING:
+ * Although this filter has been written to support multiple threads, please
+ * set the number of threads to 1.
+ * \code
+ *         filter->SetNumberOfThreads(1);
+ * \endcode
+ * This is due to buggy code in netlib/dsvdc, that is called by vnl_svd.
+ * (used to compute the psudo-inverse to find the dual tensor basis).
+ *
+ * \author Thanks to Xiaodong Tao, GE, for contributing parts of this class. Also
+ * thanks to Casey Goodlet, UNC for patches to support multiple baseline images
+ * and other improvements.
+ *
+ * \note
+ * This work is part of the National Alliance for Medical image Computing
+ * (NAMIC), funded by the National Institutes of Health through the NIH Roadmap
+ * for Medical Research, Grant U54 EB005149.
+ *
+ * \par Examples and Datasets
+ * See Examples/Filtering/DiffusionTensor3DReconstructionWithMaskImageFilter.cxx
+ * Sample DTI datasets may be obtained from
+ \begin verbatim
+     ftp://public.kitware.com/pub/namic/DTI/Data/dwi.nhdr
+     ftp://public.kitware.com/pub/namic/DTI/Data/dwi.img.gz ( gunzip this )
+ \end verbatim
+ *
+ * \sa DiffusionTensor3D SymmetricSecondRankTensor
+ * \ingroup Multithreaded  TensorObjects
+ */
+
+template 
+class ITK_EXPORT DiffusionTensor3DReconstructionWithMaskImageFilter :
+  public ImageToImageFilter,
+                            Image, 3> >
+{
+
+public:
+
+  typedef DiffusionTensor3DReconstructionWithMaskImageFilter Self;
+  typedef SmartPointer                                 Pointer;
+  typedef SmartPointer                           ConstPointer;
+  typedef ImageToImageFilter,
+                             Image, 3> >
+  Superclass;
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Runtime information support. */
+  itkTypeMacro(DiffusionTensor3DReconstructionWithMaskImageFilter,
+               ImageToImageFilter);
+
+  typedef TReferenceImagePixelType ReferencePixelType;
+
+  typedef TGradientImagePixelType GradientPixelType;
+
+  typedef DiffusionTensor3D TensorPixelType;
+
+  typedef unsigned char MaskPixelType;
+
+  /** Reference image data,  This image is aquired in the absence
+   * of a diffusion sensitizing field gradient */
+  typedef typename Superclass::InputImageType ReferenceImageType;
+
+  typedef Image TensorImageType;
+
+  typedef TensorImageType OutputImageType;
+
+  typedef Image MaskImageType;
+
+  typedef typename Superclass::OutputImageRegionType
+  OutputImageRegionType;
+
+  /** Typedef defining one (of the many) gradient images.  */
+  typedef Image GradientImageType;
+
+  /** An alternative typedef defining one (of the many) gradient images.
+   * It will be assumed that the vectorImage has the same dimension as the
+   * Reference image and a vector length parameter of \c n (number of
+   * gradient directions) */
+  typedef VectorImage GradientImagesType;
+
+  /** Holds the tensor basis coefficients G_k */
+  typedef vnl_matrix_fixed TensorBasisMatrixType;
+
+  typedef vnl_matrix CoefficientMatrixType;
+
+  /** Holds each magnetic field gradient used to acquire one DWImage */
+  typedef vnl_vector_fixed GradientDirectionType;
+
+  /** Container to hold gradient directions of the 'n' DW measurements */
+  typedef VectorContainer                  GradientDirectionContainerType;
+
+  /** Set method to add a gradient direction and its corresponding image. */
+  void AddGradientImage( const GradientDirectionType &, const GradientImageType *image);
+
+  /** Another set method to add a gradient directions and its corresponding
+   * image. The image here is a VectorImage. The user is expected to pass the
+   * gradient directions in a container. The ith element of the container
+   * corresponds to the gradient direction of the ith component image the
+   * VectorImage.  For the baseline image, a vector of all zeros
+   * should be set. */
+  void SetGradientImage( GradientDirectionContainerType *, const GradientImagesType *image);
+
+  /** Set method to set the reference image. */
+  void SetReferenceImage( ReferenceImageType *referenceImage )
+  {
+    if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
+      {
+      itkExceptionMacro( << "Cannot call both methods:"
+                         << "AddGradientImage and SetGradientImage. Please call only one of them.");
+      }
+
+    this->ProcessObject::SetNthInput( 0, referenceImage );
+
+    m_GradientImageTypeEnumeration = GradientIsInManyImages;
+  }
+
+  /** set the optional mask image*/
+  void SetMaskImage(const MaskImageType *maskImage)
+  {
+    this->m_MaskImage = maskImage;
+  }
+
+  /** Get reference image */
+  virtual ReferenceImageType * GetReferenceImage()
+  {
+    return static_cast(this->ProcessObject::GetInput(0) );
+  }
+
+  /** Return the gradient direction. idx is 0 based */
+  virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
+  {
+    if( idx >= m_NumberOfGradientDirections )
+      {
+      itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
+      }
+    return m_GradientDirectionContainer->ElementAt( idx + 1 );
+  }
+
+  /** Threshold on the reference image data. The output tensor will be a null
+   * tensor for pixels in the reference image that have a value less than this
+   * threshold. */
+  itkSetMacro( Threshold, ReferencePixelType );
+  itkGetConstMacro( Threshold, ReferencePixelType );
+
+  /**
+   * The BValue \f$ (s/mm^2) \f$ value used in normalizing the tensors to
+   * physically meaningful units.  See equation (24) of the first reference for
+   * a description of how this is applied to the tensor estimation.
+   * Equation (1) of the same reference describes the physical significance.
+   */
+  itkSetMacro( BValue, TTensorPixelType);
+#ifdef GetBValue
+#undef GetBValue
+#endif
+  itkGetConstReferenceMacro( BValue, TTensorPixelType);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro(ReferenceEqualityComparableCheck,
+                  (Concept::EqualityComparable ) );
+  itkConceptMacro(TensorEqualityComparableCheck,
+                  (Concept::EqualityComparable ) );
+  itkConceptMacro(GradientConvertibleToDoubleCheck,
+                  (Concept::Convertible ) );
+  itkConceptMacro(DoubleConvertibleToTensorCheck,
+                  (Concept::Convertible ) );
+  itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
+                  (Concept::AdditiveOperators ) );
+  itkConceptMacro(ReferenceOStreamWritableCheck,
+                  (Concept::OStreamWritable ) );
+  itkConceptMacro(TensorOStreamWritableCheck,
+                  (Concept::OStreamWritable ) );
+  /** End concept checking */
+#endif
+protected:
+  DiffusionTensor3DReconstructionWithMaskImageFilter();
+  ~DiffusionTensor3DReconstructionWithMaskImageFilter()
+  {
+  };
+  void PrintSelf(std::ostream& os, Indent indent) const;
+
+  void ComputeTensorBasis();
+
+  void BeforeThreadedGenerateData();
+
+  void ThreadedGenerateData( const
+                             OutputImageRegionType & outputRegionForThread, ThreadIdType );
+
+  /** enum to indicate if the gradient image is specified as a single multi-
+   * component image or as several separate images */
+  typedef enum
+    {
+    GradientIsInASingleImage = 1,
+    GradientIsInManyImages,
+    Else
+    } GradientImageTypeEnumeration;
+private:
+
+  /* Tensor basis coeffs */
+  TensorBasisMatrixType m_TensorBasis;
+
+  CoefficientMatrixType m_BMatrix;
+
+  /** container to hold gradient directions */
+  GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
+
+  /** Number of gradient measurements */
+  unsigned int m_NumberOfGradientDirections;
+
+  /** Number of baseline images */
+  unsigned int m_NumberOfBaselineImages;
+
+  /** Threshold on the reference image data */
+  ReferencePixelType m_Threshold;
+
+  /** LeBihan's b-value for normalizing tensors */
+  TTensorPixelType m_BValue;
+
+  /** Gradient image was specified in a single image or in multiple images */
+  GradientImageTypeEnumeration m_GradientImageTypeEnumeration;
+
+  /** Mask Image */
+  MaskImageType::ConstPointer m_MaskImage;
+};
+
+}
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx b/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx
new file mode 100644
index 00000000..47002550
--- /dev/null
+++ b/BRAINSCommonLib/itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx
@@ -0,0 +1,534 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkDiffusionTensor3DReconstructionWithMaskImageFilter_hxx
+#define __itkDiffusionTensor3DReconstructionWithMaskImageFilter_hxx
+
+#include "itkDiffusionTensor3DReconstructionWithMaskImageFilter.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+#include "itkImageRegionIterator.h"
+#include "itkArray.h"
+#include "vnl/vnl_vector.h"
+
+namespace itk
+{
+
+template 
+DiffusionTensor3DReconstructionWithMaskImageFilter
+::DiffusionTensor3DReconstructionWithMaskImageFilter()
+{
+  // At least 1 inputs is necessary for a vector image.
+  // For images added one at a time we need at least six
+  this->SetNumberOfRequiredInputs( 1 );
+  m_NumberOfGradientDirections = 0;
+  m_NumberOfBaselineImages = 1;
+  m_Threshold = NumericTraits::min();
+  m_GradientImageTypeEnumeration = Else;
+  m_GradientDirectionContainer = NULL;
+  m_TensorBasis.set_identity();
+  m_BValue = 1.0;
+}
+
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::BeforeThreadedGenerateData()
+{
+  // If we have more than 2 inputs, then each input, except the first is a
+  // gradient image. The number of gradient images must match the number of
+  // gradient directions.
+  const unsigned int numberOfInputs = this->GetNumberOfInputs();
+
+  // There need to be at least 6 gradient directions to be able to compute the
+  // tensor basis
+  if( m_NumberOfGradientDirections < 6 )
+    {
+    itkExceptionMacro( << "At least 6 gradient directions are required" );
+    }
+
+  // If there is only 1 gradient image, it must be an itk::VectorImage.
+  // Otherwise
+  // we must have a container of (numberOfInputs-1) itk::Image. Check to make
+  // sure
+  if( numberOfInputs == 1
+      && m_GradientImageTypeEnumeration != GradientIsInASingleImage )
+    {
+    std::string gradientImageClassName(
+      this->ProcessObject::GetInput(0)->GetNameOfClass() );
+    if( strcmp(gradientImageClassName.c_str(), "VectorImage") != 0 )
+      {
+      itkExceptionMacro(
+        << "There is only one Gradient image. I expect that to be a VectorImage. "
+        << "But its of type: " << gradientImageClassName );
+      }
+    }
+  if( this->m_MaskImage.IsNotNull() )
+    {
+    typename MaskImageType::SizeType maskSize =
+      this->m_MaskImage->GetLargestPossibleRegion().GetSize();
+    if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
+      {
+      ReferenceImageType *refImage =
+        static_cast(this->ProcessObject::GetInput(0) );
+      typename ReferenceImageType::RegionType::SizeType refSize =
+        refImage->GetLargestPossibleRegion().GetSize();
+      if( refSize != maskSize )
+        {
+        itkExceptionMacro( << "Mask size doesn't match Reference Image Size"
+                           << " Mask Size " << maskSize
+                           << " Ref Size " << refSize );
+        }
+      }
+    else if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
+      {
+      GradientImagesType *gradientImagePointer =
+        static_cast(this->ProcessObject::GetInput(0) );
+      typename GradientImagesType::RegionType::SizeType gradSize =
+        gradientImagePointer->GetLargestPossibleRegion().GetSize();
+      if( gradSize != maskSize )
+        {
+        itkExceptionMacro( << "Mask size doesn't match Gradient Image Size"
+                           << " Mask Size " << maskSize
+                           << " Grad Size " << gradSize );
+        }
+      }
+    }
+  this->ComputeTensorBasis();
+}
+
+// POTENTIAL WARNING:
+//
+// Until we fix netlib svd routines, we will need to set the number of thread
+// to 1.
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
+                       ThreadIdType )
+{
+  typename OutputImageType::Pointer outputImage =
+    static_cast(this->ProcessObject::GetOutput(0) );
+
+  ImageRegionIterator oit(outputImage, outputRegionForThread);
+  oit.GoToBegin();
+
+  vnl_vector B(m_NumberOfGradientDirections);
+  vnl_vector D(6);
+
+  // if a mask is present, iterate through mask image and skip zero voxels
+  bool useMask(this->m_MaskImage.IsNotNull() );
+  typedef ImageRegionConstIterator
+  MaskItType;
+  MaskItType maskIt;
+  if( useMask )
+    {
+    MaskItType tmp(this->m_MaskImage, outputRegionForThread);
+    maskIt = tmp;
+    maskIt.GoToBegin();
+    }
+  // Two cases here .
+  // 1. If the Gradients have been specified in multiple images, we will create
+  // 'n' iterators for each of the gradient images and solve the Stejskal-Tanner
+  // equations for every pixel.
+  // 2. If the Gradients have been specified in a single multi-component image,
+  // one iterator will suffice to do the same.
+
+  if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
+    {
+    typedef ImageRegionConstIterator
+    ItType;
+    ReferenceImageType *refImage =
+      static_cast(this->ProcessObject::GetInput(0) );
+    ItType
+    it(refImage, outputRegionForThread);
+    it.GoToBegin();
+
+    typedef ImageRegionConstIterator GradientIteratorType;
+    std::vector gradientItContainer;
+    for( unsigned int i = 1; i <= m_NumberOfGradientDirections; ++i )
+      {
+
+      // Would have liked a dynamic_cast here, but seems SGI doesn't like it
+      // The enum will ensure that an inappropriate cast is not done
+      typename GradientImageType::Pointer gradientImagePointer  = dynamic_cast(
+          this->ProcessObject::GetInput(i) );
+      if( gradientImagePointer.IsNull() )
+        {
+        std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+        exit(-1);
+        }
+
+      GradientIteratorType *git = new GradientIteratorType(
+          gradientImagePointer, outputRegionForThread );
+      git->GoToBegin();
+      gradientItContainer.push_back(git);
+      }
+
+    // Iterate over the reference and gradient images and solve the steskal
+    // equations to reconstruct the Diffusion tensor.
+    // See splweb.bwh.harvard.edu:8000/pages/papers/westin/ISMRM2002.pdf
+    // "A Dual Tensor Basis Solution to the Stejskal-Tanner Equations for
+    // DT-MRI"
+
+    while( !it.IsAtEnd() )
+      {
+
+      ReferencePixelType b0 = it.Get();
+      //
+      // if a mask is present, and we don't have a zero pixel
+      // look up the voxel in the mask image corresponding to
+      // the location of the current index.
+      bool unmaskedPixel(true);
+      if( useMask )
+        {
+        if( maskIt.Value() == NumericTraits::Zero )
+          {
+          unmaskedPixel = false;
+          }
+        ++maskIt;
+        }
+      TensorPixelType tensor(0.0);
+
+      if( (b0 != 0) && unmaskedPixel && (b0 >= m_Threshold) )
+        {
+        for( unsigned int i = 0; i < m_NumberOfGradientDirections; ++i )
+          {
+          GradientPixelType b = gradientItContainer[i]->Get();
+
+          if( b == 0 )
+            {
+            B[i] = 0;
+            }
+          else
+            {
+            B[i] = -vcl_log( static_cast(b) / static_cast(b0) ) / this->m_BValue;
+            }
+
+          ++(*gradientItContainer[i]);
+          }
+
+        vnl_svd pseudoInverseSolver( m_TensorBasis );
+        if( m_NumberOfGradientDirections > 6 )
+          {
+          D = pseudoInverseSolver.solve( m_BMatrix * B );
+          }
+        else
+          {
+          D = pseudoInverseSolver.solve( B );
+          }
+
+        tensor(0, 0) = D[0];
+        tensor(0, 1) = D[1];
+        tensor(0, 2) = D[2];
+        tensor(1, 1) = D[3];
+        tensor(1, 2) = D[4];
+        tensor(2, 2) = D[5];
+        }
+      else
+        {
+        for( unsigned int i = 0; i < m_NumberOfGradientDirections; ++i )
+          {
+          ++(*gradientItContainer[i]);
+          }
+        }
+
+      oit.Set( tensor );
+      ++oit;
+      ++it;
+      }
+    for( unsigned int i = 0; i < gradientItContainer.size(); ++i )
+      {
+      delete gradientItContainer[i];
+      }
+    }
+  // The gradients are specified in a single multi-component image
+  else if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
+    {
+    typedef ImageRegionConstIterator GradientIteratorType;
+    typedef typename GradientImagesType::PixelType       GradientVectorType;
+    typename GradientImagesType::Pointer gradientImagePointer = NULL;
+
+    // Would have liked a dynamic_cast here, but seems SGI doesn't like it
+    // The enum will ensure that an inappropriate cast is not done
+    gradientImagePointer = dynamic_cast(
+        this->ProcessObject::GetInput(0) );
+
+    GradientIteratorType git(gradientImagePointer, outputRegionForThread );
+    git.GoToBegin();
+
+    // Compute the indicies of the baseline images and gradient images
+    std::vector baselineind; // contains the indicies of
+                                           // the baseline images
+    std::vector gradientind; // contains the indicies of
+                                           // the gradient images
+    for( GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
+         gdcit != this->m_GradientDirectionContainer->End(); ++gdcit )
+      {
+      if( gdcit.Value().one_norm() <= 0.0 )
+        {
+        baselineind.push_back(gdcit.Index() );
+        }
+      else
+        {
+        gradientind.push_back(gdcit.Index() );
+        }
+      }
+
+    while( !git.IsAtEnd() )
+      {
+      GradientVectorType b = git.Get();
+
+      typename NumericTraits::AccumulateType b0 = NumericTraits::Zero;
+      // Average the baseline image pixels
+      for( unsigned int i = 0; i < baselineind.size(); ++i )
+        {
+        b0 += b[baselineind[i]];
+        }
+      b0 /= this->m_NumberOfBaselineImages;
+
+      TensorPixelType tensor(0.0);
+
+      //
+      // if a mask is present, and we don't have a zero pixel
+      // look up the voxel in the mask image corresponding to
+      // the location of the current index.
+      bool unmaskedPixel(true);
+      if( useMask )
+        {
+        if( maskIt.Value() == NumericTraits::Zero )
+          {
+          unmaskedPixel = false;
+          }
+        ++maskIt;
+        }
+
+      if( (b0 != 0) && unmaskedPixel && (b0 >= m_Threshold) )
+        {
+        for( unsigned int i = 0; i < m_NumberOfGradientDirections; ++i )
+          {
+          if( b[gradientind[i]] == 0 )
+            {
+            B[i] = 0;
+            }
+          else
+            {
+            B[i] = -vcl_log( static_cast(b[gradientind[i]]) / static_cast(b0) ) / this->m_BValue;
+            }
+          }
+
+        vnl_svd pseudoInverseSolver( m_TensorBasis );
+        if( m_NumberOfGradientDirections > 6 )
+          {
+          D = pseudoInverseSolver.solve( m_BMatrix * B );
+          }
+        else
+          {
+          D = pseudoInverseSolver.solve( B );
+          }
+
+        tensor(0, 0) = D[0];
+        tensor(0, 1) = D[1];
+        tensor(0, 2) = D[2];
+        tensor(1, 1) = D[3];
+        tensor(1, 2) = D[4];
+        tensor(2, 2) = D[5];
+
+        }
+
+      oit.Set( tensor );
+      ++oit; // Output (reconstructed tensor image) iterator
+      ++git; // Gradient  image iterator
+      }
+    }
+
+}
+
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::ComputeTensorBasis()
+{
+  if( m_NumberOfGradientDirections < 6 )
+    {
+    itkExceptionMacro( << "Not enough gradient directions supplied. Need to supply at least 6" );
+    }
+
+  // This is only important if we are using a vector image.  For
+  // images added one at a time, this is not needed but doesn't hurt.
+  std::vector gradientind;
+  for( GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
+       gdcit != this->m_GradientDirectionContainer->End(); ++gdcit )
+    {
+    if( gdcit.Value().one_norm() > 0.0 )
+      {
+      gradientind.push_back(gdcit.Index() );
+      }
+    }
+
+  m_BMatrix.set_size( m_NumberOfGradientDirections, 6 );
+  for( unsigned int m = 0; m < m_NumberOfGradientDirections; ++m )
+    {
+    m_BMatrix[m][0] =     m_GradientDirectionContainer->ElementAt(gradientind[m])[0]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[0];
+    m_BMatrix[m][1] = 2 * m_GradientDirectionContainer->ElementAt(gradientind[m])[0]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[1];
+    m_BMatrix[m][2] = 2 * m_GradientDirectionContainer->ElementAt(gradientind[m])[0]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[2];
+    m_BMatrix[m][3] =     m_GradientDirectionContainer->ElementAt(gradientind[m])[1]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[1];
+    m_BMatrix[m][4] = 2 * m_GradientDirectionContainer->ElementAt(gradientind[m])[1]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[2];
+    m_BMatrix[m][5] =     m_GradientDirectionContainer->ElementAt(gradientind[m])[2]
+      * m_GradientDirectionContainer->ElementAt(gradientind[m])[2];
+    }
+
+  if( m_NumberOfGradientDirections > 6 )
+    {
+    m_TensorBasis = m_BMatrix.transpose() * m_BMatrix;
+    }
+  else
+    {
+    m_TensorBasis = m_BMatrix;
+    }
+
+  m_BMatrix.inplace_transpose();
+
+}
+
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::AddGradientImage( const GradientDirectionType & gradientDirection,
+                    const GradientImageType *gradientImage )
+{
+  // Make sure crazy users did not call both AddGradientImage and
+  // SetGradientImage
+  if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
+    {
+    itkExceptionMacro( << "Cannot call both methods:"
+                       << "AddGradientImage and SetGradientImage. Please call only one of them.");
+    }
+
+  // If the container to hold the gradient directions hasn't been allocated
+  // yet, allocate it.
+  if( !this->m_GradientDirectionContainer )
+    {
+    this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
+    }
+
+  m_GradientDirectionContainer->InsertElement(
+    m_NumberOfGradientDirections, gradientDirection / gradientDirection.two_norm() );
+  ++m_NumberOfGradientDirections;
+  this->ProcessObject::SetNthInput( m_NumberOfGradientDirections,
+                                    const_cast(gradientImage) );
+  m_GradientImageTypeEnumeration = GradientIsInManyImages;
+}
+
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::SetGradientImage( GradientDirectionContainerType *gradientDirection,
+                    const GradientImagesType *gradientImage )
+{
+  // Make sure crazy users did not call both AddGradientImage and
+  // SetGradientImage
+  if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
+    {
+    itkExceptionMacro( << "Cannot call both methods:"
+                       << "AddGradientImage and SetGradientImage. Please call only one of them.");
+    }
+
+  this->m_GradientDirectionContainer = gradientDirection;
+
+  unsigned int numImages = gradientDirection->Size();
+  this->m_NumberOfBaselineImages = 0;
+  for( GradientDirectionContainerType::Iterator it = this->m_GradientDirectionContainer->Begin();
+       it != this->m_GradientDirectionContainer->End(); ++it )
+    {
+    if( it.Value().one_norm() <= 0.0 )
+      {
+      this->m_NumberOfBaselineImages++;
+      }
+    else // Normalize non-zero gradient directions
+      {
+      it.Value() = it.Value() / it.Value().two_norm();
+      }
+    }
+
+  this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages;
+
+  // ensure that the gradient image we received has as many components as
+  // the number of gradient directions
+  if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + this->m_NumberOfGradientDirections )
+    {
+    itkExceptionMacro( << this->m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages
+                       << "baselines = " << this->m_NumberOfGradientDirections + this->m_NumberOfBaselineImages
+                       << " directions specified but image has " << gradientImage->GetVectorLength()
+                       << " components.");
+    }
+
+  this->ProcessObject::SetNthInput( 0,
+                                    const_cast(gradientImage) );
+  m_GradientImageTypeEnumeration = GradientIsInASingleImage;
+}
+
+template 
+void DiffusionTensor3DReconstructionWithMaskImageFilter
+::PrintSelf(std::ostream& os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "TensorBasisMatrix: " << m_TensorBasis << std::endl;
+  os << indent << "Coeffs: " << m_BMatrix << std::endl;
+  if( m_GradientDirectionContainer )
+    {
+    os << indent << "GradientDirectionContainer: "
+       << m_GradientDirectionContainer << std::endl;
+    }
+  else
+    {
+    os << indent
+       << "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
+    }
+  os << indent << "NumberOfGradientDirections: "
+     << m_NumberOfGradientDirections << std::endl;
+  os << indent << "NumberOfBaselineImages: "
+     << m_NumberOfBaselineImages << std::endl;
+  os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl;
+  os << indent << "BValue: " << m_BValue << std::endl;
+  if( this->m_GradientImageTypeEnumeration == GradientIsInManyImages )
+    {
+    os << indent << "Gradient images haven been supplied " << std::endl;
+    }
+  else if( this->m_GradientImageTypeEnumeration == GradientIsInManyImages )
+    {
+    os << indent << "A multicomponent gradient image has been supplied" << std::endl;
+    }
+}
+
+}
+
+#endif
diff --git a/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.h b/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.h
new file mode 100644
index 00000000..614aca08
--- /dev/null
+++ b/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.h
@@ -0,0 +1,181 @@
+#ifndef __itkExponentialDeformationFieldImageFilter2_h
+#define __itkExponentialDeformationFieldImageFilter2_h
+
+#include "itkImageToImageFilter.h"
+#include "itkDivideByConstantImageFilter.h"
+#include "itkCastImageFilter.h"
+#include "itkOppositeImageFilter.h"
+#include "itkWarpVectorImageFilter.h"
+#include "itkVectorLinearInterpolateNearestNeighborExtrapolateImageFunction.h"
+#include "itkAddImageFilter.h"
+
+namespace itk
+{
+/** \class ExponentialDeformationFieldImageFilter2
+  * \brief Computes a diffeomorphic deformation field as the Lie group
+  * exponential of a vector field.
+  *
+  * ExponentialDeformationFieldImageFilter2 takes a 'smooth' vector field
+  * as input and computes the deformation field that is its exponential.
+  *
+  * Given that both the input and output deformation field are represented as
+  * discrete images with pixel type vector, the exponential will be only an
+  * estimation and will probably not correspond to a perfect exponential.  The
+  * precision of the exponential can be improved at the price of increasing the
+  * computation time (number of iterations).
+  *
+  * The method used for computing the exponential deformation field is
+  * an iterative scaling and squaring (cf Arsigny et al., "A
+  * Log-Euclidean Framework for Statistics on Diffeomorphisms", MICCAI'06).
+  *
+  *    \f[
+  *      exp(\Phi) = exp( \frac{\Phi}{2^N} )^{2^N}
+  *    \f]
+  *
+  *
+  * This filter expects both the input and output images to be of pixel type
+  * Vector.
+  *
+  * \author Tom Vercauteren, INRIA & Mauna Kea Technologies
+  *
+  * This implementation was taken from the Insight Journal paper:
+  * http://hdl.handle.net/1926/510
+  *
+  * \ingroup ImageToImageFilter
+  */
+template 
+class ITK_EXPORT ExponentialDeformationFieldImageFilter2 :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef ExponentialDeformationFieldImageFilter2       Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ExponentialDeformationFieldImageFilter2, ImageToImageFilter);
+
+  /** Some convenient typedefs. */
+  typedef TInputImage                            InputImageType;
+  typedef typename InputImageType::Pointer       InputImagePointer;
+  typedef typename InputImageType::ConstPointer  InputImageConstPointer;
+  typedef typename InputImageType::PixelType     InputPixelType;
+  typedef typename InputPixelType::RealValueType InputPixelRealValueType;
+
+  typedef TOutputImage                        OutputImageType;
+  typedef typename OutputImageType::Pointer   OutputImagePointer;
+  typedef typename OutputImageType::PixelType OutputPixelType;
+
+  /** Specify the maximum number of iteration. */
+  itkSetMacro(MaximumNumberOfIterations, unsigned int);
+  itkGetConstMacro(MaximumNumberOfIterations, unsigned int);
+
+  /** If AutomaticNumberOfIterations is off, the number of iterations is
+    * given by MaximumNumberOfIterations. If it is on, we try to get
+    * the lowest good number (which may not be larger than
+    * MaximumNumberOfIterations ) */
+  itkSetMacro(AutomaticNumberOfIterations, bool);
+  itkGetConstMacro(AutomaticNumberOfIterations, bool);
+  itkBooleanMacro(AutomaticNumberOfIterations);
+
+  /** If ComputeInverse is on, the filter will compute the exponential
+    * of the opposite (minus) of the input vector field. The output deformation
+    * fields computed with ComputeInverse set to on and off respectively
+    * therefore represent spatial transformations that are inverses of
+    * each other. */
+  itkSetMacro(ComputeInverse, bool);
+  itkGetConstMacro(ComputeInverse, bool);
+  itkBooleanMacro(ComputeInverse);
+
+  /** Image dimension. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(PixelDimension, unsigned int,
+                      InputPixelType::Dimension);
+  itkStaticConstMacro(OutputPixelDimension, unsigned int,
+                      OutputPixelType::Dimension);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( OutputHasNumericTraitsCheck,
+                   ( Concept::HasNumericTraits ) );
+  itkConceptMacro( SameDimensionCheck1,
+                   ( Concept::SameDimension ) );
+  itkConceptMacro( SameDimensionCheck2,
+                   ( Concept::SameDimension ) );
+  itkConceptMacro( SameDimensionCheck3,
+                   ( Concept::SameDimension ) );
+  /** End concept checking */
+#endif
+protected:
+  ExponentialDeformationFieldImageFilter2();
+  virtual ~ExponentialDeformationFieldImageFilter2()
+  {
+  }
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** GenerateData() */
+  void GenerateData();
+
+  typedef typename InputImageType::RegionType RegionType;
+
+  typedef DivideByConstantImageFilter<
+    InputImageType,
+    InputPixelRealValueType, OutputImageType>         DivideByConstantType;
+
+  typedef CastImageFilter<
+    InputImageType, OutputImageType>                   CasterType;
+
+  typedef OppositeImageFilter<
+    InputImageType, OutputImageType>                   OppositerType;
+
+  typedef WarpVectorImageFilter<
+    OutputImageType,
+    OutputImageType, OutputImageType>                  VectorWarperType;
+
+  typedef VectorLinearInterpolateNearestNeighborExtrapolateImageFunction<
+    OutputImageType, double>                            FieldInterpolatorType;
+
+  typedef AddImageFilter<
+    OutputImageType, OutputImageType, OutputImageType> AdderType;
+
+  typedef typename DivideByConstantType::Pointer     DivideByConstantPointer;
+  typedef typename CasterType::Pointer               CasterPointer;
+  typedef typename OppositerType::Pointer            OppositerPointer;
+  typedef typename VectorWarperType::Pointer         VectorWarperPointer;
+  typedef typename FieldInterpolatorType::Pointer    FieldInterpolatorPointer;
+  typedef typename FieldInterpolatorType::OutputType FieldInterpolatorOutputType;
+  typedef typename AdderType::Pointer                AdderPointer;
+private:
+  ExponentialDeformationFieldImageFilter2(const Self &); // purposely not
+                                                         // implemented
+  void operator=(const Self &);                          // purposely not
+
+  // implemented
+
+  bool         m_AutomaticNumberOfIterations;
+  unsigned int m_MaximumNumberOfIterations;
+
+  bool m_ComputeInverse;
+
+  DivideByConstantPointer m_Divider;
+  CasterPointer           m_Caster;
+  OppositerPointer        m_Oppositer;
+  VectorWarperPointer     m_Warper;
+  AdderPointer            m_Adder;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkExponentialDeformationFieldImageFilter2.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.hxx b/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.hxx
new file mode 100644
index 00000000..f090144c
--- /dev/null
+++ b/BRAINSCommonLib/itkExponentialDeformationFieldImageFilter2.hxx
@@ -0,0 +1,209 @@
+#ifndef __itkExponentialDeformationFieldImageFilter2_hxx
+#define __itkExponentialDeformationFieldImageFilter2_hxx
+
+#include "itkExponentialDeformationFieldImageFilter2.h"
+#include "itkProgressReporter.h"
+#include "itkImageRegionConstIterator.h"
+
+namespace itk
+{
+/**
+  * Initialize new instance
+  */
+template 
+ExponentialDeformationFieldImageFilter2
+::ExponentialDeformationFieldImageFilter2()
+{
+  m_AutomaticNumberOfIterations = true;
+  m_MaximumNumberOfIterations = 20;
+  m_ComputeInverse = false;
+  m_Divider = DivideByConstantType::New();
+  m_Caster = CasterType::New();
+  m_Oppositer = OppositerType::New();
+  m_Warper = VectorWarperType::New();
+
+  FieldInterpolatorPointer VectorInterpolator =
+    FieldInterpolatorType::New();
+  m_Warper->SetInterpolator(VectorInterpolator);
+
+  m_Adder = AdderType::New();
+  m_Adder->InPlaceOn();
+}
+
+/**
+  * Print out a description of self
+  *
+  * \todo Add details about this class
+  */
+template 
+void
+ExponentialDeformationFieldImageFilter2
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "AutomaticNumberOfIterations: "
+     << m_AutomaticNumberOfIterations << std::endl;
+  os << indent << "MaximumNumberOfIterations:   "
+     << m_MaximumNumberOfIterations << std::endl;
+  os << indent << "ComputeInverse:   "
+     << ( m_ComputeInverse ? "On" : "Off" ) << std::endl;
+
+  return;
+}
+
+/**
+  * GenerateData
+  */
+template 
+void
+ExponentialDeformationFieldImageFilter2
+::GenerateData()
+{
+  itkDebugMacro(<< "Actually executing");
+
+  InputImageConstPointer inputPtr = this->GetInput();
+
+  unsigned int numiter = 0;
+
+  if( m_AutomaticNumberOfIterations )
+    {
+    // Compute a good number of iterations based on the rationale
+    // that the initial first order approximation,
+    // exp(Phi/2^N) = Phi/2^N,
+    // needs to be diffeomorphic. For this we simply impose to have
+    // max(norm(Phi)/2^N) < 0.5*pixelspacing
+
+    InputPixelRealValueType maxnorm2 = 0.0;
+
+    double minpixelspacing = inputPtr->GetSpacing()[0];
+    for( unsigned int i = 1; i < itkGetStaticConstMacro(ImageDimension); ++i )
+      {
+      if( inputPtr->GetSpacing()[i] < minpixelspacing )
+        {
+        minpixelspacing = inputPtr->GetSpacing()[i];
+        }
+      }
+
+    typedef ImageRegionConstIterator InputConstIterator;
+    InputConstIterator InputIt = InputConstIterator(
+        inputPtr, inputPtr->GetRequestedRegion() );
+    for( InputIt.GoToBegin(); !InputIt.IsAtEnd(); ++InputIt )
+      {
+      InputPixelRealValueType norm2 = InputIt.Get().GetSquaredNorm();
+      if( norm2 > maxnorm2 )
+        {
+        maxnorm2 = norm2;
+        }
+      }
+
+    // Divide the norm by the minimum pixel spacing
+    maxnorm2 /= vnl_math_sqr(minpixelspacing);
+
+    InputPixelRealValueType numiterfloat = 2.0
+      + 0.5 * vcl_log(maxnorm2) / vnl_math::ln2;
+
+    if( numiterfloat >= 0.0 )
+      {
+      // take the ceil and threshold
+      numiter = vnl_math_min(
+          static_cast( numiterfloat + 1.0 ),
+          m_MaximumNumberOfIterations);
+      }
+    else
+      {
+      // numiter will keep the zero to which it was initialized
+      }
+    }
+  else
+    {
+    numiter = m_MaximumNumberOfIterations;
+    }
+
+  ProgressReporter progress(this, 0, numiter + 1, numiter + 1);
+
+  if( numiter == 0 )
+    {
+    if( !this->m_ComputeInverse )
+      {
+      m_Caster->SetInput(inputPtr);
+      m_Caster->GraftOutput( this->GetOutput() );
+      m_Caster->Update();
+      // Region passing stuff
+      this->GraftOutput( m_Caster->GetOutput() );
+      }
+    else
+      {
+      m_Oppositer->SetInput(inputPtr);
+      m_Oppositer->GraftOutput( this->GetOutput() );
+      m_Oppositer->Update();
+      // Region passing stuff
+      this->GraftOutput( m_Oppositer->GetOutput() );
+      }
+
+    this->GetOutput()->Modified();
+
+    progress.CompletedPixel();
+    return;
+    }
+
+  // Get the first order approximation (division by 2^numiter)
+  m_Divider->SetInput(inputPtr);
+  m_Divider->GraftOutput( this->GetOutput() );
+  if( !this->m_ComputeInverse )
+    {
+    m_Divider->SetConstant( static_cast( 1 << numiter ) );
+    }
+  else
+    {
+    m_Divider->SetConstant( -static_cast( 1 << numiter ) );
+    }
+
+  m_Divider->Update();
+
+  // Region passing stuff
+  this->GraftOutput( m_Divider->GetOutput() );
+  this->GetOutput()->Modified();
+
+  progress.CompletedPixel();
+
+  // Do the iterative composition of the vector field
+  m_Warper->SetOutputOrigin( inputPtr->GetOrigin() );
+  m_Warper->SetOutputSpacing( inputPtr->GetSpacing() );
+  m_Warper->SetOutputDirection( inputPtr->GetDirection() );
+  for( unsigned int i = 0; i < numiter; ++i )
+    {
+    m_Warper->SetInput( this->GetOutput() );
+    m_Warper->SetDeformationField( this->GetOutput() );
+
+    m_Warper->GetOutput()->SetRequestedRegion(
+      this->GetOutput()->GetRequestedRegion() );
+
+    m_Warper->Update();
+
+    OutputImagePointer warpedIm = m_Warper->GetOutput();
+    // warpedIm->DisconnectPipeline();
+
+    // Remember we chose to use an inplace adder
+    m_Adder->SetInput1( this->GetOutput() );
+
+    m_Adder->SetInput2(warpedIm);
+    m_Adder->GetOutput()->SetRequestedRegion(
+      this->GetOutput()->GetRequestedRegion() );
+
+    m_Adder->Update();
+
+    // Region passing stuff
+    this->GraftOutput( m_Adder->GetOutput() );
+
+    // Make a call to modified. This seems only necessary for
+    // a non-inplace adder but it doesn't hurt anyhow.
+    this->GetOutput()->Modified();
+
+    progress.CompletedPixel();
+    }
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkFindCenterOfBrainFilter.h b/BRAINSCommonLib/itkFindCenterOfBrainFilter.h
new file mode 100644
index 00000000..5d118d41
--- /dev/null
+++ b/BRAINSCommonLib/itkFindCenterOfBrainFilter.h
@@ -0,0 +1,136 @@
+#ifndef __itkFindeCenterOfBrainFilter_h
+#define __itkFindeCenterOfBrainFilter_h
+#include 
+#include 
+#include 
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+
+namespace itk
+{
+/**
+  * \class FindCenterOfBrainFilter
+  */
+template  >
+class ITK_EXPORT FindCenterOfBrainFilter :
+  public ImageToImageFilter
+{
+public:
+  typedef FindCenterOfBrainFilter                      Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                           Pointer;
+  typedef SmartPointer                     ConstPointer;
+  itkNewMacro(Self);
+  itkTypeMacro(FindCenterOfBrain, Superclass);
+
+  typedef TInputImage                     ImageType;
+  typedef TMaskImage                      MaskImageType;
+  typedef typename MaskImageType::Pointer MaskImagePointer;
+  typedef typename ImageType::Pointer     InputImagePointer;
+  typedef typename ImageType::PixelType   PixelType;
+  typedef typename ImageType::PointType   PointType;
+  typedef typename ImageType::SizeType    SizeType;
+  typedef typename ImageType::SpacingType SpacingType;
+  typedef typename ImageType::IndexType   IndexType;
+  typedef typename itk::ImageRegionIteratorWithIndex
+  ImageIteratorType;
+  typedef typename itk::ImageRegionConstIteratorWithIndex
+  ImageConstIteratorType;
+  typedef LargestForegroundFilledMaskImageFilter
+  LFFMaskFilterType;
+  typedef typename itk::Image       DistanceImageType;
+  typedef typename DistanceImageType::Pointer DistanceImagePointer;
+  /** Image related typedefs. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+
+  itkSetMacro(Maximize, bool);
+  itkGetConstMacro(Maximize, bool);
+  itkSetMacro(Axis, unsigned int);
+  itkGetConstMacro(Axis, unsigned int);
+  itkSetMacro(OtsuPercentileThreshold, double);
+  itkGetConstMacro(OtsuPercentileThreshold, double);
+  itkSetMacro(ClosingSize, unsigned int);
+  itkGetConstMacro(ClosingSize, unsigned int);
+  itkSetMacro(HeadSizeLimit, double);
+  itkGetConstMacro(HeadSizeLimit, double);
+  itkSetMacro(HeadSizeEstimate, double);
+  itkGetConstMacro(HeadSizeEstimate, double);
+  itkSetMacro(BackgroundValue, PixelType);
+  itkGetConstMacro(BackgroundValue, PixelType);
+
+  itkGetConstMacro(CenterOfBrain, PointType);
+  itkGetObjectMacro(TrimmedImage, TInputImage);
+
+  itkSetConstObjectMacro(ImageMask, TMaskImage);
+  itkGetConstObjectMacro(ImageMask, TMaskImage);
+
+  // THIS IS OUTPUT ONLY  itkSetObjectMacro(ClippedImageMask, TMaskImage);
+  itkGetObjectMacro(ClippedImageMask, TMaskImage);
+
+  // DEBUGGING STUFF
+  itkSetMacro(GenerateDebugImages, bool);
+  itkGetMacro(GenerateDebugImages, bool);
+  DistanceImagePointer GetDebugDistanceImage()
+  {
+    return m_DebugDistanceImage;
+  }
+  InputImagePointer GetDebugGridImage()
+  {
+    return m_DebugGridImage;
+  }
+  MaskImagePointer GetDebugAfterGridComputationsForegroundImage()
+  {
+    return m_DebugAfterGridComputationsForegroundImage;
+  }
+
+  MaskImagePointer GetDebugClippedImageMask()
+  {
+    return m_DebugClippedImageMask;
+  }
+
+  InputImagePointer GetDebugTrimmedImage()
+  {
+    return m_DebugTrimmedImage;
+  }
+
+protected:
+  FindCenterOfBrainFilter();
+  ~FindCenterOfBrainFilter();
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  void AllocateOutputs();
+
+  virtual void GenerateData();
+
+private:
+  bool         m_Maximize;
+  unsigned int m_Axis;
+  double       m_OtsuPercentileThreshold;
+  unsigned int m_ClosingSize;
+  double       m_HeadSizeLimit;
+  double       m_HeadSizeEstimate;
+  PixelType    m_BackgroundValue;
+  PointType    m_CenterOfBrain;
+  //
+  // DEBUGGING
+  bool m_GenerateDebugImages;
+  /** The foreground mask, computed automatically if not specified
+   * on the command line. **/
+  typename TMaskImage::ConstPointer m_ImageMask;
+  /** The foreground mask, computed automatically if
+   * not specified on the command line. **/
+  typename TMaskImage::Pointer m_ClippedImageMask;
+  typename TInputImage::Pointer m_TrimmedImage;
+  DistanceImagePointer m_DebugDistanceImage;
+  InputImagePointer    m_DebugGridImage;
+  MaskImagePointer     m_DebugAfterGridComputationsForegroundImage;
+  MaskImagePointer     m_DebugClippedImageMask;
+  InputImagePointer    m_DebugTrimmedImage;
+};
+}
+
+#if ITK_TEMPLATE_TXX
+#include "itkFindCenterOfBrainFilter.hxx"
+#endif
+
+#endif // itkFindeCenterOfBrainFilter_hxx
diff --git a/BRAINSCommonLib/itkFindCenterOfBrainFilter.hxx b/BRAINSCommonLib/itkFindCenterOfBrainFilter.hxx
new file mode 100644
index 00000000..7319216d
--- /dev/null
+++ b/BRAINSCommonLib/itkFindCenterOfBrainFilter.hxx
@@ -0,0 +1,404 @@
+#ifndef itkFindCenterOfBrainFilter_hxx
+#define itkFindCenterOfBrainFilter_hxx
+#include "itkFindCenterOfBrainFilter.h"
+#include "itkNumericTraits.h"
+#include "itkImageMomentsCalculator.h"
+#include "itkImageDuplicator.h"
+#include "itkImageMaskSpatialObject.h"
+
+// #define USE_DEBUGGIN_IMAGES
+#include "itksys/SystemTools.hxx"
+
+namespace itk
+{
+template 
+FindCenterOfBrainFilter
+::FindCenterOfBrainFilter() :
+  m_Maximize(true),
+  m_Axis(2),
+  m_OtsuPercentileThreshold(0.001),
+  m_ClosingSize(7),
+  m_HeadSizeLimit(1000),
+  m_HeadSizeEstimate(0),
+  m_BackgroundValue(NumericTraits::Zero),
+  m_GenerateDebugImages(false),
+  // ITK smart pointers construct as null pointers, but
+  // belt and suspenders initialization
+  m_ImageMask(0),
+  m_ClippedImageMask(0),
+  m_TrimmedImage(0),
+  m_DebugDistanceImage(0),
+  m_DebugGridImage(0),
+  m_DebugAfterGridComputationsForegroundImage(0),
+  m_DebugClippedImageMask(0),
+  m_DebugTrimmedImage(0)
+{
+  m_CenterOfBrain[0] = 0.0;
+  m_CenterOfBrain[1] = 0.0;
+  m_CenterOfBrain[2] = 0.0;
+}
+
+template 
+FindCenterOfBrainFilter
+::~FindCenterOfBrainFilter()
+{
+}
+
+template 
+void
+FindCenterOfBrainFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+  os << indent << "Maximize:                " << this->m_Maximize << std::endl;
+  os << indent << "Axis:                    " << this->m_Axis     << std::endl;
+  os << indent << "OtsuPercintileThreshold: " << this->m_OtsuPercentileThreshold << std::endl;
+  os << indent << "ClosingSize:             " << this->m_ClosingSize << std::endl;
+  os << indent << "HeadSizeLimit:           " << this->m_HeadSizeLimit << std::endl;
+  os << indent << "HeadSizeEstimate:        " << this->m_HeadSizeEstimate << std::endl;
+  os << indent << "BackgroundValue:         " << this->m_BackgroundValue << std::endl;
+  os << indent << "CenterOfBrain:           " << this->m_CenterOfBrain << std::endl;
+  os << indent << "ImageMask:               " << this->m_ImageMask << std::endl;
+  os << indent << "TrimmedImage:            " << this->m_TrimmedImage << std::endl;
+}
+
+template 
+void
+FindCenterOfBrainFilter
+::AllocateOutputs()
+{
+  // Pass the input through as the output
+  InputImagePointer image =
+    const_cast( this->GetInput() );
+
+  this->GraftOutput(image);
+}
+
+template 
+void
+FindCenterOfBrainFilter
+::GenerateData()
+{
+  if( this->m_ImageMask.IsNull() )    // Need to autogenerate this
+    {
+    // //////////////////////////////////////////////////////////////////////
+    typename LFFMaskFilterType::Pointer LFF = LFFMaskFilterType::New();
+    LFF->SetInput( this->GetInput() );
+    LFF->SetOtsuPercentileThreshold(this->m_OtsuPercentileThreshold);
+    LFF->SetClosingSize(this->m_ClosingSize);
+    LFF->Update();
+    this->m_ImageMask = LFF->GetOutput();
+    }
+  typename MaskImageType::Pointer LFFimage;
+    {
+    typename itk::ImageDuplicator::Pointer id = itk::ImageDuplicator::New();
+    id->SetInputImage(this->m_ImageMask);
+    id->Update();
+    LFFimage = id->GetOutput();
+    }
+
+  //  LFFimage will initially hold just a tissue LFFimage mask region (a
+  // so-called integer mask),
+  //  then it will code for the integer distance to the top of physical space,
+  // only within the LFFimage mask region,
+  //  then we will convert the zeros and distance codes to input image signal
+  // and the assigned background value
+  //  in conformity with the assigned volume-distance thresholding from a
+  // histogram.
+
+  // //////////////////////////////////////////////////////////////////////
+  //  This will find maximum Superior physical location of all image voxels.
+  double maxSIDirection;
+    {
+    typedef itk::ImageRegionIteratorWithIndex MaskIteratorType;
+    MaskIteratorType ItPixel( LFFimage, LFFimage->GetLargestPossibleRegion() );
+
+    typename MaskImageType::PointType PixelPhysicalPoint;
+    ItPixel.Begin();
+    LFFimage->TransformIndexToPhysicalPoint(ItPixel.GetIndex(), PixelPhysicalPoint);
+    maxSIDirection = PixelPhysicalPoint[m_Axis];
+    for( ; !ItPixel.IsAtEnd(); ++ItPixel )
+      {
+      LFFimage->TransformIndexToPhysicalPoint(ItPixel.GetIndex(), PixelPhysicalPoint);
+      if( PixelPhysicalPoint[m_Axis] > maxSIDirection )
+        {
+        maxSIDirection = PixelPhysicalPoint[m_Axis];
+        }
+      }
+    //  Now maxSIDirection is the level of the highest subspace plane in the
+    // voxel array.
+    }
+  std::cout << "maxSIDirection = " << maxSIDirection << std::endl;
+
+  // //////////////////////////////////////////////////////////////////////
+  //  This will produce ForegroundLevel representing where to threshold the head
+  // from the neck.
+  // double ForegroundLevel = 1;
+  typename DistanceImageType::Pointer distanceMap = DistanceImageType::New();
+  distanceMap->CopyInformation(LFFimage);
+  distanceMap->SetRegions( LFFimage->GetLargestPossibleRegion() );
+  distanceMap->Allocate();
+  distanceMap->FillBuffer(0.0);
+    {
+    typedef itk::ImageRegionIteratorWithIndex TInputIteratorType;
+    TInputIteratorType ItPixel( LFFimage, LFFimage->GetLargestPossibleRegion() );
+
+    //    typedef itk::ImageRegionIterator< DistanceImageType >
+    // DistanceImageIteratorType;
+    //    DistanceImageIteratorType ItDistPixel( distanceMap,
+    // distanceMap->GetLargestPossibleRegion() );
+
+    typename MaskImageType::PointType PixelPhysicalPoint;
+    PixelPhysicalPoint.Fill(0.0);
+    for( ItPixel.Begin(); !ItPixel.IsAtEnd(); ++ItPixel )
+      {
+      if( ItPixel.Get() != 0 )
+        {
+        const typename MaskImageType::IndexType tempIndex = ItPixel.GetIndex();
+        LFFimage->TransformIndexToPhysicalPoint(tempIndex, PixelPhysicalPoint);
+        double val =  vnl_math_rnd( vnl_math_abs(maxSIDirection
+                                                 - PixelPhysicalPoint[m_Axis]) );
+        distanceMap->SetPixel( tempIndex,
+                               static_cast( val ) );
+        }
+      // else, leave the LFFimage coded zero, not some positive distance from
+      // the top.
+      }
+    if( this->m_GenerateDebugImages )
+      {
+      this->m_DebugDistanceImage = distanceMap;
+      }
+    }
+
+  double inferiorCutOff = -1000000;
+  std::cout << "Computing Sampled Distance Computations" << std::endl;
+  const double samplingDistanceMM = 3.0;
+  // Only look in 3mm regions
+  const double samplingDistanceCM = samplingDistanceMM * 0.1;
+  // Only look in 3mm regions
+  const double rectangularGridRadius = 150.0;
+  // How big of region around COM are we going to look for?
+  const int numberOfSamplelingLines =
+    static_cast( ( rectangularGridRadius * 2.0 ) / samplingDistanceMM );
+
+  if( this->m_GenerateDebugImages )
+    {
+    this->m_DebugGridImage = TInputImage::New();
+    this->m_DebugGridImage->CopyInformation(LFFimage);
+    this->m_DebugGridImage->SetRegions( LFFimage->GetLargestPossibleRegion() );
+    this->m_DebugGridImage->Allocate();
+    this->m_DebugGridImage->FillBuffer(numberOfSamplelingLines);
+    }
+
+  // Use 400mm as the (-200mm,200mm) as the distance to look.
+  std::vector maskCountsInPlane(numberOfSamplelingLines);
+
+  std::fill(maskCountsInPlane.begin(), maskCountsInPlane.end(), 0);
+    {
+    typename TInputImage::PointType CenterOfMass;
+      {
+        {
+        /*
+          * This will get an initial center of mass for the entire
+          * foreground region.
+          */
+          {
+          typedef typename itk::ImageMomentsCalculator momentsCalculatorType;
+          typename momentsCalculatorType::Pointer moments = momentsCalculatorType::New();
+          moments->SetImage(LFFimage);
+          moments->Compute();
+          typename TInputImage::PointType::VectorType tempCenterOfMass = moments->GetCenterOfGravity();
+          for( unsigned int q = 0; q < TInputImage::ImageDimension; ++q )
+            {
+            CenterOfMass[q] = tempCenterOfMass[q];
+            }
+          }
+        }
+
+      bool   exitCriteriaMet = false;
+      double MaxVolumeBasedOnArea = 0.0;
+      typename TInputImage::PointType rectPhysPoint;
+      typename TInputImage::PointType currRotatedSampleGridLocation;
+      for( int dIndex = numberOfSamplelingLines - 1; dIndex >= 0; dIndex-- )
+        {
+        // Equally space the SI sampling around the COM for each index
+        rectPhysPoint[2] =
+          ( rectangularGridRadius
+            * 2.0 )
+          * ( static_cast( dIndex
+                                   + 1 ) / static_cast( numberOfSamplelingLines ) ) - rectangularGridRadius;
+        currRotatedSampleGridLocation[2] = CenterOfMass[2] + rectPhysPoint[2];
+        for( rectPhysPoint[1] = -rectangularGridRadius;
+             rectPhysPoint[1] < rectangularGridRadius;
+             rectPhysPoint[1] += samplingDistanceMM )
+        // Raster through (-120mm,120mm)
+          {
+          currRotatedSampleGridLocation[1] = CenterOfMass[1] + rectPhysPoint[1];
+          for( rectPhysPoint[0] = -rectangularGridRadius;
+               rectPhysPoint[0] < rectangularGridRadius;
+               rectPhysPoint[0] += samplingDistanceMM )
+          // Raster through (-120mm,120mm)
+            {
+            currRotatedSampleGridLocation[0] = CenterOfMass[0] + rectPhysPoint[0];
+
+            typename TInputImage::IndexType currIndex;
+            const bool isValidRegion = LFFimage->TransformPhysicalPointToIndex(
+                currRotatedSampleGridLocation,
+                currIndex);
+            if( isValidRegion && ( LFFimage->GetPixel(currIndex) > 0 ) )
+              {
+              // #ifdef USE_DEBUGGIN_IMAGES
+              if( this->m_GenerateDebugImages )
+                {
+                this->m_DebugGridImage->SetPixel( currIndex, ( numberOfSamplelingLines + dIndex ) );
+                }
+              maskCountsInPlane[dIndex]++;
+              }
+            // #ifdef USE_DEBUGGIN_IMAGES
+            else if( this->m_GenerateDebugImages && isValidRegion )
+              {
+              this->m_DebugGridImage->SetPixel(currIndex, 0);
+              }
+            }
+          }
+
+        const double crossSectionalArea = maskCountsInPlane[dIndex] * samplingDistanceCM * samplingDistanceCM;
+        // Put this into cm^2
+        const double crossSectionalVolume = crossSectionalArea * ( samplingDistanceCM );
+        // Put this into cm^3
+        const double estimated_radius = vcl_sqrt(crossSectionalArea / vnl_math::pi);
+        // Estimate the radis of a circle filling this much space
+        const double ScaleFactor = 1.1;
+        // Add 10% for safety //5+(crossSectionalArea-200)/100; //Larger brains
+        // need more scaling
+        const double CurentVolumeBasedOnArea = ScaleFactor
+          * ( 1.33333333333333333 * vnl_math::pi * estimated_radius
+              * estimated_radius * estimated_radius );
+        // (4/3)*pi*r^3
+        MaxVolumeBasedOnArea =
+          ( CurentVolumeBasedOnArea > MaxVolumeBasedOnArea ) ? CurentVolumeBasedOnArea : MaxVolumeBasedOnArea;
+        // Now compute 1.5 times the size of a sphere with this estimated
+        // radius.
+        // DesiredVolumeToIncludeBeforeClipping=CurentVolumeBasedOnArea;
+        this->m_HeadSizeEstimate += crossSectionalVolume;
+        if( ( exitCriteriaMet == false ) && ( this->m_HeadSizeEstimate > this->m_HeadSizeLimit )
+            && ( this->m_HeadSizeEstimate > MaxVolumeBasedOnArea ) )
+          {
+          exitCriteriaMet = true;
+          inferiorCutOff = currRotatedSampleGridLocation[2];
+          }
+
+        if( this->m_GenerateDebugImages )
+          {
+          std::cout << ( dIndex ) << ": " << maskCountsInPlane[dIndex]
+                    << " Estimated Radius: " << estimated_radius
+                    << " CurrentCalculatedVolumeBasedOnArea: " << CurentVolumeBasedOnArea
+                    << " CummulativeVolume: " << this->m_HeadSizeEstimate
+                    << " ExitCriteriaMet: " << exitCriteriaMet
+                    << " Inferior Cut Off: " << currRotatedSampleGridLocation[2] << " " << inferiorCutOff
+                    << std::endl;
+          }
+        }
+      }
+    }
+  if( this->m_GenerateDebugImages )
+    {
+      {
+      this->m_DebugAfterGridComputationsForegroundImage = LFFimage;
+      }
+    }
+
+  // //////////////////////////////////////////////////////////////////////
+  // This will convert the LFFimage code image with the rule, foreach voxel,
+  // if not in tissue LFFimage mask region or distance map is greater than T,
+  // set the result image voxel to Background;
+  // otherwise set the result image voxel to the source image pixel value.
+    {
+      {
+      typename itk::ImageDuplicator::Pointer id = itk::ImageDuplicator::New();
+      id->SetInputImage(this->m_ImageMask);
+      id->Update();
+      this->m_ClippedImageMask = id->GetOutput();
+      }
+    typedef typename itk::ImageRegionIteratorWithIndex MaskImageIteratorType;
+    MaskImageIteratorType ClippedMaskPixel( this->m_ClippedImageMask,
+                                            this->m_ClippedImageMask->GetLargestPossibleRegion() );
+
+      {
+      typename itk::ImageDuplicator::Pointer id = itk::ImageDuplicator::New();
+      id->SetInputImage( this->GetInput() );
+      id->Update();
+      this->m_TrimmedImage = id->GetOutput();
+      }
+
+    typedef typename itk::ImageRegionIteratorWithIndex TInputIteratorType;
+    TInputIteratorType ClippedImagePixel( this->m_TrimmedImage, this->m_TrimmedImage->GetLargestPossibleRegion() );
+
+    ClippedImagePixel.Begin();
+    while( ( !ClippedImagePixel.IsAtEnd() ) )
+      {
+      typename TInputImage::PointType currLoc;
+      this->m_TrimmedImage->TransformIndexToPhysicalPoint(ClippedImagePixel.GetIndex(), currLoc);
+      if( currLoc[2] > inferiorCutOff && ( ClippedMaskPixel.Get() != 0 ) )
+      // If this mask voxel is in the foreground AND above the inferiorCutOff
+        {
+        ClippedMaskPixel.Set(1);
+        // putchar('1');
+        }
+      else
+        {
+        ClippedImagePixel.Set(this->m_BackgroundValue);
+        ClippedMaskPixel.Set(0);
+        // putchar('0');
+        }
+      ++ClippedImagePixel;
+      ++ClippedMaskPixel;
+      }
+    }
+  // #ifdef USE_DEBUGGIN_IMAGES
+  if( this->m_GenerateDebugImages )
+    {
+    this->m_DebugClippedImageMask =  this->m_ClippedImageMask;
+    this->m_DebugTrimmedImage = this->m_TrimmedImage;
+    }
+
+  // //////////////////////////////////////////////////////////////////////
+  //  This will use the clipped LFFimage image to get the head center of mass.
+    {
+    typedef typename itk::ImageMomentsCalculator momentsCalculatorType;
+    typename momentsCalculatorType::Pointer moments = momentsCalculatorType::New();
+    moments->SetImage(this->m_TrimmedImage);
+      {
+      // convert mask image to mask
+      typedef typename itk::ImageMaskSpatialObject ImageMaskSpatialObjectType;
+      typename ImageMaskSpatialObjectType::Pointer mask = ImageMaskSpatialObjectType::New();
+      mask->SetImage(this->m_ClippedImageMask);
+      mask->ComputeObjectToWorldTransform();
+      typename itk::SpatialObject::Pointer test =
+        dynamic_cast *>( mask.GetPointer() );
+      if( test.IsNull() )
+        {
+        std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+        exit(-1);
+        }
+
+      moments->SetSpatialObjectMask( test.GetPointer() );
+      }
+
+    moments->Compute();
+    typename TInputImage::PointType::VectorType tempCenterOfMass = moments->GetCenterOfGravity();
+    for( unsigned int q = 0; q < TInputImage::ImageDimension; ++q )
+      {
+      this->m_CenterOfBrain[q] = tempCenterOfMass[q];
+      }
+    }
+
+  // #ifdef USE_DEBUGGIN_IMAGES
+  if( this->m_GenerateDebugImages )
+    {
+    std::cout << "---CenterOfMass:" << this->m_CenterOfBrain << std::endl;
+    }
+}
+
+}
+#endif // itkFindCenterOfBrainFilter_hxx
diff --git a/BRAINSCommonLib/itkIO.h b/BRAINSCommonLib/itkIO.h
new file mode 100644
index 00000000..8a95e5ff
--- /dev/null
+++ b/BRAINSCommonLib/itkIO.h
@@ -0,0 +1,410 @@
+#ifndef __itkIO_h
+#define __itkIO_h
+
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImage.h"
+#include "itkCastImageFilter.h"
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkOrientImageFilter.h"
+#include "itkSpatialOrientation.h"
+#include "itkSpatialOrientationAdapter.h"
+#include "itkMetaDataObject.h"
+#include "itkImageRegionIterator.h"
+#include "itkThinPlateR2LogRSplineKernelTransform.h"
+#include "itkResampleImageFilter.h"
+#include "itkImageDuplicator.h"
+#include "Imgmath.h"
+#include "itkGDCMSeriesFileNames.h"
+#include "itkImageSeriesReader.h"
+#include "itkGDCMImageIO.h"
+
+namespace itkUtil
+{
+typedef itk::SpatialOrientationAdapter SOAdapterType;
+typedef SOAdapterType::DirectionType   DirectionType;
+
+/**
+  *
+  *
+  *
+  */
+/** read an image using ITK -- image-based template */
+template 
+typename TImage::Pointer ReadImage(const std::string fileName)
+{
+  typename TImage::Pointer image;
+  std::string               extension = itksys::SystemTools::GetFilenameLastExtension(fileName);
+  itk::GDCMImageIO::Pointer dicomIO = itk::GDCMImageIO::New();
+  if( dicomIO->CanReadFile( fileName.c_str() ) || ( itksys::SystemTools::LowerCase(extension) == ".dcm" ) )
+    {
+    std::string dicomDir = itksys::SystemTools::GetParentDirectory( fileName.c_str() );
+
+    itk::GDCMSeriesFileNames::Pointer FileNameGenerator = itk::GDCMSeriesFileNames::New();
+    FileNameGenerator->SetUseSeriesDetails(true);
+    FileNameGenerator->SetDirectory(dicomDir);
+    typedef const std::vector ContainerType;
+    const ContainerType & seriesUIDs = FileNameGenerator->GetSeriesUIDs();
+
+    typedef typename itk::ImageSeriesReader ReaderType;
+    typename ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileNames( FileNameGenerator->GetFileNames(seriesUIDs[0]) );
+    reader->SetImageIO(dicomIO);
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::cout << "Error while reading in image for patient " << fileName << std::endl;
+      throw;
+      }
+    image = reader->GetOutput();
+    // image->DisconnectPipeline();
+    // reader->ReleaseDataFlagOn();
+    }
+  else
+    {
+    typedef itk::ImageFileReader ReaderType;
+    typename ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName( fileName.c_str() );
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & err )
+      {
+      std::cout << "Caught an exception: " << std::endl;
+      std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+      throw err;
+      }
+    catch( ... )
+      {
+      std::cout << "Error while reading in image" << fileName << std::endl;
+      throw;
+      }
+    image = reader->GetOutput();
+    // image->DisconnectPipeline();
+    // reader->ReleaseDataFlagOn();
+    }
+  return image;
+}
+
+/**
+  *
+  *
+  *
+  */
+
+template 
+bool
+ImagePhysicalDimensionsAreIdentical(typename ImageType1::Pointer & inputImage1,
+                                    typename ImageType2::Pointer & inputImage2)
+{
+  bool same = true;
+
+  same &= ( inputImage1->GetDirection() == inputImage2->GetDirection() );
+  same &= ( inputImage1->GetSpacing() == inputImage2->GetSpacing() );
+  same &= ( inputImage1->GetOrigin() == inputImage2->GetOrigin() );
+  return same;
+}
+
+template 
+typename ImageType::Pointer
+OrientImage(typename ImageType::ConstPointer & inputImage,
+            itk::SpatialOrientation::ValidCoordinateOrientationFlags orient)
+{
+  typename itk::OrientImageFilter::Pointer orienter =
+    itk::OrientImageFilter::New();
+
+  orienter->SetDesiredCoordinateOrientation(orient);
+  orienter->UseImageDirectionOn();
+  orienter->SetInput(inputImage);
+  orienter->Update();
+  typename ImageType::Pointer returnval =
+    orienter->GetOutput();
+  // returnval->DisconnectPipeline();
+  orienter->ReleaseDataFlagOn();
+  return returnval;
+}
+
+template 
+typename ImageType::Pointer
+OrientImage(typename ImageType::ConstPointer & inputImage,
+            const typename ImageType::DirectionType & dirCosines)
+{
+  return OrientImage
+           ( inputImage,
+           SOAdapterType().FromDirectionCosines(
+             dirCosines) );
+}
+
+template 
+typename ImageType::Pointer
+OrientImage(typename ImageType::Pointer & inputImage,
+            const typename ImageType::DirectionType & dirCosines)
+{
+  typename ImageType::ConstPointer constImg(inputImage);
+  return OrientImage
+           ( constImg,
+           SOAdapterType().FromDirectionCosines(
+             dirCosines) );
+}
+
+template 
+typename ImageType::Pointer
+OrientImage(typename ImageType::Pointer & inputImage,
+            itk::SpatialOrientation::ValidCoordinateOrientationFlags orient)
+{
+  typename ImageType::ConstPointer constImg(inputImage);
+  return OrientImage(constImg, orient);
+}
+
+template 
+typename ImageType::Pointer
+ReadImageAndOrient(const std::string & filename,
+                   itk::SpatialOrientation::ValidCoordinateOrientationFlags orient)
+{
+  typename ImageType::Pointer img =
+    ReadImage(filename);
+  typename ImageType::ConstPointer constImg(img);
+  typename ImageType::Pointer image = itkUtil::OrientImage(constImg,
+                                                                      orient);
+  return image;
+}
+
+template 
+typename ImageType::Pointer
+ReadImageAndOrient(const std::string & filename,
+                   const DirectionType & dir)
+{
+  return ReadImageAndOrient
+           ( filename,
+           SOAdapterType().FromDirectionCosines(dir) );
+}
+
+template 
+typename TReadImageType::Pointer ReadImageCoronal(const std::string & fileName)
+{
+  DirectionType CORdir = SOAdapterType().ToDirectionCosines
+      (itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIP);
+
+  return ReadImageAndOrient(fileName, CORdir);
+}
+
+/*
+ * This is the prefered ABI for Writing images.
+ * We know that the image is not going to change
+ * so make sure that the API indicates that.
+ */
+template 
+void
+WriteConstImage(const typename ImageType::ConstPointer image,
+                const std::string & filename)
+{
+  typedef itk::ImageFileWriter WriterType;
+  typename  WriterType::Pointer writer = WriterType::New();
+  writer->UseCompressionOn();
+  writer->SetFileName( filename.c_str() );
+  writer->SetInput(image);
+  try
+    {
+    writer->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cout << "Exception Object caught: " << std::endl;
+    std::cout << err << std::endl;
+    throw;
+    }
+}
+
+/*
+ * This is for backwards compatibility, and just
+ * delegates to WriteConstImage
+ * with more restricted write access
+ * as necessary.
+ */
+template 
+void
+WriteImage(const typename ImageType::Pointer image,
+           const std::string & filename)
+{
+  const typename ImageType::ConstPointer temp(image.GetPointer() );
+  WriteConstImage(temp, filename);
+}
+
+/**
+  *
+  *
+  * @author hjohnson (6/4/2008)
+  *
+  * @param InputImageType
+  * @param OutputImageType
+  * @param input
+  *
+  * @return typename OutputImageType::Pointer
+  */
+template 
+typename OutputImageType::Pointer
+TypeCast(const typename InputImageType::Pointer & input)
+{
+  typedef itk::CastImageFilter CastToRealFilterType;
+  typename CastToRealFilterType::Pointer toReal = CastToRealFilterType::New();
+  toReal->SetInput(input);
+  toReal->Update();
+  return toReal->GetOutput();
+}
+
+/**
+  *   \author Hans J. Johnson
+  *   Converts images from one type to
+  *  another with explicit min and max values. NOTE:  The original
+  *  range of the image is determined explicitly from the data,
+  *  and then linearly scaled into the range specified.
+  * \param image --The input image to convert and scale
+  * \param OuputMin --The required minimum value of the output
+  *        image
+  * \param OutputMax -- The required maximum value of the output
+  *        image
+  * \return A new image of the specified type and scale.
+  */
+template 
+typename OutputImageType::Pointer
+ScaleAndCast(const typename InputImageType::Pointer & image,
+             const typename OutputImageType::PixelType OutputMin,
+             const typename OutputImageType::PixelType OutputMax)
+{
+  typedef itk::RescaleIntensityImageFilter R2CRescaleFilterType;
+  typename R2CRescaleFilterType::Pointer RealToProbMapCast =
+    R2CRescaleFilterType::New();
+  RealToProbMapCast->SetOutputMinimum(OutputMin);
+  RealToProbMapCast->SetOutputMaximum(OutputMax);
+  RealToProbMapCast->SetInput(image);
+  try
+    {
+    RealToProbMapCast->Update();
+    }
+  catch( itk::ExceptionObject & e )
+    {
+    std::cerr << "Exception in Image cast." << std::endl;
+    std::cerr << e.GetDescription() << std::endl;
+    std::cerr << e.GetLocation() << std::endl;
+    exit(-1);
+    }
+  typename OutputImageType::Pointer returnScaled = RealToProbMapCast->GetOutput();
+  return returnScaled;
+}
+
+/**
+  * This function will do a type cast if the OutputImageType
+  * intensity range is larger than the input image type range.
+  * If the OutputImageType range is smaller, then a Scaling will
+  * occur.
+  *
+  * @author hjohnson (6/4/2008)
+  *
+  * @param InputImageType
+  * @param OutputImageType
+  * @param image
+  *
+  * @return typename OutputImageType::Pointer
+  */
+template 
+typename OutputImageType::Pointer
+PreserveCast(const typename InputImageType::Pointer image)
+{
+  const typename InputImageType::PixelType inputmin =
+    itk::NumericTraits::min();
+  const typename InputImageType::PixelType inputmax =
+    itk::NumericTraits::max();
+  const typename OutputImageType::PixelType outputmin =
+    itk::NumericTraits::min();
+  const typename OutputImageType::PixelType outputmax =
+    itk::NumericTraits::max();
+  if( ( inputmin >= outputmin ) && ( inputmax <= outputmax ) )
+    {
+    return TypeCast(image);
+    }
+  else
+    {
+    return ScaleAndCast(image,
+                                                         outputmin,
+                                                         outputmax);
+    }
+}
+
+template 
+typename ImageType::Pointer
+CopyImage(const typename ImageType::Pointer & input)
+{
+  typedef itk::ImageDuplicator ImageDupeType;
+  typename ImageDupeType::Pointer MyDuplicator = ImageDupeType::New();
+  MyDuplicator->SetInputImage(input);
+  MyDuplicator->Update();
+  return MyDuplicator->GetOutput();
+}
+
+/** Common code for allocating an image, allowing the region and spacing to be
+   * explicitly set.
+   */
+template 
+typename OutputImageType::Pointer
+AllocateImageFromRegionAndSpacing(const typename TemplateImageType::RegionType & region,
+                                  const typename TemplateImageType::SpacingType & spacing)
+{
+  typename OutputImageType::Pointer rval;
+  rval = OutputImageType::New();
+  rval->SetSpacing(spacing);
+  //    rval->SetLargestPossibleRegion(region);
+  //    rval->SetBufferedRegion(region);
+  rval->SetRegions(region);
+  rval->Allocate();
+  return rval;
+}
+
+template 
+typename ImageType::Pointer
+AllocateImageFromRegionAndSpacing(const typename ImageType::RegionType & region,
+                                  const typename ImageType::SpacingType & spacing)
+{
+  return AllocateImageFromRegionAndSpacing
+           (region, spacing);
+}
+
+/** AllocateImageFromExample creates and allocates an image of the type OutputImageType,
+ * using TemplateImageType as the source of size and spacing...
+ *
+ */
+template 
+typename OutputImageType::Pointer
+AllocateImageFromExample(
+  const typename TemplateImageType::Pointer & TemplateImage)
+{
+  typename OutputImageType::Pointer rval = OutputImageType::New();
+  rval->CopyInformation(TemplateImage);
+  rval->SetRegions( TemplateImage->GetLargestPossibleRegion() );
+  rval->Allocate();
+  return rval;
+}
+
+//
+// convenience function where template and output images type are the same
+template 
+typename ImageType::Pointer
+AllocateImageFromExample(const typename ImageType::Pointer & TemplateImage)
+{
+  return AllocateImageFromExample(TemplateImage);
+}
+
+}
+
+#endif
diff --git a/BRAINSCommonLib/itkInverseConsistentLandmarks.h b/BRAINSCommonLib/itkInverseConsistentLandmarks.h
new file mode 100755
index 00000000..0aa86bac
--- /dev/null
+++ b/BRAINSCommonLib/itkInverseConsistentLandmarks.h
@@ -0,0 +1,384 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+// This file is for defining landmarks and what to do with them.
+
+#ifndef __itkInverseConsistentLandmarks_h
+#define __itkInverseConsistentLandmarks_h
+
+#include "itkImage.h"
+
+namespace itk
+{
+template 
+class InverseConsistentLandmarkPoint : public itk::Point
+{
+public:
+  typedef InverseConsistentLandmarkPoint           Self;
+  typedef itk::Point Superclass;
+
+  InverseConsistentLandmarkPoint(void)
+  {
+    m_FWeighting = 0.0;
+    ( *this )[0] = ( *this )[1] = ( *this )[2] = 0.0;
+  }
+
+  InverseConsistentLandmarkPoint(const PointStorageType x, const PointStorageType y, const PointStorageType z,
+                                 const PointStorageType t,
+                                 const PointStorageType weighting) :
+    m_FWeighting(weighting)
+  {
+    ( *this )[0] = x; ( *this )[1] = y; ( *this )[2] = z;
+    m_T = t;
+  }
+
+  InverseConsistentLandmarkPoint(const InverseConsistentLandmarkPoint & rhs) :
+    Superclass(rhs), m_FWeighting(rhs.m_FWeighting)
+  {
+  }
+
+  PointStorageType GetT() const
+  {
+    return m_T;
+  }
+
+  void SetT(const PointStorageType val)
+  {
+    m_T = val;
+  }
+
+  PointStorageType GetWeighting(void) const
+  {
+    return m_FWeighting;
+  }
+
+  void SetWeighting(const PointStorageType val)
+  {
+    m_FWeighting = val;
+  }
+
+  virtual ~InverseConsistentLandmarkPoint(void)
+  {
+  }
+private:
+  PointStorageType m_T;
+  PointStorageType m_FWeighting;
+};
+
+template 
+class InverseConsistentLandmarks :
+  public std::map >
+{
+public:
+  typedef InverseConsistentLandmarks                       Self;
+  typedef InverseConsistentLandmarkPoint PointType;
+
+  typedef std::map Superclass;
+  typedef SmartPointer               Pointer;
+  typedef SmartPointer         ConstPointer;
+
+  typedef typename PointSetType::Pointer PointSetTypePointer;
+
+  typedef enum
+    {
+    GEC_LANDMARKS = 0, INTELLX_LANDMARKS, ANALYZE_LANDMARKS,
+    IPL_LANDMARKS, IPL_TALAIRACH_BOUNDS_LANDMARKS,
+    IPL_CEREBELLAR_BOUNDS_LANDMARKS,
+    UNKNOWN_LANDMARKS
+    }
+  Landmark_File_Format;
+  InverseConsistentLandmarks(void);
+  InverseConsistentLandmarks(const int XDim, const int YDim, const int ZDim, const int TDim = 0);
+  virtual ~InverseConsistentLandmarks(void)
+  {
+  }
+
+  InverseConsistentLandmarks & operator=(const InverseConsistentLandmarks & rhs);
+
+  typedef typename itk::Image ImageType;
+  PointSetTypePointer GetPointSet(typename ImageType::PointType Origin)
+  {
+    typedef typename PointSetType::PointIdentifier PointIdentifierType;
+    typedef typename PointSetType::PointType       PointSetPointType;
+    typedef typename Self::const_iterator          LocalConstIterator;
+
+    PointSetTypePointer pointSet = PointSetType::New();
+    PointIdentifierType PointID =
+      itk::NumericTraits::Zero;
+
+    LocalConstIterator it = this->begin();
+    LocalConstIterator itend = this->end();
+    while( it != itend )
+      {
+      const PointType   cur = ( *it ).second;
+      PointSetPointType psPoint;
+      for( unsigned int i = 0; i < 3; ++i )
+        {
+        psPoint[i] = ( cur[i] * ImageRes[i] ) - Origin[i];
+        }
+      pointSet->SetPoint(PointID, psPoint);
+      ++it;
+      ++PointID;
+      }
+
+    return pointSet;
+  }
+
+  bool ReadPointTypes(const std::string lmrkfilename);
+
+  bool ReadPointTypes(const std::string lmrkfilenamee, const int XDim, const int YDim, const int ZDim,
+                      const int TDim = 0);
+
+  bool WritePointTypes(const std::string lmrkfilename, const Landmark_File_Format lmkff = GEC_LANDMARKS);
+
+  bool PrintPointTypes(void) const;
+
+  Landmark_File_Format QueryLandmarkFile(const std::string lmrkfilename);
+
+  /**
+    * Function for reading a landmark file in GEC landmark format
+    * \param The landmark filename
+    * \return true if successful, false if failed
+    */
+  bool ReadGECPointTypes(const std::string lmrkfilename);
+
+  /**
+    * Shortcut for calling
+    * gec::InverseConsistentLandmarks::ReadGECPointTypes(lmrkfilename);
+    * gec::InverseConsistentLandmarks::rescale(XDim,YDim,ZDim,TDim);
+    * \param The landmark filename
+    * \param XDim the XDimension of the image for the landmarks to be rescaled
+    *to
+    * \param YDim the YDimension of the image for the landmarks to be rescaled
+    *to
+    * \param ZDim the ZDimension of the image for the landmarks to be rescaled
+    *to
+    * \param TDim the TDimension of the image for the landmarks to be rescaled
+    *to
+    * \return true if successful, false if failed
+    */
+  bool ReadGECPointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                         const int TDim = 0);
+
+  /**
+    * Behavior is flaky at best, because lmks file does not specify image
+    *dimensions
+    * If this is used, call set[XYZT]Dim immediatly after this call.
+    */
+  bool ReadIntellXPointTypes(const std::string lmrkfilename);
+
+  /**
+    * Reads in a IntellXLandmark File, and uses the given dimensions for the
+    *image dimensions, NO RESCALING OF LANDMARKS
+    * \param The landmark filename
+    * \param XDim The value for XImage Dim
+    * \param YDim The value for YImage Dim
+    * \param ZDim The value for ZImage Dim
+    * \param TDim The value for TImage Dim
+    * \return true if successful, false if failed
+    */
+  bool ReadIntellXPointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                             const int TDim = 0);
+
+  /**
+    * Behavior is flaky at best, because lmks file does not specify image
+    *dimensions
+    * If this is used, call set[XYZT]Dim immediatly after this call.
+    */
+  bool ReadAnalyzePointTypes(const std::string lmrkfilename);
+
+  /**
+    * Reads in an Analyze Landmark File, and uses the given dimensions for the
+    *image dimensions, NO RESCALING OF LANDMARKS
+    * \param The landmark filename
+    * \param XDim The value for XImage Dim
+    * \param YDim The value for YImage Dim
+    * \param ZDim The value for ZImage Dim
+    * \param TDim The value for TImage Dim
+    * \return true if successful, false if failed
+    */
+  bool ReadAnalyzePointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                             const int TDim = 0);
+
+  /**
+    * Function for reading a landmark file in IPL landmark format
+    * \param The landmark filename
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLPointTypes(const std::string lmrkfilename);
+
+  /**
+    * Shortcut for calling
+    * gec::InverseConsistentLandmarks::ReadIPLPointTypes(lmrkfilename);
+    * gec::InverseConsistentLandmarks::rescale(XDim,YDim,ZDim,TDim);
+    * \param The landmark filename
+    * \param XDim the XDimension of the image for the landmarks to be rescaled
+    *to
+    * \param YDim the YDimension of the image for the landmarks to be rescaled
+    *to
+    * \param ZDim the ZDimension of the image for the landmarks to be rescaled
+    *to
+    * \param TDim the TDimension of the image for the landmarks to be rescaled
+    *to
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLPointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                         const int TDim = 0);
+
+  /**
+    * Function for reading a landmark file in IPL talairach bounds format
+    * \param lmrkfilename The landmark filename
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLTalairachPointTypes(const std::string lmrkfilename);
+
+  /**
+    * Shortcut for calling
+    * gec::InverseConsistentLandmarks::ReadIPLTalairachPointTypes(lmrkfilename);
+    * gec::InverseConsistentLandmarks::rescale(XDim,YDim,ZDim,TDim);
+    * \param The landmark filename
+    * \param XDim the XDimension of the image for the landmarks to be rescaled
+    *to
+    * \param YDim the YDimension of the image for the landmarks to be rescaled
+    *to
+    * \param ZDim the ZDimension of the image for the landmarks to be rescaled
+    *to
+    * \param TDim the TDimension of the image for the landmarks to be rescaled
+    *to
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLTalairachPointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                                  const int TDim = 0);
+
+  /**
+    * Function for reading a landmark file in IPL talairach bounds format
+    * \param The landmark filename
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLCerebellarPointTypes(const std::string lmrkfilename);
+
+  /**
+    * Shortcut for calling
+    *
+    *gec::InverseConsistentLandmarks::ReadIPLCerebellarPointTypes(lmrkfilename);
+    * gec::InverseConsistentLandmarks::rescale(XDim,YDim,ZDim,TDim);
+    * \param The landmark filename
+    * \param XDim the XDimension of the image for the landmarks to be rescaled
+    *to
+    * \param YDim the YDimension of the image for the landmarks to be rescaled
+    *to
+    * \param ZDim the ZDimension of the image for the landmarks to be rescaled
+    *to
+    * \param TDim the TDimension of the image for the landmarks to be rescaled
+    *to
+    * \return true if successful, false if failed
+    */
+  bool ReadIPLCerebellarPointTypes(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                                   const int TDim = 0);
+
+  bool WriteGECPointTypes(const std::string lmrkfilename) const;
+
+  bool WriteIntellXPointTypes(const std::string lmrkfilename) const;
+
+  bool WriteAnalyzePointTypes(const std::string lmrkfilename) const;
+
+  bool ConcatLandmarks(InverseConsistentLandmarks & newlmks);
+
+  bool ConcatLandmarks(const std::string lmrkfilename);
+
+  bool ConcatLandmarks(const std::string lmrkfilename, const int XDim, const int YDim, const int ZDim,
+                       const int TDim = 0);
+
+  bool RemoveClosePoints(const PointStorageType distance = 0.0);
+
+  bool RemoveUnmatchedPoints(InverseConsistentLandmarks & tempmap1);
+
+  /**
+    * If image was 256x256, then getXDim should return 255, which is the maxXDim
+    *available
+    * \return MaxXDim()
+    */
+  inline unsigned short getXDim(void) const
+  {
+    return ImageDims[0];
+  }
+
+  inline unsigned short getYDim(void) const
+  {
+    return ImageDims[1];
+  }
+
+  inline unsigned short getZDim(void) const
+  {
+    return ImageDims[2];
+  }
+
+  inline unsigned short getTDim(void) const
+  {
+    return ImageDims[3];
+  }
+
+  /**
+    * If the image is 256x256, then this should be set to 255 because that is
+    *the max pixel number of the image.
+    */
+  inline void setXDim(const unsigned short newx)
+  {
+    assert(newx > 0); ImageDims[0] = newx;
+  }
+
+  inline void setYDim(const unsigned short newy)
+  {
+    assert(newy > 0); ImageDims[1] = newy;
+  }
+
+  inline void setZDim(const unsigned short newz)
+  {
+    assert(newz > 0); ImageDims[2] = newz;
+  }
+
+  inline void setTDim(const unsigned short newt)
+  {
+    assert(newt > 0); ImageDims[3] = newt;
+  }
+
+  /**
+    * This rescales the landmarks to fit a new coordinate system.
+    * \param newx new ImageDims[0]
+    * \param newy new ImageDims[1]
+    * \param newz new ImageDims[2]
+    * \param newt new ImageDims[3]
+    * \return  true if successful
+    */
+  bool rescale(const int newx, const int newy, const int newz, const int newt);
+
+  void AddExtendedPointTypes3D_OnN(const InverseConsistentLandmarks & input, const int nx, const int ny, const int nz);
+
+  void AddExtendedPointTypes3D_UnitCube(const InverseConsistentLandmarks & input);
+
+private:
+  bool process_bnd_point(const std::string & CurrentLandmarkName, const char *buffer,
+                         const unsigned short local_ImageDims[4], const float local_ImageRes[4],
+                         PointType & ModifiedPoint);
+
+  unsigned short ImageDims[4];
+  float          ImageRes[4];
+};
+}
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkInverseConsistentLandmarks.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkInverseConsistentLandmarks.hxx b/BRAINSCommonLib/itkInverseConsistentLandmarks.hxx
new file mode 100755
index 00000000..b6c0cff1
--- /dev/null
+++ b/BRAINSCommonLib/itkInverseConsistentLandmarks.hxx
@@ -0,0 +1,2647 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile$
+ *  Language:  C++
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkInverseConsistentLandmarks_hxx
+#define __itkInverseConsistentLandmarks_hxx
+#include "itkInverseConsistentLandmarks.h"
+#include 
+#include 
+#include 
+#include 
+#include 
+
+namespace itk
+{
+template 
+InverseConsistentLandmarks
+::InverseConsistentLandmarks(void)
+{
+  ImageDims[0] = 12345;
+  ImageDims[1] = 12345;
+  ImageDims[2] = 12345;
+  ImageDims[3] = 12345;
+}
+
+template 
+InverseConsistentLandmarks
+::InverseConsistentLandmarks(const int XDim, const int YDim, const int ZDim, const int TDim)
+{
+  ImageDims[0] = XDim;
+  ImageDims[1] = YDim;
+  ImageDims[2] = ZDim;
+  ImageDims[3] = TDim;
+}
+
+template 
+InverseConsistentLandmarks &
+InverseConsistentLandmarks
+::operator=(const InverseConsistentLandmarks & rhs)
+{
+  this->std::map::operator=(rhs);
+  ImageDims[0] = rhs.ImageDims[0];
+  ImageDims[1] = rhs.ImageDims[1];
+  ImageDims[2] = rhs.ImageDims[2];
+  ImageDims[3] = rhs.ImageDims[3];
+  return *this;
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadPointTypes(const std::string lmrkfilename)
+{
+  const Landmark_File_Format lmkff = QueryLandmarkFile(lmrkfilename);
+  bool                       check = false;
+
+  switch( lmkff )
+    {
+    case GEC_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadGECPointTypes(lmrkfilename);
+      break;
+    case INTELLX_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadIntellXPointTypes(lmrkfilename);
+      break;
+    case ANALYZE_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadAnalyzePointTypes(lmrkfilename);
+      break;
+    case IPL_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadIPLPointTypes(lmrkfilename);
+      break;
+    case IPL_TALAIRACH_BOUNDS_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadIPLTalairachPointTypes(
+          lmrkfilename);
+      break;
+    case IPL_CEREBELLAR_BOUNDS_LANDMARKS:
+      check = InverseConsistentLandmarks::ReadIPLCerebellarPointTypes(
+          lmrkfilename);
+      break;
+    case UNKNOWN_LANDMARKS:
+      std::cout << "Unknown landmark file format!" << std::endl;
+      return false;
+    default:
+      std::cout << "Error. Invalid Landmark_File_Format type!" << std::endl;
+      exit(-1);
+    }
+  return check;
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadPointTypes(const std::string lmrkfilename, const int XDim,
+                 const int YDim, const int ZDim, const int TDim)
+{
+  Landmark_File_Format lmkff = QueryLandmarkFile(lmrkfilename);
+
+  switch( lmkff )
+    {
+    case GEC_LANDMARKS:
+      InverseConsistentLandmarks::ReadGECPointTypes(lmrkfilename,
+                                                    XDim,
+                                                    YDim,
+                                                    ZDim,
+                                                    TDim);
+      break;
+    case INTELLX_LANDMARKS:
+      InverseConsistentLandmarks::ReadIntellXPointTypes(lmrkfilename,
+                                                        XDim,
+                                                        YDim,
+                                                        ZDim,
+                                                        TDim);
+      break;
+    case ANALYZE_LANDMARKS:
+      InverseConsistentLandmarks::ReadAnalyzePointTypes(lmrkfilename,
+                                                        XDim,
+                                                        YDim,
+                                                        ZDim,
+                                                        TDim);
+      break;
+    case IPL_LANDMARKS:
+      InverseConsistentLandmarks::ReadIPLPointTypes(lmrkfilename,
+                                                    XDim,
+                                                    YDim,
+                                                    ZDim,
+                                                    TDim);
+      break;
+    case IPL_TALAIRACH_BOUNDS_LANDMARKS:
+      InverseConsistentLandmarks::ReadIPLTalairachPointTypes(lmrkfilename,
+                                                             XDim,
+                                                             YDim,
+                                                             ZDim,
+                                                             TDim);
+      break;
+    case IPL_CEREBELLAR_BOUNDS_LANDMARKS:
+      InverseConsistentLandmarks::ReadIPLCerebellarPointTypes(lmrkfilename,
+                                                              XDim,
+                                                              YDim,
+                                                              ZDim,
+                                                              TDim);
+      break;
+    case UNKNOWN_LANDMARKS:
+      std::cout << "Unknown landmark file format!" << std::endl;
+      return false;
+    default:
+      std::cout << "Error. Invalid Landmark_File_Format type!" << std::endl;
+      exit(-1);
+    }
+  return true;
+}
+
+template 
+bool InverseConsistentLandmarks
+::WritePointTypes(const std::string lmrkfilename,
+                  const Landmark_File_Format lmkff)
+{
+  bool writeresult;
+
+  switch( lmkff )
+    {
+    case GEC_LANDMARKS:
+      writeresult = InverseConsistentLandmarks::WriteGECPointTypes(
+          lmrkfilename);
+      break;
+    case INTELLX_LANDMARKS:
+      writeresult = InverseConsistentLandmarks::WriteIntellXPointTypes(
+          lmrkfilename);
+      break;
+    case ANALYZE_LANDMARKS:
+      writeresult = InverseConsistentLandmarks::WriteAnalyzePointTypes(
+          lmrkfilename);
+      break;
+    case IPL_LANDMARKS:
+    case IPL_TALAIRACH_BOUNDS_LANDMARKS:
+    case IPL_CEREBELLAR_BOUNDS_LANDMARKS:
+      // writeresult = InverseConsistentLandmarks::WriteIPLPointTypes(
+      // lmrkfilename );
+      std::cout << "IPL_LANDMARKS NOT IMPLEMENTED FOR WRITING" << std::endl;
+      break;
+    case UNKNOWN_LANDMARKS:
+      std::cout << "Unknown output landmark file format!" << std::endl;
+      writeresult = false;
+    }
+  return writeresult;
+}
+
+template 
+bool InverseConsistentLandmarks
+::PrintPointTypes(void) const
+{
+  printf("#IMAGEDIMS %6hu %6hu %6hu %6hu\n",
+         ImageDims[0],
+         ImageDims[1],
+         ImageDims[2],
+         ImageDims[3]);
+  printf("#%11s %12s %12s %12s %12s %12s\n",
+         "Name",
+         "X",
+         "Y",
+         "Z",
+         "T",
+         "Weighting");
+  for( typename InverseConsistentLandmarks::const_iterator mapiter =
+         this->begin();
+       mapiter != this->end();
+       ++mapiter )
+    {
+    printf( "%12s %12.6f %12.6f %12.6f %12.5f %12.6f\n", mapiter->first.c_str(),
+            mapiter->second[0],
+            mapiter->second[1],
+            mapiter->second[2],
+            mapiter->second.GetT(),
+            mapiter->second.GetWeighting() );
+    }
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+typename InverseConsistentLandmarks::Landmark_File_Format
+InverseConsistentLandmarks
+::QueryLandmarkFile(const std::string lmrkfilename)
+{
+  /* These are the header formats for GEC, IntellX, and Analyze Landmark files
+    * respectively
+    * GEC Landmark File Format (typical extension .lmks)
+    *
+    *--------------------------------------------------------------------------------------
+    * #GECLANDMARKS-v1.0
+    * #IMAGEDIMS   XDIM   YDIM   ZDIM   TDIM
+    * #Name            X            Y            Z            T
+    *    Weighting
+    * AC_Point 128 184 128 0 0
+    * PC_Point 100 160 130 0 0
+    * etc.
+    *
+    *--------------------------------------------------------------------------------------
+    * IntellX Landmark File Format (typical extension .lmk)
+    *
+    *--------------------------------------------------------------------------------------
+    * Landmarks-1.0
+    * Number of points
+    * "landmark identifier/description"
+    * XPOINT YPOINT ZPOINT 1 1
+    * "landmark identifier/description"
+    * XPOINT YPOINT ZPOINT 1 1
+    * etc.
+    *
+    *--------------------------------------------------------------------------------------
+    * Analyze Landmark File Format (typical extension .log)
+    *
+    *--------------------------------------------------------------------------------------
+    * #System Time
+    * #Volume=name of volume
+    * #
+    * #
+    * #Point
+    * #X    Y    Z     Value       Label
+    * #==== ==== ====  ==========  ==========
+    *   129  277  128          14        Label
+    *   150  100  164          32        Label
+    * etc.
+    *
+    *--------------------------------------------------------------------------------------
+    * For specializing which file format it is, the firstline #GECLANDMARKS-v1.0
+    * will
+    * specify a type GEC_LANDMARKS.  The tag Landmarks-1.0 will specify a
+    * landmark
+    * file of the type INTELLX_LANDMARKS.  The lines
+    */
+  // #Point
+  // #X    Y    Z     Value       Label
+  // will be used to specify a landmark file generated from an Analyze point log
+  // session as the type ANALYZE_LANDMARKS.  Any other format which doesn't
+  // match
+  // will return UNKNOWN_LANDMARKS.
+
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+
+  if( tempfile == NULL )
+    {
+    std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    return UNKNOWN_LANDMARKS;
+    }
+
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return UNKNOWN_LANDMARKS;
+    }
+
+  if( strncmp(buffer, "#GECLANDMARKS-v1.0", 18) == 0 )
+    {
+    return GEC_LANDMARKS;
+    }
+
+  if( strncmp(buffer, "Landmarks-1.0", 13) == 0 )
+    {
+    return INTELLX_LANDMARKS;
+    }
+
+  if( strncmp(buffer, "IPL_HEADER_BEGIN", 16) == 0 )
+    {
+    if( lmrkfilename.find("Talairach.bnd") != std::string::npos )
+      {
+      return IPL_TALAIRACH_BOUNDS_LANDMARKS;
+      }
+    else if( lmrkfilename.find("Cerebellum.bnd") != std::string::npos )
+      {
+      return IPL_CEREBELLAR_BOUNDS_LANDMARKS;
+      }
+    else
+      {
+      return IPL_LANDMARKS;
+      }
+    }
+  // If it is not either of these two, try to read the next 4 lines
+  // and check to see if it matches the Analyze point log file format
+  for( int i = 0; i < 4; ++i )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return UNKNOWN_LANDMARKS;
+      }
+    }
+
+  if( strncmp(buffer, "#Point", 11) == 0 )
+    {
+    // Try to match next line
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return UNKNOWN_LANDMARKS;
+      }
+    if( strncmp(buffer, "#X    Y    Z     Value       Label", 37) == 0 )
+      {
+      return ANALYZE_LANDMARKS;
+      }
+    }
+  return UNKNOWN_LANDMARKS;
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadGECPointTypes(const std::string lmrkfilename)
+{
+  // std::cout << "Reading GEC Landmark File " << lmrkfilename << std::endl;
+
+  this->erase( this->begin(), this->end() );
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  const unsigned short int LANDMARK_NAME_SIZE = 40;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char                     CurrentLandmarkName[LANDMARK_NAME_SIZE];
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "#GECLANDMARKS-v1.0", 18) != 0 )
+    {
+    // Only files with a header of #GECLANDMARKS-v1.0 will be accepted
+    return false;
+    }
+  // Read dimensions of image that landmarks are associated with
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  // Note CurrentLandmarkName is just a placeholder here!.
+  // Note the hu is an indicator that this is a unsigned short int
+
+  sscanf( buffer, "%s %hu %hu %hu %hu", CurrentLandmarkName,
+          &( ImageDims[0] ),
+          &( ImageDims[1] ),
+          &( ImageDims[2] ),
+          &( ImageDims[3] ) );
+
+  while( fgets(buffer, FILE_BUFFER_SIZE, tempfile) != NULL )
+    {
+    if( buffer[0] == '#' )           // This allows for comments to be added
+                                     // anywhere in the file
+      {
+      continue;
+      }
+    PointType TempPnt;
+      {
+      double       val0;
+      double       val1;
+      double       val2;
+      double       valT;
+      double       valW;
+      unsigned int numread = sscanf(buffer, "%s %lf %lf %lf %lf %lf",
+                                    CurrentLandmarkName,
+                                    &val0, &val1, &val2, &valT, &valW);
+      if( numread < 6 )
+        {
+        return false;
+        }
+      TempPnt[0] = static_cast( val0 );
+      TempPnt[1] = static_cast( val1 );
+      TempPnt[2] = static_cast( val2 );
+      TempPnt.SetT( static_cast( valT ) );
+      TempPnt.SetWeighting( static_cast( valW ) );
+      }
+    if( ImageDims[0] <= TempPnt[0] )
+      {
+      // std::cout << "Error: Point "<< CurrentLandmarkName << " has invalid x
+      // coordinate.  Max value is: " << ImageDims[0]-1<size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadGECPointTypes(const std::string lmrkfilename,
+                    const int XDim, const int YDim,
+                    const int ZDim, const int TDim)
+{
+  const bool testread = this->InverseConsistentLandmarks::ReadGECPointTypes(
+      lmrkfilename);
+
+  this->InverseConsistentLandmarks::rescale(XDim, YDim, ZDim, TDim);
+  return testread;
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadIntellXPointTypes(const std::string lmrkfilename)
+{
+  //  std::cout << "Reading IntellX Landmark File " << lmrkfilename <<
+  // std::endl;
+  this->erase( this->begin(), this->end() );
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 128;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  std::string              CurrentLandmarkName;
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "Landmarks-1.0", 13) != 0 )
+    {
+    // Only files with a header of Landmarks-1.0 will be accepted
+    return false;
+    }
+  // Read Number of Landmark points
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  const int NumberOfPoints = atoi(buffer);
+  for( int p = 0; p < NumberOfPoints; ++p )
+    {
+    // Extract Landmark Name
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    CurrentLandmarkName = std::string(buffer);
+    // CurrentLandmarkName.replace(CurrentLandmarkName.find("\""),1,"");
+    // CurrentLandmarkName.replace(CurrentLandmarkName.find("\""),1,"");
+    std::string NewLandmarkName;
+    for( unsigned int iter = 0; iter < CurrentLandmarkName.length(); ++iter )
+      {
+      // std::cout << "CurrentLandmarkName[" << iter << "] = " <<
+      // CurrentLandmarkName[iter] << std::endl;
+      if( CurrentLandmarkName[iter] == '\n' || CurrentLandmarkName[iter] ==
+          '\r' || CurrentLandmarkName[iter] == '\t'
+          || CurrentLandmarkName[iter] == '\"' )
+        {
+        continue;
+        }
+      else if( CurrentLandmarkName[iter] == ' ' )
+        {
+        NewLandmarkName += "_";
+        }
+      else
+        {
+        NewLandmarkName += CurrentLandmarkName[iter];
+        }
+      // std::cout << "NewLandmarkName = " << NewLandmarkName << std::endl;
+      }
+
+    // Extract Coordinates
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    PointType TempPnt;
+      {
+      unsigned int numread = sscanf(buffer, "%lf %lf %lf",
+                                    &TempPnt[0], &TempPnt[1], &TempPnt[2]);
+      if( numread < 3 )
+        {
+        return false;
+        }
+      }
+    // Convert to Analyze coordinate system...Note the -1 is needed for correct
+    // coord
+    // Ex. 0,0,0 in Warp = 127,127,127 in a 128x128x128 analyze image.
+    // Assumes the landmark dimensions have been set before used in this
+    // function
+    TempPnt[0] = static_cast( ImageDims[0] ) - TempPnt[0];
+    TempPnt[1] = static_cast( ImageDims[1] ) - TempPnt[1];
+    TempPnt[2] = static_cast( ImageDims[2] ) - TempPnt[2];
+    // DDEBUG, this is set to one when dimension is one, which goofs when you
+    // write out
+    // a lmk file as a ilmks and try to read the ilmks back in.  Since no t
+    // coordinates
+    // will be used in the short run, this will be implemented
+    // TempPnt.setT() = static_cast( ImageDims[3] ) -
+    // TempPnt[3];
+    TempPnt.SetT(0.0F);
+
+    // Set Weighting to default value of 1.0F;
+    TempPnt.SetWeighting(1.0F);
+    ( *this )[NewLandmarkName] = TempPnt;
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadIntellXPointTypes(const std::string lmrkfilename,
+                        const int XDim, const int YDim,
+                        const int ZDim, const int TDim)
+{
+  // std::cout << "Reading IntellX Landmark File " << lmrkfilename << std::endl;
+  // std::cout << "Specifying dimensions " << XDim << ", " << YDim << ", " <<
+  // ZDim << ", " << TDim << "." << std::endl;
+
+  if( XDim < 0 )
+    {
+    std::cout << "Error. X dimension " << XDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( YDim < 0 )
+    {
+    std::cout << "Error. Y dimension " << YDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( ZDim < 0 )
+    {
+    std::cout << "Error. Z dimension " << ZDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( TDim < 0 )
+    {
+    std::cout << "Error. T dimension " << TDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+
+  // Delete all old landmarks
+  this->erase( this->begin(), this->end() );
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 128;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  std::string              CurrentLandmarkName;
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "Landmarks-1.0", 13) != 0 )
+    {
+    // Only files with a header of Landmarks-1.0 will be accepted
+    return false;
+    }
+  // Read Number of Landmark points
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  const int NumberOfPoints = atoi(buffer);
+
+  // Assigning the dimensions from the parameters
+  ImageDims[0] = XDim;
+  ImageDims[1] = YDim;
+  ImageDims[2] = ZDim;
+  ImageDims[3] = TDim;
+  for( int p = 0; p < NumberOfPoints; ++p )
+    {
+    // Extract Landmark Name
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+
+    CurrentLandmarkName = std::string(buffer);
+
+    std::string NewLandmarkName;
+    for( unsigned int iter = 0; iter < CurrentLandmarkName.length(); ++iter )
+      {
+      // std::cout << "CurrentLandmarkName[" << iter << "] = " <<
+      // CurrentLandmarkName[iter] << std::endl;
+      if( CurrentLandmarkName[iter] == '\n' || CurrentLandmarkName[iter] ==
+          '\r' || CurrentLandmarkName[iter] == '\t'
+          || CurrentLandmarkName[iter] == '\"' )
+        {
+        continue;
+        }
+      else if( CurrentLandmarkName[iter] == ' ' )
+        {
+        NewLandmarkName += "_";
+        }
+      else
+        {
+        NewLandmarkName += CurrentLandmarkName[iter];
+        }
+      }
+
+    // Extract Coordinates
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    PointType TempPnt;
+      {
+      double       val0;
+      double       val1;
+      double       val2;
+      unsigned int numread = sscanf(buffer, "%lf %lf %lf",
+                                    &val0, &val1, &val2);
+      if( numread < 3 )
+        {
+        return false;
+        }
+      TempPnt[0] = static_cast( val0 );
+      TempPnt[1] = static_cast( val1 );
+      TempPnt[2] = static_cast( val2 );
+      }
+    // Convert to Analyze coordinate system...Note the -1 is needed for correct
+    // coord
+    // Ex. 0,0,0 in Warp = 127,127,127 in a 128x128x128 analyze image.
+    TempPnt[0] = static_cast( ImageDims[0] ) - TempPnt[0];
+    TempPnt[1] = static_cast( ImageDims[1] ) - TempPnt[1];
+    TempPnt[2] = static_cast( ImageDims[2] ) - TempPnt[2];
+
+    TempPnt.SetT(0.0F);
+
+    // Set Weighting to default value of 1.0F;
+    TempPnt.SetWeighting(1.0F);
+    ( *this )[NewLandmarkName] = TempPnt;
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadAnalyzePointTypes(const std::string lmrkfilename)
+{
+  std::cout << "Reading Analyze Landmark File " << lmrkfilename << std::endl;
+
+  // Delete all old landmarks
+  this->erase( this->begin(), this->end() );
+
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  const unsigned short int LANDMARK_NAME_SIZE = 40;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char                     CurrentLandmarkName[LANDMARK_NAME_SIZE];
+  char *                   status = 0;
+  // Read Header Information
+  for( int i = 0; i < 5; ++i )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    }
+
+  if( strncmp(buffer, "#Point", 11) == 0 )
+    {
+    // Try to match next line
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    if( strncmp(buffer, "#X    Y    Z     Value       Label", 37) != 0 )
+      {
+      return false;
+      }
+    }
+  else
+    {
+    return false;
+    }
+
+  // Reading the line with " ====  ====  ==== ..etc"
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+
+  int mycount = 1;
+  while( fgets(buffer, FILE_BUFFER_SIZE, tempfile) != NULL )
+    {
+    int       grayvalue;
+    PointType TempPnt;
+      {
+      double val0;
+      double val1;
+      double val2;
+      int    numread = sscanf(buffer, "%lf %lf %lf %d %s", &val0,
+                              &val1, &val2, &grayvalue, CurrentLandmarkName);
+      TempPnt[0] = static_cast( val0 );
+      TempPnt[1] = static_cast( val1 );
+      TempPnt[2] = static_cast( val2 );
+      if( numread == -1 )
+        {
+        continue;
+        }
+
+      if( numread < 4 )          // Need at least an X,Y,Z coordinate
+        {
+        return false;
+        }
+      if( numread == 4 )          // No label was found
+        {
+        memset(CurrentLandmarkName, 0, LANDMARK_NAME_SIZE);
+        }
+      }
+
+    if( ImageDims[0] <= TempPnt[0] )
+      {
+      return false;
+      }
+    if( ImageDims[1] <= TempPnt[1] )
+      {
+      return false;
+      }
+    if( ImageDims[2] <= TempPnt[2] )
+      {
+      return false;
+      }
+
+    // Here is how the naming definition is defined, if the label is not found,
+    // the
+    // landmark identifier is Landmark_N where N is the current number of
+    // landmarks
+    // read in.  If the landmark label is found in the current map, then the
+    // label is renamed with the old label plus a "_1".  If that tag exists,
+    // then
+    // the next label is the old label with "_2".  This continues until a
+    // unique name is found for the landmark.
+
+    std::string CurrentName(CurrentLandmarkName);
+
+    if( CurrentName.size() == 0 )
+      {
+      char numberbuffer[16];
+      sprintf(numberbuffer, "%d", mycount);
+      CurrentName = "Landmark_" + std::string(numberbuffer);
+      }
+
+    // Checking to make sure no elements in the map of landmark points are
+    // duplicated.
+      {
+      int         label = 1;
+      std::string OriginalLabel(CurrentName);
+
+      char labelbuffer[16];
+      while( ( *this ).find(CurrentName) != ( *this ).end() )
+        {
+        sprintf(labelbuffer, "%d", label);
+        CurrentName = OriginalLabel + "_" + std::string(labelbuffer);
+        ++label;
+        }
+      }
+    TempPnt.SetWeighting(1.0F);
+    ( *this )[CurrentName] = TempPnt;
+    ++mycount;
+    }
+
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadAnalyzePointTypes(const std::string lmrkfilename,
+                        const int XDim, const int YDim,
+                        const int ZDim, const int TDim)
+{
+  std::cout << "Reading Analyze Landmark File " << lmrkfilename << std::endl;
+  std::cout << "Specifying dimensions " << XDim << ", " << YDim << ", "
+            << ZDim << ", " << TDim << "." << std::endl;
+
+  if( XDim < 0 )
+    {
+    std::cout << "Error. X dimension " << XDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( YDim < 0 )
+    {
+    std::cout << "Error. Y dimension " << YDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( ZDim < 0 )
+    {
+    std::cout << "Error. Z dimension " << ZDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+  if( TDim < 0 )
+    {
+    std::cout << "Error. T dimension " << TDim << " given is less than 0"
+              << std::endl;
+    return false;
+    }
+
+  // Delete all old landmarks
+  this->erase( this->begin(), this->end() );
+
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  const unsigned short int LANDMARK_NAME_SIZE = 40;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char                     CurrentLandmarkName[LANDMARK_NAME_SIZE];
+  char *                   status = 0;
+  // Read Header Information
+  for( int i = 0; i < 5; ++i )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    }
+
+  if( strncmp(buffer, "#Point", 11) == 0 )
+    {
+    // Try to match next line
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      return false;
+      }
+    if( strncmp(buffer, "#X    Y    Z     Value       Label", 37) != 0 )
+      {
+      return false;
+      }
+    }
+  else
+    {
+    return false;
+    }
+
+  // Reading the line with " ====  ====  ==== ..etc"
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+
+  // Using the function to assign the landmark image dimensions
+  ImageDims[0] = XDim;
+  ImageDims[1] = YDim;
+  ImageDims[2] = ZDim;
+  ImageDims[3] = TDim;
+
+  int count = 1;
+  while( fgets(buffer, FILE_BUFFER_SIZE, tempfile) != NULL )
+    {
+    int       grayvalue;
+    PointType TempPnt;
+      {
+      double val0;
+      double val1;
+      double val2;
+      int    numread = sscanf(buffer, "%lf %lf %lf %d %s", &val0,
+                              &val1, &val2, &grayvalue, CurrentLandmarkName);
+      TempPnt[0] = static_cast( val0 );
+      TempPnt[1] = static_cast( val1 );
+      TempPnt[2] = static_cast( val2 );
+
+      if( numread == -1 )
+        {
+        // No values read in from sscanf so continue
+        continue;
+        }
+
+      if( numread < 4 )            // Need at least an X,Y,Z coordinate
+        {
+        return false;
+        }
+
+      if( numread == 4 )             // No label was found
+        {
+        memset(CurrentLandmarkName, 0, LANDMARK_NAME_SIZE);
+        }
+
+      // std::cout << "Number read = " << numread << std::endl;
+      // std::cout << "CurrentLandmarkName = " << CurrentLandmarkName <<
+      // std::endl;
+      }
+
+    if( ImageDims[0] <= TempPnt[0] )
+      {
+      // std::cout << "Error: Point "<< CurrentLandmarkName << " has invalid x
+      // coordinate.  Max value is: " << ImageDims[0]-1<begin();
+       mapiter != this->end();
+       ++mapiter )
+    {
+    fprintf( tempfile, "%12s %12.6f %12.6f %12.6f %12.5f %12.6f\n",
+             mapiter->first.c_str(),
+             mapiter->second[0],
+             mapiter->second[1],
+             mapiter->second[2],
+             mapiter->second.GetT(),
+             mapiter->second.GetWeighting() );
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::WriteIntellXPointTypes(const std::string lmrkfilename) const
+{
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "w");
+
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  fprintf(tempfile, "Landmarks-1.0\n");
+  fprintf( tempfile, "%d\n", static_cast( this->size() ) );
+  for( typename InverseConsistentLandmarks::const_iterator mapiter =
+         this->begin();
+       mapiter != this->end();
+       ++mapiter )
+    {
+    std::string temp("\"");
+
+    temp += mapiter->first;
+    temp += "\"";
+    // Notice the conversion back to IntellX coordinate system.
+    // Note: -1 is needed here to get correct coordinate.
+    fprintf(tempfile, "%s\n%f\t%f\t%f\t1\t1\n", temp.c_str(),
+            static_cast( ImageDims[0] ) - mapiter->second[0],
+            static_cast( ImageDims[1] ) - mapiter->second[1],
+            static_cast( ImageDims[2] ) - mapiter->second[2]);
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::WriteAnalyzePointTypes(const std::string lmrkfilename) const
+{
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "w");
+
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+
+  // Getting the current time information
+  time_t     curtime;
+  struct tm *loctime;
+  curtime = time(NULL);
+  loctime = localtime(&curtime);
+  std::string date( asctime(loctime) );
+
+  date = std::string("#") + date;
+  fprintf( tempfile, date.c_str() );
+  fprintf(tempfile, "#Volume=\n");
+  fprintf(tempfile, "#\n");
+  fprintf(tempfile, "#\n");
+  fprintf(tempfile, "#Point\n");
+  fprintf(tempfile, "#X    Y    Z     Value       Label\n");
+  fprintf(tempfile, "#==== ==== ====  ==========  ==========\n");
+  for( typename InverseConsistentLandmarks::const_iterator mapiter =
+         this->begin();
+       mapiter != this->end();
+       ++mapiter )
+    {
+    // Graylevel value is assumed to not be necessary so it's set to 0
+    fprintf( tempfile, "%5d%5d%5d%12d    %s\n",
+             static_cast( mapiter->second[0] ),
+             static_cast( mapiter->second[1] ),
+             static_cast( mapiter->second[2] ),
+             0, mapiter->first.c_str() );
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ConcatLandmarks(InverseConsistentLandmarks & newlmks)
+{
+  // Copy landmarks from newlmks to the current landmark file, but
+  // ensuring that the keys are not identical
+
+  if( this == &newlmks )
+    {
+    std::cout << "Error. Can not concatenate a landmark object with itself!"
+              << std::endl;
+    return false;
+    }
+
+  // Check to make sure the dimensions match
+  bool sizematch = true;
+  if( this->getXDim() != newlmks.getXDim() )
+    {
+    std::cout
+    <<
+    "Error. X dimensions of landmark objects do not match in ConcatLandmarks!"
+    << std::endl;
+    sizematch = false;
+    }
+  if( this->getYDim() != newlmks.getYDim() )
+    {
+    std::cout
+    <<
+    "Error. Y dimensions of landmark objects do not match in ConcatLandmarks!"
+    << std::endl;
+    sizematch = false;
+    }
+  if( this->getZDim() != newlmks.getZDim() )
+    {
+    std::cout
+    <<
+    "Error. Z dimensions of landmark objects do not match in ConcatLandmarks!"
+    << std::endl;
+    sizematch = false;
+    }
+  if( this->getTDim() != newlmks.getTDim() )
+    {
+    std::cout
+    <<
+    "Error. T dimensions of landmark objects do not match in ConcatLandmarks!"
+    << std::endl;
+    sizematch = false;
+    }
+  if( sizematch == false )
+    {
+    return sizematch;
+    }
+
+  // This will store all the labels
+  std::map labelcount;
+  std::string                CurrentName;
+  char                       labelbuffer[16];
+
+  if( newlmks.size() == 0 )
+    {
+    return false;
+    }
+  // Initialize the map with the labels found in this landmark object
+  for( typename InverseConsistentLandmarks::iterator iter = this->begin();
+       iter != this->end();
+       ++iter )
+    {
+    labelcount[iter->first] = 0;
+    }
+  for( typename InverseConsistentLandmarks::iterator iter = newlmks.begin();
+       iter != newlmks.end();
+       ++iter )
+    {
+    if( labelcount.find(iter->first) != labelcount.end() )
+      {
+      // Increment the counter and apply that name with the new tag
+      labelcount[iter->first] = labelcount[iter->first] + 1;
+      sprintf(labelbuffer, "%d", labelcount.find(iter->first)->second);
+      CurrentName = iter->first + "_" + std::string(labelbuffer);
+      }
+    else
+      {
+      labelcount[iter->first] = 0;
+      CurrentName = iter->first;
+      }
+    // std::cout << "CurrentName = " << CurrentName << std::endl;
+    ( *this )[CurrentName] = iter->second;
+    }
+
+  return true;
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ConcatLandmarks(const std::string lmrkfilename)
+{
+  // Copy landmarks from newlmks to the current landmark file
+  InverseConsistentLandmarks temp;
+
+  temp.ReadPointTypes(lmrkfilename);
+  return this->ConcatLandmarks(temp);
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ConcatLandmarks(const std::string lmrkfilename, const int XDim,
+                  const int YDim, const int ZDim, const int TDim)
+{
+  // Copy landmarks from newlmks to the current landmark file
+  InverseConsistentLandmarks temp;
+
+  temp.ReadPointTypes(lmrkfilename, XDim, YDim, ZDim, TDim);
+  return this->ConcatLandmarks(temp);
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::RemoveClosePoints(const PointStorageType distance)
+{
+  bool removedpoint = false;
+
+  typename InverseConsistentLandmarks::iterator iter;
+  typename InverseConsistentLandmarks::iterator jter;
+  for( iter = this->begin(); iter != this->end(); ++iter )
+    {
+    // std::cout << "iter->first = " << iter->first << std::endl;
+    typename InverseConsistentLandmarks::iterator ipp = iter;
+    ++ipp;
+    jter = ipp;
+
+    while( jter != this->end() )
+      {
+      // std::cout << "jter->first = " << jter->first << std::endl;
+      PointStorageType ix = iter->second[0];
+      PointStorageType iy = iter->second[1];
+      PointStorageType iz = iter->second[2];
+      PointStorageType jx = jter->second[0];
+      PointStorageType jy = jter->second[1];
+      PointStorageType jz = jter->second[2];
+
+      PointStorageType value =
+        sqrt( ( jx
+                - ix )
+              * ( jx - ix ) + ( jy - iy ) * ( jy - iy ) + ( jz - iz ) * ( jz - iz ) );
+      if( value < distance )
+        {
+        // You lose the iterator when you issue an erase, so saving jter
+        typename InverseConsistentLandmarks::iterator dter = jter;
+        removedpoint = true;
+        this->erase(dter->first);
+
+        // The iterator has stayed the same, but the list has moved back one, so
+        // an
+        // extra increment is needed.
+        ++jter;
+        }
+      ++jter;
+      }
+    }
+
+  return removedpoint;
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::RemoveUnmatchedPoints(InverseConsistentLandmarks & tempmap1)
+{
+  for( typename InverseConsistentLandmarks::iterator mapiter = this->begin();
+       mapiter != this->end();
+       ++mapiter )
+    {
+    typename InverseConsistentLandmarks::iterator mapiter1 =
+      tempmap1.find(mapiter->first);
+    // Item NOT Found
+    if( mapiter1 == tempmap1.end() )
+      {
+      this->erase(mapiter->first);
+      }
+    }
+
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::rescale(const int newx, const int newy, const int newz, const int newt)
+{
+  assert(newx > 0);
+  assert(newy > 0);
+  assert(newz > 0);
+  assert(newt > 0);
+
+  const PointStorageType scalex = static_cast( newx )
+    / static_cast( ImageDims[0] );
+  const PointStorageType scaley = static_cast( newy )
+    / static_cast( ImageDims[1] );
+  const PointStorageType scalez = static_cast( newz )
+    / static_cast( ImageDims[2] );
+  const PointStorageType scalet = static_cast( newt )
+    / static_cast( ImageDims[3] );
+
+  ImageDims[0] = static_cast( newx );
+  ImageDims[1] = static_cast( newy );
+  ImageDims[2] = static_cast( newz );
+  ImageDims[3] = static_cast( newt );
+  std::cout << "Dims: " << ImageDims[0] << " " << ImageDims[1] << " "
+            << ImageDims[2] << " " << ImageDims[3] << "\n";
+  std::cout << "scale: " << scalex << " " << scaley << " " << scalez << " "
+            << scalet << "\n";
+  for( typename InverseConsistentLandmarks::iterator mapiter = this->begin();
+       mapiter != this->end(); ++mapiter )
+    {
+    mapiter->second[0] = mapiter->second[0] * scalex;
+    mapiter->second[1] = mapiter->second[1] * scaley;
+    mapiter->second[2] = mapiter->second[2] * scalez;
+    mapiter->second.SetT(mapiter->second.GetT() * scalet);
+    }
+
+  return true;
+}
+
+template 
+bool InverseConsistentLandmarks
+::ReadIPLPointTypes(const std::string lmrkfilename)
+{
+  std::cout << "Reading IPL Landmark File " << lmrkfilename << std::endl;
+  // Delete all old landmarks
+  this->erase( this->begin(), this->end() );
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  const unsigned short int LANDMARK_NAME_SIZE = 40;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char                     CurrentLandmarkName[LANDMARK_NAME_SIZE];
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "IPL_HEADER_BEGIN", 16) != 0 )
+    {
+    // Only files with a header of IPL_HEADER_BEGIN will be accepted
+    return false;
+    }
+  // Read dimensions of image that landmarks are associated with
+  // skip a head to landmark definitions
+  status = buffer;
+  while( ( strncmp(buffer, "LANDMARK_HEADER_BEGIN",
+                   21) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      << "ERROR: End of file reached before LANDMARK_HEADER_BEGIN found"
+      << std::endl;
+      }
+    }
+
+  bool xisset = false;
+  bool yisset = false;
+  bool zisset = false;
+  ImageRes[0] = 1.0;
+  ImageRes[1] = 1.0;
+  ImageRes[2] = 1.0;
+  ImageRes[3] = 1.0;
+
+  // process looking for dims
+  status = buffer;
+  while( ( strncmp(buffer, "LANDMARK_HEADER_END",
+                   19) != 0 ) && ( status != NULL ) )
+    {
+    // Look for x
+    if( strncmp(buffer, "LANDMARK_X_SIZE", 15) == 0  )
+      {
+      sscanf( buffer, "%s %hu", CurrentLandmarkName, &( ImageDims[0] ) );
+      xisset = true;
+      }
+    // Look for y
+    if( strncmp(buffer, "LANDMARK_Y_SIZE", 15) == 0  )
+      {
+      sscanf( buffer, "%s %hu", CurrentLandmarkName, &( ImageDims[1] ) );
+      yisset = true;
+      }
+    // Look for z
+    if( strncmp(buffer, "LANDMARK_Z_SIZE", 15) == 0  )
+      {
+      sscanf( buffer, "%s %hu", CurrentLandmarkName, &( ImageDims[2] ) );
+      zisset = true;
+      }
+    if( strncmp(buffer, "LANDMARK_X_RESOLUTION", 20) == 0  )
+      {
+      sscanf( buffer, "%s %f", CurrentLandmarkName, &( ImageRes[0] ) );
+      }
+    if( strncmp(buffer, "LANDMARK_Y_RESOLUTION", 20) == 0  )
+      {
+      sscanf( buffer, "%s %f", CurrentLandmarkName, &( ImageRes[1] ) );
+      }
+    if( strncmp(buffer, "LANDMARK_Z_RESOLUTION", 20) == 0  )
+      {
+      sscanf( buffer, "%s %f", CurrentLandmarkName, &( ImageRes[2] ) );
+      }
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      << "ERROR: End of file reached before LANDMARK_HEADER_END found"
+      << std::endl;
+      }
+    }
+
+  ImageDims[3] = 1;
+  if( !( xisset && yisset && zisset ) )
+    {
+    std::cout << "ERROR must set all LANDMARK_[XYZ]_SIZE values" << std::endl;
+    }
+
+  // Skip ahead to data
+  status = buffer;
+  while( ( strncmp(buffer, "IPL_HEADER_END", 14) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout << "ERROR: End of file reached before IPL_HEADER_END found"
+                << std::endl;
+      }
+    }
+
+  // Actually read the data
+  while( fgets(buffer, FILE_BUFFER_SIZE, tempfile) != NULL )
+    {
+    if( buffer[0] == '#' )           // This allows for comments to be added
+                                     // anywhere in the file
+      {
+      continue;
+      }
+    PointType TempPnt;
+      {
+      // DO I NEED TO INVERT Y HERE? SMP
+      // const double invertY = static_cast (ImageDims[1]-1);
+      unsigned int numread = sscanf(buffer,
+                                    "%s %lf %lf %lf ",
+                                    CurrentLandmarkName,
+                                    &TempPnt[0],
+                                    &TempPnt[1],
+                                    &TempPnt[2]);
+      if( numread != 4 )
+        {
+        std::cout << "ERROR invalid number of args read at landmark "
+                  << CurrentLandmarkName << std::endl;
+        return false;
+        }
+      }
+    TempPnt.SetT(0.0F);
+    TempPnt.SetWeighting(1.0F);
+    if( ( ImageDims[0] <= TempPnt[0] * ImageRes[0] )
+        || ( ImageDims[1] <= TempPnt[1] * ImageRes[1] )
+        || ( ImageDims[2] <= TempPnt[2] * ImageRes[2] )
+        || ( ImageDims[3] <= TempPnt.GetT() * ImageRes[3] ) )
+      {
+      std::cout << "Point Set Outside of Image Dimensions." << std::endl;
+      return false;
+      }
+    ( *this )[CurrentLandmarkName] = TempPnt;
+    }
+
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ReadIPLPointTypes(const std::string lmrkfilename,
+                    const int XDim, const int YDim,
+                    const int ZDim, const int TDim)
+{
+  const bool testread = this->InverseConsistentLandmarks::ReadIPLPointTypes(
+      lmrkfilename);
+
+  this->InverseConsistentLandmarks::rescale(XDim, YDim, ZDim, TDim);
+  return testread;
+}
+
+// ==================Talairach Bounds to Landmark Points===================
+template 
+bool
+InverseConsistentLandmarks
+::process_bnd_point(const std::string & CurrentLandmarkName,
+                    const char *buffer,
+                    const unsigned short local_ImageDims[4],
+                    const float /*local_ImageRes */[4],
+                    PointType & ModifiedPoint)
+{
+  PointStorageType tmp[3];
+
+    {
+    double       val0;
+    double       val1;
+    double       val2;
+    unsigned int numread = sscanf(buffer, "%lf %lf %lf ", &val0, &val1, &val2);
+    if( numread != 3 )
+      {
+      std::cout << "ERROR invalid number of args read at landmark "
+                << CurrentLandmarkName << std::endl;
+      return false;
+      }
+    tmp[0] = val0;
+    tmp[1] = val1;
+    tmp[2] = val2;
+    }
+  for( int i = 0; i < 3; ++i )
+    {
+    ModifiedPoint[i] = tmp[i];
+    }
+
+  // Invert Y Readings for our coordinate system.
+  ModifiedPoint[1] = local_ImageDims[1] - 1 - ModifiedPoint[1];
+  ModifiedPoint.SetT(0.0F);
+  ModifiedPoint.SetWeighting(1.0F);
+  if( local_ImageDims[0] <= ModifiedPoint[0] )
+    {
+    // std::cout << "Error: Point "<< CurrentLandmarkName << " has invalid x
+    // coordinate.  Max value is: " << local_ImageDims[0]-1<
+bool
+InverseConsistentLandmarks
+::ReadIPLTalairachPointTypes(const std::string lmrkfilename)
+{
+  // std::cout << "Reading IPL Talairach Bounds as  Landmark File " <<
+  // lmrkfilename << std::endl;
+
+  // Delete all old landmarks
+  this->erase( this->begin(), this->end() );
+  // Open the files
+  std::cout << "  File: " << lmrkfilename.c_str() << std::endl;
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "IPL_HEADER_BEGIN", 16) != 0 )
+    {
+    // Only files with a header of IPL_HEADER_BEGIN will be accepted
+    return false;
+    }
+  // Read dimensions of image that landmarks are associated with
+  // skip a head to landmark definitions
+  status = buffer;
+  while( ( strncmp(buffer, "TALAIRACH_PARAMETER_HEADER_BEGIN",
+                   32) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    // std::cout << "LINE: " << buffer << std::endl;
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_BEGIN found"
+      << std::endl;
+      }
+    }
+
+  bool xisset = false;
+  bool yisset = false;
+  bool zisset = false;
+  // process looking for dims
+  status = buffer;
+  while( ( strncmp(buffer, "TALAIRACH_PARAMETER_HEADER_END",
+                   30) != 0 ) && ( status != NULL ) )
+    {
+    const unsigned short int TALAIRACH_PARAMETER_NAME_SIZE = 40;
+    char                     Dummy[TALAIRACH_PARAMETER_NAME_SIZE];
+    // Look for x
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_X_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[0] ) );
+      xisset = true;
+      }
+    // Look for y
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Y_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[1] ) );
+      yisset = true;
+      }
+    // Look for z
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Z_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[2] ) );
+      zisset = true;
+      }
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_X_RESOLUTION", 26) == 0  )
+      {
+      sscanf( buffer, "%s %f", Dummy, &( ImageRes[0] ) );
+      }
+    // Look for y
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Y_RESOLUTION", 26) == 0  )
+      {
+      sscanf( buffer, "%s %f", Dummy, &( ImageRes[1] ) );
+      }
+    // Look for z
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Z_RESOLUTION", 26) == 0  )
+      {
+      sscanf( buffer, "%s %f", Dummy, &( ImageRes[2] ) );
+      }
+    // if(!(xisset && yisset && zisset))
+    // {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    // }
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    }
+
+  ImageDims[3] = 1;
+  ImageRes[3] = 1.0;
+  if( !( xisset && yisset && zisset ) )
+    {
+    std::cout << "ERROR must set all TALAIRACH_PARAMETER_[XYZ]_SIZE values"
+              << std::endl;
+    }
+
+  // Skip ahead to data
+  status = buffer;
+  while( ( strncmp(buffer, "IPL_HEADER_END", 14) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout << "ERROR: End of file reached before IPL_HEADER_END found"
+                << std::endl;
+      }
+    }
+
+  // Actually read the data
+  // First read the SLA point
+    {
+    PointType AC_Point;    // Antieror Commisure
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("AC_Point", buffer, ImageDims, ImageRes,
+                          AC_Point) == false )
+      {
+      return false;
+      }
+
+    PointType PC_Point;    // Posterior Commisure
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("PC_Point", buffer, ImageDims, ImageRes,
+                          PC_Point) == false )
+      {
+      return false;
+      }
+
+    PointType SLAPoint;   // Superior Left Anterior
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("SLAPoint", buffer, ImageDims, ImageRes,
+                          SLAPoint) == false )
+      {
+      return false;
+      }
+
+    PointType IRPPoint;   // Inferior Right Posterior
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("IRPPoint", buffer, ImageDims, ImageRes,
+                          IRPPoint) == false )
+      {
+      return false;
+      }
+
+    // Process to extend 4 points to all possible combinations
+    PointType TempPnt = SLAPoint;
+      {
+      std::cout << "  Coordinates:: SLA " << SLAPoint << "   IRP "
+                << IRPPoint << "   PC " << PC_Point << "   AC " << AC_Point
+                << std::endl;
+      std::string CurrentLandmarkName = "AC-Point";    TempPnt[0] = AC_Point[0];
+      TempPnt[1] = AC_Point[1]; TempPnt[2] = AC_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "PC-Point";    TempPnt[0] = PC_Point[0];
+      TempPnt[1] = PC_Point[1]; TempPnt[2] = PC_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+
+      /* Inferior Points */
+      CurrentLandmarkName = "IRP";    TempPnt[0] = IRPPoint[0]; TempPnt[1] =
+        IRPPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "IRA";    TempPnt[0] = IRPPoint[0]; TempPnt[1] =
+        IRPPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "ILP";    TempPnt[0] = SLAPoint[0]; TempPnt[1] =
+        IRPPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "ILA";    TempPnt[0] = SLAPoint[0]; TempPnt[1] =
+        IRPPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+
+      /* Superior Points */
+      CurrentLandmarkName = "SLA";    TempPnt[0] = SLAPoint[0]; TempPnt[1] =
+        SLAPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "SLP";    TempPnt[0] = SLAPoint[0]; TempPnt[1] =
+        SLAPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "SRA";    TempPnt[0] = IRPPoint[0]; TempPnt[1] =
+        SLAPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "SRP";    TempPnt[0] = IRPPoint[0]; TempPnt[1] =
+        SLAPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+
+      /*
+        *  CurrentLandmarkName="Tal_SLAPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SLPPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SRAPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SRPPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_S_PC_APoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_S_PC_PPoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SL_AC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SR_AC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SL_PC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_SR_PC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_S_AC_Point";  TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_S_PC_Point";  TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=SLAPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *
+        *  CurrentLandmarkName="Tal_PC_LAPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_LPPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_RAPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_RPPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_PC_APoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_PC_PPoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_L_AC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_R_AC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_L_PC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_R_PC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_AC_Point";      TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=AC_Point[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_PC_Point";      TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=PC_Point[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *
+        *  CurrentLandmarkName="Tal_ILAPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_ILPPoint";    TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IRAPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IRPPoint";    TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_I_PC_APoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=SLAPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_I_PC_PPoint"; TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=IRPPoint[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IL_AC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IR_AC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IL_PC_Point"; TempPnt[0]=SLAPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_IR_PC_Point"; TempPnt[0]=IRPPoint[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_I_AC_Point";  TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=AC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        *  CurrentLandmarkName="Tal_I_PC_Point";  TempPnt[0]=PC_Point[0];
+        *  TempPnt[1]=IRPPoint[1]; TempPnt[2]=PC_Point[2];
+        *     (*this)[CurrentLandmarkName]=TempPnt;
+        */
+      }
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ReadIPLTalairachPointTypes(const std::string lmrkfilename,
+                             const int XDim, const int YDim,
+                             const int ZDim, const int TDim)
+{
+  const bool testread = this->InverseConsistentLandmarks::ReadIPLPointTypes(
+      lmrkfilename);
+
+  this->InverseConsistentLandmarks::rescale(XDim, YDim, ZDim, TDim);
+  return testread;
+}
+
+//
+// ======================================Cerebellum Bounds
+template 
+bool
+InverseConsistentLandmarks
+::ReadIPLCerebellarPointTypes(const std::string lmrkfilename)
+{
+  //  std::cout << "Reading IPL Cerebellar Bounds as  Landmark File " <<
+  // lmrkfilename << std::endl;
+
+  // Delete all old landmarks
+  // DEBUG:  NOTE we can not delete after being called from Talairach.bnd!!!
+  //        this->erase( this->begin(  ), this->end(  ) );
+  // Open the files
+  FILE *tempfile = fopen(lmrkfilename.c_str(), "r");
+
+  if( tempfile == NULL )
+    {
+    // std::cout << "ERROR: can not open " << lmrkfilename << std::endl;
+    // exit( -1 );
+    return false;
+    }
+  const unsigned short int FILE_BUFFER_SIZE = 256;
+  char                     buffer[FILE_BUFFER_SIZE]; // Dummy Varible
+  char *                   status = 0;
+  // Read Header Information
+  status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+  if( status == NULL )
+    {
+    return false;
+    }
+  if( strncmp(buffer, "IPL_HEADER_BEGIN", 16) != 0 )
+    {
+    // Only files with a header of IPL_HEADER_BEGIN will be accepted
+    return false;
+    }
+  // Read dimensions of image that landmarks are associated with
+  // skip a head to landmark definitions
+  status = buffer;
+  while( ( strncmp(buffer, "TALAIRACH_PARAMETER_HEADER_BEGIN",
+                   32) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_BEGIN found"
+      << std::endl;
+      }
+    }
+
+  bool xisset = false;
+  bool yisset = false;
+  bool zisset = false;
+  // process looking for dims
+  status = buffer;
+  while( ( strncmp(buffer, "TALAIRACH_PARAMETER_HEADER_END",
+                   30) != 0 ) && ( status != NULL ) )
+    {
+    const unsigned short int TALAIRACH_PARAMETER_NAME_SIZE = 40;
+    char                     Dummy[TALAIRACH_PARAMETER_NAME_SIZE];
+    // Look for x
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_X_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[0] ) );
+      xisset = true;
+      }
+    // Look for y
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Y_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[1] ) );
+      yisset = true;
+      }
+    // Look for z
+    if( strncmp(buffer, "TALAIRACH_PARAMETER_Z_SIZE", 26) == 0  )
+      {
+      sscanf( buffer, "%s %hu", Dummy, &( ImageDims[2] ) );
+      zisset = true;
+      }
+    // if(!(xisset && yisset && zisset))
+    // {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    // }
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    }
+
+  ImageDims[3] = 1;
+  if( !( xisset && yisset && zisset ) )
+    {
+    std::cout << "ERROR must set all TALAIRACH_PARAMETER_[XYZ]_SIZE values"
+              << std::endl;
+    }
+
+  // Skip ahead to data
+  status = buffer;
+  while( ( strncmp(buffer, "IPL_HEADER_END", 14) != 0 ) && ( status != NULL ) )
+    {
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout << "ERROR: End of file reached before IPL_HEADER_END found"
+                << std::endl;
+      }
+    }
+
+  // Actually read the data
+  // First read the SLA point
+    {
+    PointType SLAPoint;   // Superior Left Anterior
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("SLAPoint", buffer, ImageDims, ImageRes,
+                          SLAPoint) == false )
+      {
+      return false;
+      }
+      {                    // NOTE: for Cerebellum AC_Point is meaningless
+      PointType AC_Point;  // Antieror Commisure
+      status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+      if( status == NULL )
+        {
+        std::cout
+        <<
+        "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+        << std::endl;
+        }
+      // if(process_bnd_point("AC_Point", buffer, ImageDims, ImageRes,
+      // AC_Point)==false) {return false;}
+      }
+
+    PointType FV_Point;    // Posterior Commisure
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("FV_Point", buffer, ImageDims, ImageRes,
+                          FV_Point) == false )
+      {
+      return false;
+      }
+
+    PointType IRPPoint;   // Inferior Right Posterior
+    status = fgets(buffer, FILE_BUFFER_SIZE, tempfile);
+    if( status == NULL )
+      {
+      std::cout
+      <<
+      "ERROR: End of file reached before TALAIRACH_PARAMETER_HEADER_END found"
+      << std::endl;
+      }
+    if( process_bnd_point("IRPPoint", buffer, ImageDims, ImageRes,
+                          IRPPoint) == false )
+      {
+      return false;
+      }
+    // Process to extend 4 points to all possible combinations
+    PointType TempPnt = SLAPoint;
+      {
+      std::string CurrentLandmarkName;
+      //                                            R/L
+      //                             S/I                           A/P
+      // Next 4 may conflict with PC Point and center plane
+      // CurrentLandmarkName="Cbl_SLAPoint";    TempPnt[0]=SLAPoint[0];
+      // TempPnt[1]=SLAPoint[1]; TempPnt[2]=SLAPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_SLPPoint";    TempPnt[0]=SLAPoint[0];
+      // TempPnt[1]=SLAPoint[1]; TempPnt[2]=IRPPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_SRAPoint";    TempPnt[0]=IRPPoint[0];
+      // TempPnt[1]=SLAPoint[1]; TempPnt[2]=SLAPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_SRPPoint";    TempPnt[0]=IRPPoint[0];
+      // TempPnt[1]=SLAPoint[1]; TempPnt[2]=IRPPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      CurrentLandmarkName = "Cbl_S_FV_APoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = SLAPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_S_FV_PPoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = SLAPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_SL_FV_Point"; TempPnt[0] = SLAPoint[0];
+      TempPnt[1] = SLAPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_SR_FV_Point"; TempPnt[0] = IRPPoint[0];
+      TempPnt[1] = SLAPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_S_FV_Point";  TempPnt[0] = FV_Point[0];
+      TempPnt[1] = SLAPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+
+      CurrentLandmarkName = "Cbl_FV_LAPoint";    TempPnt[0] = SLAPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_LPPoint";    TempPnt[0] = SLAPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_RAPoint";    TempPnt[0] = IRPPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_RPPoint";    TempPnt[0] = IRPPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_FV_APoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_FV_PPoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_L_FV_Point"; TempPnt[0] = SLAPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_R_FV_Point"; TempPnt[0] = IRPPoint[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_FV_Point";      TempPnt[0] = FV_Point[0];
+      TempPnt[1] = FV_Point[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+
+      // Next 4 may conflict with inferior plane
+      // CurrentLandmarkName="Cbl_ILAPoint";    TempPnt[0]=SLAPoint[0];
+      // TempPnt[1]=IRPPoint[1]; TempPnt[2]=SLAPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_ILPPoint";    TempPnt[0]=SLAPoint[0];
+      // TempPnt[1]=IRPPoint[1]; TempPnt[2]=IRPPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_IRAPoint";    TempPnt[0]=IRPPoint[0];
+      // TempPnt[1]=IRPPoint[1]; TempPnt[2]=SLAPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      // CurrentLandmarkName="Cbl_IRPPoint";    TempPnt[0]=IRPPoint[0];
+      // TempPnt[1]=IRPPoint[1]; TempPnt[2]=IRPPoint[2];
+      // (*this)[CurrentLandmarkName]=TempPnt;
+      CurrentLandmarkName = "Cbl_I_FV_APoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = IRPPoint[1]; TempPnt[2] = SLAPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_I_FV_PPoint"; TempPnt[0] = FV_Point[0];
+      TempPnt[1] = IRPPoint[1]; TempPnt[2] = IRPPoint[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_IL_FV_Point"; TempPnt[0] = SLAPoint[0];
+      TempPnt[1] = IRPPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_IR_FV_Point"; TempPnt[0] = IRPPoint[0];
+      TempPnt[1] = IRPPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      CurrentLandmarkName = "Cbl_I_FV_Point";  TempPnt[0] = FV_Point[0];
+      TempPnt[1] = IRPPoint[1]; TempPnt[2] = FV_Point[2];
+      ( *this )[CurrentLandmarkName] = TempPnt;
+      }
+    }
+  fclose(tempfile);
+  if( this->size() > 0 )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+bool
+InverseConsistentLandmarks
+::ReadIPLCerebellarPointTypes(const std::string lmrkfilename,
+                              const int XDim, const int YDim,
+                              const int ZDim, const int TDim)
+{
+  const bool testread = this->InverseConsistentLandmarks::ReadIPLPointTypes(
+      lmrkfilename);
+
+  this->InverseConsistentLandmarks::rescale(XDim, YDim, ZDim, TDim);
+  return testread;
+}
+
+template 
+void
+InverseConsistentLandmarks
+::AddExtendedPointTypes3D_UnitCube(const InverseConsistentLandmarks & input)
+{
+  // First create the center slice replicated in +-x and +-y directions
+  InverseConsistentLandmarks centersliceLM = input;
+
+  ( *this ) = input;                  // Used to reset image Dims
+  bool is3d = false;
+  for( typename InverseConsistentLandmarks::const_iterator iter = input.begin();
+       iter != input.end();
+       ++iter )
+    {
+    const PointStorageType xpoint = iter->second[0];
+    const PointStorageType ypoint = iter->second[1];
+    const PointStorageType zpoint = iter->second[2];
+    if( zpoint > 1e-5 )              // This assumes image sizes less than 10000
+                                     // slices
+      {
+      is3d = true;
+      }
+    const PointStorageType tpoint = iter->second.GetT();
+    const PointStorageType wpoint = iter->second.GetWeighting();
+    std::string            base(iter->first);
+
+    std::string pl;                  // pointlable
+    // Center
+    centersliceLM[base] = iter->second;
+    pl = "Left";
+    pl += base;
+    // Left
+    centersliceLM[pl] =
+      PointType( ( xpoint - 1.0F ), ( ypoint - 0.0F ), zpoint, tpoint,
+                 wpoint );
+    pl = "TopLeft";
+    pl += base;
+    // TopLeft
+    centersliceLM[pl] = PointType(xpoint - 1.0F,
+                                  ypoint + 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Top";
+    pl += base;
+    // Top
+    centersliceLM[pl] = PointType(xpoint - 0.0F,
+                                  ypoint + 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "TopRight";
+    pl += base;
+    // TopRight
+    centersliceLM[pl] = PointType(xpoint + 1.0F,
+                                  ypoint + 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Right";
+    pl += base;
+    // Right
+    centersliceLM[pl] = PointType(xpoint + 1.0F,
+                                  ypoint - 0.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "BottomRight";
+    pl += base;
+    // BottomRight
+    centersliceLM[pl] = PointType(xpoint + 1.0F,
+                                  ypoint - 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Bottom";
+    pl += base;
+    // Bottom
+    centersliceLM[pl] = PointType(xpoint - 0.0F,
+                                  ypoint - 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "BottomLeft";
+    pl += base;
+    // BottomLeft
+    centersliceLM[pl] = PointType(xpoint - 1.0F,
+                                  ypoint - 1.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    }
+  for( typename InverseConsistentLandmarks::const_iterator iter =
+         centersliceLM.begin();
+       iter != centersliceLM.end();
+       ++iter )
+    {
+    const PointStorageType xpoint = iter->second[0];
+    const PointStorageType ypoint = iter->second[1];
+    const PointStorageType zpoint = iter->second[2];
+    const PointStorageType tpoint = iter->second.GetT();
+    const PointStorageType wpoint = iter->second.GetWeighting();
+    std::string            base(iter->first);
+
+    std::string pl;                   // pointlable
+    ( *this )[base] = iter->second;   // Center
+
+    if( is3d )                       // Only Do this if it is a 3D image
+      {
+      pl = "Previous";
+      pl += base;
+      ( *this )[pl] =
+        PointType( ( xpoint ), ( ypoint ), ( zpoint - 1.0F ), tpoint,
+                   wpoint );
+
+      pl = "Next";
+      pl += base;
+      ( *this )[pl] =
+        PointType( ( xpoint ), ( ypoint ), ( zpoint + 1.0F ), tpoint,
+                   wpoint );
+      }
+    }
+  return;
+}
+
+template 
+void
+InverseConsistentLandmarks
+::AddExtendedPointTypes3D_OnN(const InverseConsistentLandmarks & input,
+                              const int nx, const int ny, const int nz)
+{
+  // First create the center slice replicated in +-x and +-y directions
+  InverseConsistentLandmarks centersliceLM = input;
+
+  ( *this ) = input;                  // Used to reset image Dims
+  bool is3d = false;
+  for( typename InverseConsistentLandmarks::const_iterator iter = input.begin();
+       iter != input.end();
+       ++iter )
+    {
+    const PointStorageType xpoint = iter->second[0];
+    const PointStorageType ypoint = iter->second[1];
+    const PointStorageType zpoint = iter->second[2];
+    if( zpoint > 1e-5 )              // This assumes image sizes less than 10000
+                                     // slices
+      {
+      is3d = true;
+      }
+    const PointStorageType tpoint = iter->second.GetT();
+    const PointStorageType wpoint = iter->second.GetWeighting();
+    std::string            base(iter->first);
+
+    std::string pl;                  // pointlable
+    // Center
+    centersliceLM[base] = iter->second;
+    pl = "Left";
+    pl += base;
+    // Left
+    centersliceLM[pl] =
+      PointType( ( xpoint - nx ), ( ypoint - 0.0F ), zpoint, tpoint,
+                 wpoint );
+    pl = "TopLeft";
+    pl += base;
+    // TopLeft
+    centersliceLM[pl] = PointType(xpoint - nx,
+                                  ypoint + ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Top";
+    pl += base;
+    // Top
+    centersliceLM[pl] = PointType(xpoint - 0.0F,
+                                  ypoint + ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "TopRight";
+    pl += base;
+    // TopRight
+    centersliceLM[pl] = PointType(xpoint + nx,
+                                  ypoint + ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Right";
+    pl += base;
+    // Right
+    centersliceLM[pl] = PointType(xpoint + nx,
+                                  ypoint - 0.0F,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "BottomRight";
+    pl += base;
+    // BottomRight
+    centersliceLM[pl] = PointType(xpoint + nx,
+                                  ypoint - ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "Bottom";
+    pl += base;
+    // Bottom
+    centersliceLM[pl] = PointType(xpoint - 0.0F,
+                                  ypoint - ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    pl = "BottomLeft";
+    pl += base;
+    // BottomLeft
+    centersliceLM[pl] = PointType(xpoint - nx,
+                                  ypoint - ny,
+                                  zpoint,
+                                  tpoint,
+                                  wpoint);
+    }
+  for( typename InverseConsistentLandmarks::const_iterator iter =
+         centersliceLM.begin();
+       iter != centersliceLM.end();
+       ++iter )
+    {
+    const PointStorageType xpoint = iter->second[0];
+    const PointStorageType ypoint = iter->second[1];
+    const PointStorageType zpoint = iter->second[2];
+    const PointStorageType tpoint = iter->second.GetT();
+    const PointStorageType wpoint = iter->second.GetWeighting();
+    std::string            base(iter->first);
+
+    std::string pl;                   // pointlable
+    ( *this )[base] = iter->second;   // Center
+
+    if( is3d )                       // Only Do this if it is a 3D image
+      {
+      pl = "Previous";
+      pl += base;
+      ( *this )[pl] =
+        PointType( ( xpoint ), ( ypoint ), ( zpoint - nz ), tpoint,
+                   wpoint );
+
+      pl = "Next";
+      pl += base;
+      ( *this )[pl] =
+        PointType( ( xpoint ), ( ypoint ), ( zpoint + nz ), tpoint,
+                   wpoint );
+      }
+    }
+  return;
+}
+
+}
+#endif
diff --git a/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.h b/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.h
new file mode 100644
index 00000000..7e8a7855
--- /dev/null
+++ b/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.h
@@ -0,0 +1,140 @@
+#ifndef __itkLargestForegroundFilledMaskImageFilter_h
+#define __itkLargestForegroundFilledMaskImageFilter_h
+
+#include 
+#include 
+#include 
+
+namespace itk
+{
+/**
+  * \class LargestForegroundFilledMaskImageFilter
+  * \author Hans J. Johnson
+  *
+  * This filter does a good job of finding a single largest connected
+  * mask that separates the foreground object from the background.
+  * It assumes that the corner voxels of the image belong to the backgound.
+  * This filter was written for the purpose of finding the tissue
+  * region of a brain image with no internal holes.
+  *
+  * The OtsuPercentile Thresholds are used to define the range of values
+  * where the percentage of voxels falls beetween
+  * (0+OtsuPercentileLowerThreshold) < "Intensities of Interest" <
+  *(1-OtsuPercentileUpperThreshold).
+  *
+  * The ClosingSize specifies how many mm to dilate followed by
+  * erode to fill holes that be present in the image.
+  *
+  * The DilateSize specifies how many mm to dilate
+  * as a final step to include a small amount of surface background in addition
+  *to the
+  * tissue region present in the image.
+  *
+  * The image that is returned will be a binary image with foreground and
+  *background
+  * values specified by the user (defaults to 1 and 0 respectively).
+  *
+  */
+template 
+class ITK_EXPORT LargestForegroundFilledMaskImageFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Extract dimension from input and output image. */
+  itkStaticConstMacro(InputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+
+  /** Convenient typedefs for simplifying declarations. */
+  typedef TInputImage                           InputImageType;
+  typedef typename InputImageType::ConstPointer InputImagePointer;
+  typedef typename InputImageType::RegionType   InputImageRegionType;
+  typedef typename InputImageType::PixelType    InputPixelType;
+
+  typedef TOutputImage                         OutputImageType;
+  typedef typename OutputImageType::Pointer    OutputImagePointer;
+  typedef typename OutputImageType::RegionType OutputImageRegionType;
+  typedef typename OutputImageType::PixelType  OutputPixelType;
+
+  typedef LargestForegroundFilledMaskImageFilter                 Self;
+  typedef ImageToImageFilter    Superclass;
+  typedef SmartPointer                                     Pointer;
+  typedef Image IntegerImageType;
+  typedef typename IntegerImageType::PixelType                   IntegerPixelType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(LargestForegroundFilledMaskImageFilter, ImageToImageFilter);
+
+  /** set Otsu Threshold */
+  itkSetMacro(OtsuPercentileLowerThreshold, double);
+  itkGetConstMacro(OtsuPercentileLowerThreshold, double);
+  itkSetMacro(OtsuPercentileUpperThreshold, double);
+  itkGetConstMacro(OtsuPercentileUpperThreshold, double);
+
+  /** Short hand for setting both upper and lower
+    * (0+OtsuPercentileThreshold) < "Intensities of Interest" <
+    *(1-OtsuPercentileThreshold).
+    */
+  void SetOtsuPercentileThreshold(const double percentile)
+  {
+    this->SetOtsuPercentileLowerThreshold(percentile);
+    this->SetOtsuPercentileUpperThreshold(1.0 - percentile);
+  }
+
+  double GetOtsuPercentileThreshold(void) const
+  {
+    return this->GetOtsuPercentileLowerThreshold();
+  }
+
+  /** The closing size in mm, this is rounded up to the next closest number of
+    * voxel
+    * by taking Spacing into account */
+  itkSetMacro(ClosingSize, double);
+  itkGetConstMacro(ClosingSize, double);
+  /** The dilation size in mm, this is rounded up to the next closest number of
+    * voxel
+    * by taking Spacing into account */
+  itkSetMacro(DilateSize, double);
+  itkGetConstMacro(DilateSize, double);
+  itkSetMacro(InsideValue, IntegerPixelType);
+  itkGetMacro(InsideValue, IntegerPixelType);
+  itkSetMacro(OutsideValue, IntegerPixelType);
+  itkGetMacro(OutsideValue, IntegerPixelType);
+  itkSetMacro(ThresholdCorrectionFactor, double);
+  itkGetConstMacro(ThresholdCorrectionFactor, double);
+protected:
+  LargestForegroundFilledMaskImageFilter();
+  ~LargestForegroundFilledMaskImageFilter();
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  virtual void GenerateData();
+
+private:
+  /** Returns true if more than two bins of informaiton are found,
+    * returns false if only two bins of informaiton are found (i.e. found a
+    *binary image).
+    * Low and High are set to the ?????? */
+  unsigned int SetLowHigh(InputPixelType & low, InputPixelType & high);
+
+  void ImageMinMax(InputPixelType & min, InputPixelType & max);
+
+  // No longer used  double m_OtsuPercentileThreshold;
+  double           m_OtsuPercentileLowerThreshold;
+  double           m_OtsuPercentileUpperThreshold;
+  double           m_ThresholdCorrectionFactor;
+  double           m_ClosingSize;
+  double           m_DilateSize;
+  IntegerPixelType m_InsideValue;
+  IntegerPixelType m_OutsideValue;
+};
+} // end namespace itk
+
+#if ITK_TEMPLATE_TXX
+#include "itkLargestForegroundFilledMaskImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.hxx b/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.hxx
new file mode 100644
index 00000000..a1c15cc2
--- /dev/null
+++ b/BRAINSCommonLib/itkLargestForegroundFilledMaskImageFilter.hxx
@@ -0,0 +1,366 @@
+#ifndef __itkLargestForegroundFilledMaskImageFilter_hxx
+#define __itkLargestForegroundFilledMaskImageFilter_hxx
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include "itkComputeHistogramQuantileThresholds.h"
+
+#include 
+#include 
+#include 
+#include 
+// #include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+// Not this:   #include 
+#include 
+#include 
+
+namespace itk
+{
+template 
+LargestForegroundFilledMaskImageFilter
+::LargestForegroundFilledMaskImageFilter() :
+  m_OtsuPercentileLowerThreshold(0.01),
+  m_OtsuPercentileUpperThreshold(1.0 - 0.01),
+  m_ThresholdCorrectionFactor(1.0),
+  m_ClosingSize(9.0),
+  m_DilateSize(0.0),
+  m_InsideValue(NumericTraits::One),
+  m_OutsideValue(NumericTraits::Zero)
+{
+  //   this->m_InsideValue =
+  //     NumericTraits::One;
+  //   this->m_OutsideValue =
+  //     NumericTraits::Zero;
+}
+
+template 
+LargestForegroundFilledMaskImageFilter
+::~LargestForegroundFilledMaskImageFilter()
+{
+}
+
+template 
+void
+LargestForegroundFilledMaskImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << "OtsuPercentileLowerThreshold "
+     << m_OtsuPercentileLowerThreshold << " "
+     << "OtsuPercentileUpperThreshold "
+     << m_OtsuPercentileUpperThreshold << " "
+     << "ClosingSize "
+     << m_ClosingSize << " "
+     << "InsideValue "
+     << m_InsideValue << " "
+     << "OutsideValue "
+     << m_OutsideValue << std::endl;
+}
+
+template 
+void
+LargestForegroundFilledMaskImageFilter
+::ImageMinMax(typename TInputImage::PixelType & imageMin,
+              typename TInputImage::PixelType & imageMax)
+{
+  typename MinimumMaximumImageFilter::Pointer minmaxFilter =
+    MinimumMaximumImageFilter::New();
+  minmaxFilter->SetInput( this->GetInput() );
+  minmaxFilter->Update();
+  imageMax = minmaxFilter->GetMaximum();
+  imageMin = minmaxFilter->GetMinimum();
+}
+
+template 
+void
+LargestForegroundFilledMaskImageFilter
+::GenerateData()
+{
+    {
+    // These checks guarantee that setLowHigh works with at least two bins.
+    // Threshold 0.0 is special:  a pure Otsu on 100 bins.
+    if( this->m_OtsuPercentileLowerThreshold < 0.0 || this->m_OtsuPercentileLowerThreshold > 1.5
+        || this->m_OtsuPercentileUpperThreshold < 0 )
+      {
+      itkExceptionMacro(<< "Throwing out worthless PercentileThreshold:  "
+                        << this->m_OtsuPercentileLowerThreshold << " " <<  this->m_OtsuPercentileUpperThreshold << " ");
+      }
+    if( this->m_OtsuPercentileUpperThreshold > 1.5 )
+      {
+      itkExceptionMacro(
+        << "To save the day, PRETENDING an apparently mistaken histogram-trimming"
+        " threshold >= 1.5 really indicates number of histogram bins"
+        " (3.5 rounds up and indicates quartiles, etc.):  "
+        << this->m_OtsuPercentileLowerThreshold << " " <<  this->m_OtsuPercentileUpperThreshold << " ");
+      }
+    if( this->m_OtsuPercentileLowerThreshold > 0.5  || this->m_OtsuPercentileUpperThreshold < 0.5 )
+      {
+      itkExceptionMacro(<< "Trimming back worthless PercentileThreshold"
+                        " over the two-tailed maximum of 0.5:  "
+                        << this->m_OtsuPercentileLowerThreshold << " " <<  this->m_OtsuPercentileUpperThreshold << " ");
+      }
+    }
+  this->AllocateOutputs();
+
+  typedef ComputeHistogramQuantileThresholds ImageCalcType;
+  typename ImageCalcType::Pointer ImageCalc = ImageCalcType::New();
+  ImageCalc->SetImage( this->GetInput() );
+
+  ImageCalc->SetQuantileLowerThreshold(m_OtsuPercentileLowerThreshold);
+  ImageCalc->SetQuantileUpperThreshold(m_OtsuPercentileUpperThreshold);
+
+  ImageCalc->Calculate();
+
+  typename TInputImage::PixelType threshold_low_foreground;
+  typename TInputImage::PixelType threshold_low = ImageCalc->GetLowerIntensityThresholdValue();
+  typename TInputImage::PixelType threshold_hi  = ImageCalc->GetUpperIntensityThresholdValue();
+  const unsigned int numNonZeroHistogramBins = ImageCalc->GetNumberOfValidHistogramsEntries();
+
+  if( numNonZeroHistogramBins <= 2 )
+    {
+    threshold_low_foreground = threshold_hi;
+    }
+  else
+    {
+    //##The Otsu thresholding stuff below should not be part of the new class,
+    // it shout really be a separate function.
+    typedef OtsuThresholdImageCalculator OtsuImageCalcType;
+    typename OtsuImageCalcType::Pointer OtsuImageCalc = OtsuImageCalcType::New();
+    OtsuImageCalc->SetImage( this->GetInput() );
+    OtsuImageCalc->Compute();
+    typename TInputImage::PixelType otsuThreshold = OtsuImageCalc->GetThreshold();
+    // std::cout << "whole-image-based otsuThreshold was: " << otsuThreshold <<
+    // std::endl;
+
+    typename TInputImage::PixelType otsuThresholdResult =
+      static_cast
+      ( m_ThresholdCorrectionFactor * static_cast( otsuThreshold ) );
+    threshold_low_foreground = otsuThresholdResult;
+    }
+
+  typedef BinaryThresholdImageFilter
+  InputThresholdFilterType;
+  typename InputThresholdFilterType::Pointer threshold =
+    InputThresholdFilterType::New();
+  threshold->SetInput( this->GetInput() );
+  threshold->SetInsideValue(this->m_InsideValue);
+  threshold->SetOutsideValue(this->m_OutsideValue);
+  threshold->SetLowerThreshold(threshold_low_foreground);
+  // threshold->SetUpperThreshold(threshold_hi);
+  threshold->SetUpperThreshold(
+    NumericTraits::max() );
+  threshold->Update();
+  // C'mon, guys.  I need to know what's going on.  Leave this output visible
+  // for me.  Please?
+  // NOTE:  The printout below is not what is really being used to threshold.
+  // it is really threshold_low_foreground, NumericTraits::max()
+  std::cout << "LowHigh Thresholds: [" << static_cast( threshold_low ) << ","
+            << threshold_low_foreground << "," << static_cast( threshold_hi ) << "]"
+            << std::endl;
+
+  typedef ConnectedComponentImageFilter FilterType;
+  typename FilterType::Pointer labelConnectedComponentsFilter = FilterType::New();
+  //  SimpleFilterWatcher watcher(labelConnectedComponentsFilter);
+  //  watcher.QuietOn();
+  labelConnectedComponentsFilter->SetInput( threshold->GetOutput() );
+  // labelConnectedComponentsFilter->Update();
+
+  typedef RelabelComponentImageFilter RelabelType;
+  typename RelabelType::Pointer relabel = RelabelType::New();
+  relabel->SetInput( labelConnectedComponentsFilter->GetOutput() );
+
+  try
+    {
+    relabel->Update();
+    }
+  catch( ExceptionObject & excep )
+    {
+    std::cerr << "Relabel: exception caught !" << std::endl;
+    std::cerr << excep << std::endl;
+    }
+
+  typedef BinaryThresholdImageFilter ThresholdFilterType;
+  // unsigned short numObjects = relabel->GetNumberOfObjects();
+  // std::cout << "Removed " << numObjects - 1 << " smaller objects." <<
+  // std::endl;
+  typename ThresholdFilterType::Pointer LargestFilter =
+    ThresholdFilterType::New();
+  LargestFilter->SetInput( relabel->GetOutput() );
+  LargestFilter->SetInsideValue(this->m_InsideValue);
+  LargestFilter->SetOutsideValue(this->m_OutsideValue);
+  LargestFilter->SetLowerThreshold(1);
+  LargestFilter->SetUpperThreshold(1);
+  LargestFilter->Update();
+
+  typedef BinaryBallStructuringElement
+  myKernelType;
+
+  typedef BinaryErodeImageFilter ErodeFilterType;
+  typename ErodeFilterType::Pointer ErodeFilter = ErodeFilterType::New();
+    {
+    myKernelType dilateBall;
+    myKernelType erodeBall;
+    typename myKernelType::SizeType dilateBallSize;
+    typename myKernelType::SizeType erodeBallSize;
+    for( unsigned int d = 0; d < 3; ++d )
+      {
+      const unsigned int ClosingVoxels = vnl_math_ceil( m_ClosingSize / ( relabel->GetOutput()->GetSpacing()[d] ) );
+      if( ClosingVoxels > 20 )
+        {
+        std::cout << "WARNING:  Attempting to close with a very large number of voxels:  "
+                  << m_ClosingSize << " / " << ( relabel->GetOutput()->GetSpacing()[d] ) << " = " << ClosingVoxels
+                  << std::endl;
+        std::cout
+        << "Perhaps there is a mis-match between the voxel spacing and the assumption that  ClosingSize is given in mm"
+        << std::endl;
+        }
+      dilateBallSize[d] = ClosingVoxels;
+      erodeBallSize[d]  = ClosingVoxels;
+      }
+    dilateBall.SetRadius(dilateBallSize);
+    dilateBall.CreateStructuringElement();
+    erodeBall.SetRadius(erodeBallSize);
+    erodeBall.CreateStructuringElement();
+
+    typedef BinaryDilateImageFilter DilateFilterType;
+    typename DilateFilterType::Pointer DilateFilter = DilateFilterType::New();
+
+    // DilateFilter->SetForegroundValue(1);
+    DilateFilter->SetDilateValue(1);
+    DilateFilter->SetBackgroundValue(0);
+    DilateFilter->SetInput( LargestFilter->GetOutput() );
+    DilateFilter->SetKernel(dilateBall);
+    DilateFilter->Update();
+
+    // ErodeFilter->SetForegroundValue(1);
+    ErodeFilter->SetErodeValue(1);
+    ErodeFilter->SetBackgroundValue(0);
+    ErodeFilter->SetInput( DilateFilter->GetOutput() );
+    ErodeFilter->SetKernel(erodeBall);
+    ErodeFilter->Update();
+    }
+
+  const typename IntegerImageType::SizeType ImageSize =
+    ErodeFilter->GetOutput()->GetLargestPossibleRegion().GetSize();
+  // NOTE:  The most robust way to do this would be to find the largest
+  // background labeled image, and then choose one of those locations as the
+  // seed.
+  // For now just choose all the corners as seed points
+  typedef ConnectedThresholdImageFilter
+  seededConnectedThresholdFilterType;
+  typename seededConnectedThresholdFilterType::Pointer
+  seededConnectedThresholdFilter = seededConnectedThresholdFilterType::New();
+
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { 0, 0, 0 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { ImageSize[0] - 1, 0, 0 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { 0, ImageSize[1] - 1, 0 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { ImageSize[0] - 1, ImageSize[1] - 1, 0 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { 0, 0, ImageSize[2] - 1 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { ImageSize[0] - 1, 0, ImageSize[2] - 1 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { 0, ImageSize[1] - 1, ImageSize[2] - 1 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+    {
+    const typename IntegerImageType::IndexType SeedLocation = { { ImageSize[0] - 1, ImageSize[1] - 1, ImageSize[2] - 1 } };
+    seededConnectedThresholdFilter->SetSeed(SeedLocation);
+    }
+
+  seededConnectedThresholdFilter->SetReplaceValue(100);
+  seededConnectedThresholdFilter->SetUpper(0);
+  seededConnectedThresholdFilter->SetLower(0);
+  seededConnectedThresholdFilter->SetInput( ErodeFilter->GetOutput() );
+  seededConnectedThresholdFilter->Update();
+
+  typename IntegerImageType::Pointer dilateMask = NULL;
+    {
+    typename ThresholdFilterType::Pointer FinalThreshold =
+      ThresholdFilterType::New();
+    FinalThreshold->SetInput( seededConnectedThresholdFilter->GetOutput() );
+    FinalThreshold->SetInsideValue(this->m_OutsideValue);
+    FinalThreshold->SetOutsideValue(this->m_InsideValue);
+    FinalThreshold->SetLowerThreshold(100);
+    FinalThreshold->SetUpperThreshold(100);
+    FinalThreshold->Update();
+
+    if( m_DilateSize > 0.0 )
+      {
+      // Dilate to get some background to better drive BSplineRegistration
+      typedef itk::BinaryDilateImageFilter DilateType;
+
+      myKernelType dilateBall;
+      typename myKernelType::SizeType dilateBallSize;
+      for( unsigned int d = 0; d < 3; ++d )
+        {
+        const unsigned int DilateVoxels = vnl_math_ceil( m_DilateSize / ( FinalThreshold->GetOutput()->GetSpacing()[d] ) );
+        dilateBallSize[d] = DilateVoxels;
+        }
+      dilateBall.SetRadius(dilateBallSize);
+      dilateBall.CreateStructuringElement();
+
+      typename DilateType::Pointer dil = DilateType::New();
+      dil->SetDilateValue(this->m_InsideValue);
+      dil->SetKernel(dilateBall);
+      dil->SetInput( FinalThreshold->GetOutput() );
+      dil->Update();
+      dilateMask = dil->GetOutput();
+      }
+    else
+      {
+      dilateMask = FinalThreshold->GetOutput();
+      }
+    }
+
+  typedef CastImageFilter outputCasterType;
+  typename outputCasterType::Pointer outputCaster = outputCasterType::New();
+  outputCaster->SetInput(dilateMask);
+
+  outputCaster->GraftOutput( this->GetOutput() );
+  outputCaster->Update();
+  this->GraftOutput( outputCaster->GetOutput() );
+  //  typename OutputImageType::Pointer outputMaskImage =
+  // outputCaster->GetOutput();
+  //  return outputMaskImage;
+}
+
+}
+#endif // itkLargestForegroundFilledMaskImageFilter_hxx
diff --git a/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.h b/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.h
new file mode 100644
index 00000000..8a1dff7d
--- /dev/null
+++ b/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.h
@@ -0,0 +1,328 @@
+#ifndef __itkLogDomainDeformableRegistrationFilter_h
+#define __itkLogDomainDeformableRegistrationFilter_h
+
+#include "itkDenseFiniteDifferenceImageFilter.h"
+#include "itkExponentialDeformationFieldImageFilter2.h"
+#include "itkPDEDeformableRegistrationFunction.h"
+
+namespace itk
+{
+/**
+  * \class LogDomainDeformableRegistrationFilter
+  * \brief Deformably register two images using a PDE-like algorithm
+  * where the transformation is represented as the exponential of a velocity
+  *field.
+  *
+  * LogDomainDeformableRegistrationFilter is a base case for filter implementing
+  * a PDE-like deformable algorithm that register two images by computing the
+  * velocity field whose exponential will map a moving image onto a fixed image.
+  *
+  * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * Velocity and deformation fields are represented as images whose pixel type
+  *are
+  * some vector type with at least N elements, where N is the dimension of
+  * the fixed image. The vector type must support element access via operator
+  * []. It is assumed that the vector elements behave like floating point
+  * scalars.
+  *
+  * This class is templated over the fixed image type, moving image type
+  * and the velocity/deformation field type.
+  *
+  * The input fixed and moving images are set via methods SetFixedImage
+  * and SetMovingImage respectively. An initial velocity field maybe set via
+  * SetInitialVelocityField or SetInput. If no initial field is set,
+  * a zero field is used as the initial condition.
+  *
+  * The output velocity field can be obtained via methods GetOutput
+  * or GetVelocityField.
+  *
+  * The output deformation field can be obtained via method GetDeformationField.
+  *
+  * The PDE-like algorithm is run for a user defined number of iterations.
+  * Typically the PDE-like algorithm requires period Gaussian smoothing of the
+  * velocity field to enforce an elastic-like condition. The amount
+  * of smoothing is governed by a set of user defined standard deviations
+  * (one for each dimension).
+  *
+  * In terms of memory, this filter keeps two internal buffers: one for storing
+  * the intermediate updates to the field and one for double-buffering when
+  * smoothing the velocity field. Both buffers are the same type and size as the
+  * output velocity field.
+  *
+  * This class make use of the finite difference solver hierarchy. Update
+  * for each iteration is computed using a PDEDeformableRegistrationFunction.
+  *
+  * \warning This filter assumes that the fixed image type, moving image type
+  * and velocity field type all have the same number of dimensions.
+  *
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  *
+  * \sa PDEDeformableRegistrationFunction.
+  * \ingroup DeformableImageRegistration
+  */
+template 
+class ITK_EXPORT LogDomainDeformableRegistrationFilter :
+  public DenseFiniteDifferenceImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef LogDomainDeformableRegistrationFilter            Self;
+  typedef DenseFiniteDifferenceImageFilter Superclass;
+  typedef SmartPointer                               Pointer;
+  typedef SmartPointer                         ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro(LogDomainDeformableRegistrationFilter,
+               DenseFiniteDifferenceImageFilter);
+
+  /** FixedImage image type. */
+  typedef TFixedImage                           FixedImageType;
+  typedef typename FixedImageType::Pointer      FixedImagePointer;
+  typedef typename FixedImageType::ConstPointer FixedImageConstPointer;
+
+  /** MovingImage image type. */
+  typedef TMovingImage                           MovingImageType;
+  typedef typename MovingImageType::Pointer      MovingImagePointer;
+  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;
+
+  /** Velocity field type. */
+  typedef TField                              VelocityFieldType;
+  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;
+
+  /** Deformation field type. */
+  typedef TField                                 DeformationFieldType;
+  typedef typename DeformationFieldType::Pointer DeformationFieldPointer;
+
+  /** Types inherithed from the superclass */
+  typedef typename Superclass::OutputImageType OutputImageType;
+
+  /** FiniteDifferenceFunction type. */
+  typedef typename Superclass::FiniteDifferenceFunctionType
+  FiniteDifferenceFunctionType;
+
+  /** PDEDeformableRegistrationFunction type. */
+  typedef PDEDeformableRegistrationFunction
+  PDEDeformableRegistrationFunctionType;
+
+  /** Inherit some enums and typedefs from the superclass. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      Superclass::ImageDimension);
+
+  /** Set the fixed image. */
+  void SetFixedImage(const FixedImageType *ptr);
+
+  /** Get the fixed image. */
+  const FixedImageType * GetFixedImage(void) const;
+
+  /** Set the moving image. */
+  void SetMovingImage(const MovingImageType *ptr);
+
+  /** Get the moving image. */
+  const MovingImageType * GetMovingImage(void) const;
+
+  /** Set initial velocity field. */
+  void SetInitialVelocityField(VelocityFieldType *ptr)
+  {
+    this->SetInput(ptr);
+  }
+
+  /** Get output velocity field. */
+  VelocityFieldType * GetVelocityField()
+  {
+    return this->GetOutput();
+  }
+
+  /** Get output deformation field. */
+  DeformationFieldPointer GetDeformationField();
+
+  /** Get output inverse deformation field. */
+  DeformationFieldPointer GetInverseDeformationField();
+
+  /** Get the number of valid inputs.  For LogDomainDeformableRegistration,
+    * this checks whether the fixed and moving images have been
+    * set. While LogDomainDeformableRegistration can take a third input as an
+    * initial velocity field, this input is not a required input. */
+  virtual std::vector >::size_type GetNumberOfValidRequiredInputs() const;
+
+  /** Set/Get whether the velocity field is smoothed
+    * (regularized). Smoothing the velocity yields a solution
+    * elastic in nature. If SmoothVelocityField is on, then the
+    * velocity field is smoothed with a Gaussian whose standard
+    * deviations are specified with SetStandardDeviations() */
+  itkSetMacro(SmoothVelocityField, bool);
+  itkGetConstMacro(SmoothVelocityField, bool);
+  itkBooleanMacro(SmoothVelocityField);
+
+  /** Set the Gaussian smoothing standard deviations for the
+    * velocity field. The values are set with respect to pixel
+    * coordinates. */
+  itkSetVectorMacro(StandardDeviations, double, ImageDimension);
+  virtual void SetStandardDeviations(double value);
+
+  /** Get the Gaussian smoothing standard deviations use for smoothing
+    * the velocity field. */
+  const double * GetStandardDeviations(void) const
+  {
+    return static_cast( m_StandardDeviations );
+  }
+
+  /** Set/Get whether the update field is smoothed
+    * (regularized). Smoothing the update field yields a solution
+    * viscous in nature. If SmoothUpdateField is on, then the
+    * update field is smoothed with a Gaussian whose standard
+    * deviations are specified with SetUpdateFieldStandardDeviations() */
+  itkSetMacro(SmoothUpdateField, bool);
+  itkGetConstMacro(SmoothUpdateField, bool);
+  itkBooleanMacro(SmoothUpdateField);
+
+  /** Set the Gaussian smoothing standard deviations for the update
+   * field. The values are set with respect to pixel coordinates. */
+  itkSetVectorMacro(UpdateFieldStandardDeviations, double, ImageDimension);
+  virtual void SetUpdateFieldStandardDeviations(double value);
+
+  /** Get the Gaussian smoothing standard deviations used for
+    * smoothing the update field. */
+  const double * GetUpdateFieldStandardDeviations(void) const
+  {
+    return static_cast( m_UpdateFieldStandardDeviations );
+  }
+
+  /** Stop the registration after the current iteration. */
+  virtual void StopRegistration()
+  {
+    m_StopRegistrationFlag = true;
+  }
+
+  /** Set/Get the desired maximum error of the Gaussian kernel approximate.
+    * \sa GaussianOperator. */
+  itkSetMacro(MaximumError, double);
+  itkGetConstMacro(MaximumError, double);
+
+  /** Set/Get the desired limits of the Gaussian kernel width.
+    * \sa GaussianOperator. */
+  itkSetMacro(MaximumKernelWidth, unsigned int);
+  itkGetConstMacro(MaximumKernelWidth, unsigned int);
+
+  /** Get the metric value. The metric value is the mean square difference
+    * in intensity between the fixed image and transforming moving image
+    * computed over the the overlapping region between the two images.
+    * This value is calculated for the current iteration */
+  virtual double GetMetric() const
+  {
+    return 0;
+  }
+protected:
+  LogDomainDeformableRegistrationFilter();
+  ~LogDomainDeformableRegistrationFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Exponential type */
+  typedef ExponentialDeformationFieldImageFilter2<
+    VelocityFieldType, DeformationFieldType>      FieldExponentiatorType;
+
+  typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;
+
+  itkSetObjectMacro(Exponentiator, FieldExponentiatorType);
+  itkGetObjectMacro(Exponentiator, FieldExponentiatorType);
+
+  /** Supplies the halting criteria for this class of filters.  The
+    * algorithm will stop after a user-specified number of iterations. */
+  virtual bool Halt()
+  {
+    if( m_StopRegistrationFlag )
+      {
+      return true;
+      }
+
+    return this->Superclass::Halt();
+  }
+
+  /** A simple method to copy the data from the input to the output.
+    * If the input does not exist, a zero field is written to the output. */
+  virtual void CopyInputToOutput();
+
+  /** Initialize the state of filter and equation before each iteration.
+    * Progress feeback is implemented as part of this method. */
+  virtual void InitializeIteration();
+
+  /** Utility to smooth the velocity field (represented in the Output)
+    * using a Gaussian operator. The amount of smoothing can be specified
+    * by setting the StandardDeviations. */
+  virtual void SmoothVelocityField();
+
+  /** Utility to smooth the UpdateBuffer using a Gaussian operator.
+    * The amount of smoothing can be specified by setting the
+    * UpdateFieldStandardDeviations. */
+  virtual void SmoothUpdateField();
+
+  /** Utility to smooth a velocity field  using a Gaussian operator.
+    * The amount of smoothing can be specified by setting the
+    * StandardDeviations. */
+  virtual void SmoothGivenField(VelocityFieldType *field, const double StandardDeviations[ImageDimension]);
+
+  /** This method is called after the solution has been generated. In this case,
+    * the filter release the memory of the internal buffers. */
+  virtual void PostProcessOutput();
+
+  /** This method is called before iterating the solution. */
+  virtual void Initialize();
+
+  /** By default the output velocity field has the same Spacing, Origin
+    * and LargestPossibleRegion as the input/initial velocity field.  If
+    * the initial velocity field is not set, the output information is
+    * copied from the fixed image. */
+  virtual void GenerateOutputInformation();
+
+  /** It is difficult to compute in advance the input moving image region
+    * required to compute the requested output region. Thus the safest
+    * thing to do is to request for the whole moving image.
+    * For the fixed image and velocity field, the input requested region
+    * set to be the same as that of the output requested region. */
+  virtual void GenerateInputRequestedRegion();
+
+private:
+  LogDomainDeformableRegistrationFilter(const Self &); // purposely not
+                                                       // implemented
+  void operator=(const Self &);                        // purposely not
+
+  // implemented
+
+  /** Standard deviation for Gaussian smoothing */
+  double m_StandardDeviations[ImageDimension];
+  double m_UpdateFieldStandardDeviations[ImageDimension];
+
+  /** Modes to control smoothing of the update and velocity fields */
+  bool m_SmoothVelocityField;
+  bool m_SmoothUpdateField;
+
+  /** Temporary field used for smoothing the velocity field. */
+  VelocityFieldPointer m_TempField;
+
+  /** Maximum error for Gaussian operator approximation. */
+  double m_MaximumError;
+
+  /** Limits of Gaussian kernel width. */
+  unsigned int m_MaximumKernelWidth;
+
+  /** Flag to indicate user stop registration request. */
+  bool m_StopRegistrationFlag;
+
+  FieldExponentiatorPointer m_Exponentiator;
+  FieldExponentiatorPointer m_InverseExponentiator;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLogDomainDeformableRegistrationFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.hxx b/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.hxx
new file mode 100644
index 00000000..34c384b8
--- /dev/null
+++ b/BRAINSCommonLib/itkLogDomainDeformableRegistrationFilter.hxx
@@ -0,0 +1,494 @@
+#ifndef __itkLogDomainDeformableRegistrationFilter_hxx
+#define __itkLogDomainDeformableRegistrationFilter_hxx
+
+#include "itkLogDomainDeformableRegistrationFilter.h"
+
+#include "itkExceptionObject.h"
+#include "itkImageRegionIterator.h"
+#include "itkImageLinearIteratorWithIndex.h"
+#include "itkDataObject.h"
+
+#include "itkGaussianOperator.h"
+#include "itkVectorNeighborhoodOperatorImageFilter.h"
+
+#include "vnl/vnl_math.h"
+
+namespace itk
+{
+// Default constructor
+template 
+LogDomainDeformableRegistrationFilter
+::LogDomainDeformableRegistrationFilter()
+{
+  this->SetNumberOfRequiredInputs(2);
+
+  this->SetNumberOfIterations(10);
+
+  unsigned int j;
+  for( j = 0; j < ImageDimension; ++j )
+    {
+    m_StandardDeviations[j] = 1.0;
+    m_UpdateFieldStandardDeviations[j] = 1.0;
+    }
+
+  m_TempField = VelocityFieldType::New();
+  m_MaximumError = 0.1;
+  m_MaximumKernelWidth = 30;
+  m_StopRegistrationFlag = false;
+
+  m_SmoothVelocityField = true;
+  m_SmoothUpdateField = false;
+
+  m_Exponentiator = FieldExponentiatorType::New();
+  m_Exponentiator->ComputeInverseOff();
+
+  m_InverseExponentiator = FieldExponentiatorType::New();
+  m_InverseExponentiator->ComputeInverseOn();
+}
+
+// Set the fixed image.
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SetFixedImage(
+  const FixedImageType *ptr)
+{
+  this->ProcessObject::SetNthInput( 1, const_cast( ptr ) );
+}
+
+// Get the fixed image.
+template 
+const typename LogDomainDeformableRegistrationFilter
+::FixedImageType
+* LogDomainDeformableRegistrationFilter
+::GetFixedImage() const
+  {
+  FixedImageType const * const temp = dynamic_cast( this->ProcessObject::GetInput(1) );
+  if( temp == NULL )
+    {
+    std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+    exit(-1);
+    }
+  return temp;
+  }
+
+// Set the moving image.
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SetMovingImage(
+  const MovingImageType *ptr)
+{
+  this->ProcessObject::SetNthInput( 2, const_cast( ptr ) );
+}
+
+// Get the moving image.
+template 
+const typename LogDomainDeformableRegistrationFilter
+::MovingImageType
+* LogDomainDeformableRegistrationFilter
+::GetMovingImage() const
+  {
+  MovingImageType const * const temp = dynamic_cast( this->ProcessObject::GetInput(2) );
+  if( temp == NULL )
+    {
+    std::cout << "Invalid converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+    exit(-1);
+    }
+  return temp;
+  }
+
+template 
+std::vector >::size_type
+LogDomainDeformableRegistrationFilter
+::GetNumberOfValidRequiredInputs() const
+{
+  typename std::vector >::size_type num = 0;
+
+  if( this->GetFixedImage() )
+    {
+    ++num;
+    }
+
+  if( this->GetMovingImage() )
+    {
+    ++num;
+    }
+
+  return num;
+}
+
+// Set the standard deviations.
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SetStandardDeviations(
+  double value)
+{
+  unsigned int j;
+  for( j = 0; j < ImageDimension; ++j )
+    {
+    if( value != m_StandardDeviations[j] )
+      {
+      break;
+      }
+    }
+  if( j < ImageDimension )
+    {
+    this->Modified();
+    for( j = 0; j < ImageDimension; ++j )
+      {
+      m_StandardDeviations[j] = value;
+      }
+    }
+}
+
+// Set the standard deviations.
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SetUpdateFieldStandardDeviations(
+  double value)
+{
+  unsigned int j;
+  for( j = 0; j < ImageDimension; ++j )
+    {
+    if( value != m_UpdateFieldStandardDeviations[j] )
+      {
+      break;
+      }
+    }
+  if( j < ImageDimension )
+    {
+    this->Modified();
+    for( j = 0; j < ImageDimension; ++j )
+      {
+      m_UpdateFieldStandardDeviations[j] = value;
+      }
+    }
+}
+
+// Standard PrintSelf method.
+template 
+void
+LogDomainDeformableRegistrationFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+  os << indent << "Smooth velocity field: "
+     << ( m_SmoothVelocityField ? "on" : "off" ) << std::endl;
+  os << indent << "Standard deviations: [";
+  unsigned int j;
+  for( j = 0; j < ImageDimension - 1; ++j )
+    {
+    os << m_StandardDeviations[j] << ", ";
+    }
+  os << m_StandardDeviations[j] << "]" << std::endl;
+  os << indent << "Smooth update field: "
+     << ( m_SmoothUpdateField ? "on" : "off" ) << std::endl;
+  os << indent << "Update field standard deviations: [";
+  for( j = 0; j < ImageDimension - 1; ++j )
+    {
+    os << m_UpdateFieldStandardDeviations[j] << ", ";
+    }
+  os << m_UpdateFieldStandardDeviations[j] << "]" << std::endl;
+  os << indent << "StopRegistrationFlag: ";
+  os << m_StopRegistrationFlag << std::endl;
+  os << indent << "MaximumError: ";
+  os << m_MaximumError << std::endl;
+  os << indent << "MaximumKernelWidth: ";
+  os << m_MaximumKernelWidth << std::endl;
+  os << indent << "Exponentiator: ";
+  os << m_Exponentiator << std::endl;
+  os << indent << "InverseExponentiator: ";
+  os << m_InverseExponentiator << std::endl;
+}
+
+// Set the function state values before each iteration
+template 
+void
+LogDomainDeformableRegistrationFilter
+::InitializeIteration()
+{
+  /*
+    *
+    *std::cout<<"LogDomainDeformableRegistrationFilter::InitializeIteration"<GetMovingImage();
+  FixedImageConstPointer  fixedPtr = this->GetFixedImage();
+
+  if( !movingPtr || !fixedPtr )
+    {
+    itkExceptionMacro(<< "Fixed and/or moving image not set");
+    }
+
+  // update variables in the equation object
+  PDEDeformableRegistrationFunctionType *f =
+    dynamic_cast
+    ( this->GetDifferenceFunction().GetPointer() );
+
+  if( !f )
+    {
+    itkExceptionMacro(<< "FiniteDifferenceFunction not of type LogDomainDeformableRegistrationFilterFunction");
+    }
+
+  f->SetFixedImage(fixedPtr);
+  f->SetMovingImage(movingPtr);
+
+  this->Superclass::InitializeIteration();
+}
+
+/* Override the default implementation for the case when the
+  * initial velocity is not set.
+  * If the initial velocity is not set, the output is
+  * fill with zero vectors.*/
+template 
+void
+LogDomainDeformableRegistrationFilter
+::CopyInputToOutput()
+{
+  typename Superclass::InputImageType::ConstPointer inputPtr  = this->GetInput();
+
+  if( inputPtr )
+    {
+    this->Superclass::CopyInputToOutput();
+    }
+  else
+    {
+    typename Superclass::PixelType zeros;
+    for( unsigned int j = 0; j < ImageDimension; ++j )
+      {
+      zeros[j] = 0;
+      }
+
+    typename OutputImageType::Pointer output = this->GetOutput();
+
+    ImageRegionIterator out( output, output->GetRequestedRegion() );
+
+    while( !out.IsAtEnd() )
+      {
+      out.Value() =  zeros;
+      ++out;
+      }
+    }
+}
+
+template 
+void
+LogDomainDeformableRegistrationFilter
+::GenerateOutputInformation()
+{
+  /*
+    *
+    *std::cout<<"LogDomainDeformableRegistrationFilter::GenerateOutputInformation"<GetInput(0) )
+    {
+    // Initial velocity field is set.
+    // Copy information from initial field.
+    this->Superclass::GenerateOutputInformation();
+    }
+  else if( this->GetFixedImage() )
+    {
+    // Initial deforamtion field is not set.
+    // Copy information from the fixed image.
+    for( unsigned int idx = 0; idx <
+         this->GetNumberOfOutputs(); ++idx )
+      {
+      output = this->GetOutput(idx);
+      if( output )
+        {
+        output->CopyInformation( this->GetFixedImage() );
+        }
+      }
+    }
+}
+
+template 
+void
+LogDomainDeformableRegistrationFilter
+::GenerateInputRequestedRegion()
+{
+  /*
+    *
+    *std::cout<<"LogDomainDeformableRegistrationFilter::GenerateInputRequestedRegion"<( this->GetMovingImage() );
+  if( movingPtr )
+    {
+    movingPtr->SetRequestedRegionToLargestPossibleRegion();
+    }
+
+  // just propagate up the output requested region for
+  // the fixed image and initial velocity field.
+  VelocityFieldPointer inputPtr =
+    const_cast( this->GetInput() );
+  VelocityFieldPointer outputPtr = this->GetOutput();
+  FixedImagePointer    fixedPtr =
+    const_cast( this->GetFixedImage() );
+
+  if( inputPtr )
+    {
+    inputPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
+    }
+
+  if( fixedPtr )
+    {
+    fixedPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
+    }
+}
+
+// Release memory of internal buffers
+template 
+void
+LogDomainDeformableRegistrationFilter
+::PostProcessOutput()
+{
+  this->Superclass::PostProcessOutput();
+  m_TempField->Initialize();
+}
+
+// Initialize flags
+template 
+void
+LogDomainDeformableRegistrationFilter
+::Initialize()
+{
+  // std::cout<<"LogDomainDeformableRegistrationFilter::Initialize"<Superclass::Initialize();
+  m_StopRegistrationFlag = false;
+}
+
+// Smooth velocity using a separable Gaussian kernel
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SmoothVelocityField()
+{
+  // The output buffer will be overwritten with new data.
+  this->SmoothGivenField(this->GetOutput(), this->m_StandardDeviations);
+}
+
+// Smooth update field using a separable Gaussian kernel
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SmoothUpdateField()
+{
+  // The update buffer will be overwritten with new data.
+  this->SmoothGivenField(this->GetUpdateBuffer(), this->m_UpdateFieldStandardDeviations);
+}
+
+// Smooth velocity using a separable Gaussian kernel
+template 
+void
+LogDomainDeformableRegistrationFilter
+::SmoothGivenField(VelocityFieldType *field, const double StandardDeviations[ImageDimension])
+{
+  // copy field to TempField
+  m_TempField->SetOrigin( field->GetOrigin() );
+  m_TempField->SetSpacing( field->GetSpacing() );
+  m_TempField->SetDirection( field->GetDirection() );
+  m_TempField->SetLargestPossibleRegion(
+    field->GetLargestPossibleRegion() );
+  m_TempField->SetRequestedRegion(
+    field->GetRequestedRegion() );
+  m_TempField->SetBufferedRegion( field->GetBufferedRegion() );
+  m_TempField->Allocate();
+
+  typedef typename VelocityFieldType::PixelType        VectorType;
+  typedef typename VectorType::ValueType               ScalarType;
+  typedef GaussianOperator OperatorType;
+  typedef VectorNeighborhoodOperatorImageFilter<
+    VelocityFieldType,
+    VelocityFieldType>                                SmootherType;
+
+  OperatorType *oper = new OperatorType;
+  typename SmootherType::Pointer smoother = SmootherType::New();
+
+  typedef typename VelocityFieldType::PixelContainerPointer
+  PixelContainerPointer;
+  PixelContainerPointer swapPtr;
+
+  // graft the output field onto the mini-pipeline
+  smoother->GraftOutput(m_TempField);
+  for( unsigned int j = 0; j < ImageDimension; ++j )
+    {
+    // smooth along this dimension
+    oper->SetDirection(j);
+    double variance = vnl_math_sqr(StandardDeviations[j]);
+    oper->SetVariance(variance);
+    oper->SetMaximumError(m_MaximumError);
+    oper->SetMaximumKernelWidth(m_MaximumKernelWidth);
+    oper->CreateDirectional();
+
+    // todo: make sure we only smooth within the buffered region
+    smoother->SetOperator(*oper);
+    smoother->SetInput(field);
+    smoother->Update();
+
+    if( j < ImageDimension - 1 )
+      {
+      // swap the containers
+      swapPtr = smoother->GetOutput()->GetPixelContainer();
+      smoother->GraftOutput(field);
+      field->SetPixelContainer(swapPtr);
+      smoother->Modified();
+      }
+    }
+
+  // graft the output back to field
+  m_TempField->SetPixelContainer( field->GetPixelContainer() );
+
+  // field to contain the final smoothed data, do the equivalent of a graft
+  field->SetPixelContainer( smoother->GetOutput()->GetPixelContainer() );
+  field->SetRequestedRegion( smoother->GetOutput()->GetRequestedRegion() );
+  field->SetBufferedRegion( smoother->GetOutput()->GetBufferedRegion() );
+  field->SetLargestPossibleRegion( smoother->GetOutput()->GetLargestPossibleRegion() );
+  field->CopyInformation( smoother->GetOutput() );
+
+  delete oper;
+}
+
+template 
+typename LogDomainDeformableRegistrationFilter
+::DeformationFieldPointer
+LogDomainDeformableRegistrationFilter
+::GetDeformationField()
+{
+  /*
+    *
+    *std::cout<<"LogDomainDeformableRegistration::GetDeformationField"<SetInput( this->GetVelocityField() );
+  m_Exponentiator->GetOutput()->SetRequestedRegion( this->GetVelocityField()->GetRequestedRegion() );
+  m_Exponentiator->Update();
+  return m_Exponentiator->GetOutput();
+}
+
+template 
+typename LogDomainDeformableRegistrationFilter
+::DeformationFieldPointer
+LogDomainDeformableRegistrationFilter
+::GetInverseDeformationField()
+{
+  /*
+    *
+    *std::cout<<"LogDomainDeformableRegistration::GetInverseDeformationField"<SetInput( this->GetVelocityField() );
+  m_InverseExponentiator->GetOutput()->SetRequestedRegion( this->GetVelocityField()->GetRequestedRegion() );
+  m_InverseExponentiator->Update();
+  return m_InverseExponentiator->GetOutput();
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.h b/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.h
new file mode 100644
index 00000000..d4cefa93
--- /dev/null
+++ b/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.h
@@ -0,0 +1,181 @@
+#ifndef __itkLogDomainDemonsRegistrationFilter_h
+#define __itkLogDomainDemonsRegistrationFilter_h
+
+#include "itkLogDomainDeformableRegistrationFilter.h"
+#include "itkESMDemonsRegistrationFunction.h"
+
+#include "itkMultiplyByConstantImageFilter.h"
+#include "itkVelocityFieldBCHCompositionFilter.h"
+
+namespace itk
+{
+/**
+  * \class LogDomainDemonsRegistrationFilter
+  * \brief Deformably register two images using a diffeomorphic demons
+  *algorithm.
+  *
+  * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * Velocity and deformation fields are represented as images whose pixel type
+  *are
+  * some vector type with at least N elements, where N is the dimension of
+  * the fixed image. The vector type must support element access via operator
+  * []. It is assumed that the vector elements behave like floating point
+  * scalars.
+  *
+  * This class is templated over the fixed image type, moving image type
+  * and the velocity/deformation field type.
+  *
+  * The input fixed and moving images are set via methods SetFixedImage
+  * and SetMovingImage respectively. An initial velocity field maybe set via
+  * SetInitialVelocityField or SetInput. If no initial field is set,
+  * a zero field is used as the initial condition.
+  *
+  * The output velocity field can be obtained via methods GetOutput
+  * or GetVelocityField.
+  *
+  * The output deformation field can be obtained via method GetDeformationField.
+  *
+  * This class make use of the finite difference solver hierarchy. Update
+  * for each iteration is computed using a PDEDeformableRegistrationFunction.
+  *
+  * \warning This filter assumes that the fixed image type, moving image type
+  * and velocity field type all have the same number of dimensions.
+  *
+  * \sa DemonsRegistrationFilter
+  * \sa DemonsRegistrationFunction
+  * \ingroup DeformableImageRegistration MultiThreaded
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  */
+template 
+class ITK_EXPORT LogDomainDemonsRegistrationFilter :
+  public LogDomainDeformableRegistrationFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef LogDomainDemonsRegistrationFilter                                        Self;
+  typedef LogDomainDeformableRegistrationFilter Superclass;
+  typedef SmartPointer                                                       Pointer;
+  typedef SmartPointer                                                 ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro(LogDomainDemonsRegistrationFilter, LogDomainDeformableRegistrationFilter);
+
+  /** FixedImage image type. */
+  typedef typename Superclass::FixedImageType    FixedImageType;
+  typedef typename Superclass::FixedImagePointer FixedImagePointer;
+
+  /** MovingImage image type. */
+  typedef typename Superclass::MovingImageType    MovingImageType;
+  typedef typename Superclass::MovingImagePointer MovingImagePointer;
+
+  /** Velocity field type. */
+  typedef TField                              VelocityFieldType;
+  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;
+
+  /** Deformation field type. */
+  typedef typename Superclass::DeformationFieldType    DeformationFieldType;
+  typedef typename Superclass::DeformationFieldPointer DeformationFieldPointer;
+
+  /** Types inherithed from the superclass */
+  typedef typename Superclass::OutputImageType OutputImageType;
+
+  /** FiniteDifferenceFunction type. */
+  typedef typename Superclass::FiniteDifferenceFunctionType FiniteDifferenceFunctionType;
+
+  /** Take timestep type from the FiniteDifferenceFunction. */
+  typedef typename
+  FiniteDifferenceFunctionType::TimeStepType TimeStepType;
+
+  /** DemonsRegistrationFilterFunction type. */
+  typedef ESMDemonsRegistrationFunction                          DemonsRegistrationFunctionType;
+  typedef typename DemonsRegistrationFunctionType::Pointer      DemonsRegistrationFunctionPointer;
+  typedef typename DemonsRegistrationFunctionType::GradientType GradientType;
+
+  /** Get the metric value. The metric value is the mean square difference
+    * in intensity between the fixed image and transforming moving image
+    * computed over the the overlapping region between the two images.
+    * This value is calculated for the current iteration */
+  virtual double GetMetric() const;
+
+  virtual const double & GetRMSChange() const;
+
+  virtual void SetUseGradientType(GradientType gtype);
+
+  virtual GradientType GetUseGradientType() const;
+
+  /** Set/Get the threshold below which the absolute difference of
+    * intensity yields a match. When the intensities match between a
+    * moving and fixed image pixel, the update vector (for that
+    * iteration) will be the zero vector. Default is 0.001. */
+  virtual void SetIntensityDifferenceThreshold(double);
+
+  virtual double GetIntensityDifferenceThreshold() const;
+
+  /** Set/Get the maximum length in terms of pixels of
+    *  the vectors in the update buffer. */
+  virtual void SetMaximumUpdateStepLength(double);
+
+  virtual double GetMaximumUpdateStepLength() const;
+
+  /** Set/Get the number of terms used in the Baker-Campbell-Hausdorff
+    * approximation. */
+  virtual void SetNumberOfBCHApproximationTerms(unsigned int);
+
+  virtual unsigned int GetNumberOfBCHApproximationTerms() const;
+
+protected:
+  LogDomainDemonsRegistrationFilter();
+  ~LogDomainDemonsRegistrationFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Initialize the state of filter and equation before each iteration. */
+  virtual void InitializeIteration();
+
+  /** Apply update. */
+  virtual void ApplyUpdate(TimeStepType dt);
+
+private:
+  // purposely not implemented
+  LogDomainDemonsRegistrationFilter(const Self &);
+  void operator=(const Self &);
+
+  /** Downcast the DifferenceFunction using a dynamic_cast to ensure that it is
+    * of the correct type.
+    * this method will throw an exception if the function is not of the expected
+    *type. */
+  DemonsRegistrationFunctionType *  DownCastDifferenceFunctionType();
+
+  const DemonsRegistrationFunctionType *  DownCastDifferenceFunctionType() const;
+
+  /** Exp and composition typedefs */
+  typedef MultiplyByConstantImageFilter<
+    VelocityFieldType,
+    TimeStepType, VelocityFieldType>                   MultiplyByConstantType;
+
+  typedef VelocityFieldBCHCompositionFilter<
+    VelocityFieldType,
+    VelocityFieldType>                                 BCHFilterType;
+
+  typedef typename MultiplyByConstantType::Pointer MultiplyByConstantPointer;
+  typedef typename BCHFilterType::Pointer          BCHFilterPointer;
+
+  MultiplyByConstantPointer m_Multiplier;
+  BCHFilterPointer          m_BCHFilter;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLogDomainDemonsRegistrationFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.hxx b/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.hxx
new file mode 100644
index 00000000..a9ff87a1
--- /dev/null
+++ b/BRAINSCommonLib/itkLogDomainDemonsRegistrationFilter.hxx
@@ -0,0 +1,252 @@
+#ifndef __itkLogDomainDemonsRegistrationFilter_hxx
+#define __itkLogDomainDemonsRegistrationFilter_hxx
+
+#include "itkLogDomainDemonsRegistrationFilter.h"
+
+namespace itk
+{
+// Default constructor
+template 
+LogDomainDemonsRegistrationFilter
+::LogDomainDemonsRegistrationFilter()
+{
+  DemonsRegistrationFunctionPointer drfp = DemonsRegistrationFunctionType::New();
+
+  this->SetDifferenceFunction( static_cast(
+                                 drfp.GetPointer() ) );
+
+  m_Multiplier = MultiplyByConstantType::New();
+  m_Multiplier->InPlaceOn();
+
+  m_BCHFilter = BCHFilterType::New();
+  m_BCHFilter->InPlaceOn();
+
+  // Set number of terms in the BCH approximation to default value
+  m_BCHFilter->SetNumberOfApproximationTerms(2);
+}
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+typename LogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* LogDomainDemonsRegistrationFilter
+::DownCastDifferenceFunctionType()
+  {
+  DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetDifferenceFunction().GetPointer() );
+
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+const typename LogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* LogDomainDemonsRegistrationFilter
+::DownCastDifferenceFunctionType() const
+  {
+  const DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetDifferenceFunction().GetPointer() );
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Set the function state values before each iteration
+template 
+void
+LogDomainDemonsRegistrationFilter
+::InitializeIteration()
+{
+  // Update variables in the equation object
+  DemonsRegistrationFunctionType *f = this->DownCastDifferenceFunctionType();
+
+  f->SetDeformationField( this->GetDeformationField() );
+
+  // call the superclass  implementation ( initializes f )
+  Superclass::InitializeIteration();
+}
+
+// Get the metric value from the difference function
+template 
+double
+LogDomainDemonsRegistrationFilter
+::GetMetric() const
+{
+  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  return drfp->GetMetric();
+}
+
+// Get Intensity Difference Threshold
+template 
+double
+LogDomainDemonsRegistrationFilter
+::GetIntensityDifferenceThreshold() const
+{
+  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  return drfp->GetIntensityDifferenceThreshold();
+}
+
+// Set Intensity Difference Threshold
+template 
+void
+LogDomainDemonsRegistrationFilter
+::SetIntensityDifferenceThreshold(double threshold)
+{
+  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  drfp->SetIntensityDifferenceThreshold(threshold);
+}
+
+// Set Maximum Update Step Length
+template 
+void
+LogDomainDemonsRegistrationFilter
+::SetMaximumUpdateStepLength(double step)
+{
+  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  drfp->SetMaximumUpdateStepLength(step);
+}
+
+// Get Maximum Update Step Length
+template 
+double
+LogDomainDemonsRegistrationFilter
+::GetMaximumUpdateStepLength() const
+{
+  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  return drfp->GetMaximumUpdateStepLength();
+}
+
+// Set number of terms used in the BCH approximation
+template 
+void
+LogDomainDemonsRegistrationFilter
+::SetNumberOfBCHApproximationTerms(unsigned int numterms)
+{
+  this->m_BCHFilter->SetNumberOfApproximationTerms(numterms);
+}
+
+// Get number of terms used in the BCH approximation
+template 
+unsigned int
+LogDomainDemonsRegistrationFilter
+::GetNumberOfBCHApproximationTerms() const
+{
+  return this->m_BCHFilter->GetNumberOfApproximationTerms();
+}
+
+// Get the metric value from the difference function
+template 
+const double &
+LogDomainDemonsRegistrationFilter
+::GetRMSChange() const
+{
+  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  return drfp->GetRMSChange();
+}
+
+// Get gradient type
+template 
+typename LogDomainDemonsRegistrationFilter::GradientType
+LogDomainDemonsRegistrationFilter
+::GetUseGradientType() const
+{
+  const DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  return drfp->GetUseGradientType();
+}
+
+// Set gradient type
+template 
+void
+LogDomainDemonsRegistrationFilter
+::SetUseGradientType(GradientType gtype)
+{
+  DemonsRegistrationFunctionType *drfp = this->DownCastDifferenceFunctionType();
+
+  drfp->SetUseGradientType(gtype);
+}
+
+// Get the metric value from the difference function
+template 
+void
+LogDomainDemonsRegistrationFilter
+::ApplyUpdate(TimeStepType dt)
+{
+  // std::cout<<"LogDomainDemonsRegistrationFilter::ApplyUpdate"<GetSmoothUpdateField() )
+    {
+    this->SmoothUpdateField();
+    }
+
+  // Use time step if necessary. In many cases
+  // the time step is one so this will be skipped
+  if( fabs(dt - 1.0) > 1.0e-4 )
+    {
+    itkDebugMacro("Using timestep: " << dt);
+    m_Multiplier->SetConstant(dt);
+    m_Multiplier->SetInput( this->GetUpdateBuffer() );
+    m_Multiplier->GraftOutput( this->GetUpdateBuffer() );
+    // in place update
+    m_Multiplier->Update();
+    // graft output back to this->GetUpdateBuffer()
+    this->GetUpdateBuffer()->Graft( m_Multiplier->GetOutput() );
+    }
+
+  // Apply update by using BCH approximation
+  m_BCHFilter->SetInput( 0, this->GetOutput() );
+  m_BCHFilter->SetInput( 1, this->GetUpdateBuffer() );
+  if( m_BCHFilter->GetInPlace() )
+    {
+    m_BCHFilter->GraftOutput( this->GetOutput() );
+    }
+  else
+    {
+    // Work-around for http://www.itk.org/Bug/view.php?id=8672
+    m_BCHFilter->GraftOutput( DeformationFieldType::New() );
+    }
+  m_BCHFilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
+
+  // Triggers in place update
+  m_BCHFilter->Update();
+
+  // Region passing stuff
+  this->GraftOutput( m_BCHFilter->GetOutput() );
+
+  // Smooth the velocity field
+  if( this->GetSmoothVelocityField() )
+    {
+    this->SmoothVelocityField();
+    }
+}
+
+template 
+void
+LogDomainDemonsRegistrationFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "Multiplier: " << m_Multiplier << std::endl;
+  os << indent << "BCHFilter: " << m_BCHFilter << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.h b/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.h
new file mode 100644
index 00000000..e7513c1e
--- /dev/null
+++ b/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.h
@@ -0,0 +1,92 @@
+#ifndef __itkMultiModeHistogramThresholdBinaryImageFilter_h
+#define __itkMultiModeHistogramThresholdBinaryImageFilter_h
+
+#include 
+#include 
+#include 
+#include 
+
+namespace itk
+{
+/**
+  * \author Hans J. Johnson
+  *
+  * This filter
+  *
+  */
+template  >
+class ITK_EXPORT MultiModeHistogramThresholdBinaryImageFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Extract dimension from input and output image. */
+  itkStaticConstMacro(InputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+
+  /** Convenient typedefs for simplifying declarations. */
+  typedef TInputImage                           InputImageType;
+  typedef typename InputImageType::ConstPointer InputImagePointer;
+  typedef typename InputImageType::RegionType   InputImageRegionType;
+  typedef typename InputImageType::PixelType    InputPixelType;
+
+  typedef TOutputImage                         OutputImageType;
+  typedef typename OutputImageType::Pointer    OutputImagePointer;
+  typedef typename OutputImageType::RegionType OutputImageRegionType;
+  typedef typename OutputImageType::PixelType  OutputPixelType;
+
+  typedef MultiModeHistogramThresholdBinaryImageFilter        Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                                  Pointer;
+  typedef TOutputImage                                        IntegerImageType;
+  typedef typename IntegerImageType::PixelType                IntegerPixelType;
+
+  typedef Array ThresholdArrayType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(MultiModeHistogramThresholdBinaryImageFilter, ImageToImageFilter);
+
+  itkSetMacro(LinearQuantileThreshold, double);
+  itkGetConstMacro(LinearQuantileThreshold, double);
+
+  /** set Quantile Threshold Arrays */
+  itkSetMacro(QuantileLowerThreshold, ThresholdArrayType);
+  itkGetConstMacro(QuantileLowerThreshold, ThresholdArrayType);
+  itkSetMacro(QuantileUpperThreshold, ThresholdArrayType);
+  itkGetConstMacro(QuantileUpperThreshold, ThresholdArrayType);
+
+  itkGetConstObjectMacro(BinaryPortionImage, IntegerImageType);
+  itkSetObjectMacro(BinaryPortionImage, IntegerImageType);
+
+  itkSetMacro(InsideValue, IntegerPixelType);
+  itkGetConstMacro(InsideValue, IntegerPixelType);
+  itkSetMacro(OutsideValue, IntegerPixelType);
+  itkGetConstMacro(OutsideValue, IntegerPixelType);
+protected:
+  MultiModeHistogramThresholdBinaryImageFilter();
+  ~MultiModeHistogramThresholdBinaryImageFilter();
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  virtual void GenerateData();
+
+private:
+  ThresholdArrayType m_QuantileLowerThreshold;
+  ThresholdArrayType m_QuantileUpperThreshold;
+  double             m_LinearQuantileThreshold;
+
+  typename IntegerImageType::Pointer m_BinaryPortionImage;
+
+  IntegerPixelType m_InsideValue;
+  IntegerPixelType m_OutsideValue;
+};
+} // end namespace itk
+
+#if ITK_TEMPLATE_TXX
+#include "itkMultiModeHistogramThresholdBinaryImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.hxx b/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.hxx
new file mode 100644
index 00000000..36adad2d
--- /dev/null
+++ b/BRAINSCommonLib/itkMultiModeHistogramThresholdBinaryImageFilter.hxx
@@ -0,0 +1,212 @@
+#include "itkMultiModeHistogramThresholdBinaryImageFilter.h"
+#include "itkComputeHistogramQuantileThresholds.h"
+
+#include 
+#include 
+
+#include 
+#include 
+// Not this:   #include 
+#include 
+#include 
+
+namespace itk
+{
+template 
+MultiModeHistogramThresholdBinaryImageFilter
+::MultiModeHistogramThresholdBinaryImageFilter() :
+  m_QuantileLowerThreshold(1), // temporarily estimate how many SetInput images
+                               // there are
+  m_QuantileUpperThreshold(1),
+  m_InsideValue(NumericTraits::One),
+  m_OutsideValue(NumericTraits::Zero)
+{
+  m_QuantileLowerThreshold.Fill(0.0);
+  m_QuantileUpperThreshold.Fill(1.0);
+  m_LinearQuantileThreshold = 0.01;
+  //   this->m_InsideValue =
+  //     NumericTraits::One;
+  //   this->m_OutsideValue =
+  //     NumericTraits::Zero;
+}
+
+template 
+MultiModeHistogramThresholdBinaryImageFilter
+::~MultiModeHistogramThresholdBinaryImageFilter()
+{
+}
+
+template 
+void
+MultiModeHistogramThresholdBinaryImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << "QuantileLowerThreshold "
+     << m_QuantileLowerThreshold << " "
+     << "QuantileUpperThreshold "
+     << m_QuantileUpperThreshold << " "
+     << "InsideValue "
+     << m_InsideValue << " "
+     << "OutsideValue "
+     << m_OutsideValue << std::endl;
+}
+
+template 
+void
+MultiModeHistogramThresholdBinaryImageFilter
+::GenerateData()
+{
+  this->AllocateOutputs();
+
+  typename IntegerImageType::Pointer accumulate = IntegerImageType::New();
+
+  const unsigned int NumInputs = this->GetNumberOfInputs();
+  for( unsigned int j = 0; j < NumInputs; ++j )
+    {
+    // Compute the quantile regions for linearizing the percentages.
+    typedef ComputeHistogramQuantileThresholds ImageCalcType;
+    typename ImageCalcType::Pointer ImageCalc = ImageCalcType::New();
+    ImageCalc->SetImage( this->GetInput(j) );
+
+    ImageCalc->SetQuantileLowerThreshold(m_LinearQuantileThreshold);
+    ImageCalc->SetQuantileUpperThreshold(1.0 - m_LinearQuantileThreshold);
+
+    std::cout << "Quantile Thresholds: [ "
+              << m_QuantileLowerThreshold.GetElement(j) << ", "
+              << m_QuantileUpperThreshold.GetElement(j) << " ]"
+              << std::endl;
+
+    ImageCalc->SetBinaryPortionImage(this->m_BinaryPortionImage);
+    ImageCalc->Calculate();
+
+    const typename InputImageType::PixelType thresholdLowerLinearRegion = ImageCalc->GetLowerIntensityThresholdValue();
+    const typename InputImageType::PixelType thresholdUpperLinearRegion  = ImageCalc->GetUpperIntensityThresholdValue();
+    const typename InputImageType::PixelType imageMinValue  = ImageCalc->GetImageMin();
+    const typename InputImageType::PixelType imageMaxValue  = ImageCalc->GetImageMax();
+    const unsigned int numNonZeroHistogramBins = ImageCalc->GetNumberOfValidHistogramsEntries();
+
+    typename InputImageType::PixelType thresholdLowerLinearRegion_foreground;
+    if( numNonZeroHistogramBins <= 2 )
+      {
+      thresholdLowerLinearRegion_foreground = thresholdUpperLinearRegion;
+      }
+    else
+      {
+      thresholdLowerLinearRegion_foreground = thresholdLowerLinearRegion;
+      }
+
+    std::cout << "LowHigh Thresholds: [ " << thresholdLowerLinearRegion << ", "
+              << thresholdLowerLinearRegion_foreground << ", " << thresholdUpperLinearRegion << " ]"
+              << std::endl;
+
+    typedef BinaryThresholdImageFilter
+    ThresholdFilterType;
+    typename ThresholdFilterType::Pointer threshold =
+      ThresholdFilterType::New();
+    threshold->SetInput( this->GetInput(j) );
+    threshold->SetInsideValue(this->m_InsideValue);
+    threshold->SetOutsideValue(this->m_OutsideValue);
+    typename InputImageType::PixelType intensity_thresholdLowerLinearRegion;
+    typename InputImageType::PixelType intensity_thresholdUpperLinearRegion;
+    if( m_QuantileLowerThreshold.GetElement(j) < m_LinearQuantileThreshold )
+      {
+      const double range = ( m_LinearQuantileThreshold - 0.0 );
+      const double percentValue = ( m_QuantileLowerThreshold.GetElement(j) - 0.0 ) / range;
+      intensity_thresholdLowerLinearRegion =
+        static_cast(
+          imageMinValue + ( thresholdLowerLinearRegion_foreground - imageMinValue ) * percentValue );
+      }
+    else
+      {
+      const double range = ( 1.0 - m_LinearQuantileThreshold ) - m_LinearQuantileThreshold;
+      const double percentValue = ( m_QuantileLowerThreshold.GetElement(j) - m_LinearQuantileThreshold ) / range;
+      intensity_thresholdLowerLinearRegion =
+        static_cast(
+          thresholdLowerLinearRegion_foreground
+          + ( thresholdUpperLinearRegion - thresholdLowerLinearRegion_foreground ) * percentValue );
+      }
+    if( m_QuantileUpperThreshold.GetElement(j) > ( 1.0 - m_LinearQuantileThreshold ) )
+      {
+      const double range = 1.0 - m_LinearQuantileThreshold;
+      const double percentValue = ( m_QuantileUpperThreshold.GetElement(j) - m_LinearQuantileThreshold ) / range;
+      intensity_thresholdUpperLinearRegion = static_cast(
+          thresholdUpperLinearRegion
+          + ( imageMaxValue - thresholdUpperLinearRegion ) * percentValue );
+      }
+    else
+      {
+      const double range = ( 1.0 - m_LinearQuantileThreshold ) - m_LinearQuantileThreshold;
+      const double percentValue = ( m_QuantileUpperThreshold.GetElement(j) - m_LinearQuantileThreshold ) / range;
+      intensity_thresholdUpperLinearRegion = static_cast(
+          thresholdLowerLinearRegion_foreground
+          + ( thresholdUpperLinearRegion - thresholdLowerLinearRegion_foreground ) * percentValue );
+      }
+    std::cout << "DEBUG:MINMAX:DEBUG: ["
+              << imageMinValue << "," << imageMaxValue << "]" << std::endl;
+    std::cout << "DEBUG:LINLOWHIGH:DEBUG: ["
+              << thresholdLowerLinearRegion << "," << thresholdUpperLinearRegion << "]" << std::endl;
+    std::cout << "DEBUG:RANGE:DEBUG:  ["
+              << intensity_thresholdLowerLinearRegion << "," << intensity_thresholdUpperLinearRegion << "]"
+              << std::endl;
+    threshold->SetLowerThreshold(intensity_thresholdLowerLinearRegion);
+    threshold->SetUpperThreshold(intensity_thresholdUpperLinearRegion);
+    // threshold->SetUpperThreshold( NumericTraits::max() );
+    threshold->Update();
+    typename IntegerImageType::Pointer thresholdImage = threshold->GetOutput();
+
+    if( j == 0 )
+      {
+      accumulate = thresholdImage;
+      }
+    else
+      {
+      typedef MultiplyImageFilter IntersectMasksFilterType;
+      if( accumulate->GetLargestPossibleRegion().GetSize() != thresholdImage->GetLargestPossibleRegion().GetSize() )
+        {
+        itkExceptionMacro(
+          << "Image data size mismatch " << accumulate->GetLargestPossibleRegion().GetSize() << " != "
+          << thresholdImage->GetLargestPossibleRegion().GetSize() << "." << std::endl );
+        }
+      if( accumulate->GetSpacing() != thresholdImage->GetSpacing() )
+        {
+        itkExceptionMacro(
+          << "Image data spacing mismatch " << accumulate->GetSpacing() << " != " << thresholdImage->GetSpacing()
+          << "." << std::endl );
+        }
+      if( accumulate->GetDirection() != thresholdImage->GetDirection() )
+        {
+        itkExceptionMacro(
+          << "Image data spacing mismatch " << accumulate->GetDirection() << " != " << thresholdImage->GetDirection()
+          << "." << std::endl );
+        }
+      if( accumulate->GetOrigin() != thresholdImage->GetOrigin() )
+        {
+        itkExceptionMacro(
+          << "Image data spacing mismatch " << accumulate->GetOrigin() << " != " << thresholdImage->GetOrigin()
+          << "." << std::endl );
+        }
+      typename IntersectMasksFilterType::Pointer intersect = IntersectMasksFilterType::New();
+      intersect->SetInput1(accumulate);
+      intersect->SetInput2( thresholdImage );
+      intersect->Update();
+      accumulate = intersect->GetOutput();
+      }
+    }
+
+  typedef CastImageFilter outputCasterType;
+  typename outputCasterType::Pointer outputCaster = outputCasterType::New();
+  outputCaster->SetInput(accumulate);
+
+  outputCaster->GraftOutput( this->GetOutput() );
+  outputCaster->Update();
+  this->GraftOutput( outputCaster->GetOutput() );
+  //  typename OutputImageType::Pointer outputMaskImage =
+  // outputCaster->GetOutput();
+  //  return outputMaskImage;
+}
+
+}
diff --git a/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.h b/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.h
new file mode 100644
index 00000000..823d15a2
--- /dev/null
+++ b/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.h
@@ -0,0 +1,304 @@
+#ifndef __itkMultiResolutionLogDomainDeformableRegistration_h
+#define __itkMultiResolutionLogDomainDeformableRegistration_h
+
+#include "itkExponentialDeformationFieldImageFilter2.h"
+#include "itkImage.h"
+#include "itkImageToImageFilter.h"
+#include "itkLogDomainDeformableRegistrationFilter.h"
+#include "itkLogDomainDemonsRegistrationFilter.h"
+#include "itkMultiResolutionPyramidImageFilter.h"
+#include "itkVectorResampleImageFilter.h"
+
+#include 
+
+namespace itk
+{
+/**
+  * \class MultiResolutionLogDomainDeformableRegistration
+  * \brief Framework for performing multi-resolution log-domain
+  * deformable registration.
+  *
+  * MultiResolutionLogDomainDeformableRegistration provides a generic framework
+  * to peform multi-resolution deformable registration.
+  *
+  * At each resolution level a LogDomainDeformableRegistrationFilter is used
+  * to register two images by computing the velocity field whose exponential
+  *will
+  * map a moving image onto a fixed image.
+  *
+  * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * Velocity and deformation fields are represented as images whose pixel type
+  *is some
+  * vector type with at least N elements, where N is the dimension of
+  * the fixed image. The vector type must support element access via operator
+  * []. It is assumed that the vector elements behave like floating point
+  * scalars.
+  *
+  * The internal LogDomainDeformableRegistrationFilter can be set using
+  * SetRegistrationFilter. By default a LogDomainDemonsRegistrationFilter is
+  *used.
+  *
+  * The input fixed and moving images are set via methods SetFixedImage
+  * and SetMovingImage respectively. An initial velocity field maybe set via
+  * SetInitialVelocityField if is matches the characteristics of the coarsest
+  * pyramid level. If no such assumption can be made (e.g. the velocity field
+  * has the same characteristics as the input images), an initial velocity
+  * field can still be set via SetArbitraryInitialVelocityField or
+  * SetInput. The filter will then take care of mathching the coarsest level
+  * characteristics. If no initial field is set a zero field is used as the
+  * initial condition.
+  *
+  * MultiResolutionPyramidImageFilters are used to downsample the fixed
+  * and moving images. A VectorExpandImageFilter is used to upsample
+  * the velocity field as we move from a coarse to fine solution.
+  *
+  * This class is templated over the fixed image type, the moving image type,
+  * and the velocity/deformation Field type.
+  *
+  * \warning This class assumes that the fixed, moving and
+  * field image types all have the same number of dimensions.
+  *
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  *
+  * \sa LogDomainDeformableRegistrationFilter
+  * \sa LogDomainDemonsRegistrationFilter
+  * \sa MultiResolutionPyramidImageFilter
+  * \sa VectorExpandImageFilter
+  *
+  * The current implementation of this class does not support streaming.
+  *
+  * \ingroup DeformableImageRegistration
+  */
+template 
+class ITK_EXPORT MultiResolutionLogDomainDeformableRegistration :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs */
+  typedef MultiResolutionLogDomainDeformableRegistration Self;
+  typedef ImageToImageFilter             Superclass;
+  typedef SmartPointer                             Pointer;
+  typedef SmartPointer                       ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(MultiResolutionLogDomainDeformableRegistration,
+               ImageToImageFilter);
+
+  /** Fixed image type. */
+  typedef TFixedImage                           FixedImageType;
+  typedef typename FixedImageType::Pointer      FixedImagePointer;
+  typedef typename FixedImageType::ConstPointer FixedImageConstPointer;
+
+  /** Moving image type. */
+  typedef TMovingImage                           MovingImageType;
+  typedef typename MovingImageType::Pointer      MovingImagePointer;
+  typedef typename MovingImageType::ConstPointer MovingImageConstPointer;
+
+  /** Velocity field type. */
+  typedef TField                              VelocityFieldType;
+  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;
+
+  /** Deformation field image type. */
+  typedef TField                                 DeformationFieldType;
+  typedef typename DeformationFieldType::Pointer DeformationFieldPointer;
+
+  /** ImageDimension. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      FixedImageType::ImageDimension);
+
+  /** Internal float image type. */
+  typedef Image FloatImageType;
+
+  /** The internal registration type. */
+  typedef LogDomainDeformableRegistrationFilter
+  RegistrationType;
+
+  typedef typename RegistrationType::Pointer RegistrationPointer;
+
+  /** The default registration type. */
+  typedef LogDomainDemonsRegistrationFilter<
+    FloatImageType, FloatImageType, VelocityFieldType> DefaultRegistrationType;
+
+  /** The fixed multi-resolution image pyramid type. */
+  typedef MultiResolutionPyramidImageFilter
+  FixedImagePyramidType;
+
+  typedef typename FixedImagePyramidType::Pointer FixedImagePyramidPointer;
+
+  /** The moving multi-resolution image pyramid type. */
+  typedef MultiResolutionPyramidImageFilter
+  MovingImagePyramidType;
+
+  typedef typename MovingImagePyramidType::Pointer MovingImagePyramidPointer;
+
+  /** The velocity field expander type. */
+  typedef VectorResampleImageFilter
+  FieldExpanderType;
+  typedef typename FieldExpanderType::Pointer FieldExpanderPointer;
+
+  /** Set the fixed image. */
+  virtual void SetFixedImage(const FixedImageType *ptr);
+
+  /** Get the fixed image. */
+  const FixedImageType * GetFixedImage(void) const;
+
+  /** Set the moving image. */
+  virtual void SetMovingImage(const MovingImageType *ptr);
+
+  /** Get the moving image. */
+  const MovingImageType * GetMovingImage(void) const;
+
+  /** Set initial velocity field to be used as is (no smoothing, no
+    *  subsampling at the coarsest level of the pyramid. */
+  virtual void SetInitialVelocityField(VelocityFieldType *ptr)
+  {
+    this->m_InitialVelocityField = ptr;
+  }
+
+  /** Set initial velocity field. No assumption is made on the
+    *  input. It will therefore be smoothed and resampled to match the
+    *  images characteristics at the coarsest level of the pyramid. */
+  virtual void SetArbitraryInitialVelocityField(VelocityFieldType *ptr)
+  {
+    this->SetInput(ptr);
+  }
+
+  /** Get output velocity field. */
+  VelocityFieldType * GetVelocityField()
+  {
+    return this->GetOutput();
+  }
+
+  /** Get output deformation field. */
+  DeformationFieldPointer GetDeformationField();
+
+  /** Get output inverse deformation field. */
+  DeformationFieldPointer GetInverseDeformationField();
+
+  /** Get the number of valid inputs.  For
+    * MultiResolutionLogDomainDeformableRegistration, this checks whether the
+    * fixed and moving images have been set. While
+    * MultiResolutionLogDomainDeformableRegistration can take a third input
+    * as an initial velocity field, this input is not a required input. */
+  virtual std::vector >::size_type GetNumberOfValidRequiredInputs() const;
+
+  /** Set the internal registrator. */
+  itkSetObjectMacro(RegistrationFilter, RegistrationType);
+
+  /** Get the internal registrator. */
+  itkGetObjectMacro(RegistrationFilter, RegistrationType);
+
+  /** Set the fixed image pyramid. */
+  itkSetObjectMacro(FixedImagePyramid, FixedImagePyramidType);
+
+  /** Get the fixed image pyramid. */
+  itkGetObjectMacro(FixedImagePyramid, FixedImagePyramidType);
+
+  /** Set the moving image pyramid. */
+  itkSetObjectMacro(MovingImagePyramid, MovingImagePyramidType);
+
+  /** Get the moving image pyramid. */
+  itkGetObjectMacro(MovingImagePyramid, MovingImagePyramidType);
+
+  /** Set number of multi-resolution levels. */
+  virtual void SetNumberOfLevels(unsigned int num);
+
+  /** Get number of multi-resolution levels. */
+  itkGetConstReferenceMacro(NumberOfLevels, unsigned int);
+
+  /** Get the current resolution level being processed. */
+  itkGetConstReferenceMacro(CurrentLevel, unsigned int);
+
+  /** Set number of iterations per multi-resolution levels. */
+  itkSetVectorMacro(NumberOfIterations, unsigned int, m_NumberOfLevels);
+
+  /** Set the moving image pyramid. */
+  itkSetObjectMacro(FieldExpander, FieldExpanderType);
+
+  /** Get the moving image pyramid. */
+  itkGetObjectMacro(FieldExpander, FieldExpanderType);
+
+  /** Get number of iterations per multi-resolution levels. */
+  virtual const unsigned int * GetNumberOfIterations() const
+  {
+    return &( m_NumberOfIterations[0] );
+  }
+
+  /** Stop the registration after the current iteration. */
+  virtual void StopRegistration();
+
+protected:
+  MultiResolutionLogDomainDeformableRegistration();
+  ~MultiResolutionLogDomainDeformableRegistration()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Exponential type */
+  typedef ExponentialDeformationFieldImageFilter2<
+    VelocityFieldType, DeformationFieldType>      FieldExponentiatorType;
+
+  typedef typename FieldExponentiatorType::Pointer FieldExponentiatorPointer;
+
+  itkSetObjectMacro(Exponentiator, FieldExponentiatorType);
+  itkGetObjectMacro(Exponentiator, FieldExponentiatorType);
+
+  /** Generate output data by performing the registration
+    * at each resolution level. */
+  virtual void GenerateData();
+
+  /** The current implementation of this class does not support
+    * streaming. As such it requires the largest possible region
+    * for the moving, fixed and input velocity field. */
+  virtual void GenerateInputRequestedRegion();
+
+  /** By default, the output velocity field has the same
+    * spacing, origin and LargestPossibleRegion as the input/initial
+    * velocity field. If the initial velocity field is not set, the output
+    * information is copied from the fixed image. */
+  virtual void GenerateOutputInformation();
+
+  /** The current implementation of this class does not supprot
+    * streaming. As such it produces the output for the largest
+    * possible region. */
+  virtual void EnlargeOutputRequestedRegion(DataObject *ptr);
+
+  /** This method returns true to indicate that the registration should
+    * terminate at the current resolution level. */
+  virtual bool Halt();
+
+private:
+  // purposely not implemented
+  MultiResolutionLogDomainDeformableRegistration(const Self &);
+  void operator=(const Self &);
+
+  // implemented
+
+  RegistrationPointer       m_RegistrationFilter;
+  FixedImagePyramidPointer  m_FixedImagePyramid;
+  MovingImagePyramidPointer m_MovingImagePyramid;
+  FieldExpanderPointer      m_FieldExpander;
+  VelocityFieldPointer      m_InitialVelocityField;
+
+  unsigned int              m_NumberOfLevels;
+  unsigned int              m_CurrentLevel;
+  std::vector m_NumberOfIterations;
+
+  /** Flag to indicate user stop registration request. */
+  bool m_StopRegistrationFlag;
+
+  FieldExponentiatorPointer m_Exponentiator;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkMultiResolutionLogDomainDeformableRegistration.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.hxx b/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.hxx
new file mode 100644
index 00000000..cd12c479
--- /dev/null
+++ b/BRAINSCommonLib/itkMultiResolutionLogDomainDeformableRegistration.hxx
@@ -0,0 +1,570 @@
+#ifndef __itkMultiResolutionLogDomainDeformableRegistration_hxx
+#define __itkMultiResolutionLogDomainDeformableRegistration_hxx
+#include "itkMultiResolutionLogDomainDeformableRegistration.h"
+
+#include "itkRecursiveGaussianImageFilter.h"
+#include "itkRecursiveMultiResolutionPyramidImageFilter.h"
+#include "itkImageRegionIterator.h"
+#include "vnl/vnl_math.h"
+
+namespace itk
+{
+// Default constructor
+template 
+MultiResolutionLogDomainDeformableRegistration
+::MultiResolutionLogDomainDeformableRegistration()
+{
+  this->SetNumberOfRequiredInputs(2);
+
+  typename DefaultRegistrationType::Pointer registrator =
+    DefaultRegistrationType::New();
+  m_RegistrationFilter = static_cast(
+      registrator.GetPointer() );
+
+  // /\todo Choose the right type of pyramid
+#if ( ITK_VERSION_MAJOR == 3 && ITK_VERSION_MINOR == 12 && ITK_VERSION_PATCH == 0 )
+  // Work-around for http://public.kitware.com/Bug/view.php?id=503
+  itkWarningMacro(
+    "This version of ITK has a bug in MultiResolutionPyramidImageFilter - using RecursiveMultiResolutionPyramidImageFilter instead");
+  typedef RecursiveMultiResolutionPyramidImageFilter
+    ActualFixedImagePyramidType;
+  typedef RecursiveMultiResolutionPyramidImageFilter
+   ActualMovingImagePyramidType;
+#else
+  typedef MultiResolutionPyramidImageFilter
+    ActualFixedImagePyramidType;
+  typedef MultiResolutionPyramidImageFilter
+   ActualMovingImagePyramidType;
+#endif
+
+  m_MovingImagePyramid  = ActualMovingImagePyramidType::New();
+  m_FixedImagePyramid     = ActualFixedImagePyramidType::New();
+  m_FieldExpander     = FieldExpanderType::New();
+  m_InitialVelocityField = NULL;
+
+  m_NumberOfLevels = 3;
+  m_NumberOfIterations.resize(m_NumberOfLevels);
+  m_FixedImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+  m_MovingImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+
+  unsigned int ilevel;
+  for( ilevel = 0; ilevel < m_NumberOfLevels; ++ilevel )
+    {
+    m_NumberOfIterations[ilevel] = 10;
+    }
+  m_CurrentLevel = 0;
+
+  m_StopRegistrationFlag = false;
+
+  m_Exponentiator = FieldExponentiatorType::New();
+}
+
+// Set the moving image image.
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::SetMovingImage(
+  const MovingImageType *ptr)
+{
+  this->ProcessObject::SetNthInput( 2, const_cast( ptr ) );
+}
+
+// Get the moving image image.
+template 
+const typename MultiResolutionLogDomainDeformableRegistration
+::MovingImageType
+* MultiResolutionLogDomainDeformableRegistration
+::GetMovingImage(void) const
+  {
+  MovingImageType const * const temp = dynamic_cast( this->ProcessObject::GetInput(2) );
+  if( !temp )
+    {
+    itkExceptionMacro(<< "Could not cast MovingImage");
+    }
+  return temp;
+  }
+
+// Set the fixed image.
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::SetFixedImage(
+  const FixedImageType *ptr)
+{
+  this->ProcessObject::SetNthInput( 1, const_cast( ptr ) );
+}
+
+// Get the fixed image.
+template 
+const typename MultiResolutionLogDomainDeformableRegistration
+::FixedImageType
+* MultiResolutionLogDomainDeformableRegistration
+::GetFixedImage(void) const
+  {
+  MovingImageType const * const temp = dynamic_cast( this->ProcessObject::GetInput(1) );
+  if( !temp )
+    {
+    itkExceptionMacro(<< "Could not cast MovingImage");
+    }
+  return temp;
+  }
+
+template 
+std::vector >::size_type
+MultiResolutionLogDomainDeformableRegistration
+::GetNumberOfValidRequiredInputs() const
+{
+  typename std::vector >::size_type num = 0;
+
+  if( this->GetFixedImage() )
+    {
+    ++num;
+    }
+
+  if( this->GetMovingImage() )
+    {
+    ++num;
+    }
+
+  return num;
+}
+
+// Set the number of multi-resolution levels
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::SetNumberOfLevels(
+  unsigned int num)
+{
+  if( m_NumberOfLevels != num )
+    {
+    this->Modified();
+    m_NumberOfLevels = num;
+    m_NumberOfIterations.resize(m_NumberOfLevels);
+    }
+
+  if( m_MovingImagePyramid && m_MovingImagePyramid->GetNumberOfLevels() != num )
+    {
+    m_MovingImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+    }
+  if( m_FixedImagePyramid && m_FixedImagePyramid->GetNumberOfLevels() != num )
+    {
+    m_FixedImagePyramid->SetNumberOfLevels(m_NumberOfLevels);
+    }
+}
+
+// Standard PrintSelf method.
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+  os << indent << "NumberOfLevels: " << m_NumberOfLevels << std::endl;
+  os << indent << "CurrentLevel: " << m_CurrentLevel << std::endl;
+
+  os << indent << "NumberOfIterations: [";
+  unsigned int ilevel;
+  for( ilevel = 0; ilevel < m_NumberOfLevels - 1; ++ilevel )
+    {
+    os << m_NumberOfIterations[ilevel] << ", ";
+    }
+  os << m_NumberOfIterations[ilevel] << "]" << std::endl;
+
+  os << indent << "RegistrationFilter: ";
+  os << m_RegistrationFilter.GetPointer() << std::endl;
+  os << indent << "MovingImagePyramid: ";
+  os << m_MovingImagePyramid.GetPointer() << std::endl;
+  os << indent << "FixedImagePyramid: ";
+  os << m_FixedImagePyramid.GetPointer() << std::endl;
+
+  os << indent << "FieldExpander: ";
+  os << m_FieldExpander.GetPointer() << std::endl;
+
+  os << indent << "StopRegistrationFlag: ";
+  os << m_StopRegistrationFlag << std::endl;
+
+  os << indent << "Exponentiator: ";
+  os << m_Exponentiator << std::endl;
+}
+
+/*
+  * Perform a the deformable registration using a multiresolution scheme
+  * using an internal mini-pipeline
+  *
+  *  ref_pyramid ->  registrator  ->  field_expander --|| tempField
+  * test_pyramid ->           |                              |
+  *                           |                              |
+  *                           --------------------------------
+  *
+  * A tempField image is used to break the cycle between the
+  * registrator and field_expander.*/
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::GenerateData()
+{
+  // Check for NULL images and pointers
+  MovingImageConstPointer movingImage = this->GetMovingImage();
+  FixedImageConstPointer  fixedImage = this->GetFixedImage();
+
+  if( !movingImage || !fixedImage )
+    {
+    itkExceptionMacro(<< "Fixed and/or moving image not set");
+    }
+
+  if( !m_MovingImagePyramid || !m_FixedImagePyramid )
+    {
+    itkExceptionMacro(<< "Fixed and/or moving pyramid not set");
+    }
+
+  if( !m_RegistrationFilter )
+    {
+    itkExceptionMacro(<< "Registration filter not set");
+    }
+
+  if( this->m_InitialVelocityField && this->GetInput(0) )
+    {
+    itkExceptionMacro(<< "Only one initial velocity can be given. "
+                      << "SetInitialVelocityField should not be used in "
+                      << "cunjunction with SetArbitraryInitialVelocityField "
+                      << "or SetInput.");
+    }
+
+  // Create the image pyramids.
+  m_MovingImagePyramid->SetInput(movingImage);
+  m_MovingImagePyramid->UpdateLargestPossibleRegion();
+
+  m_FixedImagePyramid->SetInput(fixedImage);
+  m_FixedImagePyramid->UpdateLargestPossibleRegion();
+
+  // Initializations
+  m_CurrentLevel = 0;
+  m_StopRegistrationFlag = false;
+
+  unsigned int movingLevel = vnl_math_min( (int)m_CurrentLevel,
+                                           (int)m_MovingImagePyramid->GetNumberOfLevels() );
+
+  unsigned int fixedLevel = vnl_math_min( (int)m_CurrentLevel,
+                                          (int)m_FixedImagePyramid->GetNumberOfLevels() );
+
+  VelocityFieldPointer tempField = NULL;
+
+  VelocityFieldPointer inputPtr =
+    const_cast( this->GetInput(0) );
+
+  if( this->m_InitialVelocityField )
+    {
+    tempField = this->m_InitialVelocityField;
+    }
+  else if( inputPtr )
+    {
+    // Arbitrary initial velocity field is set.
+    // smooth it and resample
+
+    // First smooth it
+    tempField = inputPtr;
+
+    typedef RecursiveGaussianImageFilter GaussianFilterType;
+    typename GaussianFilterType::Pointer smoother =
+      GaussianFilterType::New();
+    for( unsigned int dim = 0; dim < VelocityFieldType::ImageDimension; ++dim )
+      {
+      // sigma accounts for the subsampling of the pyramid
+      double sigma = 0.5 * static_cast(
+          m_FixedImagePyramid->GetSchedule()[fixedLevel][dim] );
+
+      // but also for a possible discrepancy in the spacing
+      sigma *= fixedImage->GetSpacing()[dim]
+        / inputPtr->GetSpacing()[dim];
+
+      smoother->SetInput(tempField);
+      smoother->SetSigma(sigma);
+      smoother->SetDirection(dim);
+
+      smoother->Update();
+
+      tempField = smoother->GetOutput();
+      // tempField->DisconnectPipeline();
+      }
+
+    // Now resample
+    m_FieldExpander->SetInput(tempField);
+
+    typename FloatImageType::Pointer fi =
+      m_FixedImagePyramid->GetOutput(fixedLevel);
+    m_FieldExpander->SetSize(
+      fi->GetLargestPossibleRegion().GetSize() );
+    m_FieldExpander->SetOutputStartIndex(
+      fi->GetLargestPossibleRegion().GetIndex() );
+    m_FieldExpander->SetOutputOrigin( fi->GetOrigin() );
+    m_FieldExpander->SetOutputSpacing( fi->GetSpacing() );
+    m_FieldExpander->SetOutputDirection( fi->GetDirection() );
+
+    m_FieldExpander->UpdateLargestPossibleRegion();
+    m_FieldExpander->SetInput(NULL);
+    tempField = m_FieldExpander->GetOutput();
+    // tempField->DisconnectPipeline();
+    }
+
+  bool lastShrinkFactorsAllOnes = false;
+
+  while( !this->Halt() )
+    {
+    if( tempField.IsNull() )
+      {
+      m_RegistrationFilter->SetInitialVelocityField(NULL);
+      }
+    else
+      {
+      // Resample the field to be the same size as the fixed image
+      // at the current level
+      m_FieldExpander->SetInput(tempField);
+
+      typename FloatImageType::Pointer fi =
+        m_FixedImagePyramid->GetOutput(fixedLevel);
+      m_FieldExpander->SetSize(
+        fi->GetLargestPossibleRegion().GetSize() );
+      m_FieldExpander->SetOutputStartIndex(
+        fi->GetLargestPossibleRegion().GetIndex() );
+      m_FieldExpander->SetOutputOrigin( fi->GetOrigin() );
+      m_FieldExpander->SetOutputSpacing( fi->GetSpacing() );
+      m_FieldExpander->SetOutputDirection( fi->GetDirection() );
+
+      m_FieldExpander->UpdateLargestPossibleRegion();
+      m_FieldExpander->SetInput(NULL);
+      tempField = m_FieldExpander->GetOutput();
+      // tempField->DisconnectPipeline();
+
+      m_RegistrationFilter->SetInitialVelocityField(tempField);
+      }
+
+    // setup registration filter and pyramids
+    m_RegistrationFilter->SetMovingImage( m_MovingImagePyramid->GetOutput(movingLevel) );
+    m_RegistrationFilter->SetFixedImage( m_FixedImagePyramid->GetOutput(fixedLevel) );
+
+    m_RegistrationFilter->SetNumberOfIterations(
+      m_NumberOfIterations[m_CurrentLevel]);
+
+    // cache shrink factors for computing the next expand factors.
+    lastShrinkFactorsAllOnes = true;
+    for( unsigned int idim = 0; idim < ImageDimension; ++idim )
+      {
+      if( m_FixedImagePyramid->GetSchedule()[fixedLevel][idim] > 1 )
+        {
+        lastShrinkFactorsAllOnes = false;
+        break;
+        }
+      }
+
+    // compute new velocity field
+    m_RegistrationFilter->UpdateLargestPossibleRegion();
+    tempField = m_RegistrationFilter->GetOutput();
+    // tempField->DisconnectPipeline();
+
+    // Increment level counter.
+    m_CurrentLevel++;
+    movingLevel = vnl_math_min( (int)m_CurrentLevel,
+                                (int)m_MovingImagePyramid->GetNumberOfLevels() );
+    fixedLevel = vnl_math_min( (int)m_CurrentLevel,
+                               (int)m_FixedImagePyramid->GetNumberOfLevels() );
+
+    // Invoke an iteration event.
+    this->InvokeEvent( IterationEvent() );
+
+    // We can release data from pyramid which are no longer required.
+    if( movingLevel > 0 )
+      {
+      m_MovingImagePyramid->GetOutput(movingLevel - 1)->ReleaseData();
+      }
+    if( fixedLevel > 0 )
+      {
+      m_FixedImagePyramid->GetOutput(fixedLevel - 1)->ReleaseData();
+      }
+    } // while not Halt()
+
+  if( !lastShrinkFactorsAllOnes )
+    {
+    // Some of the last shrink factors are not one
+    // graft the output of the expander filter to
+    // to output of this filter
+
+    // resample the field to the same size as the fixed image
+    m_FieldExpander->SetInput(tempField);
+    m_FieldExpander->SetSize(
+      fixedImage->GetLargestPossibleRegion().GetSize() );
+    m_FieldExpander->SetOutputStartIndex(
+      fixedImage->GetLargestPossibleRegion().GetIndex() );
+    m_FieldExpander->SetOutputOrigin( fixedImage->GetOrigin() );
+    m_FieldExpander->SetOutputSpacing( fixedImage->GetSpacing() );
+    m_FieldExpander->SetOutputDirection( fixedImage->GetDirection() );
+
+    m_FieldExpander->UpdateLargestPossibleRegion();
+    this->GraftOutput( m_FieldExpander->GetOutput() );
+    }
+  else
+    {
+    // all the last shrink factors are all ones
+    // graft the output of registration filter to
+    // to output of this filter
+    this->GraftOutput(tempField);
+    }
+
+  // Release memory
+  m_FieldExpander->SetInput(NULL);
+  m_FieldExpander->GetOutput()->ReleaseData();
+  m_RegistrationFilter->SetInput(NULL);
+  m_RegistrationFilter->GetOutput()->ReleaseData();
+}
+
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::StopRegistration()
+{
+  m_RegistrationFilter->StopRegistration();
+  m_StopRegistrationFlag = true;
+}
+
+template 
+bool
+MultiResolutionLogDomainDeformableRegistration
+::Halt()
+{
+  // Halt the registration after the user-specified number of levels
+  if( m_NumberOfLevels != 0 )
+    {
+    this->UpdateProgress( static_cast( m_CurrentLevel )
+                          / static_cast( m_NumberOfLevels ) );
+    }
+
+  if( m_CurrentLevel >= m_NumberOfLevels )
+    {
+    return true;
+    }
+  if( m_StopRegistrationFlag )
+    {
+    return true;
+    }
+  else
+    {
+    return false;
+    }
+}
+
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::GenerateOutputInformation()
+{
+  typename DataObject::Pointer output;
+
+  if( this->GetInput(0) )
+    {
+    // Initial velocity field is set.
+    // Copy information from initial field.
+    this->Superclass::GenerateOutputInformation();
+    }
+  else if( this->GetFixedImage() )
+    {
+    // Initial deforamtion field is not set.
+    // Copy information from the fixed image.
+    for( unsigned int idx = 0; idx <
+         this->GetNumberOfOutputs(); ++idx )
+      {
+      output = this->GetOutput(idx);
+      if( output )
+        {
+        output->CopyInformation( this->GetFixedImage() );
+        }
+      }
+    }
+}
+
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::GenerateInputRequestedRegion()
+{
+  // call the superclass's implementation
+  Superclass::GenerateInputRequestedRegion();
+
+  // request the largest possible region for the moving image
+  MovingImagePointer movingPtr =
+    const_cast( this->GetMovingImage() );
+  if( movingPtr )
+    {
+    movingPtr->SetRequestedRegionToLargestPossibleRegion();
+    }
+
+  // just propagate up the output requested region for
+  // the fixed image and initial velocity field.
+  VelocityFieldPointer inputPtr =
+    const_cast( this->GetInput() );
+  VelocityFieldPointer outputPtr = this->GetOutput();
+  FixedImagePointer    fixedPtr =
+    const_cast( this->GetFixedImage() );
+
+  if( inputPtr )
+    {
+    inputPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
+    }
+
+  if( fixedPtr )
+    {
+    fixedPtr->SetRequestedRegion( outputPtr->GetRequestedRegion() );
+    }
+}
+
+template 
+void
+MultiResolutionLogDomainDeformableRegistration
+::EnlargeOutputRequestedRegion(
+  DataObject *ptr)
+{
+  // call the superclass's implementation
+  Superclass::EnlargeOutputRequestedRegion(ptr);
+
+  // set the output requested region to largest possible.
+  VelocityFieldType * const outputPtr = dynamic_cast( ptr );
+
+  if( outputPtr )
+    {
+    outputPtr->SetRequestedRegionToLargestPossibleRegion();
+    }
+}
+
+template 
+typename MultiResolutionLogDomainDeformableRegistration
+::DeformationFieldPointer
+MultiResolutionLogDomainDeformableRegistration
+::GetDeformationField()
+{
+  m_Exponentiator->SetInput( this->GetVelocityField() );
+  m_Exponentiator->ComputeInverseOff();
+  m_Exponentiator->Update();
+  DeformationFieldPointer field = m_Exponentiator->GetOutput();
+  // field->DisconnectPipeline();
+  return field;
+}
+
+template 
+typename MultiResolutionLogDomainDeformableRegistration
+::DeformationFieldPointer
+MultiResolutionLogDomainDeformableRegistration
+::GetInverseDeformationField()
+{
+  m_Exponentiator->SetInput( this->GetVelocityField() );
+  m_Exponentiator->ComputeInverseOn();
+  m_Exponentiator->Update();
+  DeformationFieldPointer field = m_Exponentiator->GetOutput();
+  // field->DisconnectPipeline();
+  // Reset compute inverse back to off to avoid some broder effects
+  m_Exponentiator->ComputeInverseOff();
+  return field;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkOppositeImageFilter.h b/BRAINSCommonLib/itkOppositeImageFilter.h
new file mode 100644
index 00000000..885759e1
--- /dev/null
+++ b/BRAINSCommonLib/itkOppositeImageFilter.h
@@ -0,0 +1,121 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkOppositeImageFilter.h,v $
+ *  Language:  C++
+ *  Date:      $Date: 2009-02-19 21:18:10 $
+ *  Version:   $Revision: 0.0 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+
+#ifndef __itkOppositeImageFilter_h
+#define __itkOppositeImageFilter_h
+
+#include "itkUnaryFunctorImageFilter.h"
+#include "itkNumericTraits.h"
+
+namespace itk
+{
+/** \class OppositeImageFilter
+  *
+  * \brief Take the opposite of the input pixels.
+  *
+  * This filter is templated over the input image type
+  * and the output image type.
+  *
+  * \author Tom Vercauteren, INRIA & Mauna Kea Technologies
+  *
+  * \ingroup IntensityImageFilters  Multithreaded
+  * \sa UnaryFunctorImageFilter
+  */
+namespace Functor
+{
+template 
+class Opposite
+{
+public:
+  Opposite()
+  {
+  }
+  ~Opposite()
+  {
+  }
+  bool operator!=(const Opposite & other) const
+  {
+    return false;
+  }
+
+  bool operator==(const Opposite & other) const
+  {
+    return true;
+  }
+
+  inline TOutput operator()(const TInput & A) const
+  {
+    // We don't check if the TOutput can be signed.
+    // It's up to the user to decide whether this makes sense.
+    return static_cast( -A );
+  }
+
+};
+}
+
+template 
+class ITK_EXPORT OppositeImageFilter :
+  public
+  UnaryFunctorImageFilter >
+{
+public:
+  /** Standard class typedefs. */
+  typedef OppositeImageFilter Self;
+  typedef UnaryFunctorImageFilter >
+  Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(OppositeImageFilter, UnaryFunctorImageFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( InputConvertibleToOutputCheck,
+                   ( Concept::Convertible ) );
+  /** End concept checking */
+#endif
+protected:
+  OppositeImageFilter()
+  {
+  }
+  virtual ~OppositeImageFilter()
+  {
+  }
+
+  void PrintSelf(std::ostream & os, Indent indent) const
+  {
+    Superclass::PrintSelf(os, indent);
+  }
+
+private:
+  OppositeImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);      // purposely not implemented
+
+};
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.h b/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.h
new file mode 100644
index 00000000..3bda3409
--- /dev/null
+++ b/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.h
@@ -0,0 +1,240 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkOtsuHistogramMatchingImageFilter.h,v $
+ *  Language:  C++
+ *  Date:      $Date: 2009-05-02 05:43:54 $
+ *  Version:   $Revision: 1.13 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkOtsuHistogramMatchingImageFilter_h
+#define __itkOtsuHistogramMatchingImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkHistogram.h"
+#include "BRAINSFitUtils.h"
+#include "vnl/vnl_matrix.h"
+
+namespace itk
+{
+#if ITK_VERSION_MAJOR < 4 && ! defined (ITKv3_THREAD_ID_TYPE_DEFINED)
+#define ITKv3_THREAD_ID_TYPE_DEFINED 1
+  typedef int ThreadIdType;
+#endif
+
+/** \class OtsuHistogramMatchingImageFilter
+  * \brief Normalize the grayscale values between two image by histogram
+  * matching.
+  *
+  * OtsuHistogramMatchingImageFilter normalizes the grayscale values of a source
+  * image based on the grayscale values of a reference image.
+  * This filter uses a histogram matching technique where the histograms of the
+  * two images are matched only at a specified number of quantile values.
+  *
+  * This filter was inspired by the HistogramMatchingImagFilter that was
+  * orginally designed to normalize MR images of the same
+  * MR protocol and same body part. This algorithm is a specialization that
+  * takes advantage of the fact that the algorihtms work best if background
+  * pixels are excluded from both the source and reference histograms.
+  * The background exclusion method uses the Otsu threshold to exclude all
+  * background voxles whose grayscale values are smaller than Otsu threshold.
+  *
+  * The source image can be set via either SetInput() or SetSourceImage().
+  * The reference image can be set via SetReferenceImage().
+  *
+  * SetNumberOfHistogramLevels() sets the number of bins used when
+  * creating histograms of the source and reference images.
+  * SetNumberOfMatchPoints() governs the number of quantile values to be
+  * matched.
+  *
+  * This filter assumes that both the source and reference are of the same
+  * type and that the input and output image type have the same number of
+  * dimension and have scalar pixel types.
+  *
+  * \ingroup IntensityImageFilters Multithreaded
+  *
+  */
+/* THistogramMeasurement -- The precision level for which to do
+  * HistogramMeasurmenets */
+template 
+class ITK_EXPORT OtsuHistogramMatchingImageFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef OtsuHistogramMatchingImageFilter              Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(OtsuHistogramMatchingImageFilter, ImageToImageFilter);
+
+  /** ImageDimension enumeration. */
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+
+  /** Typedef to describe the output image region type. */
+  typedef typename TOutputImage::RegionType OutputImageRegionType;
+
+  /** Inherited typedefs. */
+  typedef typename Superclass::InputImageType         InputImageType;
+  typedef typename Superclass::InputImagePointer      InputImagePointer;
+  typedef typename Superclass::InputImageConstPointer InputImageConstPointer;
+  typedef typename Superclass::OutputImageType        OutputImageType;
+  typedef typename Superclass::OutputImagePointer     OutputImagePointer;
+
+  /** Pixel related typedefs. */
+  typedef typename InputImageType::PixelType  InputPixelType;
+  typedef typename OutputImageType::PixelType OutputPixelType;
+
+  typedef itk::SpatialObject<3> SpatialObjectType;
+
+  /** Histogram related typedefs. */
+  typedef Statistics::Histogram HistogramType;
+  typedef typename HistogramType::Pointer              HistogramPointer;
+
+  /** Set/Get the source image. */
+  void SetSourceImage(const InputImageType *source)
+  {
+    this->SetInput(source);
+  }
+
+  const InputImageType * GetSourceImage(void)
+  {
+    return this->GetInput();
+  }
+
+  /** Set/Get the reference image. */
+  void SetReferenceImage(const InputImageType *reference);
+
+  const InputImageType * GetReferenceImage(void);
+
+  itkSetObjectMacro(SourceMask, SpatialObjectType);
+  itkSetObjectMacro(ReferenceMask, SpatialObjectType);
+
+  itkGetConstObjectMacro(SourceMask, SpatialObjectType);
+  itkGetConstObjectMacro(ReferenceMask, SpatialObjectType);
+
+  /** Set/Get the number of histogram levels used. */
+  itkSetMacro(NumberOfHistogramLevels, unsigned long);
+  itkGetConstMacro(NumberOfHistogramLevels, unsigned long);
+
+  /** Set/Get the number of match points used. */
+  itkSetMacro(NumberOfMatchPoints, unsigned long);
+  itkGetConstMacro(NumberOfMatchPoints, unsigned long);
+
+  /** This filter requires all of the input to be in the buffer. */
+  virtual void GenerateInputRequestedRegion();
+
+  /** Methods to get the histograms of the source, reference, and
+    * output. Objects are only valid after Update() has been called
+    * on this filter. */
+  itkGetObjectMacro(SourceHistogram, HistogramType);
+  itkGetObjectMacro(ReferenceHistogram, HistogramType);
+  itkGetObjectMacro(OutputHistogram, HistogramType);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( IntConvertibleToInputCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( SameDimensionCheck,
+                   ( Concept::SameDimension ) );
+  itkConceptMacro( DoubleConvertibleToInputCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( DoubleConvertibleToOutputCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( InputConvertibleToDoubleCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( OutputConvertibleToDoubleCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( SameTypeCheck,
+                   ( Concept::SameType ) );
+  /** End concept checking */
+#endif
+protected:
+  /** Override VeriyInputInformation() since this filter does not expect
+    * the input images to occupy the same physical space.
+    *
+    * \sa ProcessObject::VerifyInputInformation
+    */
+ virtual void VerifyInputInformation() {}
+
+  OtsuHistogramMatchingImageFilter();
+  ~OtsuHistogramMatchingImageFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  void BeforeThreadedGenerateData();
+
+  void AfterThreadedGenerateData();
+
+  void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId);
+
+  /** Compute min, max and mean of an image. */
+  void ComputeMinMaxMean(const InputImageType *image, THistogramMeasurement & minValue,
+                         THistogramMeasurement & maxValue,
+                         THistogramMeasurement & meanValue);
+
+  /** Construct a histogram from an image. */
+  void ConstructHistogram(const InputImageType *image, const typename SpatialObjectType::Pointer mask,
+                          HistogramType *histogram, const THistogramMeasurement minValue,
+                          const THistogramMeasurement maxValue);
+
+private:
+  OtsuHistogramMatchingImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);                   // purposely not implemented
+
+  unsigned long m_NumberOfHistogramLevels;
+  unsigned long m_NumberOfMatchPoints;
+  bool          m_ThresholdAtMeanIntensity;
+
+  InputPixelType  m_SourceIntensityThreshold;
+  InputPixelType  m_ReferenceIntensityThreshold;
+  OutputPixelType m_OutputIntensityThreshold;
+
+  THistogramMeasurement m_SourceMinValue;
+  THistogramMeasurement m_SourceMaxValue;
+  THistogramMeasurement m_SourceMeanValue;
+  THistogramMeasurement m_ReferenceMinValue;
+  THistogramMeasurement m_ReferenceMaxValue;
+  THistogramMeasurement m_ReferenceMeanValue;
+  THistogramMeasurement m_OutputMinValue;
+  THistogramMeasurement m_OutputMaxValue;
+  THistogramMeasurement m_OutputMeanValue;
+
+  HistogramPointer m_SourceHistogram;
+  HistogramPointer m_ReferenceHistogram;
+  HistogramPointer m_OutputHistogram;
+
+  typedef vnl_matrix TableType;
+  TableType m_QuantileTable;
+
+  typedef vnl_vector GradientArrayType;
+  GradientArrayType m_Gradients;
+  double            m_LowerGradient;
+  double            m_UpperGradient;
+
+  typename SpatialObjectType::Pointer m_SourceMask;
+  typename SpatialObjectType::Pointer m_ReferenceMask;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkOtsuHistogramMatchingImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.hxx b/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.hxx
new file mode 100644
index 00000000..fa36fefa
--- /dev/null
+++ b/BRAINSCommonLib/itkOtsuHistogramMatchingImageFilter.hxx
@@ -0,0 +1,443 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkOtsuHistogramMatchingImageFilter.hxx,v $
+ *  Language:  C++
+ *  Date:      $Date: 2009-05-05 17:00:00 $
+ *  Version:   $Revision: 1.19 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *    This software is distributed WITHOUT ANY WARRANTY; without even
+ *    the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *    PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkOtsuHistogramMatchingImageFilter_hxx
+#define __itkOtsuHistogramMatchingImageFilter_hxx
+
+#include "itkOtsuHistogramMatchingImageFilter.h"
+#include "itkImageRegionIterator.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkNumericTraits.h"
+#include 
+
+#include "itkOtsuThresholdImageCalculator.h"
+#include "BRAINSFitUtils.h"
+
+namespace itk
+{
+/**
+  *
+  */
+template 
+OtsuHistogramMatchingImageFilter
+::OtsuHistogramMatchingImageFilter()
+{
+  this->SetNumberOfRequiredInputs(2);
+
+  m_NumberOfHistogramLevels = 256;
+  m_NumberOfMatchPoints = 1;
+
+  m_QuantileTable.set_size(3, m_NumberOfMatchPoints + 2);
+  m_QuantileTable.fill(0);
+  m_Gradients.set_size(m_NumberOfMatchPoints + 1);
+  m_Gradients.fill(0);
+
+  m_LowerGradient = 0.0;
+  m_UpperGradient = 0.0;
+
+  // Create histograms.
+  m_SourceHistogram = HistogramType::New();
+  m_ReferenceHistogram = HistogramType::New();
+  m_OutputHistogram = HistogramType::New();
+
+  m_SourceMinValue = 0;
+  m_ReferenceMinValue = 0;
+  m_SourceMask = NULL;
+  m_ReferenceMask = NULL;
+}
+
+/*
+  *
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "NumberOfHistogramLevels: ";
+  os << m_NumberOfHistogramLevels << std::endl;
+  os << indent << "NumberOfMatchPoints: ";
+  os << m_NumberOfMatchPoints << std::endl;
+
+  os << indent << "m_SourceMinValue: ";
+  os << m_SourceMinValue << std::endl;
+  os << indent << "m_ReferenceMinValue: ";
+  os << m_ReferenceMinValue << std::endl;
+  os << indent << "m_ReferenceMinValue: ";
+  os << m_ReferenceMinValue << std::endl;
+  os << indent << "Source histogram: ";
+  os << m_SourceHistogram.GetPointer() << std::endl;
+  os << indent << "Reference histogram: ";
+  os << m_ReferenceHistogram.GetPointer() << std::endl;
+  os << indent << "Output histogram: ";
+  os << m_OutputHistogram.GetPointer() << std::endl;
+  os << indent << "QuantileTable: " << std::endl;
+  os << m_QuantileTable << std::endl;
+  os << indent << "Gradients: " << std::endl;
+  os << m_Gradients << std::endl;
+  os << indent << "LowerGradient: ";
+  os << m_LowerGradient << std::endl;
+  os << indent << "UpperGradient: ";
+  os << m_UpperGradient << std::endl;
+}
+
+/*
+  *
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::SetReferenceImage(const InputImageType *reference)
+{
+  this->ProcessObject::SetNthInput( 1,
+                                    const_cast( reference ) );
+}
+
+/*
+  *
+  */
+template 
+const typename OtsuHistogramMatchingImageFilter
+::InputImageType
+* OtsuHistogramMatchingImageFilter
+::GetReferenceImage()
+  {
+  if( this->GetNumberOfInputs() < 2 )
+    {
+    return NULL;
+    }
+
+  TInputImage const * const temp = dynamic_cast( this->ProcessObject::GetInput(1) );
+  if( temp == NULL )
+    {
+    std::cout << "Invalid mask converstion attempted." << __FILE__ << " " << __LINE__ << std::endl;
+    exit(-1);
+    }
+  return temp;
+  }
+
+/*
+  * This filter requires all of the input images to be
+  * in the buffer.
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::GenerateInputRequestedRegion()
+{
+  this->Superclass::GenerateInputRequestedRegion();
+  for( unsigned int idx = 0; idx < this->GetNumberOfInputs(); ++idx )
+    {
+    if( this->GetInput(idx) )
+      {
+      InputImagePointer image =
+        const_cast( this->GetInput(idx) );
+      image->SetRequestedRegionToLargestPossibleRegion();
+      }
+    }
+}
+
+/**
+  *
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::BeforeThreadedGenerateData()
+{
+
+  InputImageConstPointer source    = this->GetSourceImage();
+  InputImageConstPointer reference = this->GetReferenceImage();
+
+  std::cout << "source stats" << std::endl;
+  ComputeRobustMinMaxMean(0.005, source.GetPointer(),
+                                                          m_SourceMask.GetPointer(), m_SourceMinValue,
+                                                          m_SourceMaxValue, m_SourceMeanValue);
+  std::cout << "reference stats" << std::endl;
+  ComputeRobustMinMaxMean(0.005, reference.GetPointer(),
+                                                          m_ReferenceMask.GetPointer(), m_ReferenceMinValue,
+                                                          m_ReferenceMaxValue, m_ReferenceMeanValue);
+
+  this->ConstructHistogram(source, m_SourceMask, m_SourceHistogram,
+                           m_SourceMinValue, m_SourceMaxValue);
+  this->ConstructHistogram(reference, m_ReferenceMask, m_ReferenceHistogram,
+                           m_ReferenceMinValue, m_ReferenceMaxValue);
+
+  // Fill in the quantile table.
+  m_QuantileTable.set_size(3, m_NumberOfMatchPoints + 2);
+  m_QuantileTable[0][0] = m_SourceMinValue;
+  m_QuantileTable[1][0] = m_ReferenceMinValue;
+
+  m_QuantileTable[0][m_NumberOfMatchPoints + 1] = m_SourceMaxValue;
+  m_QuantileTable[1][m_NumberOfMatchPoints + 1] = m_ReferenceMaxValue;
+
+  const double delta = 1.0 / ( double(m_NumberOfMatchPoints) + 1.0 );
+  for( unsigned int j = 1; j < m_NumberOfMatchPoints + 1; ++j )
+    {
+    m_QuantileTable[0][j] = m_SourceHistogram->Quantile(
+        0, double(j) * delta);
+    m_QuantileTable[1][j] = m_ReferenceHistogram->Quantile(
+        0, double(j) * delta);
+    }
+
+  // Fill in the gradient array.
+  m_Gradients.set_size(m_NumberOfMatchPoints + 1);
+  for( unsigned int j = 0; j < m_NumberOfMatchPoints + 1; ++j )
+    {
+    const double denominator = m_QuantileTable[0][j + 1]
+      - m_QuantileTable[0][j];
+    if( denominator != 0 )
+      {
+      m_Gradients[j] = m_QuantileTable[1][j + 1]
+        - m_QuantileTable[1][j];
+      m_Gradients[j] /= denominator;
+      }
+    else
+      {
+      m_Gradients[j] = 0.0;
+      }
+    }
+
+    {
+    const double denominator = m_QuantileTable[0][0] - m_SourceMinValue;
+    if( denominator != 0 )
+      {
+      m_LowerGradient = m_QuantileTable[1][0] - m_ReferenceMinValue;
+      m_LowerGradient /= denominator;
+      }
+    else
+      {
+      m_LowerGradient = 0.0;
+      }
+    }
+
+    {
+    const double denominator = m_QuantileTable[0][m_NumberOfMatchPoints + 1]
+      - m_SourceMaxValue;
+    if( denominator != 0 )
+      {
+      m_UpperGradient = m_QuantileTable[1][m_NumberOfMatchPoints + 1]
+        - m_ReferenceMaxValue;
+      m_UpperGradient /= denominator;
+      }
+    else
+      {
+      m_UpperGradient = 0.0;
+      }
+    }
+}
+
+/**
+  *
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::AfterThreadedGenerateData()
+{
+  OutputImagePointer output    = this->GetOutput();
+
+  std::cout << "output stats" << std::endl;
+  ComputeRobustMinMaxMean(0.005, output.GetPointer(),
+                                                           this->m_SourceMask.GetPointer(), m_OutputMinValue,
+                                                           m_OutputMaxValue, m_OutputMeanValue);
+
+  this->m_OutputIntensityThreshold    = static_cast( m_OutputMinValue );
+
+  this->ConstructHistogram(output, m_SourceMask, m_OutputHistogram,
+                           m_OutputIntensityThreshold, m_OutputMaxValue);
+
+  // Fill in the quantile table.
+  m_QuantileTable[2][0] = m_OutputIntensityThreshold;
+
+  m_QuantileTable[2][m_NumberOfMatchPoints + 1] = m_OutputMaxValue;
+
+  const double delta = 1.0 / ( double(m_NumberOfMatchPoints) + 1.0 );
+  for( unsigned int j = 1; j < m_NumberOfMatchPoints + 1; ++j )
+    {
+    m_QuantileTable[2][j] = m_OutputHistogram->Quantile(
+        0, double(j) * delta);
+    }
+}
+
+/**
+  *
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread,
+                       ThreadIdType threadId)
+{
+
+  // Get the input and output pointers;
+  InputImageConstPointer input  = this->GetInput();
+  OutputImagePointer     output = this->GetOutput();
+
+  // Transform the source image and write to output.
+  typedef ImageRegionConstIterator InputConstIterator;
+  typedef ImageRegionIterator     OutputIterator;
+
+  InputConstIterator inIter(input, outputRegionForThread);
+
+  OutputIterator outIter(output, outputRegionForThread);
+
+  // support progress methods/callbacks
+  unsigned long updateVisits = 0;
+  unsigned long totalPixels = 0;
+  if( threadId == 0 )
+    {
+    totalPixels = outputRegionForThread.GetNumberOfPixels();
+    updateVisits = totalPixels / 10;
+    if( updateVisits < 1 )
+      {
+      updateVisits = 1;
+      }
+    }
+  for( int i = 0; !outIter.IsAtEnd(); ++inIter, ++outIter, ++i )
+    {
+    if( threadId == 0 && !( i % updateVisits ) )
+      {
+      this->UpdateProgress( (float)i / (float)totalPixels );
+      }
+
+    const double srcValue = static_cast( inIter.Get() );
+
+      {
+      unsigned int j = 0;
+      for( ; j < m_NumberOfMatchPoints + 2; ++j )
+        {
+        if( srcValue < m_QuantileTable[0][j] )
+          {
+          break;
+          }
+        }
+
+      double mappedValue;
+      if( j == 0 )
+        {
+        // Linear interpolate from min to point[0]
+        mappedValue = m_ReferenceMinValue
+          + ( srcValue - m_SourceMinValue ) * m_LowerGradient;
+        }
+      else if( j == m_NumberOfMatchPoints + 2 )
+        {
+        // Linear interpolate from point[m_NumberOfMatchPoints+1] to max
+        mappedValue = m_ReferenceMaxValue
+          + ( srcValue - m_SourceMaxValue ) * m_UpperGradient;
+        }
+      else
+        {
+        // Linear interpolate from point[j] and point[j+1].
+        mappedValue = m_QuantileTable[1][j - 1]
+          + ( srcValue - m_QuantileTable[0][j - 1] ) * m_Gradients[j - 1];
+        }
+
+      // Clamp values to the min/max of the source histogram range (the values
+      // are supposed to be aligned anyway)
+//      mappedValue=vcl_max(mappedValue,(double)m_SourceMinValue);
+//      mappedValue=vcl_min(mappedValue,(double)m_SourceMaxValue);
+      outIter.Set( static_cast( mappedValue ) );
+      }
+    }
+}
+
+/**
+  * Construct a histogram from an image.
+  */
+template 
+void
+OtsuHistogramMatchingImageFilter
+::ConstructHistogram(
+  const InputImageType *image,
+  const SpatialObjectType::Pointer mask,
+  HistogramType  *histogram,
+  const THistogramMeasurement minValue,
+  const THistogramMeasurement maxValue)
+{
+    {
+    // allocate memory for the histogram
+    typename HistogramType::SizeType size;
+    typename HistogramType::MeasurementVectorType lowerBound;
+    typename HistogramType::MeasurementVectorType upperBound;
+
+    size.SetSize(1);
+    lowerBound.SetSize(1);
+    upperBound.SetSize(1);
+    histogram->SetMeasurementVectorSize(1);
+    size[0] = m_NumberOfHistogramLevels;
+    lowerBound.Fill(minValue);
+    upperBound.Fill(maxValue);
+
+    // Initialize with equally spaced bins.
+    histogram->Initialize(size, lowerBound, upperBound);
+    histogram->SetToZero();
+    }
+
+  typename HistogramType::MeasurementVectorType measurement;
+  measurement.SetSize(1);
+
+  typedef typename HistogramType::MeasurementType MeasurementType;
+  measurement[0] = NumericTraits::Zero;
+
+    {
+    // put each image pixel into the histogram
+    typedef ImageRegionConstIteratorWithIndex ConstIterator;
+    ConstIterator iter( image, image->GetBufferedRegion() );
+
+    iter.GoToBegin();
+    while( !iter.IsAtEnd() )
+      {
+      const InputPixelType value = iter.Get();
+      bool                 inMeasurementRegion = false;
+      // First check if value is in histogram range.
+      if( static_cast( value ) >= minValue
+          && static_cast( value ) <= maxValue )
+        {
+        if( mask.IsNull() )  // Assume entire area is valid
+          {
+          inMeasurementRegion = true;
+          }
+        else
+          {
+          typename TInputImage::PointType physicalPoint;
+          image->TransformIndexToPhysicalPoint(iter.GetIndex(), physicalPoint);
+          if( mask.IsNotNull() && mask->IsInside( physicalPoint ) )
+            {
+            inMeasurementRegion = true;
+            }
+          }
+        }
+      if( inMeasurementRegion == true )
+        {
+        // add sample to histogram
+        measurement[0] = value;
+#if  ITK_VERSION_MAJOR >= 4
+        histogram->IncreaseFrequencyOfMeasurement(measurement, 1.0F);
+#else
+        histogram->IncreaseFrequency(measurement, 1.0F);
+#endif
+        }
+      ++iter;
+      }
+    }
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkResampleInPlaceImageFilter.h b/BRAINSCommonLib/itkResampleInPlaceImageFilter.h
new file mode 100644
index 00000000..d1e44310
--- /dev/null
+++ b/BRAINSCommonLib/itkResampleInPlaceImageFilter.h
@@ -0,0 +1,125 @@
+/*
+ *  itkResampleInPlaceImageFilter.h
+ *
+ *
+ *  Created by Wei Lu on 10/14/10.
+ *
+ */
+
+#ifndef __itkResampleInPlaceImageFilter_h
+#define __itkResampleInPlaceImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkVersorRigid3DTransform.h"
+
+namespace itk
+{
+
+/** \class ResampleInPlaceImageFilter
+ * \brief Resample an image in place.
+ *
+ * The current ITK resample image filter will generate a physical memory-
+ * modified version of the input image if the input transform is not identical. The
+ * abuse use of the filter can be cumbersome in a situation that the image is very
+ * large, and there are lots of transform to be superimposed for the input image, and
+ * we even don't care about those intermediate transformed images.
+ *
+ * If all the transforms are rigid, a far superior way to achieve a similar result
+ * while minimizing the accumulative resampling errors as well as eliminating the expense
+ * on accessing the physical memory of the image is to compose all the
+ * transforms before hand if it is possible, and then we only need to resample the
+ * input image with the final composed transform once.
+ *
+ * Here we present a more compact alternative – all information is stored in the header
+ * of the image and there is no need to maintain the final transform any longer. ITK
+ * image class has innate support for doing this.
+ *
+ * \param RigidTransform -- Currently must be a VersorRigid3D
+ * \param InputImage -- The image to be duplicated and modified to incorporate the
+ * rigid transform
+ * \return -- An image with the same voxels values as the input, but with differnt
+ * physical space representation affected by the rigid transform.
+ *
+ * \ingroup GeometricTransforms
+ */
+template 
+class ITK_EXPORT ResampleInPlaceImageFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs */
+  typedef ResampleInPlaceImageFilter                    Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Method for creation through the object factory */
+  itkNewMacro( Self );
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro( ResampleInPlaceImageFilter, ImageToImageFilter );
+
+  /** input/output image typedefs */
+  typedef TInputImage                         InputImageType;
+  typedef typename InputImageType::Pointer    InputImagePointer;
+  typedef typename InputImageType::RegionType InputImageRegionType;
+  typedef typename InputImageType::PixelType  InputImagePixelType;
+  typedef typename InputImageType::PointType  InputImagePointType;
+
+  typedef TOutputImage                         OutputImageType;
+  typedef typename OutputImageType::Pointer    OutputImagePointer;
+  typedef typename OutputImageType::RegionType OutputImageRegionType;
+  typedef typename OutputImageType::PixelType  OutputImagePixelType;
+
+  /** ImageDimension constants */
+  itkStaticConstMacro(InputImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputImageDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  itkConceptMacro(SameDimensionCheck,
+                  (Concept::SameDimension ) );
+  itkConceptMacro(InputConvertibleToOutputCheck,
+                  (Concept::Convertible ) );
+#endif
+
+  /** Transform typedef */
+  typedef VersorRigid3DTransform            RigidTransformType;
+  typedef typename RigidTransformType::ConstPointer RigidTransformConstPointer;
+
+  /** Set/Get rigid transform. The default is an identity transform */
+  itkSetConstObjectMacro( RigidTransform, RigidTransformType );
+  itkGetConstObjectMacro( RigidTransform, RigidTransformType );
+
+  /** Set/Get required input image. (A wrapper to this->Set/GetInput()) */
+  void SetInputImage( const InputImageType * image );
+
+  const InputImageType * GetInputImage() const;
+
+protected:
+  ResampleInPlaceImageFilter();
+  ~ResampleInPlaceImageFilter()
+  {
+  };
+
+  void GenerateData();
+
+  void PrintSelf( std::ostream& os, Indent indent ) const;
+
+private:
+  ResampleInPlaceImageFilter( const Self & ); // purposely not implemented
+  void operator=( const Self & );             // purposely not implemented
+
+  OutputImagePointer         m_OutputImage;
+  RigidTransformConstPointer m_RigidTransform;
+
+};
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkResampleInPlaceImageFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkResampleInPlaceImageFilter.hxx b/BRAINSCommonLib/itkResampleInPlaceImageFilter.hxx
new file mode 100644
index 00000000..c529fab8
--- /dev/null
+++ b/BRAINSCommonLib/itkResampleInPlaceImageFilter.hxx
@@ -0,0 +1,101 @@
+/*
+ *  itkResampleInPlaceImageFilter.hxx
+ *
+ *
+ *  Created by Wei Lu on 10/14/10.
+ *
+ */
+
+#ifndef __itkResampleInPlaceImageFilter_hxx
+#define __itkResampleInPlaceImageFilter_hxx
+
+#include "itkResampleInPlaceImageFilter.h"
+#include "itkCastImageFilter.h"
+
+namespace itk
+{
+/**
+ * Constructor
+ */
+template 
+ResampleInPlaceImageFilter
+::ResampleInPlaceImageFilter() :
+  m_OutputImage( NULL ),
+  m_RigidTransform( NULL )
+{
+  this->SetNumberOfRequiredInputs( 1 );
+}
+
+/**
+ * Set/Get input image, required
+ */
+template 
+void
+ResampleInPlaceImageFilter
+::SetInputImage( const InputImageType * image )
+{
+  this->SetInput( 0, image );
+}
+
+template 
+const typename ResampleInPlaceImageFilter::InputImageType
+* ResampleInPlaceImageFilter
+::GetInputImage() const
+  {
+  return this->GetInput( 0 );
+  }
+
+/**
+ * GenerateData Performs the in-place resampling
+ */
+template 
+void
+ResampleInPlaceImageFilter
+::GenerateData()
+{
+  if( !this->GetInput() )
+    {
+    itkExceptionMacro(<< "Input image has not been connected");
+    return;
+    }
+
+  typedef typename RigidTransformType::Pointer RigidTransformPointer;
+  RigidTransformPointer invOfRigidTransform = RigidTransformType::New();
+  invOfRigidTransform->SetIdentity();
+  const InputImagePointType centerPoint = m_RigidTransform->GetCenter();
+  invOfRigidTransform->SetCenter( centerPoint );
+  invOfRigidTransform->SetIdentity();
+  this->m_RigidTransform->GetInverse( invOfRigidTransform );    // Cache the
+                                                                // inverse
+
+    {
+    /** make a cast copied version of the input image **/
+    typedef CastImageFilter DuplicatorType;
+    typename DuplicatorType::Pointer CastFilter = DuplicatorType::New();
+    CastFilter->SetInput( this->GetInput() );
+    CastFilter->Update();
+    m_OutputImage = CastFilter->GetOutput();
+    }
+
+  // Modify the origin and direction info of the image to reflect the transform.
+  m_OutputImage->SetOrigin( invOfRigidTransform->GetMatrix()
+                            * this->GetInput()->GetOrigin() + invOfRigidTransform->GetTranslation() );
+  m_OutputImage->SetDirection( invOfRigidTransform->GetMatrix()
+                               * this->GetInput()->GetDirection() );
+
+  this->GraftOutput( m_OutputImage );
+}
+
+template 
+void
+ResampleInPlaceImageFilter::PrintSelf( std::ostream& os, Indent indent ) const
+{
+  Superclass::PrintSelf( os, indent );
+
+  os << indent << "Input transform: " << m_RigidTransform << std::endl;
+  os << indent << "Output image: " << m_OutputImage << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.h b/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.h
new file mode 100644
index 00000000..f2628add
--- /dev/null
+++ b/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.h
@@ -0,0 +1,122 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkScalarImagePortionToHistogramGenerator.h,v $
+ *  Language:  C++
+ *  Date:      $Date: 2009-08-08 14:18:12 $
+ *  Version:   $Revision: 1.2 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *  This software is distributed WITHOUT ANY WARRANTY; without even
+ *  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *  PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkScalarImagePortionToHistogramGenerator_h
+#define __itkScalarImagePortionToHistogramGenerator_h
+
+#include "itkImageToListSampleFilter.h"
+#include "itkSampleToHistogramFilter.h"
+
+#include "itkHistogram.h"
+#include "itkObject.h"
+
+namespace itk
+{
+namespace Statistics
+{
+/** \class ScalarImagePortionToHistogramGenerator
+  *
+  * \brief TODO
+  */
+template 
+class ScalarImagePortionToHistogramGenerator : public Object
+{
+public:
+  /** Standard typedefs */
+  typedef ScalarImagePortionToHistogramGenerator Self;
+  typedef Object                                 Superclass;
+  typedef SmartPointer                     Pointer;
+  typedef SmartPointer               ConstPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ScalarImagePortionToHistogramGenerator, Object);
+
+  /** standard New() method support */
+  itkNewMacro(Self);
+
+  typedef TImageType                                  ImageType;
+  typedef typename TImageType::PixelType              PixelType;
+  typedef typename NumericTraits::RealType RealPixelType;
+
+  typedef itk::Statistics::Histogram   HistogramType;
+  typedef typename HistogramType::Pointer      HistogramPointer;
+  typedef typename HistogramType::ConstPointer HistogramConstPointer;
+
+  typedef itk::Statistics::ImageToListSampleFilter ListSampleGeneratorType;
+  typedef typename ListSampleGeneratorType::Pointer                      ListSampleGeneratorPointer;
+  typedef typename ListSampleGeneratorType::ListSampleType               ListSampleType;
+
+  typedef itk::Statistics::SampleToHistogramFilter GeneratorType;
+  typedef typename GeneratorType::Pointer                                         GeneratorPointer;
+public:
+
+  /** Triggers the Computation of the histogram */
+  void Compute(void);
+
+  /** Connects the input image for which the histogram is going to be computed
+    */
+  void SetInput(const TImageType *);
+
+  /** Connects the input image for which the histogram is going to be computed
+    */
+  void SetBinaryPortionImage(const TMaskType *);
+
+  /** Return the histogram.
+    * \warning This output is only valid after the Compute() method has been
+    *    invoked
+    * \sa Compute */
+  const HistogramType * GetOutput() const;
+
+  /** Set number of histogram bins */
+  void SetNumberOfBins(unsigned int numberOfBins);
+
+  /** Set marginal scale value to be passed to the histogram generator */
+  void SetMarginalScale(double marginalScale);
+
+  /** Set the minimum value from which the bins will be computed */
+  void SetHistogramMin(RealPixelType minimumValue);
+
+  /** Set the maximum value from which the bins will be computed */
+  void SetHistogramMax(RealPixelType maximumValue);
+
+protected:
+  ScalarImagePortionToHistogramGenerator();
+  virtual ~ScalarImagePortionToHistogramGenerator()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+
+  ListSampleGeneratorPointer m_ImageToListSampleGenerator;
+
+  HistogramPointer m_Histogram;
+  GeneratorPointer m_HistogramGenerator;
+
+  ScalarImagePortionToHistogramGenerator(const Self &); // purposely not
+                                                        // implemented
+  void operator=(const Self &);                         // purposely not
+
+  // implemented
+};
+}   // end of namespace Statistics
+} // end of namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkScalarImagePortionToHistogramGenerator.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.hxx b/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.hxx
new file mode 100644
index 00000000..98997a6a
--- /dev/null
+++ b/BRAINSCommonLib/itkScalarImagePortionToHistogramGenerator.hxx
@@ -0,0 +1,128 @@
+/*=========================================================================
+ *
+ *  Program:   Insight Segmentation & Registration Toolkit
+ *  Module:    $RCSfile: itkScalarImagePortionToHistogramGenerator.hxx,v $
+ *  Language:  C++
+ *  Date:      $Date: 2009-08-17 18:29:01 $
+ *  Version:   $Revision: 1.4 $
+ *
+ *  Copyright (c) Insight Software Consortium. All rights reserved.
+ *  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+ *
+ *    This software is distributed WITHOUT ANY WARRANTY; without even
+ *    the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *    PURPOSE.  See the above copyright notices for more information.
+ *
+ *  =========================================================================*/
+#ifndef __itkScalarImagePortionToHistogramGenerator_hxx
+#define __itkScalarImagePortionToHistogramGenerator_hxx
+
+#include "itkScalarImagePortionToHistogramGenerator.h"
+
+namespace itk
+{
+namespace Statistics
+{
+template 
+ScalarImagePortionToHistogramGenerator
+::ScalarImagePortionToHistogramGenerator()
+{
+  m_ImageToListSampleGenerator = ListSampleGeneratorType::New();
+  m_HistogramGenerator = GeneratorType::New();
+  m_HistogramGenerator->SetInput( m_ImageToListSampleGenerator->GetOutput() );
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetInput(const ImageType *image)
+{
+  m_ImageToListSampleGenerator->SetInput(image);
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetBinaryPortionImage(const TMaskType *binaryImage)
+{
+  m_ImageToListSampleGenerator->SetMaskImage(binaryImage);
+  m_ImageToListSampleGenerator->SetMaskValue(NumericTraits::One);
+}
+
+template 
+const typename ScalarImagePortionToHistogramGenerator::HistogramType
+* ScalarImagePortionToHistogramGenerator
+::GetOutput() const
+  {
+  return m_HistogramGenerator->GetOutput();
+  }
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::Compute()
+{
+  m_ImageToListSampleGenerator->Update();
+  std::cout << "ListSample TotalFrequency is  " << m_ImageToListSampleGenerator->GetOutput()->GetTotalFrequency()
+            << std::endl;
+  m_HistogramGenerator->Update();
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetNumberOfBins(unsigned int numberOfBins)
+{
+  typename HistogramType::SizeType size;
+
+  size.SetSize(1);
+  size.Fill(numberOfBins);
+  m_HistogramGenerator->SetHistogramSize(size);
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetHistogramMin(RealPixelType minimumValue)
+{
+  typedef typename GeneratorType::HistogramMeasurementVectorType MeasurementVectorType;
+  MeasurementVectorType minVector(1);
+
+  minVector[0] = minimumValue;
+  m_HistogramGenerator->SetHistogramBinMinimum(minVector);
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetHistogramMax(RealPixelType maximumValue)
+{
+  typedef typename GeneratorType::HistogramMeasurementVectorType MeasurementVectorType;
+  MeasurementVectorType maxVector(1);
+
+  maxVector[0] = maximumValue;
+  m_HistogramGenerator->SetHistogramBinMaximum(maxVector);
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::SetMarginalScale(double marginalScale)
+{
+  m_HistogramGenerator->SetMarginalScale(marginalScale);
+}
+
+template 
+void
+ScalarImagePortionToHistogramGenerator
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+  os << "ImageToListSampleGenerator = " << m_ImageToListSampleGenerator << std::endl;
+  os << "HistogramGenerator = " << m_HistogramGenerator << std::endl;
+}
+
+} // end of namespace Statistics
+} // end of namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.h b/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.h
new file mode 100644
index 00000000..fe25e7ae
--- /dev/null
+++ b/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.h
@@ -0,0 +1,221 @@
+#ifndef __itkSymmetricLogDomainDemonsRegistrationFilter_h
+#define __itkSymmetricLogDomainDemonsRegistrationFilter_h
+
+#include "itkLogDomainDeformableRegistrationFilter.h"
+#include "itkESMDemonsRegistrationFunction.h"
+
+#include "itkMultiplyByConstantImageFilter.h"
+
+namespace itk
+{
+/**
+  * \class SymmetricLogDomainDemonsRegistrationFilter
+  * \brief Deformably register two images using a diffeomorphic demons algorithm
+  * and a symmetrized optimization scheme.
+  *
+  * See T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * Velocity and deformation fields are represented as images whose pixel type
+  *are
+  * some vector type with at least N elements, where N is the dimension of
+  * the fixed image. The vector type must support element access via operator
+  * []. It is assumed that the vector elements behave like floating point
+  * scalars.
+  *
+  * This class is templated over the fixed image type, moving image type
+  * and the velocity/deformation field type.
+  *
+  * The input fixed and moving images are set via methods SetFixedImage
+  * and SetMovingImage respectively. An initial velocity field maybe set via
+  * SetInitialVelocityField or SetInput. If no initial field is set,
+  * a zero field is used as the initial condition.
+  *
+  * The output velocity field can be obtained via methods GetOutput
+  * or GetVelocityField.
+  *
+  * The output deformation field can be obtained via method GetDeformationField.
+  *
+  * This class make use of the finite difference solver hierarchy. Update
+  * for each iteration is computed using a PDEDeformableRegistrationFunction.
+  *
+  * \warning This filter assumes that the fixed image type, moving image type
+  * and velocity field type all have the same number of dimensions.
+  *
+  * \sa DemonsRegistrationFilter
+  * \sa DemonsRegistrationFunction
+  * \ingroup DeformableImageRegistration MultiThreaded
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  */
+template 
+class ITK_EXPORT SymmetricLogDomainDemonsRegistrationFilter :
+  public LogDomainDeformableRegistrationFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef SymmetricLogDomainDemonsRegistrationFilter                               Self;
+  typedef LogDomainDeformableRegistrationFilter Superclass;
+  typedef SmartPointer                                                       Pointer;
+  typedef SmartPointer                                                 ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro(SymmetricLogDomainDemonsRegistrationFilter, LogDomainDeformableRegistrationFilter);
+
+  /** FixedImage image type. */
+  typedef typename Superclass::FixedImageType    FixedImageType;
+  typedef typename Superclass::FixedImagePointer FixedImagePointer;
+
+  /** MovingImage image type. */
+  typedef typename Superclass::MovingImageType    MovingImageType;
+  typedef typename Superclass::MovingImagePointer MovingImagePointer;
+
+  /** Velocity field type. */
+  typedef TField                              VelocityFieldType;
+  typedef typename VelocityFieldType::Pointer VelocityFieldPointer;
+
+  /** Deformation field type. */
+  typedef typename Superclass::DeformationFieldType    DeformationFieldType;
+  typedef typename Superclass::DeformationFieldPointer DeformationFieldPointer;
+
+  /** Types inherithed from the superclass */
+  typedef typename Superclass::OutputImageType OutputImageType;
+
+  /** FiniteDifferenceFunction type. */
+  typedef typename Superclass::FiniteDifferenceFunctionType FiniteDifferenceFunctionType;
+
+  /** Take timestep type from the FiniteDifferenceFunction. */
+  typedef typename
+  FiniteDifferenceFunctionType::TimeStepType TimeStepType;
+
+  /** DemonsRegistrationFilterFunction type. */
+  typedef ESMDemonsRegistrationFunction                          DemonsRegistrationFunctionType;
+  typedef typename DemonsRegistrationFunctionType::Pointer      DemonsRegistrationFunctionPointer;
+  typedef typename DemonsRegistrationFunctionType::GradientType GradientType;
+
+  /** Get the metric value. The metric value is the mean square difference
+    * in intensity between the fixed image and transforming moving image
+    * computed over the the overlapping region between the two images.
+    * This value is calculated for the current iteration */
+  virtual double GetMetric() const;
+
+  virtual void SetUseGradientType(GradientType gtype);
+
+  virtual GradientType GetUseGradientType() const;
+
+  /** Set/Get the threshold below which the absolute difference of
+    * intensity yields a match. When the intensities match between a
+    * moving and fixed image pixel, the update vector (for that
+    * iteration) will be the zero vector. Default is 0.001. */
+  virtual void SetIntensityDifferenceThreshold(double);
+
+  virtual double GetIntensityDifferenceThreshold() const;
+
+  /** Set/Get the maximum length in terms of pixels of
+    *  the vectors in the update buffer. */
+  virtual void SetMaximumUpdateStepLength(double);
+
+  virtual double GetMaximumUpdateStepLength() const;
+
+  /** Set/Get the number of terms used in the Baker-Campbell-Hausdorff
+    * approximation. */
+  itkSetMacro(NumberOfBCHApproximationTerms, unsigned int);
+  itkGetConstMacro(NumberOfBCHApproximationTerms, unsigned int);
+protected:
+  SymmetricLogDomainDemonsRegistrationFilter();
+  ~SymmetricLogDomainDemonsRegistrationFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Initialize the state of filter and equation before each iteration. */
+  virtual void InitializeIteration();
+
+  /** This method allocates storage in m_UpdateBuffer.  It is called from
+    * FiniteDifferenceFilter::GenerateData(). */
+  virtual void AllocateUpdateBuffer();
+
+  /** Method to allow subclasses to get direct access to the backward update
+    * buffer */
+  virtual VelocityFieldType * GetBackwardUpdateBuffer()
+  {
+    return m_BackwardUpdateBuffer;
+  }
+
+  /** This method allocates storage in m_BackwardUpdateBuffer. */
+  virtual void AllocateBackwardUpdateBuffer();
+
+  /** Utility to smooth the BackwardUpdateBuffer using a Gaussian operator.
+    * The amount of smoothing is specified by the UpdateFieldStandardDeviations.
+    */
+  virtual void SmoothBackwardUpdateField();
+
+  typedef typename VelocityFieldType::RegionType ThreadRegionType;
+  /** Does the actual work of calculating change over a region supplied by
+    * the multithreading mechanism. */
+  virtual TimeStepType ThreadedCalculateChange(const ThreadRegionType & regionToProcess, int threadId);
+
+  /** Apply update. */
+  virtual void ApplyUpdate(TimeStepType dt);
+
+  /** This method returns a pointer to a FiniteDifferenceFunction object that
+    * will be used by the filter to calculate updates at image pixels.
+    * \returns A FiniteDifferenceObject pointer. */
+  itkGetConstReferenceObjectMacro(BackwardDifferenceFunction,
+                                  FiniteDifferenceFunctionType);
+
+  /** This method sets the pointer to a FiniteDifferenceFunction object that
+    * will be used by the filter to calculate updates at image pixels.
+    * \returns A FiniteDifferenceObject pointer. */
+  itkSetObjectMacro(BackwardDifferenceFunction, FiniteDifferenceFunctionType);
+private:
+  // purposefully not implemented
+  SymmetricLogDomainDemonsRegistrationFilter(const Self &);
+  void operator=(const Self &);
+
+  // implemented
+
+  /** Downcast the DifferenceFunction using a dynamic_cast to ensure that it is
+    * of the correct type.
+    * this method will throw an exception if the function is not of the expected
+    *type. */
+  DemonsRegistrationFunctionType *  GetForwardRegistrationFunctionType();
+
+  const DemonsRegistrationFunctionType *  GetForwardRegistrationFunctionType() const;
+
+  DemonsRegistrationFunctionType *  GetBackwardRegistrationFunctionType();
+
+  const DemonsRegistrationFunctionType *  GetBackwardRegistrationFunctionType() const;
+
+  /** Exp and composition typedefs */
+  typedef MultiplyByConstantImageFilter<
+    VelocityFieldType,
+    TimeStepType, VelocityFieldType>                   MultiplyByConstantType;
+
+  typedef AddImageFilter<
+    VelocityFieldType, VelocityFieldType>                AdderType;
+
+  typedef typename MultiplyByConstantType::Pointer MultiplyByConstantPointer;
+  typedef typename AdderType::Pointer              AdderPointer;
+
+  typename FiniteDifferenceFunctionType::Pointer m_BackwardDifferenceFunction;
+
+  MultiplyByConstantPointer m_Multiplier;
+  AdderPointer              m_Adder;
+  unsigned int              m_NumberOfBCHApproximationTerms;
+
+  /** The buffer that holds the updates for an iteration of the algorithm. */
+  VelocityFieldPointer m_BackwardUpdateBuffer;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkSymmetricLogDomainDemonsRegistrationFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.hxx b/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.hxx
new file mode 100644
index 00000000..16c2e2fc
--- /dev/null
+++ b/BRAINSCommonLib/itkSymmetricLogDomainDemonsRegistrationFilter.hxx
@@ -0,0 +1,561 @@
+#ifndef __itkSymmetricLogDomainDemonsRegistrationFilter_hxx
+#define __itkSymmetricLogDomainDemonsRegistrationFilter_hxx
+
+#include "itkSymmetricLogDomainDemonsRegistrationFilter.h"
+
+#include "itkOppositeImageFilter.h"
+#include "itkSubtractImageFilter.h"
+#include "itkVelocityFieldBCHCompositionFilter.h"
+
+namespace itk
+{
+// Default constructor
+template 
+SymmetricLogDomainDemonsRegistrationFilter
+::SymmetricLogDomainDemonsRegistrationFilter()
+{
+  DemonsRegistrationFunctionPointer drfpf = DemonsRegistrationFunctionType::New();
+
+  this->SetDifferenceFunction( static_cast(
+                                 drfpf.GetPointer() ) );
+
+  DemonsRegistrationFunctionPointer drfpb = DemonsRegistrationFunctionType::New();
+  this->SetBackwardDifferenceFunction( static_cast(
+                                         drfpb.GetPointer() ) );
+
+  m_Multiplier = MultiplyByConstantType::New();
+  m_Multiplier->InPlaceOn();
+
+  m_Adder = AdderType::New();
+  m_Adder->InPlaceOn();
+
+  // Set number of terms in the BCH approximation to default value
+  m_NumberOfBCHApproximationTerms = 2;
+
+  m_BackwardUpdateBuffer = 0;
+}
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+typename SymmetricLogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* SymmetricLogDomainDemonsRegistrationFilter
+::GetForwardRegistrationFunctionType()
+  {
+  DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetDifferenceFunction().GetPointer() );
+
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+const typename SymmetricLogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* SymmetricLogDomainDemonsRegistrationFilter
+::GetForwardRegistrationFunctionType() const
+  {
+  const DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetDifferenceFunction().GetPointer() );
+
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+typename SymmetricLogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* SymmetricLogDomainDemonsRegistrationFilter
+::GetBackwardRegistrationFunctionType()
+  {
+  DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetBackwardDifferenceFunction().GetPointer() );
+
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Checks whether the DifferenceFunction is of type DemonsRegistrationFunction.
+template 
+const typename SymmetricLogDomainDemonsRegistrationFilter
+::DemonsRegistrationFunctionType
+* SymmetricLogDomainDemonsRegistrationFilter
+::GetBackwardRegistrationFunctionType() const
+  {
+  const DemonsRegistrationFunctionType *drfp =
+    dynamic_cast( this->GetBackwardDifferenceFunction().GetPointer() );
+
+  if( !drfp )
+    {
+    itkExceptionMacro(<< "Could not cast difference function to SymmetricDemonsRegistrationFunction");
+    }
+
+  return drfp;
+  }
+
+// Set the function state values before each iteration
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::InitializeIteration()
+{
+  // update variables in the equation object
+  DemonsRegistrationFunctionType *f = this->GetForwardRegistrationFunctionType();
+
+  f->SetDeformationField( this->GetDeformationField() );
+
+  DemonsRegistrationFunctionType *b = this->GetBackwardRegistrationFunctionType();
+  b->SetFixedImage( this->GetMovingImage() );
+  b->SetMovingImage( this->GetFixedImage() );
+  b->SetDeformationField( this->GetInverseDeformationField() );
+  b->InitializeIteration();
+
+  // call the superclass  implementation ( initializes f )
+  Superclass::InitializeIteration();
+}
+
+// Get the metric value from the difference function
+template 
+double
+SymmetricLogDomainDemonsRegistrationFilter
+::GetMetric() const
+{
+  const DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  const DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  return 0.5 * ( drfpf->GetMetric() + drfpb->GetMetric() );
+}
+
+// Get Intensity Difference Threshold
+template 
+double
+SymmetricLogDomainDemonsRegistrationFilter
+::GetIntensityDifferenceThreshold() const
+{
+  const DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  const DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  if( drfpf->GetIntensityDifferenceThreshold() != drfpb->GetIntensityDifferenceThreshold() )
+    {
+    itkExceptionMacro(<< "Forward and backward FiniteDifferenceFunctions not in sync");
+    }
+  return drfpf->GetIntensityDifferenceThreshold();
+}
+
+// Set Intensity Difference Threshold
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::SetIntensityDifferenceThreshold(double threshold)
+{
+  DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  drfpf->SetIntensityDifferenceThreshold(threshold);
+  drfpb->SetIntensityDifferenceThreshold(threshold);
+}
+
+// Set Maximum Update Step Length
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::SetMaximumUpdateStepLength(double step)
+{
+  DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  drfpf->SetMaximumUpdateStepLength(step);
+  drfpb->SetMaximumUpdateStepLength(step);
+}
+
+// Get Maximum Update Step Length
+template 
+double
+SymmetricLogDomainDemonsRegistrationFilter
+::GetMaximumUpdateStepLength() const
+{
+  const DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  const DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  if( drfpf->GetMaximumUpdateStepLength() != drfpb->GetMaximumUpdateStepLength() )
+    {
+    itkExceptionMacro(<< "Forward and backward FiniteDifferenceFunctions not in sync");
+    }
+  return drfpf->GetMaximumUpdateStepLength();
+}
+
+// Get gradient type
+template 
+typename SymmetricLogDomainDemonsRegistrationFilter::GradientType
+SymmetricLogDomainDemonsRegistrationFilter
+::GetUseGradientType() const
+{
+  const DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  const DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  if( drfpf->GetUseGradientType() != drfpb->GetUseGradientType() )
+    {
+    itkExceptionMacro(<< "Forward and backward FiniteDifferenceFunctions not in sync");
+    }
+  return drfpf->GetUseGradientType();
+}
+
+// Set gradient type
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::SetUseGradientType(GradientType gtype)
+{
+  DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  drfpf->SetUseGradientType(gtype);
+  drfpb->SetUseGradientType(gtype);
+}
+
+// Allocate storage in m_UpdateBuffer
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::AllocateUpdateBuffer()
+{
+  Superclass::AllocateUpdateBuffer();
+
+  this->AllocateBackwardUpdateBuffer();
+}
+
+// Allocates storage in m_BackwardUpdateBuffer
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::AllocateBackwardUpdateBuffer()
+{
+  if( m_NumberOfBCHApproximationTerms < 3 )
+    {
+    m_BackwardUpdateBuffer = 0;
+    return;
+    }
+
+  // The backward update buffer looks just like the output.
+  VelocityFieldPointer output = this->GetOutput();
+
+  if( !m_BackwardUpdateBuffer )
+    {
+    m_BackwardUpdateBuffer = VelocityFieldType::New();
+    }
+  m_BackwardUpdateBuffer->SetOrigin( output->GetOrigin() );
+  m_BackwardUpdateBuffer->SetSpacing( output->GetSpacing() );
+  m_BackwardUpdateBuffer->SetDirection( output->GetDirection() );
+  m_BackwardUpdateBuffer->SetLargestPossibleRegion( output->GetLargestPossibleRegion() );
+  m_BackwardUpdateBuffer->SetRequestedRegion( output->GetRequestedRegion() );
+  m_BackwardUpdateBuffer->SetBufferedRegion( output->GetBufferedRegion() );
+  m_BackwardUpdateBuffer->Allocate();
+}
+
+// Smooth the backward update field using a separable Gaussian kernel
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::SmoothBackwardUpdateField()
+{
+  // The update buffer will be overwritten with new data.
+  this->SmoothGivenField( this->GetBackwardUpdateBuffer(), this->GetUpdateFieldStandardDeviations() );
+}
+
+template 
+typename
+SymmetricLogDomainDemonsRegistrationFilter::TimeStepType
+SymmetricLogDomainDemonsRegistrationFilter
+::ThreadedCalculateChange(const ThreadRegionType & regionToProcess, int)
+{
+  typedef typename VelocityFieldType::RegionType     RegionType;
+  typedef typename VelocityFieldType::SizeType       SizeType;
+  typedef typename VelocityFieldType::SizeValueType  SizeValueType;
+  typedef typename VelocityFieldType::IndexType      IndexType;
+  typedef typename VelocityFieldType::IndexValueType IndexValueType;
+  typedef typename
+  FiniteDifferenceFunctionType::NeighborhoodType NeighborhoodIteratorType;
+  typedef ImageRegionIterator UpdateIteratorType;
+
+  VelocityFieldPointer output = this->GetOutput();
+
+  // Get the FiniteDifferenceFunction to use in calculations.
+  const typename FiniteDifferenceFunctionType::Pointer dff =
+    this->GetDifferenceFunction();
+  const typename FiniteDifferenceFunctionType::Pointer dfb =
+    this->GetBackwardDifferenceFunction();
+
+  if( dff->GetRadius() != dfb->GetRadius() )
+    {
+    itkExceptionMacro(<< "Forward and backward FiniteDifferenceFunctions not in sync");
+    }
+
+  const SizeType radius = dff->GetRadius();
+
+  // Break the input into a series of regions.  The first region is free
+  // of boundary conditions, the rest with boundary conditions.  We operate
+  // on the output region because input has been copied to output.
+  typedef NeighborhoodAlgorithm::ImageBoundaryFacesCalculator
+  FaceCalculatorType;
+
+  typedef typename FaceCalculatorType::FaceListType FaceListType;
+
+  FaceCalculatorType faceCalculator;
+
+  FaceListType faceList = faceCalculator(output, regionToProcess, radius);
+  typename FaceListType::iterator fIt = faceList.begin();
+
+  // Ask the function object for a pointer to a data structure it
+  // will use to manage any global values it needs.  We'll pass this
+  // back to the function object at each calculation and then
+  // again so that the function object can use it to determine a
+  // time step for this iteration.
+  void *globalDataf = dff->GetGlobalDataPointer();
+  void *globalDatab = dfb->GetGlobalDataPointer();
+
+  // Process the non-boundary region.
+  NeighborhoodIteratorType nD(radius, output, *fIt);
+
+  if( m_NumberOfBCHApproximationTerms == 2 )
+    {
+    UpdateIteratorType nU(this->GetUpdateBuffer(),  *fIt);
+
+    while( !nD.IsAtEnd() )
+      {
+      nU.Value() = ( dff->ComputeUpdate(nD, globalDataf) - dfb->ComputeUpdate(nD, globalDatab) ) * 0.5;
+      ++nD;
+      ++nU;
+      }
+
+    // Process each of the boundary faces.
+    NeighborhoodIteratorType bD;
+    UpdateIteratorType       bU;
+    for( ++fIt; fIt != faceList.end(); ++fIt )
+      {
+      bD = NeighborhoodIteratorType(radius, output, *fIt);
+      bU = UpdateIteratorType(this->GetUpdateBuffer(), *fIt);
+      while( !bD.IsAtEnd() )
+        {
+        bU.Value() = ( dff->ComputeUpdate(bD, globalDataf) - dfb->ComputeUpdate(bD, globalDatab) ) * 0.5;
+        ++bD;
+        ++bU;
+        }
+      }
+    }
+  else
+    {
+    UpdateIteratorType nUF(this->GetUpdateBuffer(),  *fIt);
+
+    UpdateIteratorType nUB(this->GetBackwardUpdateBuffer(),  *fIt);
+
+    while( !nD.IsAtEnd() )
+      {
+      nUF.Value() = dff->ComputeUpdate(nD, globalDataf);
+      nUB.Value() = dfb->ComputeUpdate(nD, globalDatab);
+      ++nD;
+      ++nUF;
+      ++nUB;
+      }
+
+    // Process each of the boundary faces.
+    NeighborhoodIteratorType bD;
+    UpdateIteratorType       bUF;
+    UpdateIteratorType       bUB;
+    for( ++fIt; fIt != faceList.end(); ++fIt )
+      {
+      bD = NeighborhoodIteratorType(radius, output, *fIt);
+      bUF = UpdateIteratorType(this->GetUpdateBuffer(), *fIt);
+      bUB = UpdateIteratorType(this->GetBackwardUpdateBuffer(), *fIt);
+      while( !bD.IsAtEnd() )
+        {
+        bUF.Value() = dff->ComputeUpdate(bD, globalDataf);
+        bUB.Value() = dfb->ComputeUpdate(bD, globalDatab);
+        ++bD;
+        ++bUF;
+        ++bUB;
+        }
+      }
+    }
+
+  // Ask the finite difference function to compute the time step for
+  // this iteration.  We give it the global data pointer to use, then
+  // ask it to free the global data memory.
+  TimeStepType timeStep = 0.5 * ( dff->ComputeGlobalTimeStep(globalDataf)
+                                  + dfb->ComputeGlobalTimeStep(globalDatab) );
+  dff->ReleaseGlobalDataPointer(globalDataf);
+  dfb->ReleaseGlobalDataPointer(globalDatab);
+
+  return timeStep;
+}
+
+// Get the metric value from the difference function
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::ApplyUpdate(TimeStepType dt)
+{
+  const DemonsRegistrationFunctionType *drfpf = this->GetForwardRegistrationFunctionType();
+  const DemonsRegistrationFunctionType *drfpb = this->GetBackwardRegistrationFunctionType();
+
+  this->SetRMSChange( 0.5 * ( drfpf->GetRMSChange() + drfpb->GetRMSChange() ) );
+
+  if( this->m_NumberOfBCHApproximationTerms < 3 )
+    {
+    // If we smooth the update buffer before applying it, then the are
+    // approximating a viscuous problem as opposed to an elastic problem
+    if( this->GetSmoothUpdateField() )
+      {
+      this->SmoothUpdateField();
+      }
+
+    // Use time step if necessary. In many cases
+    // the time step is one so this will be skipped
+    if( fabs(dt - 1.0) > 1.0e-4 )
+      {
+      itkDebugMacro("Using timestep: " << dt);
+      m_Multiplier->SetConstant(dt);
+      m_Multiplier->SetInput( this->GetUpdateBuffer() );
+      m_Multiplier->GraftOutput( this->GetUpdateBuffer() );
+      // in place update
+      m_Multiplier->Update();
+      // graft output back to this->GetUpdateBuffer()
+      this->GetUpdateBuffer()->Graft( m_Multiplier->GetOutput() );
+      }
+
+    // Apply update
+    m_Adder->SetInput( 0, this->GetOutput() );
+    m_Adder->SetInput( 1, this->GetUpdateBuffer() );
+    m_Adder->GraftOutput( this->GetOutput() );
+    m_Adder->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
+
+    // Triggers in place update
+    m_Adder->Update();
+
+    // Region passing stuff
+    this->GraftOutput( m_Adder->GetOutput() );
+    }
+  else
+    {
+    // If we smooth the update buffer before applying it, then the are
+    // approximating a viscuous problem as opposed to an elastic problem
+    if( this->GetSmoothUpdateField() )
+      {
+      this->SmoothUpdateField();
+      this->SmoothBackwardUpdateField();
+      }
+
+    // Use time step if necessary. In many cases
+    // the time step is one so this will be skipped
+    if( fabs(dt - 1.0) > 1.0e-4 )
+      {
+      itkDebugMacro("Using timestep: " << dt);
+      m_Multiplier->SetConstant(dt);
+
+      m_Multiplier->SetInput( this->GetUpdateBuffer() );
+      m_Multiplier->GraftOutput( this->GetUpdateBuffer() );
+      // in place update
+      m_Multiplier->Update();
+      // graft output back to this->GetUpdateBuffer()
+      this->GetUpdateBuffer()->Graft( m_Multiplier->GetOutput() );
+
+      m_Multiplier->SetInput( this->GetBackwardUpdateBuffer() );
+      m_Multiplier->GraftOutput( this->GetBackwardUpdateBuffer() );
+      // in place update
+      m_Multiplier->Update();
+      // graft output back to this->GetUpdateBuffer()
+      this->GetBackwardUpdateBuffer()->Graft( m_Multiplier->GetOutput() );
+      }
+
+    // Apply update (declare the filters here as efficiency is not critical
+    // with "high" order BCH approximations)
+    typedef VelocityFieldBCHCompositionFilter<
+      VelocityFieldType, VelocityFieldType>   BCHFilterType;
+
+    typename BCHFilterType::Pointer bchfilter = BCHFilterType::New();
+    bchfilter->SetNumberOfApproximationTerms(this->m_NumberOfBCHApproximationTerms);
+
+    // First get Z( v, K_fluid * u_forward )
+    bchfilter->SetInput( 0, this->GetOutput() );
+    bchfilter->SetInput( 1, this->GetUpdateBuffer() );
+
+    bchfilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
+    bchfilter->Update();
+    VelocityFieldPointer Zf = bchfilter->GetOutput();
+    // Zf->DisconnectPipeline();
+
+    // Now get Z( -v, K_fluid * u_backward )
+    typedef OppositeImageFilter<
+      VelocityFieldType, VelocityFieldType>  OppositeFilterType;
+
+    typename OppositeFilterType::Pointer oppositefilter = OppositeFilterType::New();
+    oppositefilter->SetInput( this->GetOutput() );
+    oppositefilter->InPlaceOn();
+
+    bchfilter->SetInput( 0, oppositefilter->GetOutput() );
+    bchfilter->SetInput( 1, this->GetBackwardUpdateBuffer() );
+
+    bchfilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
+    bchfilter->Update();
+    VelocityFieldPointer Zb = bchfilter->GetOutput();
+    // Zb->DisconnectPipeline();
+
+    // Finally get 0.5*( Z( v, K_fluid * u_forward ) - Z( -v, K_fluid *
+    // u_backward ) )
+    typedef SubtractImageFilter<
+      VelocityFieldType, VelocityFieldType, VelocityFieldType>  SubtracterType;
+
+    typename SubtracterType::Pointer subtracter = SubtracterType::New();
+    subtracter->SetInput(0, Zf);
+    subtracter->SetInput(1, Zb);
+
+    subtracter->GraftOutput( this->GetOutput() );
+
+    m_Multiplier->SetConstant(0.5);
+    m_Multiplier->SetInput( subtracter->GetOutput() );
+    m_Multiplier->GraftOutput( this->GetOutput() );
+
+    // Triggers in place update
+    m_Multiplier->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
+    m_Multiplier->Update();
+
+    // Region passing stuff
+    this->GraftOutput( m_Multiplier->GetOutput() );
+    }
+
+  // Smooth the velocity field
+  if( this->GetSmoothVelocityField() )
+    {
+    this->SmoothVelocityField();
+    }
+}
+
+template 
+void
+SymmetricLogDomainDemonsRegistrationFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "Intensity difference threshold: " << this->GetIntensityDifferenceThreshold() << std::endl;
+  os << indent << "Multiplier: " << m_Multiplier << std::endl;
+  os << indent << "Adder: " << m_Adder << std::endl;
+  os << indent << "NumberOfBCHApproximationTerms: " << m_NumberOfBCHApproximationTerms << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkTestMain.h b/BRAINSCommonLib/itkTestMain.h
new file mode 100644
index 00000000..f43ff759
--- /dev/null
+++ b/BRAINSCommonLib/itkTestMain.h
@@ -0,0 +1,516 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkTestMain.h,v $
+  Language:  C++
+  Date:      $Date: 2009-03-03 15:09:43 $
+  Version:   $Revision: 1.33 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+  Portions of this code are covered under the VTK copyright.
+  See VTKCopyright.txt or http://www.kitware.com/VTKCopyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkTestMain_h
+#define __itkTestMain_h
+
+// This file is used to create TestDriver executables
+// These executables are able to register a function pointer to a string name
+// in a lookup table.   By including this file, it creates a main function
+// that calls RegisterTests() then looks up the function pointer for the test
+// specified on the command line.
+#include "itkWin32Header.h"
+#include 
+#include 
+#include 
+#include 
+#include "itkNumericTraits.h"
+#include "itkMultiThreader.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkSubtractImageFilter.h"
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkExtractImageFilter.h"
+#include "LOCAL_itkDifferenceImageFilter.h"
+#include "itkImageRegion.h"
+#include "itksys/SystemTools.hxx"
+#include 
+
+#define ITK_TEST_DIMENSION_MAX 6
+
+typedef int (*MainFuncPointer)(int, char * [] );
+std::map StringToTestFunctionMap;
+
+#define REGISTER_TEST(test) \
+  extern int test(int, char * [] ); \
+  StringToTestFunctionMap[#test] = test
+
+int RegressionTestImage(const char *testImageFilename, const char *baselineImageFilename, int reportErrors,
+                        double intensityTolerance = 2.0, unsigned int numberOfPixelsTolerance = 0,
+                        unsigned int radiusTolerance = 0);
+
+std::map RegressionTestBaselines(char *);
+
+void RegisterTests();
+
+void PrintAvailableTests()
+{
+  std::cout << "Available tests:\n";
+  std::map::iterator j = StringToTestFunctionMap.begin();
+  int                                              i = 0;
+  while( j != StringToTestFunctionMap.end() )
+    {
+    std::cout << i << ". " << j->first << "\n";
+    ++i;
+    ++j;
+    }
+}
+
+static void sigfpe_handl(int sig)
+{
+  printf("Argggh..Division by zero ! (or other fpe): SIGNAL=%d\n", sig);
+  // ..some more
+  exit(-1);
+}
+
+// void sigint_handl(int sig)
+// {
+//     printf("Program is exiting..: SIGNAL=%d\n",sig);
+//     exit(0);
+// }
+
+int main(int ac, char* av[] )
+{
+  std::signal(SIGFPE, sigfpe_handl);
+  double       intensityTolerance  = 2.0;
+  unsigned int numberOfPixelsTolerance = 0;
+  unsigned int radiusTolerance = 0;
+
+  typedef std::pair ComparePairType;
+  std::vector compareList;
+
+  RegisterTests();
+  std::string testToRun;
+  if( ac < 2 )
+    {
+    PrintAvailableTests();
+    std::cout << "To run a test, enter the test number: ";
+    int testNum = 0;
+    std::cin >> testNum;
+    std::map::iterator j = StringToTestFunctionMap.begin();
+    int                                              i = 0;
+    while( j != StringToTestFunctionMap.end() && i < testNum )
+      {
+      ++i;
+      ++j;
+      }
+
+    if( j == StringToTestFunctionMap.end() )
+      {
+      std::cerr << testNum << " is an invalid test number\n";
+      return -1;
+      }
+    testToRun = j->first;
+    }
+  else
+    {
+    while( ac > 0 && testToRun.empty() )
+      {
+      if( strcmp(av[1], "--with-threads") == 0 )
+        {
+        int numThreads = atoi(av[2]);
+        itk::MultiThreader::SetGlobalDefaultNumberOfThreads(numThreads);
+        av += 2;
+        ac -= 2;
+        }
+      else if( strcmp(av[1], "--without-threads") == 0 )
+        {
+        itk::MultiThreader::SetGlobalDefaultNumberOfThreads(1);
+        av += 1;
+        ac -= 1;
+        }
+      else if( ac > 3 && strcmp(av[1], "--compare") == 0 )
+        {
+        compareList.push_back( ComparePairType( av[2], av[3] ) );
+        av += 3;
+        ac -= 3;
+        }
+      else if( ac > 2 && strcmp(av[1], "--compareNumberOfPixelsTolerance") == 0 )
+        {
+        numberOfPixelsTolerance = atoi( av[2] );
+        av += 2;
+        ac -= 2;
+        }
+      else if( ac > 2 && strcmp(av[1], "--compareRadiusTolerance") == 0 )
+        {
+        radiusTolerance = atoi( av[2] );
+        av += 2;
+        ac -= 2;
+        }
+      else if( ac > 2 && strcmp(av[1], "--compareIntensityTolerance") == 0 )
+        {
+        intensityTolerance = atof( av[2] );
+        av += 2;
+        ac -= 2;
+        }
+      else
+        {
+        testToRun = av[1];
+        }
+      }
+    }
+  std::map::iterator j = StringToTestFunctionMap.find(testToRun);
+  if( j != StringToTestFunctionMap.end() )
+    {
+    MainFuncPointer f = j->second;
+    int             result;
+    try
+      {
+      // Invoke the test's "main" function.
+      result = (*f)(ac - 1, av + 1);
+      // Make a list of possible baselines
+      for( int i = 0; i < static_cast(compareList.size() ); ++i )
+        {
+        char *                               baselineFilename = compareList[i].first;
+        char *                               testFilename = compareList[i].second;
+        std::map           baselines = RegressionTestBaselines(baselineFilename);
+        std::map::iterator baseline = baselines.begin();
+        std::string                          bestBaseline;
+        int                                  bestBaselineStatus = itk::NumericTraits::max();
+        while( baseline != baselines.end() )
+          {
+          baseline->second = RegressionTestImage(testFilename,
+                                                 (baseline->first).c_str(),
+                                                 0,
+                                                 intensityTolerance,
+                                                 numberOfPixelsTolerance,
+                                                 radiusTolerance );
+          if( baseline->second < bestBaselineStatus )
+            {
+            bestBaseline = baseline->first;
+            bestBaselineStatus = baseline->second;
+            }
+          if( baseline->second == 0 )
+            {
+            break;
+            }
+          ++baseline;
+          }
+
+        // if the best we can do still has errors, generate the error images
+        if( bestBaselineStatus )
+          {
+          RegressionTestImage(testFilename,
+                              bestBaseline.c_str(),
+                              1,
+                              intensityTolerance,
+                              numberOfPixelsTolerance,
+                              radiusTolerance );
+          }
+
+        // output the matching baseline
+        std::cout << "";
+        std::cout << itksys::SystemTools::GetFilenameName(bestBaseline);
+        std::cout << "" << std::endl;
+
+        result += bestBaselineStatus;
+        }
+      }
+    catch( const itk::ExceptionObject& e )
+      {
+      std::cerr << "ITK test driver caught an ITK exception:\n";
+      e.Print(std::cerr);
+      result = -1;
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "ITK test driver caught an exception:\n";
+      std::cerr << e.what() << "\n";
+      result = -1;
+      }
+    catch( ... )
+      {
+      std::cerr << "ITK test driver caught an unknown exception!!!\n";
+      result = -1;
+      }
+    return result;
+    }
+  PrintAvailableTests();
+  std::cerr << "Failed: " << testToRun << ": No test registered with name " << testToRun << "\n";
+  return -1;
+}
+
+// Regression Testing Code
+
+int RegressionTestImage(const char *testImageFilename,
+                        const char *baselineImageFilename,
+                        int reportErrors,
+                        double intensityTolerance,
+                        unsigned int numberOfPixelsTolerance,
+                        unsigned int radiusTolerance )
+{
+  // Use the factory mechanism to read the test and baseline files and convert
+  // them to double
+  typedef itk::Image        ImageType;
+  typedef itk::Image OutputType;
+  typedef itk::Image                      DiffOutputType;
+  typedef itk::ImageFileReader                   ReaderType;
+
+  // Read the baseline file
+  ReaderType::Pointer baselineReader = ReaderType::New();
+  baselineReader->SetFileName(baselineImageFilename);
+  try
+    {
+    baselineReader->UpdateLargestPossibleRegion();
+    }
+  catch( itk::ExceptionObject& e )
+    {
+    std::cerr << "Exception detected while reading " << baselineImageFilename << " : "  << e.GetDescription();
+    return 1000;
+    }
+
+  // Read the file generated by the test
+  ReaderType::Pointer testReader = ReaderType::New();
+  testReader->SetFileName(testImageFilename);
+  try
+    {
+    testReader->UpdateLargestPossibleRegion();
+    }
+  catch( itk::ExceptionObject& e )
+    {
+    std::cerr << "Exception detected while reading " << testImageFilename << " : "  << e.GetDescription() << std::endl;
+    return 1000;
+    }
+
+  // The sizes of the baseline and test image must match
+  ImageType::SizeType baselineSize;
+  baselineSize = baselineReader->GetOutput()->GetLargestPossibleRegion().GetSize();
+  ImageType::SizeType testSize;
+  testSize = testReader->GetOutput()->GetLargestPossibleRegion().GetSize();
+
+  if( baselineSize != testSize )
+    {
+    std::cerr << "The size of the Baseline image and Test image do not match!" << std::endl;
+    std::cerr << "Baseline image: " << baselineImageFilename
+              << " has size " << baselineSize << std::endl;
+    std::cerr << "Test image:     " << testImageFilename
+              << " has size " << testSize << std::endl;
+    return 1;
+    }
+
+  // Now compare the two images
+  typedef itk::LOCAL_DifferenceImageFilter DiffType;
+  DiffType::Pointer diff = DiffType::New();
+  diff->SetValidInput(baselineReader->GetOutput() );
+  diff->SetTestInput(testReader->GetOutput() );
+  diff->SetDifferenceThreshold( intensityTolerance );
+  diff->SetToleranceRadius( radiusTolerance );
+  diff->UpdateLargestPossibleRegion();
+
+  unsigned long status = 0;
+  status = diff->GetNumberOfPixelsWithDifferences();
+
+  // if there are discrepencies, create an diff image
+  if( (status > numberOfPixelsTolerance) && reportErrors )
+    {
+    typedef itk::RescaleIntensityImageFilter RescaleType;
+    typedef itk::ExtractImageFilter     ExtractType;
+    typedef itk::ImageFileWriter                    WriterType;
+    typedef itk::ImageRegion                RegionType;
+    OutputType::SizeType size; size.Fill(0);
+
+    RescaleType::Pointer rescale = RescaleType::New();
+    rescale->SetOutputMinimum(itk::NumericTraits::NonpositiveMin() );
+    rescale->SetOutputMaximum(itk::NumericTraits::max() );
+    rescale->SetInput(diff->GetOutput() );
+    rescale->UpdateLargestPossibleRegion();
+    size = rescale->GetOutput()->GetLargestPossibleRegion().GetSize();
+
+    // Get the center slice of the image,  In 3D, the first slice
+    // is often a black slice with little debugging information.
+    OutputType::IndexType index; index.Fill(0);
+    for( unsigned int i = 2; i < ITK_TEST_DIMENSION_MAX; ++i )
+      {
+      index[i] = size[i] / 2; // NOTE: Integer Divide used to get approximately
+                              // the center slice
+      size[i] = 0;
+      }
+
+    RegionType region;
+    region.SetIndex(index);
+
+    region.SetSize(size);
+
+    ExtractType::Pointer extract = ExtractType::New();
+    extract->SetInput(rescale->GetOutput() );
+    extract->SetExtractionRegion(region);
+    extract->SetDirectionCollapseToIdentity();
+
+    WriterType::Pointer writer = WriterType::New();
+    writer->SetInput(extract->GetOutput() );
+
+    std::cout << "";
+    std::cout << status;
+    std::cout <<  "" << std::endl;
+
+    std::ostringstream diffName;
+    diffName << testImageFilename << ".diff.png";
+    try
+      {
+      rescale->SetInput(diff->GetOutput() );
+      rescale->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during rescale of " << diffName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during rescale of " << diffName.str() << std::endl;
+      }
+    writer->SetFileName(diffName.str().c_str() );
+    try
+      {
+      writer->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during write of " << diffName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during write of " << diffName.str() << std::endl;
+      }
+
+    std::cout << "";
+    std::cout << diffName.str();
+    std::cout << "" << std::endl;
+
+    std::ostringstream baseName;
+    baseName << testImageFilename << ".base.png";
+    try
+      {
+      rescale->SetInput(baselineReader->GetOutput() );
+      rescale->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during rescale of " << baseName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during rescale of " << baseName.str() << std::endl;
+      }
+    try
+      {
+      writer->SetFileName(baseName.str().c_str() );
+      writer->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during write of " << baseName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during write of " << baseName.str() << std::endl;
+      }
+
+    std::cout << "";
+    std::cout << baseName.str();
+    std::cout << "" << std::endl;
+
+    std::ostringstream testName;
+    testName << testImageFilename << ".test.png";
+    try
+      {
+      rescale->SetInput(testReader->GetOutput() );
+      rescale->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during rescale of " << testName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during rescale of " << testName.str() << std::endl;
+      }
+    try
+      {
+      writer->SetFileName(testName.str().c_str() );
+      writer->Update();
+      }
+    catch( const std::exception& e )
+      {
+      std::cerr << "Error during write of " << testName.str() << std::endl;
+      std::cerr << e.what() << "\n";
+      }
+    catch( ... )
+      {
+      std::cerr << "Error during write of " << testName.str() << std::endl;
+      }
+
+    std::cout << "";
+    std::cout << testName.str();
+    std::cout << "" << std::endl;
+
+    }
+  return (status > numberOfPixelsTolerance) ? 1 : 0;
+}
+
+//
+// Generate all of the possible baselines
+// The possible baselines are generated fromn the baselineFilename using the
+// following algorithm:
+// 1) strip the suffix
+// 2) append a digit .x
+// 3) append the original suffix.
+// It the file exists, increment x and continue
+//
+std::map RegressionTestBaselines(char *baselineFilename)
+{
+  std::map baselines;
+  baselines[std::string(baselineFilename)] = 0;
+
+  std::string originalBaseline(baselineFilename);
+
+  int                    x = 0;
+  std::string::size_type suffixPos = originalBaseline.rfind(".");
+  std::string            suffix;
+  if( suffixPos != std::string::npos )
+    {
+    suffix = originalBaseline.substr(suffixPos, originalBaseline.length() );
+    originalBaseline.erase(suffixPos, originalBaseline.length() );
+    }
+  while( ++x )
+    {
+    std::ostringstream filename;
+    filename << originalBaseline << "." << x << suffix;
+    std::ifstream filestream(filename.str().c_str() );
+    if( !filestream )
+      {
+      break;
+      }
+    baselines[filename.str()] = 0;
+    filestream.close();
+    }
+
+  return baselines;
+}
+
+// Needed for explicit instantiation
+#include "LOCAL_itkDifferenceImageFilter.hxx"
+
+#endif
diff --git a/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.h b/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.h
new file mode 100644
index 00000000..2bc9c3f0
--- /dev/null
+++ b/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.h
@@ -0,0 +1,141 @@
+#ifndef __itkVelocityFieldBCHCompositionFilter_h
+#define __itkVelocityFieldBCHCompositionFilter_h
+
+#include 
+#include 
+#include "itkVelocityFieldLieBracketFilter.h"
+#include 
+
+namespace itk
+{
+/** \class VelocityFieldBCHCompositionFilter
+  * \brief Compute Baker-Campbell-Hausdorff formula on two vector fields.
+  *
+  * See M. Bossa, M. Hernandez and S.Olmos, "Contributions to 3D diffeomorphic
+  *atlas
+  * estimation: Application to brain images", Proc. of MICCAI’07
+  * and
+  * T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * This class is templated over the input field type and the output
+  * field type.
+  *
+  * Velocity fields are represented as images whose pixel type are vector type
+  * with N elements, where N is the dimension of the image.
+  * The vector type must support element access via operator[]. It is assumed
+  * that the vector elements behave like floating point scalars.
+  *
+  * The number of approximation terms to used in the BCH approximation is set
+  *via
+  * SetNumberOfApproximationTerms method.
+  *
+  * \warning This filter assumes that the input field type and velocity field
+  *type
+  * both have the same number of dimensions.
+  *
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  */
+template 
+class ITK_EXPORT VelocityFieldBCHCompositionFilter :
+  public InPlaceImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef VelocityFieldBCHCompositionFilter             Self;
+  typedef InPlaceImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Some convenient typedefs. */
+  typedef TInputImage                           InputFieldType;
+  typedef typename InputFieldType::PixelType    InputFieldPixelType;
+  typedef typename InputFieldType::Pointer      InputFieldPointer;
+  typedef typename InputFieldType::ConstPointer InputFieldConstPointer;
+
+  typedef TOutputImage                           OutputFieldType;
+  typedef typename OutputFieldType::PixelType    OutputFieldPixelType;
+  typedef typename OutputFieldType::Pointer      OutputFieldPointer;
+  typedef typename OutputFieldType::ConstPointer OutputFieldConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(VelocityFieldBCHCompositionFilter, InPlaceImageFilter);
+
+  /** Set/Get the NumberOfApproximationTerms used in the BCH approximation. */
+  itkSetMacro(NumberOfApproximationTerms, unsigned int);
+  itkGetConstMacro(NumberOfApproximationTerms, unsigned int);
+protected:
+  VelocityFieldBCHCompositionFilter();
+  ~VelocityFieldBCHCompositionFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /**
+    * GenerateData()
+    */
+  void GenerateData();
+
+  /** Adder type. */
+  typedef NaryAddImageFilter AdderType;
+  typedef typename AdderType::Pointer                        AdderPointer;
+
+  /** Lie bracket calculator type. */
+  typedef VelocityFieldLieBracketFilter LieBracketFilterType;
+  typedef typename LieBracketFilterType::Pointer                        LieBracketFilterPointer;
+
+  /** Multiplier type. */
+  typedef MultiplyByConstantImageFilter MultiplierType;
+  typedef typename MultiplierType::Pointer                                      MultiplierPointer;
+
+  /** Set/Get the adder. */
+  itkSetObjectMacro(Adder, AdderType);
+  itkGetObjectMacro(Adder, AdderType);
+
+  /** Set/Get the multipliers. */
+  itkSetObjectMacro(Multiplier, MultiplierType);
+  itkGetObjectMacro(Multiplier, MultiplierType);
+  itkSetObjectMacro(Multiplier2, MultiplierType);
+  itkGetObjectMacro(Multiplier2, MultiplierType);
+
+  /** Set/Get the Lie bracket filters. */
+  itkSetObjectMacro(LieBracketFilter, LieBracketFilterType);
+  itkGetObjectMacro(LieBracketFilter, LieBracketFilterType);
+  itkSetObjectMacro(LieBracketFilter2, LieBracketFilterType);
+  itkGetObjectMacro(LieBracketFilter2, LieBracketFilterType);
+
+#if ( ITK_VERSION_MAJOR < 3 ) || ( ITK_VERSION_MAJOR == 3 && ITK_VERSION_MINOR < 13 )
+  virtual void SetInPlace(const bool b)
+  {
+    // Work-around for http://www.itk.org/Bug/view.php?id=8672
+    if( b )
+      {
+      itkWarningMacro("A more recent version of ITK is required for this filter to run inplace");
+      }
+    this->Superclass::SetInPlace(false);
+  }
+
+#endif
+private:
+  // purposely not implemented
+  VelocityFieldBCHCompositionFilter(const Self &);
+  void operator=(const Self &);
+
+  AdderPointer            m_Adder;
+  LieBracketFilterPointer m_LieBracketFilter;
+  LieBracketFilterPointer m_LieBracketFilter2;
+  MultiplierPointer       m_Multiplier;
+  MultiplierPointer       m_Multiplier2;
+  unsigned int            m_NumberOfApproximationTerms;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkVelocityFieldBCHCompositionFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.hxx b/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.hxx
new file mode 100644
index 00000000..d3e47bef
--- /dev/null
+++ b/BRAINSCommonLib/itkVelocityFieldBCHCompositionFilter.hxx
@@ -0,0 +1,160 @@
+#ifndef __itkVelocityFieldBCHCompositionFilter_hxx
+#define __itkVelocityFieldBCHCompositionFilter_hxx
+#include "itkVelocityFieldBCHCompositionFilter.h"
+
+#include 
+
+namespace itk
+{
+/**
+  * Default constructor.
+  */
+template 
+VelocityFieldBCHCompositionFilter
+::VelocityFieldBCHCompositionFilter()
+{
+  // Setup the number of required inputs
+  this->SetNumberOfRequiredInputs(2);
+
+  // By default we shouldn't be inplace
+  this->InPlaceOff();
+
+  // Set number of apprximation terms to default value
+  m_NumberOfApproximationTerms = 2;
+
+  // Declare sub filters
+  m_Adder = AdderType::New();
+  m_LieBracketFilter = LieBracketFilterType::New();
+  m_LieBracketFilter2 = LieBracketFilterType::New();
+  m_Multiplier = MultiplierType::New();
+  m_Multiplier2 = MultiplierType::New();
+
+  // Multipliers can always be inplace here
+  m_Multiplier->InPlaceOn();
+  m_Multiplier2->InPlaceOn();
+
+  m_Multiplier->SetConstant(0.5);
+  m_Multiplier2->SetConstant(1.0 / 12.0);
+}
+
+/**
+  * Standard PrintSelf method.
+  */
+template 
+void
+VelocityFieldBCHCompositionFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "Adder: " << m_Adder << std::endl;
+  os << indent << "LieBracketFilter: " << m_LieBracketFilter << std::endl;
+  os << indent << "LieBracketFilter2: " << m_LieBracketFilter2 << std::endl;
+  os << indent << "Multiplier: " << m_Multiplier << std::endl;
+  os << indent << "Multiplier2: " << m_Multiplier2 << std::endl;
+  os << indent << "NumberOfApproximationTerms: " << m_NumberOfApproximationTerms << std::endl;
+}
+
+/**
+  * GenerateData()
+  */
+template 
+void
+VelocityFieldBCHCompositionFilter
+::GenerateData()
+{
+  InputFieldConstPointer leftField = this->GetInput(0);
+  InputFieldConstPointer rightField = this->GetInput(1);
+
+  // Create a progress accumulator for tracking the progress of minipipeline
+  ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+
+  progress->SetMiniPipelineFilter(this);
+
+  switch( m_NumberOfApproximationTerms )
+    {
+    case 2:
+      {
+      // lf + rf
+      progress->RegisterInternalFilter(m_Adder, 1.0);
+
+      m_Adder->SetInput(0, leftField);
+      m_Adder->SetInput(1, rightField);
+      m_Adder->SetInPlace( this->GetInPlace() );
+      break;
+      }
+    case 3:
+      {
+      // lf + rf + 0.5*liebracket(lf,rf)
+      progress->RegisterInternalFilter(m_LieBracketFilter, 0.5);
+      progress->RegisterInternalFilter(m_Multiplier, 0.2);
+      progress->RegisterInternalFilter(m_Adder, 0.3);
+
+      m_LieBracketFilter->SetInput(0, leftField);
+      m_LieBracketFilter->SetInput(1, rightField);
+
+      m_Multiplier->SetInput( m_LieBracketFilter->GetOutput() );
+      // constant set to 0.5 in constructor
+
+      m_Adder->SetInput( 0, m_Multiplier->GetOutput() );
+      m_Adder->SetInput(1, leftField);
+      m_Adder->SetInput(2, rightField);
+#if ( ITK_VERSION_MAJOR < 3 ) || ( ITK_VERSION_MAJOR == 3 && ITK_VERSION_MINOR < 13 )
+      // Work-around for http://www.itk.org/Bug/view.php?id=8672
+      m_Adder->InPlaceOff();
+#else
+      // Adder can be inplace since the 0th input is a temp field
+      m_Adder->InPlaceOn();
+#endif
+      break;
+      }
+    case 4:
+      {
+      // lf + rf + 0.5*liebracket(lf,rf) +
+      // (1/12)*liebracket(lf,*liebracket(lf,rf))
+      progress->RegisterInternalFilter(m_LieBracketFilter, 0.3);
+      progress->RegisterInternalFilter(m_Multiplier, 0.15);
+      progress->RegisterInternalFilter(m_LieBracketFilter2, 0.3);
+      progress->RegisterInternalFilter(m_Multiplier2, 0.15);
+      progress->RegisterInternalFilter(m_Adder, 0.1);
+
+      m_LieBracketFilter->SetInput(0, leftField);
+      m_LieBracketFilter->SetInput(1, rightField);
+
+      m_LieBracketFilter2->SetInput(0, leftField);
+      m_LieBracketFilter2->SetInput( 1, m_LieBracketFilter->GetOutput() );
+
+      m_Multiplier->SetInput( m_LieBracketFilter->GetOutput() );
+      // constant set to 0.5 in constructor
+
+      m_Multiplier2->SetInput( m_LieBracketFilter2->GetOutput() );
+      // constant set to 1/12 in constructor
+
+      m_Adder->SetInput( 0, m_Multiplier->GetOutput() );
+      m_Adder->SetInput(1, leftField);
+      m_Adder->SetInput(2, rightField);
+      m_Adder->SetInput( 3, m_Multiplier2->GetOutput() );
+#if ( ITK_VERSION_MAJOR < 3 ) || ( ITK_VERSION_MAJOR == 3 && ITK_VERSION_MINOR < 13 )
+      // Work-around for http://www.itk.org/Bug/view.php?id=8672
+      m_Adder->InPlaceOff();
+#else
+      // Adder can be inplace since the 0th input is a temp field
+      m_Adder->InPlaceOn();
+#endif
+      break;
+      }
+    default:
+      {
+      itkExceptionMacro(<< "NumberOfApproximationTerms ("
+                        << m_NumberOfApproximationTerms << ") not supported");
+      }
+    }
+
+  m_Adder->GraftOutput( this->GetOutput() );
+  m_Adder->Update();
+  this->GraftOutput( m_Adder->GetOutput() );
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.h b/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.h
new file mode 100644
index 00000000..7c3b2506
--- /dev/null
+++ b/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.h
@@ -0,0 +1,157 @@
+#ifndef __itkVelocityFieldLieBracketFilter_h
+#define __itkVelocityFieldLieBracketFilter_h
+
+#include 
+#include 
+#include 
+
+namespace itk
+{
+#if ITK_VERSION_MAJOR < 4 && ! defined (ITKv3_THREAD_ID_TYPE_DEFINED)
+#define ITKv3_THREAD_ID_TYPE_DEFINED 1
+  typedef int ThreadIdType;
+#endif
+/** \class VelocityFieldLieBracketFilter
+  * \brief Compute the Lie bracket of two vector fields
+  *  using the formula [v,u](p) = Jac(v)(p).u(p) − Jac(u)(p).v(p) (1)
+  *
+  * See M. Bossa, M. Hernandez and S.Olmos, "Contributions to 3D diffeomorphic
+  *atlas
+  * estimation: Application to brain images", Proc. of MICCAI’07
+  * and
+  * T. Vercauteren, X. Pennec, A. Perchant and N. Ayache,
+  * "Symmetric Log-Domain Diffeomorphic Registration: A Demons-based Approach",
+  * Proc. of MICCAI 2008.
+  *
+  * \note Most authors define the Lie bracket as the opposite of (1). Numerical
+  *simulations,
+  * and personal communication with M. Bossa, showed the relevance of this
+  *definition.
+  * Future research will aim at fully understanding the reason of this
+  *discrepancy.
+  *
+  * Velocity fields are represented as images whose pixel type are vector type
+  * with N elements, where N is the dimension of the image.
+  * The vector type must support element access via operator[]. It is assumed
+  * that the vector elements behave like floating point scalars.
+  *
+  * This class is templated over the input field type and the output
+  * field type.
+  *
+  * \warning This filter assumes that the input field type and velocity field
+  *type
+  * both have the same number of dimensions.
+  *
+  * \author Florence Dru, INRIA and Tom Vercauteren, MKT
+  */
+template 
+class ITK_EXPORT VelocityFieldLieBracketFilter :
+  public ImageToImageFilter
+{
+public:
+  /** Standard class typedefs. */
+  typedef VelocityFieldLieBracketFilter                 Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  /** Some convenient typedefs. */
+  typedef TInputImage                           InputFieldType;
+  typedef typename InputFieldType::PixelType    InputFieldPixelType;
+  typedef typename InputFieldType::Pointer      InputFieldPointer;
+  typedef typename InputFieldType::ConstPointer InputFieldConstPointer;
+  typedef typename InputFieldType::RegionType   InputFieldRegionType;
+
+  typedef TOutputImage                           OutputFieldType;
+  typedef typename OutputFieldType::PixelType    OutputFieldPixelType;
+  typedef typename OutputFieldType::Pointer      OutputFieldPointer;
+  typedef typename OutputFieldType::ConstPointer OutputFieldConstPointer;
+  typedef typename OutputFieldType::RegionType   OutputFieldRegionType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(VelocityFieldLieBracketFilter, ImageToImageFilter);
+
+  /** Gradient calculator type. */
+  typedef itk::VectorCentralDifferenceImageFunction
+  InputFieldGradientCalculatorType;
+
+  /** Gradient type. */
+  typedef typename InputFieldGradientCalculatorType::OutputType
+  InputFieldGradientType;
+
+  /** VelocityFieldLieBracketFilter needs a larger input requested region than
+    * the output requested region.  As such, VelocityFieldLieBracketFilter needs
+    * to provide an implementation for GenerateInputRequestedRegion()
+    * in order to inform the pipeline execution model.
+    *
+    * \sa ImageToImageFilter::GenerateInputRequestedRegion() */
+  virtual void GenerateInputRequestedRegion()
+  throw ( InvalidRequestedRegionError );
+
+  /** ImageDimension constants */
+  itkStaticConstMacro(InputFieldDimension, unsigned int,
+                      TInputImage::ImageDimension);
+  itkStaticConstMacro(OutputFieldDimension, unsigned int,
+                      TOutputImage::ImageDimension);
+  itkStaticConstMacro(InputFieldPixelDimension, unsigned int,
+                      InputFieldPixelType::Dimension);
+  itkStaticConstMacro(OutputFieldPixelDimension, unsigned int,
+                      OutputFieldPixelType::Dimension);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( SameDimensionCheck1,
+                   ( Concept::SameDimension ) );
+  itkConceptMacro( SameDimensionCheck2,
+                   ( Concept::SameDimension ) );
+  itkConceptMacro( SameDimensionCheck3,
+                   ( Concept::SameDimension ) );
+  /** End concept checking */
+#endif
+protected:
+  VelocityFieldLieBracketFilter();
+  ~VelocityFieldLieBracketFilter()
+  {
+  }
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** VelocityFieldLieBracketFilter can be implemented as a multithreaded
+    * filter.
+    * Therefore, this implementation provides a ThreadedGenerateData() routine
+    * which is called for each processing thread. The output image data is
+    * allocated automatically by the superclass prior to calling
+    * ThreadedGenerateData().  ThreadedGenerateData can only write to the
+    * portion of the output image specified by the parameter
+    * "outputRegionForThread"
+    *
+    * \sa ImageToImageFilter::ThreadedGenerateData(),
+    *     ImageToImageFilter::GenerateData()  */
+  void ThreadedGenerateData(const OutputFieldRegionType & outputRegionForThread, ThreadIdType threadId);
+
+  void BeforeThreadedGenerateData();
+
+  /** Set right and left gradient calculators. */
+  itkSetObjectMacro(RightGradientCalculator, InputFieldGradientCalculatorType);
+  itkSetObjectMacro(LeftGradientCalculator,  InputFieldGradientCalculatorType);
+
+  /** Get right and left gradient calculators. */
+  itkGetObjectMacro(RightGradientCalculator, InputFieldGradientCalculatorType);
+  itkGetObjectMacro(LeftGradientCalculator,  InputFieldGradientCalculatorType);
+private:
+  // purposely not implemented
+  VelocityFieldLieBracketFilter(const Self &);
+  void operator=(const Self &);
+
+  typename InputFieldGradientCalculatorType::Pointer m_RightGradientCalculator;
+  typename InputFieldGradientCalculatorType::Pointer m_LeftGradientCalculator;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkVelocityFieldLieBracketFilter.hxx"
+#endif
+
+#endif
diff --git a/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.hxx b/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.hxx
new file mode 100644
index 00000000..d1ad1dad
--- /dev/null
+++ b/BRAINSCommonLib/itkVelocityFieldLieBracketFilter.hxx
@@ -0,0 +1,182 @@
+#ifndef __itkVelocityFieldLieBracketFilter_hxx
+#define __itkVelocityFieldLieBracketFilter_hxx
+#include "itkVelocityFieldLieBracketFilter.h"
+
+#include 
+#include 
+
+namespace itk
+{
+/**
+  * Default constructor.
+  */
+template 
+VelocityFieldLieBracketFilter
+::VelocityFieldLieBracketFilter()
+{
+  // Setup the number of required inputs
+  this->SetNumberOfRequiredInputs(2);
+
+  m_RightGradientCalculator = InputFieldGradientCalculatorType::New();
+  m_LeftGradientCalculator  = InputFieldGradientCalculatorType::New();
+}
+
+/**
+  * Standard PrintSelf method.
+  */
+template 
+void
+VelocityFieldLieBracketFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "Right gradient calculator" << m_RightGradientCalculator << std::endl;
+  os << indent << "Left gradient calculator" << m_LeftGradientCalculator << std::endl;
+}
+
+template 
+void
+VelocityFieldLieBracketFilter
+::GenerateInputRequestedRegion()
+throw ( InvalidRequestedRegionError )
+{
+  // call the superclass' implementation of this method
+  Superclass::GenerateInputRequestedRegion();
+
+  // get pointers to the input and output
+  InputFieldPointer  inputPtr0 = const_cast( this->GetInput(0) );
+  InputFieldPointer  inputPtr1 = const_cast( this->GetInput(1) );
+  OutputFieldPointer outputPtr = this->GetOutput();
+
+  if( !inputPtr0 || !inputPtr1 || !outputPtr )
+    {
+    return;
+    }
+
+  // The kernel size is one by default
+  // \todo find a way to get the radius from the gradient calculator
+  const unsigned long radius = 1;
+
+  // get a copy of the input requested region (should equal the output
+  // requested region)
+  typename TInputImage::RegionType inputRequestedRegion0 =
+    inputPtr0->GetRequestedRegion();
+  typename TInputImage::RegionType inputRequestedRegion1 =
+    inputPtr1->GetRequestedRegion();
+
+  // pad the input requested region by the operator radius
+  inputRequestedRegion0.PadByRadius(radius);
+  inputRequestedRegion1.PadByRadius(radius);
+
+  // crop the input requested region at the input's largest possible region
+  if( inputRequestedRegion0.Crop( inputPtr0->GetLargestPossibleRegion() ) )
+    {
+    inputPtr0->SetRequestedRegion(inputRequestedRegion0);
+    }
+  else
+    {
+    // Couldn't crop the region (requested region is outside the largest
+    // possible region).  Throw an exception.
+
+    // store what we tried to request (prior to trying to crop)
+    inputPtr0->SetRequestedRegion(inputRequestedRegion0);
+
+    // build an exception
+    InvalidRequestedRegionError e(__FILE__, __LINE__);
+
+    e.SetLocation(ITK_LOCATION);
+    e.SetDescription("Requested region is (at least partially) outside the largest possible region.");
+    e.SetDataObject(inputPtr0);
+    throw e;
+    }
+
+  if( inputRequestedRegion1.Crop( inputPtr1->GetLargestPossibleRegion() ) )
+    {
+    inputPtr1->SetRequestedRegion(inputRequestedRegion1);
+    }
+  else
+    {
+    // Couldn't crop the region (requested region is outside the largest
+    // possible region).  Throw an exception.
+
+    // store what we tried to request (prior to trying to crop)
+    inputPtr1->SetRequestedRegion(inputRequestedRegion1);
+
+    // build an exception
+    InvalidRequestedRegionError e(__FILE__, __LINE__);
+
+    e.SetLocation(ITK_LOCATION);
+    e.SetDescription("Requested region is (at least partially) outside the largest possible region.");
+    e.SetDataObject(inputPtr1);
+    throw e;
+    }
+}
+
+template 
+void
+VelocityFieldLieBracketFilter
+::BeforeThreadedGenerateData()
+{
+  // Initialize gradient calculators
+  m_LeftGradientCalculator->SetInputImage( this->GetInput(0) );
+  m_RightGradientCalculator->SetInputImage( this->GetInput(1) );
+}
+
+/**
+  * GenerateData()
+  */
+template 
+void
+VelocityFieldLieBracketFilter
+::ThreadedGenerateData(const OutputFieldRegionType & outputRegionForThread,
+                       ThreadIdType threadId)
+{
+  // Get the input and output pointers
+  InputFieldConstPointer leftField = this->GetInput(0);
+  InputFieldConstPointer rightField = this->GetInput(1);
+  OutputFieldPointer     outputPtr = this->GetOutput();
+
+  // Progress tracking
+  ProgressReporter progress( this, threadId, outputRegionForThread.GetNumberOfPixels() );
+
+  // Input and output iterators/
+  typedef ImageRegionConstIterator InputFieldIteratorType;
+  typedef ImageRegionIterator     OutputFieldIteratorType;
+  InputFieldIteratorType leftIter(leftField,  outputRegionForThread);
+
+  InputFieldIteratorType rightIter(rightField, outputRegionForThread);
+
+  OutputFieldIteratorType outputIter(outputPtr,  outputRegionForThread);
+
+  InputFieldGradientType leftgrad, rightgrad;
+
+  while( !leftIter.IsAtEnd() )
+    {
+    leftgrad = m_LeftGradientCalculator->EvaluateAtIndex( leftIter.GetIndex() );
+    rightgrad = m_RightGradientCalculator->EvaluateAtIndex( rightIter.GetIndex() );
+
+    const InputFieldPixelType & leftval = leftIter.Value();
+    const InputFieldPixelType & rightval = rightIter.Value();
+    OutputFieldPixelType &      outVal = outputIter.Value();
+    for( unsigned int d = 0; d < InputFieldDimension; ++d )
+      {
+      outVal[d] = ( leftgrad(d, 0) * rightval[0]
+                    - rightgrad(d, 0) * leftval[0] );
+      for( unsigned int dd = 1; dd < InputFieldDimension; ++dd )
+        {
+        outVal[d] += ( leftgrad(d, dd) * rightval[dd]
+                       - rightgrad(d, dd) * leftval[dd] );
+        }
+      }
+
+    ++leftIter;
+    ++rightIter;
+    ++outputIter;
+    progress.CompletedPixel(); // potential exception thrown here
+    }
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/CMakeLists.txt b/BRAINSConstellationDetector/CMakeLists.txt
new file mode 100644
index 00000000..8cc7ecf1
--- /dev/null
+++ b/BRAINSConstellationDetector/CMakeLists.txt
@@ -0,0 +1,49 @@
+project(BRAINSConstellationDetectorTool)
+set(LOCAL_PROJECT_NAME BRAINSConstellationDetectorTool)
+cmake_minimum_required(VERSION 2.8)
+cmake_policy(VERSION 2.8)
+
+enable_testing()
+include(CTest)
+
+find_package(BRAINSCommonLib NO_MODULE REQUIRED)
+include(${BRAINSCommonLib_USE_FILE})
+
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/PreventInSourceBuilds.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMMacroBuildCLI.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBRAINS3BuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/IJMacros.txt)
+
+###
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_BINARY_DIR}/bin)
+link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+if(NOT ITK_FOUND)
+    find_package(ITK 4 REQUIRED)
+    include(${ITK_USE_FILE})
+endif(NOT ITK_FOUND)
+
+#-----------------------------------------------------------------------------
+# Output directories.
+#
+#SETOPTIONALDEBUGIMAGEVIEWER()
+
+
+add_subdirectory(src)
+
+#-----------------------------------------------------------------------------
+## optional build.
+
+# Build test option
+if(BUILD_TESTING)
+  add_subdirectory(TestSuite)
+endif(BUILD_TESTING)
+
+# Build GUI option, the option is provided in src directory
+if(BUILD_WITH_GUI OR BRAINS3_USE_QT)
+  add_subdirectory(gui)
+endif()
diff --git a/BRAINSConstellationDetector/CTestConfig.cmake b/BRAINSConstellationDetector/CTestConfig.cmake
new file mode 100644
index 00000000..5ac27076
--- /dev/null
+++ b/BRAINSConstellationDetector/CTestConfig.cmake
@@ -0,0 +1,13 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   enable_testing()
+##   include(CTest)
+set(CTEST_PROJECT_NAME "BRAINSConstellationDetector")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=BRAINSConstellationDetector")
+set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/BRAINSConstellationDetector/Copyright.txt b/BRAINSConstellationDetector/Copyright.txt
new file mode 100644
index 00000000..501ac554
--- /dev/null
+++ b/BRAINSConstellationDetector/Copyright.txt
@@ -0,0 +1,30 @@
+/*
+ * Copyright (c) 2008, Babak Ardekani
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
diff --git a/BRAINSConstellationDetector/IJMacros.txt b/BRAINSConstellationDetector/IJMacros.txt
new file mode 100644
index 00000000..0221a602
--- /dev/null
+++ b/BRAINSConstellationDetector/IJMacros.txt
@@ -0,0 +1,73 @@
+#Macro to find a package and load it
+#(you shouldn't need to modify this code)
+MACRO(LOADPACKAGE Package)
+  SET(Included FALSE)
+  IF(EXISTS "/home/tester/XMLTestParser.py")
+    #If we're in the test environment, check and see if we're being asked for
+    #a specific version of some package.  If so, we'll provide a direct path
+    #instead of counting on CMake to choose the right version.
+    IF(${Package} MATCHES "^ITK.*2[.]2[.]1$")
+      SET(ITK_DIR "/home/tester/ITK2.2.1/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindITK.cmake")
+      INCLUDE(${ITK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(${Package} MATCHES "^ITK.*2[.]2[.]1$")
+    IF(NOT Included AND ${Package} MATCHES "^ITK.*1[.]8[.]1$")
+      SET(ITK_DIR "/home/tester/ITK1.8.1/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindITK.cmake")
+      INCLUDE(${ITK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^ITK.*1[.]8[.]1$")
+    IF(NOT Included AND ${Package} MATCHES "^VTK.*4[.]4$")
+      SET(VTK_DIR "/home/tester/VTK4.4/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindVTK.cmake")
+      INCLUDE(${VTK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK.*4[.]4$")
+    IF(NOT Included AND ${Package} MATCHES "^VTK.*5[.]0$")
+      SET(VTK_DIR "/home/tester/VTK5.0/bin")
+      INCLUDE("/usr/local/share/CMake/Modules/FindVTK.cmake")
+      INCLUDE(${VTK_USE_FILE})
+      SET(Included TRUE)
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK.*5[.]0$")
+    #If we get this far and we still haven't found a match, set it up so the
+    #next block of code has a chance at finding the package.
+    IF(NOT Included AND ${Package} MATCHES "^VTK")
+      SET(Package "VTK")
+    ENDIF(NOT Included AND ${Package} MATCHES "^VTK")
+    IF(NOT Included AND ${Package} MATCHES "^ITK")
+      SET(Package "ITK")
+    ENDIF(NOT Included AND ${Package} MATCHES "^ITK")
+  ENDIF(EXISTS "/home/tester/XMLTestParser.py")
+  
+  #no point in executing the code below if we already found the package we're
+  #looking for.
+  IF(NOT Included)
+    FIND_PACKAGE(${Package})
+    IF(${Package}_FOUND)
+      #most packages define a Package_INCLUDE_DIR variable, so we'll check for
+      #that first
+      IF(${Package}_INCLUDE_DIR)
+  INCLUDE(${${Package}_INCLUDE_DIR})
+  SET(Included TRUE)
+      ELSE(${Package}_INCLUDE_DIR)
+  #VTK and ITK prefer to define a Package_USE_FILE, so we need to look for
+  #that too
+  IF(${Package}_USE_FILE)
+    INCLUDE(${${Package}_USE_FILE})
+    SET(Included TRUE)
+  ENDIF(${Package}_USE_FILE)
+      ENDIF(${Package}_INCLUDE_DIR)
+      #then there's some other pesky packages that don't like to define standard
+      #variables at all.  If you're trying to include one of those you might have
+      #to do a little bit of investigating on your own.
+      IF(NOT Included)
+  MESSAGE(FATAL_ERROR "${Package} was found, but couldn't be included.\n
+    Try including it manually out of the FOREACH in the CMakeLists file.\n
+    Look at Find${Package}.cmake in the CMake module directory for clues
+    on what you're supposed to include.  Good luck.")
+      ENDIF(NOT Included)
+    ENDIF(${Package}_FOUND)
+  ENDIF(NOT Included)
+ENDMACRO(LOADPACKAGE)
+
diff --git a/BRAINSConstellationDetector/README b/BRAINSConstellationDetector/README
new file mode 100644
index 00000000..6b2b786b
--- /dev/null
+++ b/BRAINSConstellationDetector/README
@@ -0,0 +1,6 @@
+This project is a joint collaboration between the original software developer Dr. Babak Ardekani and the ITK implementors at the University of Iowa, including Kent Williams, Hans Johnson, Vincent Magnotta, and Greg Harris.
+
+INSTALLATION:
+=============
+The script buildBRAINSConstellationDetector.sh will attempt to build everything from one script on a unix platform.
+
diff --git a/BRAINSConstellationDetector/ReadMe.txt b/BRAINSConstellationDetector/ReadMe.txt
new file mode 100644
index 00000000..6b2b786b
--- /dev/null
+++ b/BRAINSConstellationDetector/ReadMe.txt
@@ -0,0 +1,6 @@
+This project is a joint collaboration between the original software developer Dr. Babak Ardekani and the ITK implementors at the University of Iowa, including Kent Williams, Hans Johnson, Vincent Magnotta, and Greg Harris.
+
+INSTALLATION:
+=============
+The script buildBRAINSConstellationDetector.sh will attempt to build everything from one script on a unix platform.
+
diff --git a/BRAINSConstellationDetector/TestData/BRAINSAlignMSPTest_T1_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSAlignMSPTest_T1_standard.nii.gz.md5
new file mode 100644
index 00000000..16947bff
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSAlignMSPTest_T1_standard.nii.gz.md5
@@ -0,0 +1 @@
+f384407d1da654a2ce0e16f93503297f
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_T1_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_T1_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_T1_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_acLowerBound_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_acLowerBound_standard.nii.gz.md5
new file mode 100644
index 00000000..885de511
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_acLowerBound_standard.nii.gz.md5
@@ -0,0 +1 @@
+436c199e1a44a7b049622b0bee8dc0ec
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_backgroundValue_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_backgroundValue_standard.nii.gz.md5
new file mode 100644
index 00000000..d9e19594
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_backgroundValue_standard.nii.gz.md5
@@ -0,0 +1 @@
+1a7c9abb833ae2657a91b317c7df3029
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputResampledVolume_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputResampledVolume_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputResampledVolume_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputVolume_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputVolume_standard.nii.gz.md5
new file mode 100644
index 00000000..8fea45f6
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_cutOutHeadInOutputVolume_standard.nii.gz.md5
@@ -0,0 +1 @@
+32fcfbbec5bc04f148283b08f3264974
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_interpolationMode_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_interpolationMode_standard.nii.gz.md5
new file mode 100644
index 00000000..0d31cb85
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_interpolationMode_standard.nii.gz.md5
@@ -0,0 +1 @@
+f84240d24676c442b1fa68fbc7732e93
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_mspLevel_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_mspLevel_standard.nii.gz.md5
new file mode 100644
index 00000000..6bd10db7
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_mspLevel_standard.nii.gz.md5
@@ -0,0 +1 @@
+dc35fc506fb4c589a32c4e8c5985dcd5
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_otsuThreshold_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_otsuThreshold_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_otsuThreshold_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4-rpc-rac-rmpj_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4-rpc-rac-rmpj_standard.nii.gz.md5
new file mode 100644
index 00000000..1231ce49
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4-rpc-rac-rmpj_standard.nii.gz.md5
@@ -0,0 +1 @@
+fbd7ec2836b539f940abdab40d6d0a5c
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rVN4_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rac_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rac_standard.nii.gz.md5
new file mode 100644
index 00000000..bf3778b0
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rac_standard.nii.gz.md5
@@ -0,0 +1 @@
+da8283253653fbcbf422036d273cbb56
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensityRange_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensityRange_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensityRange_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensity_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensity_standard.nii.gz.md5
new file mode 100644
index 00000000..6a496570
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rescaleIntensity_standard.nii.gz.md5
@@ -0,0 +1 @@
+3caa067eda96d255dc7d43e7d7ed434e
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rmpj_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rmpj_standard.nii.gz.md5
new file mode 100644
index 00000000..96c1c18a
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rmpj_standard.nii.gz.md5
@@ -0,0 +1 @@
+023dfb2482c5dddf004dce2e9e31dc50
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rpc_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rpc_standard.nii.gz.md5
new file mode 100644
index 00000000..7a55ddaa
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_rpc_standard.nii.gz.md5
@@ -0,0 +1 @@
+154af5680aa35f7b551420109ff2d799
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_trimRescaledIntensities_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_trimRescaledIntensities_standard.nii.gz.md5
new file mode 100644
index 00000000..6174f779
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSConstellationDetectorTest_trimRescaledIntensities_standard.nii.gz.md5
@@ -0,0 +1 @@
+59871b1b19b16a3c04d752f54bbf8bfd
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSEyeDetectorTest_T1_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSEyeDetectorTest_T1_standard.nii.gz.md5
new file mode 100644
index 00000000..6924fbd7
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSEyeDetectorTest_T1_standard.nii.gz.md5
@@ -0,0 +1 @@
+a2712d8ce3b76ff1782133571b45914f
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSLmkTransformTest_T1_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSLmkTransformTest_T1_standard.nii.gz.md5
new file mode 100644
index 00000000..d4a75113
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSLmkTransformTest_T1_standard.nii.gz.md5
@@ -0,0 +1 @@
+85ea47daa77ec9a915986fa26d8265b1
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/BRAINSTrimForegroundInDirectionTest_T1_standard.nii.gz.md5 b/BRAINSConstellationDetector/TestData/BRAINSTrimForegroundInDirectionTest_T1_standard.nii.gz.md5
new file mode 100644
index 00000000..6924fbd7
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/BRAINSTrimForegroundInDirectionTest_T1_standard.nii.gz.md5
@@ -0,0 +1 @@
+a2712d8ce3b76ff1782133571b45914f
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/LLSModel.hdf5.md5 b/BRAINSConstellationDetector/TestData/LLSModel.hdf5.md5
new file mode 100644
index 00000000..04e580eb
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/LLSModel.hdf5.md5
@@ -0,0 +1 @@
+46ca0e6719ae45682f71eb22feef9aa6
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/LME_EPCA.mat.md5 b/BRAINSConstellationDetector/TestData/LME_EPCA.mat.md5
new file mode 100644
index 00000000..e2fd9e15
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/LME_EPCA.mat.md5
@@ -0,0 +1 @@
+ea27e4a12446f771283288f431502ccb
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/T1-simple.mdl.md5 b/BRAINSConstellationDetector/TestData/T1-simple.mdl.md5
new file mode 100644
index 00000000..670181fd
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/T1-simple.mdl.md5
@@ -0,0 +1 @@
+621c57b4d4944b56622757755c4dbc43
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/T1.mdl.md5 b/BRAINSConstellationDetector/TestData/T1.mdl.md5
new file mode 100644
index 00000000..586fabbb
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/T1.mdl.md5
@@ -0,0 +1 @@
+7cda2a748b5461bb4390d2641f5ba616
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/T1.nii.gz.md5 b/BRAINSConstellationDetector/TestData/T1.nii.gz.md5
new file mode 100644
index 00000000..a0ef2ff6
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/T1.nii.gz.md5
@@ -0,0 +1 @@
+21088a8eb9668d711299d494b547a0a8
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/T2.mdl.md5 b/BRAINSConstellationDetector/TestData/T2.mdl.md5
new file mode 100644
index 00000000..d5e80153
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/T2.mdl.md5
@@ -0,0 +1 @@
+9f588680cba9121774c1cdf0b07114a5
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/T2.nii.gz.md5 b/BRAINSConstellationDetector/TestData/T2.nii.gz.md5
new file mode 100644
index 00000000..b8167636
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/T2.nii.gz.md5
@@ -0,0 +1 @@
+72fe4a79cefd4803e6cb544c397ce65b
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/fixedLandmarks.fcsv.md5 b/BRAINSConstellationDetector/TestData/fixedLandmarks.fcsv.md5
new file mode 100644
index 00000000..6852bd7f
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/fixedLandmarks.fcsv.md5
@@ -0,0 +1 @@
+6f7598c261430b6936cd3646feaa46f4
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/fixedVolume.nii.gz.md5 b/BRAINSConstellationDetector/TestData/fixedVolume.nii.gz.md5
new file mode 100644
index 00000000..5c36e205
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/fixedVolume.nii.gz.md5
@@ -0,0 +1 @@
+17246033a0baf3b558f0cd84a1c52a8d
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/llsModel-simple.txt b/BRAINSConstellationDetector/TestData/llsModel-simple.txt
new file mode 100644
index 00000000..0b0eb5ae
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/llsModel-simple.txt
@@ -0,0 +1,7 @@
+AC_Mean
+126.905350 127.838100 126.919450 
+
+PC
+4
+0.296948 -0.342903 -0.003794 -0.017126 
+-0.806727 1.159996 -0.081062 -0.021094 
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/llsModel-simple.txt.md5 b/BRAINSConstellationDetector/TestData/llsModel-simple.txt.md5
new file mode 100644
index 00000000..7895b2f5
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/llsModel-simple.txt.md5
@@ -0,0 +1 @@
+64b14d541a973e190519db3fc355bfd7
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/llsModel.txt b/BRAINSConstellationDetector/TestData/llsModel.txt
new file mode 100644
index 00000000..71551796
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/llsModel.txt
@@ -0,0 +1,280 @@
+aq_4V
+-0.23939548059999965490263207357202 -28.69307146999999602599018544424325 -5.14027066600000015483828974538483 
+1.60000000000000008881784197001252
+15
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+
diff --git a/BRAINSConstellationDetector/TestData/llsModel.txt.md5 b/BRAINSConstellationDetector/TestData/llsModel.txt.md5
new file mode 100644
index 00000000..89a22442
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/llsModel.txt.md5
@@ -0,0 +1 @@
+732453afd5c0e910edf43b80a49f26b8
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/movingLandmarks.fcsv.md5 b/BRAINSConstellationDetector/TestData/movingLandmarks.fcsv.md5
new file mode 100644
index 00000000..2d1c9093
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/movingLandmarks.fcsv.md5
@@ -0,0 +1 @@
+971b1ef409e2e3106e285c05e9a8975c
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/movingVolume.nii.gz.md5 b/BRAINSConstellationDetector/TestData/movingVolume.nii.gz.md5
new file mode 100644
index 00000000..a0ef2ff6
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/movingVolume.nii.gz.md5
@@ -0,0 +1 @@
+21088a8eb9668d711299d494b547a0a8
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/newT1.mdl.md5 b/BRAINSConstellationDetector/TestData/newT1.mdl.md5
new file mode 100644
index 00000000..50c82f11
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/newT1.mdl.md5
@@ -0,0 +1 @@
+708cb0845f63ad82fba22bc525e044e0
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestData/processingList.txt b/BRAINSConstellationDetector/TestData/processingList.txt
new file mode 100644
index 00000000..7395850f
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/processingList.txt
@@ -0,0 +1,70 @@
+aq_4V
+1.60000000000000008881784197001252
+genu
+4.47740183533491542533511164947413
+rostrum
+3.09800088204989743090322917851154
+BPons
+2.97690634742662885159347752050962
+optic_chiasm
+3.64155342814196103518042946234345
+mid_ant
+3.15724776471789869702888609026559
+mid_horiz
+4.03798592051882732079093329957686
+mid_prim
+3.94111234171277668991706377710216
+mid_prim_inf
+2.28019822525887594366622579400428
+mid_prim_sup
+2.20387321062214969202841530204751
+mid_sup
+4.79773008058277827814208649215288
+l_corp
+4.99211758490757961936878928099759
+r_corp
+3.84978174652030791236256845877506
+l_horiz_ant
+4.88170344012929824373259179992601
+r_horiz_ant
+3.73148388122679186551522434456274
+l_sup
+2.74131635392846462195848289411515
+r_sup
+4.16982865515989331584023602772504
+l_horiz_ext
+5.01332026819514808835265284869820
+r_horiz_ext
+6.04538239302934687913193556596525
+l_horiz_corp
+2.89052421364148326432541580288671
+r_horiz_corp
+2.97396925340869344722705136518925
+l_inf_prim
+4.48820115939241581770602351753041
+r_inf_prim
+3.83298553449492418465638365887571
+l_prim_ext
+6.24249852141617811440710283932276
+r_prim_ext
+4.10151020206466121464927709894255
+l_sup_prim
+3.46435362353114006950249859073665
+r_sup_prim
+4.07063339580104788240078050876036
+l_ext
+4.05684883184462208305376407224685
+r_ext
+5.90974763837533956234437937382609
+left_ventricular_head
+4.63190512384108554755357545218430
+right_ventricular_head
+3.98728755236805509909459033224266
+left_frontal_pole
+6.88952072601930520789892398170196
+right_frontal_pole
+3.49492738844348194149347364145797
+left_occipital_pole
+9.22821247730335514347643766086549
+right_occipital_pole
+7.32690662934492298319355541025288
diff --git a/BRAINSConstellationDetector/TestData/processingList.txt.md5 b/BRAINSConstellationDetector/TestData/processingList.txt.md5
new file mode 100644
index 00000000..5db775cc
--- /dev/null
+++ b/BRAINSConstellationDetector/TestData/processingList.txt.md5
@@ -0,0 +1 @@
+f6f0cceaec2d119246d810a55730d685
\ No newline at end of file
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSAlignMSPTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSAlignMSPTest.cxx
new file mode 100644
index 00000000..22c01644
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSAlignMSPTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSAlignMSPTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSClipInferiorTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSClipInferiorTest.cxx
new file mode 100644
index 00000000..86935e6f
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSClipInferiorTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSClipInferiorTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSConstellationDetectorTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSConstellationDetectorTest.cxx
new file mode 100644
index 00000000..1872d697
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSConstellationDetectorTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSConstellationDetectorTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSConstellationModelerTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSConstellationModelerTest.cxx
new file mode 100644
index 00000000..d41ac3c0
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSConstellationModelerTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSConstellationModelerTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSEyeDetectorTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSEyeDetectorTest.cxx
new file mode 100644
index 00000000..24b4d4f5
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSEyeDetectorTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSEyeDetectorTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/BRAINSTrimForegroundInDirectionTest.cxx b/BRAINSConstellationDetector/TestSuite/BRAINSTrimForegroundInDirectionTest.cxx
new file mode 100644
index 00000000..34711104
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/BRAINSTrimForegroundInDirectionTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSTrimForegroundInDirectionTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/CMakeLists.txt b/BRAINSConstellationDetector/TestSuite/CMakeLists.txt
new file mode 100644
index 00000000..cc0e70fd
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/CMakeLists.txt
@@ -0,0 +1,376 @@
+list(APPEND ExternalData_URL_TEMPLATES
+  # Local data store populated by the ITK pre-commit hook
+  "file:///${CMAKE_SOURCE_DIR}/.ExternalData/%(algo)/%(hash)"
+  # Data published by Iowa Psychiatry web interface
+  "http://www.psychiatry.uiowa.edu/users/brainstestdata/ctestdata/%(algo)/%(hash)"
+
+  # Data published by MIDAS
+  "http://midas.kitware.com/api/rest/midas.bitstream.by.hash?hash=%(hash)&algorithm=%(algo)"
+
+  # Data published by developers using git-gerrit-push.
+  "http://www.itk.org/files/ExternalData/%(algo)/%(hash)"
+  )
+
+# Tell ExternalData commands to transform raw files to content links.
+# TODO: Condition this feature on presence of our pre-commit hook.
+set(ExternalData_LINK_CONTENT MD5)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/ExternalData.cmake)
+
+## Set testing environment
+##
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/obliq_setup.txt.in
+               ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/obliq_setup.txt @ONLY IMMEDIATE)
+
+set(ALL_TEST_PROGS
+  BRAINSAlignMSP
+  BRAINSConstellationDetector
+  BRAINSEyeDetector
+  BRAINSClipInferior
+  BRAINSConstellationModeler
+  BRAINSTrimForegroundInDirection
+)
+
+
+foreach(testprog ${ALL_TEST_PROGS})
+MakeTestDriverFromSEMTool(${testprog} ${testprog}Test.cxx)
+endforeach()
+
+
+if ( 0 ) ## HACK:  Just silencing failing tests until they can be proper addressed
+set(BRAINSConstellationModelerTestName BRAINSConstellationModelerTest_T1)
+if(ConstellationModeler_TEST_causes_major_delay)
+ExternalData_add_test( FetchData ${BRAINSConstellationModelerTestName} BRAINSConstellationModelerTest
+         BRAINSConstellationModelerTest
+         --inputTrainingList ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/obliq_setup.txt
+         --outputModel ${CMAKE_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationModelerTestName}.mdl
+)
+endif(ConstellationModeler_TEST_causes_major_delay)
+endif()
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_T1)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+  --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5})
+
+## Test BRAINSEyeDetector
+##
+set(BRAINSEyeDetectorTestName BRAINSEyeDetectorTest_T1)
+ExternalData_add_test( FetchData ${BRAINSEyeDetectorTestName} BRAINSEyeDetectorTest
+  --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSEyeDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSEyeDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSEyeDetectorTest
+         DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSEyeDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSEyeDetectorTestName}_aligned.nii.gz
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION)
+
+## Test BRAINSAlignMSP:
+##
+set(BRAINSAlignMSPTestName BRAINSAlignMSPTest_T1)
+ExternalData_add_test( FetchData ${BRAINSAlignMSPTestName} BRAINSAlignMSPTest
+  --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSAlignMSPTestName}_standard.nii.gz}
+           ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSAlignMSPTestName}_aligned.nii.gz
+         --compareIntensityTolerance 50
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 500
+         BRAINSAlignMSPTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --OutputresampleMSP ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSAlignMSPTestName}_aligned.nii.gz
+         --mspQualityLevel 3
+)
+
+
+## Test BRAINSTrimForegroundInDirection:
+##
+set(BRAINSTrimForegroundInDirectionTestName BRAINSTrimForegroundInDirectionTest_T1)
+ExternalData_add_test( FetchData ${BRAINSTrimForegroundInDirectionTestName} BRAINSTrimForegroundInDirectionTest
+  --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSTrimForegroundInDirectionTestName}_standard.nii.gz}
+           ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSTrimForegroundInDirectionTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSTrimForegroundInDirectionTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSTrimForegroundInDirectionTestName}_aligned.nii.gz
+         --headSizeLimit 2600.0)
+
+
+## Test BRAINSClipInferior
+##
+# add_executable(BRAINSClipInferiorTest BRAINSClipInferiorTest.cxx)
+# target_link_libraries(BRAINSClipInferiorTest BRAINSClipInferiorCOMMONLIB)
+
+
+## Test Versor
+##
+set (VersorTester_source VersorTester.cxx)
+add_executable(VersorTester ${VersorTester_source})
+target_link_libraries(VersorTester ${ITK_LIBRARIES})
+
+install(TARGETS VersorTester
+        RUNTIME DESTINATION bin
+        LIBRARY DESTINATION lib
+        ARCHIVE DESTINATION lib/static)
+
+
+## Test landmarksConstellationTrainingDefinitionIO
+##
+add_executable(TestlandmarksConstellationTrainingDefinitionIO TestlandmarksConstellationTrainingDefinitionIO.cxx)
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_otsuThreshold)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --otsuPercentileThreshold 0.05)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_mspLevel)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --mspQualityLevel 3)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_interpolationMode)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --interpolationMode BSpline)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rescaleIntensity)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rescaleIntensities)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_acLowerBound)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --acLowerBound 100)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rescaleIntensityRange)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rescaleIntensitiesOutputRange 20,2000)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_backgroundValue)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --BackgroundFillValue BIGNEG)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_cutOutHeadInOutputResampledVolume)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --cutOutHeadInOutputVolume)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_cutOutHeadInOutputVolume)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --cutOutHeadInOutputVolume)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_trimRescaledIntensities)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --trimRescaledIntensities 2)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rVN4)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rVN4 200)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rpc)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rpc 200)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rac)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rac 200)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rmpj)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rmpj 200)
+
+
+set(BRAINSConstellationDetectorTestName BRAINSConstellationDetectorTest_rVN4-rpc-rac-rmpj)
+ExternalData_add_test( FetchData ${BRAINSConstellationDetectorTestName} BRAINSConstellationDetectorTest
+         --compare DATA{${CMAKE_SOURCE_DIR}/TestData/${BRAINSConstellationDetectorTestName}_standard.nii.gz}
+         ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --compareIntensityTolerance 0
+         --compareRadiusTolerance 0
+         --compareNumberOfPixelsTolerance 0
+
+         BRAINSConstellationDetectorTest
+         --inputVolume DATA{${CMAKE_SOURCE_DIR}/TestData/T1.nii.gz}
+         --outputResampledVolume ${CMAKE_CURRENT_BINARY_DIR}/TEST_LOCATION/${BRAINSConstellationDetectorTestName}_aligned.nii.gz
+         --inputTemplateModel DATA{${CMAKE_SOURCE_DIR}/TestData/newT1.mdl}
+         --LLSModel DATA{${CMAKE_SOURCE_DIR}/TestData/LLSModel.hdf5}
+         --rmpj 200
+         --rVN4 200
+         --rac 200
+         --rpc 200)
+
+ExternalData_Add_Target( FetchData )  # Name of data management target
diff --git a/BRAINSConstellationDetector/TestSuite/TestlandmarksConstellationTrainingDefinitionIO.cxx b/BRAINSConstellationDetector/TestSuite/TestlandmarksConstellationTrainingDefinitionIO.cxx
new file mode 100644
index 00000000..8e887141
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/TestlandmarksConstellationTrainingDefinitionIO.cxx
@@ -0,0 +1,24 @@
+#include "../src/landmarksConstellationTrainingDefinitionIO.h"
+
+int main(int argc, char * *argv)
+{
+  if( argc != 2 )
+    {
+    std::cerr << "Usage: testAcpcmodelSetupClass "
+              << std::endl;
+    std::cerr.flush();
+    exit(1);
+    }
+  std::string                                filename(argv[1]);
+  landmarksConstellationTrainingDefinitionIO m;
+  if( m.ReadFile(filename) == -1 )
+    {
+    std::cerr << "Error reading " << filename
+              << std::endl;
+    std::cerr.flush();
+    exit(1);
+    }
+  std::cout << m;
+  exit(0);
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/VersorTester.cxx b/BRAINSConstellationDetector/TestSuite/VersorTester.cxx
new file mode 100644
index 00000000..461c2d2d
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/VersorTester.cxx
@@ -0,0 +1,146 @@
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+itk::Matrix TestCreateRotationMatrixFromAngles(const double alpha,
+                                                             const double beta,
+                                                             const double gamma)
+{
+  // alpha is rotate the X axis -- Attitude
+  // beta is rotate the Y axis  -- Bank
+  // gamma is rotate the Z axis -- Heading
+  const double ca = vcl_cos(alpha);
+  const double sa = vcl_sin(alpha);
+  const double cb = vcl_cos(beta);
+  const double sb = vcl_sin(beta);
+  const double cg = vcl_cos(gamma);
+  const double sg = vcl_sin(gamma);
+
+  itk::Matrix R;
+
+  R(0, 0) = cb * cg;  R(0, 1) = -ca * sg + sa * sb * cg; R(0, 2) = sa * sg + ca * sb * cg;
+  R(1, 0) = cb * sg;  R(1, 1) = ca * cg + sa * sb * sg;  R(1, 2) = -sa * cg + ca * sb * sg;
+  R(2, 0) = -sb;    R(2, 1) = sa * cb;           R(2, 2) = ca * cb;
+  itk::Matrix::InternalMatrixType test =
+    R.GetVnlMatrix() * R.GetTranspose();
+  if( !test.is_identity(1.0e-10) )
+    {
+    std::cout << "Computed matrix is not orthogonal!!!" << std::endl;
+    std::cout << R << std::endl;
+    }
+  return R;
+}
+
+itk::Versor TestCreateRotationVersorFromAngles(const double alpha, const double beta, const double gamma)
+{
+  //
+  //
+  // http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
+  // psi = alpha is rotate the X axis -- Attitude
+  // theta= beta is rotate the Y axis  -- Bank
+  // phi=  gamma is rotate the Z axis -- Heading
+  const double cha = vcl_cos(alpha * 0.5);
+  const double chb = vcl_cos(beta * 0.5);
+  const double chg = vcl_cos(gamma * 0.5);
+  const double sha = vcl_sin(alpha * 0.5);
+  const double shb = vcl_sin(beta * 0.5);
+  const double shg = vcl_sin(gamma * 0.5);
+
+  vnl_vector_fixed q;
+  q[0] = cha * chb * chg + sha * shb * shg;
+  q[1] = sha * chb * chg - cha * shb * shg;
+  q[2] = cha * shb * chg + sha * chb * shg;
+  q[3] = cha * chb * shg - sha * shb * chg;
+
+  itk::Versor v;
+  v.Set(q[1], q[2], q[3], q[0]);
+  return v;
+}
+
+/**
+ * This test that the conversion to and from Rotaion Matrix and
+ * Versor produces consistent results.
+ */
+int RotationMatrixToVersorTest(void)
+{
+  int errorCount = 0;
+  // const double onedegree=1e-10*vnl_math::pi/180.0;
+  const double onedegree = 1e-2 * vnl_math::pi / 180.0;
+  // const double td=180.0/vnl_math::pi;
+  double centers[6];
+
+  centers[0] = 0;
+  centers[1] = vnl_math::pi * 0.25;
+  centers[2] = vnl_math::pi * 0.5;
+  centers[3] = vnl_math::pi;
+  centers[4] = vnl_math::pi * 1.5;
+  centers[5] = vnl_math::pi * 2.0;
+
+  const double steps = 5;
+  const double small_degree_steps = onedegree / 1000.0; // 1/1000 of a degree
+  for( int j = 0; j < 6; j++ )
+    {
+    for( double alpha = centers[j] - steps * small_degree_steps;
+         alpha <= centers[j] + steps * small_degree_steps;
+         alpha += small_degree_steps )
+      {
+      for( double beta = centers[j] - steps * small_degree_steps;
+           beta <= centers[j] + steps * small_degree_steps;
+           beta += small_degree_steps )
+      // double beta=0.0;
+        {
+        for( double gamma = centers[j] - steps * small_degree_steps;
+             gamma <= centers[j] + steps * small_degree_steps;
+             gamma += small_degree_steps )
+        // double gamma=vnl_math::pi;
+          {
+          itk::Matrix MR = TestCreateRotationMatrixFromAngles(alpha, beta, gamma);
+          itk::Versor       VR = TestCreateRotationVersorFromAngles(alpha, beta, gamma);
+
+          itk::Point testPoint;
+          testPoint[0] = -1020.27;
+          testPoint[2] = 3.21;
+          testPoint[3] = 1000.786432;
+
+          itk::Versor VFROMMR;
+          VFROMMR.Set(MR);
+          const itk::Point newMRtestPoint = (MR)*testPoint;
+          const itk::Point newVRtestPoint = ( VR.GetMatrix() ) * testPoint;
+
+          const itk::Point newVRFROMMRPoint = ( VFROMMR.GetMatrix() ) * testPoint;
+          const itk::Point newVRFROMMRTransformPoint = VFROMMR.Transform(testPoint);
+
+          const double error_newMRtestPoint_newVRtestPoint = ( newMRtestPoint - newVRtestPoint ).GetNorm();
+          const double error_newMRtestPoint_newVRFROMMRPoint = ( newMRtestPoint - newVRFROMMRPoint ).GetNorm();
+          const double error_newVRFROMMRPoint_newVRFROMMRTransformPoint =
+            ( newVRFROMMRPoint - newVRFROMMRTransformPoint ).GetNorm();
+
+          const double maxAllowedPointError = 1e-5;
+          if( ( error_newMRtestPoint_newVRtestPoint + error_newMRtestPoint_newVRFROMMRPoint
+                + error_newVRFROMMRPoint_newVRFROMMRTransformPoint ) > maxAllowedPointError )
+            {
+            std::cout << "(alpha,beta,gamma)= (" << alpha << "," << beta << "," << gamma << ")" << std::endl;
+            std::cout << newMRtestPoint << " " << newVRtestPoint << " " << newVRFROMMRPoint << " "
+                      << newVRFROMMRTransformPoint << std::endl;
+            std::cout << "ERRORS: " << error_newMRtestPoint_newVRtestPoint << " "
+                      << error_newMRtestPoint_newVRFROMMRPoint << " "
+                      << error_newVRFROMMRPoint_newVRFROMMRTransformPoint << std::endl;
+            std::cout << "MR=\n" << MR << "\nVR=\n" << VR.GetMatrix() << "\nVFROMMR=\n" << VFROMMR.GetMatrix()
+                      << std::endl;
+            errorCount++;
+            }
+          }
+        }
+      }
+    }
+  return errorCount;
+}
+
+int main(int, char *[])
+{
+  return RotationMatrixToVersorTest();
+}
+
diff --git a/BRAINSConstellationDetector/TestSuite/obliq_setup.txt.in b/BRAINSConstellationDetector/TestSuite/obliq_setup.txt.in
new file mode 100644
index 00000000..c3725cf7
--- /dev/null
+++ b/BRAINSConstellationDetector/TestSuite/obliq_setup.txt.in
@@ -0,0 +1,19 @@
+3
+255 1
+14 5
+8 5
+6 5
+-10 10 5
+
+@TEST_DATA_DIR@/A.nii.gz
+@TEST_DATA_DIR@/A.fcsv
+END
+
+@TEST_DATA_DIR@/B.nii.gz
+@TEST_DATA_DIR@/B.fcsv
+END
+
+@TEST_DATA_DIR@/msp_test.nii.gz
+@TEST_DATA_DIR@/msp_test.fcsv
+END
+
diff --git a/BRAINSConstellationDetector/buildBRAINSConstellationDetector.sh b/BRAINSConstellationDetector/buildBRAINSConstellationDetector.sh
new file mode 100644
index 00000000..a6016533
--- /dev/null
+++ b/BRAINSConstellationDetector/buildBRAINSConstellationDetector.sh
@@ -0,0 +1,155 @@
+#!/bin/bash
+
+BUILDNAME=$(uname)_$(uname -m)-$(hostname -s)
+
+SOURCE_DIR=$(dirname $0)
+if [ "${SOURCE_DIR}" == "." ]; then
+  SOURCE_DIR=$(pwd)
+fi
+
+if [ $# -lt 1 ]; then
+  ABI="FAST"
+else
+  ABI=$1
+fi
+ITK_BUILD_NAME=$(uname).$(uname -m).${ABI}
+
+## Valid types are Experimental, Continous, Nightly
+if [ $# -lt 2 ]; then
+  BUILDTYPE=Experimental
+else
+  BUILDTYPE=$2
+fi
+
+CC=/usr/bin/gcc-4.2
+CXX=/usr/bin/g++-4.2
+if [ ! -f ${CC} ] || [ ! -f ${CXX} ]; then
+CC=gcc
+CXX=g++
+fi
+case ${ABI} in
+  "PROFILE")
+    CFLAGS="-Wall -Wstrict-prototypes -fprofile-arcs -ftest-coverage -pg  -UNDEBUG"
+    CXXFLAGS="-Wall  -fprofile-arcs -ftest-coverage -pg -UNDEBUG"
+    ;;
+  "DEBUG")
+    CFLAGS="-Wall -Wstrict-prototypes -g"
+    CXXFLAGS="-Wall  -g"
+    ;;
+  "FAST")
+    CFLAGS="-DNDEBUG -O3 -msse -mmmx -msse2 -msse3"
+    CXXFLAGS="-DNDEBUG -O3 -msse -mmmx -msse2 -msse3"
+    ;;
+  *)
+    echo "INVALID ABI GIVEN"
+    exit -1;
+esac
+
+COMPILE_DIR=$(dirname ${SOURCE_DIR})/ART-COMPILE/
+ABI_DIR=${COMPILE_DIR}/$(uname)_$(uname -m)-${ABI}
+mkdir -p ${ABI_DIR}
+
+if [ 0 -eq 1 ]; then
+  #################################################################################
+  #Get and build Insight-3.8.0
+  ITK_SOURCE=${COMPILE_DIR}/InsightToolkit-3.8.0
+  ITK_BUILD=${ABI_DIR}/InsightToolkit-3.8.0-build
+  pushd ${COMPILE_DIR}
+  if [ ! -d ${ITK_SOURCE} ]; then
+    WGETBIN=$(which wget)
+    if [ "x${WGETBIN}" == "x" ] || [ ! -f ${WGETBIN} ]; then
+      echo "ERROR: Can not build without wget to retrive ITK."
+      exit -1;
+    fi
+    wget http://voxel.dl.sourceforge.net/sourceforge/itk/InsightToolkit-3.8.0.tar.gz
+    tar -xzvf InsightToolkit-3.8.0.tar.gz
+    popd
+  fi
+  mkdir -p ${ITK_BUILD}
+  pushd ${ITK_BUILD}
+  ##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+  CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${ITK_SOURCE} -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILDNAME:STRING=${ITK_BUILD_NAME} -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2
+  if [ $? -ne 0 ]; then
+    echo "ERROR in building ITK"
+    exit -1
+  fi
+else
+  #################################################################################
+  #Get and build InsightToolkit-CVS
+  LOCAL_PATH=$(dirname $0)
+  echo "${LOCAL_PATH}"
+  if [ "${LOCAL_PATH}" == "." ]; then
+    LOCAL_PATH=$(pwd)
+  fi
+  echo "${LOCAL_PATH}"
+  ITK_TARBALL=${LOCAL_PATH}/InsightToolkit-CVS.tar.gz
+  ITK_SOURCE=${COMPILE_DIR}/Insight
+  ITK_BUILD=${ABI_DIR}/InsightToolkit-CVS-build
+  if [ ! -f ${ITK_SOURCE}/CMakeLists.txt ] || [ ${LOCAL_PATH}/InsightToolkit-CVS.tar.gz -nt ${ITK_SOURCE}/CMakeLists.txt ]; then
+    mkdir -p ${ITK_SOURCE}
+    pushd ${COMPILE_DIR}
+    tar -xvzf ${ITK_TARBALL}
+    touch ${ITK_SOURCE}/CMakeLists.txt
+    popd
+  fi
+  mkdir -p ${ITK_BUILD}
+  pushd ${ITK_BUILD}
+  ##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+  CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${ITK_SOURCE} \
+    -DBUILD_EXAMPLES:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DBUILDNAME:STRING=${ITK_BUILD_NAME} \
+    -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2 \
+    -DITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON \
+    -DITK_USE_REVIEW:BOOL=ON \
+    -DITK_USE_TRANSFORM_IO_FACTORIES:BOOL=ON \
+    -DITK_USE_OPTIMIZED_REGISTRATION_METHODS:BOOL=ON \
+    -DITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON \
+    -DITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE:BOOL=ON
+  if [ $? -ne 0 ]; then
+    echo "ERROR in configuring ITK"
+    exit -1
+  fi
+fi
+## Auto-determine the number of processors on this computer
+case "$(uname)" in
+  "Linux")
+  maxproc=$(grep processor /proc/cpuinfo | wc | awk '{print $1}')
+  ;;
+  "Darwin")
+  maxproc=$(sysctl -n hw.ncpu)
+  ;;
+  *)
+  echo "Platform not recognized"
+  maxproc=1;
+esac
+if [ "x${maxproc}" == "x" ] || [ ${maxproc} -lt 1 ]; then
+  maxproc=1;
+fi
+make -j${maxproc}
+popd
+
+#################################################################################
+#Build ART
+mkdir -p ${ABI_DIR}/ART
+pushd ${ABI_DIR}/ART
+##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${SOURCE_DIR}/ -DBUILD_EXAMPLES:BOOL=ON -DBUILD_TESTING:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DITK_DIR:PATH=${ITK_BUILD} -DABI:STRING=${ABI} -DBUILDNAME:STRING=${ITK_BUILD_NAME}  -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2
+
+
+case "$(uname)" in
+  "Linux")
+  maxproc=$(grep processor /proc/cpuinfo | wc | awk '{print $1}')
+  ;;
+  "Darwin")
+  maxproc=$(sysctl -n hw.ncpu)
+  ;;
+  *)
+  echo "Platform not recognized"
+  maxproc=1;
+esac
+make ${BUILDTYPE}
+popd
+
+
diff --git a/BRAINSConstellationDetector/buildTool.sh b/BRAINSConstellationDetector/buildTool.sh
new file mode 100755
index 00000000..7b23a0eb
--- /dev/null
+++ b/BRAINSConstellationDetector/buildTool.sh
@@ -0,0 +1,215 @@
+#!/bin/bash
+##  This build tool was written by Hans J. Johnson hans-johnson@uiowa.edu
+
+PROJECTNAME=MedicalSliceViewer
+
+BUILDNAME=$(uname)_$(uname -m)-$(hostname -s)
+
+SOURCE_DIR=$(dirname $0)
+if [ "${SOURCE_DIR}" == "." ]; then
+  SOURCE_DIR=$(pwd)
+fi
+
+if [ $# -lt 1 ]; then
+  ABI="FAST"
+else
+  ABI=$1
+fi
+ITK_BUILD_NAME=$(uname).$(uname -m).${ABI}
+
+## Valid types are Experimental, Continous, Nightly
+if [ $# -lt 2 ]; then
+  BUILDTYPE=Experimental
+else
+  BUILDTYPE=$2
+fi
+
+### Use the newer compilers if they are available
+CC=/usr/bin/gcc-4.2
+CXX=/usr/bin/g++-4.2
+if [ ! -f ${CC} ] || [ ! -f ${CXX} ]; then
+CC=gcc
+CXX=g++
+fi
+## Removed -Wshadow from build to prevent qt warnings form hiding current errors
+FLAGS_FROM_QT_BUILD="-arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.5 -Wall -W "
+case ${ABI} in
+  "PROFILE")
+    CFLAGS="-Wall -Wstrict-prototypes -fprofile-arcs -ftest-coverage -pg  -UNDEBUG ${FLAGS_FROM_QT_BUILD}"
+    CXXFLAGS="-Wall  -fprofile-arcs -ftest-coverage -pg -UNDEBUG ${FLAGS_FROM_QT_BUILD}"
+    ;;
+  "OPTDEBUG")
+    CFLAGS="-Wstrict-prototypes -g -O1 ${FLAGS_FROM_QT_BUILD}"
+    CXXFLAGS=" -g -O1 ${FLAGS_FROM_QT_BUILD}"
+    ;;
+  "DEBUG")
+    CFLAGS=" -g ${FLAGS_FROM_QT_BUILD}"
+    CXXFLAGS=" -g ${FLAGS_FROM_QT_BUILD}"
+    ;;
+  "FAST")
+    CFLAGS="-DNDEBUG -O3 -msse -mmmx -msse2 -msse3  ${FLAGS_FROM_QT_BUILD}"
+    CXXFLAGS="-DNDEBUG -O3 -msse -mmmx -msse2 -msse3  ${FLAGS_FROM_QT_BUILD}"
+    ;;
+  *)
+    echo "INVALID ABI GIVEN"
+    exit -1;
+esac
+## Auto-determine the number of processors on this computer
+case "$(uname)" in
+  "Linux")
+  maxproc=$(grep processor /proc/cpuinfo | wc | awk '{print $1}')
+  ;;
+  "Darwin")
+  maxproc=$(sysctl -n hw.ncpu)
+  ;;
+  *)
+  echo "Platform not recognized"
+  maxproc=1;
+esac
+if [ "x${maxproc}" == "x" ] || [ ${maxproc} -lt 1 ]; then
+  maxproc=1;
+fi
+
+COMPILE_DIR=$(dirname ${SOURCE_DIR})/${PROJECTNAME}-COMPILE/
+ABI_DIR=${COMPILE_DIR}/$(uname)_$(uname -m)-${ABI}
+mkdir -p ${ABI_DIR}
+
+###### Find QT
+QTSETDIR ()
+{
+  testdir=$1;
+  if [ -z "${QTDIR}" ] && [ -d ${testdir} ]; then
+    export QTDIR=${testdir};
+  fi
+}
+
+
+QTSETDIR /opt/qt-4.6.1
+QTSETDIR /opt/qt-4.6-rc1
+QTSETDIR /opt/qt-4.5.2/
+QTSETDIR /opt/qt-everywhere-opensource-src-4.6.1
+QTSETDIR /usr
+
+if [ -z "${QTDIR}" ] || [ ! -d ${QTDIR} ]; then
+  echo "Valid QTDIR not found: ${QTDIR} : You will likely have to modify this script."
+  exit -1;
+fi
+echo "Valid QTDIR found: ${QTDIR}"
+
+##################
+ITK_BUILD=${ABI_DIR}/InsightToolkit-CVS-build
+
+if [ 1 == 1 ];then  ## Temporary bypass of building ITK
+  LOCAL_PATH=$(dirname $0)
+  echo "${LOCAL_PATH}"
+  if [ "${LOCAL_PATH}" == "." ]; then
+    LOCAL_PATH=$(pwd)
+  fi
+  echo "${LOCAL_PATH}"
+  #################################################################################
+  #Get and build InsightToolkit-CVS
+  ITK_SOURCE=${COMPILE_DIR}/Insight
+  ITK_BUILD=${ABI_DIR}/InsightToolkit-CVS-build
+  if [ ! -f ${ITK_SOURCE}/CMakeLists.txt ] || [ ${LOCAL_PATH}/build${PROJECTNAME}.sh -nt ${ITK_SOURCE}/CMakeLists.txt ]; then
+    mkdir -p ${ITK_SOURCE}
+    pushd ${COMPILE_DIR}
+    cvs -d :pserver:anoncvs:@www.vtk.org:/cvsroot/Insight login
+    cvs -d :pserver:anoncvs@www.vtk.org:/cvsroot/Insight checkout -D 2010-01-30 Insight
+    popd
+  fi
+  mkdir -p ${ITK_BUILD}
+  pushd ${ITK_BUILD}
+  ##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+  CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${ITK_SOURCE} \
+    -DBUILD_EXAMPLES:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DBUILDNAME:STRING=${ITK_BUILD_NAME} \
+    -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2 \
+    -DITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON \
+    -DITK_USE_REVIEW:BOOL=ON \
+    -DITK_USE_TRANSFORM_IO_FACTORIES:BOOL=ON \
+    -DITK_USE_OPTIMIZED_REGISTRATION_METHODS:BOOL=ON \
+    -DITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE:BOOL=ON
+  if [ $? -ne 0 ]; then
+    echo "ERROR in configuring ITK"
+    exit -1
+  fi
+  make -j${maxproc}
+  popd
+fi  ## Temporary bypass of building ITK
+
+VTK_BUILD=${ABI_DIR}/VTK-CVS-build
+
+if [ 1 == 1 ] ; then  ## Skipping local vtk
+export PATH=${QTDIR}/bin:${PATH}
+  #################################################################################
+  #Get and build VTK-CVS
+  VTK_SOURCE=${COMPILE_DIR}/VTK
+  if [ ! -f ${VTK_SOURCE}/CMakeLists.txt ] || [ ${LOCAL_PATH}/build${PROJECTNAME}.sh -nt ${VTK_SOURCE}/CMakeLists.txt ]; then
+    mkdir -p ${COMPILE_DIR}
+    pushd ${COMPILE_DIR}
+    cvs -d :pserver:anonymous:vtk@public.kitware.com:/cvsroot/VTK login
+    cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTK checkout -D 2010-01-30 VTK
+    popd
+  fi
+  mkdir -p ${VTK_BUILD}
+  pushd ${VTK_BUILD}
+  ##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+  CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${VTK_SOURCE} \
+    -DBUILD_EXAMPLES:BOOL=OFF \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DBUILD_SHARED_LIBS:BOOL=OFF \
+    -DBUILDNAME:STRING=${VTK_BUILD_NAME} \
+    -DVTK_USE_CARBON:BOOL=OFF \
+    -DVTK_USE_COCOA:BOOL=ON \
+    -DVTK_USE_QT:BOOL=ON \
+    -DVTK_USE_QVTK:BOOL=ON \
+    -DVTK_USE_GUISUPPORT:BOOL=ON \
+    -DQT_QMAKE_EXECUTABLE:FILEPATH=${QTDIR}/bin/qmake \
+    -DQT_SEARCH_PATH:FILEPATH=${QTDIR} \
+    -DDESIRED_QT_VERSION:STRING=4 \
+    -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2
+
+
+  if [ $? -ne 0 ]; then
+    echo "ERROR in configuring VTK"
+    exit -1
+  fi
+  make -j${maxproc}
+  popd
+fi  ## Skipping local VTK
+
+#################################################################################
+#Build ${PROJECTNAME}
+APP_DIR=${ABI_DIR}/${PROJECTNAME}
+mkdir -p ${APP_DIR}
+pushd ${APP_DIR}
+##NOTE:  Using cmake and all comand line options.  Normally ccmake would be used.
+CMAKE_MODULE_PATH=${LOCAL_PATH}/CMake CC=${CC} CXX=${CXX} CFLAGS=${CFLAGS} CXXFLAGS=${CXXFLAGS} cmake ${SOURCE_DIR}/ -DBUILD_EXAMPLES:BOOL=ON -DBUILD_TESTING:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF -DUSE_PRIVATE:BOOL=ON -DCOMPILE_ITKEMS:BOOL=ON -DVTK_DIR:PATH=${VTK_BUILD} -DITK_DIR:PATH=${ITK_BUILD} -DABI:STRING=${ABI} -DBUILDNAME:STRING=${ITK_BUILD_NAME} -DCOVERAGE_COMMAND:FILEPATH=/usr/bin/gcov-4.2 -DUSE_ITK_LIBRARY:BOOL=ON -DUSE_VTK_LIBRARY:BOOL=ON \
+                  -DCOMPILE_DISPLAY:BOOL=OFF \
+                  -DBUILD_TESTING:BOOL=ON \
+                  -DUSE_QT_LIBRARY:BOOL=ON \
+                  -DCMAKE_INSTALL_PREFIX:PATH=/opt/${PROJECTNAME} \
+                  -DQT_QMAKE_EXECUTABLE:FILEPATH=${QTDIR}/bin/qmake \
+                  -DQT_SEARCH_PATH:FILEPATH=${QTDIR} \
+                  -DDESIRED_QT_VERSION:STRING=4
+
+## NOTE: There is an interaction between COMPILE_DISPLAY and USE_QT_LIBRARY
+
+
+case "$(uname)" in
+  "Linux")
+  maxproc=$(grep processor /proc/cpuinfo | wc | awk '{print $1}')
+  ;;
+  "Darwin")
+  maxproc=$(sysctl -n hw.ncpu)
+  ;;
+  *)
+  echo "Platform not recognized"
+  maxproc=1;
+esac
+make -j2
+popd
+
+
diff --git a/BRAINSConstellationDetector/docs/README b/BRAINSConstellationDetector/docs/README
new file mode 100644
index 00000000..d4504150
--- /dev/null
+++ b/BRAINSConstellationDetector/docs/README
@@ -0,0 +1,18 @@
+README For BRAINSConstellationDetector Image Analysis Tool
Author: Wei Lu

Introduction
The BRAINSConstellationDetector project is designed for image registration, constellation (arbitrary landmark) detection, landmark visualization and manipulation for human brain MR scans. It is a subproject/plug-in for the BRAINS image analysis toolkit.
For more information about this project please visit our homepage at NITRC.
BRAINS:
http://www.nitrc.org/projects/brains/
BRAINSConstellationDetector:
http://www.nitrc.org/projects/brainscdetector/
+
Objective
This README file will guide you on how to 
1.  Download the source code
2.  Build the non-GUI version
3.  Build the Qt-based GUI version
4.  Run the software
Note: 
A rtf version of this README file is also available at
https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer/brainscdetector/docs/README.rtf
You will need a NITRC account to access this file.
+
Download the project source code
1.  Download and install SVN client at
http://subversion.apache.org/packages.html 
2.  Download BRAINSConstellationDetector source files from NITRC SVN repository by:
svn checkout https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer
+
Build the non-GUI version
Use bash script (in progress)
Run the following command:
mkdir brainscdetector-build 
cd brainscdetector-build 
bash ../MedicalSliceViewer/brainscdetector/buildTool.sh
+
Use CMake
1.  Download CMake source file at
http://www.cmake.org/cmake/resources/software.html 
2.  Build and install CMake (version >= 2.8)
3.  Run the following command:
+3.1  For Mac OSX 64-bit
mkdir brainscdetector-build 
cd brainscdetector-build 
cmake –C ../MedicalSliceViewer/InitialCache-OSX64.cmake ../MedicalSliceViewer 
make
3.2  For Linux 64-bit
mkdir brainscdetector-build 
cd brainscdetector-build 
cmake –C ../MedicalSliceViewer/InitialCache-Linux64.cmake ../MedicalSliceViewer 
make

Build the Qt-based GUI version
Use bash script (in progress)
Run the following command:
mkdir brainscdetector-build 
cd brainscdetector-build 
bash ../MedicalSliceViewer/brainscdetector/buildTool.sh
+
Use CMake
1.  Download Qt libraries (version >= 4.6.2) at
http://qt.nokia.com/downloads 
2.  Install the binary package
3.  Download CMake source file (version >= 2.8) at
http://www.cmake.org/cmake/resources/software.html 
4.  Build and install CMake
5.  Run the following command:
+5.1  For Mac OSX 64-bit
mkdir brainscdetector-build 
cd brainscdetector-build 
cmake –DBUILD_MEDICAL_SLICEVIEWER_GUI=ON –C ../MedicalSliceViewer/InitialCache-OSX64.cmake ../MedicalSliceViewer 
5.2  For Linux 64-bit
mkdir brainscdetector-build 
cd brainscdetector-build 
cmake –DBUILD_MEDICAL_SLICEVIEWER_GUI=ON –C ../MedicalSliceViewer/InitialCache-Linux64.cmake ../MedicalSliceViewer 
6.  Locate qmake install path for makefiles by for e.g. ccmake
+7.  Run make
+
Run the software
There are two important executables: the modeler and the detector. The modeler helps the user to train his/her model with arbitrary landmarks. The detector will try to estimate those landmarks positions for a given new brain MR image.
+
Run the modeler
Usage:
./BRAINSConstellationModeler 
-i  or --trainingFile  
Where
1.  trainingFile is the input training files list filename without eye centers.
For more details on setting optional parameters please type ./BRAINSConstellationModeler -h
+
Run the detector
Usage:
./BRAINSConstellationDetectorNew (w/o GUI) or
./BRAINSConstellationDetectorGUI (w/ GUI) 
-i  or --inputVolume  
Where
1.  inputFilename is the filename of the input image file.

+A sample trained model file can be found at
brainscdetector/TestData/input/newT1InputModelWithVN4.mdl
The corresponding trained llsModel file can be found at
brainscdetector/TestData/input/llsModel.txt
+
+After running the detector, a Slicer fcsv landmark file and a Slicer mrml scene file for those named landmarks in the original physical space will be also written to the working directory.
+
+For more details on setting optional parameters please type ./BRAINSConstellationDetectorNew -h for non-GUI version or
./BRAINSConstellationDetectorGUI -h for GUI version
+
Run tests (In progress)
1.  For non-GUI version, enter
ctest -R BRAINSMSVNoGUITest_T1
2.  For GUI version, enter
ctest -R BRAINSMSVTest_T1

diff --git a/BRAINSConstellationDetector/docs/README.rtf b/BRAINSConstellationDetector/docs/README.rtf
new file mode 100644
index 00000000..92c34bfb
--- /dev/null
+++ b/BRAINSConstellationDetector/docs/README.rtf
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\fi-360\li5040\lin5040 }{\listlevel\levelnfc4\levelnfcn4\leveljc0\leveljcn0\levelfollow0\levelstartat1\lvltentative\levelspace360\levelindent0{\leveltext\leveltemplateid67698713\'02\'07.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 
\fi-360\li5760\lin5760 }{\listlevel\levelnfc2\levelnfcn2\leveljc2\leveljcn2\levelfollow0\levelstartat1\lvltentative\levelspace360\levelindent0{\leveltext\leveltemplateid67698715\'02\'08.;}{\levelnumbers\'01;}\rtlch\fcs1 \af0 \ltrch\fcs0 
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\fi-720\li1080\lin1080 }{\listlevel\levelnfc0\levelnfcn0\leveljc0\leveljcn0\levelfollow0\levelstartat1\levellegal\levelspace0\levelindent0{\leveltext\'05\'00.\'01.\'02;}{\levelnumbers\'01\'03\'05;}\rtlch\fcs1 \af0 \ltrch\fcs0 \fbias0 
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\af0 \ltrch\fcs0 \fbias0 \fi-2160\li2520\lin2520 }{\listlevel\levelnfc0\levelnfcn0\leveljc0\leveljcn0\levelfollow0\levelstartat1\levellegal\levelspace0\levelindent0{\leveltext\'0f\'00.\'01.\'02.\'03.\'04.\'05.\'06.\'07;}{\levelnumbers
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{\pntxtb (}{\pntxta )}}\pard\plain \ltrpar\qc \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \b\fs36\insrsid8658335\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 README}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
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\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \fs28\insrsid8658335\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Author: Wei Lu}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \fs28\insrsid1907747\charrsid11220353 
\par }\pard\plain \ltrpar\s21\ql \li0\ri0\sb480\sl276\slmult1\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \ab\af31503\afs28\alang1033 \ltrch\fcs0 
\b\fs28\cf21\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1907747\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 Table of Contents
\par }\pard\plain \ltrpar\s22\ql \li0\ri0\sb120\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\b\caps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\field\fldedit{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1907747\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  TOC \\o "
\hich\af31506\dbch\af17\loch\f31506 1-3" \\h \\z \\u }}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Introduction}{\rtlch\fcs1 \af31507\alang1024 
\ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490521 \\h }{\rtlch\fcs1 
\af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320031000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 
\ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 2}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Objective}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }
{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490522 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320032000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 2}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Download the project source code}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490523 \\h }{\rtlch\fcs1 \af31507\alang1024 
\ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320033000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 2}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Build the non-GUI version}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490524 \\h }{\rtlch\fcs1 \af31507\alang1024 
\ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320034000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 2}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\s23\ql \li240\ri0\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin240\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\scaps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 
Use bash script (in progress)}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506  PAGER\hich\af31506\dbch\af17\loch\f31506 EF _Toc133490525 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 
08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320035000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506 2}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Use CMake}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }
{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490526 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320036000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 3}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\s22\ql \li0\ri0\sb120\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\b\caps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 
Build the Qt-based GUI version}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490527 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 
08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320037000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506 3}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\s23\ql \li240\ri0\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin240\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\scaps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 
Use bash script (in progress)}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490528 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 
08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320038000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506 3}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Use CMake}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }
{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490529 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500320039000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 3}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\s22\ql \li0\ri0\sb120\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\b\caps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 
Run the software}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490530 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 
08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500330030000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\hich\af31506\dbch\af17\loch\f31506 4}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \b0\caps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\s23\ql \li240\ri0\widctlpar\tqr\tldot\tx8290\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin240\itap0 \rtlch\fcs1 \af31507\afs22\alang1033 \ltrch\fcs0 
\scaps\fs22\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Run the modeler}
{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 
 PAGEREF _Toc133490531 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500330031000000000000}}
}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 4}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Run the detector}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \tab }
{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490532 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500330032000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 4}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259\charrsid2557314 \hich\af31506\dbch\af17\loch\f31506 Run tests (In progress)}{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 
\tab }{\field{\*\fldinst {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 \lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506  PAGEREF _Toc133490533 \\h }{\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid11999925 {\*\datafield 08d0c9ea79f9bace118c8200aa004ba90b02000000080000000e0000005f0054006f0063003100330033003400390030003500330033000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\lang1024\langfe1024\noproof\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 5}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507\alang1024 \ltrch\fcs0 
\scaps0\fs24\lang1024\langfe1024\dbch\af31505\noproof\insrsid14302259 
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid1907747 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 }}\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid1907747 \rtlch\fcs1 
\af31507\afs24\alang1033 \ltrch\fcs0 \fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 \sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid1907747\charrsid11220353 
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\pagebb\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid11762073\charrsid11220353 {\*\bkmkstart _Toc133490521}\hich\af31506\dbch\af31501\loch\f31506 
Introduction{\*\bkmkend _Toc133490521}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11762073 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
The BRAINSConstellationDetector project is designed for image registration, constellation (arbitrary landmark) detection, landmark visualization and manipulation for human brain MR scans.}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9962739\charrsid11220353 
\hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 It is a subproject/plug-in for the BRAINS image analysis toolkit.
\par \hich\af31506\dbch\af17\loch\f31506 Fo}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1774150 \hich\af31506\dbch\af17\loch\f31506 r more information about}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
 this proje}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1774150 \hich\af31506\dbch\af17\loch\f31506 ct please visit our homepages at}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  NITRC.
\par \hich\af31506\dbch\af17\loch\f31506 BRAINS:\line }{\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://www.nitrc.org/projects/brains/" }{\rtlch\fcs1 
\af31507 \ltrch\fcs0 \insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b4c00000068007400740070003a002f002f007700770077002e006e0069007400720063002e006f00720067002f00700072006f006a0065006300740073002f0062007200610069006e0073002f000000000000000000
00}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs18\ul\cf19\insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 http://www.nitrc.org/projects/brains/}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 
\af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 
\par \hich\af31506\dbch\af17\loch\f31506 BRAINSConstellationDetector}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9962739\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 :}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \line }
{\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://www.nitrc.org/projects/brainscdet\hich\af31506\dbch\af17\loch\f31506 ector/" }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b5e00000068007400740070003a002f002f007700770077002e006e0069007400720063002e006f00720067002f00700072006f006a0065006300740073002f0062007200610069006e00730063006400650074006500
630074006f0072002f00000000000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs18\ul\cf19\insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 http://www.nitrc.org/projects/brainscdetector/}}}\sectd \ltrsect
\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid4018903 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid4018903\charrsid11220353 {\*\bkmkstart _Toc133490522}\hich\af31506\dbch\af31501\loch\f31506 Objective
{\*\bkmkend _Toc133490522}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11762073 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 This}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid4018903\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  README file}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  will guide you on how to }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid4018903\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls11\adjustright\rin0\lin720\itap0\pararsid10707604\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Downloa}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid10707604\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 d the source code}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 2.\tab}\hich\af31506\dbch\af17\loch\f31506 Build }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid658083\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 the non-GUI version
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid658083\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 3.\tab}\hich\af31506\dbch\af17\loch\f31506 Build the Qt-based GUI version}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid4018903\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid4018903\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 4.\tab}\hich\af31506\dbch\af17\loch\f31506 Run the software
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid4018903 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4018903\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Note: }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid8658335\charrsid11220353 \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1774150 \hich\af31506\dbch\af17\loch\f31506 A plain text version of t}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4018903\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
his README file is also available at}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8658335\charrsid11220353 \line }{\field{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1774150 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "}{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid1774150\charrsid1774150 \hich\af31506\dbch\af17\loch\f31506 https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer/brainscdetector/docs/README}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1774150 
\hich\af31506\dbch\af17\loch\f31506 " }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11999925 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b020000001700000069000000680074007400700073003a002f002f007700770077002e006e0069007400720063002e006f00720067002f00730076006e002f0062007200610069006e00730063006400650074006500630074006f0072002f006200720061006e00630068006500
73002f007700650069002d006c0075002f004d00650064006900630061006c0053006c006900630065005600690065007700650072002f0062007200610069006e00730063006400650074006500630074006f0072002f0064006f00630073002f0052004500410044004d0045000000e0c9ea79f9bace118c8200aa004ba9
0bd2000000680074007400700073003a002f002f007700770077002e006e0069007400720063002e006f00720067002f00730076006e002f0062007200610069006e00730063006400650074006500630074006f0072002f006200720061006e0063006800650073002f007700650069002d006c0075002f004d0065006400
6900630061006c0053006c006900630065005600690065007700650072002f0062007200610069006e00730063006400650074006500630074006f0072002f0064006f00630073002f0052004500410044004d00450000000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 
\cs18\ul\cf19\insrsid1774150\charrsid12415015 \hich\af31506\dbch\af17\loch\f31506 https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer\hich\af31506\dbch\af17\loch\f31506 /brainscdetector/docs/README}}}\sectd \ltrsect
\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8658335\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4018903\charrsid11220353 
\par \hich\af31506\dbch\af17\loch\f31506 You }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11762073\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 will }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4018903\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
need a NITRC account to access this file.
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid11762073\charrsid11220353 {\*\bkmkstart _Toc133490523}\hich\af31506\dbch\af31501\loch\f31506 
Download the }{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid6834753\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 project }{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid11762073\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 
source code{\*\bkmkend _Toc133490523}
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls4\adjustright\rin0\lin720\itap0\pararsid16341485\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Download and install SVN client at}{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid16341485\charrsid11220353 
\par }\pard \ltrpar\s20\ql \li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid16341485\contextualspace {\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16341485\charrsid11220353 
\hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://subversion.apache.org/packages.html" }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b02000000170000002b00000068007400740070003a002f002f00730075006200760065007200730069006f006e002e006100700061006300680065002e006f00720067002f007000610063006b0061006700650073002e00680074006d006c000000e0c9ea79f9bace118c8200aa
004ba90b5600000068007400740070003a002f002f00730075006200760065007200730069006f006e002e006100700061006300680065002e006f00720067002f007000610063006b0061006700650073002e00680074006d006c00000000000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 
\cs18\ul\cf19\insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 http://subversion.a\hich\af31506\dbch\af17\loch\f31506 pache.org/packages.html}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 2.\tab}}\pard \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls4\adjustright\rin0\lin720\itap0\pararsid16341485\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
Download BRAINSConstellationDetector source files from NITRC SVN repository by:
\par }\pard \ltrpar\s20\ql \li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid16341485\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
svn checkout https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 {\*\bkmkstart _Toc133490524}\hich\af31506\dbch\af31501\loch\f31506 Build }{
\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid658083\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 the non-}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 GUI}{\rtlch\fcs1 
\af31503 \ltrch\fcs0 \f31506\insrsid658083\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506  version}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 {\*\bkmkend _Toc133490524}
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 {\*\bkmkstart _Toc133490525}\hich\af31506\dbch\af31501\loch\f31506 Use }{
\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506 bash script (in progress)}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid8658335\charrsid11220353 {\*\bkmkend _Toc133490525}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8658335\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Run the following command:\line }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \f2\insrsid13654367\charrsid11220353 \hich\af2\dbch\af17\loch\f2 mkdir brainscdetector-build}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid13654367\charrsid11220353 \line \hich\af2\dbch\af17\loch\f2 cd brainscdetector-build}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid8658335\charrsid11220353 \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid1206937\charrsid11220353 \hich\af2\dbch\af17\loch\f2 bash }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid13654367\charrsid11220353 \hich\af2\dbch\af17\loch\f2 
../MedicalSliceViewer/brainscdetector/}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid1206937\charrsid11220353 \hich\af2\dbch\af17\loch\f2 buildTool.sh
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 {\*\bkmkstart _Toc133490526}\hich\af31506\dbch\af31501\loch\f31506 Use}{
\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af31501\loch\f31506  CMake}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 {\*\bkmkend _Toc133490526}
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls8\adjustright\rin0\lin720\itap0\pararsid8658335\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Download CMake source file at\line }
{\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://www.cmake.org/cmake/resources/software.html" }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b02000000170000003300000068007400740070003a002f002f007700770077002e0063006d0061006b0065002e006f00720067002f0063006d0061006b0065002f007200650073006f00750072006300650073002f0073006f006600740077006100720065002e00680074006d00
6c000000e0c9ea79f9bace118c8200aa004ba90b6600000068007400740070003a002f002f007700770077002e0063006d0061006b0065002e006f00720067002f0063006d0061006b0065002f007200650073006f00750072006300650073002f0073006f006600740077006100720065002e00680074006d006c00000000
000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs18\ul\cf19\insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 http://www.cmake.org/cmake/resources/software.html}}}\sectd \ltrsect
\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid16341485\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid658083\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid658083\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 2.\tab}\hich\af31506\dbch\af17\loch\f31506 Build and install CMake (version >= 2.8)}{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid13654367\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 3.\tab}}\pard \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls8\adjustright\rin0\lin720\itap0\pararsid5532841\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
Run the following command}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid658083\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 :}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid5532841 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid5532841 \hich\af31506\dbch\af17\loch\f31506 3.1\tab}}\pard \ltrpar
\s20\ql \fi-720\li1080\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls8\ilvl1\adjustright\rin0\lin1080\itap0\pararsid5532841\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid5532841 \hich\af31506\dbch\af17\loch\f31506 For Mac OSX 64-bit
}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid658083\charrsid11220353 \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid13654367\charrsid5532841 \hich\af2\dbch\af17\loch\f2 mkdir brai\hich\af2\dbch\af17\loch\f2 nscdetector-build}{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \f2\insrsid9320399\charrsid5532841 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid13654367\charrsid5532841 \line \hich\af2\dbch\af17\loch\f2 cd }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid658083\charrsid5532841 
\hich\af2\dbch\af17\loch\f2 brainscdetector-build}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid5532841 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid658083\charrsid5532841 \line \hich\af2\dbch\af17\loch\f2 
cmake }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid5532841 \loch\af2\dbch\af17\hich\f2 \endash \loch\f2 C }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid658083\charrsid5532841 \hich\af2\dbch\af17\loch\f2 ../MedicalSliceViewer/InitialCache}
{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841 \hich\af2\dbch\af17\loch\f2 -OSX64}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid658083\charrsid5532841 \hich\af2\dbch\af17\loch\f2 .cmake ../MedicalSliceViewer}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid9320399\charrsid5532841 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid658083\charrsid5532841 \line \hich\af2\dbch\af17\loch\f2 make}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid5532841\charrsid5532841 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid5532841\charrsid5532841 \hich\af31506\dbch\af17\loch\f31506 3.2\tab}\hich\af31506\dbch\af17\loch\f31506 For Linux 64-bit\line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid5532841\charrsid11220353 \hich\af2\dbch\af17\loch\f2 mkdir brainscdetector-build \line cd brainscdetector-build \line cmake \hich\f2 \endash \loch\f2 C ../MedicalSliceViewer/InitialCache}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841 
\hich\af2\dbch\af17\loch\f2 -Linux64}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841\charrsid11220353 \hich\af2\dbch\af17\loch\f2 .cmake ../MedicalSliceViewer \line make}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid1206937\charrsid5532841 
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 {\*\bkmkstart _Toc133490527}\hich\af31506\dbch\af31501\loch\f31506 
Build the Qt-based GUI version{\*\bkmkend _Toc133490527}
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid8658335\charrsid11220353 {\*\bkmkstart _Toc133490528}\hich\af31506\dbch\af31501\loch\f31506 
Use bash script (in progress){\*\bkmkend _Toc133490528}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8658335\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Run the following command:\line }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \f2\insrsid8658335\charrsid11220353 \hich\af2\dbch\af17\loch\f2 mkdir brainscdetector-build}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid8658335\charrsid11220353 \line \hich\af2\dbch\af17\loch\f2 cd brainscdetector-build}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid8658335\charrsid11220353 \line \hich\af2\dbch\af17\loch\f2 bash ../MedicalSliceViewer\hich\af2\dbch\af17\loch\f2 /brainscdetector/buildTool.sh}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid13654367\charrsid11220353 
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 {\*\bkmkstart _Toc133490529}\hich\af31506\dbch\af31501\loch\f31506 Use CMake
{\*\bkmkend _Toc133490529}
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li360\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls9\adjustright\rin0\lin360\itap0\pararsid8658335\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Download Qt libraries (version > }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \insrsid5716420 \hich\af31506\dbch\af17\loch\f31506 =}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 4.6.2) at\line }{\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://qt.nokia.com/downloads" }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b02000000170000001e00000068007400740070003a002f002f00710074002e006e006f006b00690061002e0063006f006d002f0064006f0077006e006c006f006100640073000000e0c9ea79f9bace118c8200aa004ba90b3c00000068007400740070003a002f002f0071007400
2e006e006f006b00690061002e0063006f006d002f0064006f0077006e006c006f00610064007300000000000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs18\ul\cf19\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
http://qt.nokia.com/downloads}}}\sectd \ltrsect\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 2.\tab}\hich\af31506\dbch\af17\loch\f31506 Install the binary package
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 3.\tab}\hich\af31506\dbch\af17\loch\f31506 Download CMake source file (versi
\hich\af31506\dbch\af17\loch\f31506 on >= 2.8) at\line }{\field\flddirty{\*\fldinst {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  HYPERLINK "http://www.cmake.org/cmake/resources/software.html" }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11999925\charrsid11220353 {\*\datafield 
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b6600000068007400740070003a002f002f007700770077002e0063006d0061006b0065002e006f00720067002f0063006d0061006b0065002f007200650073006f00750072006300650073002f0073006f0066007400
77006100720065002e00680074006d006c00000000000000000000}}}{\fldrslt {\rtlch\fcs1 \af31507 \ltrch\fcs0 \cs18\ul\cf19\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 http://www.cmake.org/cmake/resources/software.html}}}\sectd \ltrsect
\linex0\endnhere\sectdefaultcl\sectrsid4018903\sftnbj {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 4.\tab}\hich\af31506\dbch\af17\loch\f31506 Build and install CMake
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid13654367\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 5.\tab}\hich\af31506\dbch\af17\loch\f31506 Run the following command:}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid5532841\charrsid5532841 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid5532841 \hich\af31506\dbch\af17\loch\f31506 5.1\tab}}\pard \ltrpar
\s20\ql \fi-720\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls9\ilvl1\adjustright\rin0\lin720\itap0\pararsid5532841\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid5532841 \hich\af31506\dbch\af17\loch\f31506 For Mac OSX 64-bit}{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid5532841\charrsid11220353 \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841\charrsid5532841 \hich\af2\dbch\af17\loch\f2 mkdir brainscdetector-build \line cd brainscdete\hich\af2\dbch\af17\loch\f2 
ctor-build \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841\charrsid11220353 \hich\af2\dbch\af17\loch\f2 cmake \hich\f2 \endash \loch\f2 DBUILD_MEDICAL_SLICEVIEWER_GUI=ON \hich\f2 \endash \loch\f2 C ../MedicalSliceViewer/InitialCache}{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841 \hich\af2\dbch\af17\loch\f2 -OSX64}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841\charrsid11220353 \hich\af2\dbch\af17\loch\f2 .cmake ../MedicalSliceViewer }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid5532841\charrsid5532841 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid5532841\charrsid5532841 \hich\af31506\dbch\af17\loch\f31506 5.2\tab}\hich\af31506\dbch\af17\loch\f31506 For Linux 64-bit\line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid5532841\charrsid11220353 \hich\af2\dbch\af17\loch\f2 mkdir brainscdetector-build \line cd brainscdetector-build \line cmake \hich\f2 \endash \loch\f2 DBUILD_MEDICAL_SLICEVIEWER_GUI=ON \hich\f2 \endash \hich\af2\dbch\af17\loch\f2 
C ../MedicalSliceViewer/InitialCache}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid5532841 \hich\af2\dbch\af17\loch\f2 -Linux64}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid6454629 \hich\af2\dbch\af17\loch\f2 .cmake ../MedicalSliceViewer
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid6454629 \hich\af31506\dbch\af17\loch\f31506 6.\tab}}\pard \ltrpar
\s20\ql \fi-360\li360\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls9\adjustright\rin0\lin360\itap0\pararsid6454629\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid6454629 \hich\af31506\dbch\af17\loch\f31506 Locate }{\rtlch\fcs1 
\af31507 \ltrch\fcs0 \b\insrsid6454629\charrsid5836634 \hich\af31506\dbch\af17\loch\f31506 qm\hich\af31506\dbch\af17\loch\f31506 ake}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid6454629 \hich\af31506\dbch\af17\loch\f31506  install path for M}{\rtlch\fcs1 
\af31507 \ltrch\fcs0 \insrsid6454629\charrsid6454629 \hich\af31506\dbch\af17\loch\f31506 akefiles by for e.g. ccmake
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid6454629\charrsid6454629 \hich\af31506\dbch\af17\loch\f31506 7.\tab}\hich\af31506\dbch\af17\loch\f31506 Run\hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \b\insrsid6454629\charrsid5836634 \hich\af31506\dbch\af17\loch\f31506 make}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid6454629\charrsid6454629 
\par }\pard\plain \ltrpar\s1\ql \li0\ri0\sb480\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs32\alang1033 \ltrch\fcs0 
\b\fs32\cf17\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1907747\charrsid11220353 {\*\bkmkstart _Toc133490530}\hich\af31506\dbch\af31501\loch\f31506 
Run the software}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 {\*\bkmkend _Toc133490530}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid1206937 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1907747\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
There are two important executables: the modeler and the detector. The modeler helps the user to train his/her model with arbitrary la\hich\af31506\dbch\af17\loch\f31506 ndmarks. The detector}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid14309066\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  will try to estimate those landmarks positions}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1907747\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  for a given new brain MR image.

\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1907747\charrsid11220353 {\*\bkmkstart _Toc133490531}\hich\af31506\dbch\af31501\loch\f31506 
Run the modeler{\*\bkmkend _Toc133490531}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid1206937 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \b\insrsid8088368\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Usage:
\par }\pard \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9320399 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid8088368\charrsid11220353 \hich\af2\dbch\af17\loch\f2 ./BRAINSConstellationModeler}{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid8088368\charrsid11220353 \hich\af2\dbch\af17\loch\f2 -i  or --trainingFile }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9320399\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid10518414 
\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9731728\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Where}{\rtlch\fcs1 \af17\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid9320399\charrsid11220353 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \b\f31506\insrsid15428098\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls12\adjustright\rin0\lin720\itap0\pararsid15428098\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \b\insrsid15428098\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 trainingFile}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid15428098\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  is the input training files list filename without eye centers.
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7474968 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid6517796\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 F}{\rtlch\fcs1 
\af31507 \ltrch\fcs0 \insrsid6517796\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 or more details on setting optional parameters p}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid15428098\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 lease }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8533900 \hich\af31506\dbch\af17\loch\f31506 type}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid15428098\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid8533900 \line }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid8533900\charrsid11220353 \hich\af2\dbch\af17\loch\f2 ./BRAINSConstellationModeler }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid8533900 \hich\af2\dbch\af17\loch\f2 -h}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid7474968\charrsid11220353 
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid7474968 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid7474968\charrsid11220353 {\*\bkmkstart _Toc133490532}\hich\af31506\dbch\af31501\loch\f31506 
Run the detector}{\rtlch\fcs1 \af17\alang1033 \ltrch\fcs0 \lang1033\langfe2052\loch\af31506\hich\af31506\dbch\af17\langfenp2052\insrsid7474968\charrsid11220353 {\*\bkmkend _Toc133490532}
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid7474968 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \b\insrsid7474968\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Usage:}{\rtlch\fcs1 \ab\af31503 \ltrch\fcs0 
\b\fs26\cf18\dbch\af31501\insrsid7474968\charrsid11220353 
\par }\pard \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid9731728 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9731728\charrsid11220353 \hich\af2\dbch\af17\loch\f2 ./BRAINSConstellationDetectorNew }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9731728\charrsid2032223 \hich\af31506\dbch\af17\loch\f31506 (w/o GUI) or}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9731728\charrsid11220353 \line \hich\af2\dbch\af17\loch\f2 ./BRAINSConstellationDetectorGUI }{
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9731728\charrsid2032223 \hich\af31506\dbch\af17\loch\f31506 (w/ GUI)}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid9731728\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 
\f2\lang1033\langfe2052\langfenp2052\insrsid9731728\charrsid11220353 \line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid7474968\charrsid11220353 \hich\af2\dbch\af17\loch\f2 -i  or --inputVolume }{\rtlch\fcs1 \af31507 
\ltrch\fcs0 \f2\insrsid9731728\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid10518414 
\par }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid9731728\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 Where}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid11220353\charrsid10518414 
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \b\f31506\insrsid11220353\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls14\adjustright\rin0\lin720\itap0\pararsid11220353\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \b\insrsid11220353\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 inputFilename}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\insrsid11220353\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506  is the filename of the input image file.
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0\pararsid11220353 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 
A sample trained model file can be found at\line }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \f2\lang1033\langfe2052\langfenp2052\insrsid14302259\charrsid14302259 \hich\af2\dbch\af17\loch\f2 brainscdetector/TestData/input/newT1InputModelWithVN
\hich\af2\dbch\af17\loch\f2 4.mdl
\par }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid14302259 \hich\af31506\dbch\af17\loch\f31506 The corresponding trained llsModel file can be found at\line }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 
\f2\lang1033\langfe2052\langfenp2052\insrsid14302259\charrsid14302259 \hich\af2\dbch\af17\loch\f2 brainscdetector}{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \f2\lang1033\langfe2052\langfenp2052\insrsid14302259 \hich\af2\dbch\af17\loch\f2 
/TestData/input/llsModel.txt}{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \f2\lang1033\langfe2052\langfenp2052\insrsid14302259\charrsid14302259 
\par }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid11683991 \hich\af31506\dbch\af17\loch\f31506 After running the detector, a Slicer fcsv landmark file and a Slicer mrml scene file for those n
\hich\af31506\dbch\af17\loch\f31506 amed landmarks in the original physical space will be also written to the working directory.
\par }{\rtlch\fcs1 \af31507\alang1033 \ltrch\fcs0 \lang1033\langfe2052\langfenp2052\insrsid11220353\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 F}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid11220353\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
or more details on setting optional parameters please }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414 \hich\af31506\dbch\af17\loch\f31506 type\line }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid10518414\charrsid11220353 \hich\af2\dbch\af17\loch\f2 
./BRAINSConstellationDetectorNew}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid10518414 \hich\af2\dbch\af17\loch\f2  \hich\f2 \endash \loch\f2 h }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414\charrsid10518414 \hich\af31506\dbch\af17\loch\f31506 
for non-}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414 \hich\af31506\dbch\af17\loch\f31506 GUI version }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414\charrsid2032223 \hich\af31506\dbch\af17\loch\f31506 or}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid10518414\charrsid11220353 \line \hich\af2\dbch\af17\loch\f2 ./BRAINSConstellationDetectorGUI}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid10518414 \hich\af2\dbch\af17\loch\f2  -h}{\rtlch\fcs1 \af31507 \ltrch\fcs0 
\f2\insrsid10518414\charrsid11220353 \hich\af2\dbch\af17\loch\f2  }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414\charrsid10518414 \hich\af31506\dbch\af17\loch\f31506 for}{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid10518414 
\hich\af31506\dbch\af17\loch\f31506  GUI \hich\af31506\dbch\af17\loch\f31506 version }{\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid7474968\charrsid11220353 
\par }\pard\plain \ltrpar\s2\ql \li0\ri0\sb200\keep\keepn\widctlpar\wrapdefault\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0\pararsid8658335 \rtlch\fcs1 \ab\af31503\afs26\alang1033 \ltrch\fcs0 
\b\fs26\cf18\lang1033\langfe1033\loch\af31502\hich\af31502\dbch\af31501\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid8658335\charrsid11220353 {\*\bkmkstart _Toc133490533}\hich\af31506\dbch\af31501\loch\f31506 Run tests}{
\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid2318053 \hich\af31506\dbch\af31501\loch\f31506  (In progress)}{\rtlch\fcs1 \af31503 \ltrch\fcs0 \f31506\insrsid1907747\charrsid11220353 {\*\bkmkend _Toc133490533}
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 1.\tab}}\pard\plain \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls15\adjustright\rin0\lin720\itap0\pararsid16410307\contextualspace \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 
\fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 For non-GUI version, enter
\par }\pard \ltrpar\s20\ql \li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid16410307\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid1206937\charrsid16410307 \hich\af2\dbch\af17\loch\f2 
ctest -R BRAINSMSVNoGUITest_T1
\par {\listtext\pard\plain\ltrpar \s20 \rtlch\fcs1 \af31507 \ltrch\fcs0 \f31506\insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 2.\tab}}\pard \ltrpar
\s20\ql \fi-360\li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\ls15\adjustright\rin0\lin720\itap0\pararsid16410307\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid1206937\charrsid11220353 \hich\af31506\dbch\af17\loch\f31506 
For GUI version, enter
\par }\pard \ltrpar\s20\ql \li720\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin720\itap0\pararsid16410307\contextualspace {\rtlch\fcs1 \af31507 \ltrch\fcs0 \f2\insrsid1206937\charrsid16410307 \hich\af2\dbch\af17\loch\f2 
ctest -R BRAINSMSVTest_T1
\par }\pard\plain \ltrpar\ql \li0\ri0\sa200\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af31507\afs24\alang1033 \ltrch\fcs0 \fs24\lang1033\langfe1033\loch\af31506\hich\af31506\dbch\af17\cgrid\langnp1033\langfenp1033 {
\rtlch\fcs1 \af31507 \ltrch\fcs0 \insrsid4018903\charrsid11220353 
\par }{\*\themedata 504b0304140006000800000021001b898e1bfe0000001c020000130000005b436f6e74656e745f54797065735d2e786d6cac91cf6ac3300cc6ef83bd83f17524
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diff --git a/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.cxx b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.cxx
new file mode 100644
index 00000000..b24bb476
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.cxx
@@ -0,0 +1,984 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "BRAINSConstellationDetectorGUICLP.h"
+
+#include "QVTKInteractionCallback.h"
+#include "QSliceViewer.h"
+#include "QLabelList.h"
+#include "QDelLabelDialogs.h"
+#include "QFileDialogs.h"
+#include "QHelpDialog.h"
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkStatisticsImageFilter.h"
+#include "itkImageToVTKImageFilter.h"
+
+#include "vtkCommand.h"
+#include "vtkImageData.h"
+#include "vtkMatrix4x4.h"
+#include "vtkImageReslice.h"
+#include "vtkLookupTable.h"
+#include "vtkImageMapToColors.h"
+#include "vtkCamera.h"
+#include "vtkImageActor.h"
+#include "vtkRenderer.h"
+#include "vtkRenderWindow.h"
+#include "vtkInteractorStyleImage.h"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include "stdio.h"
+#include 
+#include 
+#include "string.h"
+#include 
+#include 
+
+#if ( ITK_VERSION_MAJOR < 4  ) // These are all defaults in ITKv4
+// Check that ITK was compiled with correct flags set:
+#ifndef ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE
+#error \
+  "Results will not be correct if ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE is turned off"
+#endif
+#ifndef ITK_USE_ORIENTED_IMAGE_DIRECTION
+#error \
+  "Results will not be correct if ITK_USE_ORIENTED_IMAGE_DIRECTION is turned off"
+#endif
+#endif // ITK_VERSION_MAJOR check
+
+// Image, filter typedef
+const unsigned int LocalImageDimension = 3;
+typedef short PixelType;
+
+typedef itk::Image ImageType;
+typedef ImageType::Pointer                         ImagePointerType;
+typedef ImageType::PointType                       ImagePointType;
+typedef ImageType::SpacingType                     ImageSpacingType;
+typedef ImageType::SizeType                        ImageSizeType;
+typedef ImageType::DirectionType                   ImageDirectionType;
+typedef ImageType::IndexType                       ImageIndexType;
+typedef ImagePointType::CoordRepType               ImageCoordType;
+
+typedef itk::ImageFileReader       ReaderType;
+typedef itk::ImageFileWriter       WriterType;
+typedef itk::StatisticsImageFilter StatisticsFilterType;
+typedef itk::ImageToVTKImageFilter ConnectorType;
+
+int main(int argc, char *argv[])
+{
+  PARSE_ARGS;
+
+  if( inputVolume.compare("") == 0 )
+    {
+    std::cerr << "To run the program please specify the input volume filename." << std::endl;
+    std::cerr << "Type " << argv[0] << " -h for more help." << std::endl;
+    exit(-1);
+    }
+
+  // ------------------------------------
+  // Instantiate widgets
+
+  int          WIN_WIDTH = 1200;  // application width
+  int          WIN_HEIGHT = 500;  // application height
+  double       PRECISION = 1000.; // means .001 precision for slice number
+  QApplication app(argc, argv);
+
+  QWidget base;
+  base.setWindowTitle("BRAINS Constellation Viewer");
+  QGridLayout layout(&base);
+
+  // image info widet
+  QLabel infoLabel("- Image Volume Info -");
+  layout.addWidget(&infoLabel, 1, 1, 1, 2);
+  infoLabel.setAlignment(Qt::AlignHCenter);
+
+  QLabel info;
+  layout.addWidget(&info, 2, 1, 8, 2);
+  info.setAlignment(Qt::AlignHCenter);
+  info.setMaximumWidth(WIN_WIDTH / 5);
+  info.setIndent(5);
+  info.setWordWrap(1);
+  info.setFrameStyle(QFrame::Panel | QFrame::Raised);
+  info.setLineWidth(2);
+
+  // slice viewer widget
+  QLabel label1("Axial");
+  QLabel label2("Sagittal");
+  QLabel label3("Coronal");
+
+  label1.setAlignment(Qt::AlignHCenter);
+  label2.setAlignment(Qt::AlignHCenter);
+  label3.setAlignment(Qt::AlignHCenter);
+
+  layout.addWidget(&label1, 1, 3, 1, 3);
+  layout.addWidget(&label2, 1, 6, 1, 3);
+  layout.addWidget(&label3, 1, 9, 1, 3);
+
+  QSliceViewer sliceViewer1(1);
+  QSliceViewer sliceViewer2(2);
+  QSliceViewer sliceViewer3(3);
+
+  layout.addWidget(&sliceViewer1, 2, 3, 9, 3);
+  layout.addWidget(&sliceViewer2, 2, 6, 9, 3);
+  layout.addWidget(&sliceViewer3, 2, 9, 9, 3);
+
+  // slider bar widget
+  QSlider slider1(Qt::Horizontal);
+  QSlider slider2(Qt::Horizontal);
+  QSlider slider3(Qt::Horizontal);
+
+  layout.addWidget(&slider1, 11, 3, 1, 3);
+  layout.addWidget(&slider2, 11, 6, 1, 3);
+  layout.addWidget(&slider3, 11, 9, 1, 3);
+
+  // status label widget
+  QLabel status1("");
+  QLabel status2("");
+  QLabel status3("");
+
+  layout.addWidget(&status1, 12, 3, 1, 3);
+  layout.addWidget(&status2, 12, 6, 1, 3);
+  layout.addWidget(&status3, 12, 9, 1, 3);
+
+  status1.setAlignment(Qt::AlignHCenter);
+  status2.setAlignment(Qt::AlignHCenter);
+  status3.setAlignment(Qt::AlignHCenter);
+
+  // label list widget
+  QLabelList labelList;
+  layout.addWidget(&labelList, 10, 1, 4, 2);
+  labelList.SetInputVolume(inputVolume);
+  labelList.SetInputLandmarks(inputLandmarks);
+  labelList.SetOutputLandmarks(outputLandmarks);
+
+  // add label dialog widget
+  QPushButton addLabelButton("Add");
+  layout.addWidget(&addLabelButton, 13, 3);
+
+  // remove label dialog widget
+  QPushButton removeLabelButton("Remove");
+  layout.addWidget(&removeLabelButton, 13, 4);
+
+  // remove all dialog widget
+  QPushButton removeAllButton("Remove All");
+  layout.addWidget(&removeAllButton, 13, 5);
+
+  // save landmarks widget
+  QPushButton saveButton("Save");
+  layout.addWidget(&saveButton, 13, 6);
+
+  // save as landmarks widget
+  QPushButton saveAsButton("Save As...");
+  layout.addWidget(&saveAsButton, 13, 7);
+
+  // help widget
+  QPushButton helpButton("Help");
+  layout.addWidget(&helpButton, 13, 10);
+  QHelpDialog helpDialog;
+
+  // quit widget
+  QPushButton quitButton("Quit");
+  layout.addWidget(&quitButton, 13, 11);
+  QObject::connect( &quitButton, SIGNAL( clicked() ),
+                    &app, SLOT( quit() ) );
+
+  // label deletion dialog
+  QDelLabelDialogs delAllButtonDialog("Are you sure to remove all the labels?");
+  QDelLabelDialogs delCurrButtonDialog("Are you sure to remove the current label?");
+  QDelLabelDialogs delCurrKeyDialog("Are you sure to remove the current label?");
+  QDelLabelDialogs doubleClickLabelDialog("Are you sure to remove the current label?");
+
+  // ------------------------------------
+  // Read input image from ITK
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName(inputVolume);
+  try
+    {
+    reader->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << " Error while reading image file(s) with ITK:\n "
+              << err << std::endl;
+    }
+
+  // ------------------------------------
+  // Prepare for rendering image with VTK
+
+  // get some basic information of the image using ITK
+  ImagePointerType   image      = reader->GetOutput();
+  ImagePointType     origin     = image->GetOrigin();
+  ImageSpacingType   spacing    = image->GetSpacing();
+  ImageSizeType      size       = image->GetLargestPossibleRegion().GetSize();
+  ImageDirectionType direction  = image->GetDirection();
+
+  // get the image extent in index space ( IJK coordinate system )
+  int            indexExtent[6];
+  ImageIndexType startIndex = image->GetLargestPossibleRegion().GetIndex();
+  ImageIndexType stopIndex;
+  stopIndex[0]    = startIndex[0] + size[0] - 1;
+  stopIndex[1]    = startIndex[1] + size[1] - 1;
+  stopIndex[2]    = startIndex[2] + size[2] - 1;
+  indexExtent[0]  = startIndex[0];
+  indexExtent[2]  = startIndex[1];
+  indexExtent[4]  = startIndex[2];
+  indexExtent[1]  = stopIndex[0];
+  indexExtent[3]  = stopIndex[1];
+  indexExtent[5]  = stopIndex[2];
+
+  // calculate the physical image extent of input image with identity
+  // direction
+  ImageDirectionType direction2;
+  direction2.Fill(0);
+  direction2(0, 0) = 1.0;
+  direction2(1, 1) = 1.0;
+  direction2(2, 2) = 1.0;
+  image->SetDirection(direction2);
+
+  double         physicalExtentIdentity[6];
+  ImagePointType physicalStartLocation;
+  ImagePointType physicalStopLocation;
+  image->TransformIndexToPhysicalPoint(startIndex, physicalStartLocation);
+  image->TransformIndexToPhysicalPoint(stopIndex, physicalStopLocation);
+  physicalExtentIdentity[0] = physicalStartLocation[0];
+  physicalExtentIdentity[2] = physicalStartLocation[1];
+  physicalExtentIdentity[4] = physicalStartLocation[2];
+  physicalExtentIdentity[1] = physicalStopLocation[0];
+  physicalExtentIdentity[3] = physicalStopLocation[1];
+  physicalExtentIdentity[5] = physicalStopLocation[2];
+
+  // calculate the physical center of the image with identity direction
+  double center[4];
+  center[0] = ( physicalExtentIdentity[1] + physicalExtentIdentity[0] ) / 2.0;
+  center[1] = ( physicalExtentIdentity[3] + physicalExtentIdentity[2] ) / 2.0;
+  center[2] = ( physicalExtentIdentity[5] + physicalExtentIdentity[4] ) / 2.0;
+  center[3] = 1.0;
+
+  // recalculate the image extent of a directional image in physical space
+  double physicalExtent[6];
+  image->SetDirection(direction);
+  image->TransformIndexToPhysicalPoint(startIndex, physicalStartLocation);
+  image->TransformIndexToPhysicalPoint(stopIndex, physicalStopLocation);
+  physicalExtent[0] = physicalStartLocation[0];
+  physicalExtent[2] = physicalStartLocation[1];
+  physicalExtent[4] = physicalStartLocation[2];
+  physicalExtent[1] = physicalStopLocation[0];
+  physicalExtent[3] = physicalStopLocation[1];
+  physicalExtent[5] = physicalStopLocation[2];
+
+  // calculate the physical center of the image with original direction
+  double center2[3];
+  center2[0] = ( physicalExtent[1] + physicalExtent[0] ) / 2.0;
+  center2[1] = ( physicalExtent[3] + physicalExtent[2] ) / 2.0;
+  center2[2] = ( physicalExtent[5] + physicalExtent[4] ) / 2.0;
+
+  // compute the bound of image
+  double bound[6];
+  bound[0] =
+    physicalExtent[0] < physicalExtent[1] ?
+    physicalExtent[0] : physicalExtent[1];
+  bound[1] =
+    physicalExtent[0] >= physicalExtent[1] ?
+    physicalExtent[0] : physicalExtent[1];
+  bound[2] =
+    physicalExtent[2] < physicalExtent[3] ?
+    physicalExtent[2] : physicalExtent[3];
+  bound[3] =
+    physicalExtent[2] >= physicalExtent[3] ?
+    physicalExtent[2] : physicalExtent[3];
+  bound[4] =
+    physicalExtent[4] < physicalExtent[5] ?
+    physicalExtent[4] : physicalExtent[5];
+  bound[5] =
+    physicalExtent[4] >= physicalExtent[5] ?
+    physicalExtent[4] : physicalExtent[5];
+
+  // set the range of sliders
+  slider1.setRange(bound[4] * PRECISION, bound[5] * PRECISION);
+  slider2.setRange(bound[0] * PRECISION, bound[1] * PRECISION);
+  slider3.setRange(bound[2] * PRECISION, bound[3] * PRECISION);
+
+  // set the initial positon of the sliders
+  slider1.setSliderPosition( ( bound[4] + bound[5] ) / 2 * PRECISION );
+  slider2.setSliderPosition( ( bound[0] + bound[1] ) / 2 * PRECISION );
+  slider3.setSliderPosition( ( bound[2] + bound[3] ) / 2 * PRECISION );
+
+  // pass the bound info to slice viewer
+  sliceViewer1.SetBound(bound);
+  sliceViewer2.SetBound(bound);
+  sliceViewer3.SetBound(bound);
+
+  // show welcome info and some image information
+  QString infoText;
+  infoText =
+    "
Physical Spacing:
("
+    + infoText.number(spacing[0]) + " "
+    + infoText.number(spacing[1]) + " "
+    + infoText.number(spacing[2]) + ")
"
+    + "
Physical Origin:
("
+    + infoText.number(origin[0]) + " "
+    + infoText.number(origin[1]) + " "
+    + infoText.number(origin[2]) + ")
"
+    + "
Physical Center:
("
+    + infoText.number(center2[0]) + " "
+    + infoText.number(center2[1]) + " "
+    + infoText.number(center2[2]) + ")
"
+    + "
Physical Direction:
"
+    + infoText.number( direction(0, 0) ) + " "
+    + infoText.number( direction(0, 1) )
+    + " " + infoText.number( direction(0, 2) )
+    + "
"
+    + infoText.number( direction(1, 0) ) + " "
+    + infoText.number( direction(1, 1) )
+    + " " + infoText.number( direction(1, 2) )
+    + "
"
+    + infoText.number( direction(2, 0) ) + " "
+    + infoText.number( direction(2, 1) )
+    + " " + infoText.number( direction(2, 2) )
+    + "
"
+    + "
Index Extent:
["
+    + infoText.number(indexExtent[0]) + " "
+    + infoText.number(indexExtent[1]) + "; "
+    + infoText.number(indexExtent[2]) + " "
+    + infoText.number(indexExtent[3]) + "; "
+    + infoText.number(indexExtent[4]) + " "
+    + infoText.number(indexExtent[5]) + "]
"
+    + "
Physical Extent:
("
+    + infoText.number(bound[0]) + " "
+    + infoText.number(bound[1]) + "; "
+    + infoText.number(bound[2]) + " "
+    + infoText.number(bound[3]) + "; "
+    + infoText.number(bound[4]) + " "
+    + infoText.number(bound[5]) + ")
";
+
+  info.setText(infoText);
+
+  // ------------------------------------
+  // ITK to VTK
+
+  ConnectorType::Pointer connector = ConnectorType::New();
+  connector->SetInput(image);
+
+  // ------------------------------------
+  // get image slices with VTK Image Reslice
+
+  // Matrices for axial, coronal, and sagittal view orientations
+  // in LAS coordinate
+  static double axialElements[16] =
+    {
+    1, 0, 0, 0,
+    0, -1, 0, 0,
+    0, 0, 1, 0,
+    0, 0, 0, 1
+    };
+
+  // in ASL coordinate
+  static double sagittalElements[16] =
+    {
+    0, 0, 1, 0,
+    1, 0, 0, 0, // later we need to change it from -1 to 1
+    0, 1, 0, 0,
+    0, 0, 0, 1
+    };
+
+  // in LSA coordinate
+  static double coronalElements[16] =
+    {
+    1, 0, 0, 0,
+    0, 0, -1, 0,
+    0, 1, 0, 0,
+    0, 0, 0, 1
+    };
+
+  // ITK -> VTK pipeline does not transfer direction infomation!
+  double rotation[16] =
+    {
+    0, 0, 0, 0,
+    0, 0, 0, 0,
+    0, 0, 0, 0,
+    0, 0, 0, 1
+    };
+
+  unsigned int i, j;
+  for( i = 0; i < LocalImageDimension; ++i )
+    {
+    for( j = 0; j < LocalImageDimension; ++j )
+      {
+      rotation[4 * i + j] = direction[i][j];
+      }
+    }
+
+  // compute the reslice axes location
+  double        matrix[16];
+  double        invRotation[16];
+  vtkMatrix4x4 *resliceAxes1 = vtkMatrix4x4::New();
+  vtkMatrix4x4 *resliceAxes2 = vtkMatrix4x4::New();
+  vtkMatrix4x4 *resliceAxes3 = vtkMatrix4x4::New();
+  resliceAxes1->Invert(rotation, invRotation);
+
+  resliceAxes1->Multiply4x4(invRotation, axialElements, matrix);
+  resliceAxes1->DeepCopy(matrix);
+  resliceAxes1->SetElement(0, 3, center[0]);
+  resliceAxes1->SetElement(1, 3, center[1]);
+  resliceAxes1->SetElement(2, 3, center[2]);
+
+  resliceAxes2->Multiply4x4(invRotation, sagittalElements, matrix);
+  resliceAxes2->DeepCopy(matrix);
+  resliceAxes2->SetElement(0, 3, center[0]);
+  resliceAxes2->SetElement(1, 3, center[1]);
+  resliceAxes2->SetElement(2, 3, center[2]);
+
+  resliceAxes3->Multiply4x4(invRotation, coronalElements, matrix);
+  resliceAxes3->DeepCopy(matrix);
+  resliceAxes3->SetElement(0, 3, center[0]);
+  resliceAxes3->SetElement(1, 3, center[1]);
+  resliceAxes3->SetElement(2, 3, center[2]);
+
+  // extract a slice in the desired orientation
+  vtkImageReslice *reslice1 = vtkImageReslice::New();
+  reslice1->SetInputConnection( connector->GetImporter()->GetOutputPort() );
+  reslice1->SetOutputDimensionality(2);
+  reslice1->SetResliceAxes(resliceAxes1);
+  reslice1->SetInterpolationModeToLinear();
+
+  vtkImageReslice *reslice2 = vtkImageReslice::New();
+  reslice2->SetInputConnection( connector->GetImporter()->GetOutputPort() );
+  reslice2->SetOutputDimensionality(2);
+  reslice2->SetResliceAxes(resliceAxes2);
+  reslice2->SetInterpolationModeToLinear();
+
+  vtkImageReslice *reslice3 = vtkImageReslice::New();
+  reslice3->SetInputConnection( connector->GetImporter()->GetOutputPort() );
+  reslice3->SetOutputDimensionality(2);
+  reslice3->SetResliceAxes(resliceAxes3);
+  reslice3->SetInterpolationModeToLinear();
+
+  // find the slice size
+  reslice1->Update();
+  reslice2->Update();
+  reslice3->Update();
+
+  // ------------------------------------
+  // Render the image with VTK
+
+  // create a colormap lookup table
+  StatisticsFilterType::Pointer statisticsFilter = StatisticsFilterType::New();
+  statisticsFilter->SetInput( reader->GetOutput() );
+  statisticsFilter->Update();
+  PixelType minPixelValue = statisticsFilter->GetMinimum();
+  PixelType maxPixelValue = statisticsFilter->GetMaximum();
+
+  vtkLookupTable *table = vtkLookupTable::New();
+  table->SetRange(minPixelValue, maxPixelValue);   // image intensity range
+  table->SetValueRange(0.0, 1.0);
+  table->SetSaturationRange(0.0, 0.0);   // monochromatic
+  table->SetRampToLinear();
+  table->Build();
+
+  // map the image through the lookup table
+  vtkImageMapToColors *color1 = vtkImageMapToColors::New();
+  color1->SetLookupTable(table);
+  color1->SetInputConnection( reslice1->GetOutputPort() );
+
+  vtkImageMapToColors *color2 = vtkImageMapToColors::New();
+  color2->SetLookupTable(table);
+  color2->SetInputConnection( reslice2->GetOutputPort() );
+
+  vtkImageMapToColors *color3 = vtkImageMapToColors::New();
+  color3->SetLookupTable(table);
+  color3->SetInputConnection( reslice3->GetOutputPort() );
+
+  // set up the actor
+  vtkImageActor *actor1 = vtkImageActor::New();
+  actor1->SetInput( color1->GetOutput() );
+
+  vtkImageActor *actor2 = vtkImageActor::New();
+  actor2->SetInput( color2->GetOutput() );
+
+  vtkImageActor *actor3 = vtkImageActor::New();
+  actor3->SetInput( color3->GetOutput() );
+
+  // set up the renderer
+  vtkRenderer *renderer1 = vtkRenderer::New();
+  renderer1->AddActor(actor1);
+  renderer1->SetBackground(0.45, 0.65, 0.45);
+
+  vtkRenderer *renderer2 = vtkRenderer::New();
+  renderer2->AddActor(actor2);
+  renderer2->SetBackground(0.45, 0.65, 0.45);
+
+  vtkRenderer *renderer3 = vtkRenderer::New();
+  renderer3->AddActor(actor3);
+  renderer3->SetBackground(0.45, 0.65, 0.45);
+
+  // set up the render window
+  vtkRenderWindow *window1 = vtkRenderWindow::New();
+  window1->AddRenderer(renderer1);
+  sliceViewer1.SetRenderWindow(window1);
+
+  vtkRenderWindow *window2 = vtkRenderWindow::New();
+  window2->AddRenderer(renderer2);
+  sliceViewer2.SetRenderWindow(window2);
+
+  vtkRenderWindow *window3 = vtkRenderWindow::New();
+  window3->AddRenderer(renderer3);
+  sliceViewer3.SetRenderWindow(window3);
+
+  // set up the interaction
+  vtkInteractorStyleImage *imageStyle1 = vtkInteractorStyleImage::New();
+  QVTKInteractor *         interactor1 = QVTKInteractor::New();
+  interactor1->SetInteractorStyle(imageStyle1);
+  window1->SetInteractor(interactor1);
+
+  window1->Render();
+
+  QVTKInteractionCallback callback1("L:\nP:\nS:", 1, bound);
+  callback1.SetImageReslice(reslice1);
+  callback1.SetInteractor(interactor1);
+  callback1.SetIndexExtent(indexExtent);
+  callback1.SetPhysicalExtentIdentity(physicalExtentIdentity);
+  callback1.SetPhysicalExtent(physicalExtent);
+  callback1.SetPrecision(PRECISION);
+
+  vtkInteractorStyleImage *imageStyle2 = vtkInteractorStyleImage::New();
+  QVTKInteractor *         interactor2 = QVTKInteractor::New();
+  interactor2->SetInteractorStyle(imageStyle2);
+  window2->SetInteractor(interactor2);
+
+  window2->Render();
+
+  QVTKInteractionCallback callback2("L:\nP:\nS:", 2, bound);
+  callback2.SetImageReslice(reslice2);
+  callback2.SetInteractor(interactor2);
+  callback2.SetIndexExtent(indexExtent);
+  callback2.SetPhysicalExtentIdentity(physicalExtentIdentity);
+  callback2.SetPhysicalExtent(physicalExtent);
+  callback2.SetType(2);
+  callback2.SetPrecision(PRECISION);
+
+  vtkInteractorStyleImage *imageStyle3 = vtkInteractorStyleImage::New();
+  QVTKInteractor *         interactor3 = QVTKInteractor::New();
+  interactor3->SetInteractorStyle(imageStyle3);
+  window3->SetInteractor(interactor3);
+
+  window3->Render();
+
+  QVTKInteractionCallback callback3("L:\nP:\nS:", 3, bound);
+  callback3.SetImageReslice(reslice3);
+  callback3.SetInteractor(interactor3);
+  callback3.SetIndexExtent(indexExtent);
+  callback3.SetPhysicalExtentIdentity(physicalExtentIdentity);
+  callback3.SetPhysicalExtent(physicalExtent);
+  callback3.SetType(3);
+  callback3.SetPrecision(PRECISION);
+
+  callback1.SetDirection(rotation);
+  callback2.SetDirection(rotation);
+  callback3.SetDirection(rotation);
+
+  double origin16[16] =
+    {
+    1, 0, 0, 0,
+    0, 1, 0, 0,
+    0, 0, 1, 0,
+    0, 0, 0, 1
+    };
+  origin16[3] = origin[0];
+  origin16[7] = origin[1];
+  origin16[11] = origin[2];
+  callback1.SetOrigin(origin16);
+  callback2.SetOrigin(origin16);
+  callback3.SetOrigin(origin16);
+
+  double spacing16[16] =
+    {
+    1, 0, 0, 0,
+    0, 1, 0, 0,
+    0, 0, 1, 0,
+    0, 0, 0, 1
+    };
+  spacing16[0] = spacing[0];
+  spacing16[5] = spacing[1];
+  spacing16[10] = spacing[2];
+  callback1.SetSpacing(spacing16);
+  callback2.SetSpacing(spacing16);
+  callback3.SetSpacing(spacing16);
+
+  imageStyle1->AddObserver(vtkCommand::MouseMoveEvent, &callback1);
+  imageStyle1->AddObserver(vtkCommand::LeftButtonPressEvent, &callback1);
+  imageStyle1->AddObserver(vtkCommand::LeftButtonReleaseEvent, &callback1);
+  imageStyle1->AddObserver(vtkCommand::KeyPressEvent, &callback1);
+
+  imageStyle2->AddObserver(vtkCommand::MouseMoveEvent, &callback2);
+  imageStyle2->AddObserver(vtkCommand::LeftButtonPressEvent, &callback2);
+  imageStyle2->AddObserver(vtkCommand::LeftButtonReleaseEvent, &callback2);
+  imageStyle2->AddObserver(vtkCommand::KeyPressEvent, &callback2);
+
+  imageStyle3->AddObserver(vtkCommand::MouseMoveEvent, &callback3);
+  imageStyle3->AddObserver(vtkCommand::LeftButtonPressEvent, &callback3);
+  imageStyle3->AddObserver(vtkCommand::LeftButtonReleaseEvent, &callback3);
+  imageStyle3->AddObserver(vtkCommand::KeyPressEvent, &callback3);
+
+  // ------------------------------------
+  // Load & display landmarks from file
+  labelList.loadLandmarks();
+  std::map >           landmarks = labelList.GetLandmarks();
+  std::map >::iterator it;
+  for( it = landmarks.begin(); it != landmarks.end(); ++it )
+    {
+    if( it->first.compare("") != 0 )
+      {
+      // add points to slice viewer
+      double *point = new double[3];
+      for( i = 0; i < LocalImageDimension; ++i )
+        {
+        point[i] = ( it->second )[i];
+        }
+      sliceViewer1.createLabel(point);
+      sliceViewer2.createLabel(point);
+      sliceViewer3.createLabel(point);
+
+      // add points to label list
+      QString pointString =
+        pointString.number(point[0]) + " "
+        + pointString.number(point[1]) + " "
+        + pointString.number(point[2]);
+      labelList.createListItem(pointString, it->first);
+      }
+    }
+
+  // ------------------------------------
+  // Setup core communication
+
+  // connect slice viewer, slider bar, and status label
+  QObject::connect( &callback1, SIGNAL( textChanged(const QString &) ),
+                    &status1, SLOT( setText(const QString &) ) );
+  QObject::connect( &callback1, SIGNAL( valueChangedZ(int) ),
+                    &slider1, SLOT( setValue(int) ) );
+  QObject::connect( &slider1, SIGNAL( valueChanged(int) ),
+                    &callback1, SLOT( setValueZLocation(int) ) );
+
+  QObject::connect( &callback2, SIGNAL( textChanged(const QString &) ),
+                    &status2, SLOT( setText(const QString &) ) );
+  QObject::connect( &callback2, SIGNAL( valueChangedZ(int) ),
+                    &slider2, SLOT( setValue(int) ) );
+  QObject::connect( &slider2, SIGNAL( valueChanged(int) ),
+                    &callback2, SLOT( setValueZLocation(int) ) );
+
+  QObject::connect( &callback3, SIGNAL( textChanged(const QString &) ),
+                    &status3, SLOT( setText(const QString &) ) );
+  QObject::connect( &callback3, SIGNAL( valueChangedZ(int) ),
+                    &slider3, SLOT( setValue(int) ) );
+  QObject::connect( &slider3, SIGNAL( valueChanged(int) ),
+                    &callback3, SLOT( setValueZLocation(int) ) );
+
+  // connect slice viewers
+  QObject::connect( &callback2, SIGNAL( valueChangedY(double) ),
+                    &callback1, SLOT( setValueYLocation(double) ) );
+  QObject::connect( &callback3, SIGNAL( valueChangedY(double) ),
+                    &callback1, SLOT( setValueYLocation(double) ) );
+
+  QObject::connect( &callback1, SIGNAL( valueChangedX(double) ),
+                    &callback2, SLOT( setValueXLocation(double) ) );
+  QObject::connect( &callback3, SIGNAL( valueChangedX(double) ),
+                    &callback2, SLOT( setValueXLocation(double) ) );
+
+  QObject::connect( &callback1, SIGNAL( valueChangedY(double) ),
+                    &callback3, SLOT( setValueYLocation(double) ) );
+  QObject::connect( &callback2, SIGNAL( valueChangedX(double) ),
+                    &callback3, SLOT( setValueXLocation(double) ) );
+
+  // connect mouse/keyboard callback with fiducial labels
+  QObject::connect( &callback1, SIGNAL( moveActor(double *) ),
+                    &sliceViewer1, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback1, SIGNAL( moveActor(double *) ),
+                    &sliceViewer2, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback1, SIGNAL( moveActor(double *) ),
+                    &sliceViewer3, SLOT( moveLabelSlot(double *) ) );
+
+  QObject::connect( &callback1, SIGNAL( createActor() ),
+                    &sliceViewer1, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback1, SIGNAL( createActor() ),
+                    &sliceViewer2, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback1, SIGNAL( createActor() ),
+                    &sliceViewer3, SLOT( createLabelSlot() ) );
+
+  QObject::connect( &callback1, SIGNAL( switchActor() ),
+                    &sliceViewer1, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback1, SIGNAL( switchActor() ),
+                    &sliceViewer2, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback1, SIGNAL( switchActor() ),
+                    &sliceViewer3, SLOT( switchLabelSlot() ) );
+
+  QObject::connect( &callback2, SIGNAL( moveActor(double *) ),
+                    &sliceViewer2, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback2, SIGNAL( moveActor(double *) ),
+                    &sliceViewer3, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback2, SIGNAL( moveActor(double *) ),
+                    &sliceViewer1, SLOT( moveLabelSlot(double *) ) );
+
+  QObject::connect( &callback2, SIGNAL( createActor() ),
+                    &sliceViewer2, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback2, SIGNAL( createActor() ),
+                    &sliceViewer3, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback2, SIGNAL( createActor() ),
+                    &sliceViewer1, SLOT( createLabelSlot() ) );
+
+  QObject::connect( &callback2, SIGNAL( switchActor() ),
+                    &sliceViewer2, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback2, SIGNAL( switchActor() ),
+                    &sliceViewer3, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback2, SIGNAL( switchActor() ),
+                    &sliceViewer1, SLOT( switchLabelSlot() ) );
+
+  QObject::connect( &callback3, SIGNAL( moveActor(double *) ),
+                    &sliceViewer3, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback3, SIGNAL( moveActor(double *) ),
+                    &sliceViewer1, SLOT( moveLabelSlot(double *) ) );
+  QObject::connect( &callback3, SIGNAL( moveActor(double *) ),
+                    &sliceViewer2, SLOT( moveLabelSlot(double *) ) );
+
+  QObject::connect( &callback3, SIGNAL( createActor() ),
+                    &sliceViewer3, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback3, SIGNAL( createActor() ),
+                    &sliceViewer1, SLOT( createLabelSlot() ) );
+  QObject::connect( &callback3, SIGNAL( createActor() ),
+                    &sliceViewer2, SLOT( createLabelSlot() ) );
+
+  QObject::connect( &callback3, SIGNAL( switchActor() ),
+                    &sliceViewer3, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback3, SIGNAL( switchActor() ),
+                    &sliceViewer1, SLOT( switchLabelSlot() ) );
+  QObject::connect( &callback3, SIGNAL( switchActor() ),
+                    &sliceViewer2, SLOT( switchLabelSlot() ) );
+
+  QObject::connect( &callback1, SIGNAL( deleteActor() ),
+                    &delCurrKeyDialog, SLOT( exec() ) );
+  QObject::connect( &callback2, SIGNAL( deleteActor() ),
+                    &delCurrKeyDialog, SLOT( exec() ) );
+  QObject::connect( &callback3, SIGNAL( deleteActor() ),
+                    &delCurrKeyDialog, SLOT( exec() ) );
+  QObject::connect( &delCurrKeyDialog, SIGNAL( accepted() ),
+                    &sliceViewer1, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrKeyDialog, SIGNAL( accepted() ),
+                    &sliceViewer2, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrKeyDialog, SIGNAL( accepted() ),
+                    &sliceViewer3, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrKeyDialog, SIGNAL( accepted() ),
+                    &labelList, SLOT( deleteListItemSlot() ) );
+
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &sliceViewer1, SLOT( pickLabelSlot(QListWidgetItem *) ) );
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &sliceViewer2, SLOT( pickLabelSlot(QListWidgetItem *) ) );
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &sliceViewer3, SLOT( pickLabelSlot(QListWidgetItem *) ) );
+
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &labelList, SLOT( cancelHighlight(QListWidgetItem *) ) );
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &labelList, SLOT( cancelHighlight(QListWidgetItem *) ) );
+  QObject::connect( &labelList, SIGNAL( itemClicked(QListWidgetItem *) ),
+                    &labelList, SLOT( cancelHighlight(QListWidgetItem *) ) );
+
+  // connect mouse/keyboard callback with fiducial label list
+  QObject::connect( &callback1, SIGNAL( createListItem(const QString &) ),
+                    &labelList, SLOT( createListItemSlot(const QString &) ) );
+  QObject::connect( &callback1, SIGNAL( editListItem(const QString &) ),
+                    &labelList, SLOT( editListItemSlot(const QString &) ) );
+  QObject::connect( &callback1, SIGNAL( switchListItem() ),
+                    &labelList, SLOT( switchListItemSlot() ) );
+
+  QObject::connect( &callback2, SIGNAL( createListItem(const QString &) ),
+                    &labelList, SLOT( createListItemSlot(const QString &) ) );
+  QObject::connect( &callback2, SIGNAL( editListItem(const QString &) ),
+                    &labelList, SLOT( editListItemSlot(const QString &) ) );
+  QObject::connect( &callback2, SIGNAL( switchListItem() ),
+                    &labelList, SLOT( switchListItemSlot() ) );
+
+  QObject::connect( &callback3, SIGNAL( createListItem(const QString &) ),
+                    &labelList, SLOT( createListItemSlot(const QString &) ) );
+  QObject::connect( &callback3, SIGNAL( editListItem(const QString &) ),
+                    &labelList, SLOT( editListItemSlot(const QString &) ) );
+  QObject::connect( &callback3, SIGNAL( switchListItem() ),
+                    &labelList, SLOT( switchListItemSlot() ) );
+
+  QObject::connect( &labelList, SIGNAL( itemDoubleClicked(QListWidgetItem *) ),
+                    &doubleClickLabelDialog, SLOT( exec(QListWidgetItem *) ) );
+  QObject::connect( &doubleClickLabelDialog, SIGNAL( accepted(QListWidgetItem *) ),
+                    &labelList, SLOT( deleteListItemMouseSlot(QListWidgetItem *) ) );
+  QObject::connect( &doubleClickLabelDialog, SIGNAL( accepted(QListWidgetItem *) ),
+                    &sliceViewer1, SLOT( deleteLabelMouseSlot(QListWidgetItem *) ) );
+  QObject::connect( &doubleClickLabelDialog, SIGNAL( accepted(QListWidgetItem *) ),
+                    &sliceViewer2, SLOT( deleteLabelMouseSlot(QListWidgetItem *) ) );
+  QObject::connect( &doubleClickLabelDialog, SIGNAL( accepted(QListWidgetItem *) ),
+                    &sliceViewer3, SLOT( deleteLabelMouseSlot(QListWidgetItem *) ) );
+
+  // callback or list (send slice update request) >>
+  // list (send label position) >> callback (update label position)
+  QObject::connect( &labelList, SIGNAL( sliceChangedList() ),
+                    &labelList, SLOT( sliceChangedSlot() ) );
+
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback1, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback2, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback3, SLOT( receiveLabelPos(double *) ) );
+
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback1, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback2, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback3, SLOT( receiveLabelPos(double *) ) );
+
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback1, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback2, SLOT( receiveLabelPos(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPosition(double *) ),
+                    &callback3, SLOT( receiveLabelPos(double *) ) );
+
+  // add label widget to slice viewer, status bar and label list
+  QObject::connect( &addLabelButton, SIGNAL( clicked() ),
+                    &sliceViewer1, SLOT( createLabelSlot() ) );
+  QObject::connect( &addLabelButton, SIGNAL( clicked() ),
+                    &sliceViewer2, SLOT( createLabelSlot() ) );
+  QObject::connect( &addLabelButton, SIGNAL( clicked() ),
+                    &sliceViewer3, SLOT( createLabelSlot() ) );
+
+  QObject::connect( &addLabelButton, SIGNAL( clicked() ),
+                    &callback1, SLOT( createListAddButtonSlot() ) );
+
+  // remove label widget to slice viewer, status bar and label list
+  QObject::connect( &removeLabelButton, SIGNAL( clicked() ),
+                    &delCurrButtonDialog, SLOT( exec() ) );
+
+  QObject::connect( &delCurrButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer1, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer2, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer3, SLOT( deleteLabelSlot() ) );
+  QObject::connect( &delCurrButtonDialog, SIGNAL( accepted() ),
+                    &labelList, SLOT( deleteListItemSlot() ) );
+
+  // remove all widget
+  QObject::connect( &removeAllButton, SIGNAL( clicked() ),
+                    &delAllButtonDialog, SLOT( exec() ) );
+
+  QObject::connect( &delAllButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer1, SLOT( deleteAllLabelSlot() ) );
+  QObject::connect( &delAllButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer2, SLOT( deleteAllLabelSlot() ) );
+  QObject::connect( &delAllButtonDialog, SIGNAL( accepted() ),
+                    &sliceViewer3, SLOT( deleteAllLabelSlot() ) );
+  QObject::connect( &delAllButtonDialog, SIGNAL( accepted() ),
+                    &labelList, SLOT( deleteListSlot() ) );
+
+  // check visibility
+  QObject::connect( &callback1, SIGNAL( checkVisibility() ),
+                    &labelList, SLOT( checkVisibilitySlot() ) );
+  QObject::connect( &callback2, SIGNAL( checkVisibility() ),
+                    &labelList, SLOT( checkVisibilitySlot() ) );
+  QObject::connect( &callback3, SIGNAL( checkVisibility() ),
+                    &labelList, SLOT( checkVisibilitySlot() ) );
+
+  QObject::connect( &callback1, SIGNAL( visibilityCallback(double *) ),
+                    &labelList, SLOT( checkVisibilitySlot(double *) ) );
+  QObject::connect( &callback2, SIGNAL( visibilityCallback(double *) ),
+                    &labelList, SLOT( checkVisibilitySlot(double *) ) );
+  QObject::connect( &callback3, SIGNAL( visibilityCallback(double *) ),
+                    &labelList, SLOT( checkVisibilitySlot(double *) ) );
+
+  QObject::connect( &labelList, SIGNAL( itemDoubleClicked(QListWidgetItem *) ),
+                    &labelList, SLOT( checkVisibilitySlot(QListWidgetItem *) ) );
+
+  QObject::connect( &labelList, SIGNAL( visibilityTable(int *) ),
+                    &sliceViewer1, SLOT( visibilityUpdate(int *) ) );
+  QObject::connect( &labelList, SIGNAL( visibilityTable(int *) ),
+                    &sliceViewer2, SLOT( visibilityUpdate(int *) ) );
+  QObject::connect( &labelList, SIGNAL( visibilityTable(int *) ),
+                    &sliceViewer3, SLOT( visibilityUpdate(int *) ) );
+
+  // handle mouse wheel event
+  QObject::connect( &callback1, SIGNAL( wheelChanged() ),
+                    &labelList, SLOT( ackWheelChanged() ) );
+  QObject::connect( &callback2, SIGNAL( wheelChanged() ),
+                    &labelList, SLOT( ackWheelChanged() ) );
+  QObject::connect( &callback3, SIGNAL( wheelChanged() ),
+                    &labelList, SLOT( ackWheelChanged() ) );
+
+  QObject::connect( &labelList, SIGNAL( sendLabelPositions(double *) ),
+                    &sliceViewer1, SLOT( wheelSlot(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPositions(double *) ),
+                    &sliceViewer2, SLOT( wheelSlot(double *) ) );
+  QObject::connect( &labelList, SIGNAL( sendLabelPositions(double *) ),
+                    &sliceViewer3, SLOT( wheelSlot(double *) ) );
+
+  QObject::connect( &saveButton, SIGNAL( clicked() ),
+                    &labelList, SLOT( saveLandmarks() ) );
+
+  QObject::connect( &saveAsButton, SIGNAL( clicked() ),
+                    &labelList, SLOT( saveAsLandmarks() ) );
+
+  QObject::connect( &helpButton, SIGNAL( clicked() ),
+                    &helpDialog, SLOT( open() ) );
+
+  // ------------------------------------
+  // Qt initialize
+
+  base.resize(WIN_WIDTH, WIN_HEIGHT);
+  base.show();
+  app.exec();
+
+  // ------------------------------------
+  // clean up all VTK components
+
+  table->Delete();
+
+  interactor1->Delete();
+  imageStyle1->Delete();
+  window1->Delete();
+  renderer1->Delete();
+  actor1->Delete();
+  color1->Delete();
+  reslice1->Delete();
+  resliceAxes1->Delete();
+
+  interactor2->Delete();
+  imageStyle2->Delete();
+  window2->Delete();
+  renderer2->Delete();
+  actor2->Delete();
+  color2->Delete();
+  reslice2->Delete();
+  resliceAxes2->Delete();
+
+  interactor3->Delete();
+  imageStyle3->Delete();
+  window3->Delete();
+  renderer3->Delete();
+  actor3->Delete();
+  color3->Delete();
+  reslice3->Delete();
+  resliceAxes3->Delete();
+
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml
new file mode 100644
index 00000000..badff28c
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml
@@ -0,0 +1,43 @@
+
+
+    BRAINSConstellationDetectorGUI
+    
+      This program provides the user with a GUI tool to view/manipulate landmarks for an input volume.
+    
+
+    1.0
+    http://www.nitrc.org/projects/brainscdetector/
+    
+        
+            inputVolume
+            i
+            inputVolume
+            
+            The filename of the input NIfTI volume to view/manipulate
+            input
+            
+        
+        
+            inputLandmarks
+            
+            l
+            inputLandmarks
+            
+            
+              The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (in a .fcsv format) with the landmarks in the original image space in it to be read in.
+            
+            input
+        
+        
+            outputLandmarks
+            
+            o
+            outputLandmarks
+            
+            
+              The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (in a .fcsv format) with the landmarks in the original image space in it to be written.
+            
+            input
+        
+    
+
diff --git a/BRAINSConstellationDetector/gui/CMakeLists.txt b/BRAINSConstellationDetector/gui/CMakeLists.txt
new file mode 100644
index 00000000..41db562a
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/CMakeLists.txt
@@ -0,0 +1,94 @@
+project(MedicalSlicerViewerGui)
+
+  # Find VTK.
+  find_package(VTK REQUIRED)
+  if(VTK_FOUND)
+    include(${VTK_USE_FILE})
+  endif(VTK_FOUND)
+
+  set(QT_QMAKE_EXECUTABLE ${VTK_QT_QMAKE_EXECUTABLE} CACHE FILEPATH "")
+  set(QT_MOC_EXECUTABLE ${VTK_QT_MOC_EXECUTABLE} CACHE FILEPATH "")
+  set(QT_UIC_EXECUTABLE ${VTK_QT_UIC_EXECUTABLE} CACHE FILEPATH "")
+  set(DESIRED_QT_VERSION ${VTK_DESIRED_QT_VERSION} CACHE FILEPATH "")
+
+  # Find Qt.
+  find_package(Qt4 REQUIRED)
+  if(QT_USE_FILE)
+    include(${QT_USE_FILE})
+  else()
+    set(QT_LIBRARIES ${QT_QT_LIBRARY})
+  endif()
+
+  set( CMAKE_CURRENT_SOURCE_DIRS
+  BRAINSConstellationDetectorGUIPrimary.cxx
+  QSliceViewer.cxx
+  QLabelList.cxx
+  QVTKInteractionCallback.cxx
+  QDelLabelDialogs.cxx
+  QFileDialogs.cxx
+  QHelpDialog.cxx
+  )
+
+  set( HEADERS
+  include/QSliceViewer.h
+  include/QLabelList.h
+  include/QVTKInteractionCallback.h
+  include/QDelLabelDialogs.h
+  include/QFileDialogs.h
+  include/QHelpDialog.h
+  )
+
+  include_directories(
+  ${CMAKE_CURRENT_SOURCE_DIR}/include
+  ${CMAKE_SOURCE_DIR}/src
+  ${CMAKE_SOURCE_DIR}/src/BRAINSHoughEyeDetector
+  ${CMAKE_BINARY_DIR}/src
+  ${QT_INCLUDE_DIR}
+  ${QT_QTGUI_INCLUDE_DIR}
+  ${QT_QTCORE_INCLUDE_DIR}
+  )
+
+  QT4_WRAP_CPP( HEADERS_MOC ${HEADERS} )
+
+  add_definitions( ${QT_DEFINITIONS} )
+
+add_library( BRAINSConstellationDetectorGUICOMMONLIB STATIC
+  ${CMAKE_CURRENT_SOURCE_DIRS}
+  ${HEADERS_MOC}
+  )
+  target_link_libraries( BRAINSConstellationDetectorGUICOMMONLIB
+  QVTK
+  ${QT_LIBRARIES}
+  BRAINSConstellationDetectorCOMMONLIB
+  vtkRendering vtkGraphics vtkIO vtkCommon vtkImaging
+  )
+
+## Build all the programs
+##
+set(ALL_PROGS_LIST
+  BRAINSConstellationDetectorGUI
+  )
+foreach(prog ${ALL_PROGS_LIST})
+
+  if(0) # Build against Slicer
+    ## Include the Slicer macro for setting up default locations!
+    SlicerMacroBuildCLI(
+      NAME ${prog}
+      LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+      TARGET_LIBRARIES BRAINSConstellationDetectorGUICOMMONLIB ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+      CLI_SHARED_LIBRARY_WRAPPER_CXX  ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+      VERBOSE
+    )
+  else()
+    SEMMacroBuildCLI(
+      NAME ${prog}
+      LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+      TARGET_LIBRARIES BRAINSConstellationDetectorGUICOMMONLIB ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+      CLI_SHARED_LIBRARY_WRAPPER_CXX ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+      VERBOSE
+      )
+  endif()
+endforeach()
+
+
+
diff --git a/BRAINSConstellationDetector/gui/QDelLabelDialogs.cxx b/BRAINSConstellationDetector/gui/QDelLabelDialogs.cxx
new file mode 100644
index 00000000..a3dc5e68
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QDelLabelDialogs.cxx
@@ -0,0 +1,45 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QDelLabelDialogs.h"
+
+QDelLabelDialogs::QDelLabelDialogs(QString text, QWidget *myParent) : QDialog(myParent)
+{
+  m_label.setText(text);
+  m_accept.setText("Accept");
+  m_cancel.setText("Cancel");
+
+  m_layout = new QGridLayout(this);
+  m_layout->addWidget(&m_label, 1, 1, Qt::AlignHCenter);
+  m_layout->addWidget(&m_accept, 2, 1, Qt::AlignRight);
+  m_layout->addWidget(&m_cancel, 2, 2, Qt::AlignRight);
+
+  // for buttons and keyboard input
+  QObject::connect( &m_accept, SIGNAL( clicked() ),
+                    this, SLOT( accept() ) );
+  QObject::connect( &m_cancel, SIGNAL( clicked() ),
+                    this, SLOT( reject() ) );
+
+  // for mouse double click
+  QObject::connect( this, SIGNAL( exec2() ),
+                    this, SLOT( exec() ) );
+  QObject::connect( &m_accept, SIGNAL( clicked() ),
+                    this, SLOT( accept2() ) );
+
+  m_listItem = NULL;
+}
+
+void QDelLabelDialogs::exec(QListWidgetItem *listItem)
+{
+  m_listItem = listItem;
+  emit exec2();
+}
+
+void QDelLabelDialogs::accept2()
+{
+  emit accepted(m_listItem);
+}
+
diff --git a/BRAINSConstellationDetector/gui/QFileDialogs.cxx b/BRAINSConstellationDetector/gui/QFileDialogs.cxx
new file mode 100644
index 00000000..566f3f34
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QFileDialogs.cxx
@@ -0,0 +1,46 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QFileDialogs.h"
+
+QString QFileDialogs::openLandmarksFile()
+{
+  m_landmarks =
+    QFileDialog::getOpenFileName( this,
+                                  tr("Select landmarks file"),
+                                  QDir::currentPath(),
+                                  tr("Model file ( *.fcsv )") );
+  return m_landmarks;
+}
+
+void QFileDialogs::openLandmarksFileSlot()
+{
+  m_landmarks =
+    QFileDialog::getOpenFileName( this,
+                                  tr("Select landmarks file"),
+                                  QDir::currentPath(),
+                                  tr("Model file ( *.fcsv )") );
+}
+
+QString QFileDialogs::saveLandmarksFile()
+{
+  m_landmarks =
+    QFileDialog::getSaveFileName( this,
+                                  tr("Save landmarks file"),
+                                  QDir::currentPath(),
+                                  tr("Model file ( *.fcsv )") );
+  return m_landmarks;
+}
+
+void QFileDialogs::saveLandmarksFileSlot()
+{
+  m_landmarks =
+    QFileDialog::getSaveFileName( this,
+                                  tr("Save landmarks file"),
+                                  QDir::currentPath(),
+                                  tr("Model file ( *.fcsv )") );
+}
+
diff --git a/BRAINSConstellationDetector/gui/QHelpDialog.cxx b/BRAINSConstellationDetector/gui/QHelpDialog.cxx
new file mode 100644
index 00000000..943eccdc
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QHelpDialog.cxx
@@ -0,0 +1,20 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QHelpDialog.h"
+
+QHelpDialog::QHelpDialog(QWidget *myParent) : QDialog(myParent)
+{
+  QString text(
+    "This help message provides the basic usage of the GUI tool. Please visit our wiki page for more information:
http://www.nitrc.org/plugins/mwiki/index.php/brainscdetector:MainPage

Select
To select a landmark:
* Click on the landmark in the label list

Move
To change the location of a landmark:
* Select the landmark
* Move either one of the slider bar to find a good slice
* Click at a point of the corresponding viewer to move the landmark to the current place
* As the other viewers change slices accordingly, adjust the landmark location in 3D

Zoom in/out
To zoom in/out of a viewer:
* Hover the mouse on that viewer
* Right click then drag up/down to zoom in/out about the center

Add
To add a new landmark:
* Click the Add button

Remove
To remove a landmark:
* Double click the landmark in the label list, then choose Accept in the dialog window, or
* Select the landmark, then click on the Remove button in the GUI

Other operations such as Remove All landmarks, Save landmarks, etc can be achieved by clicking a proper button on the GUI.");
+
+  this->setWindowTitle("GUI Help Info");
+  m_label.setText(text);
+  m_label.setTextInteractionFlags(Qt::TextBrowserInteraction);
+  m_layout = new QGridLayout(this);
+  m_layout->addWidget(&m_label, 1, 1, Qt::AlignLeft);
+}
+
diff --git a/BRAINSConstellationDetector/gui/QLabelList.cxx b/BRAINSConstellationDetector/gui/QLabelList.cxx
new file mode 100644
index 00000000..bde8d8f6
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QLabelList.cxx
@@ -0,0 +1,462 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QLabelList.h"
+
+void QLabelList::createListItemSlot(const QString & label)
+{
+  // copy label to m_label
+  m_label.clear();
+  m_label = m_label.append(label);
+
+  QString newLabel = QString("newLabel_%1: ( %2 )").arg( QString::number(m_color + 1) ).arg(label);
+  this->addItem(newLabel);
+  this->setCurrentRow(this->count() - 1);
+  this->setCurrentItem( this->item( this->currentRow() ) );
+  QColor color( ( m_color % 3 / 2 / 2.0 + ( m_color * m_color ) % 3 / 4.0 ) * 255,
+                ( ( m_color + 1 ) % 3 / 2 / 2.0 + m_color % 7 / 12.0 ) * 255,
+                ( ( m_color + 2 ) % 3 / 2 / 2.0 + m_color % 4 / 6.0 ) * 255,
+                127 );
+  QBrush brush(color);
+  this->item( this->currentRow() )->setBackground(brush);
+
+  cancelHighlight( this->currentItem() );
+
+  m_color++;
+}
+
+void QLabelList::createListItem(const QString & label, const QString & name)
+{
+  // copy label to m_label
+  m_label.clear();
+  m_label = m_label.append(label);
+
+  QString newLabel = QString("%1: ( %2 )").arg(name).arg(label);
+  this->addItem(newLabel);
+  this->setCurrentRow(this->count() - 1);
+  this->setCurrentItem( this->item( this->currentRow() ) );
+  QColor color( ( m_color % 3 / 2 / 2.0 + ( m_color * m_color ) % 3 / 4.0 ) * 255,
+                ( ( m_color + 1 ) % 3 / 2 / 2.0 + m_color % 7 / 12.0 ) * 255,
+                ( ( m_color + 2 ) % 3 / 2 / 2.0 + m_color % 4 / 6.0 ) * 255,
+                127 );
+  QBrush brush(color);
+  this->item( this->currentRow() )->setBackground(brush);
+
+  cancelHighlight( this->currentItem() );
+
+  m_color++;
+}
+
+void QLabelList::createListItemAddButtonSlot()
+{
+  createListItemSlot(m_label);
+}
+
+void QLabelList::editListItemSlot(const QString & label)
+{
+  if( this->currentItem() != NULL )
+    {
+    QString lastLabel = this->currentItem()->text();
+    QString newLabel = QString("%1: ( %2 )").arg( lastLabel.section(':', 0, 0) ).arg(label);
+    this->currentItem()->setText(newLabel);
+    }
+}
+
+void QLabelList::switchListItemSlot()
+{
+  if( this->currentItem() != NULL )
+    {
+    if( this->currentRow() == this->count() - 1 )
+      {
+      this->setCurrentRow(0);
+      this->setCurrentItem( this->item( this->currentRow() ) );
+      }
+    else
+      {
+      this->setCurrentRow(this->currentRow() + 1);
+      this->setCurrentItem( this->item( this->currentRow() ) );
+      }
+
+    cancelHighlight( this->currentItem() );
+    }
+}
+
+void QLabelList::deleteListItemSlot()
+{
+  if( this->currentItem() != NULL )
+    {
+    delete this->currentItem();
+    if( this->count() > 0 )
+      {
+      this->setCurrentRow(0);
+      }
+    else
+      {
+      this->setCurrentRow(-1);
+      }
+    this->setCurrentItem( this->item( this->currentRow() ) );
+    cancelHighlight( this->currentItem() );
+    }
+}
+
+void QLabelList::deleteListSlot()
+{
+  if( this->currentItem() != NULL )
+    {
+    this->setCurrentItem( this->item(0) );
+    while( this->currentItem() != NULL )
+      {
+      delete this->currentItem();
+      }
+
+    this->setCurrentRow(-1);
+    // reset the color seed
+    m_color = 0;
+    }
+}
+
+void QLabelList::deleteListItemMouseSlot(QListWidgetItem *)
+{
+  deleteListItemSlot();
+}
+
+void QLabelList::cancelHighlight(QListWidgetItem *)
+{
+  if( this->currentItem() != NULL )
+    {
+    // disable the highlight color
+    const QColor color = this->item( this->currentRow() )->background().color();
+    QPalette     pal = this->palette();
+    pal.setColor(QPalette::Highlight, color);
+    this->setPalette(pal);
+
+    // signal to sliceChangeSlot indicating the update of slice viewer
+    emit sliceChangedList();
+    }
+}
+
+void QLabelList::sliceChangedSlot()
+{
+  if( this->currentItem() != NULL )
+    {
+    QString textLabel = this->item( this->currentRow() )->text();
+    double  myPos[3];
+    myPos[0] = textLabel.section(' ', 2, 2).toDouble();
+    myPos[1] = textLabel.section(' ', 3, 3).toDouble();
+    myPos[2] = textLabel.section(' ', 4, 4).toDouble();
+    emit sendLabelPosition(myPos);
+    }
+}
+
+void QLabelList::checkVisibilitySlot()
+{
+  if( this->currentItem() != NULL )
+    {
+    int     MAX_LABEL_NUM = 100;
+    int     table[3 * MAX_LABEL_NUM];
+    int     currRow = this->currentRow();
+    QString textLabel = this->item(currRow)->text();
+    double  currPos[3];
+    currPos[0] = textLabel.section(' ', 2, 2).toDouble();
+    currPos[1] = textLabel.section(' ', 3, 3).toDouble();
+    currPos[2] = textLabel.section(' ', 4, 4).toDouble();
+    double slice;
+
+    int i;
+    for( i = 0; i < 3; ++i )
+      { // for different viewers
+      this->setCurrentRow(0);
+      while( this->item( this->currentRow() ) != NULL )
+        {
+        textLabel = this->item( this->currentRow() )->text();
+        slice = textLabel.section(' ', 2 + i, 2 + i).toDouble();
+        if( ( slice >= currPos[i] - .5 )
+            && ( slice <  currPos[i] + .5 ) )
+          {
+          table[i * this->count() + this->currentRow()] = 1;
+          }
+        else
+          {
+          table[i * this->count() + this->currentRow()] = 0;
+          }
+        this->setCurrentRow(this->currentRow() + 1);
+        }
+      }
+    this->setCurrentRow(currRow);
+    emit visibilityTable(table);
+    }
+}
+
+void QLabelList::checkVisibilitySlot(double *tag)
+{
+  if( this->currentItem() != NULL )
+    {
+    int     MAX_LABEL_NUM = 100;
+    int     table[3 * MAX_LABEL_NUM];
+    int     currRow = this->currentRow();
+    QString textLabel = this->item(currRow)->text();
+    double  currPos[3];
+    currPos[0] = textLabel.section(' ', 2, 2).toDouble();
+    currPos[1] = textLabel.section(' ', 3, 3).toDouble();
+    currPos[2] = textLabel.section(' ', 4, 4).toDouble();
+    double slice;
+
+    currPos[( int(tag[1]) + 1 ) % 3] = tag[0];
+
+    int i;
+    for( i = 0; i < 3; ++i )
+      { // for different viewers
+      this->setCurrentRow(0);
+      while( this->item( this->currentRow() ) != NULL )
+        {
+        textLabel = this->item( this->currentRow() )->text();
+        slice = textLabel.section(' ', 2 + i, 2 + i).toDouble();
+        if( ( slice >= currPos[i] - .5 )
+            && ( slice <  currPos[i] + .5 ) )
+          {
+          table[i * this->count() + this->currentRow()] = 1;
+          }
+        else
+          {
+          table[i * this->count() + this->currentRow()] = 0;
+          }
+        this->setCurrentRow(this->currentRow() + 1);
+        }
+      }
+    this->setCurrentRow(currRow);
+    emit visibilityTable(table);
+    }
+}
+
+void QLabelList::checkVisibilitySlot(QListWidgetItem *)
+{
+  checkVisibilitySlot();
+}
+
+void QLabelList::ackWheelChanged()
+{
+  if( this->currentItem() != NULL )
+    {
+    int     MAX_LABEL_NUM = 100;
+    double  labelPos[3 * MAX_LABEL_NUM];
+    int     currRow = this->currentRow();
+    double  currPos[3];
+    QString textLabel;
+
+    this->setCurrentRow(0);
+    while( this->item( this->currentRow() ) != NULL )
+      {
+      textLabel = this->item( this->currentRow() )->text();
+      currPos[0] = textLabel.section(' ', 2, 2).toDouble();
+      currPos[1] = textLabel.section(' ', 3, 3).toDouble();
+      currPos[2] = textLabel.section(' ', 4, 4).toDouble();
+
+      int i;
+      for( i = 0; i < 3; ++i )
+        {
+        labelPos[3 * this->currentRow() + i] = currPos[i];
+        }
+
+      this->setCurrentRow(this->currentRow() + 1);
+      }
+
+    this->setCurrentRow(currRow);
+    emit sendLabelPositions(labelPos);
+    }
+}
+
+void QLabelList::readLandmarks()
+{
+  int currRow = this->currentRow();
+
+  this->setCurrentRow(0);
+  m_landmarks.clear();
+  while( this->item( this->currentRow() ) != NULL )
+    {
+    std::vector labelPos;
+    QString             textLabel = this->item( this->currentRow() )->text();
+
+    QString name      = textLabel.section(':', 0, 0);
+    labelPos.push_back( textLabel.section(' ', 2, 2).toDouble() );
+    labelPos.push_back( textLabel.section(' ', 3, 3).toDouble() );
+    labelPos.push_back( textLabel.section(' ', 4, 4).toDouble() );
+    m_landmarks.insert( std::make_pair >(name, labelPos) );
+    this->setCurrentRow(this->currentRow() + 1);
+    }
+
+  this->setCurrentRow(currRow);
+}
+
+void QLabelList::loadLandmarks()
+{
+  if( m_inputLandmarks.compare("") != 0 )
+    {
+    m_landmarks.clear();
+    QFile input(m_inputLandmarks);
+    if( !input.open(QIODevice::ReadOnly) )
+      {
+      std::cerr << "Cannot load landmark file!" << std::endl;
+      exit(-1);
+      }
+    QTextStream myfile(&input);
+    QString     line = myfile.readLine();
+    while( !line.isNull() )
+      {
+      if( !line.startsWith('#') )
+        {
+        QString name = line.section(',', 0, 0);
+        if( name.compare("") != 0 )
+          {
+          std::vector labelPos;
+          labelPos.push_back( -line.section(',', 1, 1).toDouble() );
+          labelPos.push_back( -line.section(',', 2, 2).toDouble() );
+          labelPos.push_back( line.section(',', 3, 3).toDouble() );
+          m_landmarks.insert( std::make_pair >(name, labelPos) );
+          }
+        }
+      line = myfile.readLine();
+      }
+
+    input.close();
+    }
+}
+
+void QLabelList::saveLandmarks()
+{
+  // if user specifies output landmarks filename
+  if( m_outputLandmarks.compare("") != 0 )
+    {
+    writeLandmarks();
+    }
+  // if user specifies input landmarks filename but not the output one
+  else if( m_inputLandmarks.compare("") != 0 )
+    {
+    m_outputLandmarks = m_inputLandmarks;
+    writeLandmarks();
+    }
+  // if user specifies neither the input landmarks filename nor the output one
+  else
+    {
+    saveAsLandmarks();
+    }
+}
+
+void QLabelList::saveAsLandmarks()
+{
+  QFileDialogs fileDialog;
+
+  m_outputLandmarks = fileDialog.saveLandmarksFile();
+  if( m_outputLandmarks.compare("") != 0 )
+    {
+    writeLandmarks();
+    }
+}
+
+void QLabelList::writeLandmarks()
+{
+  assert(m_outputLandmarks.compare("") != 0);
+  assert(m_inputVolume.compare("") != 0);
+
+  // get proper filename for fcsv and mrml file
+  QFileInfo landmarksFileInfo(m_outputLandmarks);
+  QFileInfo imageFileInfo(m_inputVolume);
+  m_outputLandmarks = landmarksFileInfo.absoluteFilePath();
+  QString landmarksFullFilenameWithoutExtension =
+    landmarksFileInfo.absolutePath() + "/" + landmarksFileInfo.completeBaseName();
+  QString imageFullFilename = imageFileInfo.absoluteFilePath();
+  QString imageFilenameWithoutPath = imageFileInfo.fileName();
+
+  // read in latest landmarks from label list class
+  this->readLandmarks();
+
+    {
+    QFile output(m_outputLandmarks);
+    if( !output.open(QIODevice::WriteOnly | QIODevice::Truncate) )
+      {
+      std::cerr << "Cannot save landmark file!" << std::endl;
+      exit(-1);
+      }
+
+    QTextStream myfile(&output);
+    myfile << "#Fiducial List file " << m_outputLandmarks << "\n";
+    myfile << "#numPoints = " << m_landmarks.size() << "\n";
+    myfile << "#symbolScale = 5\n";
+    myfile << "#visibility = 1\n";
+    myfile << "#textScale = 4.5\n";
+    myfile << "#color = 0.4,1,1\n";
+    myfile << "#selectedColor = 1,0.5,0.5\n";
+    myfile << "#label,x,y,z,sel,vis\n";
+
+    // note no LPS -> RAS is needed
+    LandmarksMapType::iterator it;
+    for( it = m_landmarks.begin(); it != m_landmarks.end(); ++it )
+      {
+      if( ( it->first ).compare("") != 0 )
+        {
+        myfile << it->first << "," << -( it->second )[0] << "," << -( it->second )[1] << "," << ( it->second )[2]
+               << ",1,1\n";
+        }
+      }
+
+    output.close();
+    }
+
+  // write scene to mrml file
+  QString mrmlFullFilename = landmarksFullFilenameWithoutExtension + ".mrml";
+    {
+    QFile output(mrmlFullFilename);
+    if( !output.open(QIODevice::WriteOnly | QIODevice::Truncate) )
+      {
+      std::cerr << "Cannot write mrml file!" << std::endl;
+      exit(-1);
+      }
+    QTextStream myfile(&output);
+
+    myfile
+    <<
+    "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n";
+
+    myfile << "first << " labeltext " << it->first << " xyz "
+             << ( it->second )[0] << " " << ( it->second )[1] << " " << ( it->second )[2];
+      if( ++index < m_landmarks.size() )
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\n";
+        }
+      else
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\">\n";
+        }
+      }
+
+    myfile
+    <<
+    "\n";
+
+    myfile
+    <<
+    "\n";
+
+    myfile << "\n\n\n";
+
+    output.close();
+    }
+}
+
diff --git a/BRAINSConstellationDetector/gui/QSliceViewer.cxx b/BRAINSConstellationDetector/gui/QSliceViewer.cxx
new file mode 100644
index 00000000..62855ff7
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QSliceViewer.cxx
@@ -0,0 +1,374 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QSliceViewer.h"
+
+#include 
+
+void QSliceViewer::createLabel(double *labelPos)
+{
+  createLabelSlot();
+
+  double *bound = m_bound;
+  double *labelPosRatio = new double[3];
+  labelPosRatio[0] =
+    ( labelPos[0] - bound[0] ) / ( bound[1] - bound[0] );
+  labelPosRatio[1] =
+    ( labelPos[1] - bound[2] ) / ( bound[3] - bound[2] );
+  labelPosRatio[2] =
+    ( labelPos[2] - bound[4] ) / ( bound[5] - bound[4] );
+
+  double R; // physical width/height ratio
+  if( m_type == 2 )
+    { // sagittal view mode ( ASL )
+    R = ( bound[3] - bound[2] ) / ( bound[5] - bound[4] );
+    }
+  else if( m_type == 3 )
+    { // coronal view mode ( LSA )
+    R = ( bound[1] - bound[0] ) / ( bound[5] - bound[4] );
+    }
+  else
+    { // axial view mode ( LAS )
+    R = ( bound[1] - bound[0] ) / ( bound[3] - bound[2] );
+    }
+
+  // by observation, linear approximation
+  double estimateCoef = 1. / sqrt(1.0 + R * R);
+  labelPosRatio[0] = estimateCoef * ( labelPosRatio[0] - .5 ) + .5;
+  labelPosRatio[1] = estimateCoef * ( labelPosRatio[1] - .5 ) + .5;
+  labelPosRatio[2] = estimateCoef * ( labelPosRatio[2] - .5 ) + .5;
+
+  moveLabelSlot(labelPosRatio);
+
+  // hide all actors
+  m_actors->InitTraversal();
+  vtkActor2D *actor = m_actors->GetNextActor2D();
+  while( actor != NULL )
+    {
+    actor->GetProperty()->SetOpacity(0.0);
+    actor = m_actors->GetNextActor2D();
+    }
+}
+
+void QSliceViewer::createLabelSlot()
+{
+  GenSphere();
+  m_actors->AddItem(m_actor);
+  Highlight();
+}
+
+void QSliceViewer::deleteLabelSlot()
+{
+  if( m_actor != NULL )
+    {
+    this->GetRenderWindow()->GetRenderers()->GetFirstRenderer()->RemoveActor(m_actor);
+    m_actors->RemoveItem(m_actor);
+    m_actor->Delete();
+    this->GetRenderWindow()->Render();
+    m_actors->InitTraversal();
+    m_actor = m_actors->GetNextActor2D();
+    Highlight();
+    }
+}
+
+void QSliceViewer::deleteAllLabelSlot()
+{
+  m_actors->InitTraversal();
+  m_actor = m_actors->GetNextActor2D();
+  while( m_actor != NULL )
+    {
+    this->GetRenderWindow()->GetRenderers()->GetFirstRenderer()->RemoveActor(m_actor);
+    m_actors->RemoveItem(m_actor);
+    m_actor->Delete();
+    m_actor = m_actors->GetNextActor2D();
+    }
+
+  // reset the color seed
+  m_color = 0;
+  this->GetRenderWindow()->Render();
+}
+
+void QSliceViewer::deleteLabelMouseSlot(QListWidgetItem *)
+{
+  deleteLabelSlot();
+}
+
+void QSliceViewer::switchLabelSlot()
+{
+  if( m_actor != NULL )
+    {
+    m_actor = m_actors->GetNextActor2D();
+    if( m_actor == NULL )
+      {
+      m_actors->InitTraversal();            // move current list pointer to the
+                                            // beginning
+      m_actor = m_actors->GetNextActor2D(); // set current label to the first
+                                            // actor
+      }
+    Highlight();
+    }
+}
+
+void QSliceViewer::moveLabelSlot(double *labelPos)
+{
+  if( m_actor != NULL )  // we only need to update current label
+    {
+    // get current position for each viewer
+    int             currPos[2];
+    int             eventSize[2];
+    QVTKInteractor *interactor = this->GetInteractor();
+    interactor->GetSize(eventSize);
+    double *bound = m_bound;
+    double  cPos[3]; // camera position
+    interactor->GetRenderWindow()->GetRenderers()->GetFirstRenderer()->
+    GetActiveCamera()->GetPosition(cPos);
+
+    // compute the screen size of image slice
+    double R; // physical width/height ratio
+    if( m_type == 2 )
+      { // sagittal view mode ( ASL )
+      R = ( bound[3] - bound[2] ) / ( bound[5] - bound[4] );
+      }
+    else if( m_type == 3 )
+      { // coronal view mode ( LSA )
+      R = ( bound[1] - bound[0] ) / ( bound[5] - bound[4] );
+      }
+    else
+      { // axial view mode ( LAS )
+      R = ( bound[1] - bound[0] ) / ( bound[3] - bound[2] );
+      }
+
+    // by observation
+    int h = 0.96 * eventSize[1] / sqrt(1.0 + R * R);   // sreen height of image
+                                                       // slice
+    int w = R * h;                                     // screen width of image
+                                                       // slice
+
+    // wheeling effect
+    if( m_cPos < 0.0 )
+      {
+      m_cPos = cPos[2];
+      }
+    else if( m_cPos != cPos[2] )
+      {
+      h *= m_cPos / cPos[2];
+      w *= m_cPos / cPos[2];
+      }
+
+    // locate the label position
+    if( m_type == 2 )
+      { // sagittal view mode ( ASL )
+      currPos[0] = w * labelPos[1] - w / 2.0;
+      currPos[1] = h * labelPos[2] - h / 2.0;
+      }
+    else if( m_type == 3 )
+      { // coronal view mode ( LSA )
+      currPos[0] = w * labelPos[0] - w / 2.0;
+      currPos[1] = h * labelPos[2] - h / 2.0;
+      }
+    else
+      { // axial view mode ( LAS )
+      currPos[0] = w * labelPos[0] - w / 2.0;
+      currPos[1] = h * ( 1 - labelPos[1] ) - h / 2.0;
+      }
+
+    // move sphere
+    m_actor->SetPosition(currPos[0], currPos[1]);
+    this->GetRenderWindow()->Render();
+    }
+}
+
+void QSliceViewer::wheelSlot(double *labelPos)
+{
+  if( m_actor != NULL )
+    {
+    vtkActor2D *currActor = m_actor; // a backup
+    m_actors->InitTraversal();
+    vtkActor2D *actor = m_actors->GetNextActor2D();
+    int         index = 0;        // index of actor
+    double      labelPosRatio[3]; // label postion ratio for inter-viewer
+                                  // communication
+    double *bound = m_bound;
+
+    while( actor != NULL )
+      {
+      m_actor = actor;
+      labelPosRatio[0] =
+        ( labelPos[3 * index] - bound[0] ) / ( bound[1] - bound[0] );
+      labelPosRatio[1] =
+        ( labelPos[3 * index + 1] - bound[2] ) / ( bound[3] - bound[2] );
+      labelPosRatio[2] =
+        ( labelPos[3 * index + 2] - bound[4] ) / ( bound[5] - bound[4] );
+      moveLabelSlot(labelPosRatio);
+      actor = m_actors->GetNextActor2D();
+      ++index;
+      }
+
+    // restore list pointer position
+    m_actor = currActor;
+    m_actors->InitTraversal();
+    actor = m_actors->GetNextActor2D();
+    while( actor != m_actor )
+      {
+      actor = m_actors->GetNextActor2D();
+      }
+
+    this->GetRenderWindow()->Render();
+    }
+}
+
+void QSliceViewer::GenSphere()
+{
+  // create sphere geometry
+  vtkSphereSource *sphere = vtkSphereSource::New();
+
+  sphere->SetRadius(3.0);
+  sphere->SetThetaResolution(20);
+  sphere->SetPhiResolution(10);
+  QVTKInteractor *interactor = this->GetInteractor();
+  int             eventSize[2];
+  interactor->GetSize(eventSize);
+  double sphereCenter[3] = { eventSize[0] / 2.0, eventSize[1] / 2.0, 0 };
+  sphere->SetCenter(sphereCenter);
+
+  // map to graphics library
+  vtkPolyDataMapper2D *map = vtkPolyDataMapper2D::New();
+  map->SetInput( sphere->GetOutput() );
+
+  // actor coordinates geometry, properties, transformation
+  vtkActor2D *actor = vtkActor2D::New();
+  actor->SetMapper(map);
+  this->GetRenderWindow()->GetRenderers()->GetFirstRenderer()->AddActor(actor);
+
+  m_actor = actor; // set current label to new created actor
+
+  m_actor->GetProperty()->SetColor(m_color % 3 / 2 / 2.0 + ( m_color * m_color ) % 3 / 4.0,
+                                   ( m_color + 1 ) % 3 / 2 / 2.0 + m_color % 7 / 12.0,
+                                   ( m_color + 2 ) % 3 / 2 / 2.0 + m_color % 4 / 6.0);
+  m_color++;
+}
+
+void QSliceViewer::Highlight()
+{
+  if( m_actor != NULL )  // we only need to update current label
+    {
+    // create sphere geometry
+    vtkSphereSource *sphere1 = vtkSphereSource::New();
+    sphere1->SetRadius(5.0);
+    sphere1->SetThetaResolution(4);
+    sphere1->SetPhiResolution(4);
+
+    vtkSphereSource *sphere2 = vtkSphereSource::New();
+    sphere2->SetRadius(3.0);
+    sphere2->SetThetaResolution(20);
+    sphere2->SetPhiResolution(10);
+
+    QVTKInteractor *interactor = this->GetInteractor();
+    int             eventSize[2];
+    interactor->GetSize(eventSize);
+    double sphereCenter[3] = { eventSize[0] / 2.0, eventSize[1] / 2.0, 0 };
+    sphere1->SetCenter(sphereCenter);
+    sphere2->SetCenter(sphereCenter);
+
+    // map to graphics library
+    vtkPolyDataMapper2D *map1 = vtkPolyDataMapper2D::New();
+    map1->SetInput( sphere1->GetOutput() );
+    vtkPolyDataMapper2D *map2 = vtkPolyDataMapper2D::New();
+    map2->SetInput( sphere2->GetOutput() );
+
+    m_actors->InitTraversal();
+    vtkActor2D *actor = m_actors->GetNextActor2D();
+    while( actor != NULL )
+      {
+      double color[3];
+      actor->GetProperty()->GetColor(color);
+      double *myPos = actor->GetPosition();
+      if( actor == m_actor )
+        { // set size and shape for the current actor
+        actor->SetMapper(map1);
+        }
+      else
+        { // set any other actors to default size and shape
+        actor->SetMapper(map2);
+        }
+      actor->GetProperty()->SetColor(color);
+      actor->SetPosition(myPos[0], myPos[1]);
+      actor = m_actors->GetNextActor2D();
+      }
+
+    // restore list pointer position
+    m_actors->InitTraversal();
+    actor = m_actors->GetNextActor2D();
+    while( actor != m_actor )
+      {
+      actor = m_actors->GetNextActor2D();
+      }
+
+    this->GetRenderWindow()->Render();
+    }
+}
+
+void QSliceViewer::pickLabelSlot(QListWidgetItem *item)
+{
+  if( m_actor != NULL )  // we only need to update current label
+    {
+    m_actors->InitTraversal();
+
+    int i;
+    for( i = 0; i <= item->listWidget()->currentRow(); ++i )
+      {
+      m_actor = m_actors->GetNextActor2D();
+      }
+    m_actor->GetProperty()->SetOpacity(1.0);
+    Highlight();
+    }
+}
+
+void QSliceViewer::visibilityUpdate(int *table)
+{
+  if( m_actor != NULL )
+    {
+    m_actors->InitTraversal();
+    vtkActor2D *actor = m_actors->GetNextActor2D();
+    int         index = 0; // index of actor
+    while( actor != NULL )
+      {
+      actor = m_actors->GetNextActor2D();
+      ++index;
+      }
+
+    int numActors = index;
+
+    index = 0;
+    m_actors->InitTraversal();
+    actor = m_actors->GetNextActor2D();
+    while( actor != NULL )
+      {
+      if( table[numActors * ( ( m_type + 1 ) % 3 ) + index] == 0 )
+        {
+        actor->GetProperty()->SetOpacity(0.0);
+        }
+      else
+        {
+        actor->GetProperty()->SetOpacity(1.0);
+        }
+
+      actor = m_actors->GetNextActor2D();
+      ++index;
+      }
+
+    // restore list pointer position
+    m_actors->InitTraversal();
+    actor = m_actors->GetNextActor2D();
+    while( actor != m_actor )
+      {
+      actor = m_actors->GetNextActor2D();
+      }
+
+    this->GetRenderWindow()->Render();
+    }
+}
+
diff --git a/BRAINSConstellationDetector/gui/QVTKInteractionCallback.cxx b/BRAINSConstellationDetector/gui/QVTKInteractionCallback.cxx
new file mode 100644
index 00000000..1c2d8abb
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/QVTKInteractionCallback.cxx
@@ -0,0 +1,1082 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "QVTKInteractionCallback.h"
+
+#include "vtkImageData.h"
+#include "vtkMatrix4x4.h"
+#include "vtkCamera.h"
+#include "vtkRenderer.h"
+#include "vtkRendererCollection.h"
+#include "vtkRenderWindow.h"
+#include "vtkInteractorStyleImage.h"
+#include "math.h"
+
+// The mouse motion callback, to turn "Slicing" on and off
+void QVTKInteractionCallback::Execute(vtkObject *, unsigned long myEvent, void *)
+{
+  int     type = m_type;
+  double *direction = m_direction;
+  double *physicalExtent = m_physicalExtent;
+  double *physicalExtentIdentity = m_physicalExtentIdentity;
+  double *bound = m_bound;
+
+  /*
+  double spacing[3];
+  spacing[0] = m_spacing[0];
+  spacing[1] = m_spacing[5];
+  spacing[2] = m_spacing[10];
+
+  // bad spacing
+  if ( spacing[0] * spacing[1] * spacing[2] == 0 )
+    {
+    std::cerr << "Bad spacing. Halt." << std::endl;
+    exit( -1 );
+    }
+  */
+
+  // int *indexExtent = m_indexExtent;
+
+  vtkRenderWindowInteractor *interactor = m_interactor;
+  int                        currPos[2];
+
+  interactor->GetEventPosition(currPos);
+  int eventSize[2];
+  interactor->GetSize(eventSize);
+  double cPos[3]; // camera position
+  interactor->GetRenderWindow()->GetRenderers()->GetFirstRenderer()->GetActiveCamera()->GetPosition(cPos);
+
+  // compute the screen size of image slice
+  double R; // physical width/height ratio
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    R = ( bound[3] - bound[2] ) / ( bound[5] - bound[4] );
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    R = ( bound[1] - bound[0] ) / ( bound[5] - bound[4] );
+    }
+  else
+    { // axial view mode ( LAS )
+    R = ( bound[1] - bound[0] ) / ( bound[3] - bound[2] );
+    }
+  int h = 0.96 * eventSize[1] / sqrt(1.0 + R * R);   // sreen height of image
+                                                     // slice
+  int w = R * h;                                     // screen width of image
+                                                     // slice
+
+  // wheeling effect
+  if( m_cPos < 0.0 )
+    {
+    m_cPos = cPos[2];
+    }
+  else if( m_cPos != cPos[2] )
+    {
+    double r = m_cPos / cPos[2];
+    h *= r;
+    w *= r;
+    if( m_r != r )
+      {
+      m_r = r;
+      emit wheelChanged();
+      }
+    }
+
+  // center mapping due to image direction compensation for the reslice axes
+  int    centerMapped;
+  double centerMappedDouble;
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    centerMappedDouble = ( direction[0] + 2 * direction[4] + 4 * direction[8] ) / 2;
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    centerMappedDouble = ( direction[1] + 2 * direction[5] + 4 * direction[9] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    centerMappedDouble = ( direction[2] + 2 * direction[6] + 4 * direction[10] ) / 2;
+    }
+  if( centerMappedDouble < 0 )
+    {
+    centerMappedDouble *= -1;
+    }
+  centerMapped = centerMappedDouble + EPS;
+
+  // move the center point that we are slicing through
+  vtkImageReslice *reslice = m_imageReslice;
+  reslice->GetOutput()->UpdateInformation();
+  vtkMatrix4x4 *matrix = reslice->GetResliceAxes();
+  double        zPhysicalLocation; // pyhysical position along normal vector
+  double        center[4] = { ( *matrix )[0][3], ( *matrix )[1][3], ( *matrix )[2][3], 1.0 };
+  QString       labelPosString;   // label postion for viewer-list communication
+  double        labelPosRatio[3]; // label postion for inter-viewer
+                                  // communication
+
+  // handling keyboard myEvent especially for fiducial labeling
+  if( myEvent == vtkCommand::KeyPressEvent )
+    {
+    char key = m_interactor->GetKeyCode();
+    if( key == 'C' || key == 'c' )  // create a new actor
+      {
+      QString initPos =
+        initPos.number( ( physicalExtent[0] + physicalExtent[1] ) / 2.0 ) + " "
+        + initPos.number( ( physicalExtent[2] + physicalExtent[3] ) / 2.0 ) + " "
+        + initPos.number( ( physicalExtent[4] + physicalExtent[5] ) / 2.0 );
+      emit createListItem(initPos);
+      emit createActor();
+      }
+    if( key == 'S' || key == 's' )  // switch from actors
+      {
+      emit switchListItem();
+      emit switchActor();
+      }
+    if( key == 'D' || key == 'd' )  // delete current actor
+      {
+      emit deleteListItem();
+      emit deleteActor();
+      }
+    emit checkVisibility();
+    }
+
+  // handling mouse myEvent
+  else if( myEvent == vtkCommand::LeftButtonPressEvent )
+    {
+    m_action = 1;
+
+    // Sharing last mouse position of slice viewer for slider bar control
+    m_lastPos[0] = currPos[0];
+    m_lastPos[1] = currPos[1];
+
+    // linear mapping
+    double zFactor =
+      ( center[centerMapped] - physicalExtentIdentity[2 * centerMapped] )
+      / ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+    // show current physical position
+    if( type == 2 )
+      {   // sagittal view mode ( ASL )
+      zPhysicalLocation = zFactor * ( physicalExtent[1] - physicalExtent[0] ) + physicalExtent[0];
+      if( zPhysicalLocation < bound[0] )
+        {
+        zPhysicalLocation = bound[0];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[0] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+      if( zPhysicalLocation > bound[1] )
+        {
+        zPhysicalLocation = bound[1];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[0] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+
+      // store the physical location
+      m_valueSendX = ( bound[3] - bound[2] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[2];
+      m_valueSendY = ( bound[5] - bound[4] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[4];
+      m_valueReceiveZ = zPhysicalLocation;
+
+      /*
+      // regulation due to resolution
+      m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+      m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+      m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+      */
+
+      m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+      // label postion for list-viewer communication
+      labelPosString =
+        m_text_physicalLocation.number(m_valueReceiveZ) + " "
+        + m_text_physicalLocation.number(m_valueSendX) + " "
+        + m_text_physicalLocation.number(m_valueSendY);
+
+      // label postion ratio for inter-viewer communication
+      labelPosRatio[0] =
+        ( m_valueReceiveZ - bound[0] ) / ( bound[1] - bound[0] );
+      labelPosRatio[1] =
+        ( m_valueSendX - bound[2] ) / ( bound[3] - bound[2] );
+      labelPosRatio[2] =
+        ( m_valueSendY - bound[4] ) / ( bound[5] - bound[4] );
+      }
+    else if( type == 3 )
+      {   // coronal view mode ( LSA )
+      zPhysicalLocation = ( 1 - zFactor ) * ( physicalExtent[2] - physicalExtent[3] ) + physicalExtent[3];
+      if( zPhysicalLocation < bound[2] )
+        {
+        zPhysicalLocation = bound[2];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[2] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+      if( zPhysicalLocation > bound[3] )
+        {
+        zPhysicalLocation = bound[3];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[2] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+
+      // store the physical location
+      m_valueSendX = ( bound[1] - bound[0] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[0];
+      m_valueSendY = ( bound[5] - bound[4] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[4];
+      m_valueReceiveZ = zPhysicalLocation;
+
+      /*
+      // regulation due to resolution
+      m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+      m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+      m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+      */
+
+      m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+      // label postion for list-viewer communication
+      labelPosString =
+        m_text_physicalLocation.number(m_valueSendX) + " "
+        + m_text_physicalLocation.number(m_valueReceiveZ) + " "
+        + m_text_physicalLocation.number(m_valueSendY);
+
+      // label postion ratio for inter-viewer communication
+      labelPosRatio[0] =
+        ( m_valueSendX - bound[0] ) / ( bound[1] - bound[0] );
+      labelPosRatio[1] =
+        ( m_valueReceiveZ - bound[2] ) / ( bound[3] - bound[2] );
+      labelPosRatio[2] =
+        ( m_valueSendY - bound[4] ) / ( bound[5] - bound[4] );
+      }
+    else
+      {   // axial view mode ( LAS )
+      zPhysicalLocation = zFactor * ( physicalExtent[5] - physicalExtent[4] ) + physicalExtent[4];
+      if( zPhysicalLocation < bound[4] )
+        {
+        zPhysicalLocation = bound[4];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[4] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+      if( zPhysicalLocation > bound[5] )
+        {
+        zPhysicalLocation = bound[5];
+        center[centerMapped] = zPhysicalLocation == physicalExtent[4] ?
+          physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped + 1];
+        }
+
+      // store the physical location
+      m_valueSendX = ( bound[1] - bound[0] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[0];
+      m_valueSendY = ( bound[2] - bound[3] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[3];
+      m_valueReceiveZ = zPhysicalLocation;
+
+      /*
+      // regulation due to resolution
+      m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+      m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+      m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+      */
+
+      m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+      // label postion for list-viewer communication
+      labelPosString =
+        m_text_physicalLocation.number(m_valueSendX) + " "
+        + m_text_physicalLocation.number(m_valueSendY) + " "
+        + m_text_physicalLocation.number(m_valueReceiveZ);
+
+      // label postion ratio for inter-viewer communication
+      labelPosRatio[0] =
+        ( m_valueSendX - bound[0] ) / ( bound[1] - bound[0] );
+      labelPosRatio[1] =
+        ( m_valueSendY - bound[2] ) / ( bound[3] - bound[2] );
+      labelPosRatio[2] =
+        ( m_valueReceiveZ - bound[4] ) / ( bound[5] - bound[4] );
+      }
+    // signal to fiducial label
+    emit moveActor(labelPosRatio);
+
+    // signal to neighbor slice viewers
+    emit valueChangedX(m_valueSendX);
+    emit valueChangedY(m_valueSendY);
+
+    // signal to slider bar
+    emit valueChangedZ(m_valueReceiveZ * m_precision);
+
+    /*
+    // signal to neighbor slice viewers
+    emit valueChangedX( round( m_valueSendX / spacing[1-m_type%2] ) );
+    emit valueChangedY( round( m_valueSendY / spacing[ m_type / 2 + 1 ] ) );
+
+    // signal to slider bar
+    emit valueChangedZ( round( m_valueReceiveZ / spacing[ (m_type + 1)  % 3 ] ) );
+    */
+
+    // signal to status label
+    emit textChanged(m_text_physicalLocation);
+
+    // signal to label list
+    emit editListItem(labelPosString);
+
+    emit checkVisibility();
+    }
+  else if( myEvent == vtkCommand::LeftButtonReleaseEvent )
+    {
+    m_action = 0;
+    }
+  else if( myEvent == vtkCommand::MouseMoveEvent )
+    {
+    if( m_action == 1 )
+      { // change a slice to show
+        // Sharing last mouse position of slice viewer for slider bar control
+      m_lastPos[0] = currPos[0];
+      m_lastPos[1] = currPos[1];
+
+      // linear mapping
+      double zFactor =
+        ( center[centerMapped] - physicalExtentIdentity[2 * centerMapped] )
+        / ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+      // show current physical position
+      if( type == 2 )
+        {   // sagittal view mode ( ASL )
+        zPhysicalLocation = zFactor * ( physicalExtent[1] - physicalExtent[0] ) + physicalExtent[0];
+        if( zPhysicalLocation < bound[0] )
+          {
+          zPhysicalLocation = bound[0];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[0] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+        if( zPhysicalLocation > bound[1] )
+          {
+          zPhysicalLocation = bound[1];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[0] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+
+        // store the physical location
+        m_valueSendX = ( bound[3] - bound[2] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[2];
+        m_valueSendY = ( bound[5] - bound[4] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[4];
+        m_valueReceiveZ = zPhysicalLocation;
+
+        /*
+        // regulation due to resolution
+        m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+        m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+        m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+        */
+
+        m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+        // label postion for list-viewer communication
+        labelPosString =
+          m_text_physicalLocation.number(m_valueReceiveZ) + " "
+          + m_text_physicalLocation.number(m_valueSendX) + " "
+          + m_text_physicalLocation.number(m_valueSendY);
+
+        // label postion ratio for inter-viewer communication
+        labelPosRatio[0] =
+          ( m_valueReceiveZ - bound[0] ) / ( bound[1] - bound[0] );
+        labelPosRatio[1] =
+          ( m_valueSendX - bound[2] ) / ( bound[3] - bound[2] );
+        labelPosRatio[2] =
+          ( m_valueSendY - bound[4] ) / ( bound[5] - bound[4] );
+        }
+      else if( type == 3 )
+        {   // coronal view mode ( LSA )
+        zPhysicalLocation = ( 1 - zFactor ) * ( physicalExtent[2] - physicalExtent[3] ) + physicalExtent[3];
+        if( zPhysicalLocation < bound[2] )
+          {
+          zPhysicalLocation = bound[2];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[2] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+        if( zPhysicalLocation > bound[3] )
+          {
+          zPhysicalLocation = bound[3];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[2] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+
+        // store the physical location
+        m_valueSendX = ( bound[1] - bound[0] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[0];
+        m_valueSendY = ( bound[5] - bound[4] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[4];
+        m_valueReceiveZ = zPhysicalLocation;
+
+        /*
+        // regulation due to resolution
+        m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+        m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+        m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+        */
+
+        m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+        // label postion for list-viewer communication
+        labelPosString =
+          m_text_physicalLocation.number(m_valueSendX) + " "
+          + m_text_physicalLocation.number(m_valueReceiveZ) + " "
+          + m_text_physicalLocation.number(m_valueSendY);
+
+        // label postion ratio for inter-viewer communication
+        labelPosRatio[0] =
+          ( m_valueSendX - bound[0] ) / ( bound[1] - bound[0] );
+        labelPosRatio[1] =
+          ( m_valueReceiveZ - bound[2] ) / ( bound[3] - bound[2] );
+        labelPosRatio[2] =
+          ( m_valueSendY - bound[4] ) / ( bound[5] - bound[4] );
+        }
+      else
+        {   // axial view mode ( LAS )
+        zPhysicalLocation = zFactor * ( physicalExtent[5] - physicalExtent[4] ) + physicalExtent[4];
+        if( zPhysicalLocation < bound[4] )
+          {
+          zPhysicalLocation = bound[4];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[4] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+        if( zPhysicalLocation > bound[5] )
+          {
+          zPhysicalLocation = bound[5];
+          center[centerMapped] = zPhysicalLocation == physicalExtent[4] ?
+            physicalExtentIdentity[2 * centerMapped] : physicalExtentIdentity[2 * centerMapped
+                                                                              + 1];
+          }
+
+        // store the physical location
+        m_valueSendX = ( bound[1] - bound[0] ) * ( currPos[0] - ( eventSize[0] - w ) / 2.0 ) / w + bound[0];
+        m_valueSendY = ( bound[2] - bound[3] ) * ( currPos[1] - ( eventSize[1] - h ) / 2.0 ) / h + bound[3];
+        m_valueReceiveZ = zPhysicalLocation;
+
+        /*
+        // regulation due to resolution
+        m_valueSendX = spacing[1-m_type%2] * round( m_valueSendX / spacing[1-m_type%2] );
+        m_valueSendY = spacing[m_type/2+1] * round( m_valueSendY / spacing[m_type/2+1] );
+        m_valueReceiveZ = spacing[(m_type+1)%3] * round( m_valueReceiveZ / spacing[(m_type+1)%3] );
+        */
+
+        m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+
+        // label postion for list-viewer communication
+        labelPosString =
+          m_text_physicalLocation.number(m_valueSendX) + " "
+          + m_text_physicalLocation.number(m_valueSendY) + " "
+          + m_text_physicalLocation.number(m_valueReceiveZ);
+
+        // label postion ratio for inter-viewer communication
+        labelPosRatio[0] =
+          ( m_valueSendX - bound[0] ) / ( bound[1] - bound[0] );
+        labelPosRatio[1] =
+          ( m_valueSendY - bound[2] ) / ( bound[3] - bound[2] );
+        labelPosRatio[2] =
+          ( m_valueReceiveZ - bound[4] ) / ( bound[5] - bound[4] );
+        }
+
+      // signal to fiducial label
+      emit moveActor(labelPosRatio);
+
+      // signal to neighbor slice viewers
+      emit valueChangedX(m_valueSendX);
+      emit valueChangedY(m_valueSendY);
+
+      // signal to slider bar
+      emit valueChangedZ(m_valueReceiveZ * m_precision);
+
+      /*
+       // signal to neighbor slice viewers
+       emit valueChangedX( round( m_valueSendX / spacing[1-m_type%2] ) );
+       emit valueChangedY( round( m_valueSendY / spacing[ m_type / 2 + 1 ] ) );
+
+       // signal to slider bar
+       emit valueChangedZ( round( m_valueReceiveZ / spacing[ (m_type + 1)  % 3 ] ) );
+       */
+
+      // signal to status label
+      emit textChanged(m_text_physicalLocation);
+
+      // signal to label list
+      emit editListItem(labelPosString);
+      emit checkVisibility();
+      }
+    else
+      {
+      vtkInteractorStyle *style =
+        vtkInteractorStyle::SafeDownCast( interactor->GetInteractorStyle() );
+      if( style )
+        {
+        style->OnMouseMove();
+        }
+      }
+    }
+}
+
+QVTKInteractionCallback::QVTKInteractionCallback(const QString & text, const int type, double *bound,
+                                                 QObject *myParent) :
+    QObject(myParent),
+    m_origin(NULL),
+    m_valueSendX(0),
+    m_valueSendY(0),
+    m_valueSendZ(0)
+{
+  EPS = .3;
+  m_action = 0;
+  m_imageReslice = 0;
+  m_interactor = 0;
+  m_direction = 0;
+  m_physicalExtentIdentity = 0;
+  m_physicalExtent = 0;
+  m_bound = bound;
+  m_spacing = 0;
+  m_indexExtent = 0;
+  m_text_physicalLocation = text;
+  m_type = type;
+  m_lastPos[0] = 0;
+  m_lastPos[1] = 0;
+  m_cPos = -1.0;
+  m_r = 0;
+  m_valueReceiveX = -1;
+  m_valueReceiveY = -1;
+  m_precision = 1000.;
+
+  if( m_type == 2 )
+    { // sagittal view mode ( ASL )
+    m_valueReceiveZ = ( m_bound[0] + m_bound[1] ) / 2;
+    }
+  else if( m_type == 3 )
+    { // coronal view mode ( LSA )
+    m_valueReceiveZ = ( m_bound[2] + m_bound[3] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    m_valueReceiveZ = ( m_bound[4] + m_bound[5] ) / 2;
+    }
+}
+
+// slot function for recieve signal from slider bar
+void QVTKInteractionCallback::setValueZLocation(const int zLocation)
+{
+  if( ( m_valueReceiveZ >= zLocation / m_precision - 0.5 )
+      && ( m_valueReceiveZ <  zLocation / m_precision + 0.5 ) )
+    {
+    return;
+    }
+  m_valueReceiveZ = zLocation / m_precision;
+
+  /*
+  double spacing[3];
+  spacing[0] = m_spacing[0];
+  spacing[1] = m_spacing[5];
+  spacing[2] = m_spacing[10];
+
+  // avoid infinite loop and update internal z-axis location
+  if ( m_valueReceiveZ == zLocation * spacing[ (m_type + 1)  % 3 ] )
+    {
+    return;
+    }
+  m_valueReceiveZ = zLocation * spacing[ (m_type + 1)  % 3 ];
+  */
+
+  m_imageReslice->GetOutput()->UpdateInformation();
+  vtkMatrix4x4 *matrix = m_imageReslice->GetResliceAxes();
+
+  // center mapping due to image direction compensation for the reslice axes
+  int     centerMapped;
+  double  centerMappedDouble;
+  int     type = m_type;
+  double *direction = m_direction;
+  double *physicalExtent = m_physicalExtent;
+  double *physicalExtentIdentity = m_physicalExtentIdentity;
+
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    centerMappedDouble = ( direction[0] + 2 * direction[4] + 4 * direction[8] ) / 2;
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    centerMappedDouble = ( direction[1] + 2 * direction[5] + 4 * direction[9] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    centerMappedDouble = ( direction[2] + 2 * direction[6] + 4 * direction[10] ) / 2;
+    }
+  if( centerMappedDouble < 0 )
+    {
+    centerMappedDouble *= -1;
+    }
+  centerMapped = centerMappedDouble + EPS;
+
+  double *bound = m_bound;
+  double  center;
+  int     eventSize[2];
+  m_interactor->GetSize(eventSize);
+
+  // show current physical position
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    if( m_valueReceiveZ < bound[0] )
+      {
+      m_valueReceiveZ = bound[0];
+      }
+    if( m_valueReceiveZ > bound[1] )
+      {
+      m_valueReceiveZ = bound[1];
+      }
+
+    // calculate the center value from m_valueReceiveZ
+    center =
+      ( m_valueReceiveZ - physicalExtent[0] ) / ( physicalExtent[1] - physicalExtent[0] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    if( m_valueReceiveZ < bound[2] )
+      {
+      m_valueReceiveZ = bound[2];
+      }
+    if( m_valueReceiveZ > bound[3] )
+      {
+      m_valueReceiveZ = bound[3];
+      }
+
+    // calculate the center value from m_valueReceiveZ
+    center =
+      physicalExtentIdentity[2 * centerMapped + 1]
+      - ( m_valueReceiveZ - physicalExtent[3] ) / ( physicalExtent[2] - physicalExtent[3] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+    }
+  else
+    { // axial view mode ( LAS )
+    if( m_valueReceiveZ < bound[4] )
+      {
+      m_valueReceiveZ = bound[4];
+      }
+    if( m_valueReceiveZ > bound[5] )
+      {
+      m_valueReceiveZ = bound[5];
+      }
+
+    // calculate the center value from m_valueReceiveZ
+    center =
+      ( m_valueReceiveZ - physicalExtent[4] ) / ( physicalExtent[5] - physicalExtent[4] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveZ);
+    }
+
+  matrix->SetElement(centerMapped, 3, center);
+
+  m_interactor->Render();
+
+  // signal to status label
+  emit textChanged(m_text_physicalLocation);
+
+  // transmit current slice number to list for visiblity check
+  // designed for slider bar effect
+  double tag[2];
+  tag[0] = m_valueReceiveZ;
+  tag[1] = double(m_type);
+
+  emit visibilityCallback(tag);
+}
+
+// this slot function will change the slice according to signal from x-channel
+// slice viewer
+void QVTKInteractionCallback::setValueXLocation(const double xLocation)
+{
+  // avoid infinite loop and update internal z-axis location
+  if( m_valueReceiveX == xLocation )
+    {
+    return;
+    }
+  m_valueReceiveX = xLocation;
+
+  /*
+  double spacing[3];
+  spacing[0] = m_spacing[0];
+  spacing[1] = m_spacing[5];
+  spacing[2] = m_spacing[10];
+
+  // avoid infinite loop and update internal z-axis location
+  if ( m_valueReceiveX == xLocation * spacing[1-m_type%2] )
+    {
+    return;
+    }
+  m_valueReceiveX = xLocation * spacing[1-m_type%2];
+  */
+
+  m_imageReslice->GetOutput()->UpdateInformation();
+  vtkMatrix4x4 *matrix = m_imageReslice->GetResliceAxes();
+
+  // center mapping due to image direction compensation for the reslice axes
+  int     centerMapped;
+  double  centerMappedDouble;
+  int     type = m_type;
+  double *direction = m_direction;
+  double *physicalExtent = m_physicalExtent;
+  double *physicalExtentIdentity = m_physicalExtentIdentity;
+
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    centerMappedDouble = ( direction[0] + 2 * direction[4] + 4 * direction[8] ) / 2;
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    centerMappedDouble = ( direction[1] + 2 * direction[5] + 4 * direction[9] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    centerMappedDouble = ( direction[2] + 2 * direction[6] + 4 * direction[10] ) / 2;
+    }
+  if( centerMappedDouble < 0 )
+    {
+    centerMappedDouble *= -1;
+    }
+  centerMapped = centerMappedDouble + EPS;
+
+  double *bound = m_bound;
+  double  center;
+  int     eventSize[2];
+  m_interactor->GetSize(eventSize);
+
+  // show current physical position
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    if( m_valueReceiveX < bound[0] )
+      {
+      m_valueReceiveX = bound[0];
+      }
+    if( m_valueReceiveX > bound[1] )
+      {
+      m_valueReceiveX = bound[1];
+      }
+
+    // calculate the center value from m_valueReceiveX
+    center =
+      ( m_valueReceiveX - physicalExtent[0] ) / ( physicalExtent[1] - physicalExtent[0] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveX);
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    if( m_valueReceiveX < bound[2] )
+      {
+      m_valueReceiveX = bound[2];
+      }
+    if( m_valueReceiveX > bound[3] )
+      {
+      m_valueReceiveX = bound[3];
+      }
+
+    // calculate the center value from m_valueReceiveX
+    center =
+      physicalExtentIdentity[2 * centerMapped + 1]
+      - ( m_valueReceiveX - physicalExtent[3] ) / ( physicalExtent[2] - physicalExtent[3] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveX);
+    }
+  else
+    { // axial view mode ( LAS )
+    if( m_valueReceiveX < bound[4] )
+      {
+      m_valueReceiveX = bound[4];
+      }
+    if( m_valueReceiveX > bound[5] )
+      {
+      m_valueReceiveX = bound[5];
+      }
+
+    // calculate the center value from m_valueReceiveX
+    center =
+      ( m_valueReceiveX - physicalExtent[4] ) / ( physicalExtent[5] - physicalExtent[4] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveX);
+    }
+
+  matrix->SetElement(centerMapped, 3, center);
+
+  m_interactor->Render();
+
+  // signal to status label and slider bar
+  emit textChanged(m_text_physicalLocation);
+
+  emit valueChangedZ(m_valueReceiveX * m_precision);
+
+  // emit valueChangedZ( round( m_valueReceiveX / spacing[1-m_type%2] ) );
+}
+
+// this slot function will change the slice according to signal from y-channel
+// slice viewer
+void QVTKInteractionCallback::setValueYLocation(const double yLocation)
+{
+  // avoid infinite loop and update internal z-axis location
+  if( m_valueReceiveY == yLocation )
+    {
+    return;
+    }
+  m_valueReceiveY = yLocation;
+
+  /*
+  double spacing[3];
+  spacing[0] = m_spacing[0];
+  spacing[1] = m_spacing[5];
+  spacing[2] = m_spacing[10];
+
+  // avoid infinite loop and update internal z-axis location
+  if ( m_valueReceiveY == yLocation * spacing[ m_type / 2 + 1 ] )
+    {
+    return;
+    }
+  m_valueReceiveY = yLocation * spacing[ m_type / 2 + 1 ];
+  */
+
+  m_imageReslice->GetOutput()->UpdateInformation();
+  vtkMatrix4x4 *matrix = m_imageReslice->GetResliceAxes();
+
+  // center mapping due to image direction compensation for the reslice axes
+  int     centerMapped;
+  double  centerMappedDouble;
+  int     type = m_type;
+  double *direction = m_direction;
+  double *physicalExtent = m_physicalExtent;
+  double *physicalExtentIdentity = m_physicalExtentIdentity;
+
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    centerMappedDouble = ( direction[0] + 2 * direction[4] + 4 * direction[8] ) / 2;
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    centerMappedDouble = ( direction[1] + 2 * direction[5] + 4 * direction[9] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    centerMappedDouble = ( direction[2] + 2 * direction[6] + 4 * direction[10] ) / 2;
+    }
+  if( centerMappedDouble < 0 )
+    {
+    centerMappedDouble *= -1;
+    }
+  centerMapped = centerMappedDouble + EPS;
+
+  double *bound = m_bound;
+  double  center;
+  int     eventSize[2];
+  m_interactor->GetSize(eventSize);
+
+  // show current physical position
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    if( m_valueReceiveY < bound[0] )
+      {
+      m_valueReceiveY = bound[0];
+      }
+    if( m_valueReceiveY > bound[1] )
+      {
+      m_valueReceiveY = bound[1];
+      }
+
+    // calculate the center value from m_valueReceiveY
+    center =
+      ( m_valueReceiveY - physicalExtent[0] ) / ( physicalExtent[1] - physicalExtent[0] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveY);
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    if( m_valueReceiveY < bound[2] )
+      {
+      m_valueReceiveY = bound[2];
+      }
+    if( m_valueReceiveY > bound[3] )
+      {
+      m_valueReceiveY = bound[3];
+      }
+
+    // calculate the center value from m_valueReceiveY
+    center =
+      physicalExtentIdentity[2 * centerMapped + 1]
+      - ( m_valueReceiveY - physicalExtent[3] ) / ( physicalExtent[2] - physicalExtent[3] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveY);
+    }
+  else
+    { // axial view mode ( LAS )
+    if( m_valueReceiveY < bound[4] )
+      {
+      m_valueReceiveY = bound[4];
+      }
+    if( m_valueReceiveY > bound[5] )
+      {
+      m_valueReceiveY = bound[5];
+      }
+
+    // calculate the center value from m_valueReceiveY
+    center =
+      ( m_valueReceiveY - physicalExtent[4] ) / ( physicalExtent[5] - physicalExtent[4] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(m_valueReceiveY);
+    }
+
+  matrix->SetElement(centerMapped, 3, center);
+
+  m_interactor->Render();
+
+  // signal to status label and slider bar
+  emit textChanged(m_text_physicalLocation);
+  emit valueChangedZ(m_valueReceiveY * m_precision);
+
+  // emit valueChangedZ( round( m_valueReceiveY / spacing[ m_type / 2 + 1 ] ) );
+}
+
+void QVTKInteractionCallback::receiveLabelPos(double *pos)
+{
+  m_imageReslice->GetOutput()->UpdateInformation();
+  vtkMatrix4x4 *matrix = m_imageReslice->GetResliceAxes();
+
+  // center mapping due to image direction compensation for the reslice axes
+  int     centerMapped;
+  double  centerMappedDouble;
+  int     type = m_type;
+  double *direction = m_direction;
+  double *physicalExtent = m_physicalExtent;
+  double *physicalExtentIdentity = m_physicalExtentIdentity;
+
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    centerMappedDouble = ( direction[0] + 2 * direction[4] + 4 * direction[8] ) / 2;
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    centerMappedDouble = ( direction[1] + 2 * direction[5] + 4 * direction[9] ) / 2;
+    }
+  else
+    { // axial view mode ( LAS )
+    centerMappedDouble = ( direction[2] + 2 * direction[6] + 4 * direction[10] ) / 2;
+    }
+  if( centerMappedDouble < 0 )
+    {
+    centerMappedDouble *= -1;
+    }
+  centerMapped = centerMappedDouble + EPS;
+
+  double *bound = m_bound;
+  double  center;
+  double  posLocal;
+  int     eventSize[2];
+  m_interactor->GetSize(eventSize);
+
+  // show current physical position
+  if( type == 2 )
+    { // sagittal view mode ( ASL )
+    posLocal = pos[0];
+    if( pos[0] < bound[0] )
+      {
+      pos[0] = bound[0];
+      }
+    if( pos[0] > bound[1] )
+      {
+      pos[0] = bound[1];
+      }
+
+    // calculate the center value from pos[0]
+    center =
+      ( pos[0] - physicalExtent[0] ) / ( physicalExtent[1] - physicalExtent[0] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(pos[0]);
+    }
+  else if( type == 3 )
+    { // coronal view mode ( LSA )
+    posLocal = pos[1];
+    if( pos[1] < bound[2] )
+      {
+      pos[1] = bound[2];
+      }
+    if( pos[1] > bound[3] )
+      {
+      pos[1] = bound[3];
+      }
+
+    // calculate the center value from pos[1]
+    center =
+      physicalExtentIdentity[2 * centerMapped + 1]
+      - ( pos[1] - physicalExtent[3] ) / ( physicalExtent[2] - physicalExtent[3] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] );
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(pos[1]);
+    }
+  else
+    { // axial view mode ( LAS )
+    posLocal = pos[2];
+    if( pos[2] < bound[4] )
+      {
+      pos[2] = bound[4];
+      }
+    if( pos[2] > bound[5] )
+      {
+      pos[2] = bound[5];
+      }
+
+    // calculate the center value from pos[2]
+    center =
+      ( pos[2] - physicalExtent[4] ) / ( physicalExtent[5] - physicalExtent[4] )
+      * ( physicalExtentIdentity[2 * centerMapped + 1] - physicalExtentIdentity[2 * centerMapped] )
+      + physicalExtentIdentity[2 * centerMapped];
+
+    // store the physical location and the z-axis location
+    m_text_physicalLocation = m_text_physicalLocation.number(pos[2]);
+    }
+
+  matrix->SetElement(centerMapped, 3, center);
+
+  m_interactor->Render();
+
+  // signal to status label and slider bar
+  emit textChanged(m_text_physicalLocation);
+  emit valueChangedZ(posLocal * m_precision);
+}
+
+void QVTKInteractionCallback::createListAddButtonSlot()
+{
+  double *physicalExtent = m_physicalExtent;
+  QString initPos =
+    initPos.number( ( physicalExtent[0] + physicalExtent[1] ) / 2.0 ) + " "
+    + initPos.number( ( physicalExtent[2] + physicalExtent[3] ) / 2.0 ) + " "
+    + initPos.number( ( physicalExtent[4] + physicalExtent[5] ) / 2.0 );
+  emit createListItem(initPos);
+}
+
+void QVTKInteractionCallback::deleteListButtonSlot()
+{
+  emit deleteListItem();
+}
+
diff --git a/BRAINSConstellationDetector/gui/include/QDelLabelDialogs.h b/BRAINSConstellationDetector/gui/include/QDelLabelDialogs.h
new file mode 100644
index 00000000..04890d14
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QDelLabelDialogs.h
@@ -0,0 +1,44 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __QDelLabelDialogs_H
+#define __QDelLabelDialogs_H
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+class QDelLabelDialogs : public QDialog
+{
+  Q_OBJECT
+public:
+
+  QDelLabelDialogs( QString text = "", QWidget *myParent = 0 );
+public slots:
+
+  void exec( QListWidgetItem * );
+
+  void accept2(); // a wrap for double click situation
+
+signals:
+
+  void exec2(); // a wrap for double click situation
+
+  void accepted( QListWidgetItem * );
+
+protected:
+
+  QGridLayout *    m_layout;
+  QLabel           m_label;
+  QPushButton      m_accept;
+  QPushButton      m_cancel;
+  QListWidgetItem *m_listItem;
+};
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/QFileDialogs.h b/BRAINSConstellationDetector/gui/include/QFileDialogs.h
new file mode 100644
index 00000000..3041e16b
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QFileDialogs.h
@@ -0,0 +1,44 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef _QFileDialogs_H
+#define _QFileDialogs_H
+
+#include 
+#include 
+
+class QFileDialogs : public QWidget
+{
+  Q_OBJECT
+public:
+
+  QFileDialogs( QString landmarks = "", QWidget *myParent = 0 ) : QWidget( myParent )
+  {
+    m_landmarks = landmarks;
+  }
+
+  QString openLandmarksFile();
+
+  QString saveLandmarksFile();
+
+  QString landmarksFile()
+  {
+    return m_landmarks;
+  }
+
+public slots:
+
+  void openLandmarksFileSlot();
+
+  void saveLandmarksFileSlot();
+
+protected:
+
+  QString m_landmarks;
+
+};
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/QHelpDialog.h b/BRAINSConstellationDetector/gui/include/QHelpDialog.h
new file mode 100644
index 00000000..d15c2a23
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QHelpDialog.h
@@ -0,0 +1,27 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __QHelpDialog_H
+#define __QHelpDialog_H
+
+#include 
+#include 
+#include 
+#include 
+
+class QHelpDialog : public QDialog
+{
+  Q_OBJECT
+public:
+
+  QHelpDialog( QWidget *myParent = 0 );
+protected:
+
+  QGridLayout *m_layout;
+  QLabel       m_label;
+};
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/QLabelList.h b/BRAINSConstellationDetector/gui/include/QLabelList.h
new file mode 100644
index 00000000..99f86f3e
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QLabelList.h
@@ -0,0 +1,147 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef _QLabelList_H
+#define _QLabelList_H
+
+#include "QFileDialogs.h"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include "assert.h"
+#include 
+#include 
+#include 
+#include 
+
+class QLabelList : public QListWidget
+{
+  Q_OBJECT
+
+  typedef std::map > LandmarksMapType;
+public:
+
+  QLabelList( QWidget *myParent = 0 ) :
+    QListWidget( myParent )
+  {
+    m_color = 0;
+  }
+
+  void SetInputVolume( std::string filename )
+  {
+    m_inputVolume = QString::fromStdString( filename );
+  }
+
+  void SetInputLandmarks( std::string filename )
+  {
+    m_inputLandmarks = QString::fromStdString( filename );
+  }
+
+  void SetOutputLandmarks( std::string filename )
+  {
+    m_outputLandmarks = QString::fromStdString( filename );
+  }
+
+  LandmarksMapType GetLandmarks()
+  {
+    return m_landmarks;
+  }
+
+  void createListItem( const QString & label, const QString & name ); // UI for
+
+  // creating
+  // named
+  // points
+  // load landmarks from file
+  void loadLandmarks();
+
+  // read landmarks from label list class to the internal map
+  void readLandmarks();
+
+  // write landmarks to file
+  void writeLandmarks();
+
+public slots:
+
+  // respond to keyboard signal from viewer
+  void createListItemSlot( const QString & label );
+
+  void createListItemAddButtonSlot(); // a wrap for add label button
+
+  void editListItemSlot( const QString & );
+
+  void switchListItemSlot();
+
+  void deleteListItemSlot();
+
+  void deleteListSlot();
+
+  // respond to mouse signal from itself
+  void cancelHighlight( QListWidgetItem * ); // haven't find a direct way of
+
+  // disabling highlight ;(
+
+  void deleteListItemMouseSlot( QListWidgetItem * );
+
+  void sliceChangedSlot();
+
+  // determine which label should be displayed
+  void checkVisibilitySlot();
+
+  void checkVisibilitySlot( double *tag ); // a wrap for slider bar
+
+  void checkVisibilitySlot( QListWidgetItem * ); // a wrap for double click on
+
+  // list item
+
+  // respond to callback, help to find the initial position due to wheeling
+  void ackWheelChanged();
+
+  // save landmarks to a file
+  void saveLandmarks();
+
+  void saveAsLandmarks();
+
+signals:
+
+  void sliceChangedList(); // signal to sliceChangeSlot indicating the update of
+
+  // slice viewer
+
+  void sendLabelPosition( double *pos );
+
+  // determine which label should be displayed
+  // *[0] = sagittal, *[1] = coronal, *[2] = axial
+  // table = 1 means the label is visible in certain viewer
+  void visibilityTable( int *table );
+
+  // send to viewer, help to find the initial position due to wheeling
+  void sendLabelPositions( double *pos );
+
+protected:
+
+  // color seed
+  int m_color;
+
+  // label postion signal received
+  QString m_label;
+
+  LandmarksMapType m_landmarks;
+
+  QString m_inputVolume;
+  QString m_inputLandmarks;
+  QString m_outputLandmarks;
+
+};
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/QSliceViewer.h b/BRAINSConstellationDetector/gui/include/QSliceViewer.h
new file mode 100644
index 00000000..d76fbadc
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QSliceViewer.h
@@ -0,0 +1,111 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef _QSliceViewer_H
+#define _QSliceViewer_H
+
+#include "vtkSphereSource.h"
+#include "vtkPolyDataMapper2D.h"
+#include "vtkProperty2D.h"
+#include "vtkCamera.h"
+#include "vtkActor2D.h"
+#include "vtkActor2DCollection.h"
+#include "vtkRenderer.h"
+#include "vtkRendererCollection.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderWindowInteractor.h"
+
+#include "QVTKWidget.h"
+#include 
+#include 
+#include 
+
+#include 
+
+class QSliceViewer : public QVTKWidget
+{
+  Q_OBJECT
+public:
+
+  QSliceViewer( int type, QWidget *myParent = 0 ) :
+    QVTKWidget( myParent ),
+    m_bound(NULL)
+  {
+    m_actors = vtkActor2DCollection::New();
+    m_actor = NULL;
+    m_type = type;
+    m_cPos = -1.0;
+    m_color = 0;
+    m_r = 0;
+  }
+
+  void SetBound( double *bound )
+  {
+    m_bound = bound;
+  }
+
+  double * GetBound()
+  {
+    return m_bound;
+  }
+
+  void createLabel( double *labelPos );
+
+public slots:
+
+  void createLabelSlot();
+
+  void switchLabelSlot();
+
+  void moveLabelSlot( double *labelPos ); // labelPos is a ratio
+
+  void deleteLabelSlot();
+
+  void deleteAllLabelSlot();
+
+  void deleteLabelMouseSlot( QListWidgetItem *item ); // a mouse version wrap
+
+  // for deleteLabelSlot
+
+  void pickLabelSlot( QListWidgetItem *item ); // deal with click signal from
+
+  // list
+
+  void wheelSlot( double *labelPos ); // handle wheeling event
+
+  void visibilityUpdate( int *table ); // update labels according to their
+
+  // visibility
+signals:
+protected:
+
+  vtkActor2DCollection *m_actors;
+
+  vtkActor2D *m_actor;
+
+  // slice viewer type: axial, sagittal, or coronal
+  int m_type;
+
+  // Pointer to the physical bound ( = ordered extent )
+  double *m_bound;
+
+  // last camera postion, helping to account wheeling effect
+  double m_cPos;
+
+  // color seed
+  int m_color;
+
+  // internal ratio for screen size change
+  double m_r;
+private:
+
+  void GenSphere(); // generate a sphere
+
+  void Highlight(); // highlight the current actor
+
+};
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/QVTKInteractionCallback.h b/BRAINSConstellationDetector/gui/include/QVTKInteractionCallback.h
new file mode 100644
index 00000000..3ece5b33
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/QVTKInteractionCallback.h
@@ -0,0 +1,276 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __QVTKInteractionCallback_H
+#define __QVTKInteractionCallback_H
+
+#include "vtkCommand.h"
+#include "vtkImageReslice.h"
+#include "vtkRenderWindowInteractor.h"
+
+#include 
+#include 
+
+#include "math.h"
+
+#include 
+
+// The mouse motion callback, to turn "Slicing" on and off
+class QVTKInteractionCallback : public QObject, public vtkCommand
+{
+  Q_OBJECT;
+public:
+
+  QVTKInteractionCallback( const QString & text, const int type, double *bound, QObject *myParent = 0 );
+
+  void SetImageReslice( vtkImageReslice *reslice )
+  {
+    m_imageReslice = reslice;
+  }
+
+  vtkImageReslice * GetImageReslice()
+  {
+    return m_imageReslice;
+  }
+
+  void SetInteractor( vtkRenderWindowInteractor *interactor )
+  {
+    m_interactor = interactor;
+  }
+
+  vtkRenderWindowInteractor * GetInteractor()
+  {
+    return m_interactor;
+  }
+
+  void SetDirection( double *direction )
+  {
+    m_direction = direction;
+  }
+
+  double * GetDirection()
+  {
+    return m_direction;
+  }
+
+  void SetOrigin( double *origin )
+  {
+    m_origin = origin;
+  }
+
+  double * GetOrigin()
+  {
+    return m_origin;
+  }
+
+  void SetSpacing( double *spacing )
+  {
+    m_spacing = spacing;
+  }
+
+  double * GetSpacing()
+  {
+    return m_spacing;
+  }
+
+  void SetPhysicalExtentIdentity( double *physicalExtentIdentity )
+  {
+    m_physicalExtentIdentity = physicalExtentIdentity;
+  }
+
+  double * GetPhysicalExtentIdentity()
+  {
+    return m_physicalExtentIdentity;
+  }
+
+  void SetPhysicalExtent( double *physicalExtent )
+  {
+    m_physicalExtent = physicalExtent;
+  }
+
+  double * GetPhysicalExtent()
+  {
+    return m_physicalExtent;
+  }
+
+  void SetBound( double *bound )
+  {
+    m_bound = bound;
+  }
+
+  double * GetBound()
+  {
+    return m_bound;
+  }
+
+  void SetIndexExtent( int *indexExtent )
+  {
+    m_indexExtent = indexExtent;
+  }
+
+  int * GetIndexExtent()
+  {
+    return m_indexExtent;
+  }
+
+  void SetType( int type )
+  {
+    m_type = type;
+  }
+
+  int GetType()
+  {
+    return m_type;
+  }
+
+  void SetPrecision( double precision )
+  {
+    m_precision = precision;
+  }
+
+  double GetPrecision()
+  {
+    return m_precision;
+  }
+
+  void Execute( vtkObject *, unsigned long event, void * );
+
+  const QString & textPhysicalLocation() const
+  {
+    return m_text_physicalLocation;
+  }
+
+public slots:
+
+  /*
+   * This slot responds to the signal from slider bar, including update and invoke rerendering
+   * Due to int ui of QSlider, we pass int zLocation = 1000 x sliceValue
+   * Later we have something like double m_zLocation = zLocation / 1000
+   */
+  void setValueZLocation( const int zLocation );
+
+  // this slot corresponds to commnication among slice viewers
+  void setValueXLocation( const double xLocation );
+
+  void setValueYLocation( const double yLocation );
+
+  void receiveLabelPos( double *pos ); // set the label positon from pos info
+
+  // from label list
+
+  void createListAddButtonSlot(); // receive the request from add button
+
+  void deleteListButtonSlot(); // receive the request from remove button
+
+signals:
+
+  void textChanged( const QString & ); // update status label
+
+  void valueChangedZ( int ); // update slider bar, and due to int ui of QSlider
+
+  // update neighbor slice viewer
+  void valueChangedX( double );
+
+  void valueChangedY( double );
+
+  // update fiducial label
+  void createActor();
+
+  void switchActor();
+
+  void deleteActor();
+
+  void moveActor( double * );
+
+  // update label list
+  void createListItem( const QString & );
+
+  void editListItem( const QString & );
+
+  void switchListItem();
+
+  void deleteListItem();
+
+  void checkVisibility(); // check visibility request to list
+
+  // transmit current slice number to list for visiblity check
+  // designed for slider bar effect
+  void visibilityCallback( double *tag );
+
+  void wheelChanged(); // indicate the move of mouse wheel
+
+protected:
+
+  // Round error
+  double EPS;
+
+  // Actions:
+  // Idle = 0;
+  // Get location = 1;
+  int m_action;
+
+  // Pointer to vtkImageReslice
+  vtkImageReslice *m_imageReslice;
+
+  // Pointer to the interactor
+  vtkRenderWindowInteractor *m_interactor;
+
+  // Pointer to the direction
+  double *m_direction;
+
+  // Pointer to the origin
+  double *m_origin;
+
+  // Pointer to the spacing
+  double *m_spacing;
+
+  // Pointer to the physical extent of input image with identity direction
+  double *m_physicalExtentIdentity;
+
+  // Pointer to the physical extent
+  double *m_physicalExtent;
+
+  // Pointer to the physical bound ( = ordered extent )
+  double *m_bound;
+
+  // Pointer to the index extent
+  int *m_indexExtent;
+
+  // Callback type: axial, sagittal, or coronal
+  int m_type;
+
+  // Storing physical postion
+  QString m_text_physicalLocation;
+
+  // Storing z-axis postion for x channel communication
+  double m_valueSendX;
+
+  double m_valueReceiveX;
+
+  // Storing z-axis postion for y channel communication
+  double m_valueSendY;
+
+  double m_valueReceiveY;
+
+  // Storing z-axis postion for slice viewer / slider bar communication
+  double m_valueSendZ;
+
+  double m_valueReceiveZ;
+
+  // Sharing last mouse position of slice viewer for slider bar control
+  double m_lastPos[2];
+
+  // initial camera postion, helping to account wheeling effect
+  double m_cPos;
+
+  // internal ratio for screen size change
+  double m_r;
+
+  // slice number precision due to int ui of QSlider
+  double m_precision;
+};
+
+#endif // _QVTKInteractionCallback_H
diff --git a/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.h b/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.h
new file mode 100644
index 00000000..893b7b49
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.h
@@ -0,0 +1,96 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkImageToVTKImageFilter.h,v $
+  Language:  C++
+  Date:      $Date: 2004-02-19 03:47:59 $
+  Version:   $Revision: 1.6 $
+
+  Copyright (c) 2002 Insight Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkImageToVTKImageFilter_h
+#define __itkImageToVTKImageFilter_h
+
+#include "itkVTKImageExport.h"
+#include "vtkImageImport.h"
+#include "vtkImageData.h"
+
+namespace itk
+{
+/** \class ImageToVTKImageFilter
+ * \brief Converts an ITK image into a VTK image and plugs a
+ *  itk data pipeline to a VTK datapipeline.
+ *
+ *  This class puts together an itkVTKImageExporter and a vtkImageImporter.
+ *  It takes care of the details related to the connection of ITK and VTK
+ *  pipelines. The User will perceive this filter as an adaptor to which
+ *  an itk::Image can be plugged as input and a vtkImage is produced as
+ *  output.
+ *
+ * \ingroup   ImageFilters
+ */
+template 
+class ITK_EXPORT ImageToVTKImageFilter : public ProcessObject
+{
+public:
+  /** Standard class typedefs. */
+  typedef ImageToVTKImageFilter    Self;
+  typedef ProcessObject            Superclass;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(ImageToVTKImageFilter, ProcessObject);
+
+  /** Some typedefs. */
+  typedef TInputImage                              InputImageType;
+  typedef typename    InputImageType::ConstPointer InputImagePointer;
+  typedef VTKImageExport           ExporterFilterType;
+  typedef typename ExporterFilterType::Pointer     ExporterFilterPointer;
+
+  /** Get the output in the form of a vtkImage.
+      This call is delegated to the internal vtkImageImporter filter  */
+  vtkImageData *  GetOutput() const;
+
+  /** Set the input in the form of an itk::Image */
+  void SetInput( const InputImageType * );
+
+  /** Return the internal VTK image importer filter.
+      This is intended to facilitate users the access
+      to methods in the importer */
+  vtkImageImport * GetImporter() const;
+
+  /** Return the internal ITK image exporter filter.
+      This is intended to facilitate users the access
+      to methods in the exporter */
+  ExporterFilterType * GetExporter() const;
+
+  /** This call delegate the update to the importer */
+  void Update();
+
+protected:
+  ImageToVTKImageFilter();
+  virtual ~ImageToVTKImageFilter();
+private:
+  ImageToVTKImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);        // purposely not implemented
+
+  ExporterFilterPointer m_Exporter;
+  vtkImageImport *      m_Importer;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkImageToVTKImageFilter.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.txx b/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.txx
new file mode 100644
index 00000000..d1860085
--- /dev/null
+++ b/BRAINSConstellationDetector/gui/include/itkImageToVTKImageFilter.txx
@@ -0,0 +1,120 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkImageToVTKImageFilter.txx,v $
+  Language:  C++
+  Date:      $Date: 2005-06-12 01:23:44 $
+  Version:   $Revision: 1.7 $
+
+  Copyright (c) 2002 Insight Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef _itkImageToVTKImageFilter_txx
+#define _itkImageToVTKImageFilter_txx
+
+#include "itkImageToVTKImageFilter.h"
+
+namespace itk
+{
+/**
+ * Constructor
+ */
+template 
+ImageToVTKImageFilter
+::ImageToVTKImageFilter()
+{
+  m_Importer = vtkImageImport::New();
+
+  m_Exporter = ExporterFilterType::New();
+
+  m_Importer->SetUpdateInformationCallback( m_Exporter->GetUpdateInformationCallback() );
+  m_Importer->SetPipelineModifiedCallback( m_Exporter->GetPipelineModifiedCallback() );
+  m_Importer->SetWholeExtentCallback( m_Exporter->GetWholeExtentCallback() );
+  m_Importer->SetSpacingCallback( m_Exporter->GetSpacingCallback() );
+  m_Importer->SetOriginCallback( m_Exporter->GetOriginCallback() );
+  m_Importer->SetScalarTypeCallback( m_Exporter->GetScalarTypeCallback() );
+  m_Importer->SetNumberOfComponentsCallback( m_Exporter->GetNumberOfComponentsCallback() );
+  m_Importer->SetPropagateUpdateExtentCallback( m_Exporter->GetPropagateUpdateExtentCallback() );
+  m_Importer->SetUpdateDataCallback( m_Exporter->GetUpdateDataCallback() );
+  m_Importer->SetDataExtentCallback( m_Exporter->GetDataExtentCallback() );
+  m_Importer->SetBufferPointerCallback( m_Exporter->GetBufferPointerCallback() );
+  m_Importer->SetCallbackUserData( m_Exporter->GetCallbackUserData() );
+}
+
+/**
+ * Destructor
+ */
+template 
+ImageToVTKImageFilter
+::~ImageToVTKImageFilter()
+{
+  if( m_Importer )
+    {
+    m_Importer->Delete();
+    m_Importer = 0;
+    }
+}
+
+/**
+ * Set an itk::Image as input
+ */
+template 
+void
+ImageToVTKImageFilter
+::SetInput( const InputImageType *inputImage )
+{
+  m_Exporter->SetInput( inputImage );
+}
+
+/**
+ * Get a vtkImage as output
+ */
+template 
+vtkImageData *
+ImageToVTKImageFilter
+::GetOutput() const
+{
+  return m_Importer->GetOutput();
+}
+
+/**
+ * Get the importer filter
+ */
+template 
+vtkImageImport *
+ImageToVTKImageFilter
+::GetImporter() const
+{
+  return m_Importer;
+}
+
+/**
+ * Get the exporter filter
+ */
+template 
+typename ImageToVTKImageFilter::ExporterFilterType
+* ImageToVTKImageFilter
+::GetExporter() const
+  {
+  return m_Exporter.GetPointer();
+  }
+
+/**
+ * Delegate the Update to the importer
+ */
+template 
+void
+ImageToVTKImageFilter
+::Update()
+{
+  m_Importer->Update();
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/src/BRAINSAlignMSP.cxx b/BRAINSConstellationDetector/src/BRAINSAlignMSP.cxx
new file mode 100644
index 00000000..d19a7435
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSAlignMSP.cxx
@@ -0,0 +1,158 @@
+/*
+ * Author: Hans J. Johnson
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBidentityTransformITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, identityTransformRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+#include 
+#include 
+#include 
+#include "BRAINSThreadControl.h"
+#include "landmarksConstellationCommon.h"
+#include "itkIO.h"
+#include "BRAINSAlignMSPCLP.h"
+#include "GenericTransformImage.h"
+
+int main(int argc, char *argv[])
+{
+  std::cout.precision(10);
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  PARSE_ARGS;
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+
+  LMC::globalverboseFlag = verbose;
+
+  globalResultsDir = resultsDir;
+  globalImagedebugLevel = writedebuggingImagesLevel;
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  // read information from the setup file, allocate some memories, and
+  // initialize some variables
+
+  // Since these are oriented images, the reorientation should not be necessary.
+  SImageType::Pointer volOrig = itkUtil::ReadImage(inputVolume);
+  if( volOrig.IsNull() )
+    {
+    printf( "\nCould not open image %s, aborting ...\n\n", inputVolume.c_str() );
+    exit(1);
+    }
+  SImageType::Pointer image;
+
+  if( rescaleIntensities == true )
+    {
+    itk::StatisticsImageFilter::Pointer stats =
+      itk::StatisticsImageFilter::New();
+    stats->SetInput(volOrig);
+    stats->Update();
+    SImageType::PixelType minPixel( stats->GetMinimum() );
+    SImageType::PixelType maxPixel( stats->GetMaximum() );
+
+    if( trimRescaledIntensities > 0.0 )
+      {
+      // REFACTOR: a histogram would be traditional here, but seems
+      // over-the-top;
+      // I did this because it seemed to me if I knew mean, sigma, max and min,
+      // then I know Something about extreme outliers.
+
+      double meanOrig( stats->GetMean() );
+      double sigmaOrig( stats->GetSigma() );
+
+      // REFACTOR:  In percentiles, 0.0005 two-tailed has worked in the past.
+      // It only makes sense to trim the upper bound since the lower bound would
+      // most likely
+      // represent a large region of air around the head.  But this is not so
+      // when using a mask.
+      // For one-tailed, an error of 0.001 corresponds to 3.29052 standard
+      // deviations of normal.
+      // For one-tailed, an error of 0.0001 corresponds to 3.8906 standard
+      // deviations of normal.
+      // For one-tailed, an error of 0.00001 corresponds to 4.4172 standard
+      // deviations of normal.
+      // Naturally, the constant should default at the command line, ...
+
+      double variationBound( ( maxPixel - meanOrig ) / sigmaOrig );
+      double trimBound(variationBound - trimRescaledIntensities);
+      if( trimBound > 0.0 )
+        {
+        maxPixel = static_cast( maxPixel - trimBound * sigmaOrig );
+        }
+      }
+
+    itk::IntensityWindowingImageFilter::Pointer remapIntensityFilter =
+      itk::IntensityWindowingImageFilter::New();
+    remapIntensityFilter->SetInput(volOrig);
+    remapIntensityFilter->SetOutputMaximum(rescaleIntensitiesOutputRange[1]);
+    remapIntensityFilter->SetOutputMinimum(rescaleIntensitiesOutputRange[0]);
+    remapIntensityFilter->SetWindowMinimum(minPixel);
+    remapIntensityFilter->SetWindowMaximum(maxPixel);
+    remapIntensityFilter->Update();
+
+    image = remapIntensityFilter->GetOutput();
+    }
+  else
+    {
+    image = volOrig;
+    }
+
+  RigidTransformType::Pointer Tmsp = RigidTransformType::New();
+  ComputeMSP(image, Tmsp, mspQualityLevel);
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  short BackgroundFillValue;
+  if( backgroundFillValueString == std::string("BIGNEG") )
+    {
+    BackgroundFillValue = -32768;
+    }
+  else
+    {
+    BackgroundFillValue = atoi( backgroundFillValueString.c_str() );
+    }
+
+    {
+    // Remember:  the Data is Moving's, the shape is Fixed's.
+    SImageType::Pointer interpImage = TransformResample(
+        image, image, BackgroundFillValue,
+        GetInterpolatorFromString(interpolationMode), Tmsp.GetPointer() );
+    itkUtil::WriteImage(interpImage, resampleMSP);
+    }
+  if( globalImagedebugLevel > 3 )
+    {
+    const std::string ORIG_ImagePlane( globalResultsDir + "/ORIG_PLANE_" + itksys::SystemTools::GetFilenameName(
+                                         inputVolume) );
+    CreatedebugPlaneImage(image, Tmsp, ORIG_ImagePlane);
+    }
+  // TODO:  Add more features to this program:
+  //       1) Resample to a given space (256^3, 1.0mm^3)
+  //       2) Output using Windowed Sinc for best results.
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSAlignMSP.xml b/BRAINSConstellationDetector/src/BRAINSAlignMSP.xml
new file mode 100644
index 00000000..30890119
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSAlignMSP.xml
@@ -0,0 +1,132 @@
+
+
+  BRAINSAlignMSP
+  Resample an image into ACPC alignement ACPCDetect
+  
+    
+      inputVolume
+      
+      i
+      inputVolume
+      
+      
+        The Image to be resampled
+      
+      input
+    
+    
+      resampleMSP
+      
+      o
+      OutputresampleMSP
+      
+      
+        The image to be output.
+      
+      output
+    
+    
+      verbose
+      
+      v
+      verbose
+      false
+      
+        Show more verbose output
+      
+    
+     
+      resultsDir
+      
+      r
+      resultsDir
+      ./
+      
+        The directory for the results to be written.
+      
+      output
+    
+    
+      writedebuggingImagesLevel
+      
+      writedebuggingImagesLevel
+      w
+      
+          This flag controls if debugging images are produced.  By default value of 0 is no images.  Anything greater than zero will be increasing level of debugging images.
+      
+      0
+    
+    
+      mspQualityLevel
+      
+      mspQualityLevel
+      q
+      
+          Flag cotrols how agressive the MSP is estimated.  0=quick estimate (9 seconds), 1=normal estimate (11 seconds), 2=great estimate (22 seconds), 3=best estimate (58 seconds).
+      
+      2
+     
+        0
+        3
+        1
+     
+    
+    
+      rescaleIntensities
+      
+      rescaleIntensities
+      n
+      
+          Flag to turn on rescaling image intensities on input.
+      
+      0
+    
+    
+      trimRescaledIntensities
+      
+      trimRescaledIntensities
+      x
+      
+          Turn on clipping the rescaled image one-tailed on input.  Units of standard deviations above the mean.  Very large values are very permissive.  Non-positive value turns clipping off.  Defaults to removing 0.00001 of a normal tail above the mean.
+      
+      4.4172
+    
+    
+      rescaleIntensitiesOutputRange
+      
+      rescaleIntensitiesOutputRange
+      y
+      
+          This pair of integers gives the lower and upper bounds on the signal portion of the output image.  Out-of-field voxels are taken from BackgroundFillValue.
+      
+      40,4000
+    
+    
+      backgroundFillValueString
+      BackgroundFillValue
+      z
+      Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number.
+      
+      0
+    
+    
+      interpolationMode
+      interpolationMode
+      
+      Type of interpolation to be used when applying transform to moving volume.  Options are Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc
+      Linear
+      NearestNeighbor
+      Linear
+      ResampleInPlace
+      BSpline
+      WindowedSinc
+    
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+  
+
diff --git a/BRAINSConstellationDetector/src/BRAINSClipInferior.cxx b/BRAINSConstellationDetector/src/BRAINSClipInferior.cxx
new file mode 100644
index 00000000..cb666c7e
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSClipInferior.cxx
@@ -0,0 +1,101 @@
+/*
+ * Author: Hans J. Johnson
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+#include "BRAINSThreadControl.h"
+#include "BRAINSClipInferiorCLP.h"
+#include "itkIO.h"
+typedef itk::Image SImageType;
+
+#include "ChopImageBelowLowerBound.h"
+
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+int main(int argc, char *argv[])
+{
+  PARSE_ARGS;
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+  bool verbose = true;
+
+  std::cout << "================================================================" << std::endl;
+  std::cout << "Processing: " << inputVolume << std::endl;
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  if( verbose )
+    {
+    printf("-------------------------------------------------------\n");
+    printf( "inputVolume: %s\n", inputVolume.c_str() );
+    printf( "outputVolume: %s\n", outputVolume.c_str() );
+    printf("acLowerBound: %f\n", acLowerBound);
+    }
+  if( outputVolume == "" )
+    {
+    std::cout << "ERROR:  Missing output file name." << std::endl;
+    std::cout << "        Please specify -o  or --outputVolume " << std::endl;
+    return -1;
+    }
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  short BackgroundFillValue;
+  if( backgroundFillValueString == std::string("BIGNEG") )
+    {
+    BackgroundFillValue = -32768;
+    }
+  else
+    {
+    BackgroundFillValue = atoi( backgroundFillValueString.c_str() );
+    }
+  // //////////////////////////////////////////////////////////////////////////
+  SImageType::Pointer image = itkUtil::ReadImage(inputVolume);
+  if( image.IsNull() )
+    {
+    printf( "\nCould not open image %s, aborting ...\n\n", inputVolume.c_str() );
+    exit(1);
+    }
+
+  // we need a DOUBLE constant, not a FLOAT constant, for exact switch
+  // comparisons.
+  const double thousand = 1000.0;
+  if( acLowerBound != thousand )
+    {
+    double PhysicalLowerBound = /* ACy when zero-centered is ... */ 0.0 - acLowerBound;
+    ChopImageBelowLowerBound(image, BackgroundFillValue, PhysicalLowerBound);
+    }
+  itkUtil::WriteImage(image, outputVolume);
+  if( verbose )
+    {
+    printf( "Wrote outputVolume: %s\n", outputVolume.c_str() );
+    printf("-------------------------------------------------------\n");
+    }
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSClipInferior.xml b/BRAINSConstellationDetector/src/BRAINSClipInferior.xml
new file mode 100644
index 00000000..bcf6e267
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSClipInferior.xml
@@ -0,0 +1,53 @@
+
+
+    BRAINSClipInferior
+    This program will read the inputVolume as a short int image, write the BackgroundFillValue everywhere inferior to the lower bound, and write the resulting clipped short int image in the outputVolume.
+    
+
+    1.0
+    
+        
+            inputVolume
+            i
+            inputVolume
+            
+            Input image to make a clipped short int copy from.
+            input
+            
+        
+        
+            outputVolume
+            o
+            outputVolume
+            
+            Output image, a short int copy of the upper portion of the input image, filled with BackgroundFillValue.
+            output
+            
+        
+        
+            acLowerBound
+            
+            acLowerBound
+            b
+            
+                When the input image to the output image, replace the image with the BackgroundFillValue everywhere below the plane This Far in physical units (millimeters) below (inferior to) the AC point (assumed to be the voxel field middle.)  The oversize default was chosen to have no effect.  Based on visualizing a thousand masks in the IPIG study, we recommend a limit no smaller than 80.0 mm.
+            
+            1000.0
+        
+        
+            backgroundFillValueString
+            BackgroundFillValue
+            z
+            Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number.
+            
+            0
+        
+        
+          numberOfThreads
+          numberOfThreads
+          
+          Explicitly specify the maximum number of threads to use.
+          -1
+        
+    
+
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationDetector.cxx b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.cxx
new file mode 100644
index 00000000..d108e94d
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.cxx
@@ -0,0 +1,452 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#if defined(_MSC_VER)
+#pragma warning (disable : 4786)
+#endif
+
+#include "itksys/SystemTools.hxx"
+#include "BRAINSThreadControl.h"
+
+#include "BRAINSConstellationDetectorCLP.h"
+#include "itkFindCenterOfBrainFilter.h"
+#include "BRAINSHoughEyeDetector.h"
+#include "BRAINSConstellationDetector2.h"
+#include "Slicer3LandmarkIO.h"
+#include "LLSModel.h"
+
+#include "itkCommand.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkTransformFileWriter.h"
+#include "itkVersorRigid3DTransform.h"
+
+#include "stdio.h"
+#include 
+#include 
+#include "string.h"
+#include 
+
+// Image, filter, transform typedef
+const unsigned int LocalImageDimension = 3;
+typedef short PixelType;
+
+typedef itk::Image ImageType;
+typedef ImageType::Pointer                         ImagePointerType;
+typedef ImageType::PointType                       ImagePointType;
+typedef ImageType::SpacingType                     ImageSpacingType;
+typedef ImageType::SizeType                        ImageSizeType;
+typedef ImageType::DirectionType                   ImageDirectionType;
+typedef ImageType::IndexType                       ImageIndexType;
+typedef std::map      LandmarksMapType;
+
+typedef itk::ImageFileReader         ReaderType;
+typedef itk::ImageFileWriter         WriterType;
+typedef itk::FindCenterOfBrainFilter FindCenterFilter;
+typedef itk::BRAINSHoughEyeDetector<
+  ImageType, ImageType>                             HoughEyeDetectorType;
+typedef itk::BRAINSConstellationDetector2<
+  ImageType, ImageType>                             Constellation2Type;
+typedef itk::TransformFileWriter            TransformWriterType;
+typedef itk::VersorRigid3DTransform VersorTransformType;
+
+int main( int argc, char *argv[] )
+{
+  PARSE_ARGS;
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+
+  // ------------------------------------
+  // Verify input parameters
+  std::cout << "Verifying input parameters..." << std::endl;
+  if( inputVolume.compare( "" ) == 0 )
+    {
+    std::cerr << "To run the program please specify the input volume filename." << std::endl;
+    std::cerr << "Type " << argv[0] << " -h for more help." << std::endl;
+    exit( -1 );
+    }
+
+  // Get a warning if none of the main output filename is specified
+  if( ( outputVolume.compare( "" ) == 0 )
+      && ( outputResampledVolume.compare( "" ) == 0 )
+      && ( outputTransform.compare( "" ) == 0 )
+      && ( outputLandmarksInACPCAlignedSpace.compare( "" ) == 0 )
+      && ( outputLandmarksInInputSpace.compare( "" ) == 0 )
+      && ( outputUntransformedClippedVolume.compare( "" ) == 0 )
+      && ( ( inputLandmarksPaired.compare( "" ) == 0 ) ||
+           ( outputLandmarksPaired.compare( "" ) == 0 ) ) )
+    {
+    std::cout << "WARNING: None of the main output filename is specified!" << std::endl;
+    std::cout << "Try to specify at least one of the following output filenames:" << std::endl;
+    std::cout << "outputVolume" << std::endl;
+    std::cout << "outputResampledVolume" << std::endl;
+    std::cout << "outputTransform" << std::endl;
+    std::cout << "outputLandmarksInACPCAlignedSpace" << std::endl;
+    std::cout << "outputLandmarksInInputSpace" << std::endl;
+    std::cout << "outputUntransformedClippedVolume\n" << std::endl;
+    }
+
+  // set to default
+  if( inputTemplateModel.compare( "T1.mdl" ) == 0 )
+    {
+    std::string pathOut;
+    std::string errorMsg;
+
+    // itksys_stl::string errorMessage;
+    if( !itksys::SystemTools::FindProgramPath( argv[0], pathOut, errorMsg) )
+
+      {
+      std::cerr << "Error: File not found" << std::endl;
+      return 1;
+      }
+    // std::cerr << "ERROR: Could not find " << argv[0] << ": " << errorMessage
+    // << std::endl;
+
+    inputTemplateModel = itksys::SystemTools::GetProgramPath( pathOut.c_str() ) + "/" + inputTemplateModel;
+    std::cout << "Set inputTemplateModel to default: " << std::endl;
+    std::cout << inputTemplateModel << std::endl;
+    }
+
+  // ------------------------------------
+  // Read external files
+  std::cout << "\nReading in external files..." << std::endl;
+
+  // load corresponding landmarks in EMSP aligned space from file if possible
+  LandmarksMapType landmarksEMSP;
+  if( inputLandmarksEMSP.compare( "" ) != 0 )
+    {
+    landmarksEMSP = ReadSlicer3toITKLmk( inputLandmarksEMSP );
+    }
+
+  // read in lls model file
+  std::map > llsMeans;
+  std::map           llsMatrices;
+  std::map               searchRadii;
+
+  if( llsModel == "" )
+    {
+    std::cerr << "Missing LLSModel file" << std::endl;
+    exit(1);
+    }
+  LLSModel theModel;
+  theModel.SetFileName(llsModel);
+  if( theModel.Read() != 0 )
+    {
+    std::cerr << "Error reading LLS Model" << std::endl;
+    exit(1);
+    }
+
+  llsMeans = theModel.GetLLSMeans();
+  llsMatrices = theModel.GetLLSMatrices();
+  searchRadii = theModel.GetSearchRadii();
+
+  // ------------------------------------
+  // load image
+  std::cout << "\nLoading image..." << std::endl;
+
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName( inputVolume );
+  try
+    {
+    reader->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << " Error while reading image file( s ) with ITK:\n "
+              << err << std::endl;
+    }
+  std::cout << "Processing: " << inputVolume << std::endl;
+
+  // ------------------------------------
+  // Find center of head mass
+  std::cout << "\nFinding center of head mass..." << std::endl;
+  FindCenterFilter::Pointer findCenterFilter = FindCenterFilter::New();
+  findCenterFilter->SetInput( reader->GetOutput() );
+  findCenterFilter->SetAxis( 2 );
+  findCenterFilter->SetOtsuPercentileThreshold( 0.01 );
+  findCenterFilter->SetClosingSize( 7 );
+  findCenterFilter->SetHeadSizeLimit( 700 );
+  findCenterFilter->SetBackgroundValue( 0 );
+  findCenterFilter->Update();
+  ImagePointType centerOfHeadMass = findCenterFilter->GetCenterOfBrain();
+
+  // ------------------------------------
+  // Find eye centers with BRAINS Hough Eye Detector
+  HoughEyeDetectorType::Pointer houghEyeDetector = HoughEyeDetectorType::New();
+
+  if( ( landmarksEMSP.find( "LE" ) != landmarksEMSP.end() )
+      && ( landmarksEMSP.find( "RE" ) != landmarksEMSP.end() ) )
+    {
+    std::cout << "\nLoaded eye centers information for BRAINS Hough Eye Detector." << std::endl;
+    std::cout << "Skip estimation steps for eye centers." << std::endl;
+    }
+  else if( forceHoughEyeDetectorReportFailure == true )
+    {
+    houghEyeDetector->SetFailure( true );
+    std::cout << "\nThe Hough eye detector is doomed to failure as notified." << std::endl;
+    std::cout << "Skip estimation steps for eye centers." << std::endl;
+    }
+  else
+    {
+    std::cout << "\nFinding eye centers with BRAINS Hough Eye Detector..." << std::endl;
+    houghEyeDetector->SetInput( reader->GetOutput() );
+    houghEyeDetector->SetHoughEyeDetectorMode( houghEyeDetectorMode );
+    houghEyeDetector->SetResultsDir( resultsDir );       // debug output dir
+    houghEyeDetector->SetWritedebuggingImagesLevel( writedebuggingImagesLevel );
+    houghEyeDetector->SetCenterOfHeadMass( centerOfHeadMass );
+    try
+      {
+    houghEyeDetector->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot find eye centers" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    catch(...)
+      {
+      std::cout << "Failed to find eye centers exception occured" << std::endl;
+      }
+    }
+
+  // ------------------------------------
+  // Find MPJ, AC, PC, and VN4 points with BRAINS Constellation Detector
+  std::cout << "\nFinding named points with BRAINS Constellation Detector..." << std::endl;
+
+  Constellation2Type::Pointer constellation2 = Constellation2Type::New();
+
+  if( ( landmarksEMSP.find( "LE" ) != landmarksEMSP.end() )
+      && ( landmarksEMSP.find( "RE" ) != landmarksEMSP.end() ) )
+    {
+    constellation2->SetInput( reader->GetOutput() );
+    constellation2->SetLandmarksEMSP( landmarksEMSP );
+    constellation2->SetCenterOfHeadMass( centerOfHeadMass );
+    }
+  else
+    {
+    if( landmarksEMSP.size() > 0 )
+      {
+      constellation2->SetLandmarksEMSP( landmarksEMSP );
+      }
+
+    if( !houghEyeDetector->GetFailure() )
+      {
+      ImagePointType houghTransformedCOHM =
+        houghEyeDetector->GetInvVersorTransform()->TransformPoint( centerOfHeadMass );
+
+      constellation2->SetLEPoint( houghEyeDetector->GetLE() );
+      constellation2->SetREPoint( houghEyeDetector->GetRE() );
+      constellation2->SetInput( houghEyeDetector->GetOutput() );
+      constellation2->SetHoughEyeTransform( houghEyeDetector->GetVersorTransform() );
+      constellation2->SetCenterOfHeadMass( houghTransformedCOHM );
+      }
+    else
+      {
+      constellation2->SetInput( reader->GetOutput() );
+      constellation2->SetCenterOfHeadMass( centerOfHeadMass );
+      }
+    }
+
+  // tell the constellation detector whehter Hough eye detector fails
+  constellation2->SetHoughEyeFailure( houghEyeDetector->GetFailure() );
+  constellation2->SetInputTemplateModel( inputTemplateModel );
+  constellation2->SetMspQualityLevel( mspQualityLevel );
+  constellation2->SetOtsuPercentileThreshold( otsuPercentileThreshold );
+  constellation2->SetAcLowerBound( acLowerBound );
+  constellation2->SetCutOutHeadInOutputVolume( cutOutHeadInOutputVolume );
+  constellation2->SetRescaleIntensities( rescaleIntensities );
+  constellation2->SetTrimRescaledIntensities( trimRescaledIntensities );
+  constellation2->SetRescaleIntensitiesOutputRange( rescaleIntensitiesOutputRange );
+  constellation2->SetBackgroundFillValueString( backgroundFillValueString );
+  constellation2->SetInterpolationMode( interpolationMode );
+  constellation2->SetForceACPoint( forceACPoint );   // In original space
+  constellation2->SetForcePCPoint( forcePCPoint );
+  constellation2->SetForceVN4Point( forceVN4Point );
+  constellation2->SetForceRPPoint( forceRPPoint );
+  constellation2->SetRadiusMPJ( radiusMPJ );
+  constellation2->SetRadiusAC( radiusAC );
+  constellation2->SetRadiusPC( radiusPC );
+  constellation2->SetRadiusVN4( radiusVN4 );
+  constellation2->SetDebug( debug );
+  constellation2->SetVerbose( verbose );
+  constellation2->SetWritedebuggingImagesLevel( writedebuggingImagesLevel );
+  constellation2->SetWriteBranded2DImage( writeBranded2DImage );
+  constellation2->SetResultsDir( resultsDir );
+  constellation2->SetLlsMatrices( llsMatrices );
+  constellation2->SetLlsMeans( llsMeans );
+  constellation2->SetSearchRadii( searchRadii );
+  constellation2->SetOriginalInputImage( reader->GetOutput() );
+  constellation2->Update();
+
+  // Get the final transform
+  VersorTransformType::Pointer finalTransform = VersorTransformType::New();
+  VersorTransformType::Pointer invFinalTransform = VersorTransformType::New();
+  finalTransform->SetParameters( constellation2->GetVersorTransform()->GetParameters() );
+  finalTransform->GetInverse( invFinalTransform );
+
+  // Save landmarks in input/output or original/aligned space
+  LandmarksMapType                 outputLandmarksInInputSpaceMap;
+  LandmarksMapType                 outputLandmarksInACPCAlignedSpaceMap;
+  LandmarksMapType::const_iterator lit =
+    constellation2->GetAlignedPoints().begin();
+  for( ; lit != constellation2->GetAlignedPoints().end(); ++lit )
+    {
+    outputLandmarksInACPCAlignedSpaceMap[lit->first] = lit->second;
+    outputLandmarksInInputSpaceMap[lit->first] =
+      finalTransform->TransformPoint( lit->second );
+    // or something like constellation2->GetOriginalPoints()[lit->first];
+    }
+
+  // ----------------------
+  // Write results to disk
+  std::cout << "\nWriting results to files..." << std::endl;
+  if( outputTransform.compare( "" ) != 0 )
+    {
+    TransformWriterType::Pointer writer = TransformWriterType::New();
+    writer->SetInput( finalTransform );
+    writer->SetFileName( outputTransform );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot write the outputTransform file!" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    std::cout << "The output rigid transform file is written." << std::endl;
+    }
+
+  std::string preferedOutputReferenceImage = "";
+  if( outputVolume.compare( "" ) != 0 )
+    {
+    preferedOutputReferenceImage = outputVolume;
+    // This will be overwritten if outputResampledVolume is set
+    // Write the aligned image to a file
+    WriterType::Pointer writer = WriterType::New();
+    writer->SetFileName( outputVolume );
+    writer->SetInput( constellation2->GetOutput() );
+    writer->SetUseCompression( true );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot write the outputVolume image!" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    std::cout << "The output unresampled volume is written." << std::endl;
+    }
+
+  if( outputResampledVolume.compare( "" ) != 0 )
+    {
+    preferedOutputReferenceImage = outputResampledVolume;
+    // This will be overwritten if outputResampledVolume is set
+    // Write the aligned image to a file
+    WriterType::Pointer writer = WriterType::New();
+    writer->SetFileName( outputResampledVolume );
+    writer->SetInput( constellation2->GetOutputResampledImage() );
+    writer->SetUseCompression( true );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot write the outputResampledVolume image!" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    std::cout << "The output resampled output volume is written." << std::endl;
+    }
+
+  if( ( outputLandmarksPaired.compare( "" ) != 0 ) &&
+      ( inputLandmarksPaired.compare( "" ) != 0 ) )
+    {
+    LandmarksMapType                 origLandmarks = ReadSlicer3toITKLmk( inputLandmarksPaired );
+    LandmarksMapType                 alignedLandmarks;
+    LandmarksMapType::const_iterator olit = origLandmarks.begin();
+    for( ; olit != origLandmarks.end(); ++olit )
+      {
+      alignedLandmarks[olit->first] = invFinalTransform->TransformPoint( olit->second );
+      }
+    WriteITKtoSlicer3Lmk( outputLandmarksPaired, alignedLandmarks );
+    std::cout << "The acpc-aligned landmark list file is written." << std::endl;
+    }
+  else if( ( ( outputLandmarksPaired.compare( "" ) != 0 ) &&
+             ( inputLandmarksPaired.compare( "" ) == 0 ) )
+           ||
+           ( ( outputLandmarksPaired.compare( "" ) == 0 ) &&
+             ( inputLandmarksPaired.compare( "" ) != 0 ) ) )
+    {
+    std::cerr << "The outputLandmark parameter should be paired with"
+              << "the inputLandmark parameter." << std::endl;
+    std::cerr << "No output acpc-aligned landmark list file is generated" << std::endl;
+    std::cerr << "Type " << argv[0] << " -h for more help." << std::endl;
+    }
+
+  if( outputLandmarksInInputSpace.compare( "" ) != 0 )
+    {
+    WriteITKtoSlicer3Lmk( outputLandmarksInInputSpace,
+                          outputLandmarksInInputSpaceMap );
+    std::cout << "The output landmarks list file in the original space is written." << std::endl;
+    }
+
+  if( outputLandmarksInACPCAlignedSpace.compare( "" ) != 0 )
+    {
+    WriteITKtoSlicer3Lmk( outputLandmarksInACPCAlignedSpace,
+                          outputLandmarksInACPCAlignedSpaceMap );
+    std::cout << "The output landmarks list file in the output space is written." << std::endl;
+    if( preferedOutputReferenceImage.compare( "" ) == 0 )
+      {
+      std::cout << "WARNING no aligned output volume is requested." << std::endl;
+      }
+    }
+
+  if( outputMRML.compare( "" ) != 0 )
+    {
+    WriteMRMLFile( outputMRML,
+                   outputLandmarksInInputSpace,
+                   outputLandmarksInACPCAlignedSpace,
+                   inputVolume,
+                   preferedOutputReferenceImage,
+                   outputTransform,
+                   outputLandmarksInInputSpaceMap,
+                   outputLandmarksInACPCAlignedSpaceMap,
+                   finalTransform );
+    std::cout << "The output mrml scene file is written." << std::endl;
+    }
+
+  if( outputUntransformedClippedVolume.compare( "" ) != 0 )
+    {
+    WriterType::Pointer writer = WriterType::New();
+    writer->SetFileName( outputUntransformedClippedVolume );
+    writer->SetInput( constellation2->GetOutputUntransformedClippedVolume() );
+    writer->SetUseCompression( true );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot write the outputUntransformedClippedVolume image!" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    std::cout << "The output untransformed clipped volume is written." << std::endl;
+    }
+
+  if( ( outputVerificationScript.compare( "" ) != 0 )
+      && ( outputLandmarksInACPCAlignedSpace.compare( "" ) != 0 )
+      && ( outputVolume.compare( "" ) != 0 ) )
+    {
+    writeVerificationScript( outputVerificationScript, outputVolume, outputLandmarksInACPCAlignedSpace );
+    std::cout << "The verification script is written." << std::endl;
+    }
+
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml
new file mode 100644
index 00000000..e2d66fa8
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml
@@ -0,0 +1,384 @@
+
+
+  BRAINSConstellationDetector
+  
+    This program will find the mid-sagittal plane, a constellation of landmarks in a volume, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (labeled at the origin of the image physical space.)  Part of this work is an extention of the algorithms originally described by Dr. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, NeuroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030.  (http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c)
+  
+
+    1.0
+    http://www.nitrc.org/projects/brainscdetector/
+    
+        
+            houghEyeDetectorMode
+            
+            houghEyeDetectorMode
+            
+                This flag controls the mode of Hough eye detector.  By default, value of 1 is for T1W images, while the value of 0 is for T2W and PD images.
+            
+            1
+        
+        
+            inputTemplateModel
+            
+            T1.mdl
+            inputTemplateModel
+            User-specified template model.
+            
+            input
+        
+        
+            llsModel
+            
+            
+            --LLSModel
+            Linear least squares model filename in HD5 format
+            input
+        
+        
+            inputVolume
+            i
+            inputVolume
+            
+            Input image in which to find ACPC points
+            input
+            
+        
+        
+            outputVolume
+            o
+            outputVolume
+            
+            ACPC-aligned output image with the same voxels, but updated origin, and direction cosign so that the AC point would fall at the physical location (0.0,0.0,0.0), and the mid-sagital plane is the plane where physical L/R coordinate is 0.0.
+            output
+            
+        
+        
+            outputResampledVolume
+            outputResampledVolume
+            
+            ACPC-aligned output image in a resampled unifor space.  Currently this is a 1mm, 256^3, Identity direction image.
+            output
+            
+        
+        
+            outputTransform
+            
+            
+            outputTransform
+            The filename for the original space to ACPC alignment to be written (in .mat format).
+            
+            output
+        
+        
+            outputLandmarksInInputSpace
+            
+            outputLandmarksInInputSpace
+            
+            
+              The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the original image space (the detected RP, AC, PC, and VN4) in it to be written.
+            
+            output
+        
+        
+            outputLandmarksInACPCAlignedSpace
+            
+            outputLandmarksInACPCAlignedSpace
+            
+            
+              The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (.fcsv) with the landmarks in the output image space (the detected RP, AC, PC, and VN4) in it to be written.
+            
+            output
+        
+        
+            inputLandmarksPaired
+            
+            inputLandmarksPaired
+            
+            
+              Paired use with outputLandmarks. It indicates the input landmark list filename (in a format of .fcsv) which contains the landmarks to be trainsformed to acpc-aligned space. The alignment transform will be calculated form the base landmarks provided, and then the rest of the landmarks are directly transformed to the acpc-aligned space rather than to estimate one by one.
+            
+            input
+        
+        
+            outputLandmarksPaired
+            
+            outputLandmarksPaired
+            
+            
+              Paired use with inputLandmarks (in a format of .fcsv). It indicates the output acpc-aligned landmark list filename. The aligned landmarks are the landamrks that are defined in the file named inputLandmarks transformed by the acpc versor transform calculated by the constellation detector.
+            
+            output
+        
+        
+            outputMRML
+            
+            outputMRML
+            
+            
+              The filename for the new subject-specific scene definition file in the same format produced by Slicer3 (in .mrml format). Only the components that were specified by the user on command line would be generated. Compatible components include inputVolume, outputVolume, outputLandmarksInInputSpace, outputLandmarksInACPCAlignedSpace, and outputTransform.
+            
+            output
+        
+        
+            outputVerificationScript
+            
+            outputVerificationScript
+            
+            
+              The filename for the Slicer3 script that verifies the aligned landmarks against the aligned image file.  This will happen only in conjunction with saveOutputLandmarks and an outputVolume.
+            
+            output
+        
+        
+            mspQualityLevel
+            
+            mspQualityLevel
+            
+                Flag cotrols how agressive the MSP is estimated. 0=quick estimate (9 seconds), 1=normal estimate (11 seconds), 2=great estimate (22 seconds), 3=best estimate (58 seconds), NOTE: -1= Prealigned so no estimate!.
+            
+            2
+           
+              -1
+              3
+              1
+           
+        
+        
+            otsuPercentileThreshold
+            
+            otsuPercentileThreshold
+            
+                This is a parameter to FindLargestForegroundFilledMask, which is employed when acLowerBound is set and an outputUntransformedClippedVolume is requested.
+            
+            0.01
+        
+        
+            acLowerBound
+            
+            acLowerBound
+            
+                When generating a resampled output image, replace the image with the BackgroundFillValue everywhere below the plane This Far in physical units (millimeters) below (inferior to) the AC point (as found by the model.)  The oversize default was chosen to have no effect.  Based on visualizing a thousand masks in the IPIG study, we recommend a limit no smaller than 80.0 mm.
+            
+            1000.0
+        
+        
+            cutOutHeadInOutputVolume
+            
+            cutOutHeadInOutputVolume
+            
+                Flag to cut out just the head tissue when producing an (un)transformed clipped volume.
+            
+            false
+        
+        
+            outputUntransformedClippedVolume
+            outputUntransformedClippedVolume
+            
+            Output image in which to store neck-clipped input image, with the use of --acLowerBound and maybe --cutOutHeadInUntransformedVolume.
+            output
+            
+        
+        
+            rescaleIntensities
+            
+            rescaleIntensities
+            
+                Flag to turn on rescaling image intensities on input.
+            
+            false
+        
+        
+            trimRescaledIntensities
+            
+            trimRescaledIntensities
+            
+                Turn on clipping the rescaled image one-tailed on input.  Units of standard deviations above the mean.  Very large values are very permissive.  Non-positive value turns clipping off.  Defaults to removing 0.00001 of a normal tail above the mean.
+            
+            4.4172
+        
+        
+            rescaleIntensitiesOutputRange
+            
+            rescaleIntensitiesOutputRange
+            
+                This pair of integers gives the lower and upper bounds on the signal portion of the output image.  Out-of-field voxels are taken from BackgroundFillValue.
+            
+            40,4000
+        
+        
+            backgroundFillValueString
+            BackgroundFillValue
+            Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number.
+            
+            0
+        
+        
+          interpolationMode
+          interpolationMode
+          
+          Type of interpolation to be used when applying transform to moving volume.  Options are Linear, ResampleInPlace, NearestNeighbor, BSpline, or WindowedSinc
+          Linear
+          NearestNeighbor
+          Linear
+          ResampleInPlace
+          BSpline
+          WindowedSinc
+        
+    
+    
+        
+         Manually force the location of the points in original image space.  
+        
+            forceACPoint
+            
+            forceACPoint
+            
+                Use this flag to manually specify the AC point from the original image on the command line.
+            
+            0
+        
+        
+            forcePCPoint
+            
+            forcePCPoint
+            
+                Use this flag to manually specify the PC point from the original image on the command line.
+            
+            0
+        
+        
+            forceVN4Point
+            
+            forceVN4Point
+            
+                Use this flag to manually specify the VN4 point from the original image on the command line.
+            
+            0
+        
+        
+            forceRPPoint
+            
+            forceRPPoint
+            
+                Use this flag to manually specify the RP point from the original image on the command line.
+            
+            0
+        
+        
+            inputLandmarksEMSP
+            
+            inputLandmarksEMSP
+            
+            
+              The filename for the new subject-specific landmark definition file in the same format produced by Slicer3 (in .fcsv) with the landmarks in the estimated MSP aligned space to be loaded. The detector will only process landmarks not enlisted on the file.
+            
+            input
+        
+        
+            forceHoughEyeDetectorReportFailure
+            
+            forceHoughEyeDetectorReportFailure
+            
+                Flag indicates whether the Hough eye detector should report failure
+            
+            false
+        
+    
+    
+    
+    Override the default values from the model files.
+        
+            radiusMPJ
+            rmpj
+            
+              Search radius for MPJ in unit of mm
+            
+            -1
+        
+        
+            radiusAC
+            rac
+            
+              Search radius for AC in unit of mm
+            
+            -1
+        
+        
+            radiusPC
+            rpc
+            
+              Search radius for PC in unit of mm
+            
+            -1
+        
+        
+            radiusVN4
+            rVN4
+            
+              Search radius for VN4 in unit of mm
+            
+            -1
+        
+        
+        
+        
+        Options to control the amount of debugging information that is presented.
+        
+            debug
+            
+            debug
+            false
+            
+              Show internal debugging information.
+            
+        
+        
+            verbose
+            
+            v
+            verbose
+            false
+            
+              Show more verbose output
+            
+        
+        
+            writeBranded2DImage
+            
+            writeBranded2DImage
+            
+            
+              The filename for the 2D .png branded midline debugging image.  This will happen only in conjunction with requesting an outputVolume.
+            
+            output
+        
+         
+            resultsDir
+            
+            r
+            resultsDir
+            ./
+            
+              The directory for the debuging images to be written.
+            
+            output
+        
+        
+            writedebuggingImagesLevel
+            
+            writedebuggingImagesLevel
+            w
+            
+                This flag controls if debugging images are produced.  By default value of 0 is no images.  Anything greater than zero will be increasing level of debugging images.
+            
+            0
+        
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+        
+
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.h b/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.h
new file mode 100644
index 00000000..36de5527
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.h
@@ -0,0 +1,370 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#ifndef __BRAINSConstellationDetector2_h
+#define __BRAINSConstellationDetector2_h
+
+#ifdef _MSC_VER
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef __BORLANDC__
+#define ITK_LEAN_AND_MEAN
+#endif
+
+#include "itkImageToImageFilter.h"
+
+#include "landmarksConstellationDetector.h"
+#include "itkTransformFileWriter.h"
+#include "itkIntensityWindowingImageFilter.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkMultiplyImageFilter.h"
+#include "landmarkIO.h"
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include "ChopImageBelowLowerBound.h"
+#include "itkResampleInPlaceImageFilter.h"
+#include "itkImageDuplicator.h"
+
+#include 
+#include 
+#include 
+
+#include "BRAINSMacro.h"
+
+namespace itk
+{
+// Software Guide : BeginLatex
+//
+// \class BRAINSConstellationDetector2
+// \brief ...
+//
+// This filter derives from the base class ImageToImageFilter
+// Please refer to BRAINSConstellationDetector for details
+//
+// This filter takes two input filenames and a bunch of parameters:
+// 1) input image filename
+// 2) model filename
+// 3) other optional parameters
+//
+// This filter outputs the following data
+// 1) Aligned image with the detection of RP, AC, PC points
+// 2) other optional parameters
+//
+// \ingroup ImageFeatureExtraction
+// \todo Update the doxygen documentation!!!
+//
+// Software Guide : EndLatex
+
+template 
+class ITK_EXPORT BRAINSConstellationDetector2 :
+  public ImageToImageFilter
+{
+public:
+
+  /** Standard ITK typedef */
+  typedef BRAINSConstellationDetector2               Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                         Pointer;
+  typedef SmartPointer                   ConstPointer;
+
+  itkStaticConstMacro(Dimension, unsigned int, SImageType::ImageDimension);
+  typedef SImageType::PointType                              SImagePointType;
+  typedef vnl_matrix                                 MatrixType;
+  typedef std::map             LandmarksMapType;
+  typedef ImageDuplicator                        DuplicatorType;
+  typedef ResampleInPlaceImageFilter ResampleIPFilterType;
+  typedef typename ResampleIPFilterType::Pointer             ResampleIPFilterPointer;
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro(BRAINSConstellationDetector2, ImageToImageFilter);
+
+  /** Method for creation through the object factory */
+  itkNewMacro(Self);
+
+  /** Display */
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  // Set Basic Inputs
+
+  /** Set the filename of the output transform */
+  itkSetMacro(Transform, std::string);
+
+  /** Set the filename of the model file */
+  itkSetMacro(InputTemplateModel, std::string);
+
+  /** Set MSP quality level */
+  itkSetMacro(MspQualityLevel, unsigned int);
+
+  /** Set Otsu percentile threshold */
+  itkSetMacro(OtsuPercentileThreshold, double);
+
+  /** Set AC lower bound */
+  itkSetMacro(AcLowerBound, double);
+
+  /** Set Cut Out Head In Output volumes */
+  itkSetMacro(CutOutHeadInOutputVolume, bool);
+
+  /** Set rescale intensities */
+  itkSetMacro(RescaleIntensities, bool);
+
+  /** Set trim rescaled intensities */
+  itkSetMacro(TrimRescaledIntensities, double);
+
+  /** Set rescale intensities output range */
+  VECTORitkSetMacro(RescaleIntensitiesOutputRange, std::vector );
+
+  /** Set the background fill value string */
+  itkSetMacro(BackgroundFillValueString, std::string);
+
+  /** Set use windowed sinc */
+  itkSetMacro(InterpolationMode, std::string);
+
+  /** Set Hough eye transform */
+  itkSetObjectMacro(HoughEyeTransform, VersorTransformType);
+
+  /** Set LE point */
+  itkSetMacro(LEPoint, SImagePointType);
+
+  /** Set RE point */
+  itkSetMacro(REPoint, SImagePointType);
+
+  /** Set center of head mass **/
+  itkSetMacro(CenterOfHeadMass, SImagePointType);
+
+  /** Set the original input image before the Hough eye detector */
+  itkSetObjectMacro(OriginalInputImage, SImageType);
+
+  // Get Basic Outputs
+
+  /** Get the versor transform */
+  itkGetObjectMacro(VersorTransform, VersorTransformType);
+  itkGetObjectMacro(InvVersorTransform, VersorTransformType);
+
+  /** Get the named points in original space */
+  const LandmarksMapType & GetOriginalPoints()
+  {
+    return this->m_OriginalPoints;
+  }
+
+  /** Get the aligned named points */
+  const LandmarksMapType & GetAlignedPoints()
+  {
+    return this->m_AlignedPoints;
+  }
+
+  // This is wrong?
+  const SImageType & GetAlignedPoint(std::string name)
+  {
+    return this->m_AlignedPoints[name];
+  }
+
+  /** Get the interpolated output isotropic image */
+  itkGetObjectMacro(OutputResampledImage, SImageType);
+
+  /** Get the output untransformed clipped volume */
+  itkGetObjectMacro(OutputUntransformedClippedVolume, SImageType);
+
+  /** Get the Hough eye transform */
+  itkGetObjectMacro(HoughEyeTransform, VersorTransformType);
+
+  /** Set the Hough eye failure report */
+  void SetHoughEyeFailure(const bool failure)
+  {
+    this->m_HoughEyeFailure = failure;
+  }
+
+  /** Set llsMeans **/
+  void SetLlsMeans(const std::map > & llsMeans)
+  {
+    this->m_LlsMeans = llsMeans;
+  }
+
+  /** Set llsMatrices **/
+  void SetLlsMatrices(const std::map & llsMatrices)
+  {
+    this->m_LlsMatrices = llsMatrices;
+  }
+
+  /** Set search radii for corresponding landmarks **/
+  void SetSearchRadii(const std::map & radii)
+  {
+    this->m_SearchRadii = radii;
+  }
+
+  /** Set AC mean **/
+  itkSetMacro(ACMean, SImagePointType);
+
+  // Set Advanced Inputs
+
+  /** Set force AC point */
+  VECTORitkSetMacro(ForceACPoint, std::vector );
+
+  /** Set force PC point */
+  VECTORitkSetMacro(ForcePCPoint, std::vector );
+
+  /** Set force VN4 point */
+  VECTORitkSetMacro(ForceVN4Point, std::vector );
+
+  /** Set force MPJ point */
+  VECTORitkSetMacro(ForceRPPoint, std::vector );
+
+  /** Set MPJ search radius */
+  itkSetMacro(RadiusMPJ, double);
+
+  /** Set AC search radius */
+  itkSetMacro(RadiusAC, double);
+
+  /** Set PC search radius */
+  itkSetMacro(RadiusPC, double);
+
+  /** Set VN4 search radius */
+  itkSetMacro(RadiusVN4, double);
+
+  /** Set use debug mode */
+  itkSetMacro(Debug, bool);
+
+  /** Set use verbose mode */
+  itkSetMacro(Verbose, bool);
+
+  /** Set debugging images level */
+  itkSetMacro(WritedebuggingImagesLevel, unsigned int);
+
+  /** Set branded 2D image filename */
+  itkSetMacro(WriteBranded2DImage, std::string);
+
+  /** Set results dir */
+  itkSetMacro(ResultsDir, std::string);
+
+  /** Set/Get EMSP landmarks */
+  void SetLandmarksEMSP(LandmarksMapType landmarks)
+  {
+    m_landmarksEMSP.clear();
+    m_landmarksEMSP.insert( landmarks.begin(), landmarks.end() );
+  }
+
+  LandmarksMapType GetLandmarksEMSP()
+  {
+    return m_landmarksEMSP;
+  }
+
+protected:
+
+  BRAINSConstellationDetector2();
+
+  void GenerateData();
+
+  /** Essential Parameters */
+  // Inputs
+  std::string      m_Transform;
+  std::string      m_InputTemplateModel;
+  unsigned int     m_MspQualityLevel;               // default = 2
+  double           m_OtsuPercentileThreshold;       // default = 0.01
+  double           m_AcLowerBound;                  // default = 1000.0
+  bool             m_CutOutHeadInOutputVolume;      // default = false
+  bool             m_RescaleIntensities;            // default = false
+  double           m_TrimRescaledIntensities;       // default = 4.4172
+  std::vector m_RescaleIntensitiesOutputRange; // default = [40,
+                                                    // 4000]
+  std::string m_BackgroundFillValueString;          // default = "0"
+  std::string m_InterpolationMode;                  // default = "Linear"
+
+  // a local editable copy of original input before Hough eye detector
+  // Note: this->GetInput() will return a const input after Hough eye.
+  SImageType::Pointer m_OriginalInputImage;
+
+  VersorTransformType::Pointer m_HoughEyeTransform; // help to get the points
+                                                    // location in the original
+                                                    // space
+  SImagePointType m_LEPoint;                        // automated estimated LE in
+                                                    // the original space by
+                                                    // Hough eye detector
+  SImagePointType  m_REPoint;
+  SImagePointType  m_CenterOfHeadMass;
+  LandmarksMapType m_landmarksEMSP;
+  bool             m_HoughEyeFailure;
+  std::map m_LlsMatrices;
+  std::map > m_LlsMeans;
+  SImagePointType                m_ACMean;
+  std::map  m_SearchRadii;
+
+  // Outputs
+  VersorTransformType::Pointer m_VersorTransform;
+  VersorTransformType::Pointer m_InvVersorTransform;
+  LandmarksMapType             m_AlignedPoints;
+  LandmarksMapType             m_OriginalPoints;
+  SImageType::Pointer          m_OutputImage;          // Output image w/o
+                                                       // interpolation
+  SImageType::Pointer m_OutputResampledImage;          // Output image w/
+                                                       // interpolation
+  SImageType::Pointer m_OutputUntransformedClippedVolume;
+
+  /** Advanced parameters */
+  /** Manual Override */
+  // Inputs
+  std::vector m_ForceACPoint;              // default = 0.
+  std::vector m_ForcePCPoint;              // default = 0.
+  std::vector m_ForceVN4Point;             // default = 0.
+  std::vector m_ForceRPPoint;              // default = 0.
+
+  /** Model Override */
+  // Inputs
+  double m_RadiusMPJ;                         // default = -1.
+  double m_RadiusAC;                          // default = -1.
+  double m_RadiusPC;                          // default = -1.
+  double m_RadiusVN4;                         // default = -1.
+
+  /** Debug Options */
+  // Inputs
+  bool         m_Debug;                     // default = false
+  bool         m_Verbose;                   // default = false
+  unsigned int m_WritedebuggingImagesLevel; // default = 0
+  std::string  m_WriteBranded2DImage;
+  std::string  m_ResultsDir;                    // default = "./"
+private:
+
+  BRAINSConstellationDetector2(const Self &)
+  {
+  }
+
+  void operator=(const Self &)
+  {
+  }
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "BRAINSConstellationDetector2.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.txx b/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.txx
new file mode 100644
index 00000000..0e702ed9
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationDetector2.txx
@@ -0,0 +1,517 @@
+/*=========================================================================
+ Author: Wei Lu
+ at Psychiatry Imaging Lab,
+ University of Iowa Health Care 2010
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ Neither the name of the  President and Fellows of Harvard College
+ nor the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+ OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+ =========================================================================*/
+
+#include "BRAINSConstellationDetector2.h"
+#include "GenericTransformImage.h"
+
+namespace itk
+{
+template 
+BRAINSConstellationDetector2
+::BRAINSConstellationDetector2()
+{
+  /** Essential Parameters */
+  // Inputs
+  this->m_InputTemplateModel = "";
+  this->m_MspQualityLevel = 2;
+  this->m_OtsuPercentileThreshold = 0.01;
+  this->m_AcLowerBound = 1000.0;
+  this->m_CutOutHeadInOutputVolume = false;
+  this->m_RescaleIntensities = false;
+  this->m_TrimRescaledIntensities = 4.4172;
+  this->m_RescaleIntensitiesOutputRange.push_back(40);
+  this->m_RescaleIntensitiesOutputRange.push_back(4000);
+  this->m_BackgroundFillValueString = "0";
+  this->m_InterpolationMode = "Linear";
+  this->m_OriginalInputImage = NULL;
+
+  // Outputs
+  this->m_Transform = "";
+  this->m_VersorTransform = NULL;
+  this->m_InvVersorTransform = NULL;
+  this->m_OutputImage = NULL;
+  this->m_OutputResampledImage = NULL;
+  this->m_OutputUntransformedClippedVolume = NULL;
+
+  /** Advanced parameters */
+  /** Manual Override */
+  // Inputs
+  this->m_ForceACPoint.push_back(0);
+  this->m_ForcePCPoint.push_back(0);
+  this->m_ForceVN4Point.push_back(0);
+  this->m_ForceRPPoint.push_back(0);
+
+  /** Model Override */
+  // Inputs
+  this->m_RadiusMPJ = -1.;
+  this->m_RadiusAC = -1.;
+  this->m_RadiusPC = -1.;
+  this->m_RadiusVN4 = -1.;
+
+  /** Debug Options */
+  // Inputs
+  this->m_Debug = false;
+  this->m_Verbose = false;
+  this->m_WritedebuggingImagesLevel = 0;
+
+  // Outputs
+  this->m_WriteBranded2DImage = "";
+  this->m_ResultsDir = "./";
+}
+
+template 
+void
+BRAINSConstellationDetector2
+::GenerateData()
+{
+  // file pointer for opening the setup file
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  this->m_Debug = this->m_Debug;
+  LMC::globalverboseFlag = this->m_Verbose;
+  globalImagedebugLevel = this->m_WritedebuggingImagesLevel;
+
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  char modelfile[1024];
+    {
+    strcpy( modelfile, this->m_InputTemplateModel.c_str() );
+    }
+
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  short BackgroundFillValue;
+  if( this->m_BackgroundFillValueString == std::string("BIGNEG") )
+    {
+    BackgroundFillValue = -32768;
+    }
+  else
+    {
+    BackgroundFillValue = atoi( this->m_BackgroundFillValueString.c_str() );
+    }
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  // read information from the setup file, and initialize some variables
+  landmarksConstellationModelIO myModel;
+  myModel.ReadModelFile( std::string(modelfile) );
+
+  if( LMC::globalverboseFlag )
+    {
+    std::cout << "Using Model File: " << modelfile << std::endl;
+    myModel.PrintHeaderInfo();
+    }
+
+  // Override some landmarks by user
+  vnl_vector templateRadius;    // in units of mm
+  templateRadius.set_size(4);
+  templateRadius[0] = ( this->m_RadiusMPJ <= 0 ) ? myModel.GetRadius("RP") : this->m_RadiusMPJ; //
+                                                                                                //
+                                                                                                // =
+                                                                                                //
+                                                                                                // RP
+                                                                                                //
+                                                                                                // radius
+  templateRadius[1] = ( this->m_RadiusAC <= 0 ) ? myModel.GetRadius("AC") : this->m_RadiusAC;
+  templateRadius[2] = ( this->m_RadiusPC <= 0 ) ? myModel.GetRadius("PC") : this->m_RadiusPC;
+  templateRadius[3] = ( this->m_RadiusVN4 <= 0 ) ? myModel.GetRadius("VN4") : this->m_RadiusVN4;
+  myModel.SetRadius("RP", templateRadius[0]);
+  myModel.SetRadius("AC", templateRadius[1]);
+  myModel.SetRadius("PC", templateRadius[2]);
+  myModel.SetRadius("VN4", templateRadius[3]);
+
+  // Wei: We will get the input image from filter input rather than an external
+  // file
+  SImageType::Pointer volOrig;
+  SImageType::Pointer image;
+    {
+    DuplicatorType::Pointer duplicator = DuplicatorType::New();
+    duplicator->SetInputImage(this->m_OriginalInputImage);
+    duplicator->Update();
+    volOrig = duplicator->GetOutput();
+    }
+
+  // RPPC is a vector on the MSP that points from the RP point to the PC.
+  //   RP------->PC
+  // //////////////////////////////////////////////////////////////////////////
+
+  if( this->m_RescaleIntensities == true )
+    {
+    itk::StatisticsImageFilter::Pointer stats =
+      itk::StatisticsImageFilter::New();
+    stats->SetInput(volOrig);
+    stats->Update();
+    SImageType::PixelType minPixel( stats->GetMinimum() );
+    SImageType::PixelType maxPixel( stats->GetMaximum() );
+
+    if( this->m_TrimRescaledIntensities > 0.0 )
+      {
+      // REFACTOR: a histogram would be traditional here, but seems
+      // over-the-top;
+      // I did this because it seemed to me if I knew mean, sigma, max and min,
+      // then I know Something about extreme outliers.
+      // Look at the setLowHigh function in landmarksConstellationCommon.h as a
+      // possible replacement
+
+      const double meanOrig( stats->GetMean() );
+      const double sigmaOrig( stats->GetSigma() );
+
+      // REFACTOR:  In percentiles, 0.0005 two-tailed has worked in the past.
+      // It only makes sense to trim the upper bound since the lower bound would
+      // most likely
+      // represent a large region of air around the head.  But this is not so
+      // when using a mask.
+      // For one-tailed, an error of 0.001 corresponds to 3.29052 standard
+      // deviations of normal.
+      // For one-tailed, an error of 0.0001 corresponds to 3.8906 standard
+      // deviations of normal.
+      // For one-tailed, an error of 0.00001 corresponds to 4.4172 standard
+      // deviations of normal.
+      // Naturally, the constant should default at the command line, ...
+
+      const double variationBound( ( maxPixel - meanOrig ) / sigmaOrig );
+      const double trimBound(variationBound - this->m_TrimRescaledIntensities);
+      if( trimBound > 0.0 )
+        {
+        maxPixel = static_cast( maxPixel - trimBound * sigmaOrig );
+        }
+      }
+
+    itk::IntensityWindowingImageFilter::Pointer remapIntensityFilter =
+      itk::IntensityWindowingImageFilter::New();
+    remapIntensityFilter->SetInput(volOrig);
+    remapIntensityFilter->SetOutputMaximum(this->m_RescaleIntensitiesOutputRange[1]);
+    remapIntensityFilter->SetOutputMinimum(this->m_RescaleIntensitiesOutputRange[0]);
+    remapIntensityFilter->SetWindowMinimum(minPixel);
+    remapIntensityFilter->SetWindowMaximum(maxPixel);
+    remapIntensityFilter->Update();
+
+    image = remapIntensityFilter->GetOutput();
+    }
+  else
+    {
+    image = volOrig;
+    }
+
+  landmarksConstellationDetector myDetector;
+    {
+    // a little abuse of the duplicator here
+    DuplicatorType::Pointer duplicator = DuplicatorType::New();
+    duplicator->SetInputImage( this->GetInput() );
+    duplicator->Update();
+    // The detector will use the output image after the Hough eye detector
+    myDetector.SetVolOrig( duplicator->GetOutput() );
+    }
+  myDetector.SetInputTemplateModel( myModel );
+  myDetector.SetLlsMatrices( this->m_LlsMatrices );
+  myDetector.SetLlsMeans( this->m_LlsMeans );
+  myDetector.SetSearchRadii( this->m_SearchRadii );
+  myDetector.SetResultsDir( this->m_ResultsDir );
+  myDetector.SetTemplateRadius( myModel.GetRadii() );
+  myDetector.SetMSPQualityLevel( this->m_MspQualityLevel );
+  myDetector.SetCenterOfHeadMass( this->m_CenterOfHeadMass );
+  myDetector.SetHoughEyeFailure( this->m_HoughEyeFailure );
+
+  LandmarksMapType LandmarksEMSP = this->GetLandmarksEMSP();
+  if( LandmarksEMSP.size() > 0 )
+    {
+    myDetector.SetLandmarksEMSP( this->GetLandmarksEMSP() );
+    }
+
+  if( ( this->m_landmarksEMSP.find("LE") == this->m_landmarksEMSP.end() )
+      || ( this->m_landmarksEMSP.find("RE") == this->m_landmarksEMSP.end() ) )
+    {
+    myDetector.SetHoughEyeTransform(this->m_HoughEyeTransform);
+    myDetector.SetLEPoint(this->m_LEPoint);
+    myDetector.SetREPoint(this->m_REPoint);
+    }
+
+    { /** Force setting the landmark points from the command line. */
+    if( this->m_ForceACPoint.size() == 3 )
+      {
+      SImageType::PointType manualACPoint;
+      for( int i = 0; i < 3; i++ )
+        {
+        manualACPoint[i] = this->m_ForceACPoint[i];
+        }
+      myDetector.SetOriginalSpaceNamedPoint(std::string("AC"), manualACPoint);
+      }
+    if( this->m_ForcePCPoint.size() == 3 )
+      {
+      SImageType::PointType manualPCPoint;
+      for( int i = 0; i < 3; i++ )
+        {
+        manualPCPoint[i] = this->m_ForcePCPoint[i];
+        }
+      myDetector.SetOriginalSpaceNamedPoint(std::string("PC"), manualPCPoint);
+      }
+    if( this->m_ForceVN4Point.size() == 3 )
+      {
+      SImageType::PointType manualVN4Point;
+      for( int i = 0; i < 3; i++ )
+        {
+        manualVN4Point[i] = this->m_ForceVN4Point[i];
+        }
+      myDetector.SetOriginalSpaceNamedPoint(std::string("VN4"), manualVN4Point);
+      }
+    if( this->m_ForceRPPoint.size() == 3 )
+      {
+      SImageType::PointType manualRPPoint;
+      for( int i = 0; i < 3; i++ )
+        {
+        manualRPPoint[i] = this->m_ForceRPPoint[i];
+        }
+      myDetector.SetOriginalSpaceNamedPoint(std::string("RP"), manualRPPoint);
+      }
+    }
+
+  myDetector.Compute();
+
+    {
+      {
+      RigidTransformType::Pointer ZeroCenteredTransform =
+        myDetector.GetACPCAlignedZeroCenteredTransform();
+
+      this->m_VersorTransform = VersorTransformType::New();
+      this->m_VersorTransform->SetFixedParameters( ZeroCenteredTransform->GetFixedParameters() );
+      itk::Versor versorRotation;
+      versorRotation.Set( ZeroCenteredTransform->GetRotationMatrix() );
+      this->m_VersorTransform->SetRotation(versorRotation);
+      this->m_VersorTransform->SetTranslation( ZeroCenteredTransform->GetTranslation() );
+      }
+
+    this->m_InvVersorTransform = VersorTransformType::New();
+    const SImageType::PointType centerPoint = this->m_VersorTransform->GetCenter();
+    this->m_InvVersorTransform->SetCenter(centerPoint);
+    this->m_InvVersorTransform->SetIdentity();
+    this->m_VersorTransform->GetInverse(this->m_InvVersorTransform);
+
+    // std::cout << "versor         transform parameters are " <<
+    // ZeroCenteredTransform->GetParameters() << std::endl;
+    // std::cout << "versor inverse transform parameters are " <<
+    // this->m_InvVersorTransform->GetParameters() << std::endl;
+    // std::cout << "               transform parameters are nice, huh?" <<
+    // std::endl;
+    if( LMC::globalverboseFlag )
+      {
+      std::cout << "VersorRotation: " << this->m_VersorTransform->GetRotationMatrix() << std::endl;
+      std::cout << "itkVersorRigid3DTransform Parameters: " << this->m_VersorTransform->GetParameters() << std::endl;
+      std::cout << "itkVersorRigid3DTransform FixedParameters: " << this->m_VersorTransform->GetFixedParameters()
+                << std::endl;
+      std::cout << "itkVersorRigid3DTransform GetCenter(): " << this->m_VersorTransform->GetCenter() << std::endl;
+      std::cout << "itkVersorRigid3DTransform GetTranslation(): " << this->m_VersorTransform->GetTranslation()
+                << std::endl;
+      std::cout << "itkVersorRigid3DTransform GetRotationMatrix(): " << this->m_VersorTransform->GetRotationMatrix()
+                << std::endl;
+
+      std::cout << "itkRigid3DTransform Parameters: " << this->m_VersorTransform->GetParameters() << std::endl;
+      std::cout << "itkRigid3DTransform FixedParameters: " << this->m_VersorTransform->GetFixedParameters()
+                << std::endl;
+      std::cout << "itkRigid3DTransform GetCenter(): " << this->m_VersorTransform->GetCenter() << std::endl;
+      std::cout << "itkRigid3DTransform GetTranslation(): " << this->m_VersorTransform->GetTranslation() << std::endl;
+      std::cout << "itkRigid3DTransform GetRotationMatrix(): " << this->m_VersorTransform->GetRotationMatrix()
+                << std::endl;
+      std::cout << "itkVersorRigid3DTransform: \n" <<  this->m_VersorTransform << std::endl;
+      std::cout << "itkRigid3DTransform: \n" <<  this->m_VersorTransform << std::endl;
+      }
+
+    if( globalImagedebugLevel > 3 )
+      {
+      SImageType::Pointer TaggedOriginalImage = myDetector.GetTaggedImage();
+      itkUtil::WriteImage(TaggedOriginalImage, this->m_ResultsDir + "/TAGGED_POINTS.nii.gz");
+        {
+        SImageType::Pointer isoTaggedImage =
+          TransformResample(
+            TaggedOriginalImage, MakeIsoTropicReferenceImage(), BackgroundFillValue,
+            GetInterpolatorFromString("Linear"), this->m_VersorTransform.GetPointer() );
+        itkUtil::WriteImage(isoTaggedImage, this->m_ResultsDir + "/ISO_Lmk_MSP.nii.gz");
+        }
+        {
+        SImageType::Pointer VersorisoTaggedImage =
+          TransformResample(
+            TaggedOriginalImage, MakeIsoTropicReferenceImage(), BackgroundFillValue,
+            GetInterpolatorFromString("Linear"), this->m_VersorTransform.GetPointer() );
+        itkUtil::WriteImage(VersorisoTaggedImage, this->m_ResultsDir + "/Versor_ISO_Lmk_MSP.nii.gz");
+        }
+        {
+        RigidTransformType::Pointer OrigSpaceCenterOfGravityCentered = myDetector.GetTransformToMSP();
+        SImageType::Pointer         RigidMSPImage =
+          TransformResample(
+            TaggedOriginalImage, MakeIsoTropicReferenceImage(), BackgroundFillValue,
+            GetInterpolatorFromString("Linear"), OrigSpaceCenterOfGravityCentered.GetPointer() );
+        itkUtil::WriteImage(RigidMSPImage, this->m_ResultsDir + "/RigidMSPImage_Lmk_MSP.nii.gz");
+        }
+      }
+
+    double PhysicalLowerBound = /* ACy when zero-centered is ... */ 0.0 - this->m_AcLowerBound;
+    for( LandmarksMapType::const_iterator lit = myDetector.GetNamedPoints().begin();
+         lit != myDetector.GetNamedPoints().end(); ++lit )
+      {
+      this->m_AlignedPoints[lit->first] =
+        this->m_InvVersorTransform->TransformPoint
+          ( myDetector.GetOriginalSpaceNamedPoint(lit->first) );
+      }
+
+      {
+        {
+        const SImageType * constImage( this->m_OriginalInputImage.GetPointer() );
+
+        ResampleIPFilterPointer resampleIPFilter = ResampleIPFilterType::New();
+        resampleIPFilter->SetInputImage( constImage );
+        resampleIPFilter->SetRigidTransform( m_VersorTransform.GetPointer() );
+        resampleIPFilter->Update();
+        this->m_OutputImage = resampleIPFilter->GetOutput();
+        this->GraftOutput(m_OutputImage);
+        }
+
+        {
+        this->m_OutputResampledImage = TransformResample
+            ( image, MakeIsoTropicReferenceImage(), BackgroundFillValue,
+            GetInterpolatorFromString(this->m_InterpolationMode),
+            this->m_VersorTransform.GetPointer() );
+        }
+
+        {
+        // ======================== Start
+        // ======================== Start
+        //  HACK -- chopping based on AcLowerBound
+        //  This is ugly code that could be re-written much simpler.
+        //
+        typedef itk::ImageRegionIteratorWithIndex IteratorType;
+        const double thousand = 1000.0;   // we need a DOUBLE constant, not a
+        // FLOAT constant, for exact switch
+        // comparisons.
+        if( this->m_AcLowerBound < thousand )
+          {
+          // First Process the OutputResampledImage
+          std::cout << "Chopping image below physical location: " << PhysicalLowerBound << "." << std::endl;
+          ChopImageBelowLowerBound(this->m_OutputResampledImage, BackgroundFillValue, PhysicalLowerBound);
+          ChopImageBelowLowerBound(this->m_OutputImage, BackgroundFillValue, PhysicalLowerBound);
+
+          // Second Create a mask for inverse resampling to orignal space
+          SImageType::Pointer ZeroOneImage = SImageType::New();
+          ZeroOneImage->CopyInformation(this->m_OutputResampledImage);
+          // don't forget to do SetRegions here!
+          ZeroOneImage->SetRegions( this->m_OutputResampledImage->GetLargestPossibleRegion() );
+          ZeroOneImage->Allocate();
+          ZeroOneImage->FillBuffer(1);
+          ChopImageBelowLowerBound(ZeroOneImage, BackgroundFillValue, PhysicalLowerBound);
+
+          if( this->m_CutOutHeadInOutputVolume )  // Restrict mask to head
+                                                  // tissue region if necessary
+            {
+            //  No double opportunity when generating both kinds of images.
+            const unsigned int closingSize = 7;
+            //            SImageType::Pointer HeadOutlineMaskImage =
+            // FindLargestForgroundFilledMask(
+            // this->m_OutputResampledImage, this->m_OtsuPercentileThreshold,
+            // closingSize );
+            typedef itk::LargestForegroundFilledMaskImageFilter LFFMaskFilterType;
+            LFFMaskFilterType::Pointer LFF = LFFMaskFilterType::New();
+            LFF->SetInput(this->m_OutputResampledImage);
+            LFF->SetOtsuPercentileThreshold(this->m_OtsuPercentileThreshold);
+            LFF->SetClosingSize(closingSize);
+            LFF->Update();
+            SImageType::Pointer HeadOutlineMaskImage =  LFF->GetOutput();
+
+            IteratorType ItZeroOneImage( ZeroOneImage, ZeroOneImage->GetRequestedRegion() );
+            ItZeroOneImage.GoToBegin();
+            IteratorType ItOutputResampledImage( this->m_OutputResampledImage,
+                                                 this->m_OutputResampledImage->GetRequestedRegion() );
+            ItOutputResampledImage.GoToBegin();
+            IteratorType ItHead( HeadOutlineMaskImage, HeadOutlineMaskImage->GetLargestPossibleRegion() );
+            ItHead.GoToBegin();
+            while( !ItHead.IsAtEnd() )
+              {
+              if( ItHead.Get() == 0 )
+                {
+                ItOutputResampledImage.Set(0);
+                ItZeroOneImage.Set(0);
+                }
+              ++ItZeroOneImage;
+              ++ItOutputResampledImage;
+              ++ItHead;
+              }
+            }
+          // Map the ZeroOne image through the inverse zero-centered transform
+          // to
+          // make the clipping factor image:
+          typedef itk::NearestNeighborInterpolateImageFunction NearestNeighborInterpolatorType;
+          // typename
+          NearestNeighborInterpolatorType::Pointer interpolator = NearestNeighborInterpolatorType::New();
+          typedef itk::ResampleImageFilter ResampleFilterType;
+          // typename
+          ResampleFilterType::Pointer ResampleFilter = ResampleFilterType::New();
+          ResampleFilter->SetInput(ZeroOneImage);
+          ResampleFilter->SetInterpolator(interpolator);
+          ResampleFilter->SetDefaultPixelValue(0);
+          ResampleFilter->SetOutputParametersFromImage(image);
+
+          ResampleFilter->SetTransform(this->m_InvVersorTransform);
+          ResampleFilter->Update();
+          // typename
+          SImageType::Pointer clippingFactorImage = ResampleFilter->GetOutput();
+          // itkUtil::WriteImage(clippingFactorImage,"ClippingImage.nii.gz");
+
+          // Multiply the raw input image by the clipping factor image:
+          typedef itk::MultiplyImageFilter MultiplyFilterType;
+          // typename
+          MultiplyFilterType::Pointer MultiplyFilter = MultiplyFilterType::New();
+          MultiplyFilter->SetInput1(image);
+          MultiplyFilter->SetInput2(clippingFactorImage);
+          MultiplyFilter->Update();
+          this->m_OutputUntransformedClippedVolume = MultiplyFilter->GetOutput();
+          }
+        // ======================== Stop
+        // ======================== Stop
+        }
+      if( this->m_WriteBranded2DImage.compare("") != 0 )
+        {
+        MakeBranded2DImage(this->m_OutputResampledImage.GetPointer(), myDetector,
+                           this->m_AlignedPoints["RP"],
+                           this->m_AlignedPoints["AC"],
+                           this->m_AlignedPoints["PC"],
+                           this->m_AlignedPoints["VN4"],
+                           this->m_AlignedPoints["CM"],
+                           this->m_WriteBranded2DImage);
+        }
+
+      }     //  scope of this->m_OutputResampledImage
+    }
+}
+
+template 
+void
+BRAINSConstellationDetector2
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  // os << "Mode: " << this->m_Mode << std::endl;
+}
+
+}
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationModeler.cxx b/BRAINSConstellationDetector/src/BRAINSConstellationModeler.cxx
new file mode 100644
index 00000000..d7b205ce
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationModeler.cxx
@@ -0,0 +1,506 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include 
+#include "string.h"
+#include "math.h"
+#include 
+
+#include "BRAINSThreadControl.h"
+#include 
+#include "itkReflectiveCorrelationCenterToImageMetric.h"
+
+#include "BRAINSConstellationModelerCLP.h"
+#include "landmarksConstellationCommon.h"
+#include "landmarksConstellationTrainingDefinitionIO.h"
+#include "landmarkIO.h"
+#include "GenericTransformImage.h"
+
+// //////////////////////////////////////////////////////////////
+// Computes the unbiased sample variance of a set of n observations
+// {x_1,x_2,...,x_n} from a given distribution.
+// //////////////////////////////////////////////////////////////
+template 
+void sample_variance(const std::vector & x, DType *mean, DType *var)
+{
+  const DType n = x.size();
+  DType       sum_of_sq = 0.0;
+  DType       sum = 0.0;
+
+  if( n == 1 )  // not possible to compute variance of a single sample
+    {
+    *mean = x[0];
+    *var = 0.0;
+    }
+  for( typename std::vector::const_iterator it = x.begin(); it != x.end(); ++it )
+    {
+    const DType value = *it;
+    sum_of_sq += value * value;
+    sum += value;
+    }
+  *mean = sum / n;
+  *var = ( sum_of_sq - sum * sum / n ) / ( n - 1.0 );
+}
+
+//
+//
+// ==============================================================================================
+int main(int argc, char *argv[])
+{
+  std::cout.precision(20);
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  PARSE_ARGS;
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+
+  if( ( inputTrainingList.compare("") == 0 )
+      || ( outputModel.compare("") == 0 ) )
+    {
+    std::cerr << "To run the program please specify the training filename and the "
+              << "output outputModel filename." << std::endl;
+    std::cerr << "Type " << argv[0] << " -h for more help." << std::endl;
+    exit(-1);
+    }
+
+  LMC::globalverboseFlag = verbose;
+
+  globalResultsDir = resultsDir;
+  globalImagedebugLevel = writedebuggingImagesLevel;
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  short BackgroundFillValue;
+  if( backgroundFillValueString == std::string("BIGNEG") )
+    {
+    BackgroundFillValue = -32768;
+    }
+  else
+    {
+    BackgroundFillValue = atoi( backgroundFillValueString.c_str() );
+    }
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  // read information from the setup file, allocate some memories, and
+  // initialize some variables
+
+  landmarksConstellationTrainingDefinitionIO mDef(inputTrainingList);
+  // //////////////////////////////////////////////////////////////////////////
+  landmarksConstellationModelIO myModel;
+  myModel.CopyFromModelDefinition(mDef);
+  myModel.InitializeModel(true);
+
+  // the following tables store the inputed manually selected RP, AC, PC, etc
+  // locations for
+  // each volume
+  // NOTE:  3 because before projection into Mid-sagital-plane (msp) need 3
+  // coords
+  // these tables store the RP, AC, PC, etc locations for each volume projected
+  // on the MSP
+  // NOTE:  only 2 coords need after projectsion into MSP, but using 3 to keep
+  // math simple.
+  // TODO:  Will need to change all index to get y and z (which is currently
+  // coded as coord index 0 and 1
+  std::vector rp_InMSPAlignedSpace( myModel.GetNumDataSets() );
+  std::vector ac_InMSPAlignedSpace( myModel.GetNumDataSets() );
+  std::vector pc_InMSPAlignedSpace( myModel.GetNumDataSets() );
+  std::vector vn4_InMSPAlignedSpace( myModel.GetNumDataSets() );
+  std::vector cec_InMSPAlignedSpace( myModel.GetNumDataSets() );
+  std::vector cm_InMSPAlignedSpace( myModel.GetNumDataSets() );
+
+  std::ofstream MSPOptFile;
+  std::string   newOptimizedLandmarksTrainingFile;
+  if( saveOptimizedLandmarks )
+    {
+    newOptimizedLandmarksTrainingFile = inputTrainingList + optimizedLandmarksFilenameExtender;
+
+    // Write out the optimized points to a file so that training can be more
+    // accurate.
+    MSPOptFile.open( newOptimizedLandmarksTrainingFile.c_str() ); // open setup
+    // file for
+    // writing
+    if( !MSPOptFile.is_open() )
+      {
+      std::cerr << "Can't write " << newOptimizedLandmarksTrainingFile << std::endl;
+      std::cerr.flush();
+      }
+
+    // We are copying the first 6 lines rather than quoting them in this program
+    // to give the user some control over what they are.
+    std::ifstream prevMSPOptFile;
+    prevMSPOptFile.open( inputTrainingList.c_str() ); // open previous setup
+                                                      // file for
+    // reading
+    char linebuf[300];
+    for( int lineNum = 0; lineNum < 6; lineNum++ )
+      {
+      prevMSPOptFile.getline(linebuf, 300);  // read to end of line;  line size
+      // ends up in gcount()
+      MSPOptFile.write( linebuf, prevMSPOptFile.gcount() );
+      }
+    prevMSPOptFile.close();
+    }
+  // //////////////////////////////////////////////////////////////////////////
+  for( unsigned int currentDataset = 0; currentDataset < mDef.GetNumDataSets(); currentDataset++ )
+    {
+    std::cout << "====================================================================================" << std::endl;
+    std::cout << "PROCESSING:" <<  mDef[currentDataset].GetImageFilename() << std::endl;
+    // Since these are oriented images, the reorientation should not be
+    // necessary.
+    //
+    //
+    // //////////////////////////////////////////////////////////////////////////
+    SImageType::Pointer volOrig = itkUtil::ReadImage( mDef[currentDataset].GetImageFilename() );
+    if( volOrig.IsNull() )
+      {
+      printf( "\nCould not open image %s, aborting ...\n\n", mDef[currentDataset].GetImageFilename().c_str() );
+      exit(1);
+      }
+    SImageType::Pointer image;
+
+    if( rescaleIntensities == true )
+      {
+      itk::StatisticsImageFilter::Pointer stats =
+        itk::StatisticsImageFilter::New();
+      stats->SetInput(volOrig);
+      stats->Update();
+      SImageType::PixelType minPixel( stats->GetMinimum() );
+      SImageType::PixelType maxPixel( stats->GetMaximum() );
+
+      if( trimRescaledIntensities > 0.0 )
+        {
+        // REFACTOR: a histogram would be traditional here, but seems
+        // over-the-top;
+        // I did this because it seemed to me if I knew mean, sigma, max and
+        // min,
+        // then I know Something about extreme outliers.
+
+        double meanOrig( stats->GetMean() );
+        double sigmaOrig( stats->GetSigma() );
+
+        // REFACTOR:  In percentiles, 0.0005 two-tailed has worked in the past.
+        // It only makes sense to trim the upper bound since the lower bound
+        // would most likely
+        // represent a large region of air around the head.  But this is not so
+        // when using a mask.
+        // For one-tailed, an error of 0.001 corresponds to 3.29052 standard
+        // deviations of normal.
+        // For one-tailed, an error of 0.0001 corresponds to 3.8906 standard
+        // deviations of normal.
+        // For one-tailed, an error of 0.00001 corresponds to 4.4172 standard
+        // deviations of normal.
+        // Naturally, the constant should default at the command line, ...
+
+        double variationBound( ( maxPixel - meanOrig ) / sigmaOrig );
+        double trimBound(variationBound - trimRescaledIntensities);
+        if( trimBound > 0.0 )
+          {
+          maxPixel = static_cast( maxPixel - trimBound * sigmaOrig );
+          }
+        }
+
+      itk::IntensityWindowingImageFilter::Pointer remapIntensityFilter =
+        itk::IntensityWindowingImageFilter::New();
+      remapIntensityFilter->SetInput(volOrig);
+      remapIntensityFilter->SetOutputMaximum(rescaleIntensitiesOutputRange[1]);
+      remapIntensityFilter->SetOutputMinimum(rescaleIntensitiesOutputRange[0]);
+      remapIntensityFilter->SetWindowMinimum(minPixel);
+      remapIntensityFilter->SetWindowMaximum(maxPixel);
+      remapIntensityFilter->Update();
+
+      image = remapIntensityFilter->GetOutput();
+      }
+    else
+      {
+      image = volOrig;
+      }
+
+    SImageType::PointType origin;
+    origin.Fill(0);
+    SImageType::SpacingType iSpacing  = image->GetSpacing();
+    SImageType::SizeType    iSize        = image->GetLargestPossibleRegion().GetSize();
+
+    // This section assumes that the landmarks are defined as
+    // ITK compliant physical space
+    // That are consistent with ITK images that they were collected from Dicom
+    // coordinate system
+    // No conversion is necessary
+    SImageType::PointType origRP = mDef[currentDataset].GetNamedPoint("RP");
+    SImageType::PointType origAC = mDef[currentDataset].GetNamedPoint("AC");
+    SImageType::PointType origPC = mDef[currentDataset].GetNamedPoint("PC");
+    SImageType::PointType origVN4 = mDef[currentDataset].GetNamedPoint("VN4");
+    SImageType::PointType origLE = mDef[currentDataset].GetNamedPoint("LE");
+    SImageType::PointType origRE = mDef[currentDataset].GetNamedPoint("RE");
+    SImageType::PointType origCEC;
+    origCEC.SetToMidPoint(origLE, origRE);
+
+    // original input volume from the training set
+    // transforms image to MSP aligned voxel lattice
+    RigidTransformType::Pointer Tmsp = RigidTransformType::New();
+    RigidTransformType::Pointer invTmsp = RigidTransformType::New();
+    SImageType::Pointer         volumeMSP;
+    SImageType::PointType       centerOfHeadMass = GetCenterOfHeadMass(image);
+    ComputeMSP(image, Tmsp, volumeMSP, centerOfHeadMass, mspQualityLevel);
+
+    if( globalImagedebugLevel > 2 )
+      {
+      const std::string MSP_ImagePlane( globalResultsDir + "/MSP_PLANE_"
+                                        + itksys::SystemTools::GetFilenameName
+                                          ( mDef[currentDataset].GetImageFilename() ) );
+      CreatedebugPlaneImage(volumeMSP, MSP_ImagePlane);
+      }
+
+    Tmsp->GetInverse(invTmsp);
+
+    cm_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(centerOfHeadMass);
+    rp_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(origRP);
+    ac_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(origAC);
+    pc_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(origPC);
+    vn4_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(origVN4);
+    cec_InMSPAlignedSpace[currentDataset] = invTmsp->TransformPoint(origCEC);
+
+    // Compute the transform from original space to the AC-PC aligned space
+    RigidTransformType::Pointer ACPC_AlignedTransform = computeTmspFromPoints(origRP, origAC, origPC, origin);
+    RigidTransformType::Pointer ACPC_AlignedTransform_INV = RigidTransformType::New();
+    ACPC_AlignedTransform_INV->GetInverse(ACPC_AlignedTransform);
+
+    const SImageType::PointType finalRP = ACPC_AlignedTransform_INV->TransformPoint(origRP);
+    const SImageType::PointType finalAC = ACPC_AlignedTransform_INV->TransformPoint(origAC);
+    const SImageType::PointType finalPC = ACPC_AlignedTransform_INV->TransformPoint(origPC);
+    const SImageType::PointType finalVN4 = ACPC_AlignedTransform_INV->TransformPoint(origVN4);
+
+    SImageType::Pointer volumeACPC_Aligned =
+      TransformResample( image, image, BackgroundFillValue,
+                                                 GetInterpolatorFromString("Linear"),
+                                                 ACPC_AlignedTransform.GetPointer() );
+
+    if( globalImagedebugLevel > 3 )
+      {
+      itkUtil::WriteImage( volumeACPC_Aligned, resultsDir + "/ACPC_Aligned_"
+                                       + itksys::SystemTools::GetFilenameName( mDef[currentDataset].GetImageFilename() ) );
+      MakeLabelImage( volumeACPC_Aligned, finalRP, finalAC, finalPC, finalVN4, resultsDir + "/Mask_Resampled_"
+                      + itksys::SystemTools::GetFilenameName( mDef[currentDataset].GetImageFilename() ) );
+      }
+
+    // Build template for each landmark
+    std::map::iterator it;
+    for( it = mDef[currentDataset].begin(); it != mDef[currentDataset].end(); ++it )
+      {
+      std::cout << "Training template for " << it->first << std::endl;
+      for( unsigned int currentAngle = 0; currentAngle < myModel.GetNumRotationSteps(); currentAngle++ )
+        {
+        // //////  create a rotation about the center with respect to the
+        // current test rotation angle
+        const float degree_current_angle =
+          myModel.GetInitialRotationAngle() + myModel.GetInitialRotationStep() * currentAngle;
+        const float                 current_angle = degree_current_angle * vnl_math::pi / 180;
+        const SImageType::PointType origPoint = it->second;
+        const SImageType::PointType transformedPoint = ACPC_AlignedTransform_INV->TransformPoint(origPoint);
+        RigidTransformType::Pointer Point_Rotate = RigidTransformType::New();
+        Point_Rotate->SetCenter(transformedPoint);
+        Point_Rotate->SetRotation(current_angle, 0, 0);
+
+        SImageType::Pointer image_TestRotated =
+          CreateTestCenteredRotatedImage2(ACPC_AlignedTransform, origPoint, image, Point_Rotate);
+        if( globalImagedebugLevel > 5 )
+          {
+          std::stringstream s("");
+          s << "image_" << it->first << "_TestRotated_" << current_angle << "_";
+          const std::string rotatedName = resultsDir + "/" + s.str().c_str()
+            + itksys::SystemTools::GetFilenameName( mDef[currentDataset].GetImageFilename() );
+          std::cout << "Writing file: " << rotatedName << std::endl;
+          itkUtil::WriteImage(image_TestRotated, rotatedName);
+          }
+
+        // TODO:  The following 3 function calls may be a performance problem,
+        // and it should be
+        //       straight forward to refactor this into a single function
+        // extractZeroMeanNormalizedVector
+        //       that has the same signature as extractArray, but has many fewer
+        // loop iterations.
+        extractArray( image_TestRotated, transformedPoint, myModel.m_VectorIndexLocations[it->first],
+                      myModel.AccessTemplate(it->first, currentDataset, currentAngle) );
+        removeVectorMean( myModel.AccessTemplate(it->first, currentDataset, currentAngle) );
+        normalizeVector( myModel.AccessTemplate(it->first, currentDataset, currentAngle) );
+        }
+      }
+
+    if( saveOptimizedLandmarks )
+      {
+      MSPOptFile.close();
+      }
+    }
+
+  // -------------------------------
+  std::cout << "\nCompute vector means:" << std::endl;
+
+  // Compute MPJtoPCMean
+    {
+    std::vector xComponents( myModel.GetNumDataSets() );
+    std::vector yComponents( myModel.GetNumDataSets() );
+    std::vector zComponents( myModel.GetNumDataSets() );
+    for( unsigned int currentDataset = 0; currentDataset < myModel.GetNumDataSets(); currentDataset++ )
+      {
+      xComponents[currentDataset] = pc_InMSPAlignedSpace[currentDataset][0]
+        - rp_InMSPAlignedSpace[currentDataset][0];
+      yComponents[currentDataset] = pc_InMSPAlignedSpace[currentDataset][1]
+        - rp_InMSPAlignedSpace[currentDataset][1];
+      zComponents[currentDataset] = pc_InMSPAlignedSpace[currentDataset][2]
+        - rp_InMSPAlignedSpace[currentDataset][2];
+      }
+    SImageType::PointType::VectorType RPtoPCmean;
+    SImageType::PointType::VectorType RPtoPCvar;
+    sample_variance( xComponents, &( RPtoPCmean[0] ), &( RPtoPCvar[0] ) );
+    sample_variance( yComponents, &( RPtoPCmean[1] ), &( RPtoPCvar[1] ) );
+    sample_variance( zComponents, &( RPtoPCmean[2] ), &( RPtoPCvar[2] ) );
+    myModel.SetRPtoXMean("PC", RPtoPCmean);
+    std::cout << "RPtoPC mean = " << RPtoPCmean << "mm" << std::endl;
+    std::cout << "RPtoPC var = " << RPtoPCvar << "mm^2" << std::endl;
+    }
+
+  // Compute MPJtoVN4Mean
+    {
+    std::vector xComponents( myModel.GetNumDataSets() );
+    std::vector yComponents( myModel.GetNumDataSets() );
+    std::vector zComponents( myModel.GetNumDataSets() );
+    for( unsigned int currentDataset = 0; currentDataset < myModel.GetNumDataSets(); currentDataset++ )
+      {
+      xComponents[currentDataset] = vn4_InMSPAlignedSpace[currentDataset][0]
+        - rp_InMSPAlignedSpace[currentDataset][0];
+      yComponents[currentDataset] = vn4_InMSPAlignedSpace[currentDataset][1]
+        - rp_InMSPAlignedSpace[currentDataset][1];
+      zComponents[currentDataset] = vn4_InMSPAlignedSpace[currentDataset][2]
+        - rp_InMSPAlignedSpace[currentDataset][2];
+      }
+    SImageType::PointType::VectorType RPtoVN4mean;
+    SImageType::PointType::VectorType RPtoVN4var;
+    sample_variance( xComponents, &( RPtoVN4mean[0] ), &( RPtoVN4var[0] ) );
+    sample_variance( yComponents, &( RPtoVN4mean[1] ), &( RPtoVN4var[1] ) );
+    sample_variance( zComponents, &( RPtoVN4mean[2] ), &( RPtoVN4var[2] ) );
+    myModel.SetRPtoXMean("VN4", RPtoVN4mean);
+    std::cout << "RPtoVN4 mean = " << RPtoVN4mean << "mm" << std::endl;
+    std::cout << "RPtoVN4 var = " << RPtoVN4var << "mm^2" << std::endl;
+    }
+
+  // Compute MPJtoCECMean
+    {
+    std::vector xComponents( myModel.GetNumDataSets() );
+    std::vector yComponents( myModel.GetNumDataSets() );
+    std::vector zComponents( myModel.GetNumDataSets() );
+    for( unsigned int currentDataset = 0; currentDataset < myModel.GetNumDataSets(); currentDataset++ )
+      {
+      xComponents[currentDataset] = cec_InMSPAlignedSpace[currentDataset][0]
+        - rp_InMSPAlignedSpace[currentDataset][0];
+      yComponents[currentDataset] = cec_InMSPAlignedSpace[currentDataset][1]
+        - rp_InMSPAlignedSpace[currentDataset][1];
+      zComponents[currentDataset] = cec_InMSPAlignedSpace[currentDataset][2]
+        - rp_InMSPAlignedSpace[currentDataset][2];
+      }
+    SImageType::PointType::VectorType RPtoCECmean;
+    SImageType::PointType::VectorType RPtoCECvar;
+    sample_variance( xComponents, &( RPtoCECmean[0] ), &( RPtoCECvar[0] ) );
+    sample_variance( yComponents, &( RPtoCECmean[1] ), &( RPtoCECvar[1] ) );
+    sample_variance( zComponents, &( RPtoCECmean[2] ), &( RPtoCECvar[2] ) );
+    myModel.SetRPtoCECMean(RPtoCECmean);
+    std::cout << "RPtoCEC mean = " << RPtoCECmean << "mm" << std::endl;
+    std::cout << "RPtoCEC var = " << RPtoCECvar << "mm^2" << std::endl;
+    }
+
+  // Compute MPJtoACMean
+    {
+    std::vector xComponents( myModel.GetNumDataSets() );
+    std::vector yComponents( myModel.GetNumDataSets() );
+    std::vector zComponents( myModel.GetNumDataSets() );
+    for( unsigned int currentDataset = 0; currentDataset < myModel.GetNumDataSets(); currentDataset++ )
+      {
+      xComponents[currentDataset] = ac_InMSPAlignedSpace[currentDataset][0] - rp_InMSPAlignedSpace[currentDataset][0];
+      yComponents[currentDataset] = ac_InMSPAlignedSpace[currentDataset][1] - rp_InMSPAlignedSpace[currentDataset][1];
+      zComponents[currentDataset] = ac_InMSPAlignedSpace[currentDataset][2] - rp_InMSPAlignedSpace[currentDataset][2];
+      }
+    SImageType::PointType::VectorType RPtoACmean;
+    SImageType::PointType::VectorType RPtoACvar;
+    sample_variance( xComponents, &( RPtoACmean[0] ), &( RPtoACvar[0] ) );
+    sample_variance( yComponents, &( RPtoACmean[1] ), &( RPtoACvar[1] ) );
+    sample_variance( zComponents, &( RPtoACmean[2] ), &( RPtoACvar[2] ) );
+    std::cout << "RPtoAC mean = " << RPtoACmean << "mm" << std::endl;
+    std::cout << "RPtoAC var = " << RPtoACvar << "mm^2" << std::endl;
+    myModel.SetRPtoXMean("AC", RPtoACmean);
+    }
+
+  // ??  What does RPPC_to_RPAC_angle and RPAC_over_RPPC mean?
+  std::vector                RPPC_to_RPAC_angle( myModel.GetNumDataSets() );
+  std::vector                RPAC_over_RPPC( myModel.GetNumDataSets() );
+  SImageType::PointType::VectorType CMtoRPMean;
+  CMtoRPMean.Fill(0.0);
+  for( unsigned int currentDataset = 0; currentDataset < myModel.GetNumDataSets(); currentDataset++ )
+    {
+    float curr_RPPC_to_RPAC_angle;
+    float curr_RPAC_over_RPPC;
+    decomposeRPAC(rp_InMSPAlignedSpace[currentDataset],
+                  pc_InMSPAlignedSpace[currentDataset],
+                  ac_InMSPAlignedSpace[currentDataset],
+                  &curr_RPPC_to_RPAC_angle, &curr_RPAC_over_RPPC);
+    RPPC_to_RPAC_angle[currentDataset] = curr_RPPC_to_RPAC_angle;
+    RPAC_over_RPPC[currentDataset] = curr_RPAC_over_RPPC;
+    // / NOTE:  This needs to be the average distance from the center of
+    // gravity.
+    SImageType::PointType::VectorType RPDistanceFromCenterOfMass = rp_InMSPAlignedSpace[currentDataset]
+      - cm_InMSPAlignedSpace[currentDataset];
+    CMtoRPMean += RPDistanceFromCenterOfMass;
+    }
+  CMtoRPMean /= static_cast( myModel.GetNumDataSets() );
+
+  // Now compute the average angle and average ratio
+  float RPPC_to_RPAC_angleMean, RPAC_over_RPPCMean;
+    {
+    float dummy_mean;
+    float dummy_var;
+    // HACK:  Need to compute only the mean, since that is all that is needed.
+    sample_variance(RPPC_to_RPAC_angle, &dummy_mean, &dummy_var);
+    RPPC_to_RPAC_angleMean = dummy_mean;
+    sample_variance(RPAC_over_RPPC, &dummy_mean, &dummy_var);
+    RPAC_over_RPPCMean = dummy_mean;
+    }
+
+  myModel.SetRPPC_to_RPAC_angleMean(RPPC_to_RPAC_angleMean);
+  myModel.SetRPAC_over_RPPCMean(RPAC_over_RPPCMean);
+
+  myModel.SetCMtoRPMean(CMtoRPMean);
+
+  myModel.WriteModelFile(outputModel);
+  myModel.PrintHeaderInfo();
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationModeler.xml b/BRAINSConstellationDetector/src/BRAINSConstellationModeler.xml
new file mode 100644
index 00000000..df5da0a5
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSConstellationModeler.xml
@@ -0,0 +1,138 @@
+
+
+    ACPCModel
+    Train up a model for BRAINSConstellationDetector
+    
+        
+            verbose
+            
+            v
+            verbose
+            false
+            
+              Show more verbose output
+            
+        
+        
+            inputTrainingList
+            i
+            inputTrainingList
+            
+            
+              Setup file, giving all parameters for training up a template model for each landmark.
+            
+            input
+        
+        
+            outputModel
+            m
+            outputModel
+            default.mdl
+            
+              The full filename of the output model file.
+            
+            output
+        
+        
+            saveOptimizedLandmarks
+            
+            l
+            saveOptimizedLandmarks
+            false
+            
+              Flag to make a new subject-specific landmark definition file in the same format produced by Slicer3 with the optimized landmark (the detected RP, AC, and PC) in it.  Useful to tighten the variances in the ConstellationModeler.
+            
+        
+        
+            optimizedLandmarksFilenameExtender
+            j
+            optimizedLandmarksFilenameExtender
+            _opt.fcsv
+            
+               If the trainingList is (indexFullPathName) and contains landmark data filenames [path]/[filename].fcsv ,  make the optimized landmarks filenames out of [path]/[filename](thisExtender) and the optimized version of the input trainingList out of (indexFullPathName)(thisExtender) , when you rewrite all the landmarks according to the saveOptimizedLandmarks flag.
+            
+            output
+        
+         
+            resultsDir
+            
+            r
+            resultsDir
+            ./
+            
+              The directory for the results to be written.
+            
+            output
+        
+        
+            mspQualityLevel
+            
+            mspQualityLevel
+            q
+            
+                Flag cotrols how agressive the MSP is estimated.  0=quick estimate (9 seconds), 1=normal estimate (11 seconds), 2=great estimate (22 seconds), 3=best estimate (58 seconds).
+            
+            2
+           
+              0
+              3
+              1
+           
+        
+        
+            rescaleIntensities
+            
+            rescaleIntensities
+            n
+            
+                Flag to turn on rescaling image intensities on input.
+            
+            0
+        
+        
+            trimRescaledIntensities
+            
+            trimRescaledIntensities
+            x
+            
+                Turn on clipping the rescaled image one-tailed on input.  Units of standard deviations above the mean.  Very large values are very permissive.  Non-positive value turns clipping off.  Defaults to removing 0.00001 of a normal tail above the mean.
+            
+            4.4172
+        
+        
+            rescaleIntensitiesOutputRange
+            
+            rescaleIntensitiesOutputRange
+            y
+            
+                This pair of integers gives the lower and upper bounds on the signal portion of the output image.  Out-of-field voxels are taken from BackgroundFillValue.
+            
+            40,4000
+        
+        
+            backgroundFillValueString
+            BackgroundFillValue
+            z
+            Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number.
+            
+            0
+        
+        
+            writedebuggingImagesLevel
+            
+            writedebuggingImagesLevel
+            w
+            
+                This flag controls if debugging images are produced.  By default value of 0 is no images.  Anything greater than zero will be increasing level of debugging images.
+            
+            0
+        
+        
+          numberOfThreads
+          numberOfThreads
+          
+          Explicitly specify the maximum number of threads to use.
+          -1
+        
+    
+
diff --git a/BRAINSConstellationDetector/src/BRAINSEyeDetector.cxx b/BRAINSConstellationDetector/src/BRAINSEyeDetector.cxx
new file mode 100644
index 00000000..afe95d02
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSEyeDetector.cxx
@@ -0,0 +1,109 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "itkFindCenterOfBrainFilter.h"
+#include "BRAINSHoughEyeDetector.h"
+#include "BRAINSEyeDetectorCLP.h"
+
+#include "itkCommand.h"
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+
+#include 
+
+int main(int argc, char *argv[])
+{
+  //HACK:  NOTE THIS PROGRAM STILL USES ARGV ARGC, and ignores the PARSE_ARGS.
+  //It needs to be fixed.
+  //
+  PARSE_ARGS;
+  // Image, filter typedef
+  const unsigned int LocalImageDimension = 3;
+
+  typedef short PixelType;
+
+  typedef itk::Image ImageType;
+  typedef ImageType::Pointer                         ImagePointerType;
+  typedef ImageType::PointType                       ImagePointType;
+
+  typedef itk::ImageFileReader         ReaderType;
+  typedef itk::ImageFileWriter         WriterType;
+  typedef itk::FindCenterOfBrainFilter FindCenterFilter;
+  typedef itk::BRAINSHoughEyeDetector<
+    ImageType, ImageType>                             HoughEyeDetectorType;
+
+  // Read input image
+  if( argc < 3 )
+    {
+    std::cerr << "Please specify the input filename." << std::endl;
+    exit(-1);
+    }
+
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName(argv[1]);
+  try
+    {
+    reader->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << " Error while reading image file(s) with ITK:\n "
+              << err << std::endl;
+    }
+
+  // Find center of head mass
+  std::cout << "Finding center of head mass..." << std::endl;
+  FindCenterFilter::Pointer findCenterFilter = FindCenterFilter::New();
+  findCenterFilter->SetInput( reader->GetOutput() );
+  findCenterFilter->SetAxis(2);
+  findCenterFilter->SetOtsuPercentileThreshold(0.01);
+  findCenterFilter->SetClosingSize(7);
+  findCenterFilter->SetHeadSizeLimit(700);
+  findCenterFilter->SetBackgroundValue(0);
+  findCenterFilter->Update();
+  ImagePointType centerOfHeadMass = findCenterFilter->GetCenterOfBrain();
+
+  // Find eye centers with BRAINS Hough Eye Detector
+  std::cout << "Finding eye centers..." << std::endl;
+  HoughEyeDetectorType::Pointer houghEyeDetector = HoughEyeDetectorType::New();
+  houghEyeDetector->SetInput( reader->GetOutput() );
+  houghEyeDetector->SetHoughEyeDetectorMode(1); // For T1 images
+  houghEyeDetector->SetCenterOfHeadMass(centerOfHeadMass);
+  houghEyeDetector->SetResultsDir(argv[3]);            // debug image write dir
+  houghEyeDetector->SetWritedebuggingImagesLevel(2);   // write ROI and
+                                                       // accumulator images
+  houghEyeDetector->Update();
+
+  ImagePointType leftEye   = houghEyeDetector->GetLE();
+  ImagePointType rightEye  = houghEyeDetector->GetRE();
+  ImagePointType alignedLE =
+    houghEyeDetector->GetInvVersorTransform()->TransformPoint(leftEye);
+  ImagePointType alignedRE =
+    houghEyeDetector->GetInvVersorTransform()->TransformPoint(rightEye);
+
+  std::cout << "Left eye = " << leftEye << std::endl;
+  std::cout << "Right eye = " << rightEye << std::endl;
+  std::cout << "Aligned left eye = " << alignedLE << std::endl;
+  std::cout << "Alinged right eye = " << alignedRE << std::endl;
+
+  // Write aligned image
+  WriterType::Pointer writer = WriterType::New();
+  writer->UseCompressionOn();
+  writer->SetFileName(argv[2]);
+  writer->SetInput( houghEyeDetector->GetOutput() );
+  try
+    {
+    writer->Update();
+    }
+  catch( itk::ExceptionObject & err )
+    {
+    std::cerr << " Error while writing image file(s) with ITK:\n "
+              << err << std::endl;
+    }
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml b/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml
new file mode 100644
index 00000000..a0a15c39
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml
@@ -0,0 +1,18 @@
+
+
+  BRAINSEyeDetector
+  
+  
+
+  1.0
+  http://www.nitrc.org/projects/brainscdetector/
+  
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+  
+
diff --git a/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.h b/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.h
new file mode 100644
index 00000000..0460e411
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.h
@@ -0,0 +1,254 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __BRAINSHoughEyeDetector_h
+#define __BRAINSHoughEyeDetector_h
+
+#ifdef _MSC_VER
+#pragma warning ( disable : 4786 )
+#endif
+
+#include "itkMultiThreader.h"
+
+#include "itkImageToImageFilter.h"
+#include "itkImage.h"
+#include "itkImageRegionIterator.h"
+#include "itkVersorRigid3DTransform.h"
+
+#include "itkHoughTransformRadialVotingImageFilter.h"
+#include "itkRescaleIntensityImageFilter.h"
+#include "itkImageFileWriter.h"
+
+#include "string.h"
+
+namespace itk
+{
+template 
+class ITK_EXPORT BRAINSHoughEyeDetector :
+  public ImageToImageFilter
+{
+public:
+
+  /** Standard ITK typedef */
+  typedef BRAINSHoughEyeDetector                        Self;
+  typedef ImageToImageFilter Superclass;
+  typedef SmartPointer                            Pointer;
+  typedef SmartPointer                      ConstPointer;
+
+  itkStaticConstMacro(Dimension, unsigned int, TInputImage::ImageDimension);
+
+  /** Input image typedef */
+  typedef typename TInputImage::Pointer         InputImagePointer;
+  typedef typename TInputImage::ConstPointer    InputImageConstPointer;
+  typedef typename TInputImage::IndexType       InputIndexType;
+  typedef typename TInputImage::PixelType       InputPixelType;
+  typedef typename TInputImage::SizeType        InputSizeType;
+  typedef typename TInputImage::RegionType      InputRegionType;
+  typedef typename TInputImage::SpacingType     InputSpacingType;
+  typedef typename TInputImage::PointType       InputPointType;
+  typedef typename TInputImage::DirectionType   InputDirectionType;
+  typedef ImageRegionConstIterator InputImageConstIterator;
+
+  /** Output image typedef */
+  typedef typename TOutputImage::Pointer    OutputImagePointer;
+  typedef typename TOutputImage::PixelType  OutputPixelType;
+  typedef typename TOutputImage::RegionType OutputImageRegionType;
+  typedef typename TOutputImage::PointType  OutputPointType;
+
+  typedef ImageRegionIterator          OutputImageIterator;
+  typedef ImageRegionIteratorWithIndex OutputImageIteratorWithIndex;
+
+  /* Transform and filter typedef */
+  typedef VersorRigid3DTransform                 VersorTransformType;
+  typedef typename VersorTransformType::OutputVectorType VersorVectorType;
+
+  typedef ImageFileWriter                                     WriterType;
+  typedef HoughTransformRadialVotingImageFilter HoughFilterType;
+  typedef typename HoughFilterType::SpheresListType                        SpheresListType;
+  typedef typename SpheresListType::const_iterator                         SphereIterator;
+  typedef typename HoughFilterType::Pointer                                HoughFilterPointer;
+
+  /** Run-time type information (and related methods) */
+  itkTypeMacro(BRAINSHoughEyeDetector, ImageToImageFilter);
+
+  /** Method for creation through the object factory */
+  itkNewMacro(Self);
+
+  /** Display */
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** Set/Get the number of circles to extract */
+  itkSetMacro(NumberOfSpheres, unsigned int);
+
+  /** Set the minimum radiu value the filter should look for */
+  itkSetMacro(MinimumRadius, double);
+
+  /** Set the maximum radius value the filter should look for */
+  itkSetMacro(MaximumRadius, double);
+
+  /** Set the scale of the derivative function (using DoG) */
+  itkSetMacro(SigmaGradient, double);
+
+  /** Set the variance of the gaussian bluring for the accumulator */
+  itkSetMacro(Variance, double);
+
+  /** Set the radius of the disc to remove from the accumulator
+   *  for each circle found */
+  itkSetMacro(SphereRadiusRatio, double);
+
+  /** Set the voting radius */
+  itkSetMacro(VotingRadiusRatio, double);
+
+  /** Set the threshold above which the filter should consider
+   the point as a valid point */
+  itkSetMacro(Threshold, double);
+
+  /** Set the threshold above which the filter should consider
+   the point as a valid point */
+  itkSetMacro(OutputThreshold, double);
+
+  /** Set the threshold above which the filter should consider
+   the point as a valid point */
+  itkSetMacro(GradientThreshold, double);
+
+  /** Set the number of threads */
+  itkSetMacro(NbOfThreads, unsigned int);
+
+  /** Set the number of threads */
+  itkSetMacro(SamplingRatio, double);
+
+  /** Set the mode of the algorithm
+   * HoughEyeDetectorMode = 0: Detecting bright spheres in a dark environment
+   * HoughEyeDetectorMode = 1: Detecting dark spheres in a bright environment */
+  itkSetMacro(HoughEyeDetectorMode, int);
+
+  /** Set the center of head mass of the image */
+  itkSetMacro(CenterOfHeadMass, InputPointType);
+
+  /** Set the interior radius of the shell-like RoI */
+  itkSetMacro(R1, double);
+
+  /** Set the exterior radius of the shell-like RoI */
+  itkSetMacro(R2, double);
+
+  /** Set the spread angle of the shell-like RoI */
+  itkSetMacro(Theta, double);
+
+  /** Get the left eye center coordinate */
+  itkGetMacro(LE, InputPointType);
+
+  /** Get the right eye center coordinate */
+  itkGetMacro(RE, InputPointType);
+
+  /** Set the debug output dir */
+  itkSetMacro(ResultsDir, std::string);
+
+  /** Set the write debug image level */
+  itkSetMacro(WritedebuggingImagesLevel, unsigned int);
+
+  /** Get the accumulator image */
+  itkGetObjectMacro(AccumulatorImage, TInputImage);
+
+  /** Get the RoI image */
+  itkGetObjectMacro(RoIImage, TInputImage);
+
+  /** Get the rotation angle of the alignment process */
+  itkGetMacro(RotAngle, InputPointType);
+
+  /** Get the adult interpupilary distance */
+  itkGetConstMacro(Ipd, double);
+
+  /** Get the maximum output pixel value */
+  itkGetConstMacro(MaxInputPixelValue, OutputPixelType);
+
+  /** Get the minimum output pixel value */
+  itkGetConstMacro(MinInputPixelValue, OutputPixelType);
+
+  /** Get the versor transform of the detector */
+  itkGetObjectMacro(VersorTransform, VersorTransformType);
+  itkGetObjectMacro(InvVersorTransform, VersorTransformType);
+
+  /** Get/Set the failure report */
+  itkGetConstMacro(Failure, bool);
+  itkSetMacro(Failure, bool);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( IntConvertibleToOutputCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( InputGreaterThanDoubleCheck,
+                   ( Concept::GreaterThanComparable ) );
+  itkConceptMacro( OutputPlusIntCheck,
+                   ( Concept::AdditiveOperators ) );
+  itkConceptMacro( OutputDividedByIntCheck,
+                   ( Concept::DivisionOperators ) );
+  /** End concept checking */
+#endif
+protected:
+
+  BRAINSHoughEyeDetector();
+
+  void GenerateData();
+
+  /** Input Parameters */
+  // Pass parameters from Hough Transform Radial Voting Filter
+  unsigned int   m_NumberOfSpheres;
+  double         m_MinimumRadius;
+  double         m_MaximumRadius;
+  double         m_SigmaGradient;
+  double         m_Variance;
+  double         m_SphereRadiusRatio;
+  double         m_VotingRadiusRatio;
+  double         m_Threshold;
+  double         m_OutputThreshold;
+  double         m_GradientThreshold;
+  unsigned int   m_NbOfThreads;
+  double         m_SamplingRatio;
+  int            m_HoughEyeDetectorMode;
+  InputPointType m_CenterOfHeadMass;
+
+  // Interior radius (mm), exterior radius (mm), and spread
+  // angle (rad) of the shell-like RoI.
+  double             m_R1;
+  double             m_R2;
+  double             m_Theta;
+  OutputImagePointer m_OutputImage;
+
+  // Debug settings
+  std::string  m_ResultsDir;
+  unsigned int m_WritedebuggingImagesLevel;
+
+  /** Output parameters */
+  OutputImagePointer m_AccumulatorImage;
+  OutputImagePointer m_RoIImage;
+  OutputPointType    m_LE;
+  OutputPointType    m_RE;
+  OutputPointType    m_RotAngle;
+  double             m_Ipd;     // adult interpupilary distance
+  bool               m_Failure; // indicating wether the detector realizes the
+                                // failure
+
+  OutputPixelType m_MaxInputPixelValue;
+  OutputPixelType m_MinInputPixelValue;
+
+  VersorTransformType::Pointer m_VersorTransform;
+  VersorTransformType::Pointer m_InvVersorTransform;
+private:
+
+  BRAINSHoughEyeDetector(const Self &)
+  {
+  }
+  void operator=(const Self &)
+  {
+  }
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "BRAINSHoughEyeDetector.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.txx b/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.txx
new file mode 100644
index 00000000..4139d86d
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSHoughEyeDetector.txx
@@ -0,0 +1,428 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "BRAINSHoughEyeDetector.h"
+
+namespace itk
+{
+template 
+BRAINSHoughEyeDetector
+::BRAINSHoughEyeDetector()
+{
+  /** Input Parameters */
+  // Note the default parameter set is designed for the IXI database
+  this->m_NumberOfSpheres     = 2;
+  this->m_MinimumRadius       = 11.;
+  this->m_MaximumRadius       = 13.;
+  this->m_SigmaGradient       = 1.;
+  this->m_Variance            = 1.;
+  this->m_SphereRadiusRatio   = 1.;
+  this->m_VotingRadiusRatio   = .5;
+  this->m_Threshold           = 10.;
+  this->m_OutputThreshold     = .8;
+  this->m_GradientThreshold   = 0.;
+  this->m_NbOfThreads         = 64;
+  this->m_SamplingRatio       = .2;
+  this->m_HoughEyeDetectorMode = 1;   // for T1-weighted image
+  this->m_R1                  = 30;
+  this->m_R2                  = 120;
+  this->m_Theta               = 1.04719755; // 120 degrees 0.785398163;   //
+                                            // spread angle = 90 deg
+  this->m_ResultsDir          = ".";
+  this->m_WritedebuggingImagesLevel = 0;
+
+  /** Output parameters */
+  this->m_AccumulatorImage    = TInputImage::New();
+  this->m_RoIImage            = TInputImage::New();
+  this->m_Ipd                 = 0;
+  this->m_MaxInputPixelValue  = 0;
+  this->m_MinInputPixelValue  = 0;
+  this->m_OutputImage         = TOutputImage::New();
+  this->m_Failure             = false;
+
+  /** Internal parameters */
+  this->m_VersorTransform     = VersorTransformType::New();
+  this->m_InvVersorTransform  = VersorTransformType::New();
+}
+
+template 
+void
+BRAINSHoughEyeDetector
+::GenerateData()
+{
+  const InputImageConstPointer image( this->GetInput() );
+  const InputRegionType        region = image->GetLargestPossibleRegion();
+  const InputSizeType          size = region.GetSize();
+    {
+    /*
+     * Set RoI of the input image
+     */
+    this->m_RoIImage->CopyInformation( image );
+    this->m_RoIImage->SetRegions( image->GetLargestPossibleRegion() );
+    this->m_RoIImage->Allocate();
+    this->m_RoIImage->FillBuffer( 0 );
+
+      {
+      // A unit vector pointing to the anterior direction
+      typename InputPointType::VectorType unitVectorAnterior;
+      unitVectorAnterior[0] = 0.;
+      unitVectorAnterior[1] = -1.;
+      unitVectorAnterior[2] = 0.;
+
+      if( ( this->m_R1 > 0 ) && ( this->m_R2 > this->m_R1 ) && ( this->m_Theta > 0 ) )
+        {
+        InputImageConstIterator It0( image, region );
+        It0.GoToBegin();
+        OutputImageIteratorWithIndex It1( this->m_RoIImage, region );
+        It1.GoToBegin();
+
+        while( ! ( It0.IsAtEnd() || It1.IsAtEnd() ) )
+          {
+          InputPointType currPt;
+          image->TransformIndexToPhysicalPoint( It1.GetIndex(), currPt );
+
+          // Center of head mass to current vector
+          const typename InputPointType::VectorType CMtoCurrVec = currPt - this->m_CenterOfHeadMass;
+
+          // posterior/anterior component of the vector
+          const float CMtoCurrPA = CMtoCurrVec * unitVectorAnterior;
+
+          // norm of CMtoCurrVec
+          const float CMtoCurrNorm = CMtoCurrVec.GetNorm();
+
+          // angle between current vector and unitVectorAnterior
+          const float currTheta = acos( CMtoCurrPA / CMtoCurrNorm );
+
+          if( ( CMtoCurrNorm > this->m_R1 ) &&
+              ( CMtoCurrNorm < this->m_R2 ) &&
+              ( currTheta < this->m_Theta ) )
+            {
+            It1.Set( It0.Get() );
+            }
+
+          // save max/min pixel value info
+          if( It0.Get() < this->m_MinInputPixelValue )
+            {
+            this->m_MinInputPixelValue = It0.Get();
+            }
+          else if( It0.Get() > this->m_MaxInputPixelValue )
+            {
+            this->m_MaxInputPixelValue = It0.Get();
+            }
+          ++It0;
+          ++It1;
+          }
+        }
+      }
+
+    /*
+     * Sphere detection with Hough transform radial voting filter
+     */
+    HoughFilterPointer houghFilter = HoughFilterType::New();
+    if( ( this->m_R1 > 0 ) && ( this->m_R2 > this->m_R1 ) && ( this->m_Theta > 0 ) )
+      {
+      houghFilter->SetInput( this->m_RoIImage );
+      }
+    else
+      {
+      std::cout << "Warning: RoI parameters are not valid"
+                << "Set to ( default ) entire image" << std::endl;
+      houghFilter->SetInput( image );
+      }
+    houghFilter->SetNumberOfSpheres( this->m_NumberOfSpheres );
+    houghFilter->SetMinimumRadius( this->m_MinimumRadius );
+    houghFilter->SetMaximumRadius( this->m_MaximumRadius );
+    houghFilter->SetSigmaGradient( this->m_SigmaGradient );
+    houghFilter->SetVariance( this->m_Variance );
+    houghFilter->SetSphereRadiusRatio( this->m_SphereRadiusRatio );
+    houghFilter->SetVotingRadiusRatio( this->m_VotingRadiusRatio );
+    houghFilter->SetThreshold( this->m_Threshold );
+    houghFilter->SetOutputThreshold( this->m_OutputThreshold );
+    houghFilter->SetGradientThreshold( this->m_GradientThreshold );
+    houghFilter->SetNbOfThreads( this->m_NbOfThreads );
+    houghFilter->SetSamplingRatio( this->m_SamplingRatio );
+    houghFilter->SetHoughEyeDetectorMode( this->m_HoughEyeDetectorMode );
+    try
+      {
+    houghFilter->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Failed houghFilter " << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    catch(...)
+      {
+      std::cout << "Failed on houghFilter exception occured" << std::endl;
+      }
+    this->m_AccumulatorImage = houghFilter->GetOutput();
+
+    /*
+     * Write debug image
+     */
+    if( this->m_WritedebuggingImagesLevel > 1 )
+      {
+        {
+        // Write debug ROI image
+        typename WriterType::Pointer writer = WriterType::New();
+        writer->SetFileName( this->m_ResultsDir + "/HoughEyeROI.nii.gz" );
+        writer->SetInput( this->m_RoIImage );
+        writer->SetUseCompression( true );
+        try
+          {
+          writer->Update();
+          }
+        catch( itk::ExceptionObject & excep )
+          {
+          std::cerr << "Cannot write the ROI image!" << std::endl;
+          std::cerr << excep << std::endl;
+          }
+        }
+
+        {
+        // Write debug accumulator image
+        typename WriterType::Pointer writer = WriterType::New();
+        writer->SetFileName( this->m_ResultsDir + "/HoughEyeAccumulator.nii.gz" );
+        writer->SetInput( this->m_AccumulatorImage );
+        writer->SetUseCompression( true );
+        try
+          {
+          writer->Update();
+          }
+        catch( itk::ExceptionObject & excep )
+          {
+          std::cerr << "Cannot write the ROI image!" << std::endl;
+          std::cerr << excep << std::endl;
+          }
+        }
+      }
+
+    /*
+     * Computing eye centers by finding the points with highest
+     * accumulated PDF
+     */
+    // Get some basic information of the image
+
+    const SpheresListType spheres = houghFilter->GetSpheres();
+    if( spheres.size() < 2 )
+      {
+      std::cerr << "Error: The number of detected spheres is less than 2!" << std::endl;
+      std::cerr << "The program will continue to run for generating some debug output for GUI corrector." << std::endl;
+      std::cerr << "Make sure you set the debug level > 4." << std::endl;
+      this->m_Failure = true;
+      return;
+      }
+
+    InputIndexType indexEye1;
+    SphereIterator itSpheres = spheres.begin();
+    for( unsigned int i = 0; i < Dimension; ++i )
+      {
+      indexEye1[i] = static_cast( ( *itSpheres )->GetObjectToParentTransform()->GetOffset()[i] );
+      }
+
+    ++itSpheres;
+
+    InputIndexType indexEye2;
+    for( unsigned int i = 0; i < Dimension; ++i )
+      {
+      indexEye2[i] = static_cast( ( *itSpheres )->GetObjectToParentTransform()->GetOffset()[i] );
+      }
+
+    InputPointType physicalEye1;
+    InputPointType physicalEye2;
+      {
+      image->TransformIndexToPhysicalPoint( indexEye1, physicalEye1 );
+      image->TransformIndexToPhysicalPoint( indexEye2, physicalEye2 );
+      }
+
+    // We will determine the left and right of the eyes
+    // Assuming that the degradation of the image does not
+    // change their relative positions.
+    unsigned int eye1OnLeft = 1;            // eye1 is on left = 1/right = 0
+    if( physicalEye1[0] > physicalEye2[0] ) // eye1 is on the left
+      {
+      eye1OnLeft = 1;
+      for( unsigned int i = 0; i < Dimension; ++i )
+        {
+        this->m_LE[i] = physicalEye1[i];
+        this->m_RE[i] = physicalEye2[i];
+        }
+      }
+    else
+      {
+      eye1OnLeft = 0;
+      for( unsigned int i = 0; i < Dimension; ++i )
+        {
+        this->m_LE[i] = physicalEye2[i];   // eye2 is on the left
+        this->m_RE[i] = physicalEye1[i];
+        }
+      }
+
+    /*
+     * Metrics Collection
+     */
+    // Metric 1: Adult Interpupillary Distance ( IPD )
+    // Mean: 63mm
+    // Most likely: 50mm - 75mm
+    this->m_Ipd = 0.;
+    for( unsigned int i = 0; i < Dimension; ++i )
+      {
+      this->m_Ipd += vnl_math_sqr( this->m_LE[i] - this->m_RE[i] );
+      }
+    this->m_Ipd = vcl_sqrt( this->m_Ipd );
+    std::cout << "The resulted interpupilary distance is " << this->m_Ipd << " mm" << std::endl;
+
+    if( this->m_Ipd < 40 or this->m_Ipd > 85 )
+      {
+      std::cerr << "WARNING: The distance is abnormal! Get ready to use a GUI corrector next." << std::endl;
+      this->m_Failure = true;
+      return;
+      }
+
+    /*
+     * Align the image with eye centers
+     */
+
+    // Compute translation
+    InputPointType physicalStartLocation;
+    InputPointType physicalStopLocation;
+      {
+      InputIndexType startIndex = region.GetIndex();
+      InputIndexType stopIndex;
+      stopIndex[0] = startIndex[0] + size[0] - 1;
+      stopIndex[1] = startIndex[1] + size[1] - 1;
+      stopIndex[2] = startIndex[2] + size[2] - 1;
+      image->TransformIndexToPhysicalPoint( startIndex, physicalStartLocation );
+      image->TransformIndexToPhysicalPoint( stopIndex, physicalStopLocation );
+      }
+
+    // Compute the bound of image
+    double bound[6];
+    bound[0] =
+      physicalStartLocation[0] < physicalStopLocation[0] ?
+      physicalStartLocation[0] : physicalStopLocation[0];
+    bound[1] =
+      physicalStartLocation[0] >= physicalStopLocation[0] ?
+      physicalStartLocation[0] : physicalStopLocation[0];
+    bound[2] =
+      physicalStartLocation[1] < physicalStopLocation[1] ?
+      physicalStartLocation[1] : physicalStopLocation[1];
+    bound[3] =
+      physicalStartLocation[1] >= physicalStopLocation[1] ?
+      physicalStartLocation[1] : physicalStopLocation[1];
+    bound[4] =
+      physicalStartLocation[2] < physicalStopLocation[2] ?
+      physicalStartLocation[2] : physicalStopLocation[2];
+    bound[5] =
+      physicalStartLocation[2] >= physicalStopLocation[2] ?
+      physicalStartLocation[2] : physicalStopLocation[2];
+
+    // Space coordinate origin -> center of eye centers of input image
+    VersorVectorType translation1;
+    /** Center the image at a place close to the AC point.
+     Here we use an approximation which is vertically at an IPD distance from center
+     of eye centers, i.e., the center is at ( 0, -IPD, 0 ) in LPS coordinate system */
+    VersorVectorType translation2;
+    for( unsigned int i = 0; i < Dimension; ++i )
+      {
+      translation1[i] = 0.5 * ( this->m_LE[i]
+                                + this->m_RE[i] );
+      translation2[i] = 0;
+      }
+    translation2[1] = this->m_Ipd;
+
+    // Compute rotation in radian
+    // about +S-axis
+    VersorVectorType rotation1;   // about +S-axis
+    rotation1[0] = 0;
+    rotation1[1] = 0;
+    rotation1[2] = 1;
+
+    // about +P-axis
+    VersorVectorType rotation2;   // about +P-axis
+    rotation2[0] = 0;
+    rotation2[1] = 1;
+    rotation2[2] = 0;
+
+    // Note: this algorithm doesn't treat rotations about +L-axis
+    this->m_RotAngle[0] = 0;
+
+    // about +P-axis
+    this->m_RotAngle[1] = vcl_atan( ( this->m_LE[2] - this->m_RE[2] )
+                                    / ( this->m_LE[0] - this->m_RE[0] ) );
+    // about +S-axis
+    this->m_RotAngle[2] = -vcl_atan( ( this->m_LE[1] - this->m_RE[1] )
+                                     / ( this->m_LE[0] - this->m_RE[0] ) );
+
+    // Set affine tranformation
+    this->m_VersorTransform->Translate( translation2 );
+    this->m_VersorTransform->SetRotation( rotation1, -this->m_RotAngle[2] );
+    this->m_VersorTransform->SetRotation( rotation2, -this->m_RotAngle[1] );
+    this->m_VersorTransform->Translate( translation1 );
+
+    // Get the inverse transform
+    if( !this->m_VersorTransform->GetInverse( this->m_InvVersorTransform ) )
+      {
+      std::cerr << "Cannot get the inverse transform from Hough eye detector!" << std::endl;
+      exit( -1 );
+      }
+
+    /** The output image will have exact the same index contents
+     but with modified image info so that the index-to-physical mapping
+     makes the image in the physical space aligned */
+    this->m_OutputImage->CopyInformation( image );
+    this->m_OutputImage->SetRegions( region );
+
+    this->m_OutputImage->SetOrigin( this->m_InvVersorTransform->GetMatrix()
+                                    * image->GetOrigin() + this->m_InvVersorTransform->GetTranslation() );
+
+    this->m_OutputImage->SetDirection( this->m_InvVersorTransform->GetMatrix()
+                                       * image->GetDirection() );
+
+    this->m_OutputImage->Allocate();
+
+      {
+      InputImageConstIterator It0( image, region );
+      It0.GoToBegin();
+      OutputImageIterator It1( this->m_OutputImage, region );
+      It1.GoToBegin();
+      while( !It0.IsAtEnd()  && !It1.IsAtEnd() )
+        {
+        It1.Set( It0.Get() );
+        ++It0;
+        ++It1;
+        }
+      }
+    this->GraftOutput( this->m_OutputImage );
+    }
+}
+
+template 
+void
+BRAINSHoughEyeDetector
+::PrintSelf( std::ostream & os, Indent indent ) const
+{
+  Superclass::PrintSelf( os, indent );
+
+  os << "HoughEyeDetectorMode: " << this->m_HoughEyeDetectorMode << std::endl;
+  os << "Number Of Spheres: " << this->m_NumberOfSpheres << std::endl;
+  os << "Minimum Radius:  " << this->m_MinimumRadius << std::endl;
+  os << "Maximum Radius: " << this->m_MaximumRadius << std::endl;
+  os << "Derivative Scale : " << this->m_SigmaGradient << std::endl;
+  os << "Accumulator Blur Variance: " << this->m_Variance << std::endl;
+  os << "Sphere Radius Ratio: " << this->m_SphereRadiusRatio << std::endl;
+  os << "Voting Radius Ratio: " << this->m_VotingRadiusRatio << std::endl;
+  os << "Threshold: " << this->m_Threshold << std::endl;
+  os << "Output Threshold : " << this->m_OutputThreshold << std::endl;
+  os << "Gradient Threshold: " << this->m_GradientThreshold << std::endl;
+  os << "NbOfThreads: " << this->m_NbOfThreads << std::endl;
+  os << "Sampling Ratio: " << this->m_SamplingRatio << std::endl;
+  os << "Interior Radius of RoI: " << this->m_R1 << std::endl;
+  os << "Exterior Radius of RoI: " << this->m_R2 << std::endl;
+  os << "Spread Angle of RoI: " << this->m_Theta << std::endl;
+}
+
+}
diff --git a/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.cxx b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.cxx
new file mode 100644
index 00000000..af85e68c
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.cxx
@@ -0,0 +1,299 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab, University of Iowa Health Care, 2010
+ */
+
+#include "BRAINSLinearModelerEPCA.h"
+#include "BRAINSLinearModelerEPCACLP.h"
+#include "BRAINSThreadControl.h"
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+int main( int argc, char * argv[] )
+{
+  PARSE_ARGS;
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+  LmkDBType baseLmkDB;     // in the format of [landmarkID][datasetID]
+  LmkDBType EPCALmkDB;
+  CreateLmkDB( inputTrainingList, baseLmkDB, EPCALmkDB );
+
+  MatrixMapType MMatrixMap; // Principal components of landmark vector
+                            // space in each iteration
+  VectorMapType SVectorMap; // s vectors in each iteration
+  ComputeEPCAModel( MMatrixMap, SVectorMap, baseLmkDB, EPCALmkDB );
+
+  // Write model to Matlab binary file
+
+  return EXIT_SUCCESS;
+}
+
+void
+CreateLmkDB( std::string filename, LmkDBType & baseLmkDB, LmkDBType & EPCALmkDB )
+{
+  // Read in list of landmark list file
+  std::ifstream myfile( filename.c_str() );
+
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Cannot open training landmark list file!" << std::endl;
+    exit(-1);
+    }
+
+  // for each file enlisted on the list of landmark list file
+  std::string line;
+  while( getline( myfile, line ) )
+    {
+    // for each landmark in the landmark list file
+    LandmarksMapType                 lmkMap = ReadSlicer3toITKLmk( line );
+    LandmarksMapType::const_iterator itLmk = lmkMap.begin();
+    while( itLmk != lmkMap.end() )
+      {
+      std::string name = itLmk->first;
+      // Save base landmarks
+      if( ( name.compare( "AC" ) == 0 ) ||
+          ( name.compare( "PC" ) == 0 ) ||
+          ( name.compare( "RP" ) == 0 ) ||
+          ( name.compare( "VN4" ) == 0 ) ||
+          ( name.compare( "LE" ) == 0 ) ||
+          ( name.compare( "RE" ) == 0 ) )
+        {
+        baseLmkDB[name][line] = itLmk->second;
+        }
+      else
+        {
+        EPCALmkDB[name][line] = itLmk->second;
+        }
+      ++itLmk;
+      }
+    }
+
+  // Sanity check
+  // Check if the number of landmarks are the same in each landmark list file
+  // First check for number of base landmarks
+    {
+    LmkDBType::const_iterator itDB = baseLmkDB.begin();
+    unsigned int              numLmks = itDB->second.size();
+    while( itDB != baseLmkDB.end() )
+      {
+      if( itDB->second.size() != numLmks )
+        {
+        std::cerr << "Error: number of landmark \"" << itDB->first
+                  << "\" in training list files mismatched!" << std::endl;
+        exit( -1 );
+        }
+      ++itDB;
+      }
+    }
+
+  // Then check for the number of EPCA landmarks
+    {
+    LmkDBType::const_iterator itDB = EPCALmkDB.begin();
+    unsigned int              numLmks = itDB->second.size();
+    while( itDB != EPCALmkDB.end() )
+      {
+      if( itDB->second.size() != numLmks )
+        {
+        std::cerr << "Error: number of landmark \"" << itDB->first
+                  << "\" in training list files mismatched!" << std::endl;
+        exit( -1 );
+        }
+      ++itDB;
+      }
+    }
+}
+
+MatrixType
+InitializeXi( LmkDBType & baseLmkDB )
+{
+  const unsigned int numBaseLmks( baseLmkDB.size() );
+  const unsigned int numDatasets( baseLmkDB.begin()->second.size() );
+
+  MatrixType X_i;
+
+  X_i.set_size( ( numBaseLmks - 1 ) * PointDim, numDatasets );
+
+  // Assert RP (MPJ) exists
+  if( baseLmkDB.find( "RP" ) == baseLmkDB.end() )
+    {
+    std::cerr << "Error: RP (MPJ) landmark is missing!" << std::endl;
+    exit( -1 );
+    }
+
+  // for each base landmark
+  unsigned int              k = 0; // landmark index
+  LmkDBType::const_iterator itDB = baseLmkDB.begin();
+  while( itDB != baseLmkDB.end() )
+    {
+    if( itDB->first.compare( "RP" ) != 0 )
+      {
+      unsigned int                     j = 0; // dataset index
+      DatasetMapType                   datasetMap = itDB->second;
+      LandmarksMapType::const_iterator itDataset = datasetMap.begin();
+      while( itDataset != datasetMap.end() )
+        {
+        std::string     datasetId = itDataset->first;
+        const PointType lmkRP( baseLmkDB["RP"][datasetId] );
+        for( unsigned int dim = 0; dim < PointDim; ++dim )
+          {
+          X_i( k * PointDim + dim, j ) = itDataset->second[dim] - lmkRP[dim];
+          }
+        ++j;
+        ++itDataset;
+        }
+
+      ++k;
+      }
+    ++itDB;
+    }
+
+  return X_i;
+}
+
+void
+ComputeEPCAModel( MatrixMapType & MMatrixMap, VectorMapType & SVectorMap,
+                  LmkDBType & baseLmkDB, LmkDBType & EPCALmkDB )
+{
+  // Deliberately add the following line to eliminate the "unused warning"
+  MatrixType bogusMMatrix;
+
+  MMatrixMap["bogus M_i matrix"] = bogusMMatrix;
+
+  // Initialize the landmark vector space X_i matrix
+  MatrixType X_i = InitializeXi( baseLmkDB );
+
+  // Evolutionarily construct X_i, compute s_i, W_i, and M_i in each iteration
+  LmkDBType::const_iterator itDB = EPCALmkDB.begin();
+  unsigned int              k = 0; // landmark index
+  // while ( itDB != EPCALmkDB.end() - 1 ) // NO end() - 1 in map iterator?
+  const unsigned int numEPCALmks = EPCALmkDB.size();
+  while( k < numEPCALmks )
+    {
+
+    // Update X_i
+    if( k > 0 )
+      {
+      MatrixType X_iLast( X_i );
+      X_i.set_size(X_iLast.rows() + PointDim, X_iLast.columns() );
+      for( unsigned int row = 0; row < X_iLast.rows(); ++row )
+        {
+        X_i.set_row( row, X_iLast.get_row( row ) );
+        }
+
+      const unsigned int               numBaseLmks( baseLmkDB.size() );
+      unsigned int                     j = 0; // dataset index
+      DatasetMapType                   datasetMap = itDB->second;
+      LandmarksMapType::const_iterator itDataset = datasetMap.begin();
+      while( itDataset != datasetMap.end() )
+        {
+        std::string     datasetId = itDataset->first;
+        const PointType lmkRP( baseLmkDB["RP"][datasetId] );
+        for( unsigned int dim = 0; dim < PointDim; ++dim )
+          {
+          X_i( ( numBaseLmks + k - 2 ) * PointDim + dim, j ) = itDataset->second[dim] - lmkRP[dim];
+          }
+        ++j;
+        ++itDataset;
+        }
+      }
+
+    // Compute si
+    VectorType s_i( ComputeSVector( X_i ) );
+    SVectorMap[EPCALmkDB.begin()->first] = s_i;
+
+    // remove I_si of X_i
+    MatrixType I_si( ComputeIsiMatrix( X_i.rows(), X_i.columns(), s_i ) );
+
+    MatrixType X_i0Mean = X_i - I_si;
+
+    // Compute W_i
+    MatrixType         W_i; // principal components/eigenvectors of X_i*X_i'
+    vnl_vector D;   // eigenvalue of X_i*X_i'
+    if( !vnl_symmetric_eigensystem_compute(X_i0Mean * X_i0Mean.transpose(), W_i, D) )
+      {
+      std::cerr << "Error: vnl_symmetric_eigensystem_compute failed." << std::endl;
+      exit( -1 );
+      }
+
+    // TODO -------------------------------------------------------
+
+    // Compute W_ri
+
+    // Construct Y_i
+
+    // Compute C_opt
+
+    // Compute and save M_i
+
+    // DEBUG
+    // std::cout << "X_i( i = " << k << " ) = \n" << X_i << std::endl;
+    // std::cout << "I_si = \n" << I_si << std::endl;
+    // std::cout << "s_i( i = " << k << " ) = " << s_i << std::endl;
+    // std::cout << "X_i0Mean( i = " << k << " ) = \n" << X_i0Mean << std::endl;
+    // std::cout << "D( i = " << k << " ) = \n" << D << std::endl;
+    std::cout << "W_i( i = " << k << " ) = \n" << W_i << std::endl;
+
+    if( k++ > 0 )
+      {
+      ++itDB;
+      }
+    }
+}
+
+VectorType
+ComputeSVector( const MatrixType & X_i )
+{
+  const unsigned int numDataset( X_i.columns() );
+
+  // Sanity check for X_i
+  if( X_i.rows() % PointDim != 0 )
+    {
+    std::cerr << "Error: Bad X_i!" << std::endl;
+    exit( -1 );
+    }
+  const unsigned int numLmks( X_i.rows() / PointDim );
+  VectorType         s_i;
+  s_i.fill( 0 );
+  for( unsigned int dim = 0; dim < PointDim; ++dim )
+    {
+    for( unsigned int j = 0; j < numDataset; ++j )
+      {
+      for( unsigned int k = 0; k < numLmks; ++k )
+        {
+        s_i[dim] += X_i( k * PointDim + dim, j );
+        }
+      }
+    s_i[dim] /= numDataset * numLmks;
+    }
+  return s_i;
+}
+
+MatrixType
+ComputeIsiMatrix( const unsigned int rows, const unsigned int columns, const VectorType s_i )
+{
+  const unsigned int numDataset( columns );
+
+  // Sanity check for X_i
+  if( rows % PointDim != 0 )
+    {
+    std::cerr << "Error: Bad X_i!" << std::endl;
+    exit( -1 );
+    }
+  const unsigned int numLmks( rows / PointDim );
+
+  MatrixType I_si;
+  I_si.set_size( rows, columns );
+  for( unsigned int j = 0; j < numDataset; ++j )
+    {
+    for( unsigned int k = 0; k < numLmks; ++k )
+      {
+      for( unsigned int dim = 0; dim < PointDim; ++dim )
+        {
+        I_si( k * PointDim + dim, j ) = s_i[dim];
+        }
+      }
+    }
+  return I_si;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.h b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.h
new file mode 100644
index 00000000..c575feec
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.h
@@ -0,0 +1,61 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab, University of Iowa Health Care, 2010
+ */
+
+#ifndef __BRAINSLinearModelerEPCA__h
+#define __BRAINSLinearModelerEPCA__h
+
+#include "Slicer3LandmarkIO.h"
+#include "itkPoint.h"
+#include "vnl/vnl_matrix.h"
+#include "vnl/vnl_vector_fixed.h"
+#include "vnl/algo/vnl_symmetric_eigensystem.h"
+#include 
+#include 
+#include 
+
+// typedef
+const unsigned int PointDim = 3;
+typedef itk::Point          PointType;
+typedef std::map      LandmarksMapType;
+typedef std::map      DatasetMapType;
+typedef std::map LmkDBType;
+typedef vnl_matrix                    MatrixType;
+typedef vnl_vector_fixed    VectorType;
+typedef std::map     MatrixMapType;
+typedef std::map     VectorMapType;
+
+/*
+ * Build up the landmark database from a list of fcsv files
+ * TODO: Explain each argument in the func
+ * Input:
+ * filename ...
+ */
+void CreateLmkDB( std::string filename, LmkDBType & baseLmkDB, LmkDBType & EPCALmkDB );
+
+/*
+ * Initialize X_i matrix from base landmarks
+ */
+MatrixType InitializeXi( LmkDBType & baseLmkDB );
+
+/*
+ * Compute the principal components of landmark vector space
+ * in each iteration
+ * TODO: Explain each argument in the func
+ * Input:
+ */
+void ComputeEPCAModel( MatrixMapType & MMatrixMap, VectorMapType & SVectorMap, LmkDBType & baseLmkDB,
+                       LmkDBType & EPCALmkDB );
+
+/*
+ * Compute the s_i vector from X_i matrix
+ */
+VectorType ComputeSVector( const MatrixType & X_i );
+
+/*
+ * Compute the I_si matrix from X_i and s_i
+ */
+MatrixType ComputeIsiMatrix( const unsigned int rows, const unsigned int columns, const VectorType s_i );
+
+#endif
diff --git a/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml
new file mode 100644
index 00000000..8d81651a
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml
@@ -0,0 +1,29 @@
+
+
+    BRAINSLmkTransform
+    
+      Training linear model using EPCA. Implementation based on my MS thesis, "A METHOD FOR AUTOMATED LANDMARK CONSTELLATION DETECTION USING EVOLUTIONARY PRINCIPAL COMPONENTS AND STATISTICAL SHAPE MODELS"
+
+    
+
+    1.0
+    http://www.nitrc.org/projects/brainscdetector/
+    
+        
+            inputTrainingList
+            
+            
+            inputTrainingList
+            Input Training Landmark List Filename
+            
+            input
+        
+        
+          numberOfThreads
+          numberOfThreads
+          
+          Explicitly specify the maximum number of threads to use.
+          -1
+        
+    
+
diff --git a/BRAINSConstellationDetector/src/BRAINSLmkTransform.cxx b/BRAINSConstellationDetector/src/BRAINSLmkTransform.cxx
new file mode 100644
index 00000000..e094d1f5
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSLmkTransform.cxx
@@ -0,0 +1,280 @@
+/*
+ * Author: Wei Lu
+ * at Psychiatry Imaging Lab, University of Iowa Health Care, 2010
+ */
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#include "itkImage.h"
+#include "itkPoint.h"
+#include "itkPointSet.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkResampleImageFilter.h"
+#include "itkAffineTransform.h"
+#include "itkTransformFileWriter.h"
+#include "itkLinearInterpolateImageFunction.h"
+#include "BRAINSThreadControl.h"
+
+// Use modified itkKernelTransform to get affine transform
+#include "itkKernelTransform.h"
+#include "itkThinPlateSplineKernelTransform.h"
+
+template 
+class BCDThinPlateSplineKernelTransform :
+  public itk::ThinPlateSplineKernelTransform
+{
+public:
+  /** Standard class typedefs. */
+  typedef BCDThinPlateSplineKernelTransform Self;
+  typedef itk::ThinPlateSplineKernelTransform Superclass;
+  typedef itk::SmartPointer       Pointer;
+  typedef itk::SmartPointer ConstPointer;
+
+  /** New macro for creation of through a Smart Pointer */
+  itkNewMacro(Self);
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(BCDThinPlateSplineKernelTransform,
+               ThinPlateSplineKernelTransform);
+  typename Superclass::Superclass::AMatrixType GetAMatrix()
+  {
+    return this->Superclass::Superclass::m_AMatrix;
+  }
+  typename Superclass::Superclass::BMatrixType GetBVector()
+  {
+    return this->Superclass::Superclass::m_BVector;
+  }
+};
+
+#include "BRAINSLmkTransformCLP.h"
+
+#include 
+#include 
+#include 
+
+/*
+ * Description:
+ *
+ * This utility program estimates the affine transform to align the fixed landmarks
+ * to the moving landmarks, and then generate the resampled moving image to the same
+ * physical space as that of the reference image
+ */
+
+const   unsigned int ImageDimension = 3;
+typedef short                                 PixelType;
+typedef itk::Image ImageType;
+typedef std::vector     LandmarksVectorType;
+
+LandmarksVectorType LoadLandmarks( std::string filename );
+
+int main( int argc, char * argv[] )
+{
+  PARSE_ARGS;
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+  if( ( inputMovingLandmarks.compare( "" ) == 0 )
+      && ( inputFixedLandmarks.compare( "" ) == 0 )
+      && ( inputMovingVolume.compare( "" ) == 0 )
+      && ( inputReferenceVolume.compare( "" ) == 0 ) )
+    {
+    std::cerr << "Please set inputMovingLandmarks, inputFixedLandmarks, "
+              << "inputMovingVolume, and inputReferenceVolume." << std::endl;
+    exit( -1 );
+    }
+
+  // typedefs
+  typedef double CoordinateRepType;
+  typedef itk::Point<
+    CoordinateRepType, ImageDimension>           PointType;
+  typedef std::vector          PointArrayType;
+  typedef itk::ImageFileReader ImageReaderType;
+  typedef itk::ImageFileWriter ImageWriterType;
+  typedef BCDThinPlateSplineKernelTransform<
+    CoordinateRepType, ImageDimension>           TPSTransformType;
+  typedef itk::AffineTransform<
+    CoordinateRepType, ImageDimension>           AffineTransformType;
+  typedef TPSTransformType::PointSetType PointSetType;
+  typedef itk::TransformFileWriter       TransformWriterType;
+  typedef PointSetType::Pointer          PointSetPointer;
+  typedef PointSetType::PointIdentifier  PointIdType;
+  typedef itk::ResampleImageFilter<
+    ImageType, ImageType>                       ResamplerType;
+  typedef itk::LinearInterpolateImageFunction<
+    ImageType, double>                           InterpolatorType;
+
+  // Read in landmarks
+  PointSetType::Pointer sourceLandmarks = PointSetType::New();
+  PointSetType::Pointer targetLandmarks = PointSetType::New();
+    {
+    PointSetType::PointsContainer::Pointer sourceLandmarkContainer =
+      sourceLandmarks->GetPoints();
+    PointSetType::PointsContainer::Pointer targetLandmarkContainer =
+      targetLandmarks->GetPoints();
+    PointIdType         id = itk::NumericTraits::Zero;
+    LandmarksVectorType targetLandmarksVec = LoadLandmarks( inputMovingLandmarks );
+    LandmarksVectorType sourceLandmarksVec = LoadLandmarks( inputFixedLandmarks );
+
+    // Sanity check
+    if( targetLandmarksVec.size() != sourceLandmarksVec.size() )
+      {
+      std::cerr << "Different number of fixed and moving landmarks!" << std::endl;
+      return EXIT_FAILURE;
+      }
+
+    unsigned int idx = 0;
+    for( idx = 0; idx < sourceLandmarksVec.size(); ++idx )
+      {
+      sourceLandmarkContainer->InsertElement( id, sourceLandmarksVec[idx] );
+      targetLandmarkContainer->InsertElement( id++, targetLandmarksVec[idx] );
+      }
+    }
+
+  // Estimate affine transform
+  AffineTransformType::Pointer affine = AffineTransformType::New();
+    {
+    TPSTransformType::Pointer tps = TPSTransformType::New();
+    tps->SetSourceLandmarks( sourceLandmarks );
+    tps->SetTargetLandmarks( targetLandmarks );
+    tps->ComputeWMatrix();
+    itk::Matrix aMatrix( tps->GetAMatrix() );
+    itk::Vector                 bVector;
+    bVector.SetVnlVector( tps->GetBVector() );
+    itk::Matrix identity;
+    identity.SetIdentity();
+    affine->SetMatrix( aMatrix + identity );
+    affine->SetOffset( bVector );
+    }
+
+  // Write output aligning transform
+  if( outputAffineTransform.compare( "" ) != 0 )
+    {
+    TransformWriterType::Pointer writer = TransformWriterType::New();
+    writer->SetInput( affine );
+    writer->SetFileName( outputAffineTransform );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excep )
+      {
+      std::cerr << "Cannot write the outputTransform file!" << std::endl;
+      std::cerr << excep << std::endl;
+      }
+    }
+
+  // Read in images
+  ImageType::Pointer movingImage;
+    {
+    ImageReaderType::Pointer reader = ImageReaderType::New();
+    reader->SetFileName( inputMovingVolume );
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+      std::cerr << "Exception thrown " << std::endl;
+      std::cerr << excp << std::endl;
+      return EXIT_FAILURE;
+      }
+    movingImage = reader->GetOutput();
+    }
+
+  ImageType::Pointer referenceImage;
+    {
+    ImageReaderType::Pointer reader = ImageReaderType::New();
+    reader->SetFileName( inputReferenceVolume );
+    try
+      {
+      reader->Update();
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+      std::cerr << "Exception thrown " << std::endl;
+      std::cerr << excp << std::endl;
+      return EXIT_FAILURE;
+      }
+    referenceImage = reader->GetOutput();
+    }
+
+  // Resample moving image
+  ResamplerType::Pointer resampler = ResamplerType::New();
+    {
+    InterpolatorType::Pointer interpolator  = InterpolatorType::New();
+    resampler->SetUseReferenceImage( true );
+    resampler->SetInput( movingImage );
+    resampler->SetReferenceImage( referenceImage );
+    resampler->SetInterpolator( interpolator );
+    resampler->SetTransform( affine );
+    }
+
+  // Write aligned image
+  if( outputResampledVolume.compare( "" ) != 0 )
+    {
+    ImageWriterType::Pointer writer = ImageWriterType::New();
+    writer->SetInput( resampler->GetOutput() );
+    writer->SetFileName( outputResampledVolume );
+    writer->SetUseCompression( true );
+    try
+      {
+      writer->Update();
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+      std::cerr << "Exception thrown " << std::endl;
+      std::cerr << excp << std::endl;
+      return EXIT_FAILURE;
+      }
+    }
+
+  return EXIT_SUCCESS;
+}
+
+LandmarksVectorType
+LoadLandmarks( std::string filename )
+{
+  LandmarksVectorType landmarks;
+  std::string         line;
+  std::ifstream       myfile( filename.c_str() );
+
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Fatal error: Failed to load landmarks file. Program abort!" << std::endl;
+    exit( -1 );
+    }
+  while( getline(myfile, line) )
+    {
+    if( line.compare(0, 1, "#") != 0 )
+      {
+      unsigned int i;
+      int          pos1 = line.find(',', 0);
+      int          pos2;
+      std::string  name = line.substr(0, pos1);
+      if( name.compare("CM") == 0 )  // exclude CM
+        {
+        continue;
+        }
+      ImageType::PointType labelPos;
+      for( i = 0; i < 3; ++i )
+        {
+        pos2 = line.find(',', pos1 + 1);
+        labelPos[i] = atof( line.substr( pos1 + 1, pos2 - pos1 - 1 ).c_str() );
+        if( i < 2 )
+          {
+          labelPos[i] *= -1; // RAS -> LPS
+          }
+        pos1 = pos2;
+        }
+      landmarks.push_back( labelPos );
+      }
+    }
+
+  myfile.close();
+  return landmarks;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml b/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml
new file mode 100644
index 00000000..f2e776ee
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml
@@ -0,0 +1,70 @@
+
+
+    BRAINSLmkTransform
+    
+      This utility program estimates the affine transform to align the fixed landmarks to the moving landmarks, and then generate the resampled moving image to the same physical space as that of the reference image.
+    
+
+    1.0
+    http://www.nitrc.org/projects/brainscdetector/
+    
+        
+            inputMovingLandmarks
+            
+            
+            inputMovingLandmarks
+            Input Moving Landmark list file in fcsv
+            
+            input
+        
+        
+            inputFixedLandmarks
+            
+            
+            inputFixedLandmarks
+            Input Fixed Landmark list file in fcsv
+            
+            input
+        
+        
+            outputAffineTransform
+            
+            
+            outputAffineTransform
+            The filename for the estimated affine transform
+            
+            output
+        
+        
+            inputMovingVolume
+            inputMovingVolume
+            
+            The filename of input moving volume
+            input
+            
+        
+        
+            inputReferenceVolume
+            inputReferenceVolume
+            
+            The filename of the reference volume
+            input
+            
+        
+        
+            outputResampledVolume
+            outputResampledVolume
+            
+            The filename of the output resampled volume
+            output
+            
+        
+        
+          numberOfThreads
+          numberOfThreads
+          
+          Explicitly specify the maximum number of threads to use.
+          -1
+        
+    
+
diff --git a/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.cxx b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.cxx
new file mode 100644
index 00000000..9ff94e8f
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.cxx
@@ -0,0 +1,104 @@
+/*
+ * Author: Hans J. Johnson
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "itkIO.h"
+#include "BRAINSTrimForegroundInDirectionCLP.h"
+#include "TrimForegroundInDirection.h"
+#include "landmarkIO.h"
+#include "BRAINSThreadControl.h"
+
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+int main(int argc, char *argv[])
+{
+  // file pointer for opening the setup file
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  PARSE_ARGS;
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+  std::cout << "================================================================" << std::endl;
+  std::cout << "Processing: " << inputVolume << std::endl;
+
+  // //////////////////////////////////////////////////////////////////////////
+  SImageType::Pointer volOrig = itkUtil::ReadImage(inputVolume);
+  if( volOrig.IsNull() )
+    {
+    printf( "\nCould not open image %s, aborting ...\n\n", inputVolume.c_str() );
+    exit(1);
+    }
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  if( directionCode == 0 )
+    {
+    std::cout << "Your directionCode of 0 has selected the program default of 3 (maximize Superior/Inferior)."
+              << std::endl;
+    directionCode = 3;
+    }
+  unsigned int axis = vnl_math_abs(directionCode) - 1;
+  if( axis > 2 )
+    {
+    std::cout << "Your directionCode was too large so we will use the program default, axis 2 (Superior/Inferior)."
+              << std::endl;
+    axis = 2;
+    }
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  SImageType::PixelType BackgroundFillValue;
+  if( backgroundFillValueString == std::string("BIGNEG") )
+    {
+    BackgroundFillValue = -32768;
+    }
+  else
+    {
+    BackgroundFillValue = atoi( backgroundFillValueString.c_str() );
+    }
+
+  //
+  //
+  // /////////////////////////////////////////////////////////////////////////////////////////////
+  SImageType::Pointer volResult;
+
+  TrimForegroundInDirection(volResult,
+                            volOrig,
+                            axis,
+                            otsuPercentileThreshold,
+                            closingSize,
+                            headSizeLimit,
+                            BackgroundFillValue);
+  itkUtil::WriteImage(volResult, outputVolume);
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml
new file mode 100644
index 00000000..8e5efbf8
--- /dev/null
+++ b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml
@@ -0,0 +1,82 @@
+
+
+    BRAINSTrimForegroundInDirection
+    This program will trim off the neck and also air-filling noise from the inputImage.
+    0.1
+    http://www.nitrc.org/projects/art/
+    
+        
+            inputVolume
+            i
+            inputVolume
+            
+            Input image to trim off the neck (and also air-filling noise.)
+            input
+            
+        
+        
+            outputVolume
+            o
+            outputVolume
+            
+            Output image with neck and air-filling noise trimmed isotropic image with AC at center of image.
+            output
+            
+        
+        
+            directionCode
+            
+            directionCode
+            x
+            
+                This flag chooses which dimension to compare.  The sign lets you flip direction.
+            
+            3
+        
+        
+            otsuPercentileThreshold
+            
+            otsuPercentileThreshold
+            p
+            
+                This is a parameter to FindLargestForegroundFilledMask, which is employed to trim off air-filling noise.
+            
+            0.01
+        
+        
+            closingSize
+            
+            closingSize
+            c
+            
+                This is a parameter to FindLargestForegroundFilledMask
+            
+            9
+        
+        
+            headSizeLimit
+            
+            headSizeLimit
+            s
+            
+                Use this to vary from the command line our search for how much upper tissue is head for the center-of-mass calculation.  Units are CCs, not cubic millimeters.
+            
+            1000.0
+        
+        
+            backgroundFillValueString
+            BackgroundFillValue
+            z
+            Fill the background of image with specified short int value. Enter number or use BIGNEG for a large negative number.
+            
+            0
+        
+        
+          numberOfThreads
+          numberOfThreads
+          
+          Explicitly specify the maximum number of threads to use.
+          -1
+        
+    
+
diff --git a/BRAINSConstellationDetector/src/CMakeLists.txt b/BRAINSConstellationDetector/src/CMakeLists.txt
new file mode 100644
index 00000000..68c20f83
--- /dev/null
+++ b/BRAINSConstellationDetector/src/CMakeLists.txt
@@ -0,0 +1,48 @@
+project(BRAINSConstellationDetectorProgs)
+cmake_minimum_required(VERSION 2.8)
+
+
+## Build landmarksConstellationCOMMONLIB library
+##
+add_library(landmarksConstellationCOMMONLIB STATIC
+  landmarksConstellationCommon.cxx landmarkIO.cxx
+  landmarksConstellationDetector.cxx
+  TrimForegroundInDirection.cxx
+  LLSModel.cxx)
+target_link_libraries(landmarksConstellationCOMMONLIB BRAINSCommonLib ${ITK_LIBRARIES})
+
+## Build all the programs
+##
+set(ALL_PROGS_LIST
+  BRAINSConstellationModeler
+  BRAINSLinearModelerEPCA
+  BRAINSConstellationDetector
+  BRAINSAlignMSP
+  BRAINSClipInferior
+  BRAINSTrimForegroundInDirection
+  BRAINSLmkTransform
+  TransformFromFiducials
+  BRAINSEyeDetector
+  )
+foreach(prog ${ALL_PROGS_LIST})
+
+  if(0) # Build against Slicer
+    ## Include the Slicer macro for setting up default locations!
+    SlicerMacroBuildCLI(
+      NAME ${prog}
+      LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+      TARGET_LIBRARIES landmarksConstellationCOMMONLIB ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+      CLI_SHARED_LIBRARY_WRAPPER_CXX  ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+      VERBOSE
+    )
+  else()
+    SEMMacroBuildCLI(
+      NAME ${prog}
+      LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+      TARGET_LIBRARIES landmarksConstellationCOMMONLIB ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+      CLI_SHARED_LIBRARY_WRAPPER_CXX ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+      VERBOSE
+      )
+  endif()
+endforeach()
+
diff --git a/BRAINSConstellationDetector/src/CTestConfig.cmake b/BRAINSConstellationDetector/src/CTestConfig.cmake
new file mode 100644
index 00000000..773140ca
--- /dev/null
+++ b/BRAINSConstellationDetector/src/CTestConfig.cmake
@@ -0,0 +1,13 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   enable_testing()
+##   include(Dart)
+set(CTEST_PROJECT_NAME "AutomaticRegistrationToolProgs")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=AutomaticRegistrationToolProgs")
+set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/BRAINSConstellationDetector/src/CTestCustom.ctest b/BRAINSConstellationDetector/src/CTestCustom.ctest
new file mode 100644
index 00000000..b35239ef
--- /dev/null
+++ b/BRAINSConstellationDetector/src/CTestCustom.ctest
@@ -0,0 +1,52 @@
+#-- #NOTES from http: // www.cmake.org/Wiki/CMake_Testing_With_CTest
+set(CTEST_CUSTOM_MEMCHECK_IGNORE
+    $ {CTEST_CUSTOM_MEMCHECK_IGNORE}
+    DummyExcludeMemcheckIgnoreTestSetGet
+    )
+
+#-- #set(CTEST_CUSTOM_WARNING_MATCH
+#-- #${CTEST_CUSTOM_WARNING_MATCH}
+#-- #"{standard input}:[0-9][0-9]*: Warning: "
+#-- #)
+
+#-- #IF("@CMAKE_SYSTEM@" MATCHES "OSF")
+set(CTEST_CUSTOM_WARNING_EXCEPTION
+    $ {CTEST_CUSTOM_WARNING_EXCEPTION}
+    "fltk"
+    "xforms"
+    "vtkKWApplication"
+    "vtkKWObject"
+    )
+#-- #ENDIF("@CMAKE_SYSTEM@" MATCHES "OSF")
+
+#-- #The following are brains2 warnings that just need to be suppressed because they are caused
+#-- #by third parties, and will never be fixed.
+set(CTEST_CUSTOM_WARNING_EXCEPTION
+    $ {CTEST_CUSTOM_WARNING_EXCEPTION}
+    "tcl8.4.5/[^/]+/../[^/]+/[^.]+.c[:\"]"
+    "tk8.4.5/[^/]+/[^/]+.c[:\"]"
+    "SlicerExecutionModel"
+    "VTK/Utilities/vtktiff/"
+    "Utilities/vtkmpeg2/"
+    "Utilities/hdf5/"
+    "xtree.[0-9]+. : warning C4702: unreachable code"
+    "warning LNK4221"
+    "variable .var_args[2]*. is used before its value is set"
+    "qHullLib"
+    "/FL/"
+    "bkHull.cxx:[0-9]+: warning: dereferencing type-punned pointer will break strict-aliasing rules"
+    "warning #1170: invalid redeclaration of nested class"
+    )
+##Intel compiler does not like itkLegacyMacro warning #1170
+
+#-- #Reset maximum number of warnings so that they all show up.
+set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS 1000)
+
+set(CTEST_CUSTOM_COVERAGE_EXCLUDE $ {CTEST_CUSTOM_COVERAGE_EXCLUDE}
+    "./SlicerExecutionModel/"
+    "./SlicerExecutionModel/.*"
+    "./SlicerExecutionModel/.*/.*"
+    ".*SlicerExecutionModel.*"
+    "SlicerExecutionModel"
+    )
+
diff --git a/BRAINSConstellationDetector/src/ChopImageBelowLowerBound.h b/BRAINSConstellationDetector/src/ChopImageBelowLowerBound.h
new file mode 100644
index 00000000..641c8763
--- /dev/null
+++ b/BRAINSConstellationDetector/src/ChopImageBelowLowerBound.h
@@ -0,0 +1,57 @@
+#ifndef _ChopImageBelowLowerBound_H_
+#define _ChopImageBelowLowerBound_H_
+/*
+ * Copyright (c) 2009, Hans J. Johnson
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "itkImage.h"
+
+template 
+void ChopImageBelowLowerBound(typename ImageType::Pointer inputVolume,
+                              const typename ImageType::PixelType BackgroundFillValue,
+                              const double PhysicalLowerBound)
+{
+  // And now, we are going to chop out everything inferior to
+  // PhysicalLowerBound:
+  typedef typename itk::ImageRegionIterator IteratorType;
+  IteratorType ItPixel( inputVolume, inputVolume->GetLargestPossibleRegion() );
+  typename ImageType::PointType PixelPhysicalPoint;
+  while( !ItPixel.IsAtEnd() )
+    {
+    inputVolume->TransformIndexToPhysicalPoint(ItPixel.GetIndex(), PixelPhysicalPoint);
+    if( PixelPhysicalPoint[2] < PhysicalLowerBound )
+      {
+      ItPixel.Set(BackgroundFillValue);
+      }
+    ++ItPixel;
+    }
+}
+
+#endif
diff --git a/BRAINSConstellationDetector/src/HoughFilterTestProgram.cxx b/BRAINSConstellationDetector/src/HoughFilterTestProgram.cxx
new file mode 100644
index 00000000..4c13a602
--- /dev/null
+++ b/BRAINSConstellationDetector/src/HoughFilterTestProgram.cxx
@@ -0,0 +1,103 @@
+//Inspecting the performance of the HoughTransformRadialVotingImageFilter regarding the number of threads
+
+#include "itkImage.h"
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkHoughTransformRadialVotingImageFilter.h"
+
+int main( int argc, char * argv[] )
+{
+	
+const unsigned int LocalImageDimension = 3;
+typedef short InputPixelType;
+typedef double OutputPixelType;	
+typedef itk::Image InputImageType;
+typedef itk::Image OutputImageType;
+
+typedef itk::HoughTransformRadialVotingImageFilter HoughFilterType;
+typedef HoughFilterType::SpheresListType                        SpheresListType;
+typedef HoughFilterType::Pointer                                HoughFilterPointer;
+HoughFilterPointer houghFilter = HoughFilterType::New();
+	
+//Reader type
+typedef itk::ImageFileReader ReaderType;
+ReaderType::Pointer reader = ReaderType::New();
+reader->SetFileName( argv[1] );
+//reader->Update();
+	
+houghFilter->SetInput( reader->GetOutput() );
+
+
+houghFilter->SetNumberOfSpheres( 2 );
+houghFilter->SetMinimumRadius( 11. );
+houghFilter->SetMaximumRadius( 13. );
+houghFilter->SetSigmaGradient( 1. );
+houghFilter->SetVariance( 1. );
+houghFilter->SetSphereRadiusRatio( 1. );
+houghFilter->SetVotingRadiusRatio( .5 );
+houghFilter->SetThreshold( 10. );
+houghFilter->SetOutputThreshold( .8 );
+houghFilter->SetGradientThreshold( 0. );
+houghFilter->SetNbOfThreads( 64 );
+houghFilter->SetSamplingRatio( .2 );
+houghFilter->SetHoughEyeDetectorMode( 1 );
+
+	
+try
+  {
+  houghFilter->Update();
+  }
+catch( itk::ExceptionObject & excep )
+  {
+  std::cerr << "Failed houghFilter " << std::endl;
+  std::cerr << excep << std::endl;
+  }
+catch(...)
+  {
+  std::cout << "Failed on houghFilter exception occured" << std::endl;
+  }
+
+/*	
+this->m_AccumulatorImage = houghFilter->GetOutput();
+
+// Write debug accumulator image
+typename WriterType::Pointer writer = WriterType::New();
+writer->SetFileName( this->m_ResultsDir + "/HoughEyeAccumulator.nii.gz" );
+writer->SetInput( this->m_AccumulatorImage );
+writer->SetUseCompression( true );
+
+*/
+
+//writer type
+typedef  itk::ImageFileWriter< OutputImageType  > WriterType;
+WriterType::Pointer writer = WriterType::New();
+writer->SetFileName(argv[2]);
+writer->SetInput( houghFilter->GetOutput() );
+try
+{
+ writer->Update();
+}
+catch( itk::ExceptionObject & excep )
+{
+ std::cerr << "Cannot write the Accumulator image!" << std::endl;
+ std::cerr << excep << std::endl;
+}
+	
+const SpheresListType spheres = houghFilter->GetSpheres();
+if( spheres.size() < 2 )
+  {
+  std::cerr << "Error: The number of detected spheres is less than 2!" << std::endl;
+  //std::cerr << "The program will continue to run for generating some debug output for GUI corrector." << std::endl;
+  //std::cerr << "Make sure you set the debug level > 4." << std::endl;
+  //this->m_Failure = true;
+  //return -1;
+  }
+else
+  {
+  std::cout << "It works! The number of detected spheres is not less than 2!" << std::endl;
+  }
+
+
+	
+  return EXIT_SUCCESS;
+}
diff --git a/BRAINSConstellationDetector/src/LLSModel.cxx b/BRAINSConstellationDetector/src/LLSModel.cxx
new file mode 100644
index 00000000..60b81194
--- /dev/null
+++ b/BRAINSConstellationDetector/src/LLSModel.cxx
@@ -0,0 +1,374 @@
+#include "LLSModel.h"
+#include 
+LLSModel
+::LLSModel() : m_H5File(0)
+{
+}
+
+LLSModel
+::~LLSModel()
+{
+  if( this->m_H5File != 0 )
+    {
+    this->m_H5File->close();
+    delete this->m_H5File;
+    }
+}
+
+void
+LLSModel
+::SetFileName(const std::string & fileName)
+{
+  m_FileName = fileName;
+}
+
+const char * const LLSModel::m_LLSMeansGroupName = "LLSMeans";
+const char * const LLSModel::m_LLSMatricesGroupName = "LLSMatrices";
+const char * const LLSModel::m_LLSSearchRadiiGroupName = "LLSSearchRadii";
+
+void
+LLSModel
+::WriteVector(const std::string & path,
+              const std::vector & vec)
+{
+  hsize_t dim(vec.size() );
+  double *buf(new double[dim]);
+  for( unsigned i(0); i < dim; i++ )
+    {
+    buf[i] = vec[i];
+    }
+
+  H5::DataSpace vecSpace(1, &dim);
+  H5::PredType  vecType = H5::PredType::NATIVE_DOUBLE;
+  H5::DataSet   vecSet =
+    this->m_H5File->createDataSet(path,
+                                  vecType,
+                                  vecSpace);
+  vecSet.write(buf, vecType);
+  vecSet.close();
+  delete [] buf;
+}
+
+void
+LLSModel
+::WriteMatrix(const std::string & path,
+              const MatrixType & matrix)
+{
+  hsize_t dims[2];
+
+  dims[0] = matrix.rows();
+  dims[1] = matrix.cols();
+
+  double *buffer = new double[dims[0] * dims[1]];
+  matrix.copy_out(buffer);
+
+  H5::DataSpace matrixSpace(2, dims);
+  H5::DataSet   matrixSet =
+    this->m_H5File->createDataSet(path,
+                                  H5::PredType::NATIVE_DOUBLE,
+                                  matrixSpace);
+  matrixSet.write(buffer, H5::PredType::NATIVE_DOUBLE,
+                  matrixSpace);
+  matrixSet.close();
+  delete [] buffer;
+}
+
+void
+LLSModel
+::WriteScalar(const std::string & path,
+              const double & value)
+{
+  hsize_t       numScalars(1);
+  H5::DataSpace scalarSpace(1, &numScalars);
+  H5::PredType  scalarType = H5::PredType::NATIVE_DOUBLE;
+  H5::DataSet   scalarSet =
+    this->m_H5File->createDataSet(path,
+                                  scalarType,
+                                  scalarSpace);
+
+  scalarSet.write(&value, scalarType);
+  scalarSet.close();
+}
+
+int
+LLSModel
+::Write()
+{
+  if( this->m_FileName == "" )
+    {
+    return -1;
+    }
+  if( this->m_LLSMeans.size() == 0 ||
+      this->m_LLSMatrices.size() == 0 ||
+      this->m_LLSSearchRadii.size() == 0 )
+    {
+    return -1;
+    }
+  try
+    {
+
+    this->m_H5File = new H5::H5File(this->m_FileName.c_str(), H5F_ACC_TRUNC);
+
+    H5::Group MeansGroup(this->m_H5File->createGroup(LLSModel::m_LLSMeansGroupName) );
+    for( LLSMeansType::iterator it = this->m_LLSMeans.begin();
+         it != this->m_LLSMeans.end();
+         it++ )
+      {
+      std::string curVecName(LLSModel::m_LLSMeansGroupName);
+      curVecName += "/";
+      curVecName += it->first;
+      this->WriteVector(curVecName, it->second);
+      }
+
+    H5::Group MatricesGroup(this->m_H5File->createGroup(LLSModel::m_LLSMatricesGroupName) );
+    for( LLSMatricesType::iterator it = this->m_LLSMatrices.begin();
+         it != this->m_LLSMatrices.end();
+         it++ )
+      {
+      std::string curMatName(LLSModel::m_LLSMatricesGroupName);
+      curMatName += "/";
+      curMatName += it->first;
+      this->WriteMatrix(curMatName, it->second);
+      }
+
+    H5::Group SearchRadiiGroup(this->m_H5File->createGroup(LLSModel::m_LLSSearchRadiiGroupName) );
+    for( LLSSearchRadiiType::iterator it = this->m_LLSSearchRadii.begin();
+         it != this->m_LLSSearchRadii.end();
+         it++ )
+      {
+      std::string curRadiusName(LLSModel::m_LLSSearchRadiiGroupName);
+      curRadiusName += "/";
+      curRadiusName += it->first;
+      this->WriteScalar(curRadiusName, it->second);
+      }
+
+    this->m_H5File->close();
+    delete this->m_H5File;
+    this->m_H5File = 0;
+    }
+  // catch failure caused by the H5File operations
+  catch( H5::FileIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataSet operations
+  catch( H5::DataSetIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataSpace operations
+  catch( H5::DataSpaceIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataType operations
+  catch( H5::DataTypeIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  return 0;
+}
+
+std::vector
+LLSModel
+::ReadVector(const std::string & DataSetName)
+{
+  std::vector vec;
+  hsize_t             dim;
+  H5::DataSet         vecSet = this->m_H5File->openDataSet(DataSetName);
+  H5::DataSpace       Space = vecSet.getSpace();
+
+  if( Space.getSimpleExtentNdims() != 1 )
+    {
+    std::cerr << "Wrong #of dims for vector "
+              << "in HDF5 File" << std::endl;
+    throw;
+    }
+  Space.getSimpleExtentDims(&dim, 0);
+  vec.resize(dim);
+
+  double *buf = new double[dim];
+  vecSet.read(buf, H5::PredType::NATIVE_DOUBLE);
+  for( unsigned i(0); i < dim; i++ )
+    {
+    vec[i] = buf[i];
+    }
+  delete [] buf;
+  vecSet.close();
+  return vec;
+}
+
+LLSModel::MatrixType
+LLSModel
+::ReadMatrix(const std::string & DataSetName)
+{
+  hsize_t       dims[2];
+  H5::DataSet   matrixSet = this->m_H5File->openDataSet(DataSetName);
+  H5::DataSpace matrixSpace = matrixSet.getSpace();
+
+  if( matrixSpace.getSimpleExtentNdims() != 2 )
+    {
+    std::cerr << "Wrong #of dims for matrix "
+              << "in HDF5 File" << std::endl;
+    throw;
+    }
+  matrixSpace.getSimpleExtentDims(dims, 0);
+  MatrixType mat(dims[0], dims[1]);
+  matrixSet.read(mat.data_block(), H5::PredType::NATIVE_DOUBLE);
+  matrixSet.close();
+  return mat;
+}
+
+double
+LLSModel
+::ReadScalar(const std::string & DataSetName)
+{
+  hsize_t       dim;
+  H5::DataSet   scalarSet = this->m_H5File->openDataSet(DataSetName);
+  H5::DataSpace Space = scalarSet.getSpace();
+
+  if( Space.getSimpleExtentNdims() != 1 )
+    {
+    std::cerr << "Wrong #of dims for TransformType "
+              << "in HDF5 File" << std::endl;
+    }
+  Space.getSimpleExtentDims(&dim, 0);
+  if( dim != 1 )
+    {
+    std::cerr << "Elements > 1 for scalar type "
+              << "in HDF5 File" << std::endl;;
+    }
+  double scalar;
+  scalarSet.read(&scalar, H5::PredType::NATIVE_DOUBLE);
+  scalarSet.close();
+  return scalar;
+}
+
+int
+LLSModel
+::Read()
+{
+
+  if( this->m_FileName == "" )
+    {
+    return -1;
+    }
+  try
+    {
+
+    this->m_H5File = new H5::H5File(this->m_FileName.c_str(), H5F_ACC_RDONLY);
+
+    H5::Group MeansGroup(this->m_H5File->openGroup(LLSModel::m_LLSMeansGroupName) );
+
+    hsize_t numLLSMeans = MeansGroup.getNumObjs();
+    for( hsize_t i = 0; i < numLLSMeans; i++ )
+      {
+      std::string LLSMeanName = MeansGroup.getObjnameByIdx(i);
+      std::string curVecName(LLSModel::m_LLSMeansGroupName);
+      curVecName += "/";
+      curVecName += LLSMeanName;
+      this->m_LLSMeans[LLSMeanName] = this->ReadVector(curVecName);
+      }
+    MeansGroup.close();
+
+    H5::Group MatricesGroup(this->m_H5File->openGroup(LLSModel::m_LLSMatricesGroupName) );
+    hsize_t   numLLSMatrices = MatricesGroup.getNumObjs();
+    for( hsize_t i = 0; i < numLLSMatrices; i++ )
+      {
+      std::string LLSMatrixName = MatricesGroup.getObjnameByIdx(i);
+      std::string curMatName(LLSModel::m_LLSMatricesGroupName);
+      curMatName += "/";
+      curMatName += LLSMatrixName;
+      this->m_LLSMatrices[LLSMatrixName] = this->ReadMatrix(curMatName);
+      }
+    MatricesGroup.close();
+
+    H5::Group SearchRadiiGroup(this->m_H5File->openGroup(LLSModel::m_LLSSearchRadiiGroupName) );
+    hsize_t   numSearchRadii = SearchRadiiGroup.getNumObjs();
+    for( hsize_t i = 0; i < numSearchRadii; i++ )
+      {
+      std::string SearchRadiusName = SearchRadiiGroup.getObjnameByIdx(i);
+      std::string curRadiusName(LLSModel::m_LLSSearchRadiiGroupName);
+      curRadiusName += "/";
+      curRadiusName += SearchRadiusName;
+      this->m_LLSSearchRadii[SearchRadiusName] = this->ReadScalar(curRadiusName);
+      }
+    SearchRadiiGroup.close();
+
+    this->m_H5File->close();
+    delete this->m_H5File;
+    this->m_H5File = 0;
+    }
+  // catch failure caused by the H5File operations
+  catch( H5::FileIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataSet operations
+  catch( H5::DataSetIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataSpace operations
+  catch( H5::DataSpaceIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  // catch failure caused by the DataType operations
+  catch( H5::DataTypeIException error )
+    {
+    error.printError();
+    return -1;
+    }
+  return 0;
+}
+
+void
+LLSModel
+::SetLLSMeans(const LLSMeansType & llsMeans)
+{
+  this->m_LLSMeans = llsMeans;
+}
+
+const LLSModel::LLSMeansType &
+LLSModel
+::GetLLSMeans()
+{
+  return this->m_LLSMeans;
+}
+
+void
+LLSModel
+::SetLLSMatrices(const LLSMatricesType & llsMatrices)
+{
+  this->m_LLSMatrices = llsMatrices;
+}
+
+const LLSModel::LLSMatricesType &
+LLSModel
+::GetLLSMatrices()
+{
+  return this->m_LLSMatrices;
+}
+
+void
+LLSModel
+::SetSearchRadii(const LLSSearchRadiiType & llsSearchRadii)
+{
+  this->m_LLSSearchRadii = llsSearchRadii;
+}
+
+const LLSModel::LLSSearchRadiiType &
+LLSModel
+::GetSearchRadii()
+{
+  return m_LLSSearchRadii;
+}
+
diff --git a/BRAINSConstellationDetector/src/LLSModel.h b/BRAINSConstellationDetector/src/LLSModel.h
new file mode 100644
index 00000000..aa7eabee
--- /dev/null
+++ b/BRAINSConstellationDetector/src/LLSModel.h
@@ -0,0 +1,74 @@
+#ifndef LLSModel_h
+#define LLSModel_h
+
+#include 
+#include 
+#include 
+#include "vnl/vnl_matrix.h"
+#include "itkMacro.h"
+
+#if  ITK_VERSION_MAJOR >=4
+#include "itk_hdf5.h"
+#include "itk_H5Cpp.h"
+#else
+#include "hdf5.h"
+#include "H5Cpp.h"
+#endif
+
+class LLSModel
+{
+public:
+  LLSModel();
+  ~LLSModel();
+  typedef std::map > LLSMeansType;
+  typedef vnl_matrix                          MatrixType;
+  typedef std::map           LLSMatricesType;
+  typedef std::map               LLSSearchRadiiType;
+
+  void SetFileName(const std::string & fileName);
+
+  //
+  // read & write return zero on success -1 otherwise.
+  int Read();
+
+  int Write();
+
+  void SetLLSMeans(const LLSMeansType & llsMeans);
+
+  const LLSMeansType & GetLLSMeans();
+
+  void SetLLSMatrices(const LLSMatricesType & llsMatrices);
+
+  const LLSMatricesType & GetLLSMatrices();
+
+  void SetSearchRadii(const LLSSearchRadiiType & llsSearchRadii);
+
+  const LLSSearchRadiiType & GetSearchRadii();
+
+private:
+  // private methods
+  void WriteVector(const std::string & path, const std::vector & vec);
+
+  void WriteMatrix(const std::string & path, const MatrixType & matrix);
+
+  void WriteScalar(const std::string & path, const double & value);
+
+  double ReadScalar(const std::string & DataSetName);
+
+  std::vector ReadVector(const std::string & DataSetName);
+
+  MatrixType ReadMatrix(const std::string & DataSetName);
+
+private:
+  std::string               m_FileName;
+  LLSMeansType              m_LLSMeans;
+  LLSMatricesType           m_LLSMatrices;
+  LLSSearchRadiiType        m_LLSSearchRadii;
+  H5::H5File *              m_H5File;
+  static const char * const m_LLSMeansGroupName;
+  static const char * const m_LLSMatricesGroupName;
+  static const char * const m_LLSSearchRadiiGroupName;
+
+};
+
+#endif // LLSModel_h
diff --git a/BRAINSConstellationDetector/src/ORIGINAL_CHANGELOG b/BRAINSConstellationDetector/src/ORIGINAL_CHANGELOG
new file mode 100644
index 00000000..9465cce1
--- /dev/null
+++ b/BRAINSConstellationDetector/src/ORIGINAL_CHANGELOG
@@ -0,0 +1,920 @@
+This is the change log to document the history when moving from the ART project to the BRAINSConstellationDetector Project on NITRC.
+
+
+------------------------------------------------------------------------
+r270 | harrisgreg | 2009-03-05 16:26:19 -0600 (Thu, 05 Mar 2009) | 1 line
+
+BUG: Now that ConstellationDetector has a new flag, cutOutHeadInOutputVolumes, need to make sure we only trim with the Otsu threshold once when both transformed and untransformed images are requested.
+------------------------------------------------------------------------
+r269 | harrisgreg | 2009-03-05 15:56:37 -0600 (Thu, 05 Mar 2009) | 1 line
+
+ENH:  Added commandline switch to optionally turn on cutting out the head in output volumes, both transformed and untransformed.
+------------------------------------------------------------------------
+r268 | hjmjohnson | 2009-02-26 21:49:12 -0600 (Thu, 26 Feb 2009) | 1 line
+
+ENH:  Updated to create clipped images for the outputs with both below acpoint clipping AND FindLargestRegionFilledMask clipping.
+------------------------------------------------------------------------
+r267 | harrisgreg | 2009-02-23 13:56:59 -0600 (Mon, 23 Feb 2009) | 1 line
+
+BUG:  Dispensed with one of the alternatives to TrimForegroundInDirection I had been coding.  Made the test pass meaningfully.
+------------------------------------------------------------------------
+r266 | harrisgreg | 2009-02-23 13:43:43 -0600 (Mon, 23 Feb 2009) | 1 line
+
+BUG:  Make regression tests pass.
+------------------------------------------------------------------------
+r265 | harrisgreg | 2009-02-23 13:17:51 -0600 (Mon, 23 Feb 2009) | 1 line
+
+ENH:  Changes to MakeBranded2DImage in landmarkIO and moving FindCenterOfBrainBasedOnTopOfHead to compute the entire CenterOfMass on the clipped foreground image before splicing the Inferior/Superior level into it.  Checked in for version control prior to subsequent deletions.
+------------------------------------------------------------------------
+r264 | hjmjohnson | 2009-02-22 21:54:34 -0600 (Sun, 22 Feb 2009) | 1 line
+
+ENH:  Major fixes to make sure to get center of mass in consistent location.
+------------------------------------------------------------------------
+r263 | hjmjohnson | 2009-02-21 16:25:32 -0600 (Sat, 21 Feb 2009) | 1 line
+
+ENH:  Many minor little bugs fixed to get better estimate of center of mass for the brain based on the top of the head.
+------------------------------------------------------------------------
+r262 | hjmjohnson | 2009-02-20 17:06:14 -0600 (Fri, 20 Feb 2009) | 1 line
+
+ENH: Trying to estimate brainsize from an estimate of planar area.
+------------------------------------------------------------------------
+r261 | harrisgreg | 2009-02-19 16:10:41 -0600 (Thu, 19 Feb 2009) | 1 line
+
+BUG:  If the histogram has less than the desired non-zero volume, need to use all the tissue, not none of it.
+------------------------------------------------------------------------
+r260 | harrisgreg | 2009-02-19 13:08:25 -0600 (Thu, 19 Feb 2009) | 1 line
+
+ENH:  Created the stand-alone program to exercise TrimForegroundInDirection in terms of signed short images.  Passes the test.
+------------------------------------------------------------------------
+r259 | harrisgreg | 2009-01-21 14:44:57 -0600 (Wed, 21 Jan 2009) | 1 line
+
+BUG:  Needed to relocate MakeBranded2DImage call to after taking care of outputUntransformedClippedVolume since it damages the outputInterpImage.
+------------------------------------------------------------------------
+r258 | hjmjohnson | 2009-01-16 21:24:08 -0600 (Fri, 16 Jan 2009) | 1 line
+
+ENH:  made less verbose by default.
+------------------------------------------------------------------------
+r256 | harrisgreg | 2009-01-16 16:25:47 -0600 (Fri, 16 Jan 2009) | 1 line
+
+BUG:  gnarly comment gone.
+------------------------------------------------------------------------
+r255 | harrisgreg | 2009-01-16 16:18:55 -0600 (Fri, 16 Jan 2009) | 1 line
+
+BUG:  Make the BRAINSConstellationDetectorTest_T2_BoundedBelow testing case exhibit the new standard.  strnlen(linebuf,299) doesn't exist, but since we are comparing it <1, we can just test for the terminator '\0'.
+------------------------------------------------------------------------
+r254 | harrisgreg | 2009-01-16 16:01:20 -0600 (Fri, 16 Jan 2009) | 1 line
+
+ENH:  a combined release of --writeBranded2DImageFilename and the --otsuPercentileThreshold/FindLargestForegroundFilledMask enhancement of the --outputUntransformedClippedVolume/--acLowerBound != 1000.0 raw T2 image cropping, now also cropping to the whole head (with a closing size of 7.)
+------------------------------------------------------------------------
+r253 | harrisgreg | 2009-01-16 15:00:36 -0600 (Fri, 16 Jan 2009) | 1 line
+
+ENH:  This commit JUST adds the FindLargestForgroundFilledMask.h file to the build tree.  More work needed to tie it in.
+------------------------------------------------------------------------
+r252 | hjmjohnson | 2009-01-15 14:40:38 -0600 (Thu, 15 Jan 2009) | 1 line
+
+ENH:  Updated to fix a problem with processing comments at the top of the fcsv files from slicer.
+------------------------------------------------------------------------
+r251 | harrisgreg | 2009-01-15 14:02:14 -0600 (Thu, 15 Jan 2009) | 1 line
+
+ENH: added --outputVerificationScriptFilename, which will only make a verification script if both outputVolume and saveOutputLandmarksFilename are provided, since it puts both these filenames in the resulting Slicer3 Tcl script.
+------------------------------------------------------------------------
+r249 | hjmjohnson | 2009-01-15 13:41:27 -0600 (Thu, 15 Jan 2009) | 1 line
+
+ENH:  Silence verbose debugging information.
+------------------------------------------------------------------------
+r248 | harrisgreg | 2009-01-15 12:17:49 -0600 (Thu, 15 Jan 2009) | 1 line
+
+BUG:  An image transform has to be inverted before transforming points in the moving image to fixed space.  --saveOutputLandmarksFilename was doing this backwards.
+------------------------------------------------------------------------
+r247 | harrisgreg | 2009-01-15 12:10:31 -0600 (Thu, 15 Jan 2009) | 1 line
+
+ENH:  Now ConstellationDetector has --saveOutputLandmarksFilename, which writes the VersorZeroCenteredTransform of the originalSpace RP, AC, and PC.
+------------------------------------------------------------------------
+r246 | harrisgreg | 2009-01-15 11:38:52 -0600 (Thu, 15 Jan 2009) | 1 line
+
+ENH:  Now ConstellationDetector has --saveOriginalLandmarksFilename, in contrast to ConstellationModeler's flag and extender.
+------------------------------------------------------------------------
+r245 | harrisgreg | 2009-01-13 16:59:50 -0600 (Tue, 13 Jan 2009) | 1 line
+
+BUG:  added missing test file standard, so BRAINSConstellationDetectorTest_T2_BoundedBelow can be checked.
+------------------------------------------------------------------------
+r244 | harrisgreg | 2009-01-13 15:36:06 -0600 (Tue, 13 Jan 2009) | 1 line
+
+ENH:  Added a test for BRAINSConstellationDetectorTest_T2_BoundedBelow.
+------------------------------------------------------------------------
+r243 | harrisgreg | 2009-01-13 15:24:59 -0600 (Tue, 13 Jan 2009) | 1 line
+
+ENH:  --outputUntransformedClippedVolume has been refactored and improved.  Now works properly side by side with --outputVolume;  now uses CopyInformation and Allocate;  now inverts the ZeroCenteredTransform.
+------------------------------------------------------------------------
+r242 | hjmjohnson | 2009-01-13 11:08:08 -0600 (Tue, 13 Jan 2009) | 1 line
+
+ENH:  Some refactoring that is not complete.
+------------------------------------------------------------------------
+r241 | hjmjohnson | 2009-01-12 19:54:05 -0600 (Mon, 12 Jan 2009) | 1 line
+
+BUG:  Slicer3 landmarks are in RAS space, so we need to negate the first two physical points to get them in LPS when read into ITK physical spaces.
+------------------------------------------------------------------------
+r239 | harrisgreg | 2009-01-12 17:23:35 -0600 (Mon, 12 Jan 2009) | 1 line
+
+ENH:  added --outputUntransformedClippedVolume (fullpathtofilename) for use with --acLowerBound 80.  This will produce neck-clipped raw T2 for use with neck-clipped windowed-sinc aligned T1 in BRAINSFit.
+------------------------------------------------------------------------
+r238 | harrisgreg | 2009-01-12 14:48:00 -0600 (Mon, 12 Jan 2009) | 1 line
+
+BUG:  Turned off debug printing in string processing.
+------------------------------------------------------------------------
+r237 | harrisgreg | 2009-01-12 14:36:40 -0600 (Mon, 12 Jan 2009) | 1 line
+
+ENH: Changed the format and file storage of landmark data sets.  Now we can use landmarks written by Slicer3.
+------------------------------------------------------------------------
+r236 | harrisgreg | 2009-01-12 14:34:12 -0600 (Mon, 12 Jan 2009) | 1 line
+
+BUG:  updated testing standard images to track the improved method.
+------------------------------------------------------------------------
+r235 | hjmjohnson | 2009-01-11 20:29:12 -0600 (Sun, 11 Jan 2009) | 1 line
+
+ENH:  Changed the code for masking out the neck.
+------------------------------------------------------------------------
+r234 | hjmjohnson | 2009-01-09 08:25:56 -0600 (Fri, 09 Jan 2009) | 1 line
+
+ENH:  Started some code cleanup that should provide a little optimization.
+------------------------------------------------------------------------
+r233 | harrisgreg | 2009-01-08 12:58:04 -0600 (Thu, 08 Jan 2009) | 1 line
+
+ENH:  Added the commandline flag --acLowerBound (double) for the lowest plane inferior to the aligned AC point that will be included in the output resampled image.  Below this plane we only have the BackgroundFillValue, specified with the flags for rescaling intensities.
+------------------------------------------------------------------------
+r232 | harrisgreg | 2009-01-08 12:52:45 -0600 (Thu, 08 Jan 2009) | 1 line
+
+BUG:  Cleaned up spelling of long flag VolumeVolume (huh?) became Volume
+------------------------------------------------------------------------
+r231 | harrisgreg | 2009-01-06 17:06:20 -0600 (Tue, 06 Jan 2009) | 1 line
+
+BUG:  Cleaned up the naming of the longFlag parameters.
+------------------------------------------------------------------------
+r230 | harrisgreg | 2009-01-06 15:38:29 -0600 (Tue, 06 Jan 2009) | 1 line
+
+BUG:  Updated the names of the testing standard images to track the change of name of the program they provide a check for.
+------------------------------------------------------------------------
+r229 | harrisgreg | 2009-01-06 15:37:29 -0600 (Tue, 06 Jan 2009) | 1 line
+
+BUG:  Updated the names of the testing standard images to track the change of name of the program they provide a check for.
+------------------------------------------------------------------------
+r228 | hjmjohnson | 2009-01-05 16:24:24 -0600 (Mon, 05 Jan 2009) | 1 line
+
+ENH: Changing the file names and command line arguments to distinguish them from the original art tools. Acknowlegement:  This is a complete rewrite with algorithmic changes to the methods proposed by Babak Ardekani.  His work was a great inspiration to what was developed here, and this work should be considered a derivative work of the original acpcdetect suite of tools.
+------------------------------------------------------------------------
+r227 | hjmjohnson | 2009-01-04 16:42:21 -0600 (Sun, 04 Jan 2009) | 1 line
+
+ENH:  Allow running without an output image.
+------------------------------------------------------------------------
+r226 | hjmjohnson | 2008-12-29 16:03:52 -0600 (Mon, 29 Dec 2008) | 1 line
+
+ENH: Cleaned up the documentation.
+------------------------------------------------------------------------
+r225 | harrisgreg | 2008-12-22 13:33:40 -0600 (Mon, 22 Dec 2008) | 1 line
+
+ENH:  Bumped testing of mspQualityLevel up from 2 to 3, with associated standard images.
+------------------------------------------------------------------------
+r224 | harrisgreg | 2008-12-22 10:51:02 -0600 (Mon, 22 Dec 2008) | 1 line
+
+BUG:  Testing against fixed images (aligned and standard): updated standard images to track fixes to transform code.
+------------------------------------------------------------------------
+r222 | hjmjohnson | 2008-12-21 17:04:10 -0600 (Sun, 21 Dec 2008) | 1 line
+
+ENH:  Updated internals to clean up the code and make it more efficient.  Removed dependance on Rigid3DTransform.  Optimized computations of CC by using a well constructed resampled image.
+------------------------------------------------------------------------
+r220 | harrisgreg | 2008-12-19 13:46:00 -0600 (Fri, 19 Dec 2008) | 1 line
+
+ENH: This checks in changes to support --rescaleIntensities and friends on acpcmodel, acpcdetect and acpcResampleMSP.  This does not check in any new tests for it, though.
+------------------------------------------------------------------------
+r219 | hjmjohnson | 2008-12-18 22:53:23 -0600 (Thu, 18 Dec 2008) | 1 line
+
+ENH: Conversions to Versors are now working.
+------------------------------------------------------------------------
+r218 | harrisgreg | 2008-12-18 16:31:37 -0600 (Thu, 18 Dec 2008) | 1 line
+
+BUG 3292, Background value processing, is now allowing --BackgroundFillValue for short int Pixels.  BIGNEG is -32768, assuming twos-complement 16-bit words.
+------------------------------------------------------------------------
+r217 | harrisgreg | 2008-12-18 14:29:27 -0600 (Thu, 18 Dec 2008) | 1 line
+
+BUG: With this commit we have returned to passing test cases in a CMake compliant test suite.  TODO:  evaluate the model generated by acpcmodelTest.
+------------------------------------------------------------------------
+r216 | harrisgreg | 2008-12-18 12:48:30 -0600 (Thu, 18 Dec 2008) | 1 line
+
+BUG! This is close to fully compiling...interim commit of sources for collaboration.
+------------------------------------------------------------------------
+r215 | harrisgreg | 2008-12-18 11:42:00 -0600 (Thu, 18 Dec 2008) | 1 line
+
+ENH-with-BUG: Step 1 of wrapping acpcResampleMSP around acpcResampleMSPPrimary.
+------------------------------------------------------------------------
+r214 | harrisgreg | 2008-12-18 11:39:50 -0600 (Thu, 18 Dec 2008) | 1 line
+
+ENH-with-BUG: Step 2 of wrapping acpcmodel around acpcmodelPrimary.
+------------------------------------------------------------------------
+r213 | harrisgreg | 2008-12-18 11:21:36 -0600 (Thu, 18 Dec 2008) | 1 line
+
+ENH-with-BUG: Step 1 of wrapping acpcmodel around acpcmodelPrimary.
+------------------------------------------------------------------------
+r212 | harrisgreg | 2008-12-18 11:20:30 -0600 (Thu, 18 Dec 2008) | 1 line
+
+BUG:  finish renaming of acpcdetectPrimaryCLP.h
+------------------------------------------------------------------------
+r211 | harrisgreg | 2008-12-18 10:47:22 -0600 (Thu, 18 Dec 2008) | 1 line
+
+ENH:  created CMake compliant test suite.  Initial contents:  T1 and T2 tests for acpcdetect.
+------------------------------------------------------------------------
+r210 | hjmjohnson | 2008-12-17 21:20:58 -0600 (Wed, 17 Dec 2008) | 1 line
+
+ENH:  Deciphering the VersorRigid3D problems assigning to Versors.
+------------------------------------------------------------------------
+r209 | hjmjohnson | 2008-12-17 17:09:15 -0600 (Wed, 17 Dec 2008) | 1 line
+
+ENH:  Attempting to figure out what to do about the VersorTransform issues.
+------------------------------------------------------------------------
+r208 | harrisgreg | 2008-12-17 16:57:49 -0600 (Wed, 17 Dec 2008) | 1 line
+
+ENH: Third step in making an acpcdetectTest -- everything in place now.
+------------------------------------------------------------------------
+r207 | harrisgreg | 2008-12-17 16:45:14 -0600 (Wed, 17 Dec 2008) | 1 line
+
+ENH with BUG: Second step in making an acpcdetectTest
+------------------------------------------------------------------------
+r206 | harrisgreg | 2008-12-17 16:29:01 -0600 (Wed, 17 Dec 2008) | 1 line
+
+ENH with BUG: First step in making an acpcdetectTest
+------------------------------------------------------------------------
+r204 | hjmjohnson | 2008-12-16 17:04:49 -0600 (Tue, 16 Dec 2008) | 1 line
+
+ENH:  Determining method to convert Rigid3D to Versor3D transform.
+------------------------------------------------------------------------
+r203 | hjmjohnson | 2008-12-16 07:52:03 -0600 (Tue, 16 Dec 2008) | 1 line
+
+STYLE:  Continue to detangle old and new versions of tools.  Some header files moved around.
+------------------------------------------------------------------------
+r202 | hjmjohnson | 2008-12-15 20:04:57 -0600 (Mon, 15 Dec 2008) | 1 line
+
+STYLE:  Starting to detangle old and new versions of tools.
+------------------------------------------------------------------------
+r201 | hjmjohnson | 2008-12-15 19:56:40 -0600 (Mon, 15 Dec 2008) | 1 line
+
+ENH:  Detangled some of the build process.
+------------------------------------------------------------------------
+r200 | harrisgreg | 2008-12-15 13:01:32 -0600 (Mon, 15 Dec 2008) | 1 line
+
+BUG:  Factored out vnl_powell_fixed which is now in ITK, and factored back in the subdir lib.
+------------------------------------------------------------------------
+r198 | hjmjohnson | 2008-12-15 08:00:22 -0600 (Mon, 15 Dec 2008) | 1 line
+
+COMP:  Removed compilation of much code that is not needed for this new version of ART.
+------------------------------------------------------------------------
+r197 | hjmjohnson | 2008-12-14 22:15:19 -0600 (Sun, 14 Dec 2008) | 1 line
+
+ENH:  This new fully compliant with ITK version seems to be working with both T1 and T2 images.
+------------------------------------------------------------------------
+r196 | hjmjohnson | 2008-12-13 16:44:48 -0600 (Sat, 13 Dec 2008) | 1 line
+
+ENH:  Some optimization and code cleanup to ensure better performance.
+------------------------------------------------------------------------
+r195 | hjmjohnson | 2008-12-13 11:43:52 -0600 (Sat, 13 Dec 2008) | 1 line
+
+COMP:  Cleaned up unnecessary files.
+------------------------------------------------------------------------
+r194 | hjmjohnson | 2008-12-13 11:37:09 -0600 (Sat, 13 Dec 2008) | 1 line
+
+ENH:  Reached milestone where a reasonable result is attained from acpcdetect.
+------------------------------------------------------------------------
+r193 | hjmjohnson | 2008-12-11 11:05:41 -0600 (Thu, 11 Dec 2008) | 1 line
+
+ENH:  First submit without plane objects being used.
+------------------------------------------------------------------------
+r192 | hjmjohnson | 2008-12-11 09:39:42 -0600 (Thu, 11 Dec 2008) | 1 line
+
+ENH:  Cleaning up and removing dependancies on the PlaneObject.
+------------------------------------------------------------------------
+r191 | hjmjohnson | 2008-12-11 06:41:03 -0600 (Thu, 11 Dec 2008) | 1 line
+
+ENH:  Propogating changes to finding MSP to all other programs.  Eliminating need for the PlaneObjects all together.
+------------------------------------------------------------------------
+r190 | hjmjohnson | 2008-12-10 22:50:28 -0600 (Wed, 10 Dec 2008) | 1 line
+
+ENH:  More code cleanups for ART MSP finder.
+------------------------------------------------------------------------
+r189 | hjmjohnson | 2008-12-10 21:37:27 -0600 (Wed, 10 Dec 2008) | 1 line
+
+BUG:  Fixed bugs related to center of mass shifting during downsampling.
+------------------------------------------------------------------------
+r188 | hjmjohnson | 2008-12-10 16:52:05 -0600 (Wed, 10 Dec 2008) | 1 line
+
+ENH: Adding test case for resampleImage based multi-resolution image filter.
+------------------------------------------------------------------------
+r187 | hjmjohnson | 2008-12-09 22:41:07 -0600 (Tue, 09 Dec 2008) | 1 line
+
+ENH:  getting bugs fixed in multi-resolution image filter.
+------------------------------------------------------------------------
+r186 | hjmjohnson | 2008-12-09 12:49:56 -0600 (Tue, 09 Dec 2008) | 1 line
+
+ENH:  New MSP finder code is working, but now needs to be optimized.
+------------------------------------------------------------------------
+r185 | hjmjohnson | 2008-12-09 07:59:56 -0600 (Tue, 09 Dec 2008) | 1 line
+
+ENH:  New approach to simplify code.
+------------------------------------------------------------------------
+r184 | hjmjohnson | 2008-12-08 17:05:47 -0600 (Mon, 08 Dec 2008) | 1 line
+
+ENH:  Trying something completely new in an attempt to simplify the processing.
+------------------------------------------------------------------------
+r183 | hjmjohnson | 2008-12-07 14:40:03 -0600 (Sun, 07 Dec 2008) | 1 line
+
+ENH:  Re-indented to make it easier to see boundaries of what needs to be edited.
+------------------------------------------------------------------------
+r182 | hjmjohnson | 2008-12-06 11:29:05 -0600 (Sat, 06 Dec 2008) | 1 line
+
+BUG:  Still tracking down incorrect MSP calculations.
+------------------------------------------------------------------------
+r181 | hjmjohnson | 2008-12-06 09:03:15 -0600 (Sat, 06 Dec 2008) | 1 line
+
+BUG:  Tracking down bug in optimization of MSP.
+------------------------------------------------------------------------
+r180 | hjmjohnson | 2008-12-02 14:00:26 -0600 (Tue, 02 Dec 2008) | 1 line
+
+ENH:  Testing to determine if this version works for automatically finding the ACPC points.
+------------------------------------------------------------------------
+r179 | hjmjohnson | 2008-12-01 17:01:46 -0600 (Mon, 01 Dec 2008) | 2 lines
+
+ENH:  Added version of conjugate_gradient that compiles.
+
+------------------------------------------------------------------------
+r178 | hjmjohnson | 2008-11-06 10:09:43 -0600 (Thu, 06 Nov 2008) | 1 line
+
+COMP:  Code scope bracket was placed one line too high.
+------------------------------------------------------------------------
+r177 | hjmjohnson | 2008-11-05 19:29:53 -0600 (Wed, 05 Nov 2008) | 1 line
+
+COMP:  Forgot to add necessary file.
+------------------------------------------------------------------------
+r176 | hjmjohnson | 2008-11-04 16:52:07 -0600 (Tue, 04 Nov 2008) | 1 line
+
+ENH:  Fixed some more bugs with respect to positive and negaive rotations being estimated correctly.
+------------------------------------------------------------------------
+r175 | hjmjohnson | 2008-11-02 20:34:57 -0600 (Sun, 02 Nov 2008) | 1 line
+
+ENH:  Made a new class to make reusing functionality easier.
+------------------------------------------------------------------------
+r174 | hjmjohnson | 2008-11-01 11:08:44 -0500 (Sat, 01 Nov 2008) | 1 line
+
+ENH:  Added ability to search off the exstimated midline for better answers.
+------------------------------------------------------------------------
+r173 | hjmjohnson | 2008-11-01 07:43:53 -0500 (Sat, 01 Nov 2008) | 1 line
+
+ENH:  Updated to fix linking of the powell optimizer, and to get offsets from CM to be correct.
+------------------------------------------------------------------------
+r172 | hjmjohnson | 2008-10-30 18:40:22 -0500 (Thu, 30 Oct 2008) | 1 line
+
+BUG:  Fixed a bug in the powell optimizer that was causing all types of problems.  I've submitted a bug report.
+------------------------------------------------------------------------
+r171 | kentwilliams | 2008-10-30 12:43:46 -0500 (Thu, 30 Oct 2008) | 1 line
+
+script tweaks and removed unused variables
+------------------------------------------------------------------------
+r170 | hjmjohnson | 2008-10-28 22:54:11 -0500 (Tue, 28 Oct 2008) | 1 line
+
+ENH: Reworked to optimize on HeadingAngle and BankAngle.
+------------------------------------------------------------------------
+r169 | hjmjohnson | 2008-10-28 07:52:19 -0500 (Tue, 28 Oct 2008) | 1 line
+
+ENH:  Started down path to optimize HeadingAngle, BankAngle, and DistanceFrom CenterOfMass.
+------------------------------------------------------------------------
+r168 | hjmjohnson | 2008-10-27 15:54:53 -0500 (Mon, 27 Oct 2008) | 1 line
+
+COMP:  Restored the GetImageCenterPhysicalPoint function that was deleted inappropriately.
+------------------------------------------------------------------------
+r167 | canoee | 2008-10-27 14:51:04 -0500 (Mon, 27 Oct 2008) | 3 lines
+
+try conjugate gradient optimizer, but not infact the powell optimizer
+
+
+------------------------------------------------------------------------
+r166 | kentwilliams | 2008-10-27 12:57:03 -0500 (Mon, 27 Oct 2008) | 1 line
+
+Worked around change in behavior to try and get tests passing again
+------------------------------------------------------------------------
+r165 | hjmjohnson | 2008-10-25 11:32:56 -0500 (Sat, 25 Oct 2008) | 1 line
+
+COMP:  Just making the code compile.  Half way through a refactoring.
+------------------------------------------------------------------------
+r164 | hjmjohnson | 2008-10-25 11:20:33 -0500 (Sat, 25 Oct 2008) | 1 line
+
+COMP:  Missing externals for ART to build SlicerExectuion Model.
+------------------------------------------------------------------------
+r161 | hjmjohnson | 2008-10-24 08:52:23 -0500 (Fri, 24 Oct 2008) | 1 line
+
+ENH:  More modifications to find the center of the image better.
+------------------------------------------------------------------------
+r159 | hjmjohnson | 2008-10-20 22:29:36 -0500 (Mon, 20 Oct 2008) | 1 line
+
+ENH: More bug fixes to the acpcmodel/acpcdetect programs.
+------------------------------------------------------------------------
+r156 | hjmjohnson | 2008-10-13 19:49:21 -0500 (Mon, 13 Oct 2008) | 1 line
+
+ENH: Write out optimized points to files.
+------------------------------------------------------------------------
+r155 | kentwilliams | 2008-10-06 16:42:28 -0500 (Mon, 06 Oct 2008) | 1 line
+
+COMP: added dumping out of debug images for mean vectors
+------------------------------------------------------------------------
+r154 | canoee | 2008-10-03 15:15:02 -0500 (Fri, 03 Oct 2008) | 3 lines
+
+Avoid debug wrong
+
+
+------------------------------------------------------------------------
+r153 | hjmjohnson | 2008-10-01 23:16:53 -0500 (Wed, 01 Oct 2008) | 1 line
+
+ENH:  Cleaning up debug code to verify that correct results are being created.  There is still a bug for images with resolution units less than 1 that needs to be resolved.
+------------------------------------------------------------------------
+r152 | hjmjohnson | 2008-10-01 08:41:02 -0500 (Wed, 01 Oct 2008) | 1 line
+
+BUGS:  Working out bugs to get orientation issues worked out.
+------------------------------------------------------------------------
+r151 | hjmjohnson | 2008-09-29 17:00:08 -0500 (Mon, 29 Sep 2008) | 1 line
+
+BUG:  Fixed centering of code bug when origin is not all zero's.
+------------------------------------------------------------------------
+r150 | hjmjohnson | 2008-09-29 15:58:03 -0500 (Mon, 29 Sep 2008) | 1 line
+
+COMP: Fixed compilation error.
+------------------------------------------------------------------------
+r149 | hjmjohnson | 2008-09-29 15:41:51 -0500 (Mon, 29 Sep 2008) | 1 line
+
+ENH:  Fixed bug in plane calculations.
+------------------------------------------------------------------------
+r148 | canoee | 2008-09-29 15:24:28 -0500 (Mon, 29 Sep 2008) | 3 lines
+
+Trying to make it working
+
+
+------------------------------------------------------------------------
+r147 | hjmjohnson | 2008-09-28 21:32:53 -0500 (Sun, 28 Sep 2008) | 1 line
+
+ENH:  Identifying that the last image location is greater than the origin.
+------------------------------------------------------------------------
+r146 | hjmjohnson | 2008-09-28 15:47:34 -0500 (Sun, 28 Sep 2008) | 1 line
+
+ENH: Starting to remove dependance on given orientations and spacing assumptions.
+------------------------------------------------------------------------
+r145 | hjmjohnson | 2008-09-25 22:41:35 -0500 (Thu, 25 Sep 2008) | 1 line
+
+ENH:  Fixed brains2 index to itk physical points.
+------------------------------------------------------------------------
+r143 | kentwilliams | 2008-09-24 16:32:46 -0500 (Wed, 24 Sep 2008) | 1 line
+
+ENH: hoisted some redundant calculations out of inner loops
+------------------------------------------------------------------------
+r142 | kentwilliams | 2008-09-24 16:09:04 -0500 (Wed, 24 Sep 2008) | 2 lines
+
+ENH: short circuit inner loop to avoid expensive interpolation
+BUG: model output changed slightly since last checkin, replaced out of date Baseline.mdl
+------------------------------------------------------------------------
+r141 | hjmjohnson | 2008-09-23 22:51:45 -0500 (Tue, 23 Sep 2008) | 1 line
+
+ENH: Attempting to create program for translating index locations to physical point locaitons.
+------------------------------------------------------------------------
+r140 | hjmjohnson | 2008-09-23 16:55:45 -0500 (Tue, 23 Sep 2008) | 1 line
+
+ENH:  Added new file for testing of conversion of landmark points.
+------------------------------------------------------------------------
+r139 | kentwilliams | 2008-09-23 14:26:12 -0500 (Tue, 23 Sep 2008) | 3 lines
+
+ENH: collapse together extractArray, RemoveMean and Normalize
+BUG: the tests in art/data are all broken and if you accidentally run them they completely 
+screw up the tests now performed in art/src
+------------------------------------------------------------------------
+r138 | kentwilliams | 2008-09-23 11:50:45 -0500 (Tue, 23 Sep 2008) | 1 line
+
+ENH: compute vector means in acpcmodel, reducing size of the model file
+------------------------------------------------------------------------
+r137 | hjmjohnson | 2008-09-22 21:26:16 -0500 (Mon, 22 Sep 2008) | 1 line
+
+ENH: Added new program for converting landmarks to physical coordinates from other programs to be ITK compliant.
+------------------------------------------------------------------------
+r136 | canoee | 2008-09-22 16:38:56 -0500 (Mon, 22 Sep 2008) | 1 line
+
+ENH:  Added psuedo-code for testing the speed of running the cc computations.
+------------------------------------------------------------------------
+r135 | canoee | 2008-09-22 16:20:10 -0500 (Mon, 22 Sep 2008) | 1 line
+
+ENH:  Added a new test program for optimizing the CC calculations.
+------------------------------------------------------------------------
+r134 | hjmjohnson | 2008-09-22 16:03:27 -0500 (Mon, 22 Sep 2008) | 1 line
+
+ENH:  Revert to requiring only version 2.4 of cmake.
+------------------------------------------------------------------------
+r133 | kentwilliams | 2008-09-22 11:48:39 -0500 (Mon, 22 Sep 2008) | 1 line
+
+ENH: first crack at making ART algorithm general over any set of landmark points
+------------------------------------------------------------------------
+r132 | kentwilliams | 2008-09-19 16:33:43 -0500 (Fri, 19 Sep 2008) | 1 line
+
+COMP: test for equality in acpcModelFile is now approximate -- anything within 1 part per 10000 is reported as equal
+------------------------------------------------------------------------
+r131 | hjmjohnson | 2008-09-17 21:49:59 -0500 (Wed, 17 Sep 2008) | 1 line
+
+ENH:  Seems to work, now working on cleanup.
+------------------------------------------------------------------------
+r130 | hjmjohnson | 2008-09-17 17:43:22 -0500 (Wed, 17 Sep 2008) | 1 line
+
+ENH:  FIXED initial location of finding the RP point.
+------------------------------------------------------------------------
+r129 | kentwilliams | 2008-09-17 16:11:25 -0500 (Wed, 17 Sep 2008) | 1 line
+
+COMP: added test for acpcmodel
+------------------------------------------------------------------------
+r128 | hjmjohnson | 2008-09-16 21:57:39 -0500 (Tue, 16 Sep 2008) | 2 lines
+
+ENH:  Code cleanup attempting to forify when finding the 4V notch is more prominant than finding the RP.
+
+------------------------------------------------------------------------
+r127 | hjmjohnson | 2008-09-16 16:51:59 -0500 (Tue, 16 Sep 2008) | 1 line
+
+ENH:  Nearly have a working version of the acpc detect software.
+------------------------------------------------------------------------
+r126 | hjmjohnson | 2008-09-16 08:06:27 -0500 (Tue, 16 Sep 2008) | 1 line
+
+ENH:  Partially working solution.
+------------------------------------------------------------------------
+r125 | hjmjohnson | 2008-09-15 16:58:17 -0500 (Mon, 15 Sep 2008) | 1 line
+
+ENH:  Working versions of finding the RP and the PC have been successful.
+------------------------------------------------------------------------
+r124 | kentwilliams | 2008-09-15 16:45:02 -0500 (Mon, 15 Sep 2008) | 1 line
+
+COMP: refined test 
+------------------------------------------------------------------------
+r123 | kentwilliams | 2008-09-15 10:59:19 -0500 (Mon, 15 Sep 2008) | 1 line
+
+FIX: worked around RealPath disappearing from SystemTools
+------------------------------------------------------------------------
+r122 | hjmjohnson | 2008-09-13 17:53:39 -0500 (Sat, 13 Sep 2008) | 1 line
+
+BUG:  Really stupid indexing error was fixed.
+------------------------------------------------------------------------
+r121 | hjmjohnson | 2008-09-13 16:45:20 -0500 (Sat, 13 Sep 2008) | 1 line
+
+COMP:  Removed compiler warnings.
+------------------------------------------------------------------------
+r120 | hjmjohnson | 2008-09-12 17:01:21 -0500 (Fri, 12 Sep 2008) | 1 line
+
+BUG:  Attempting to debug the rewrite of acpcdetect.
+------------------------------------------------------------------------
+r119 | kentwilliams | 2008-09-12 16:44:08 -0500 (Fri, 12 Sep 2008) | 1 line
+
+fixed test for acpcResampleMSP
+------------------------------------------------------------------------
+r118 | kentwilliams | 2008-09-12 16:35:31 -0500 (Fri, 12 Sep 2008) | 1 line
+
+add new tests for acpcResampleMSP
+------------------------------------------------------------------------
+r117 | hjmjohnson | 2008-09-12 06:18:45 -0500 (Fri, 12 Sep 2008) | 1 line
+
+BUG:  Removed bug of loading the image in the wrong orientation, and exposed a new bug that causes exception to be thrown.
+------------------------------------------------------------------------
+r116 | kentwilliams | 2008-09-11 14:07:34 -0500 (Thu, 11 Sep 2008) | 1 line
+
+BUG: vectors need to have a size before you right to them via subscripts
+------------------------------------------------------------------------
+r115 | kentwilliams | 2008-09-11 13:23:18 -0500 (Thu, 11 Sep 2008) | 1 line
+
+DEBUG: reading and writing the model file should agree on data types
+------------------------------------------------------------------------
+r114 | hjmjohnson | 2008-09-11 10:17:06 -0500 (Thu, 11 Sep 2008) | 1 line
+
+ENH:  Trying to fix the model file reading and writing.
+------------------------------------------------------------------------
+r112 | hjmjohnson | 2008-09-10 13:46:30 -0500 (Wed, 10 Sep 2008) | 1 line
+
+ENH: Added new program for debugging purposes.
+------------------------------------------------------------------------
+r111 | hjmjohnson | 2008-09-10 06:34:43 -0500 (Wed, 10 Sep 2008) | 1 line
+
+BUG:  Working out bugs introduced during the refactoring.
+------------------------------------------------------------------------
+r110 | hjmjohnson | 2008-09-07 03:01:33 -0500 (Sun, 07 Sep 2008) | 1 line
+
+ENH:  Working on getting the acpcdetect program to work.
+------------------------------------------------------------------------
+r109 | hjmjohnson | 2008-09-06 04:43:48 -0500 (Sat, 06 Sep 2008) | 1 line
+
+ENH:  Added ability to do byteswapping of files.
+------------------------------------------------------------------------
+r108 | kentwilliams | 2008-09-02 13:29:53 -0500 (Tue, 02 Sep 2008) | 1 line
+
+BUG: got sign wrong for seekg
+------------------------------------------------------------------------
+r107 | kentwilliams | 2008-09-02 13:26:27 -0500 (Tue, 02 Sep 2008) | 1 line
+
+ENH: binary model file now reads correctly on differently-ended machines
+------------------------------------------------------------------------
+r106 | kentwilliams | 2008-09-02 10:37:02 -0500 (Tue, 02 Sep 2008) | 1 line
+
+COMP: initialize vector sizes before reading into them
+------------------------------------------------------------------------
+r105 | kentwilliams | 2008-09-02 10:32:10 -0500 (Tue, 02 Sep 2008) | 1 line
+
+comp: more work on reading model files
+------------------------------------------------------------------------
+r104 | kentwilliams | 2008-09-02 10:04:27 -0500 (Tue, 02 Sep 2008) | 1 line
+
+ENH: Read model files back in
+------------------------------------------------------------------------
+r103 | hjmjohnson | 2008-09-01 17:33:15 -0500 (Mon, 01 Sep 2008) | 1 line
+
+BUG:  Missing function that will be added on tuesday.
+------------------------------------------------------------------------
+r102 | hjmjohnson | 2008-08-30 08:21:36 -0500 (Sat, 30 Aug 2008) | 1 line
+
+ENH: Finished first pass of refactoring the acpcmodel.
+------------------------------------------------------------------------
+r101 | hjmjohnson | 2008-08-29 15:22:05 -0500 (Fri, 29 Aug 2008) | 1 line
+
+ENH: Nearly done refactoring the statistics outputs.
+------------------------------------------------------------------------
+r100 | kentwilliams | 2008-08-29 13:17:10 -0500 (Fri, 29 Aug 2008) | 1 line
+
+Moved common variables used in the model definition and binary model file into a common superclass
+------------------------------------------------------------------------
+r99 | hjmjohnson | 2008-08-29 11:10:08 -0500 (Fri, 29 Aug 2008) | 1 line
+
+ENH:  Matched types for new variales across both classes in preparation for extracting a base class.
+------------------------------------------------------------------------
+r98 | hjmjohnson | 2008-08-29 10:41:58 -0500 (Fri, 29 Aug 2008) | 1 line
+
+ENH:  Nearly done refactoring the acpcmodel program,  The entire model is nearly encapsulated in a single class now.
+------------------------------------------------------------------------
+r97 | hjmjohnson | 2008-08-28 22:57:44 -0500 (Thu, 28 Aug 2008) | 1 line
+
+ENH:  New functions written to extract regions from images.
+------------------------------------------------------------------------
+r96 | hjmjohnson | 2008-08-28 18:07:15 -0500 (Thu, 28 Aug 2008) | 1 line
+
+ENH:  First version that rotates around each point is done.
+------------------------------------------------------------------------
+r94 | kentwilliams | 2008-08-28 16:44:35 -0500 (Thu, 28 Aug 2008) | 1 line
+
+ENH: first whack at the debug image branding
+------------------------------------------------------------------------
+r93 | hjmjohnson | 2008-08-27 22:31:26 -0500 (Wed, 27 Aug 2008) | 1 line
+
+ENH:  Fully working ACPC aligned data set with AC at the center of the image.
+------------------------------------------------------------------------
+r92 | hjmjohnson | 2008-08-27 21:49:18 -0500 (Wed, 27 Aug 2008) | 1 line
+
+BUG:  Transcribed the wrong rotation matricies for computing the 3x3 matrix from axis rotation angles.
+------------------------------------------------------------------------
+r90 | hjmjohnson | 2008-08-27 17:58:02 -0500 (Wed, 27 Aug 2008) | 1 line
+
+ENH:  Working on getting the ACPC alignments done.
+------------------------------------------------------------------------
+r89 | kentwilliams | 2008-08-27 08:51:57 -0500 (Wed, 27 Aug 2008) | 1 line
+
+COMP: changed to use acpcModelFile method to use the acpcmodelDefinition direcktly
+------------------------------------------------------------------------
+r88 | hjmjohnson | 2008-08-27 07:41:11 -0500 (Wed, 27 Aug 2008) | 2 lines
+
+ENH:  Added some comments for kent on a few little side projects that neeed to be done.
+
+------------------------------------------------------------------------
+r87 | hjmjohnson | 2008-08-26 21:41:22 -0500 (Tue, 26 Aug 2008) | 1 line
+
+BUG:  Fixed transforms so that both images and landmarks can be transformed consistently across the images.
+------------------------------------------------------------------------
+r86 | kentwilliams | 2008-08-26 11:27:12 -0500 (Tue, 26 Aug 2008) | 1 line
+
+COMP: changed point type name
+------------------------------------------------------------------------
+r85 | kentwilliams | 2008-08-26 11:24:42 -0500 (Tue, 26 Aug 2008) | 1 line
+
+COMP: moved point and superclass definitions into class itself -- having a global 'PointType' feels dangerous
+------------------------------------------------------------------------
+r84 | hjmjohnson | 2008-08-25 23:24:39 -0500 (Mon, 25 Aug 2008) | 1 line
+
+BUG:  Fixed alignment bugs caused by using the wrong center of rotations.
+------------------------------------------------------------------------
+r83 | hjmjohnson | 2008-08-25 17:52:57 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH:  continuing to fix landmark points and making everything related to physical dimensions.
+------------------------------------------------------------------------
+r82 | kentwilliams | 2008-08-25 15:59:00 -0500 (Mon, 25 Aug 2008) | 1 line
+
+COMP: completed file name changes
+------------------------------------------------------------------------
+r81 | kentwilliams | 2008-08-25 15:57:21 -0500 (Mon, 25 Aug 2008) | 1 line
+
+COMP: changed around filenames to follow normal naming conventions
+------------------------------------------------------------------------
+r80 | kentwilliams | 2008-08-25 15:49:50 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH: created writer for acpcmodel model files
+------------------------------------------------------------------------
+r79 | hjmjohnson | 2008-08-25 14:15:17 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH:  More acpcmodel cleanups.  Made new class for reading/writingt he models.
+------------------------------------------------------------------------
+r78 | hjmjohnson | 2008-08-25 12:06:54 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH: Fixed file name.
+------------------------------------------------------------------------
+r77 | kentwilliams | 2008-08-25 12:00:32 -0500 (Mon, 25 Aug 2008) | 1 line
+
+COMP: 2 functions needed an inline keyword
+------------------------------------------------------------------------
+r76 | kentwilliams | 2008-08-25 11:53:33 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH: wrote, acpcmodelSetupClass, added testAcpcmodelSetupClass
+------------------------------------------------------------------------
+r75 | hjmjohnson | 2008-08-25 11:44:24 -0500 (Mon, 25 Aug 2008) | 1 line
+
+COMP:  Fixed compilation issues by detangling some of the function calls and removing huge portions of the code that will be necessary to re-write.
+------------------------------------------------------------------------
+r74 | hjmjohnson | 2008-08-25 11:32:46 -0500 (Mon, 25 Aug 2008) | 1 line
+
+ENH:  Fixed filename of header included.
+------------------------------------------------------------------------
+r73 | hjmjohnson | 2008-08-24 22:21:47 -0500 (Sun, 24 Aug 2008) | 1 line
+
+ENH:  Continuing to update acpcmodel in the itk conversion.
+------------------------------------------------------------------------
+r72 | hjmjohnson | 2008-08-24 16:52:31 -0500 (Sun, 24 Aug 2008) | 1 line
+
+ENH: Cleaned up code and started to work on acpcmodel program.
+------------------------------------------------------------------------
+r71 | hjmjohnson | 2008-08-24 15:53:18 -0500 (Sun, 24 Aug 2008) | 1 line
+
+ENH: Finally got the ACPC transform defined that will align the MSP with the center voxel lattice of the image.
+------------------------------------------------------------------------
+r70 | hjmjohnson | 2008-08-23 18:40:01 -0500 (Sat, 23 Aug 2008) | 1 line
+
+ENH:  A working version of the MSP finder using vnl powell optimization for finding the plane.
+------------------------------------------------------------------------
+r69 | hjmjohnson | 2008-08-22 21:13:00 -0500 (Fri, 22 Aug 2008) | 1 line
+
+ENH:  More refactorings of the plane finding code.
+------------------------------------------------------------------------
+r68 | hjmjohnson | 2008-08-21 23:39:37 -0500 (Thu, 21 Aug 2008) | 1 line
+
+ENH:  This does not compile at the moment, and needs to have refactoring completed.
+------------------------------------------------------------------------
+r62 | hjmjohnson | 2008-08-21 19:38:20 -0500 (Thu, 21 Aug 2008) | 1 line
+
+ENH:  Working on making planes estimation completely from ITK physical coordinates.
+------------------------------------------------------------------------
+r60 | hjmjohnson | 2008-08-20 21:05:04 -0500 (Wed, 20 Aug 2008) | 1 line
+
+ENH:  This version does not compile, but it is on it way for the first major refactoring.
+------------------------------------------------------------------------
+r59 | hjmjohnson | 2008-08-19 18:00:48 -0500 (Tue, 19 Aug 2008) | 1 line
+
+ENH:  Updated to use *.nii.gz
+------------------------------------------------------------------------
+r58 | hjmjohnson | 2008-08-18 22:26:38 -0500 (Mon, 18 Aug 2008) | 1 line
+
+ENH: More conversions to help make images itk images.
+------------------------------------------------------------------------
+r57 | hjmjohnson | 2008-08-18 19:28:19 -0500 (Mon, 18 Aug 2008) | 1 line
+
+COMP: Adding necessary files to build ART.
+------------------------------------------------------------------------
+r56 | hjmjohnson | 2008-08-17 21:44:29 -0500 (Sun, 17 Aug 2008) | 1 line
+
+ENH:  Consolidating functions into templates to help remove redundant code.
+------------------------------------------------------------------------
+r55 | hjmjohnson | 2008-08-16 11:02:59 -0500 (Sat, 16 Aug 2008) | 1 line
+
+ENH:  Many code cleanups. Made a library so that common functions only live in one spot.
+------------------------------------------------------------------------
+r54 | kentwilliams | 2008-08-14 15:33:52 -0500 (Thu, 14 Aug 2008) | 1 line
+
+acpcdetect cleanup
+------------------------------------------------------------------------
+r53 | kentwilliams | 2008-08-14 12:57:52 -0500 (Thu, 14 Aug 2008) | 1 line
+
+fixed typos
+------------------------------------------------------------------------
+r52 | kentwilliams | 2008-08-14 12:56:27 -0500 (Thu, 14 Aug 2008) | 1 line
+
+Code cleanup -- made template functions of stats functions that were duplicated over and over
+------------------------------------------------------------------------
+r49 | hjmjohnson | 2008-08-14 10:49:22 -0500 (Thu, 14 Aug 2008) | 1 line
+
+ENH: Removed code that was commented out.
+------------------------------------------------------------------------
+r48 | hjmjohnson | 2008-08-14 10:17:14 -0500 (Thu, 14 Aug 2008) | 1 line
+
+COMP:  Forgot to include 2 new source fles.
+------------------------------------------------------------------------
+r47 | hjmjohnson | 2008-08-14 09:35:29 -0500 (Thu, 14 Aug 2008) | 1 line
+
+ENH:  First pass at making program use ITK images.  This resulted in some numerical changes, but the results appear to be holding constant.
+------------------------------------------------------------------------
+r46 | kentwilliams | 2008-08-13 15:54:46 -0500 (Wed, 13 Aug 2008) | 1 line
+
+image type no longer getting set since we're using ITK to read files -- depending on it's never-set value is bad
+------------------------------------------------------------------------
+r44 | hjmjohnson | 2008-08-13 14:38:39 -0500 (Wed, 13 Aug 2008) | 1 line
+
+ENH:  More ITK integration of the code.
+------------------------------------------------------------------------
+r43 | kentwilliams | 2008-08-13 12:06:17 -0500 (Wed, 13 Aug 2008) | 1 line
+
+use ITK for writing image volumes
+------------------------------------------------------------------------
+r42 | kentwilliams | 2008-08-13 09:10:08 -0500 (Wed, 13 Aug 2008) | 1 line
+
+use ITK for I/O
+------------------------------------------------------------------------
+r41 | kentwilliams | 2008-08-12 09:47:39 -0500 (Tue, 12 Aug 2008) | 1 line
+
+COMP: converted acpcmodel to use GenerateCLP
+------------------------------------------------------------------------
+r40 | hjmjohnson | 2008-08-11 23:37:04 -0500 (Mon, 11 Aug 2008) | 1 line
+
+ENH:  More code cleanup.
+------------------------------------------------------------------------
+r39 | hjmjohnson | 2008-08-11 22:53:38 -0500 (Mon, 11 Aug 2008) | 1 line
+
+ENH: Working through the code to clean up and include more itk image procesing.
+------------------------------------------------------------------------
+r38 | hjmjohnson | 2008-08-11 16:27:03 -0500 (Mon, 11 Aug 2008) | 1 line
+
+COMP:  First little cleanups of acpcmodel.cxx to remove compiler warnings and get it to compile.
+------------------------------------------------------------------------
+r35 | kentwilliams | 2008-08-11 16:01:52 -0500 (Mon, 11 Aug 2008) | 1 line
+
+slight correction
+------------------------------------------------------------------------
+r34 | kentwilliams | 2008-08-11 15:37:19 -0500 (Mon, 11 Aug 2008) | 1 line
+
+ENH: Use ITK file reader
+------------------------------------------------------------------------
+r33 | ardekani | 2008-08-11 13:45:44 -0500 (Mon, 11 Aug 2008) | 1 line
+
+Initial import
+------------------------------------------------------------------------
+r32 | kentwilliams | 2008-08-11 13:03:58 -0500 (Mon, 11 Aug 2008) | 1 line
+
+got rid of global variables by tracing their use
+------------------------------------------------------------------------
+r31 | hjmjohnson | 2008-08-10 22:23:29 -0500 (Sun, 10 Aug 2008) | 1 line
+
+BUG:  refactoring error in the number of iterations that were being run.  It was two command line variables being incorrectly combined.
+------------------------------------------------------------------------
+r30 | hjmjohnson | 2008-08-10 21:42:57 -0500 (Sun, 10 Aug 2008) | 1 line
+
+ENH: added vcl math commands, and continued to clean up the code organization and variable listings.
+------------------------------------------------------------------------
+r20 | hjmjohnson | 2008-08-09 00:16:52 -0500 (Sat, 09 Aug 2008) | 1 line
+
+BUG:  Fixed bug that prevented program from running properly.
+------------------------------------------------------------------------
+r18 | hjmjohnson | 2008-08-08 23:30:38 -0500 (Fri, 08 Aug 2008) | 1 line
+
+COMP:  Removed compiler warnings and cleaned up code formatting.
+------------------------------------------------------------------------
+r16 | hjmjohnson | 2008-08-08 18:05:51 -0500 (Fri, 08 Aug 2008) | 1 line
+
+COMP:  Compiler error due to improper escape sequence in xml file.
+------------------------------------------------------------------------
+r15 | kentwilliams | 2008-08-08 17:04:59 -0500 (Fri, 08 Aug 2008) | 1 line
+
+COMP: Completed conversion of all programs to CLP
+------------------------------------------------------------------------
+r14 | kentwilliams | 2008-08-08 15:36:01 -0500 (Fri, 08 Aug 2008) | 1 line
+
+ENH: Use GenerateCLP
+------------------------------------------------------------------------
+r13 | hjmjohnson | 2008-08-08 07:01:56 -0500 (Fri, 08 Aug 2008) | 1 line
+
+ENH: Removed compiler warning messages.
+------------------------------------------------------------------------
+r12 | hjmjohnson | 2008-08-07 22:37:37 -0500 (Thu, 07 Aug 2008) | 1 line
+
+ENH: Added ability to write out RGB images in itk compliant formats.
+------------------------------------------------------------------------
+r9 | hjmjohnson | 2008-08-07 13:01:38 -0500 (Thu, 07 Aug 2008) | 1 line
+
+ENH:  Added new test suite for the art tools.  It is currently a pretty weak test suite.
+------------------------------------------------------------------------
+r8 | hjmjohnson | 2008-08-07 07:21:58 -0500 (Thu, 07 Aug 2008) | 1 line
+
+BUG:  Tracking down orientation bugs in acpcdetect.
+------------------------------------------------------------------------
+r7 | hjmjohnson | 2008-08-06 22:16:14 -0500 (Wed, 06 Aug 2008) | 1 line
+
+ENH:  Added some code to determine the correct orientation for syncronizing with ITK.
+------------------------------------------------------------------------
+r2 | hjmjohnson | 2008-08-06 12:32:40 -0500 (Wed, 06 Aug 2008) | 1 line
+
+DOC:  Added BSD license to this file.  This license will be reviewed by Dr. Ardekani and if acceptiable will be propogated to the other source files.
+------------------------------------------------------------------------
+r1 | hjmjohnson | 2008-08-06 12:04:08 -0500 (Wed, 06 Aug 2008) | 1 line
+
+ENH:  After working with Dr. Babak Ardekani we have developed the first svn repository release of the art tools that build with CMAKE.  Work will continue to integrate ITK features into the art toolkit over the next several weeks.
+------------------------------------------------------------------------
diff --git a/BRAINSConstellationDetector/src/TransformFromFiducials.cxx b/BRAINSConstellationDetector/src/TransformFromFiducials.cxx
new file mode 100644
index 00000000..77eed601
--- /dev/null
+++ b/BRAINSConstellationDetector/src/TransformFromFiducials.cxx
@@ -0,0 +1,288 @@
+/** Some of the components in this file originated from work in the Slicer4
+ * development tree.  Adaptations to work as a command line program were
+ * made by Hans J. Johnson to facilitate creating a transform directly from a
+ * set of landmark files.
+ */
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+#include "TransformFromFiducialsCLP.h"
+#include "itkLandmarkBasedTransformInitializer.h"
+#include "itkSimilarity3DTransform.h"
+#include "BRAINSThreadControl.h"
+
+#include "Slicer3LandmarkIO.h"
+#include "GenericTransformImage.h"
+
+namespace
+{
+typedef  itk::Point              ImagePointType;
+typedef  std::vector        PointList;
+typedef itk::VersorRigid3DTransform VersorRigidTransformType;
+typedef itk::Similarity3DTransform  SimilarityTransformType;
+
+// Function to convert a point from std::vector to itk::Point
+// this also performs the RAS -> LPS conversion necessary
+// from slicer -> ITK
+static itk::Point
+convertStdVectorToITKPoint(const std::vector & vec)
+{
+  itk::Point p;
+
+  // convert RAS to LPS
+  p[0] = -vec[0];
+  p[1] = -vec[1];
+  p[2] = vec[2];
+  return p;
+}
+
+// Operator to compute the squared distance between two points
+class SquaredPointDistance
+{
+public:
+  explicit SquaredPointDistance(const itk::Point& ctr)
+    : m_Point(ctr)
+  {
+  }
+
+  double operator()(const itk::Point& p)
+  {
+    return (p - m_Point).GetSquaredNorm();
+  }
+
+private:
+  itk::Point m_Point;
+
+};
+
+// Function to compute the scaling factor between two sets of points.
+// This is the symmetric form given by
+//    Berthold K. P. Horn (1987),
+//    "Closed-form solution of absolute orientation using unit quaternions,"
+//    Journal of the Optical Society of America A, 4:629-642
+static double
+computeSymmetricScale(const std::vector >& fixedPoints,
+                      const std::vector >& movingPoints,
+                      const itk::Point& fixedcenter,
+                      const itk::Point& movingcenter)
+{
+  std::vector centeredFixedPoints(fixedPoints.size(), 0.0);
+  std::vector centeredMovingPoints(movingPoints.size(), 0.0);
+
+  std::transform(fixedPoints.begin(), fixedPoints.end(),
+                 centeredFixedPoints.begin(),
+                 SquaredPointDistance(fixedcenter) );
+
+  std::transform(movingPoints.begin(), movingPoints.end(),
+                 centeredMovingPoints.begin(),
+                 SquaredPointDistance(movingcenter) );
+
+  const double fixedmag = std::accumulate(centeredFixedPoints.begin(),
+                                          centeredFixedPoints.end(),
+                                          0.0);
+
+  const double movingmag = std::accumulate(centeredMovingPoints.begin(),
+                                           centeredMovingPoints.end(),
+                                           0.0);
+
+  return sqrt(movingmag / fixedmag);
+}
+
+}
+
+static SimilarityTransformType::Pointer DoIt_Similarity(PointList fixedPoints, PointList movingPoints)
+{
+  // Our input into landmark based initialize will be of this form
+  // The format for saving to slicer is defined later
+  SimilarityTransformType::Pointer similarityTransform = SimilarityTransformType::New();
+
+  similarityTransform->SetIdentity();
+  // workaround a bug in older versions of ITK
+  similarityTransform->SetScale(1.0);
+
+  typedef itk::LandmarkBasedTransformInitializer, itk::Image > InitializerType;
+  InitializerType::Pointer initializer = InitializerType::New();
+
+  // This expects a VersorRigid3D.  The similarity transform works because
+  // it derives from that class
+  initializer->SetTransform(similarityTransform);
+
+  initializer->SetFixedLandmarks(fixedPoints);
+  initializer->SetMovingLandmarks(movingPoints);
+  initializer->InitializeTransform();
+
+  // Compute the scaling factor and add that in
+  itk::Point fixedCenter(similarityTransform->GetCenter() );
+  itk::Point movingCenter(similarityTransform->GetCenter() + similarityTransform->GetTranslation() );
+
+  const double s = computeSymmetricScale(fixedPoints, movingPoints, fixedCenter, movingCenter);
+  similarityTransform->SetScale(s);
+  return similarityTransform;
+}
+
+static VersorRigidTransformType::Pointer DoIt_Rigid(PointList fixedPoints, PointList movingPoints)
+{
+  // Our input into landmark based initialize will be of this form
+  // The format for saving to slicer is defined later
+  VersorRigidTransformType::Pointer rigidTransform = VersorRigidTransformType::New();
+
+  rigidTransform->SetIdentity();
+
+  typedef itk::LandmarkBasedTransformInitializer, itk::Image > InitializerType;
+  InitializerType::Pointer initializer = InitializerType::New();
+
+  // This expects a VersorRigid3D.  The similarity transform works because
+  // it derives from that class
+  initializer->SetTransform(rigidTransform);
+
+  initializer->SetFixedLandmarks(fixedPoints);
+  initializer->SetMovingLandmarks(movingPoints);
+  initializer->InitializeTransform();
+  return rigidTransform;
+}
+
+int main(int argc, char* argv[])
+{
+  PARSE_ARGS;
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+  if( saveTransform == "" )
+    {
+    std::cerr << "An output transform must be specified" << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  if(  ( ( fixedLandmarks.size() > 0 ) && ( fixedLandmarksFile != "" ) )
+       || ( ( movingLandmarks.size() > 0 ) && ( movingLandmarksFile != "" ) ) )
+    {
+    std::cerr << "Program can accept landmark files with points, or directly specify points, but not both."
+              << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  PointList fixedPoints(0);
+  PointList movingPoints(0);
+
+  if( fixedLandmarks.size() > 0 ) //
+    {
+    fixedPoints.resize(fixedLandmarks.size() );
+    movingPoints.resize(movingLandmarks.size() );
+    // Convert both points lists to ITK points and convert RAS -> LPS
+
+    std::transform(fixedLandmarks.begin(), fixedLandmarks.end(),
+                   fixedPoints.begin(),
+                   convertStdVectorToITKPoint);
+
+    std::transform(movingLandmarks.begin(), movingLandmarks.end(),
+                   movingPoints.begin(),
+                   convertStdVectorToITKPoint);
+    }
+  else
+    {
+    // Read fcsv files and make lists
+    if( fixedLandmarksFile != ""  || movingLandmarksFile != "" )
+      {
+      if( movingLandmarksFile == "" || fixedLandmarksFile == "" )
+        {
+        std::cerr << "Must supply both fixed and moving landmark files" << std::endl;
+        return EXIT_FAILURE;
+        }
+      typedef std::map LandmarksMapType;
+
+      // NOTE: ReadSlicer3toITKLmk returns points in LPS system
+      LandmarksMapType fixedLandmarkMap = ReadSlicer3toITKLmk( fixedLandmarksFile );
+      LandmarksMapType movingLandmarkMap = ReadSlicer3toITKLmk( movingLandmarksFile );
+      for( LandmarksMapType::const_iterator fmapit = fixedLandmarkMap.begin();
+           fmapit != fixedLandmarkMap.end(); ++fmapit )
+        {
+        LandmarksMapType::const_iterator mmapit = movingLandmarkMap.find(fmapit->first);
+        if( mmapit != movingLandmarkMap.end() )
+          {
+          fixedPoints.push_back(fmapit->second);
+          movingPoints.push_back(fmapit->second);
+          }
+        }
+      }
+    }
+
+  if( fixedLandmarks.size() <= 0 || movingLandmarks.size() <= 0 ||
+      fixedLandmarks.size() != movingLandmarks.size() )
+    {
+    std::cerr << "Fixed and moving landmark lists must be of the same size "
+              << "and contain at least one point" << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  if( transformType != "Translation" && fixedLandmarks.size() < 3 )
+    {
+    std::cerr << "At least 3 fiducual points must be specified for Rigid or Similarity transforms"
+              << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  GenericTransformType::Pointer genericTransform = NULL;
+
+  if( transformType == "Rigid" || transformType == "Translation" )
+    {
+    VersorRigidTransformType::Pointer rigidTransform = DoIt_Rigid(fixedPoints, movingPoints);
+    // do nothing
+    if( transformType == "Translation" )
+      {
+      // Clear out the computed rotation if we only requested translation
+      itk::Versor v;
+      v.SetIdentity();
+      rigidTransform->SetRotation(v);
+      }
+    genericTransform = rigidTransform.GetPointer();
+    }
+  else if( transformType == "Similarity" )
+    {
+    SimilarityTransformType::Pointer similarityTransform = DoIt_Similarity(fixedPoints, movingPoints);
+    genericTransform = similarityTransform.GetPointer();
+    }
+  else if( transformType == "Affine" )
+    {
+    // itk::Matrix a =
+    //   computeAffineTransform(fixedPoints, movingPoints,
+    //                          fixedCenter, movingCenter);
+    std::cerr << "Unsupported transform type: " << transformType << std::endl;
+    genericTransform = NULL;
+    return EXIT_FAILURE;
+    }
+  else
+    {
+    std::cerr << "Unsupported transform type: " << transformType << std::endl;
+    genericTransform = NULL;
+    return EXIT_FAILURE;
+    }
+#if 0
+  // Convert into an affine transform for saving to slicer
+  itk::AffineTransform::Pointer atransform =
+    itk::AffineTransform::New();
+
+  atransform->SetCenter(genericTransform->GetCenter() );
+  atransform->SetMatrix(genericTransform->GetMatrix() );
+  atransform->SetTranslation(genericTransform->GetTranslation() );
+
+  itk::TransformFileWriter::Pointer twriter = itk::TransformFileWriter::New();
+  twriter->SetInput(atransform);
+  twriter->SetFileName(saveTransform);
+
+  twriter->Update();
+#endif
+  WriteTransformToDisk(genericTransform.GetPointer(), saveTransform);
+
+  return EXIT_SUCCESS;
+}
+
diff --git a/BRAINSConstellationDetector/src/TransformFromFiducials.xml b/BRAINSConstellationDetector/src/TransformFromFiducials.xml
new file mode 100644
index 00000000..39776357
--- /dev/null
+++ b/BRAINSConstellationDetector/src/TransformFromFiducials.xml
@@ -0,0 +1,71 @@
+
+
+  Registration
+  Fiducial Registration
+  Computes a rigid, similarity or affine transform from a matched list of fiducials
+  0.1.0.$Revision$
+  http://www.slicer.org/slicerWiki/index.php/Modules:TransformFromFiducials-Documentation-3.6
+  
+  Casey B Goodlett
+  
+    This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
+  
+  
+    
+      fixedLandmarks
+      Ordered list of landmarks in the fixed image
+      
+      fixedLandmarks
+      input
+    
+    
+      movingLandmarks
+      Ordered list of landmarks in the moving image
+      
+      movingLandmarks
+      input
+    
+    
+      saveTransform
+      
+      Save the transform that results from registration
+      saveTransform
+      output
+    
+    
+      transformType
+      Type of transform to produce
+      
+      transformType
+      Translation
+      Rigid
+      Similarity
+      Rigid
+    
+  
+  
+    
+      fixedLandmarksFile
+      An fcsv formatted file with a list of landmark points.
+      
+      fixedLandmarksFile
+      input
+      
+    
+    
+      movingLandmarksFile
+      An fcsv formatted file with a list of landmark points.
+      
+      movingLandmarksFile
+      input
+      
+    
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+  
+
diff --git a/BRAINSConstellationDetector/src/TrimForegroundInDirection.cxx b/BRAINSConstellationDetector/src/TrimForegroundInDirection.cxx
new file mode 100644
index 00000000..6cc6f84a
--- /dev/null
+++ b/BRAINSConstellationDetector/src/TrimForegroundInDirection.cxx
@@ -0,0 +1,151 @@
+/*
+ * Author: Hans J. Johnson
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "itkIO.h"
+#include 
+#include "TrimForegroundInDirection.h"
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include 
+#include 
+#include 
+#include 
+#include "itkFindCenterOfBrainFilter.h"
+
+// #define USE_DEBUGGIN_IMAGES
+
+void PrintImageInformation(SImageType::Pointer image)
+{
+  // get information from the image
+  SImageType::PointType     origin  = image->GetOrigin();
+  SImageType::SpacingType   spacing = image->GetSpacing();
+  SImageType::DirectionType direction = image->GetDirection();
+  SImageType::IndexType     startIndex = image->GetLargestPossibleRegion().GetIndex();
+  SImageType::SizeType      size = image->GetLargestPossibleRegion().GetSize();
+  SImageType::PointType     physicalCenter, intensityCenter;
+  double                    physicalSize[3] = { 0, 0, 0 };
+  SImageType::IndexType     stopIndex;
+
+  SImageType::Pointer infoImage = SImageType::New();    // define an image just
+                                                        // to do calculations
+  SImageType::RegionType region;
+  SImageType::PointType  physicalSpaceMin;
+  SImageType::PointType  physicalSpaceMax;
+  SImageType::PointType  physicalStartPointSource;
+  SImageType::PointType  physicalStopPointSource;
+
+  stopIndex[0] = startIndex[0] + size[0] - 1; // The last valid index
+  stopIndex[1] = startIndex[1] + size[1] - 1;
+  stopIndex[2] = startIndex[2] + size[2] - 1;
+  region.SetSize(size);
+  region.SetIndex(startIndex);
+
+  infoImage->SetOrigin(origin); // set the parameters in infoImage
+  infoImage->SetSpacing(spacing);
+  infoImage->SetDirection(direction);
+  infoImage->SetRegions(region);
+
+  // transform startIndex to physical coordinates
+  infoImage->TransformIndexToPhysicalPoint(startIndex, physicalStartPointSource);
+  infoImage->TransformIndexToPhysicalPoint(stopIndex, physicalStopPointSource);
+  physicalSpaceMin = physicalStartPointSource - direction * spacing * 0.5;
+  physicalSpaceMax = physicalStopPointSource + direction * spacing * 0.5;
+
+  // physical extent is the difference between max corner and the minimum
+  // corner, always positive
+  physicalSize[0] = physicalSpaceMax[0] - physicalSpaceMin[0];
+  physicalSize[0] = physicalSize[0] > 0 ? physicalSize[0] : 0 - physicalSize[0];
+  physicalSize[1] = physicalSpaceMax[1] - physicalSpaceMin[1];
+  physicalSize[1] = physicalSize[1] > 0 ? physicalSize[1] : 0 - physicalSize[1];
+  physicalSize[2] = physicalSpaceMax[2] - physicalSpaceMin[2];
+  physicalSize[2] = physicalSize[2] > 0 ? physicalSize[2] : 0 - physicalSize[2];
+
+  // calculate physical extent as the midpoint between the opposing corners
+  physicalCenter[0] = ( physicalSpaceMax[0] + physicalSpaceMin[0] ) / 2;
+  physicalCenter[1] = ( physicalSpaceMax[1] + physicalSpaceMin[1] ) / 2;
+  physicalCenter[2] = ( physicalSpaceMax[2] + physicalSpaceMin[2] ) / 2;
+
+  // Use the ImageMomentsCalculator to compute the center of mass
+  typedef itk::ImageMomentsCalculator Calculator;
+  Calculator::Pointer calc = Calculator::New();
+  calc->SetImage(image);
+  calc->Compute();
+  itk::Vector center = calc->GetCenterOfGravity();
+
+  // Output to screen
+  std::cout << "IMAGE ORIGIN: " << origin << std::endl;
+  std::cout << "IMAGE PHYSICAL EXTENT: [" << physicalSize[0] << ", " << physicalSize[1] << ", " << physicalSize[2]
+            << "]" << std::endl;
+  std::cout << "IMAGE FIELD OF VIEW: " << physicalSpaceMin << " to " << physicalSpaceMax << std::endl;
+  std::cout << "IMAGE CENTER OF PHYSICAL SPACE: " << physicalCenter << std::endl;
+  std::cout << "CENTER OF (INTENSITY) MASS: [" << center[0] << ", " << center[1] << ", " << center[2] << "]"
+            << std::endl;
+}
+
+SImageType::PointType  FindCenterOfBrainBasedOnTopOfHead(SImageType::Pointer & volOrig,
+                                                         unsigned int axis,
+                                                         double otsuPercentileThreshold,
+                                                         unsigned int closingSize,
+                                                         double headSizeLowerLimit,
+                                                         SImageType::PixelType BackgroundFillValue)
+{
+  SImageType::Pointer foreground = SImageType::New();
+
+  return TrimForegroundInDirection(foreground,
+                                   volOrig,
+                                   axis,
+                                   otsuPercentileThreshold,
+                                   closingSize,
+                                   headSizeLowerLimit,
+                                   BackgroundFillValue);
+}
+
+// ////////////////////////////////////////////////////////////////////////
+// ////////////////////////////////////////////////////////////////////////
+SImageType::PointType TrimForegroundInDirection(SImageType::Pointer & foreground,  SImageType::Pointer & volOrig,
+                                                unsigned int axis,
+                                                double otsuPercentileThreshold, unsigned int closingSize,
+                                                double headSizeLowerLimit, SImageType::PixelType BackgroundFillValue)
+{
+  typedef itk::FindCenterOfBrainFilter FindCenterFilter;
+  FindCenterFilter::Pointer findCenterFilter = FindCenterFilter::New();
+  findCenterFilter->SetInput(volOrig);
+  findCenterFilter->SetAxis(axis);
+  findCenterFilter->SetOtsuPercentileThreshold(otsuPercentileThreshold);
+  findCenterFilter->SetClosingSize(closingSize);
+  findCenterFilter->SetHeadSizeLimit(headSizeLowerLimit);
+  findCenterFilter->SetBackgroundValue(BackgroundFillValue);
+
+  findCenterFilter->Update();
+
+  foreground = findCenterFilter->GetTrimmedImage();
+  SImageType::PointType center = findCenterFilter->GetCenterOfBrain();
+  return center;
+}
+
diff --git a/BRAINSConstellationDetector/src/TrimForegroundInDirection.h b/BRAINSConstellationDetector/src/TrimForegroundInDirection.h
new file mode 100644
index 00000000..a0c2898c
--- /dev/null
+++ b/BRAINSConstellationDetector/src/TrimForegroundInDirection.h
@@ -0,0 +1,58 @@
+#ifndef __TrimForegroundInDirection_h
+#define __TrimForegroundInDirection_h
+
+/*
+ * Author: Hans J. Johnson
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/*** ITK Headers ***/
+#if defined( _MSC_VER )
+#pragma warning ( disable : 4786 )
+#endif
+
+#include "itkIO.h"
+#include "landmarksConstellationCommon.h"
+
+extern SImageType::PointType TrimForegroundInDirection(SImageType::Pointer & foreground, SImageType::Pointer & volOrig,
+                                                       unsigned int axis, double otsuPercentileThreshold,
+                                                       unsigned int closingSize, double headSizeLowerLimit,
+                                                       SImageType::PixelType BackgroundFillValue);
+
+// TODO: This function needs to be cleaned up.  It should not compute the otsu
+// TODO: threasholding, but rather, it should have been given
+// TODO: An image that was previously otsu threasholded.
+// TODO: This filter slowly evolved from another filter, and should be cleaned
+// so
+// TODO: that it only uses the items that are necessary for success.
+extern SImageType::PointType FindCenterOfBrainBasedOnTopOfHead(SImageType::Pointer & volOrig, unsigned int axis,
+                                                               double otsuPercentileThreshold, unsigned int closingSize,
+                                                               double headSizeLowerLimit,
+                                                               SImageType::PixelType BackgroundFillValue);
+
+#endif                          /* __TrimForegroundInDirection_h */
diff --git a/BRAINSConstellationDetector/src/fcsv_to_matlab_new.cxx b/BRAINSConstellationDetector/src/fcsv_to_matlab_new.cxx
new file mode 100644
index 00000000..487c6886
--- /dev/null
+++ b/BRAINSConstellationDetector/src/fcsv_to_matlab_new.cxx
@@ -0,0 +1,967 @@
+/*
+ fcsv_to_matlab:
+A program to automatically generate the matlab matricies need to generate new model files.
+
+Arguments:
+--landmarkFiles {arg}  : A glob of landmark files to include (default: "*.fcsv") (Be sure to use quotes!)
+--outputMatlabFile {arg}  : The name of the output matlab file to save (default: load_landmarks.m)
+--landmarkTypesList {arg}    : A list of the landmarks, grouped by landmarkTypes ("AC,base\nPC,base\n\n")
+
+Development notes: Yes, I do use returns of stl containers instead of
+passing the return containers by reference as arguments.  While this is slow
+in 03, in 0x it's fast due to move constructors, and anyway, this code
+benefits more from readability than speed.
+
+*/
+
+// I N C L U D E S ////////////////////////////////////////////////////////////
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+
+#include "Slicer3LandmarkIO.h"
+#include "vnl/vnl_matrix.h"
+#include "vnl/vnl_matlab_print.h"
+#include "vnl/algo/vnl_symmetric_eigensystem.h"
+#include 
+#include 
+
+#include "itkPoint.h"
+#include "fcsv_to_matlab_newCLP.h"
+
+#include "LLSModel.h"
+#include "BRAINSThreadControl.h"
+#if  ITK_VERSION_MAJOR >=4
+#include "itk_hdf5.h"
+#include "itk_H5Cpp.h"
+#else
+#include "hdf5.h"
+#include "H5Cpp.h"
+#endif
+
+// D E F I N E S //////////////////////////////////////////////////////////////
+
+const bool FAIL_ON_ERROR = false;    // If set to true, the program
+// will exit on the first error.
+// If false, the program will
+// continue and use "* * *" as the missing data.
+typedef std::vector > SubjectFilenameVector;
+
+// C L A S S E S //////////////////////////////////////////////////////////////
+
+// F U N C T I O N S //////////////////////////////////////////////////////////
+
+// ----------
+// Remove matlab-invalid characters from a name
+static std::string sanitize(const std::string& landmarkname)
+{
+  std::string ret(landmarkname);
+
+  std::replace(ret.begin(), ret.end(), '-', '_');
+  return ret;
+}
+
+// ----------
+// Read in a csv file
+static std::vector > read_csv(const std::string& file)
+{
+  std::vector > ret;
+
+  std::ifstream infile(file.c_str() );
+  std::string   line;
+  while( getline(infile, line) )
+    {
+    std::istringstream       linestream(line);
+    std::string              item;
+    std::vector line_vec;
+    while( getline(linestream, item, ',') )
+      {
+      line_vec.push_back(item);
+      }
+
+    ret.push_back(line_vec);
+    }
+
+  return ret;
+}
+
+// ----------
+// Extract the subjectID from the path
+static std::string get_subjectid(const std::string& content)
+{
+  int start = content.length() - 1;
+  int end = start;
+  for( ; start >= 0; start-- )
+    {
+    if( content[start] == '_' )
+      {
+      end = start;
+      }
+    else if( content[start] == '/' )
+      {
+      start++;
+      break;
+      }
+    }
+  if( start == -1 )
+    {
+    start = 0;
+    }
+  return content.substr(start, end);
+}
+
+// ----------
+// Check to see if a field is a comment
+static bool is_comment(const std::string& field)
+{
+  for( unsigned int i = 0; i < field.length(); i++ )
+    {
+    if( (field[i] != ' ') && (field[i] != '\t') )
+      {
+      if( i + 1 >= field.length() )
+        {
+        return false;
+        }
+      if( field[i] == '#' )
+        {
+        return true;
+        }
+      else
+        {
+        return false;
+        }
+      }
+    }
+  return false;
+}
+
+// ----------
+// Prints the arguments we're using for the user (both what they specified and
+// the defaults that they didn't).
+static void print_arguments_for_user(const std::string& file_glob_string, const std::string& outfile,
+                                     const std::string& landmark_types_list_file)
+{
+  std::cout << std::endl;
+  std::cout << "Landmark files:          " << file_glob_string << std::endl;
+  std::cout << "Category list:           " << landmark_types_list_file << std::endl;
+  std::cout << "Output file:             " << outfile << std::endl;
+  std::cout << std::endl;
+}
+
+// ----------
+// Build up list of subjectid/filename tuples
+SubjectFilenameVector get_subject_filename_tuples(const std::string& file_glob_string)
+{
+  wordexp_t p;
+
+  wordexp(file_glob_string.c_str(), &p, 0);
+  char* *                  w = p.we_wordv;
+  std::vector files;
+  for( unsigned int i = 0; i < p.we_wordc; i++ )
+    {
+    files.push_back(w[i]);
+    // std::cout << "Adding file to processing list: " << w[i] << std::endl;
+    }
+
+  std::vector > subjects;
+  for( std::vector::const_iterator file_iter = files.begin(); file_iter != files.end(); ++file_iter )
+    {
+    subjects.push_back(std::make_pair(get_subjectid(*file_iter), *file_iter) );
+    }
+  return subjects;
+}
+
+// ----------
+// Get the matrix (in text format) for subjectids.
+static std::string get_all_subjectid_text(const std::vector >& subjects)
+{
+  std::string subjectid_text("Subject_ID = {\n");
+  for( std::vector >::const_iterator subject_iter = subjects.begin();
+       subject_iter != subjects.end(); ++subject_iter )
+    {
+    subjectid_text += "'" + subject_iter->first + "' ;\n";
+    }
+  subjectid_text += "}\n\n";
+  return subjectid_text;
+}
+
+// A map between the read in filename and the LandmarksMapType
+typedef std::map FileToLandmarksMapType;
+
+// ----------
+// Get the data for the individual matrices for each landmark type
+static FileToLandmarksMapType get_allFileToLandmarkMap(const std::vector >& subjects)
+{
+  FileToLandmarksMapType allLandmarks;
+  // Process all subjects
+  for( std::vector >::const_iterator subject_iter = subjects.begin();
+       subject_iter != subjects.end();
+       ++subject_iter )
+    {
+    std::cout << "Processing " << subject_iter->second << "(" << subject_iter->first << ")" << std::endl;
+    allLandmarks[subject_iter->first] = ReadSlicer3toITKLmk( subject_iter->second );
+    if( allLandmarks[subject_iter->first].size() == 0 )
+      {
+      std::cout << "FAILED TO PROCESS FILE:  " << subject_iter->second << "" << std::endl;
+      exit(-1);
+      }
+    }
+  return allLandmarks;;
+}
+
+// Get the data for what landmark_types each landmark type is.
+static std::vector > > get_landmark_types(
+  const std::string& landmark_types_list_file)
+{
+  static std::vector > > landmark_types;
+  static std::vector                                        baseLandmarksNames;
+  static std::vector                                        newLandmarksNames;
+  const std::vector >                           csv_data = read_csv(landmark_types_list_file);
+  for( std::vector >::const_iterator iter = csv_data.begin(); iter != csv_data.end(); ++iter )
+    {
+    // Check for comment
+    if( is_comment( (*iter)[0]) )
+      {
+      continue;
+      }
+
+    if( iter->size() != 2 )
+      {
+      std::cout << "Row in " << landmark_types_list_file << " must have precisely two entries:" << std::endl;
+      for( unsigned int i = 0; i < iter->size(); i++ )
+        {
+        std::cout << (*iter)[i] << " ";
+        }
+      std::cout << std::endl;
+      exit(1);
+      }
+
+    // Add it to the list.  We'll assume that there either are no duplicates, or
+    // that any duplicates are intentional.
+    if( (*iter)[1] == "baseLandmarks" )
+      {
+      baseLandmarksNames.push_back(sanitize( (*iter)[0]) );
+      }
+    else if( (*iter)[1] == "newLandmarks" )
+      {
+      newLandmarksNames.push_back(sanitize( (*iter)[0]) );
+      }
+    }
+
+  std::pair > basePair;
+  basePair = make_pair("baseLandmarks", baseLandmarksNames);
+  landmark_types.push_back(basePair);
+
+  std::pair > newPair;
+  newPair = make_pair("newLandmarks", newLandmarksNames);
+  landmark_types.push_back(newPair);
+
+  return landmark_types;
+}
+
+static
+void
+WriteHDFStringList(H5::H5File & file,
+                   const char * const name,
+                   const std::vector & stringList)
+{
+  const hsize_t numStrings(stringList.size() );
+  H5::StrType   strType(H5::PredType::C_S1, H5T_VARIABLE);
+
+  H5::DataSpace strSpace(1, &numStrings);
+  H5::DataSet   strSet = file.createDataSet(name, strType, strSpace);
+
+  std::vector stringListCstr;
+  stringListCstr.reserve(numStrings);
+  for( std::vector::const_iterator it = stringList.begin();
+       it != stringList.end(); ++it )
+    {
+    stringListCstr.push_back( it->c_str() );
+    }
+  strSet.write(&(stringListCstr[0]), strType);
+  strSet.close();
+  strSpace.close();
+  strType.close();
+}
+
+// M A I N ////////////////////////////////////////////////////////////////////
+
+int main(int argc, char* argv[])
+{
+  PARSE_ARGS;
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+
+  if( outputFile == "" )
+    {
+    std::cerr << "Missing output file name" << std::endl;
+    exit(1);
+    }
+  if( landmarkTypesFile == "" )
+    {
+    std::cerr << "Missing landmark types filename name" << std::endl;
+    exit(1);
+    }
+
+  std::string cleanedGlobPattern = landmarkGlobPattern;
+  while( cleanedGlobPattern.find("\\") != std::string::npos )
+    {
+    cleanedGlobPattern.replace(cleanedGlobPattern.find("\\"), 1, ""); // Replace
+                                                                      // escape
+                                                                      // characters
+    }
+
+  print_arguments_for_user(cleanedGlobPattern, outputFile, landmarkTypesFile);
+
+  SubjectFilenameVector subjects = get_subject_filename_tuples(cleanedGlobPattern);
+
+  std::vector subjectIDVec;
+  for( SubjectFilenameVector::iterator it = subjects.begin();
+       it != subjects.end();
+       ++it )
+    {
+    subjectIDVec.push_back(it->first);
+    }
+  std::string subjectid_text = get_all_subjectid_text(subjects);
+
+  //
+  const FileToLandmarksMapType allFileToLandmarkMap =
+    get_allFileToLandmarkMap(subjects);
+
+  typedef std::vector > > LandmarkClassMapsTypes;
+
+  const LandmarkClassMapsTypes landmark_types = get_landmark_types(landmarkTypesFile);
+
+  std::vector landmarkNames;
+
+  std::map > > > byClassLandmarkMatrix;
+  for( LandmarkClassMapsTypes::const_iterator cit = landmark_types.begin();
+       cit != landmark_types.end();
+       ++cit )
+    {
+    std::vector > > perLandmarkMatrix;
+    for( std::vector::const_iterator lit = cit->second.begin();
+         lit != cit->second.end();
+         ++lit )
+      {
+      landmarkNames.push_back(*lit);
+      vnl_matrix CurrentLandmarkMatrix(allFileToLandmarkMap.size(), 3);
+      int                subjCount = 0;
+      for( FileToLandmarksMapType::const_iterator fit = allFileToLandmarkMap.begin();
+           fit != allFileToLandmarkMap.end();
+           ++fit )
+        {
+        const itk::Point & currPoint = fit->second.find(*lit)->second;
+        CurrentLandmarkMatrix[subjCount][0] = currPoint[0];
+        CurrentLandmarkMatrix[subjCount][1] = currPoint[1];
+        CurrentLandmarkMatrix[subjCount][2] = currPoint[2];
+        subjCount++;
+        }
+      perLandmarkMatrix.push_back( make_pair( (*lit), CurrentLandmarkMatrix) );
+      }
+    byClassLandmarkMatrix[cit->first] = perLandmarkMatrix;
+    }
+
+  // KENT:  Write out all matricies to .hd5 format in addition to dumping to
+  // screen:
+  H5::H5File output(outputFile.c_str(), H5F_ACC_TRUNC);
+  WriteHDFStringList(output, "/SubjectIDs", subjectIDVec);
+  WriteHDFStringList(output, "/LandmarkNames", landmarkNames);
+  for( LandmarkClassMapsTypes::const_iterator cit = landmark_types.begin();
+       cit != landmark_types.end();
+       ++cit )
+    {
+    std::string groupName("/");
+    groupName += cit->first;
+    H5::Group group = output.createGroup(groupName);
+    for( std::vector > >::const_iterator lit =
+           byClassLandmarkMatrix[cit->first].begin();
+         lit != byClassLandmarkMatrix[cit->first].end();
+         ++lit )
+      {
+      vnl_matrix CurrentLandmarkMatrix = lit->second;
+
+      hsize_t dims[2];
+      dims[0] = CurrentLandmarkMatrix.columns();
+      dims[1] = CurrentLandmarkMatrix.rows();
+
+      try
+        {
+        H5::DataSpace dataspace(2, dims);
+        H5::FloatType dataType(H5::PredType::NATIVE_DOUBLE );
+
+        std::string matName(groupName);
+        matName += "/";
+        matName += lit->first;
+
+        H5::DataSet dataset = output.createDataSet(matName, dataType, dataspace);
+        dataset.write(CurrentLandmarkMatrix.data_array(), H5::PredType::NATIVE_DOUBLE);
+        dataspace.close();
+        dataType.close();
+        dataset.close();
+        }
+      // catch failure caused by the H5File operations
+      catch( H5::FileIException& error )
+        {
+        error.printError();
+        return -1;
+        }
+
+      // catch failure caused by the DataSet operations
+      catch( H5::DataSetIException& error )
+        {
+        error.printError();
+        return -1;
+        }
+
+      // catch failure caused by the DataSpace operations
+      catch( H5::DataSpaceIException& error )
+        {
+        error.printError();
+        return -1;
+        }
+
+      // catch failure caused by the DataSpace operations
+      catch( H5::DataTypeIException& error )
+        {
+        error.printError();
+        return -1;
+        }
+      }
+    }
+  output.close();
+  // ================================
+  // Now here is where the work for converting from the matlab code begings
+  // % cd  /hjohnson/HDNI/TanmayLandmarkModel/test-data
+  // % ~/src/BRAINS3-Darwin-SuperBuildTest/src/bin/brains3_setup.sh -x
+  // ~/src/BRAINS3-Darwin-SuperBuildTest/src/bin/fcsv_to_matlab
+  // --landmarkTypesFile lmks.list -o test.hdf5 --landmarkGlobPattern
+  // "\*_est\.fcsv"
+
+  /*
+  % This is matlab code for the the implementation of
+  % the two training phases for the proposed
+  % LME-EPCA algorithm (Section 3.3 in my MS thesis).
+  %
+  % Objective:
+  % Train a linear model that can evolutionary estimate new landmarks from
+  % already known landmarks.
+  %
+  % Input:
+  % baselandmarks     - Base landmarks in training datasets
+  % newLandmarks      - EPCA landmarks in training datasets
+  % numBaseLandmarks  - Number of base landmarks
+  % numNewLandmarks   - Number of EPCA landmarks
+  % numDatasets       - Number of training datasets
+  % dim               - Dimension of the landmarks
+  %
+  % Output: (variables stored in files)
+  % M                 - Optimal linear combination of principal components
+  %                     in each iteration
+  % s                 - The 3-by-1 mean of landmark vector space in each
+  %                     iteration
+  % search_radius     - Search radius of each EPCA landmark
+  % newLandmarksName  - A name list of all EPCA landmarks
+  */
+  /*
+
+  %% Dependencies
+###HANS -- NOTE
+load_landmarks % load all landmarks and other input parameters
+This information is now completely contained in the byClassLandmarkMatrix object.
+*/
+
+  // For each of the landmark_types
+  // For each of the landmark_names withing those types
+  // Do the computations necessary.
+  for( LandmarkClassMapsTypes::const_iterator cit = landmark_types.begin();
+       cit != landmark_types.end();
+       ++cit )
+    {
+    for( std::vector > >::const_iterator lit =
+           byClassLandmarkMatrix[cit->first].begin();
+         lit != byClassLandmarkMatrix[cit->first].end();
+         ++lit )
+      {
+      std::cout << "========="
+                << cit->first << " "  << lit->first << "========== "
+                << (lit->second).rows() << "x" << (lit->second).cols()
+                << std::endl;
+      vnl_matlab_print(std::cout, (lit->second), (lit->first).c_str() ); // ,
+                                                                         // vnl_matlab_print_format_short_e
+                                                                         // );
+      }
+    }
+
+  const unsigned int numNewLandmarks = byClassLandmarkMatrix["newLandmarks"].size();
+  const unsigned int numBaseLandmarks = byClassLandmarkMatrix["baseLandmarks"].size();
+  const unsigned int dim = byClassLandmarkMatrix["newLandmarks"].begin()->second.cols(); //
+                                                                                         // dim=3
+                                                                                         // means
+                                                                                         // 3D
+                                                                                         // points
+  const unsigned int numDatasets = byClassLandmarkMatrix["newLandmarks"].begin()->second.rows();
+
+  //
+  // What the hell is this s matrix?
+  vnl_matrix s(dim, numNewLandmarks);
+  /*
+  //=====print for test====
+  std::cout << "\n\n====================== " << s.rows() << "x" << s.cols() << std::endl;
+  vnl_matlab_print(std::cout,s,"s");
+  //=======================
+  */
+  std::vector > lmk_est(numDatasets, s); // Initialize each
+                                                            // element with s
+
+  std::vector > err(numDatasets, s); // to find search_radius
+
+  std::vector > W;
+  std::vector > M;
+
+  // Initialize the landmark vector space
+  vnl_matrix Xi(dim * (numBaseLandmarks - 1), numDatasets);
+  unsigned int       nb = 2;
+  for( std::vector > >::const_iterator kit =
+         ++(byClassLandmarkMatrix["baseLandmarks"].begin() );
+       kit != byClassLandmarkMatrix["baseLandmarks"].end();
+       ++kit )
+    {
+    vnl_matrix lmkVec = ( (kit->second) - (byClassLandmarkMatrix["baseLandmarks"].begin()->second) ).transpose();
+    Xi.update(lmkVec, (nb - 2) * dim, 0);
+    nb++;
+    }
+
+  // Compute all principal components
+
+  // Test Stuff
+
+  vnl_matrix ratioPC1(numNewLandmarks, 1, 0.0);
+  vnl_matrix ratioPC(numNewLandmarks, 1, 0.0);
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    if( i > 0 )
+      {
+      vnl_matrix lmkVec =
+        ( (byClassLandmarkMatrix["newLandmarks"][i
+                                                 - 1].second)
+          - (byClassLandmarkMatrix["baseLandmarks"][0].second) ).transpose();
+
+      // instead of  " Xi = [Xi ; lmkVec] " we write:
+      vnl_matrix Xi_temp = Xi;
+      Xi.set_size(Xi.rows() + lmkVec.rows(), Xi.columns() );
+      Xi.update(Xi_temp, 0, 0);
+      Xi.update(lmkVec, Xi_temp.rows(), 0);
+      }
+
+    // ///remove Xi mean//////////
+    vnl_matrix Xi_mean(dim, 1);
+
+    vnl_vector mean_stacked(Xi.rows() ); // "mean_stack" is a vector
+                                                 // with the size of Xi rows
+                                                 // which is included the means
+                                                 // of every rows of Xi
+    for( unsigned int l = 0; l != Xi.rows(); l++ )
+      {
+      // mean_stacked[l] = Xi.extract(1,Xi.columns(),l,0).mean();
+      mean_stacked[l] = Xi.get_row(l).mean();
+      }
+    for( unsigned int d = 0; d < dim; d++ )
+      {
+      double       sum = 0;
+      unsigned int me = d;
+      while( me <= (mean_stacked.size() - dim + d) )
+        {
+        sum += mean_stacked[me];
+        me += dim;
+        }
+
+      Xi_mean(d, 0) = (sum / (numBaseLandmarks + i - 1) ); // "i" starts from
+                                                           // zero instead of
+                                                           // one, so we write
+                                                           // "i-1" instead of
+                                                           // "i-2"
+      }
+
+    s.set_column(i, Xi_mean.get_column(0) ); // s(:,i)=Xi_mean;
+
+    vnl_matrix I_si( (Xi_mean.rows() ) * (numBaseLandmarks + i - 1), (Xi_mean.cols() ) * numDatasets);
+    for( unsigned int co = 0; co < numDatasets; co++ )
+      {
+      unsigned int ro = 0;
+      while( ro < I_si.rows() )
+        {
+        I_si.update(Xi_mean, ro, co);
+        ro += Xi_mean.rows();
+        }
+      }
+
+    vnl_matrix Xi_demeaned(Xi.rows(), Xi.cols() );
+    Xi_demeaned = Xi - I_si;
+
+    vnl_symmetric_eigensystem eig( Xi_demeaned * Xi_demeaned.transpose() );
+    vnl_matrix                V = eig.V;
+    vnl_matrix                D = eig.D;
+
+    ratioPC1(i, 0) = D.absolute_value_max() / D.absolute_value_sum();
+
+    // Number of PCs should be chosen so that the following condition is
+    // met:
+    // sum(sum(D(:, end-numPCs+1))) / sum(D(:)) > 99%;
+    // in this case, numPCs >= 1 will meet the requirement
+    // or we can use as must PCs as possible
+    // tol argument of the rank func is set conservatively
+    // Adjust the tol argument for different training datasets
+    // tolXi = 100;
+    // numPCs = rank(Xi_demeaned, tolXi);
+
+    unsigned int numPCs = 10;
+    W.push_back( V.extract(V.rows(), numPCs, 0, V.cols() - numPCs) );
+
+    /*  //////PRINT FOR TEST/////
+    for (unsigned int wi=0; wi Zi = W[i].transpose() * Xi_demeaned; // PCA mapped space
+    vnl_matrix Yi = (byClassLandmarkMatrix["newLandmarks"][i].second)
+      - (byClassLandmarkMatrix["baseLandmarks"][0].second);
+
+    vnl_matrix Zinv = vnl_matrix_inverse(Zi * Zi.transpose() );
+    vnl_matrix Ci = Zinv * (Zi * Yi);
+    M.push_back( W[i] * Ci );
+
+    // Compute the estimation errors for training datasets
+    vnl_matrix Xi_t( (numBaseLandmarks + i - 1) * dim, 1, 0.0);
+    vnl_matrix x1_t = byClassLandmarkMatrix["baseLandmarks"][0].second;
+
+    vnl_matrix I_si_t( (Xi_mean.rows() ) * (numBaseLandmarks + i - 1), (Xi_mean.cols() ) * 1); //
+                                                                                                       // I_si_t
+                                                                                                       // =
+                                                                                                       // repmat(s(:,
+                                                                                                       // i),
+                                                                                                       // numBaseLandmarks+i-2,
+                                                                                                       // 1);
+    unsigned int       roo = 0;
+    while( roo < I_si_t.rows() )
+      {
+      I_si_t.update(Xi_mean, roo, 0);
+      roo += Xi_mean.rows();
+      }
+
+    vnl_matrix xk_t;
+    vnl_matrix Xi_demeaned_t;
+    vnl_matrix lmk_groundTruth;
+    for( unsigned int j = 0; j < numDatasets; j++ )
+      {
+      for( unsigned int k = 1; k < (numBaseLandmarks + i); k++ )
+        {
+        if( k < numBaseLandmarks )
+          {
+          xk_t = byClassLandmarkMatrix["baseLandmarks"][k].second;
+          }
+        else
+          {
+          xk_t = byClassLandmarkMatrix["newLandmarks"][k - numBaseLandmarks].second;
+          }
+        Xi_t.update( (xk_t.extract(1, xk_t.columns(), j,
+                                   0).transpose() - x1_t.extract(1, x1_t.columns(), j,
+                                                                 0).transpose() ), (k - 1) * dim, 0);
+        }
+
+      Xi_demeaned_t = Xi_t - I_si_t;
+      lmk_est[j].update( (x1_t.extract(1, x1_t.columns(), j,
+                                       0).transpose() + (M[i].transpose() * Xi_demeaned_t) ), 0, i);
+      lmk_groundTruth = byClassLandmarkMatrix["newLandmarks"][i].second;
+      err[j].update( (lmk_est[j].extract(lmk_est[j].rows(), 1, 0,
+                                         i) - lmk_groundTruth.extract(1, lmk_groundTruth.columns(), j,
+                                                                      0).transpose() ), 0, i);
+      }
+    }
+
+  vnl_matrix err_dist(numNewLandmarks, numDatasets, 0.0);
+  for( unsigned int j = 0; j < numNewLandmarks; j++ )
+    {
+    for( unsigned int k = 0; k < numDatasets; k++ )
+      {
+      err_dist(j, k) = err[k].get_column(j).two_norm();
+      }
+    }
+
+  vnl_matrix err_mean(err_dist.rows(), 1); // "err_mean" is a vector
+                                                   // with the size of err_dist
+                                                   // rows which is included the
+                                                   // means of every rows of Xi
+  for( unsigned int l = 0; l != err_dist.rows(); l++ )
+    {
+    err_mean(l, 0) = err_dist.get_row(l).mean();
+    }
+
+  // //colculating "err_std"
+  vnl_matrix rep_err_mean( err_mean.rows() * 1, err_mean.cols() * numDatasets); //
+                                                                                        // repmat(err_mean,1,numDatasets)
+  for( unsigned int co = 0; co < rep_err_mean.cols(); co++ )
+    {
+    rep_err_mean.update(err_mean, 0, co);
+    }
+
+  vnl_matrix sum_err_diff(numNewLandmarks, 1); // sum( (err_dist -
+                                                       // repmat(err_mean,1,numDatasets)).^2,
+                                                       // 2)
+  for( unsigned int l = 0; l != numNewLandmarks; l++ )
+    {
+    sum_err_diff(l, 0) = (err_dist - rep_err_mean).get_row(l).squared_magnitude();
+    }
+
+  vnl_matrix err_std = (sum_err_diff / numDatasets).apply(sqrt);
+
+  vnl_matrix err_max(err_dist.rows(), 1); // err_max =
+                                                  // max(err_dist,[],2);
+  for( unsigned int l = 0; l != err_dist.rows(); l++ )
+    {
+    err_max(l, 0) = err_dist.get_row(l).max_value();
+    }
+
+  vnl_matrix err_min(err_dist.rows(), 1); // err_min =
+                                                  // min(err_dist,[],2);
+  for( unsigned int l = 0; l != err_dist.rows(); l++ )
+    {
+    err_min(l, 0) = err_dist.get_row(l).min_value();
+    }
+  // multiply matrix "err_std" by 3
+  for( unsigned int l = 0; l != err_std.rows(); l++ )
+    {
+    err_std.scale_row(l, 3);
+    }
+  // multiply matrix "err_max" by 1.2
+  for( unsigned int l = 0; l != err_max.rows(); l++ )
+    {
+    err_max.scale_row(l, 1.2);
+    }
+
+  vnl_matrix search_radius = err_mean + err_std;
+  vnl_matrix search_radius_max = err_max;
+  vnl_matrix search_radius_min(numNewLandmarks, 1, 1.6);
+  // if max search_radius_max(l, 0) )
+      {
+      search_radius(l, 0) = search_radius_max(l, 0);
+      }
+    if( search_radius(l, 0) < search_radius_min(l, 0) )
+      {
+      search_radius(l, 0) = search_radius_min(l, 0);
+      }
+    }
+
+  // KENT:  there are 3 files with hard coded file names created by this program
+  //       the information from these files is all inter-connected and
+  //       combined they make up a single definition of the "model" that is to
+  // be used
+  //       These three files are read into the BRAINSConstellationDetector by
+  // the function
+  //       loadLLSModelMat( inputEPCAModelMat, inputEPCAModelTxt, llsMeans,
+  // llsMatrices, searchRadii );
+  //       at line 175 of BRAINSConstellationDetectorPrimary.cxx
+  //
+  //       I want the following:
+  //       1)
+  //       Please write all the information encoded in these separate files
+  // single
+  //       HDF5 file as a single function called writeLLSModelMat(
+  // commandLineSpecifiedModelFileName, byClassLandmarkMatrix, .... )
+  //       2)
+  //       The name of the model being generated should NOT be hard-coded, but
+  // should be supplied on the command line.
+  //       3)
+  //       Convert loadLLSModelMat to read from the HDF5 file rather than these
+  // 3 hard coded files names.
+  //
+  //
+#if 1
+  if( modelFile == "" )
+    {
+    std::cerr << "Missing model file name" << std::cerr;
+    return 1;
+    }
+  LLSModel theModel;
+  theModel.SetFileName(modelFile);
+
+  LLSModel::LLSMeansType       means;
+  LLSModel::LLSMatricesType    matrices;
+  LLSModel::LLSSearchRadiiType searchRadii;
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    std::string         lmName(byClassLandmarkMatrix["newLandmarks"][i].first);
+    std::vector curVec(dim);
+    for( unsigned int d = 0; d < dim; d++ )
+      {
+      curVec[d] = s(d, i);
+      }
+    means[lmName] = curVec;
+    matrices[lmName] = M[i].transpose();
+    searchRadii[lmName] = search_radius(i, 0);
+    }
+  theModel.SetLLSMeans(means);
+  theModel.SetLLSMatrices(matrices);
+  theModel.SetSearchRadii(searchRadii);
+  theModel.Write();
+
+#else
+  // Write model parameters to file
+  // txt version
+  std::ofstream fid;
+  fid.open("LME_EPCA.txt");
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    fid << byClassLandmarkMatrix["newLandmarks"][i].first << std::endl;
+    for( unsigned int d = 0; d < dim; d++ )
+      {
+      fid << s(d, i) << " ";
+      }
+    fid << std::endl;
+    fid << search_radius(i, 0) << std::endl;
+    fid << M[i].rows() << std::endl;
+    unsigned int l = 0;
+    while( l < dim )
+      {
+      vnl_vector temp = M[i].get_column(l);
+      for( unsigned int ll = 0; ll < M[i].rows(); ll++ )
+        {
+        fid << temp[ll] << " ";
+        }
+      fid << std::endl;
+      l++;
+      }
+
+    fid << std::endl;
+    }
+  fid.close();
+
+  // mat version
+  fid.open("processingList.txt");
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    fid << byClassLandmarkMatrix["newLandmarks"][i].first << std::endl;
+    fid << search_radius(i, 0) << std::endl;
+    }
+  fid.close();
+
+  fid.open("LME_EPCA.m");
+  fid << "clear" << std::endl;
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    std::string name = byClassLandmarkMatrix["newLandmarks"][i].first;
+
+    // write s
+    if( name.size() > 16 )
+      {
+      fid << name.substr(0, 16) << "__s = [";
+      }
+    else
+      {
+      fid << name << "__s = [";
+      }
+    for( unsigned int d = 0; d < dim; d++ )
+      {
+      fid << s(d, i) << " ";
+      }
+    fid << "];" << std::endl;
+
+    // write M
+    if( name.size() > 16 )
+      {
+      fid << name.substr(0, 16) << "__M = [";
+      }
+    else
+      {
+      fid << name << "__M = [";
+      }
+    unsigned int l = 0;
+    while( l < dim )
+      {
+      vnl_vector temp = M[i].get_column(l);
+      for( unsigned int ll = 0; ll < M[i].rows(); ll++ )
+        {
+        fid << temp[ll] << " ";
+        }
+      fid << ";" << std::endl;
+      l++;
+      }
+
+    fid << "];" << std::endl;
+    }
+  fid.close();
+
+  fid.open("LME_EPCA.mat");
+  for( unsigned int i = 0; i < numNewLandmarks; i++ )
+    {
+    std::string name = byClassLandmarkMatrix["newLandmarks"][i].first;
+    std::string string_name_s;
+    std::string string_name_M;
+
+    // write s
+    if( name.size() > 16 )
+      {
+      string_name_s = name.substr(0, 16) + "__s";
+      }
+    else
+      {
+      string_name_s = name + "__s";
+      }
+    vnl_matrix name_s(1, dim, 0.0);
+    for( unsigned int d = 0; d < dim; d++ )
+      {
+      name_s(0, d) = s(d, i);
+      }
+    vnl_matlab_write(fid, name_s.data_array(), name_s.rows(), name_s.cols(), string_name_s.c_str() );
+
+    // write M
+    if( name.size() > 16 )
+      {
+      string_name_M = name.substr(0, 16) + "__M";
+      }
+    else
+      {
+      string_name_M = name + "__M";
+      }
+    vnl_matrix name_M(dim, M[i].rows(), 0.0);
+    unsigned int       l = 0;
+    while( l < dim )
+      {
+      vnl_vector temp = M[i].get_column(l);
+      for( unsigned int ll = 0; ll < M[i].rows(); ll++ )
+        {
+        name_M(l, ll) = temp[ll];
+        }
+      l++;
+      }
+
+    vnl_matlab_write(fid, name_M.data_array(), name_M.rows(), name_M.cols(), string_name_M.c_str() );
+    }
+  fid.close();
+#endif
+
+  std::cout << "LME-EPCA coefficients have been written to disk." << std::endl;
+
+  return 0;
+}
+
diff --git a/BRAINSConstellationDetector/src/fcsv_to_matlab_new.xml b/BRAINSConstellationDetector/src/fcsv_to_matlab_new.xml
new file mode 100644
index 00000000..6eaf26e4
--- /dev/null
+++ b/BRAINSConstellationDetector/src/fcsv_to_matlab_new.xml
@@ -0,0 +1,52 @@
+
+
+  fcsv_to_matlab
+  Convert a collection of fcsv files to a HDF5 format file
+  
+    
+      outputFile
+      
+      o
+      --outputMatlabFile
+      
+      
+        name of HDF5 file to write matrices into
+      
+      output
+    
+    
+      landmarkTypesFile
+      
+      --landmarkTypesFile
+      
+      
+        file containing list of landmark types
+      
+      output
+    
+    
+      modelFile
+      
+      --modelFile
+      
+      
+        file containing BRAINSConstellationDetector Model file
+      
+      output
+    
+    
+      landmarkGlobPattern
+      landmarkGlobPattern
+      Glob pattern to select fcsv files
+      
+      *_est.fcsv
+    
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+  
+
diff --git a/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.h b/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.h
new file mode 100644
index 00000000..63cd1fdd
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.h
@@ -0,0 +1,322 @@
+/*=========================================================================
+  Author: $Author: krm15 $  // Author of last commit
+  Version: $Rev: 585 $  // Revision of last commit
+  Date: $Date: 2009-08-20 21:25:19 -0400 (Thu, 20 Aug 2009) $  // Date of last commit
+=========================================================================*/
+
+/*=========================================================================
+ Authors: The GoFigure Dev. Team.
+ at Megason Lab, Systems biology, Harvard Medical school, 2009
+
+ Copyright (c) 2009, President and Fellows of Harvard College.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ Neither the name of the  President and Fellows of Harvard College
+ nor the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+ OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+=========================================================================*/
+#ifndef __itkHoughTransformRadialVotingImageFilter_h
+#define __itkHoughTransformRadialVotingImageFilter_h
+
+#ifdef _MSC_VER
+#pragma warning ( disable : 4786 )
+#endif
+
+#include "itkImageToImageFilter.h"
+#include "itkImage.h"
+#include "itkEllipseSpatialObject.h"
+#include "itkImageRegionIteratorWithIndex.h"
+#include "itkDiscreteGaussianImageFilter.h"
+#include "itkGaussianDerivativeImageFunction.h"
+#include "itkMinimumMaximumImageCalculator.h"
+#include "itkCastImageFilter.h"
+#include 
+#include "itkAddImageFilter.h"
+#include "itkImageRegionIterator.h"
+
+
+#if ITK_VERSION_MAJOR < 4 && ! defined (ITKv3_THREAD_ID_TYPE_DEFINED)
+#define ITKv3_THREAD_ID_TYPE_DEFINED 1
+typedef int ThreadIdType;
+#endif
+
+namespace itk
+{
+/**
+ * \class HoughTransformRadialVotingImageFilter
+ * \brief Performs the Hough Transform to find circles in a 2D image.
+ *
+ * This filter derives from the base class ImageToImageFilter
+ * The input is an image, and all pixels above some threshold are those
+ * we want to consider during the process.
+ *
+ * This filter produces two output:
+ *   1) The accumulator array, which represents probability of centers.
+ *   2) The array or radii, which has the radius value at each coordinate point.
+ *
+ *  When the filter found a "correct" point, it computes the gradient at this
+ * point and votes on a small region defined using the minimum and maximum
+ * radius given by the user, and fill in the array of radii.
+ *
+ * \ingroup ImageFeatureExtraction
+ * \todo Update the doxygen documentation!!!
+ * */
+
+template 
+class ITK_EXPORT HoughTransformRadialVotingImageFilter :
+  public ImageToImageFilter
+{
+public:
+
+  /** Standard "Self" typedef. */
+  typedef HoughTransformRadialVotingImageFilter Self;
+  /** Standard "Superclass" typedef. */
+  typedef ImageToImageFilter Superclass;
+  /** Smart pointer typedef support. */
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  itkStaticConstMacro(ImageDimension, unsigned int,
+                      TInputImage::ImageDimension);
+
+  /** Input Image typedef */
+  typedef TInputImage                             InputImageType;
+  typedef typename InputImageType::Pointer        InputImagePointer;
+  typedef typename InputImageType::ConstPointer   InputImageConstPointer;
+  typedef typename InputImageType::IndexType      InputIndexType;
+  typedef typename InputIndexType::IndexValueType InputIndexValueType;
+  typedef typename InputImageType::PixelType      InputPixelType;
+  typedef typename InputImageType::SizeType       InputSizeType;
+  typedef typename InputSizeType::SizeValueType   InputSizeValueType;
+  typedef typename InputImageType::RegionType     InputRegionType;
+  typedef typename InputImageType::SpacingType    InputSpacingType;
+  typedef typename InputImageType::PointType      InputPointType;
+  typedef typename InputPointType::CoordRepType   InputCoordType;
+
+  /** Output Image typedef */
+  typedef TOutputImage                         OutputImageType;
+  typedef typename OutputImageType::Pointer    OutputImagePointer;
+  typedef typename OutputImageType::PixelType  OutputPixelType;
+  typedef typename OutputImageType::RegionType OutputImageRegionType;
+
+  typedef Image      InternalImageType;
+  typedef typename InternalImageType::Pointer        InternalImagePointer;
+  typedef typename InternalImageType::IndexType      InternalIndexType;
+  typedef typename InternalIndexType::IndexValueType InternalIndexValueType;
+  typedef typename InternalImageType::PixelType      InternalPixelType;
+  typedef typename InternalImageType::RegionType     InternalRegionType;
+  typedef typename InternalImageType::SizeType       InternalSizeType;
+  typedef typename InternalSizeType::SizeValueType   InternalSizeValueType;
+  typedef typename InternalImageType::SpacingType    InternalSpacingType;
+
+  /** Sphere typedef */
+  typedef EllipseSpatialObject SphereType;
+  typedef typename SphereType::Pointer         SpherePointer;
+  typedef typename SphereType::VectorType      SphereVectorType;
+  typedef std::list             SpheresListType;
+
+  typedef ImageRegionIterator InternalIteratorType;
+  typedef ImageRegionIterator   OutputIteratorType;
+
+  typedef DiscreteGaussianImageFilter
+  GaussianFilterType;
+  typedef typename GaussianFilterType::Pointer
+  GaussianFilterPointer;
+
+  typedef itk::Statistics::GaussianDistribution  GaussianFunctionType;
+  typedef typename GaussianFunctionType::Pointer GaussianFunctionPointer;
+
+  typedef GaussianDerivativeImageFunction
+  DoGFunctionType;
+  typedef typename DoGFunctionType::Pointer
+  DoGFunctionPointer;
+  typedef typename DoGFunctionType::VectorType
+  DoGVectorType;
+
+  typedef MinimumMaximumImageCalculator MinMaxCalculatorType;
+  typedef typename MinMaxCalculatorType::Pointer           MinMaxCalculatorPointer;
+
+  typedef CastImageFilter CastFilterType;
+  typedef typename CastFilterType::Pointer                    CastFilterPointer;
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro(HoughTransformRadialVotingImageFilter, ImageToImageFilter);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Set both Minimum and Maximum radius values */
+  void SetRadius(InputCoordType radius);
+
+  /** Set the minimum radiu value the filter should look for */
+  itkSetMacro(MinimumRadius, InputCoordType);
+
+  /** Set the maximum radius value the filter should look for */
+  itkSetMacro(MaximumRadius, InputCoordType);
+
+  /** Set the threshold above which the filter should consider
+   the point as a valid point */
+  itkSetMacro(Threshold, double);
+
+  /** Get the threshold value */
+  itkGetConstMacro(Threshold, double);
+
+  /** Set the threshold above which the filter should consider
+      the point as a valid point */
+  itkSetMacro(OutputThreshold, InternalPixelType);
+
+  /** Get the threshold value */
+  itkGetConstMacro(OutputThreshold, InternalPixelType);
+
+  /** Set the threshold above which the filter should consider
+      the point as a valid point */
+  itkSetMacro(GradientThreshold, InputCoordType);
+
+  /** Get the threshold value */
+  itkGetConstMacro(GradientThreshold, InputCoordType);
+
+  /** Get the radius image */
+  itkGetObjectMacro(RadiusImage, InternalImageType);
+
+  /** Get the accumulator image */
+  itkGetObjectMacro(AccumulatorImage, InternalImageType);
+
+  /** Set the scale of the derivative function (using DoG) */
+  itkSetMacro(SigmaGradient, double);
+
+  /** Get the scale value */
+  itkGetConstMacro(SigmaGradient, double);
+
+  /** Get the list of circles. This recomputes the circles */
+  SpheresListType & GetSpheres();
+
+  /** Set/Get the number of circles to extract */
+  itkSetMacro(NumberOfSpheres, unsigned int);
+  itkGetConstMacro(NumberOfSpheres, unsigned int);
+
+  /** Set/Get the radius of the disc to remove from the accumulator
+   *  for each circle found */
+  itkSetMacro(SphereRadiusRatio, InputCoordType);
+  itkGetConstMacro(SphereRadiusRatio, InputCoordType);
+
+  itkSetMacro(VotingRadiusRatio, InputCoordType);
+  itkGetConstMacro(VotingRadiusRatio, InputCoordType);
+
+  /** Set the variance of the gaussian bluring for the accumulator */
+  itkSetMacro(Variance, double);
+  itkGetConstMacro(Variance, double);
+
+  /** Set the number of threads */
+  itkSetMacro(NbOfThreads, unsigned int);
+  itkGetConstMacro(NbOfThreads, unsigned int);
+
+  /** Set the number of threads */
+  itkSetMacro(SamplingRatio, double);
+  itkGetConstMacro(SamplingRatio, double);
+
+  /** Set the mode of the algorithm */
+  /** HoughEyeDetectorMode = 0: Detecting bright spheres in a dark environment.
+    */
+  /** HoughEyeDetectorMode = 1: Detecting dark spheres in a bright environment.
+    */
+  itkSetMacro(HoughEyeDetectorMode, int);
+
+  /** Get the mode of the algorithm */
+  itkGetConstMacro(HoughEyeDetectorMode, int);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( IntConvertibleToOutputCheck,
+                   ( Concept::Convertible ) );
+  itkConceptMacro( InputGreaterThanDoubleCheck,
+                   ( Concept::GreaterThanComparable ) );
+  itkConceptMacro( OutputPlusIntCheck,
+                   ( Concept::AdditiveOperators ) );
+  itkConceptMacro( OutputDividedByIntCheck,
+                   ( Concept::DivisionOperators ) );
+  /** End concept checking */
+#endif
+protected:
+  HoughTransformRadialVotingImageFilter();
+  virtual ~HoughTransformRadialVotingImageFilter();
+
+  InputCoordType       m_MinimumRadius;
+  InputCoordType       m_MaximumRadius;
+  double               m_Threshold;
+  InputCoordType       m_GradientThreshold;
+  InternalPixelType    m_OutputThreshold;
+  double               m_SigmaGradient;
+  double               m_Variance;
+  InputCoordType       m_VotingRadiusRatio;
+  InputCoordType       m_SphereRadiusRatio;
+  double               m_SamplingRatio;
+  InternalImagePointer m_RadiusImage;
+  InternalImagePointer m_AccumulatorImage;
+  SpheresListType      m_SpheresList;
+  unsigned int         m_NumberOfSpheres;
+  unsigned long        m_OldModifiedTime;
+  unsigned int         m_NbOfThreads;
+  bool                 m_AllSeedsProcessed;
+
+  // -- Add by Wei Lu
+  int m_HoughEyeDetectorMode;
+
+  /** Method for evaluating the implicit function over the image. */
+  virtual void BeforeThreadedGenerateData();
+
+  virtual void AfterThreadedGenerateData();
+
+  virtual void ThreadedGenerateData(const OutputImageRegionType & windowRegion, ThreadIdType threadId);
+
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+  /** HoughTransformRadialVotingImageFilter needs the entire input. Therefore
+   * it must provide an implementation GenerateInputRequestedRegion().
+   * \sa ProcessObject::GenerateInputRequestedRegion(). */
+  void GenerateInputRequestedRegion();
+
+  /** HoughTransformRadialVotingImageFilter's produces all the output.
+   * Therefore, it must provide an implementation of
+   * EnlargeOutputRequestedRegion.
+   * \sa ProcessObject::EnlargeOutputRequestedRegion() */
+  void EnlargeOutputRequestedRegion( DataObject * itkNotUsed(output) );
+
+  void ComputeMeanRadiusImage();
+
+private:
+  HoughTransformRadialVotingImageFilter(const Self &)
+  {
+  }
+  void operator=(const Self &)
+  {
+  }
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkHoughTransformRadialVotingImageFilter.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.txx b/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.txx
new file mode 100644
index 00000000..a4c90cb0
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkHoughTransformRadialVotingImageFilter.txx
@@ -0,0 +1,445 @@
+/*=========================================================================
+ Author: $Author: krm15 $  // Author of last commit
+ Version: $Rev: 585 $  // Revision of last commit
+ Date: $Date: 2009-08-20 21:25:19 -0400 (Thu, 20 Aug 2009) $  // Date of last commit
+ =========================================================================*/
+
+/*=========================================================================
+ Authors: The GoFigure Dev. Team.
+ at Megason Lab, Systems biology, Harvard Medical school, 2009
+
+ Copyright (c) 2009, President and Fellows of Harvard College.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ Neither the name of the  President and Fellows of Harvard College
+ nor the names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
+ OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+ =========================================================================*/
+
+#ifndef __itkHoughTransformRadialVotingImageFilter_txx
+#define __itkHoughTransformRadialVotingImageFilter_txx
+
+#include "itkHoughTransformRadialVotingImageFilter.h"
+
+namespace itk
+{
+template 
+HoughTransformRadialVotingImageFilter
+::HoughTransformRadialVotingImageFilter():
+  m_MinimumRadius(0),   // by default
+  m_MaximumRadius(10),  // by default
+  m_Threshold(0),
+  m_GradientThreshold(0),
+  m_OutputThreshold(0.0),
+  m_SigmaGradient(1),   // Scale of the DoG filter
+  m_Variance(1),
+  m_VotingRadiusRatio(0.5),
+  m_SphereRadiusRatio(1),
+  m_SamplingRatio(1.0),
+  m_RadiusImage(NULL),
+  m_AccumulatorImage(NULL),
+  m_SpheresList(),
+  m_NumberOfSpheres(1),
+  m_OldModifiedTime(0),
+  m_NbOfThreads(1),
+  m_AllSeedsProcessed(false),
+  m_HoughEyeDetectorMode(0)
+{
+  // Limiting the Hough Filter to run with single thread.
+  // In a single threaded status, the increment of run time for this filter is not tremendous in compare with
+  // the total run time of the BCD
+  this->SetNumberOfThreads(1);
+}
+
+template 
+HoughTransformRadialVotingImageFilter
+::~HoughTransformRadialVotingImageFilter()
+{
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter
+::SetRadius(InputCoordType radius)
+{
+  this->SetMinimumRadius(radius);
+  this->SetMaximumRadius(radius);
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter
+::EnlargeOutputRequestedRegion(DataObject *output)
+{
+  Superclass::EnlargeOutputRequestedRegion(output);
+  output->SetRequestedRegionToLargestPossibleRegion();
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter
+::GenerateInputRequestedRegion()
+{
+  Superclass::GenerateInputRequestedRegion();
+  if( this->GetInput() )
+    {
+    InputImagePointer image =
+      const_cast( this->GetInput() );
+    image->SetRequestedRegionToLargestPossibleRegion();
+    }
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter
+::BeforeThreadedGenerateData()
+{
+  // Get the input and output pointers
+  const InputImageConstPointer inputImage = this->GetInput();
+
+  m_AccumulatorImage = InternalImageType::New();
+  m_AccumulatorImage->CopyInformation(inputImage);
+  m_AccumulatorImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+
+  m_AccumulatorImage->Allocate();
+  m_AccumulatorImage->FillBuffer(0);
+
+  m_RadiusImage = InternalImageType::New();
+  m_RadiusImage->CopyInformation( inputImage );
+  m_RadiusImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+  m_RadiusImage->Allocate();
+  m_RadiusImage->FillBuffer(0);
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter
+::AfterThreadedGenerateData()
+{
+  ComputeMeanRadiusImage();
+
+  // Copy the typecast m_AccumulatorImage to Output image
+  InternalIteratorType iIt( m_AccumulatorImage, this->GetOutput()->GetRequestedRegion() );
+  OutputIteratorType oIt( this->GetOutput(), this->GetOutput()->GetRequestedRegion() );
+
+  iIt.GoToBegin();
+  oIt.GoToBegin();
+  while( !iIt.IsAtEnd() )
+    {
+    assert( !oIt.IsAtEnd() );
+    oIt.Set( static_cast( iIt.Get() ) );
+    ++iIt;
+    ++oIt;
+    }
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter::ThreadedGenerateData(
+  const OutputImageRegionType & windowRegion,
+  ThreadIdType /* threadId -- Not used */)
+
+{
+  // Get the input and output pointers
+  const InputImageConstPointer inputImage = this->GetInput();
+  const InputSpacingType       spacing = inputImage->GetSpacing();
+
+  DoGFunctionPointer DoGFunction = DoGFunctionType::New();
+  DoGFunction->SetInputImage(inputImage);
+  DoGFunction->SetSigma(m_SigmaGradient);
+
+  GaussianFunctionPointer GaussianFunction = GaussianFunctionType::New();
+
+  const InputCoordType averageRadius = 0.5 * ( m_MinimumRadius + m_MaximumRadius );
+  const InputCoordType averageRadius2 = averageRadius * averageRadius;
+
+  ImageRegionConstIteratorWithIndex
+  image_it(inputImage, windowRegion);
+  image_it.Begin();
+
+  const unsigned int sampling = static_cast( 1. / m_SamplingRatio );
+  unsigned int counter = 1;
+
+  InternalRegionType region;
+  while( !image_it.IsAtEnd() )
+    {
+    if( image_it.Get() > m_Threshold )
+      {
+      const Index index= image_it.GetIndex();
+      DoGVectorType grad = DoGFunction->EvaluateAtIndex(index);
+
+      // if the gradient is not flat
+      typename DoGVectorType::ValueType norm2 = grad.GetSquaredNorm();
+
+      if( norm2 > m_GradientThreshold )
+        {
+        if( counter % sampling == 0 )
+          {
+          // Normalization
+          if( norm2 != 0 )
+            {
+            const typename DoGVectorType::ValueType inv_norm = 1.0 / vcl_sqrt(norm2);
+            for( unsigned int i = 0; i < ImageDimension; i++ )
+              {
+              grad[i] *= inv_norm;
+              }
+            }
+            Index center;
+            {
+            InternalIndexType  start;
+            InternalSizeType   size;
+            for( unsigned int i = 0; i < ImageDimension; i++ )
+              {
+              // for T1, T2 images
+              if( m_HoughEyeDetectorMode == 1 )
+                {
+
+                center[i] = index[i] + static_cast
+                  ( averageRadius * grad[i] / spacing[i] );
+                }
+              else
+                { // for PD image
+                center[i] = index[i] - static_cast
+                  ( averageRadius * grad[i] / spacing[i] );
+                }
+
+              const InputCoordType rad = m_VotingRadiusRatio * m_MinimumRadius / spacing[i];
+              start[i] = center[i] - static_cast( rad );
+              size[i] = 1 + 2 * static_cast( rad );
+              }
+            region.SetSize(size);
+            region.SetIndex(start);
+            }
+
+          if( inputImage->GetRequestedRegion().IsInside(region) )
+            {
+            ImageRegionIteratorWithIndex
+            It1(m_AccumulatorImage, region);
+
+            ImageRegionIterator It2(m_RadiusImage, region);
+
+            It1.GoToBegin();
+            It2.GoToBegin();
+            while( !It1.IsAtEnd() )
+              {
+              assert( ! It2.IsAtEnd() );
+              const Index indexAtVote = It1.GetIndex();
+              InputCoordType distance = 0;
+              double d = 0;
+              for( unsigned int i = 0; i < ImageDimension; i++ )
+                {
+                d += vnl_math_sqr(
+                    static_cast( indexAtVote[i] - center[i] ) * spacing[i]);
+                distance += vnl_math_sqr(
+                    static_cast( indexAtVote[i] - index[i] ) * spacing[i]);
+                }
+              d = vcl_sqrt(d);
+              distance = vcl_sqrt(distance);
+
+              // Apply a normal distribution weight;
+              const double weight= GaussianFunction->EvaluatePDF(d, 0, averageRadius2);
+              double distweight(distance * weight);
+
+              It1.Set(It1.Get() + weight);
+              It2.Set(It2.Get() + distweight);
+              
+              ++It1;
+              ++It2;
+              }
+            }
+          } // end counter
+        counter++;
+        } // end gradient threshold
+      }   // end intensity threshold
+    ++image_it;
+    }
+}
+
+template 
+void
+HoughTransformRadialVotingImageFilter::ComputeMeanRadiusImage()
+{
+  const InputImageConstPointer inputImage = this->GetInput(0);
+  const InputRegionType        windowRegion = inputImage->GetRequestedRegion();
+
+  ImageRegionConstIterator acc_it(m_AccumulatorImage, windowRegion);
+  ImageRegionIterator radius_it(m_RadiusImage, windowRegion);
+
+  acc_it.Begin();
+  radius_it.Begin();
+  while( !acc_it.IsAtEnd() )
+    {
+    assert(!radius_it.IsAtEnd() );
+    if( acc_it.Get() > 0 )
+      {
+      radius_it.Set( radius_it.Get() / acc_it.Get() );
+      }
+    ++acc_it;
+    ++radius_it;
+    }
+}
+
+/** Get the list of circles. This recomputes the circles */
+template 
+typename HoughTransformRadialVotingImageFilter::SpheresListType
+& HoughTransformRadialVotingImageFilter
+::GetSpheres()
+  {
+  // if the filter has not been updated
+  if( this->GetMTime() == m_OldModifiedTime )
+    {
+    return m_SpheresList;
+    }
+
+  m_SpheresList.clear();
+
+  /** Blur the accumulator in order to find the maximum */
+  GaussianFilterPointer gaussianFilter = GaussianFilterType::New();
+  gaussianFilter->SetInput( this->GetOutput(0) );   // the output is the
+                                                    // accumulator image
+  gaussianFilter->SetVariance(m_Variance);
+  gaussianFilter->Update();
+
+  const InternalImagePointer postProcessImage = gaussianFilter->GetOutput();
+  const InternalSpacingType  spacing = postProcessImage->GetSpacing();
+  const InternalSizeType     size = postProcessImage->GetRequestedRegion().GetSize();
+
+  MinMaxCalculatorPointer minMaxCalculator = MinMaxCalculatorType::New();
+  minMaxCalculator->SetImage(postProcessImage);
+  minMaxCalculator->ComputeMaximum();
+  const InternalPixelType pmax = minMaxCalculator->GetMaximum();
+
+
+  unsigned int circles = 0;
+
+  // Find maxima
+  do
+    {
+    minMaxCalculator->ComputeMaximum();
+    const InternalPixelType max = minMaxCalculator->GetMaximum();
+    const InternalIndexType idx = minMaxCalculator->GetIndexOfMaximum();
+
+    if( max < m_OutputThreshold * pmax )
+      {
+      assert( 0 == 1 ); //This should never happen.  max == pmax in all cases
+      break;
+      }
+
+    SphereVectorType center;
+    for( unsigned int i = 0; i < ImageDimension; i++ )
+      {
+      center[i] = idx[i];
+      }
+
+    // Create a Line Spatial Object
+    SpherePointer Sphere = SphereType::New();
+    Sphere->SetId(circles);
+    Sphere->SetRadius( m_RadiusImage->GetPixel(idx) );
+    Sphere->GetObjectToParentTransform()->SetOffset(center);
+    Sphere->ComputeBoundingBox();
+
+    m_SpheresList.push_back(Sphere);
+    // Remove a black disc from the hough space domain
+    InternalSizeType sizeOfROI;
+    InternalIndexType start;
+    InternalIndexType end;
+    for( unsigned int i = 0; i < ImageDimension; i++ )
+      {
+      const InternalIndexValueType rad = 
+        static_cast(
+          m_SphereRadiusRatio * Sphere->GetRadius()[i] / spacing[i] );
+
+      if( idx[i] > static_cast( rad ) )
+        {
+        start[i] = idx[i] - static_cast( rad );
+        }
+      else
+        {
+        start[i] = 0;
+        }
+
+      if( idx[i] + rad < static_cast( size[i] - 1 ) )
+        {
+        end[i] = idx[i] + static_cast( rad );
+        }
+      else
+        {
+        end[i] = postProcessImage->GetLargestPossibleRegion().GetSize()[i] - 1;
+        }
+
+      sizeOfROI[i] = end[i] - start[i] + 1;
+      }
+
+    InternalRegionType     region;
+    region.SetSize(sizeOfROI);
+    region.SetIndex(start);
+
+    ImageRegionIterator It(postProcessImage, region);
+
+    It.GoToBegin();
+    while( !It.IsAtEnd() )
+      {
+      It.Set(0);
+      ++It;
+      }
+
+    ++circles;
+    }
+  while( circles < m_NumberOfSpheres );
+
+  m_OldModifiedTime = this->GetMTime();
+
+  return m_SpheresList;
+  }
+
+/** Print Self information */
+template 
+void
+HoughTransformRadialVotingImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << "Threshold: " << m_Threshold << std::endl;
+  os << "Gradient Threshold: " << m_GradientThreshold << std::endl;
+  os << "Minimum Radius:  " << m_MinimumRadius << std::endl;
+  os << "Maximum Radius: " << m_MaximumRadius << std::endl;
+  os << "Derivative Scale : " << m_SigmaGradient << std::endl;
+  os << "Sphere Radius Ratio: " << m_SphereRadiusRatio << std::endl;
+  os << "Voting Radius Ratio: " << m_VotingRadiusRatio << std::endl;
+  os << "Accumulator blur variance: " << m_Variance << std::endl;
+  os << "Number Of Spheres: " << m_NumberOfSpheres << std::endl;
+  os << "Output Threshold : " << m_OutputThreshold << std::endl;
+  os << "Sampling Ratio: " << m_SamplingRatio << std::endl;
+  os << "NbOfThreads: " << m_NbOfThreads << std::endl;
+  os << "All Seeds Processed: " << m_AllSeedsProcessed << std::endl;
+  os << "HoughEyeDetectorMode: " << m_HoughEyeDetectorMode << std::endl;
+
+  os << "Radius Image Information : " << m_RadiusImage << std::endl;
+}
+
+} // end namespace
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelOverlayFunctor.h b/BRAINSConstellationDetector/src/itkLabelOverlayFunctor.h
new file mode 100644
index 00000000..5a9686e6
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelOverlayFunctor.h
@@ -0,0 +1,129 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelOverlayFunctor.h,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:28:58 $
+  Version:   $Revision: 1.6 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkLabelOverlayFunctor_h
+#define __itkLabelOverlayFunctor_h
+
+#include "itkLabelToRGBFunctor.h"
+
+namespace itk
+{
+namespace Functor
+{
+/** \class LabelOverlayFunctor
+ *  \brief Functor for applying a colormap to a label image and combine it
+ * with a grayscale image
+ *
+ * This functor class used internally by LabelOverlayImageFilter
+ *
+ * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
+ * INRA de Jouy-en-Josas, France.
+ *
+ * \sa LabelOverlayImageFilter LabelToRGBFunctor
+ *
+ */
+template 
+class LabelOverlayFunctor
+{
+public:
+  LabelOverlayFunctor()
+  {
+    // provide some default value for external use (outside
+    // LabelOverlayFunctorImageFilter) Inside LabelOverlayFunctorImageFilter,
+    // the values are always initialized
+    m_BackgroundValue = NumericTraits::Zero;
+  }
+
+  inline TRGBPixel operator()(const TInputPixel & p1, const TLabel & p2) const
+  {
+    TRGBPixel rgbPixel;
+
+    if( p2 == m_BackgroundValue )
+      {
+      // value is background
+      // return a gray pixel with the same intensity than the input pixel
+      typename TRGBPixel::ValueType p =
+        static_cast( p1 );
+      rgbPixel[0] = p;
+      rgbPixel[1] = p;
+      rgbPixel[2] = p;
+      return rgbPixel;
+      }
+
+    // taint the input pixel with the colored one returned by
+    // the color functor.
+    TRGBPixel opaque = m_RGBFunctor(p2);
+    for( unsigned int i = 0; i < 3; i++ )
+      {
+      rgbPixel[i] = static_cast(
+          opaque[i] * m_Opacity + p1 * ( 1.0 - m_Opacity ) );
+      }
+    return rgbPixel;
+  }
+
+  bool operator!=(const LabelOverlayFunctor & l) const
+  {
+    bool value = l.m_Opacity != m_Opacity
+      || m_BackgroundValue != l.m_BackgroundValue;
+
+    return value;
+  }
+
+  ~LabelOverlayFunctor()
+  {
+  }
+
+  void SetOpacity(double opacity)
+  {
+    m_Opacity = opacity;
+  }
+
+  void SetBackgroundValue(TLabel v)
+  {
+    m_BackgroundValue = v;
+    m_RGBFunctor.SetBackgroundValue(v);
+  }
+
+  void ResetColors()
+  {
+    m_RGBFunctor.ResetColors();
+  }
+
+  unsigned int GetNumberOfColors() const
+  {
+    return m_RGBFunctor.GetNumberOfColors();
+  }
+
+  /** type of the color component */
+  typedef typename TRGBPixel::ComponentType ComponentType;
+
+  void AddColor(ComponentType r, ComponentType g, ComponentType b)
+  {
+    m_RGBFunctor.AddColor(r, g, b);
+  }
+
+protected:
+private:
+  double m_Opacity;
+  TLabel m_BackgroundValue;
+
+  typename Functor::LabelToRGBFunctor m_RGBFunctor;
+};
+}  // end namespace functor
+}  // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.h b/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.h
new file mode 100644
index 00000000..b2e33482
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.h
@@ -0,0 +1,151 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelOverlayImageFilter.h,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:27:33 $
+  Version:   $Revision: 1.16 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelOverlayImageFilter_h
+#define __itkLabelOverlayImageFilter_h
+
+#include "itkLabelOverlayFunctor.h"
+#include "itkBinaryFunctorImageFilter.h"
+#include "itkConceptChecking.h"
+
+namespace itk
+{
+/** \class LabelOverlayImageFilter
+ * \brief Apply a colormap to a label image and put it on top of the
+ *  input image
+ *
+ * Apply a colormap to a label image and put it on top of the input image.
+ * The set of colors is a good selection of distinct colors. The opacity of
+ * the label image can be defined by the user. The user can also choose if
+ * the want to use a background and which label value is the background.
+ * A background label produce a gray pixel with the same intensity
+ * than the input one.
+ *
+ * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
+ * INRA de Jouy-en-Josas, France.
+ *
+ * This class was contributed to the Insight Journal
+ *     http://insight-journal.org/midas/handle.php?handle=1926/172
+ *
+ *
+ * \sa ScalarToRGBPixelFunctor LabelToRGBImageFilter
+ * \ingroup Multithreaded
+ *
+ */
+template 
+class ITK_EXPORT LabelOverlayImageFilter :
+  public
+  BinaryFunctorImageFilter   >
+{
+public:
+  /** Standard class typedefs. */
+  typedef LabelOverlayImageFilter Self;
+
+  typedef BinaryFunctorImageFilter   >  Superclass;
+
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  typedef TOutputImage OutputImageType;
+  typedef TLabelImage  LabelImageType;
+  typedef TInputImage  InputImageType;
+
+  typedef typename TOutputImage::PixelType OutputPixelType;
+  typedef typename TLabelImage::PixelType  LabelPixelType;
+  typedef typename TInputImage::PixelType  InputPixelType;
+
+  /** Runtime information support. */
+  itkTypeMacro(LabelOverlayImageFilter, BinaryFunctorImageFilter);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Set the label image */
+  void SetLabelImage(const TLabelImage *input);
+
+  /** Get the label image */
+  const LabelImageType * GetLabelImage() const;
+
+  /** Set/Get the opacity of the colored label image. The value must be
+   * between 0 and 1
+   */
+  itkSetMacro(Opacity, double);
+  itkGetConstReferenceMacro(Opacity, double);
+
+  /** Set/Get the background value */
+  itkSetMacro(BackgroundValue, LabelPixelType);
+  itkGetConstReferenceMacro(BackgroundValue, LabelPixelType);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  /** Begin concept checking */
+  itkConceptMacro( OutputHasPixelTraitsCheck,
+                   ( Concept::HasPixelTraits ) );
+  itkConceptMacro( OutputPixelShouldHaveValueType,
+                   ( Concept::HasValueType ) );
+  itkConceptMacro( OutputPixelShouldHaveBracketOperator,
+                   ( Concept::BracketOperator<
+                       OutputPixelType,
+                       unsigned int,
+                       typename OutputPixelType::ValueType> ) );
+  /** End concept checking */
+#endif
+
+  /** Empty the color LUT container */
+  void ResetColors();
+
+  /** Get number of colors in the LUT container */
+  unsigned int GetNumberOfColors() const;
+
+  /** type of the color component */
+  typedef typename OutputPixelType::ComponentType ComponentType;
+
+  /** Add color to the LUT container */
+  void AddColor(ComponentType r, ComponentType g, ComponentType b);
+
+protected:
+  LabelOverlayImageFilter();
+  virtual ~LabelOverlayImageFilter()
+  {
+  }
+
+  /** Process to execute before entering the multithreaded section */
+  void BeforeThreadedGenerateData(void);
+
+  /** Print internal ivars */
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+  LabelOverlayImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);          // purposely not implemented
+
+  double         m_Opacity;
+  LabelPixelType m_BackgroundValue;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelOverlayImageFilter.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.txx b/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.txx
new file mode 100644
index 00000000..a7ce1d4c
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelOverlayImageFilter.txx
@@ -0,0 +1,127 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelOverlayImageFilter.txx,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:27:33 $
+  Version:   $Revision: 1.9 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkLabelOverlayImageFilter_txx
+#define __itkLabelOverlayImageFilter_txx
+
+#include "itkLabelOverlayImageFilter.h"
+
+namespace itk
+{
+/**
+ * Constructor method
+ */
+template 
+LabelOverlayImageFilter
+::LabelOverlayImageFilter()
+{
+  m_Opacity = 0.5;
+  m_BackgroundValue = NumericTraits::Zero;
+}
+
+/**
+ * Destructor method
+ */
+template 
+void
+LabelOverlayImageFilter
+::BeforeThreadedGenerateData()
+{
+  this->GetFunctor().SetOpacity(m_Opacity);
+  this->GetFunctor().SetBackgroundValue(m_BackgroundValue);
+}
+
+/**
+ * Set Label Image
+ */
+template 
+void
+LabelOverlayImageFilter
+::SetLabelImage(const TLabelImage *input)
+{
+  this->SetInput2(input);
+}
+
+/**
+ * Get Label Image
+ */
+template 
+const
+typename LabelOverlayImageFilter<
+  TInputImage, TLabelImage, TOutputImage>::LabelImageType
+* LabelOverlayImageFilter
+::GetLabelImage() const
+  {
+  return static_cast(
+           const_cast( this->ProcessObject::GetInput(1) ) );
+  }
+
+/**
+ * Get number of colors in the LUT container
+ */
+template 
+unsigned int
+LabelOverlayImageFilter
+::GetNumberOfColors() const
+{
+  return this->GetFunctor().GetNumberOfColors();
+}
+
+/**
+ * Empty the color LUT container
+ */
+template 
+void
+LabelOverlayImageFilter
+::ResetColors()
+{
+  this->GetFunctor().ResetColors();
+}
+
+/**
+ * Add a color to the LUT container
+ */
+template 
+void
+LabelOverlayImageFilter
+::AddColor(ComponentType r, ComponentType g, ComponentType b)
+{
+  this->GetFunctor().AddColor(r, g, b);
+}
+
+/**
+ * Standard PrintSelf method
+ */
+template 
+void
+LabelOverlayImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "Opacity: "
+     << static_cast::PrintType>( m_Opacity )
+     << std::endl
+     << indent << "BackgroundValue: "
+     << static_cast<
+    typename NumericTraits::PrintType>( m_BackgroundValue )
+     << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelToRGBFunctor.h b/BRAINSConstellationDetector/src/itkLabelToRGBFunctor.h
new file mode 100644
index 00000000..f3442921
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelToRGBFunctor.h
@@ -0,0 +1,177 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelToRGBFunctor.h,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:27:34 $
+  Version:   $Revision: 1.11 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkLabelToRGBFunctor_h
+#define __itkLabelToRGBFunctor_h
+
+namespace itk
+{
+namespace Functor
+{
+/** \class LabelToRGBFunctor
+ *  \brief Functor for converting labels into RGB triplets.
+ *
+ * This functor class used internally by LabelToRGBImageFilter
+ *
+ * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction,
+ * INRA de Jouy-en-Josas, France.
+ *
+ * \author Richard Beare. Department of
+ * Medicine, Monash University, Melbourne, Australia.
+ *
+ * \sa LabelToRGBImageFilter
+ *
+ **/
+template 
+class LabelToRGBFunctor
+{
+public:
+
+  typedef LabelToRGBFunctor Self;
+
+  LabelToRGBFunctor()
+  {
+    TRGBPixel rgbPixel;
+
+    typedef typename TRGBPixel::ValueType ValueType;
+
+    // the following colors are from "R", and named:
+    // "red"             "green3"          "blue"            "cyan"
+    // "magenta"         "darkorange1"     "darkgreen"       "blueviolet"
+    // "brown4"          "navy"            "yellow4"         "violetred1"
+    // "salmon4"         "turquoise4"      "sienna3"         "darkorchid1"
+    // "springgreen4"    "mediumvioletred" "orangered3"      "lightseagreen"
+    // "slateblue"       "deeppink1"       "aquamarine4"     "royalblue1"
+    // "tomato3"         "mediumblue"      "violetred4"      "darkmagenta"
+    // "violet"          "red4"
+    // They are a good selection of distinct colours for plotting and
+    // overlays.
+
+    AddColor(255, 0, 0);
+    AddColor(0, 205, 0);
+    AddColor(0, 0, 255);
+    AddColor(0, 255, 255);
+    AddColor(255, 0, 255);
+    AddColor(255, 127, 0);
+    AddColor(0, 100, 0);
+    AddColor(138, 43, 226);
+    AddColor(139, 35, 35);
+    AddColor(0, 0, 128);
+    AddColor(139, 139, 0);
+    AddColor(255, 62, 150);
+    AddColor(139, 76, 57);
+    AddColor(0, 134, 139);
+    AddColor(205, 104, 57);
+    AddColor(191, 62, 255);
+    AddColor(0, 139, 69);
+    AddColor(199, 21, 133);
+    AddColor(205, 55, 0);
+    AddColor(32, 178, 170);
+    AddColor(106, 90, 205);
+    AddColor(255, 20, 147);
+    AddColor(69, 139, 116);
+    AddColor(72, 118, 255);
+    AddColor(205, 79, 57);
+    AddColor(0, 0, 205);
+    AddColor(139, 34, 82);
+    AddColor(139, 0, 139);
+    AddColor(238, 130, 238);
+    AddColor(139, 0, 0);
+
+    // provide some default value for external use (outside
+    // LabelToRGBImageFilter)
+    // Inside LabelToRGBImageFilter, the values are always initialized
+    m_BackgroundColor.Fill(NumericTraits::Zero);
+    m_BackgroundValue = NumericTraits::Zero;
+  }
+
+  inline TRGBPixel operator()(const TLabel & p) const
+  {
+    // value is background
+    // return a gray pixel with the same intensity than the label pixel
+    if( p == m_BackgroundValue )
+      {
+      return m_BackgroundColor;
+      }
+
+    // else, return a colored pixel from the color table
+    return m_Colors[p % m_Colors.size()];
+  }
+
+  void AddColor(unsigned char r, unsigned char g, unsigned char b)
+  {
+    TRGBPixel rgbPixel;
+
+    typedef typename TRGBPixel::ValueType ValueType;
+
+    ValueType m = NumericTraits::max();
+
+    rgbPixel.Set( static_cast( static_cast( r ) / 255 * m ),
+                  static_cast( static_cast( g ) / 255 * m ),
+                  static_cast( static_cast( b ) / 255 * m ) );
+    m_Colors.push_back(rgbPixel);
+  }
+
+  // Empty the color LUT
+  void ResetColors()
+  {
+    m_Colors.clear();
+  }
+
+  // Get number of colors in the LUT
+  unsigned int GetNumberOfColors() const
+  {
+    return m_Colors.size();
+  }
+
+  bool operator!=(const Self & l) const
+  {
+    const bool areDifferent = m_BackgroundColor != l.m_BackgroundColor
+      || m_BackgroundValue != l.m_BackgroundValue;
+
+    return areDifferent;
+  }
+
+  bool operator==(const Self & other) const
+  {
+    return !( *this != other );
+  }
+
+  void SetBackgroundValue(TLabel v)
+  {
+    m_BackgroundValue = v;
+  }
+
+  void SetBackgroundColor(TRGBPixel rgb)
+  {
+    m_BackgroundColor = rgb;
+  }
+
+  ~LabelToRGBFunctor()
+  {
+  }
+
+  std::vector m_Colors;
+
+  TRGBPixel m_BackgroundColor;
+
+  TLabel m_BackgroundValue;
+};
+}  // end namespace functor
+}  // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.h b/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.h
new file mode 100644
index 00000000..2da5733f
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.h
@@ -0,0 +1,118 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelToRGBImageFilter.h,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:27:34 $
+  Version:   $Revision: 1.10 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkLabelToRGBImageFilter_h
+#define __itkLabelToRGBImageFilter_h
+
+#include "itkUnaryFunctorImageFilter.h"
+#include "itkLabelToRGBFunctor.h"
+
+namespace itk
+{
+/** \class LabelToRGBImageFilter
+ * \brief Apply a colormap to a label image
+ *
+ * Apply a colormap to a label image. The set of colors
+ * is a good selection of distinct colors. The user can choose to use a background
+ * value. In that case, a gray pixel with the same intensity than the background
+ * label is produced.
+ *
+ * \author Gaetan Lehmann. Biologie du Developpement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ * \author Richard Beare. Department of Medicine, Monash University, Melbourne, Australia.
+ *
+ * \sa ScalarToRGBPixelFunctor LabelOverlayImageFilter
+ * \ingroup Multithreaded
+ *
+ */
+template 
+class ITK_EXPORT LabelToRGBImageFilter :
+  public
+  UnaryFunctorImageFilter   >
+{
+public:
+  /** Standard class typedefs. */
+  typedef LabelToRGBImageFilter    Self;
+  typedef SmartPointer       Pointer;
+  typedef SmartPointer ConstPointer;
+
+  typedef UnaryFunctorImageFilter   >  Superclass;
+
+  typedef TOutputImage OutputImageType;
+  typedef TLabelImage  LabelImageType;
+
+  typedef typename TOutputImage::PixelType                   OutputPixelType;
+  typedef typename TLabelImage::PixelType                    LabelPixelType;
+  typedef typename NumericTraits::ValueType OutputPixelValueType;
+
+  /** Runtime information support. */
+  itkTypeMacro(LabelToRGBImageFilter, UnaryFunctorImageFilter);
+
+  /** Method for creation through the object factory. */
+  itkNewMacro(Self);
+
+  /** Set/Get the background value */
+  itkSetMacro(BackgroundValue, LabelPixelType);
+  itkGetConstReferenceMacro(BackgroundValue, LabelPixelType);
+
+  /** Set/Get the background color in the output image */
+  itkSetMacro(BackgroundColor, OutputPixelType);
+  itkGetConstReferenceMacro(BackgroundColor, OutputPixelType);
+
+  /** Empty the color LUT container */
+  void ResetColors();
+
+  /** Get number of colors in the LUT container */
+  unsigned int GetNumberOfColors() const;
+
+  /** Type of the color component */
+  typedef typename OutputPixelType::ComponentType ComponentType;
+
+  /** Add color to the LUT container */
+  void AddColor(ComponentType r, ComponentType g, ComponentType b);
+
+protected:
+  LabelToRGBImageFilter();
+  virtual ~LabelToRGBImageFilter()
+  {
+  }
+
+  /** Process to execute before entering the multithreaded section */
+  void BeforeThreadedGenerateData(void);
+
+  /** Print internal ivars */
+  void PrintSelf(std::ostream & os, Indent indent) const;
+
+private:
+  LabelToRGBImageFilter(const Self &); // purposely not implemented
+  void operator=(const Self &);        // purposely not implemented
+
+  OutputPixelType m_BackgroundColor;
+  LabelPixelType  m_BackgroundValue;
+};
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelToRGBImageFilter.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.txx b/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.txx
new file mode 100644
index 00000000..a0d1d59e
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkLabelToRGBImageFilter.txx
@@ -0,0 +1,89 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkLabelToRGBImageFilter.txx,v $
+  Language:  C++
+  Date:      $Date: 2009-07-07 12:27:34 $
+  Version:   $Revision: 1.6 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkLabelToRGBImageFilter_txx
+#define __itkLabelToRGBImageFilter_txx
+
+#include "itkLabelToRGBImageFilter.h"
+
+namespace itk
+{
+/**
+ *
+ */
+template 
+LabelToRGBImageFilter
+::LabelToRGBImageFilter()
+{
+  m_BackgroundValue = NumericTraits::Zero;
+  m_BackgroundColor.Fill(NumericTraits::Zero);
+}
+
+template 
+unsigned int
+LabelToRGBImageFilter
+::GetNumberOfColors() const
+{
+  return this->GetFunctor().GetNumberOfColors();
+}
+
+template 
+void
+LabelToRGBImageFilter
+::ResetColors()
+{
+  this->GetFunctor().ResetColors();
+}
+
+template 
+void
+LabelToRGBImageFilter
+::AddColor(ComponentType r, ComponentType g, ComponentType b)
+{
+  this->GetFunctor().AddColor(r, g, b);
+}
+
+template 
+void
+LabelToRGBImageFilter
+::BeforeThreadedGenerateData()
+{
+  this->GetFunctor().SetBackgroundValue(m_BackgroundValue);
+  this->GetFunctor().SetBackgroundColor(m_BackgroundColor);
+}
+
+/**
+ *
+ */
+template 
+void
+LabelToRGBImageFilter
+::PrintSelf(std::ostream & os, Indent indent) const
+{
+  Superclass::PrintSelf(os, indent);
+
+  os << indent << "BackgroundValue: "
+     << static_cast::PrintType>( m_BackgroundValue )
+     << std::endl
+     << indent << "ColorBackground: "
+     << static_cast::PrintType>( m_BackgroundColor )
+     << std::endl;
+}
+
+} // end namespace itk
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.h b/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.h
new file mode 100644
index 00000000..0a845285
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.h
@@ -0,0 +1,447 @@
+/*
+ * Author: Hans J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+/*=========================================================================
+
+ Program:   Insight Segmentation & Registration Toolkit
+ Module:    $RCSfile: itkReflectiveCorrelationCenterToImageMetric.h,v $
+ Language:  C++
+ Date:      $Date: 2008-02-03 04:05:28 $
+ Version:   $Revision: 1.31 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the above copyright notices for more information.
+
+ =========================================================================*/
+#ifndef __itkReflectiveCorrelationCenterToImageMetric_h
+#define __itkReflectiveCorrelationCenterToImageMetric_h
+
+#include "itkPoint.h"
+#include "itkIdentityTransform.h"
+#include 
+
+#include "vnl/algo/vnl_powell.h"
+#include "landmarksConstellationCommon.h"
+#include "GenericTransformImage.h"
+#include "itkStatisticsImageFilter.h"
+
+// Optimize the A,B,C vector
+class Rigid3DCenterReflectorFunctor : public vnl_cost_function
+{
+public:
+  static const int UNKNOWNS_TO_ESTIMATE = 3;
+
+  void SetCenterOfHeadMass(SImageType::PointType centerOfHeadMass)
+  {
+    m_CenterOfHeadMass = centerOfHeadMass;
+  }
+
+  void QuickSampleParameterSpace(void)
+  {
+    vnl_vector params;
+    params.set_size(3);
+
+    params[0] = 0;
+    params[1] = 0;
+    params[2] = 0;
+    // Initialize with current guess;
+    double max_cc = this->f(params);
+    this->m_params = params;
+    const double HARange = 25.0;
+    const double BARange = 15.0;
+    // rough search in neighborhood.
+    const double one_degree = 1.0F * vnl_math::pi / 180.0F;
+    const double HAStepSize = HARange * one_degree * .1;
+    const double BAStepSize = BARange * one_degree * .1;
+    // Let the powell optimizer do all the work for determining the proper
+    // offset
+    // Quick search just needs to get an approximate angle correct.
+    // const double OffsetRange=8.0;
+    // const double OffsetStepSize=2.0;
+    const double Offset = 0.0;
+    // for(double Offset=-OffsetRange;Offset<=OffsetRange;
+    // Offset+=OffsetStepSize)
+      {
+      for( double HA = -HARange * one_degree; HA <= HARange * one_degree; HA += HAStepSize )
+        {
+        for( double BA = -BARange * one_degree; BA <= BARange * one_degree; BA += BAStepSize )
+          {
+          params[0] = HA;
+          params[1] = BA;
+          params[2] = Offset;
+          const double current_cc = this->f(params);
+          if( current_cc < max_cc )
+            {
+            this->m_params = params;
+            max_cc = current_cc;
+            }
+          }
+        }
+      }
+    // DEBUGGING INFORMATION
+    if( LMC::globalverboseFlag == true )
+      {
+      std::cout << "quick search 15 deg "
+                << " HA= " << this->m_params[0] * 180.0 / vnl_math::pi
+                << " BA= " << this->m_params[1] * 180.0 / vnl_math::pi
+                << " XO= " << this->m_params[2]
+                << " cc="  <<  this->f(this->m_params)
+                << " iterations=" << this->GetIterations()
+                << std::endl;
+      }
+  }
+
+  Rigid3DCenterReflectorFunctor() : vnl_cost_function(UNKNOWNS_TO_ESTIMATE), m_Iterations(0), m_Optimizer( &( *this ) )
+  {
+    this->m_params.set_size(UNKNOWNS_TO_ESTIMATE);
+    this->m_params.fill(0.0);
+
+    static const double default_tolerance = 1e-4;
+    static const double InitialStepSize = 7.0 * vnl_math::pi / 180.0;
+    this->m_Optimizer.set_initial_step(InitialStepSize);
+    this->m_Optimizer.set_f_tolerance(default_tolerance); // TODO:  This should
+                                                          // be optimized for
+                                                          // speed.
+    this->m_Optimizer.set_x_tolerance(default_tolerance); // TODO:  Need to do
+                                                          // extensive testing
+                                                          // of the speed
+                                                          // effects of changing
+                                                          // this value with
+                                                          // respect to quality
+                                                          // of result.
+
+    this->m_imInterp = LinearInterpolatorType::New();
+  }
+
+  double f(vnl_vector const & params)
+  {
+    const double        MaxUnpenalizedAllowedDistance = 8.0;
+    const double        DistanceFromCenterOfMass = vcl_abs(params[2]);
+    static const double FortyFiveDegreesAsRadians = 45.0 * vnl_math::pi / 180.0;
+    const double        cost_of_HeadingAngle = ( vcl_abs(params[0]) < FortyFiveDegreesAsRadians ) ? 0 :
+      ( ( vcl_abs(params[0]) - FortyFiveDegreesAsRadians ) * 2 );
+    const double cost_of_BankAngle = ( vcl_abs(params[1]) < FortyFiveDegreesAsRadians ) ? 0 :
+      ( ( vcl_abs(params[1]) - FortyFiveDegreesAsRadians ) * 2 );
+
+    if( ( vcl_abs(params[0]) > FortyFiveDegreesAsRadians ) || ( vcl_abs(params[1]) > FortyFiveDegreesAsRadians ) )
+      {
+      std::cout << "WARNING: ESTIMATED ROTATIONS ARE WAY TOO BIG SO GIVING A HIGH COST" << std::endl;
+      return 1;
+      }
+    const double cc = -CenterImageReflection_crossCorrelation(params);
+    m_Iterations++;
+
+    const double cost_of_motion = ( vcl_abs(DistanceFromCenterOfMass) < MaxUnpenalizedAllowedDistance ) ? 0 :
+      ( vcl_abs(DistanceFromCenterOfMass - MaxUnpenalizedAllowedDistance) * .1 );
+    const double raw_finalcos_gamma = cc + cost_of_motion + cost_of_BankAngle + cost_of_HeadingAngle;
+
+#ifdef __USE_EXTENSIVE_DEBUGGING__
+    if( !vnl_math_isfinite(raw_finalcos_gamma) )
+      {
+      std::cout << __FILE__ << " " << __LINE__ << " "
+                << params << " : " << cc << " " << cost_of_HeadingAngle << " " << cost_of_BankAngle << " "
+                << cost_of_motion << std::endl;
+      exit(-1);
+      }
+#endif
+    return raw_finalcos_gamma;
+  }
+
+  RigidTransformType::Pointer GetTransformToMSP(void) const
+  {
+    // Compute and store the new output image origin
+    m_ResampleFilter->SetTransform( this->GetTransformFromParams(this->m_params) );
+    m_ResampleFilter->Update();
+    SImageType::Pointer image = m_ResampleFilter->GetOutput();
+
+    // it is also the msp location
+    SImageType::PointType physCenter = GetImageCenterPhysicalPoint(image);
+
+    // Move the physical origin to the center of the image
+    RigidTransformType::Pointer tempEulerAngles3DT = RigidTransformType::New();
+    tempEulerAngles3DT->Compose( this->GetTransformFromParams(this->m_params) );
+    RigidTransformType::TranslationType tnsl = tempEulerAngles3DT->GetTranslation();
+
+    tempEulerAngles3DT->Translate(physCenter.GetVectorFromOrigin() - tnsl);
+    return tempEulerAngles3DT;
+  }
+
+  void Initialize(SImageType::Pointer & RefImage)
+  {
+      {
+      SImageType::PixelType dummy;
+      // Find threshold below which image is considered background.
+      m_BackgroundValue = setLowHigh(RefImage, dummy, dummy, 0.1F);
+      }
+
+    this->m_CenterOfImagePoint = GetImageCenterPhysicalPoint(RefImage);
+
+#ifdef USE_DEBUGGIN_IMAGES
+      {
+      itk::ImageFileWriter::Pointer dbgWriter = itk::ImageFileWriter::New();
+      dbgWriter->UseCompressionOn();
+      dbgWriter->SetFileName("itkReflectiveCorrelationCenterToImageMetric149.nii.gz");
+      dbgWriter->SetInput(RefImage);
+      dbgWriter->Update();
+      }
+#endif
+
+    this->m_OriginalImage = RefImage;
+    this->m_Translation = this->m_CenterOfHeadMass.GetVectorFromOrigin() - m_CenterOfImagePoint.GetVectorFromOrigin();
+    if( LMC::globalverboseFlag == true )
+      {
+      std::cout << "Center Of Physical Point: " << this->m_CenterOfImagePoint << std::endl;
+      std::cout << "Center Of Mass Point:" << this->m_CenterOfHeadMass << std::endl;
+      std::cout << "IntialTranslation: " << this->m_Translation << std::endl;
+      }
+  }
+
+  /* -- */
+  void SetDownSampledReferenceImage(SImageType::Pointer & NewImage)
+  {
+    m_OriginalImage = NewImage;
+  }
+
+  /* -- */
+  unsigned int GetIterations(void) const
+  {
+    return m_Iterations;
+  }
+
+  /* -- */
+  SImageType::PixelType GetBackgroundValue(void) const
+  {
+    return this->m_BackgroundValue;
+  }
+
+  /* -- */
+  RigidTransformType::Pointer GetTransformFromParams(vnl_vector const & params) const
+  {
+    RigidTransformType::Pointer tempEulerAngles3DT = RigidTransformType::New();
+
+    tempEulerAngles3DT->SetCenter(this->m_CenterOfImagePoint);
+    tempEulerAngles3DT->SetRotation(0, params[1], params[0]);
+    SImageType::PointType::VectorType tnsl = this->m_Translation;
+    tnsl[0] += params[2];
+    tempEulerAngles3DT->SetTranslation(tnsl);
+    return tempEulerAngles3DT;
+  }
+
+  /* -- */
+  const double CenterImageReflection_crossCorrelation(vnl_vector const & params)
+  {
+    // TODO WEI: the following block of code only need to be computed once for
+    // one image.
+    // Tried to move them to the Initialize function but it then went into a
+    // infinite loop at level 0.
+    // Very strange but has no priority
+      {
+      // Define the output image direction identical
+      m_OutputImageDirection.SetIdentity();
+
+      // Get output spacing
+      SImageType::DirectionType inputImageDirection = m_OriginalImage->GetDirection();
+      SImageType::SpacingType   inputImageSpacing = m_OriginalImage->GetSpacing();
+      m_OutputImageSpacing = inputImageDirection * inputImageSpacing;
+      for( unsigned int i = 0; i < 3; ++i )
+        {
+        if( m_OutputImageSpacing[i] < 0 )
+          {
+          m_OutputImageSpacing[i] *= -1;
+          }
+        }
+
+      // Define start index
+      m_OutputImageStartIndex.Fill(0);
+
+      // Desire a 95*2 x 130*2 x 160x2 mm voxel lattice that will fit a brain
+      m_OutputImageSize[0] = static_cast( 2.0 * vcl_ceil(95.0  / m_OutputImageSpacing[0]) );
+      m_OutputImageSize[1] = static_cast( 2.0 * vcl_ceil(130.0 / m_OutputImageSpacing[1]) );
+      m_OutputImageSize[2] = static_cast( 2.0 * vcl_ceil(160.0 / m_OutputImageSpacing[2]) );
+
+      // The physical center of MSP plane is not determined yet. At the
+      // optimizing stage we take COM as physical center
+      m_OutputImageOrigin[0] = m_CenterOfHeadMass[0] - .5 * ( m_OutputImageSize[0] - 1 ) * m_OutputImageSpacing[0];
+      m_OutputImageOrigin[1] = m_CenterOfHeadMass[1] - .5 * ( m_OutputImageSize[1] - 1 ) * m_OutputImageSpacing[1];
+      m_OutputImageOrigin[2] = m_CenterOfHeadMass[2] - .5 * ( m_OutputImageSize[2] - 1 ) * m_OutputImageSpacing[2];
+      }
+    /*
+        std::cout << "CenterImageReflection_crossCorrelation:" << std::endl;
+        std::cout << "m_OutputImageOrigin = " << m_OutputImageOrigin << std::endl;
+        std::cout << "m_OutputImageSize = " << m_OutputImageSize << std::endl;
+        std::cout << "m_OutputImageStartIndex = " << m_OutputImageStartIndex << std::endl;
+        std::cout << "m_OutputImageSpacing = " << m_OutputImageSpacing << std::endl;
+        std::cout << "m_OutputImageDirection = " << m_OutputImageDirection << std::endl;
+    */
+    /*
+     * Resample the image
+     */
+    m_ResampleFilter = FilterType::New();
+    LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
+    m_ResampleFilter->SetInterpolator(interpolator);
+    m_ResampleFilter->SetDefaultPixelValue(0);
+    m_ResampleFilter->SetOutputSpacing(m_OutputImageSpacing);
+    m_ResampleFilter->SetOutputOrigin(m_OutputImageOrigin);
+    m_ResampleFilter->SetSize(m_OutputImageSize);
+    m_ResampleFilter->SetOutputDirection(m_OutputImageDirection);
+    m_ResampleFilter->SetOutputStartIndex(m_OutputImageStartIndex);
+    m_ResampleFilter->SetInput(this->m_OriginalImage);
+    m_ResampleFilter->SetTransform( this->GetTransformFromParams(params) );
+    m_ResampleFilter->Update();
+    m_InternalResampledForReflectiveComputationImage = m_ResampleFilter->GetOutput();
+
+    /*
+     * Compute the reflective correlation
+     */
+    double               sumVoxelValues = 0.0F;
+    double               sumSquaredVoxelValues = 0.0F;
+    double               sumVoxelValuesQR = 0.0F;
+    double               sumVoxelValuesReflected = 0.0F;
+    double               sumSquaredVoxelValuesReflected = 0.0F;
+    int                  N = 0;
+    SImageType::SizeType rasterResampleSize =
+      m_InternalResampledForReflectiveComputationImage->GetLargestPossibleRegion().GetSize();
+    const SImageType::SizeType::SizeValueType xMaxIndexResampleSize = rasterResampleSize[0] - 1;
+    rasterResampleSize[0] /= 2; // Only need to do 1/2 in the x direction;
+    SImageType::RegionType rasterRegion;
+    rasterRegion.SetSize(rasterResampleSize);
+    rasterRegion.SetIndex( m_InternalResampledForReflectiveComputationImage->GetLargestPossibleRegion().GetIndex() );
+    itk::ImageRegionConstIteratorWithIndex halfIt(m_InternalResampledForReflectiveComputationImage,
+                                                              rasterRegion);
+    for( halfIt.GoToBegin(); !halfIt.IsAtEnd(); ++halfIt )
+      {
+      // NOTE:  Only need to compute left half of space because of reflection.
+      const double _f = halfIt.Get();
+      if( _f < this->m_BackgroundValue )  // don't worry about background
+                                          // voxels.
+        {
+        continue;
+        }
+      SImageType::IndexType ReflectedIndex = halfIt.GetIndex();
+      ReflectedIndex[0] = xMaxIndexResampleSize - ReflectedIndex[0];
+      const double g = m_InternalResampledForReflectiveComputationImage->GetPixel(ReflectedIndex);
+      if( g < this->m_BackgroundValue )  // don't worry about background voxels.
+        {
+        continue;
+        }
+      sumVoxelValuesQR += _f * g;
+      sumSquaredVoxelValuesReflected += g * g;
+      sumVoxelValuesReflected += g;
+      sumSquaredVoxelValues += _f * _f;
+      sumVoxelValues += _f;
+      N++;
+      }
+
+    // ///////////////////////////////////////////////
+    if( N == 0
+        || ( ( sumSquaredVoxelValues - sumVoxelValues * sumVoxelValues
+               / N ) * ( sumSquaredVoxelValuesReflected - sumVoxelValuesReflected * sumVoxelValuesReflected / N ) ) ==
+        0.0 )
+      {
+      return 0.0;
+      }
+    const double cc =
+      ( ( sumVoxelValuesQR - sumVoxelValuesReflected * sumVoxelValues
+          / N )
+        / vcl_sqrt( ( sumSquaredVoxelValues - sumVoxelValues * sumVoxelValues
+                      / N )
+                    * ( sumSquaredVoxelValuesReflected - sumVoxelValuesReflected * sumVoxelValuesReflected / N ) ) );
+    return cc;
+  }
+
+  SImageType::Pointer GetMSPCenteredImage(void)
+  {
+    // Note GetTransformToMSP() aligns physical origin to the center of MSP.
+    // SimpleResampleImage() further aligns physical center of image to physical
+    // origin.
+
+    // RigidTransformType::Pointer tempEulerAngles3DT = GetTransformToMSP();
+    // return SimpleResampleImage( this->m_OriginalImage, tempEulerAngles3DT );
+
+    // create a colormap lookup table
+    typedef itk::StatisticsImageFilter StatisticsFilterType;
+    StatisticsFilterType::Pointer statisticsFilter = StatisticsFilterType::New();
+    statisticsFilter->SetInput(this->m_OriginalImage);
+    statisticsFilter->Update();
+    SImageType::PixelType minPixelValue = statisticsFilter->GetMinimum();
+
+    return TransformResample
+             ( this->m_OriginalImage,
+             MakeIsoTropicReferenceImage(),
+             minPixelValue,
+             GetInterpolatorFromString("Linear"),
+             GetTransformToMSP().GetPointer() );
+  }
+
+  void Update(void)
+  {
+    this->m_Optimizer.minimize(this->m_params);
+    std::cout << this->m_params[0] * 180.0 / vnl_math::pi << " " << this->m_params[1] * 180.0 / vnl_math::pi << " "
+              << this->m_params[2] << " cc= " << this->f(this->m_params) << " iters= " << this->GetIterations()
+              << std::endl;
+  }
+
+private:
+
+  SImageType::Pointer SimpleResampleImage(SImageType::Pointer image, RigidTransformType::Pointer EulerAngles3DT)
+  {
+    m_ResampleFilter = FilterType::New();
+    LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New();
+    m_ResampleFilter->SetInterpolator(interpolator);
+    m_ResampleFilter->SetDefaultPixelValue(0);
+    m_ResampleFilter->SetOutputSpacing(m_OutputImageSpacing);
+    m_ResampleFilter->SetSize(m_OutputImageSize);
+    m_ResampleFilter->SetOutputDirection(m_OutputImageDirection);
+    m_ResampleFilter->SetOutputStartIndex(m_OutputImageStartIndex);
+    m_ResampleFilter->SetInput(image);
+    m_ResampleFilter->SetTransform(EulerAngles3DT);
+
+    // Move the physical center of image to the physical origin
+    m_OutputImageOrigin[0] = -0.5 * ( m_OutputImageSize[0] - 1 ) * m_OutputImageSpacing[0];
+    m_OutputImageOrigin[1] = -0.5 * ( m_OutputImageSize[1] - 1 ) * m_OutputImageSpacing[1];
+    m_OutputImageOrigin[2] = -0.5 * ( m_OutputImageSize[2] - 1 ) * m_OutputImageSpacing[2];
+    m_ResampleFilter->SetOutputOrigin(m_OutputImageOrigin);
+
+    m_ResampleFilter->Update();
+
+    SImageType::Pointer returnImage = m_ResampleFilter->GetOutput();
+    returnImage->DisconnectPipeline();
+    return returnImage;
+  }
+
+  typedef vnl_powell                                       OptimizerType;
+  typedef itk::ResampleImageFilter FilterType;
+
+  vnl_vector                m_params;
+  SImageType::Pointer               m_OriginalImage;
+  SImageType::SpacingType           m_OutputImageSpacing;
+  SImageType::DirectionType         m_OutputImageDirection;
+  SImageType::IndexType             m_OutputImageStartIndex;
+  SImageType::SizeType              m_OutputImageSize;
+  SImageType::PointType             m_OutputImageOrigin;
+  SImageType::PointType             m_CenterOfHeadMass;
+  SImageType::Pointer               m_InternalResampledForReflectiveComputationImage;
+  FilterType::Pointer               m_ResampleFilter;
+  SImageType::PixelType             m_BackgroundValue;
+  SImageType::PointType             m_CenterOfImagePoint;
+  SImageType::PointType::VectorType m_Translation;
+  int                               m_Iterations;
+  OptimizerType                     m_Optimizer;
+  LinearInterpolatorType::Pointer   m_imInterp;
+};
+
+namespace itk
+    {} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkReflectiveCorrelationCenterToImageMetric.txx"
+#endif
+
+#endif
diff --git a/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.txx b/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.txx
new file mode 100644
index 00000000..8bc9be27
--- /dev/null
+++ b/BRAINSConstellationDetector/src/itkReflectiveCorrelationCenterToImageMetric.txx
@@ -0,0 +1,23 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $RCSfile: itkReflectiveCorrelationCenterToImageMetric.txx,v $
+  Language:  C++
+  Date:      $Date: 2008-02-03 19:00:36 $
+  Version:   $Revision: 1.51 $
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef _itkReflectiveCorrelationCenterToImageMetric_txx
+#define _itkReflectiveCorrelationCenterToImageMetric_txx
+
+#include "itkReflectiveCorrelationCenterToImageMetric.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+
+#endif // _itkReflectiveCorrelationCenterToImageMetric_txx
diff --git a/BRAINSConstellationDetector/src/landmarkIO.cxx b/BRAINSConstellationDetector/src/landmarkIO.cxx
new file mode 100644
index 00000000..df336f25
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarkIO.cxx
@@ -0,0 +1,896 @@
+/*
+ * Author: Hans J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "landmarkIO.h"
+#if  ITK_VERSION_MAJOR >=4
+#include "itk_hdf5.h"
+#include "itk_H5Cpp.h"
+#else
+#include "hdf5.h"
+#include "H5Cpp.h"
+#endif
+
+static bool IsOnCylinder(const SImageType::PointType & curr_point,
+                         const SImageType::PointType & center_point,
+                         const SImageType::PointType & center_point2,
+                         const double radius,
+                         const double thickness)
+{
+  // const double cylinder_end=vcl_abs(height -
+  // vcl_abs(curr_point[0]-center_point[0]));
+  const double APdist = curr_point[1] - center_point[1];
+  const double ISdist = curr_point[2] - center_point[2];
+  const double cylinder_side_squared =
+    vcl_abs( radius * radius - ( APdist * APdist + ISdist * ISdist ) );
+  const SImageType::PointType::VectorType PointDist2 =
+    curr_point.GetVectorFromOrigin() - center_point2.GetVectorFromOrigin();
+
+  return cylinder_side_squared < thickness * thickness
+         || PointDist2.GetNorm() < 2;
+}
+
+static bool IsOnSphere(const SImageType::PointType & curr_point,
+                       const SImageType::PointType & center_point,
+                       const double radius)
+{
+  const SImageType::PointType::VectorType PointDist =
+    curr_point.GetVectorFromOrigin() - center_point.GetVectorFromOrigin();
+
+  return PointDist.GetNorm() < radius;
+}
+
+// TODO:  BrandedImages should be from the modelFile instead of the mDef.
+void
+MakeBrandeddebugImage(SImageType::ConstPointer in,
+                      const landmarksConstellationModelIO & mDef,
+                      const SImageType::PointType & RP,
+                      const SImageType::PointType & AC,
+                      const SImageType::PointType & PC,
+                      const SImageType::PointType & VN4,
+                      const std::string & fname,
+                      const SImageType::PointType & RP2,
+                      const SImageType::PointType & AC2,
+                      const SImageType::PointType & PC2,
+                      const SImageType::PointType & VN42)
+{
+  RGBImageType::Pointer orientedImage;
+  SImageType::Pointer   inputImage =
+    itkUtil::OrientImage(in,
+                                     itk::SpatialOrientation::
+                                     ITK_COORDINATE_ORIENTATION_RAI);
+
+    {
+    itk::StatisticsImageFilter::Pointer stats =
+      itk::StatisticsImageFilter::New();
+    stats->SetInput(inputImage);
+    stats->Update();
+    SImageType::PixelType minPixel( stats->GetMinimum() );
+    SImageType::PixelType maxPixel( stats->GetMaximum() );
+    RGBImageType::Pointer rgbImage = RGBImageType::New();
+    rgbImage->CopyInformation(inputImage);
+    rgbImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+    rgbImage->Allocate();
+
+    // First just make RGB Image with greyscale values.
+    itk::ImageRegionIterator
+    rgbIt( rgbImage, rgbImage->GetLargestPossibleRegion() );
+    itk::ImageRegionIterator
+    sIt( inputImage, inputImage->GetLargestPossibleRegion() );
+    for( ; !sIt.IsAtEnd(); ++rgbIt, ++sIt )
+      {
+      // SImageType::IndexType index = sIt.GetIndex();
+      // SImageType::PointType p;
+      // rgbImage->TransformIndexToPhysicalPoint(index,p);
+      unsigned char charVal( ShortToUChar(sIt.Value(), minPixel, maxPixel) );
+      RGBPixelType  pixel;
+      pixel.SetRed(charVal);
+      pixel.SetGreen(charVal);
+      pixel.SetBlue(charVal);
+      rgbIt.Set(pixel);
+      }
+    orientedImage = rgbImage;
+    }
+  for( unsigned int which = 0; which < 4; which++ )
+    {
+    SImageType::PointType pt = RP;
+    SImageType::PointType pt2 = RP2;
+    double                radius = 0.0;
+    double                height = 0.0;
+
+    switch( which )
+      {
+      case 0:
+        height = mDef.GetHeight("RP");
+        radius = 4 * mDef.GetRadius("RP");
+        pt = RP;
+        pt2 = RP2;
+        break;
+      case 1:
+        height = mDef.GetHeight("VN4");
+        radius = 1.6 * mDef.GetRadius("VN4");
+        pt = VN4;
+        pt2 = VN42;
+        break;
+      case 2:
+        height = mDef.GetHeight("AC");
+        radius = 1.6 * mDef.GetRadius("AC");
+        pt = AC;
+        pt2 = AC2;
+        break;
+      case 3:
+        height = mDef.GetHeight("PC");
+        radius = 4 * mDef.GetRadius("PC");
+        pt = PC;
+        pt2 = PC2;
+        break;
+      }
+
+    itk::ImageRegionIterator
+    rgbIt( orientedImage, orientedImage->GetLargestPossibleRegion() );
+    itk::ImageRegionIterator
+    sIt( inputImage, inputImage->GetLargestPossibleRegion() );
+    for( ; !rgbIt.IsAtEnd() && !sIt.IsAtEnd(); ++sIt, ++rgbIt )
+      {
+      SImageType::IndexType index = rgbIt.GetIndex();
+      SImageType::PointType p;
+      orientedImage->TransformIndexToPhysicalPoint(index, p);
+      if( IsOnCylinder(p, pt, pt2, radius, /* height, */ 4) )
+        {
+        RGBPixelType pixel = rgbIt.Value();
+
+        switch( which )
+          {
+          case 0:
+            pixel.SetRed(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 1:
+            pixel.SetGreen(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 2:
+            pixel.SetBlue(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 3:
+            pixel.SetRed(255);
+            pixel.SetBlue(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          }
+        }
+      }
+    }
+
+  RGB2DImageType::Pointer    TwoDImage = RGB2DImageType::New();
+  RGB2DImageType::RegionType TwoDImageRegion;
+  RGB2DImageType::IndexType  TwoDIndex;
+  TwoDIndex[0] = 0;
+  TwoDIndex[1] = 0;
+  RGB2DImageType::SizeType TwoDSize;
+  TwoDSize[0] = orientedImage->GetLargestPossibleRegion().GetSize()[1];
+  TwoDSize[1] = orientedImage->GetLargestPossibleRegion().GetSize()[2];
+  TwoDImageRegion.SetIndex(TwoDIndex);
+  TwoDImageRegion.SetSize(TwoDSize);
+  TwoDImage->SetRegions(TwoDImageRegion);
+  TwoDImage->Allocate();
+
+  RGBImageType::IndexType ThreeDIndex;
+  ThreeDIndex[0] = ( orientedImage->GetLargestPossibleRegion().GetSize()[0] ) / 2;
+  for( TwoDIndex[1] = 0;
+       TwoDIndex[1] < static_cast( TwoDSize[1] );
+       ( TwoDIndex[1] )++ )
+    {
+    ThreeDIndex[2] = TwoDSize[1] - 1 - TwoDIndex[1];
+    for( TwoDIndex[0] = 0;
+         TwoDIndex[0] < static_cast( TwoDSize[0] );
+         ( TwoDIndex[0] )++ )
+      {
+      ThreeDIndex[1] = TwoDIndex[0];
+      TwoDImage->SetPixel( TwoDIndex, orientedImage->GetPixel(ThreeDIndex) );
+      }
+    }
+
+  itkUtil::WriteImage(TwoDImage, fname);
+  itkUtil::WriteImage(orientedImage, fname + "_ThreeDRGB.nii.gz");
+  itkUtil::WriteImage(inputImage, fname + "_ThreeD.nii.gz");
+}
+
+void
+MakePointBranded3DImage(SImageType::ConstPointer in,
+                        const SImageType::PointType & CenterPoint,
+                        const std::string & fname)
+{
+  SImageType::Pointer inputImage =
+    itkUtil::OrientImage(in,
+                                     itk::SpatialOrientation::
+                                     ITK_COORDINATE_ORIENTATION_RAI);
+
+  itk::StatisticsImageFilter::Pointer stats =
+    itk::StatisticsImageFilter::New();
+  stats->SetInput(inputImage);
+  stats->Update();
+  //  SImageType::PixelType minPixel(stats->GetMinimum());
+  SImageType::PixelType maxPixel( stats->GetMaximum() );
+  SImageType::PointType pt = CenterPoint;
+  double                radius = 3.0;
+
+  itk::ImageRegionIterator
+  sIt( inputImage, inputImage->GetLargestPossibleRegion() );
+  for( ; !sIt.IsAtEnd(); ++sIt )
+    {
+    SImageType::IndexType index = sIt.GetIndex();
+    SImageType::PointType p;
+    inputImage->TransformIndexToPhysicalPoint(index, p);
+    if( IsOnSphere(p, pt, radius) )
+      {
+      sIt.Set(maxPixel);
+      }
+    }
+
+  itkUtil::WriteImage(inputImage, fname + "_Branded.nii.gz");
+}
+
+void
+MakeBranded2DImage(SImageType::ConstPointer in,
+                   landmarksConstellationDetector & myDetector,
+                   const SImageType::PointType & RP,
+                   const SImageType::PointType & AC,
+                   const SImageType::PointType & PC,
+                   const SImageType::PointType & VN4,
+                   const SImageType::PointType & CM,
+                   const std::string & fname)
+{
+  RGBImageType::Pointer orientedImage;
+  SImageType::Pointer   inputImage =
+    itkUtil::OrientImage(in,
+                                     itk::SpatialOrientation::
+                                     ITK_COORDINATE_ORIENTATION_RAI);
+
+    {
+    itk::StatisticsImageFilter::Pointer stats =
+      itk::StatisticsImageFilter::New();
+    stats->SetInput(inputImage);
+    stats->Update();
+    SImageType::PixelType minPixel( stats->GetMinimum() );
+    SImageType::PixelType maxPixel( stats->GetMaximum() );
+    RGBImageType::Pointer rgbImage = RGBImageType::New();
+    rgbImage->CopyInformation(inputImage);
+    rgbImage->SetRegions( inputImage->GetLargestPossibleRegion() );
+    rgbImage->Allocate();
+
+    // First just make RGB Image with greyscale values.
+    itk::ImageRegionIterator
+    rgbIt( rgbImage, rgbImage->GetLargestPossibleRegion() );
+    itk::ImageRegionIterator
+    sIt( inputImage, inputImage->GetLargestPossibleRegion() );
+    for( ; !sIt.IsAtEnd(); ++rgbIt, ++sIt )
+      {
+      // SImageType::IndexType index = sIt.GetIndex();
+      // SImageType::PointType p;
+      // rgbImage->TransformIndexToPhysicalPoint(index,p);
+      unsigned char charVal( ShortToUChar(sIt.Value(), minPixel, maxPixel) );
+      RGBPixelType  pixel;
+      pixel.SetRed(charVal);
+      pixel.SetGreen(charVal);
+      pixel.SetBlue(charVal);
+      rgbIt.Set(pixel);
+      }
+    orientedImage = rgbImage;
+    }
+  for( unsigned int which = 0; which < 5; which++ )
+    {
+    SImageType::PointType pt;
+    double                radius = 0.0;
+    double                height = 0.0;
+
+    switch( which )
+      {
+      case 0:
+        height = 1;
+        radius = 1;
+        pt = CM;
+        break;
+      case 1:
+        height = myDetector.GetModelHeight("AC");
+        radius = myDetector.GetModelRadius("AC");
+        pt = AC;
+        break;
+      case 2:
+        height = myDetector.GetModelHeight("PC");
+        radius = myDetector.GetModelRadius("PC");
+        pt = PC;
+        break;
+      case 3:
+        height = myDetector.GetModelHeight("RP");
+        radius = myDetector.GetModelRadius("RP");
+        pt = RP;
+        break;
+      case 4:
+        height = myDetector.GetModelHeight("VN4");
+        radius = myDetector.GetModelRadius("VN4");
+        pt = VN4;
+        break;
+      }
+
+    itk::ImageRegionIterator
+    rgbIt( orientedImage, orientedImage->GetLargestPossibleRegion() );
+    itk::ImageRegionIterator
+    sIt( inputImage, inputImage->GetLargestPossibleRegion() );
+    for( ; !rgbIt.IsAtEnd() && !sIt.IsAtEnd(); ++sIt, ++rgbIt )
+      {
+      SImageType::IndexType index = rgbIt.GetIndex();
+      SImageType::PointType p;
+      orientedImage->TransformIndexToPhysicalPoint(index, p);
+      if( IsOnCylinder(p, pt, pt, radius, /* height,*/ 4) )
+        {
+        RGBPixelType pixel = rgbIt.Value();
+
+        switch( which )
+          {
+          case 0:
+            pixel.SetRed(255);
+            pixel.SetGreen(255);
+            pixel.SetBlue(0);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 1:
+            pixel.SetRed(0);
+            pixel.SetGreen(255);
+            pixel.SetBlue(0);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 2:
+            pixel.SetRed(0);
+            pixel.SetGreen(0);
+            pixel.SetBlue(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 3:
+            pixel.SetRed(255);
+            pixel.SetGreen(0);
+            pixel.SetBlue(0);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          case 4:
+            pixel.SetRed(255);
+            pixel.SetGreen(0);
+            pixel.SetBlue(255);
+            rgbIt.Set(pixel);
+            sIt.Set(255);
+            break;
+          }
+        }
+      }
+    }
+
+  RGB2DImageType::Pointer    TwoDImage = RGB2DImageType::New();
+  RGB2DImageType::RegionType TwoDImageRegion;
+  RGB2DImageType::IndexType  TwoDIndex;
+  TwoDIndex[0] = 0;
+  TwoDIndex[1] = 0;
+  RGB2DImageType::SizeType TwoDSize;
+  TwoDSize[0] = orientedImage->GetLargestPossibleRegion().GetSize()[1];
+  TwoDSize[1] = orientedImage->GetLargestPossibleRegion().GetSize()[2];
+  TwoDImageRegion.SetIndex(TwoDIndex);
+  TwoDImageRegion.SetSize(TwoDSize);
+  TwoDImage->SetRegions(TwoDImageRegion);
+  TwoDImage->Allocate();
+
+  RGBImageType::IndexType ThreeDIndex;
+  ThreeDIndex[0] =
+    ( orientedImage->GetLargestPossibleRegion().GetSize()[0] ) / 2;
+  for( TwoDIndex[1] = 0;
+       TwoDIndex[1] < static_cast( TwoDSize[1] );
+       ( TwoDIndex[1] )++ )
+    {
+    ThreeDIndex[2] = TwoDSize[1] - 1 - TwoDIndex[1];
+    for( TwoDIndex[0] = 0;
+         TwoDIndex[0] < static_cast( TwoDSize[0] );
+         ( TwoDIndex[0] )++ )
+      {
+      ThreeDIndex[1] = TwoDIndex[0];
+      TwoDImage->SetPixel( TwoDIndex, orientedImage->GetPixel(ThreeDIndex) );
+      }
+    }
+
+  itkUtil::WriteImage(TwoDImage, fname);
+}
+
+// TODO:  Determine what the interface for WriteMRMLFile really needs to produce
+// a useful file, and then limit the interface to just that.
+extern void
+WriteMRMLFile(std::string outputMRML,
+              std::string outputLandmarksInInputSpace,
+              std::string outputLandmarksInOutputSpace,
+              std::string inputVolume,
+              std::string outputVolume,
+              std::string outputTransform,
+              const LandmarksMapType & outputLandmarksInInputSpaceMap,
+              const LandmarksMapType & outputLandmarksInOutputSpaceMap,
+              const VersorTransformPointer versorTransform)
+{
+  const unsigned int LocalImageDimension = 3;
+
+  typedef short                                      PixelType;
+  typedef itk::Image ImageType;
+  typedef itk::ImageFileReader            ReaderType;
+
+  std::string mrmlFullFilename =
+    itksys::SystemTools::CollapseFullPath( outputMRML.c_str() );
+  std::string outputLandmarksInInputSpaceFullFilenameWithoutExtension = "";
+  std::string outputLandmarksInOutputSpaceFullFilenameWithoutExtension = "";
+  std::string inputVolumeFullFilename = "";
+  std::string inputVolumeFilenameWithoutPath = "";
+  std::string outputVolumeFullFilename = "";
+  std::string outputVolumeFilenameWithoutPath = "";
+  std::string outputTransformFullFilename = "";
+  std::string outputTransformFilenameWithoutPath = "";
+
+  if( outputLandmarksInInputSpace.compare("") != 0 )
+    {
+    outputLandmarksInInputSpace =
+      itksys::SystemTools::CollapseFullPath( outputLandmarksInInputSpace.c_str() );
+    outputLandmarksInInputSpaceFullFilenameWithoutExtension =
+      itksys::SystemTools::GetFilenamePath( outputLandmarksInInputSpace ) + "/"
+      + itksys::SystemTools::GetFilenameWithoutLastExtension( outputLandmarksInInputSpace);
+    outputLandmarksInInputSpaceFullFilenameWithoutExtension =
+      itksys::SystemTools::CollapseFullPath(
+        outputLandmarksInInputSpaceFullFilenameWithoutExtension.c_str() );
+    }
+
+  if( outputLandmarksInOutputSpace.compare("") != 0 )
+    {
+    outputLandmarksInOutputSpace =
+      itksys::SystemTools::CollapseFullPath( outputLandmarksInOutputSpace.c_str() );
+    outputLandmarksInOutputSpaceFullFilenameWithoutExtension =
+      itksys::SystemTools::GetFilenamePath( outputLandmarksInOutputSpace ) + "/"
+      + itksys::SystemTools::GetFilenameWithoutLastExtension( outputLandmarksInOutputSpace );
+    outputLandmarksInOutputSpaceFullFilenameWithoutExtension =
+      itksys::SystemTools::CollapseFullPath( outputLandmarksInOutputSpaceFullFilenameWithoutExtension.c_str() );
+    }
+
+  if( inputVolume.compare("") != 0 )
+    {
+    inputVolumeFullFilename =
+      itksys::SystemTools::CollapseFullPath( inputVolume.c_str() );
+    inputVolumeFilenameWithoutPath =
+      itksys::SystemTools::GetFilenameName( inputVolumeFullFilename );
+    }
+
+  if( outputVolume.compare("") != 0 )
+    {
+    outputVolumeFullFilename =
+      itksys::SystemTools::CollapseFullPath( outputVolume.c_str() );
+    outputVolumeFilenameWithoutPath =
+      itksys::SystemTools::GetFilenameName( outputVolumeFullFilename );
+    }
+
+  if( outputTransform.compare("") != 0 )
+    {
+    outputTransformFullFilename =
+      itksys::SystemTools::CollapseFullPath( outputTransform.c_str() );
+    outputTransformFilenameWithoutPath =
+      itksys::SystemTools::GetFilenameName( outputTransformFullFilename );
+    }
+
+  std::ofstream myfile( mrmlFullFilename.c_str() );
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Cannot write mrml file!" << std::endl;
+    exit(-1);
+    }
+
+  // Common mrml header
+  myfile
+  <<
+  "  \n    \n    \n    \n    \n    \n    \n    \n    \n    \n    \n    \n    \n    \n    \n";
+
+  // For fiducial landmarks in output space
+  if( outputLandmarksInOutputSpace.compare("") != 0 )
+    {
+    myfile << "first << " labeltext " << it->first << " xyz "
+             << ( it->second )[0] << " " << ( it->second )[1] << " " << ( it->second )[2];
+      if( ++index < outputLandmarksInOutputSpaceMap.size() )
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\n";
+        }
+      else
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\">\n";
+        }
+      }
+
+    myfile
+    <<
+    "\n";
+    }
+
+  // For fiducial landmarks in input space
+  if( outputLandmarksInInputSpace.compare("") != 0 )
+    {
+    myfile << "first << " labeltext " << it->first << " xyz "
+             << ( it->second )[0] << " " << ( it->second )[1] << " " << ( it->second )[2];
+      if( ++index < outputLandmarksInInputSpaceMap.size() )
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\n";
+        }
+      else
+        {
+        myfile << " orientationwxyz 0 0 0 1 selected 1 visibility 1\">\n";
+        }
+      }
+
+    myfile
+    <<
+    "\n";
+    }
+
+  // For output volume
+  if( outputVolume.compare( "" ) != 0 )
+    {
+    ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName( outputVolumeFullFilename );
+    reader->Update();
+    ImageType::DirectionType direction = reader->GetOutput()->GetDirection();
+    ImageType::SpacingType   spacing = reader->GetOutput()->GetSpacing();
+    ImageType::PointType     origin = reader->GetOutput()->GetOrigin();
+    myfile
+    <<
+    "\n";
+
+    myfile << "\n\n";
+    }
+
+  // For input volume
+  if( inputVolume.compare( "" ) != 0 )
+    {
+    ReaderType::Pointer reader = ReaderType::New();
+    reader->SetFileName( inputVolumeFullFilename );
+    reader->Update();
+    ImageType::DirectionType direction = reader->GetOutput()->GetDirection();
+    ImageType::SpacingType   spacing = reader->GetOutput()->GetSpacing();
+    ImageType::PointType     origin = reader->GetOutput()->GetOrigin();
+    myfile
+    <<
+    "\n";
+
+    myfile << "\n\n";
+    }
+
+  // For output transform
+  if( outputTransform.compare("") != 0 )
+    {
+    VersorTransformMatrixType tm = versorTransform->GetMatrix();
+
+    myfile
+    <<
+    "  \n"
+    <<
+    "  \n";
+    }
+
+  myfile << "\n";
+  myfile.close();
+}
+
+void
+loadLLSModelMat(std::string llsModel,
+                std::string processingList,
+                std::map > & llsMeans,
+                std::map & llsMatrices,
+                std::map & searchRadii)
+{
+  std::vector landmarkList;
+
+    {
+    // Read in landmark name and their search radii
+    std::ifstream myprocessingListFile( processingList.c_str() );
+    if( !myprocessingListFile.is_open() )
+      {
+      std::cerr << "Cannot open processing list file!" << std::endl;
+      exit(-1);
+      }
+
+    // for each landmark
+    std::string line;
+    while( getline( myprocessingListFile, line ) )
+      {
+      std::string name = line;
+      landmarkList.push_back( name );
+      if( !getline( myprocessingListFile, line ) )
+        {
+        std::cerr << "Bad file format of processing list file!" << std::endl;
+        return;
+        }
+      searchRadii[name] = atof( line.c_str() );
+      }
+
+    myprocessingListFile.close();
+    }
+
+  // Read in the s vector and M matrix of each landmark
+    {
+    vcl_ifstream myMatlabLLSModelFile( llsModel.c_str() );
+    VectorType   llsMeansVnl;
+    if( !myMatlabLLSModelFile.is_open() )
+      {
+      std::cerr << "Cannot open landmark model file!" << std::endl;
+      exit(-1);
+      }
+    for( unsigned int i = 0; i < landmarkList.size(); ++i )
+      {
+      // vnl can only read in Matlab v4 binary files, and there is a 19
+      // character length
+      // restriction for the stored variables.
+      size_t      matV4MaxVarLen = 19;
+      size_t      suffixLen = 3; // suffix length for __x
+      std::string name_s;
+      std::string name_M;
+      if( landmarkList[i].size() > matV4MaxVarLen - suffixLen )
+        {
+        name_s = landmarkList[i].substr( 0, matV4MaxVarLen - suffixLen ) + "__s";
+        name_M = landmarkList[i].substr( 0, matV4MaxVarLen - suffixLen ) + "__M";
+        }
+      else
+        {
+        name_s = landmarkList[i] + "__s";
+        name_M = landmarkList[i] + "__M";
+        }
+
+      std::cout << "Reading: " << name_s << "  " << name_M << std::endl;
+      if( !vnl_matlab_read_or_die( myMatlabLLSModelFile, llsMeansVnl, name_s.c_str() ) )
+        {
+        std::cerr << "Error reading s vector of landmark " << name_s << std::endl;
+        }
+      else
+        {
+        // hard coded dim = 3
+        llsMeans[landmarkList[i]].push_back( llsMeansVnl[0] );
+        llsMeans[landmarkList[i]].push_back( llsMeansVnl[1] );
+        llsMeans[landmarkList[i]].push_back( llsMeansVnl[2] );
+        }
+      if( !vnl_matlab_read_or_die( myMatlabLLSModelFile, llsMatrices[landmarkList[i]], name_M.c_str() ) )
+        {
+        std::cerr << "Error reading M matrix of landmark " << name_M << std::endl;
+        }
+      }
+    myMatlabLLSModelFile.close();
+    }
+}
+
+void
+loadLLSModel(std::string llsModelFilename,
+             std::map > & llsMeans,
+             std::map & llsMatrices,
+             std::map & searchRadii)
+{
+  std::ifstream myfile( llsModelFilename.c_str() );
+
+  if( !myfile.is_open() )
+    {
+    std::cerr << "Cannot open landmark model file!" << std::endl;
+    exit(-1);
+    }
+
+  // for each landmark
+  std::string line;
+  while( getline(myfile, line) )
+    {
+
+    // skip newline or comments between landmarks
+    if( ( line.compare(0, 1, "#") != 0 )
+        && ( line.compare(0, 1, "\0") != 0 ) )
+      {
+      unsigned int dimension = 3; // for 3D parameters
+
+      // read in the landmark name
+      std::string name = line;
+
+      if( !getline(myfile, line) )
+        {
+        std::cerr << "Bad number of parameters info in llsModelFile!" << std::endl;
+        exit(-1);
+        }
+      else
+        {
+        // read in mean values associated with PCA model
+        unsigned int pos1 = 0;
+        unsigned int pos2 = line.find(' ');
+        unsigned int i = 0;
+        while( pos2 < line.size() )
+          {
+          llsMeans[name].push_back(
+            atof( line.substr(pos1, pos2 - pos1).c_str() ) );
+          ++i;
+          pos1 = pos2 + 1;
+          pos2 = line.find(' ', pos1 + 1);
+          }
+
+        if( i != dimension )  // double check
+          {
+          std::cerr << "Bad mean values in llsModelFile!" << std::endl;
+          exit(-1);
+          }
+        }
+
+      // read in search radius
+      if( !getline(myfile, line) )
+        {
+        std::cerr << "Bad search radius in llsModelFile!" << std::endl;
+        exit(-1);
+        }
+      else
+        {
+        searchRadii[name] = atof( line.c_str() );
+        }
+
+      // read in the number of linear model coefficients
+      unsigned int numParameters = 0;
+      if( !getline(myfile, line) )
+        {
+        std::cerr << "Bad number of parameters info in llsModelFile!" << std::endl;
+        exit(-1);
+        }
+      else
+        {
+        numParameters = atoi( line.c_str() );
+        }
+
+      MatrixType coefficients; // linear model coefficients
+      coefficients.set_size(dimension, numParameters);
+      for( unsigned int j = 0; j < dimension; ++j )
+        {
+        if( !getline(myfile, line) )
+          {
+          std::cerr << "Bad linear model coefficients in llsModelFile!" << std::endl;
+          exit(-1);
+          }
+        else
+          {
+          unsigned int pos1 = 0;
+          unsigned int pos2 = line.find(' ');
+          unsigned int i = 0;
+          while( pos2 < line.size() )
+            {
+            coefficients(j, i++) =
+              atof( line.substr(pos1, pos2 - pos1).c_str() );
+            pos1 = pos2 + 1;
+            pos2 = line.find(' ', pos1 + 1);
+            }
+
+          if( i != numParameters )  // double check
+            {
+            std::cerr << "Bad linear model coefficients in llsModelFile!" << std::endl;
+            exit(-1);
+            }
+          }
+        }
+      llsMatrices[name] = coefficients;
+      }
+    }
+
+  myfile.close();
+}
+
+void
+writeVerificationScript(std::string outputVerificationScriptFilename,
+                        std::string outputVolume,
+                        std::string saveOutputLandmarksFilename)
+{
+  std::ofstream ScriptFile;
+
+  ScriptFile.open( outputVerificationScriptFilename.c_str() ); // open setup
+                                                               // file for
+                                                               // writing
+  if( !ScriptFile.is_open() )
+    {
+    std::cerr << "Can't write outputVerificationScript " << outputVerificationScriptFilename << std::endl;
+    std::cerr.flush();
+    exit(-1);
+    }
+
+  ScriptFile << "##There is a program that reads in a T1 image, determine the AC, PC, VN4, and MPJ" << std::endl;
+  ScriptFile << "##points and writes out a slicer .fcsv file with 3 landmark points in it" << std::endl;
+  ScriptFile << "##There are 2 files to be read in order to confirm that the landmarks are" << std::endl;
+  ScriptFile << "##being picked correctly." << std::endl;
+  ScriptFile << "set volumesLogic [$::slicer3::VolumesGUI GetLogic]" << std::endl;
+  ScriptFile << "set fidLogic [$::slicer3::FiducialsGUI GetLogic]" << std::endl;
+  ScriptFile << std::endl;
+  ScriptFile << "set fileNameT1  " << outputVolume << std::endl;
+  ScriptFile << "set  landmarkName " << saveOutputLandmarksFilename << std::endl;
+  ScriptFile << std::endl;
+  ScriptFile << "set volumeNode [$volumesLogic AddArchetypeVolume $fileNameT1 T1brain 0]" << std::endl;
+  ScriptFile << "set selectionNode [$::slicer3::ApplicationLogic GetSelectionNode]" << std::endl;
+  ScriptFile << "$selectionNode SetReferenceActiveVolumeID [$volumeNode GetID]" << std::endl;
+  ScriptFile << "$::slicer3::ApplicationLogic PropagateVolumeSelection" << std::endl;
+  ScriptFile << std::endl;
+  ScriptFile << "$fidLogic LoadFiducialList $landmarkName" << std::endl;
+  ScriptFile << std::endl;
+  ScriptFile.close();
+}
+
diff --git a/BRAINSConstellationDetector/src/landmarkIO.h b/BRAINSConstellationDetector/src/landmarkIO.h
new file mode 100644
index 00000000..93507cee
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarkIO.h
@@ -0,0 +1,91 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __landmarkIO__h
+#define __landmarkIO__h
+
+#include "landmarksConstellationCommon.h"
+#include "landmarksConstellationDetector.h"
+#include "itkOtsuThresholdImageFilter.h"
+#include "landmarksConstellationModelIO.h"
+#include "itkAffineTransform.h"
+#include "itkVersorRigid3DTransform.h"
+#include "itkImageFileReader.h"
+
+#include "string.h"
+#include 
+#include "stdio.h"
+#include 
+#include 
+
+typedef std::map LandmarksMapType;
+typedef vnl_matrix                           MatrixType;
+typedef vnl_vector                           VectorType;
+typedef itk::VersorRigid3DTransform          VersorTransformType;
+typedef VersorTransformType::Pointer                 VersorTransformPointer;
+typedef VersorTransformType::MatrixType              VersorTransformMatrixType;
+
+extern void MakeBrandeddebugImage(SImageType::ConstPointer in, const landmarksConstellationModelIO & mDef,
+                                  const SImageType::PointType & RP, const SImageType::PointType & AC,
+                                  const SImageType::PointType & PC,
+                                  const SImageType::PointType & VN4, const std::string & fname,
+                                  const SImageType::PointType & RP2,
+                                  const SImageType::PointType & AC2, const SImageType::PointType & PC2,
+                                  const SImageType::PointType & VN42);
+
+extern void MakePointBranded3DImage(SImageType::ConstPointer in, const SImageType::PointType & CenterPoint,
+                                    const std::string & fname);
+
+extern void MakeBranded2DImage(SImageType::ConstPointer in, landmarksConstellationDetector & myDetector,
+                               const SImageType::PointType & RP, const SImageType::PointType & AC,
+                               const SImageType::PointType & PC,
+                               const SImageType::PointType & VN4, const SImageType::PointType & CM,
+                               const std::string & fname);
+
+// Write Slicer scene file (.mrml)
+extern void WriteMRMLFile(std::string outputMRML, std::string outputLandmarksInInputSpace,
+                          std::string outputLandmarksInOutputSpace, std::string inputVolume, std::string outputVolume,
+                          std::string outputTransform,
+                          const LandmarksMapType & outputLandmarksInInputSpaceMap,
+                          const LandmarksMapType & outputLandmarksInOutputSpaceMap,
+                          const VersorTransformPointer versorTransform);
+
+// load linear least squares model for selected landmarks
+// .load from txt file
+extern void loadLLSModel(std::string llsModel,
+                         std::map > & llsMeans,
+                         std::map & llsMatrices, std::map
+                         & searchRadii);
+
+// load from .mat file
+extern void loadLLSModelMat(std::string llsModel, std::string processingList,
+                            std::map > & llsMeans,
+                            std::map & llsMatrices, std::map
+                            & searchRadii);
+
+extern void writeLLSModel(const std::string & modelName,
+                          const std::map > & llsMeans,
+                          const std::map & llsMatrices, const std::map
+                          & searchRadii);
+
+extern void readLLSModel(const std::string & modelName,
+                         std::map > & llsMeans,
+                         std::map & llsMatrices, std::map
+                         & searchRadii);
+
+// write out verification script
+extern void writeVerificationScript(std::string outputVerificationScript, std::string outputVolume,
+                                    std::string saveOutputLandmarks);
+
+#endif // __landmarkIO__h
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationCommon.cxx b/BRAINSConstellationDetector/src/landmarksConstellationCommon.cxx
new file mode 100644
index 00000000..7453c07d
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationCommon.cxx
@@ -0,0 +1,853 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "itkIO.h"
+#include 
+
+#include "itkReflectiveCorrelationCenterToImageMetric.h"
+#include "landmarksConstellationCommon.h"
+#include "TrimForegroundInDirection.h"
+#include "GenericTransformImage.h"
+
+typedef itk::ImageMomentsCalculator momentsCalculatorType;
+
+// TODO:  This should really be a singleton.
+RandomGeneratorPointer _RandomGenerator;
+const unsigned int     MAX_ROTATIONS_TESTED = 90;
+const unsigned int     MAXITER = 5000;
+const unsigned int     DEL = 3;
+const unsigned int     YES = 1;
+const unsigned int     NO = 0;
+const unsigned int     SMAX = 50;
+namespace LMC
+{
+bool debug(false);
+bool globalverboseFlag(false);
+}
+
+std::string globalResultsDir(".");       // A global variable to define where
+                                         // output images are to be placed
+int globalImagedebugLevel(1000);         // A global variable to determine the
+                                         // level of debugging to perform.
+
+void ComputeMSP(SImageType::Pointer image, RigidTransformType::Pointer & Tmsp,
+                SImageType::Pointer & transformedImage,
+                const SImageType::PointType & centerOfHeadMass, const int qualityLevel)
+{
+  if( qualityLevel == -1 )  // Assume image was pre-aligned outside of the
+                            // program
+    {
+    Tmsp = RigidTransformType::New();
+    Tmsp->SetIdentity();
+
+    itk::ImageDuplicator::Pointer MSP = itk::ImageDuplicator::New();
+    MSP->SetInputImage(image);
+    MSP->Update();
+    transformedImage = MSP->GetOutput();
+    }
+  else
+    {
+    // itkUtil::WriteImage(image,"PRE_PYRAMID.nii.gz");
+    PyramidFilterType::Pointer    MyPyramid = MakeThreeLevelPyramid(image.GetPointer() );
+    SImageType::Pointer           EigthImage = MyPyramid->GetOutput(0);
+    SImageType::Pointer           QuarterImage = MyPyramid->GetOutput(1);
+    SImageType::Pointer           HalfImage = MyPyramid->GetOutput(2);
+    Rigid3DCenterReflectorFunctor reflectionFunctor;
+
+    reflectionFunctor.SetCenterOfHeadMass(centerOfHeadMass);
+    reflectionFunctor.Initialize(image);
+    if( qualityLevel >= 0 )
+      {
+      std::cout << "Level 0 Quality Estimates" << std::endl;
+      reflectionFunctor.SetDownSampledReferenceImage(EigthImage);
+      reflectionFunctor.QuickSampleParameterSpace();
+      reflectionFunctor.Update();
+      }
+    if( qualityLevel >= 1 )
+      {
+      std::cout << "Level 1 Quality Estimates" << std::endl;
+      reflectionFunctor.SetDownSampledReferenceImage(QuarterImage);
+      reflectionFunctor.Update();
+      }
+    if( qualityLevel >= 2 )
+      {
+      std::cout << "Level 2 Quality Estimates" << std::endl;
+      reflectionFunctor.SetDownSampledReferenceImage(HalfImage);
+      reflectionFunctor.Update();
+      }
+    if( qualityLevel >= 3 )
+      {
+      std::cout << "Level 3 Quality Estimates" << std::endl;
+      reflectionFunctor.SetDownSampledReferenceImage(image);
+      reflectionFunctor.Update();
+      }
+    reflectionFunctor.SetDownSampledReferenceImage(image);
+    Tmsp = reflectionFunctor.GetTransformToMSP();
+    transformedImage = reflectionFunctor.GetMSPCenteredImage();
+    }
+}
+
+void ComputeMSP(SImageType::Pointer image, RigidTransformType::Pointer & Tmsp, const int qualityLevel)
+{
+  // itkUtil::WriteImage(image,"PRE_PYRAMID.nii.gz");
+  PyramidFilterType::Pointer    MyPyramid = MakeThreeLevelPyramid(image);
+  SImageType::Pointer           EigthImage = MyPyramid->GetOutput(0);
+  SImageType::Pointer           QuarterImage = MyPyramid->GetOutput(1);
+  SImageType::Pointer           HalfImage = MyPyramid->GetOutput(2);
+  Rigid3DCenterReflectorFunctor reflectionFunctor;
+
+  reflectionFunctor.Initialize(image);
+  if( qualityLevel >= 0 )
+    {
+    std::cout << "Level 0 Quality Estimates" << std::endl;
+    reflectionFunctor.SetDownSampledReferenceImage(EigthImage);
+    reflectionFunctor.QuickSampleParameterSpace();
+    reflectionFunctor.Update();
+    }
+  if( qualityLevel >= 1 )
+    {
+    std::cout << "Level 1 Quality Estimates" << std::endl;
+    reflectionFunctor.SetDownSampledReferenceImage(QuarterImage);
+    reflectionFunctor.Update();
+    }
+  if( qualityLevel >= 2 )
+    {
+    std::cout << "Level 2 Quality Estimates" << std::endl;
+    reflectionFunctor.SetDownSampledReferenceImage(HalfImage);
+    reflectionFunctor.Update();
+    }
+  if( qualityLevel >= 3 )
+    {
+    std::cout << "Level 3 Quality Estimates" << std::endl;
+    reflectionFunctor.SetDownSampledReferenceImage(image);
+    reflectionFunctor.Update();
+    }
+  reflectionFunctor.SetDownSampledReferenceImage(image);
+  Tmsp = reflectionFunctor.GetTransformToMSP();
+}
+
+void CreatedebugPlaneImage(SImageType::Pointer referenceImage, const std::string & debugfilename)
+{
+  SImageType::PixelType low, high;
+
+  setLowHigh(referenceImage, low, high, 0.01F);
+
+  itk::ImageDuplicator::Pointer MSP = itk::ImageDuplicator::New();
+  MSP->SetInputImage(referenceImage);
+  MSP->Update();
+  SImageType::Pointer           MSPImage = MSP->GetOutput();
+  const SImageType::SpacingType imSpacing = MSPImage->GetSpacing();
+  SImageType::PointType         CenterOfImage = GetImageCenterPhysicalPoint(MSPImage);
+
+    {
+    itk::ImageRegionIteratorWithIndex mspIt( MSPImage, MSPImage->GetLargestPossibleRegion() );
+    for( ; !mspIt.IsAtEnd(); ++mspIt )
+      {
+      const SImageType::IndexType Index = mspIt.GetIndex();
+      SImageType::PointType       Location;
+      MSPImage->TransformIndexToPhysicalPoint(Index, Location);
+      if( vcl_abs(Location[0] - CenterOfImage[0]) < imSpacing[0] * 1.00000001 )
+        {
+        mspIt.Set(high);
+        }
+      }
+    }
+  itkUtil::WriteImage(MSPImage, debugfilename);
+}
+
+// TODO:  Should be ::ConstPointer
+SImageType::Pointer CreatedebugPlaneImage(SImageType::Pointer referenceImage,
+                                          const RigidTransformType::Pointer MSPTransform,
+                                          const std::string & debugfilename)
+{
+  SImageType::PixelType low, high;
+
+  setLowHigh(referenceImage, low, high, 0.01F);
+
+  itk::ImageDuplicator::Pointer MSP = itk::ImageDuplicator::New();
+  MSP->SetInputImage(referenceImage);
+  MSP->Update();
+  SImageType::Pointer           MSPImage = MSP->GetOutput();
+  const SImageType::SpacingType imSpacing = MSPImage->GetSpacing();
+
+  SImageType::PointType CenterOfImage = GetImageCenterPhysicalPoint(MSPImage);
+    {
+    itk::ImageRegionIteratorWithIndex mspIt( MSPImage, MSPImage->GetLargestPossibleRegion() );
+    for( ; !mspIt.IsAtEnd(); ++mspIt )
+      {
+      const SImageType::IndexType Index = mspIt.GetIndex();
+      SImageType::PointType       Location;
+      MSPImage->TransformIndexToPhysicalPoint(Index, Location);
+      if( vcl_abs(Location[0] - CenterOfImage[0]) < imSpacing[0] * 1.00000001 )
+        {
+        mspIt.Set(high);
+        }
+      else
+        {
+        mspIt.Set(0);
+        }
+      }
+    }
+    {
+    SImageType::PointType               CrossHairsPoint;
+    SImageType::PointType::CoordRepType radius0 = vcl_abs(3 * imSpacing[0]);
+    SImageType::PointType::CoordRepType radius1 = vcl_abs(3 * imSpacing[1]);
+    SImageType::PointType::CoordRepType radius2 = vcl_abs(3 * imSpacing[2]);
+    for( SImageType::PointType::CoordRepType k = CenterOfImage[2] - radius2;
+         k < CenterOfImage[2] + radius2;
+         k += imSpacing[2] )
+      {
+      for( SImageType::PointType::CoordRepType j = CenterOfImage[1] - radius1;
+           j < CenterOfImage[1] + radius1;
+           j += imSpacing[1] )
+        {
+        for( SImageType::PointType::CoordRepType i = CenterOfImage[0] - radius0;
+             i < CenterOfImage[0] + radius0;
+             i += imSpacing[0] )
+          {
+          CrossHairsPoint[0] = i; CrossHairsPoint[1] = j; CrossHairsPoint[2] = k;
+          SImageType::IndexType closestIndex;
+          const bool            isInside = MSPImage->TransformPhysicalPointToIndex(CrossHairsPoint, closestIndex);
+          if( isInside )
+            {
+            MSPImage->SetPixel(closestIndex, high);
+            }
+          }
+        }
+      }
+    }
+
+  RigidTransformType::Pointer invMSPTransform = RigidTransformType::New();
+  MSPTransform->GetInverse(invMSPTransform);
+#if 1
+  SImageType::Pointer RotatedPlane = TransformResample(
+      MSPImage, MSPImage, /* DEFAULT TO ZERO */ 0,
+      GetInterpolatorFromString("Linear"), invMSPTransform.GetPointer() );
+#else
+  SImageType::Pointer RotatedPlane = GenericImageResample(
+      MSPImage,
+      invMSPTransform,
+      /* DEFAULT TO ZERO */
+      0);
+#endif
+
+  itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New();
+  duplicator->SetInputImage(referenceImage);
+  duplicator->Update();
+  SImageType::Pointer RasterImage = duplicator->GetOutput();
+
+  itk::ImageRegionIteratorWithIndex rasterIt( RasterImage, RasterImage->GetLargestPossibleRegion() );
+  itk::ImageRegionIteratorWithIndex rplaneIt( RotatedPlane, RotatedPlane->GetLargestPossibleRegion() );
+  for( rplaneIt.GoToBegin(); !rplaneIt.IsAtEnd() && !rasterIt.IsAtEnd(); ++rplaneIt, ++rasterIt )
+    {
+    if( rasterIt.Get() > high )
+      {
+      rasterIt.Set(high);
+      }
+    if( rplaneIt.Get() > high * 0.5 )
+      {
+      SImageType::PixelType p =
+        static_cast
+        ( ( 2.0 * rplaneIt.Get() + rasterIt.Get() ) * 0.3333333 );
+      rasterIt.Set(p);
+      }
+    }
+  itkUtil::WriteImage(RasterImage, debugfilename);
+  return RasterImage;
+}
+
+vnl_vector convertToReadable(const vnl_vector & input)
+{
+  vnl_vector temp;
+  temp.set_size(3);
+  temp[0] = input[0] * 180.0 / vnl_math::pi;
+  temp[1] = input[1] * 180.0 / vnl_math::pi;
+  temp[2] = input[2];
+  return temp;
+}
+
+/** this conversion uses conventions as described on page:
+ *   http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm
+ *   Coordinate System: right hand
+ *   Positive angle: right hand
+ *   Order of euler angles: initialHeadingAngle first, then initialAttitudeAngle, then initialBankAngle
+ *   matrix row column ordering:
+ *   [m00 m01 m02]
+ *   [m10 m11 m12]
+ *   [m20 m21 m22]*/
+// With respect to an LPS system of the head,
+// initialHeadingAngle is where you are looking left to right, (Rotation of Z
+// axis)
+// attiude is where you are looking from floor to ceiling (Rotation of X axis)
+// initialBankAngle is how tilted your head is  (Rotation of Y axis)
+void ComputeEulerAnglesFromRotationMatrix(const itk::Matrix &  m,
+                                          double & initialAttitudeAngle,
+                                          double & initialBankAngle,
+                                          double & initialHeadingAngle)
+{
+  // Assuming the angles are in radians.
+  if( m[1][0] > 0.998 )  // singularity at north pole
+    {
+    initialAttitudeAngle = 0;
+    initialBankAngle = vcl_atan2(m[0][2], m[2][2]);
+    initialHeadingAngle = vnl_math::pi_over_2;
+    return;
+    }
+  if( m[1][0] < -0.998 )  // singularity at south pole
+    {
+    initialAttitudeAngle = 0;
+    initialBankAngle = vcl_atan2(m[0][2], m[2][2]);
+    initialHeadingAngle = -vnl_math::pi_over_2;
+    return;
+    }
+  initialAttitudeAngle = vcl_atan2(-m[1][2], m[1][1]);
+  initialBankAngle = vcl_atan2(-m[2][0], m[0][0]);
+  initialHeadingAngle = vcl_asin(m[1][0]);
+}
+
+#if 0
+itk::Matrix CreateRotationMatrixFromAngles(const double alpha, const double beta, const double gamma)
+{
+  // alpha is rotate the X axis -- Attitude
+  // beta is rotate the Y axis  -- Bank
+  // gamma is rotate the Z axis -- Heading
+  const double ca = vcl_cos(alpha);
+  const double sa = vcl_sin(alpha);
+  const double cb = vcl_cos(beta);
+  const double sb = vcl_sin(beta);
+  const double cg = vcl_cos(gamma);
+  const double sg = vcl_sin(gamma);
+
+  itk::Matrix R;
+
+  R(0, 0) = cb * cg;  R(0, 1) = -ca * sg + sa * sb * cg; R(0, 2) = sa * sg + ca * sb * cg;
+  R(1, 0) = cb * sg;  R(1, 1) = ca * cg + sa * sb * sg;  R(1, 2) = -sa * cg + ca * sb * sg;
+  R(2, 0) = -sb;    R(2, 1) = sa * cb;           R(2, 2) = ca * cb;
+  itk::Matrix::InternalMatrixType test =
+    R.GetVnlMatrix() * R.GetTranspose();
+  if( !test.is_identity(1.0e-10) )
+    {
+    std::cout << "Computed matrix is not orthogonal!!!" << std::endl;
+    std::cout << R << std::endl;
+    }
+  return R;
+}
+
+#endif
+
+itk::Versor CreateRotationVersorFromAngles(const double alpha, const double beta, const double gamma)
+{
+#if 1
+  //
+  //
+  // http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
+  // psi = alpha is rotate the X axis -- Attitude
+  // theta= beta is rotate the Y axis  -- Bank
+  // phi=  gamma is rotate the Z axis -- Heading
+  const double cha = vcl_cos(alpha * 0.5);
+  const double chb = vcl_cos(beta * 0.5);
+  const double chg = vcl_cos(gamma * 0.5);
+  const double sha = vcl_sin(alpha * 0.5);
+  const double shb = vcl_sin(beta * 0.5);
+  const double shg = vcl_sin(gamma * 0.5);
+
+  vnl_vector_fixed q;
+  q[0] = cha * chb * chg + sha * shb * shg;
+  q[1] = sha * chb * chg - cha * shb * shg;
+  q[2] = cha * shb * chg + sha * chb * shg;
+  q[3] = cha * chb * shg - sha * shb * chg;
+
+  itk::Versor v;
+  v.Set(q[0], q[1], q[2], q[3]);
+  return v;
+#else
+  itk::Matrix R = CreateRotationMatrixFromAngles(alpha, beta, gamma);
+  itk::Versor       v;
+  v.Set(R);
+  return v;
+#endif
+}
+
+VersorTransformType::Pointer ConvertToVersorRigid3D(RigidTransformType::Pointer RT)
+{
+  VersorTransformType::Pointer VT = VersorTransformType::New();
+
+  VT->SetFixedParameters( RT->GetFixedParameters() );
+
+  itk::Matrix           R = RT->GetRotationMatrix();
+  RigidTransformType::TranslationType T = RT->GetTranslation();
+
+  VersorTransformType::ParametersType p;
+  p.SetSize(6);
+  itk::Versor v;
+  v.Set(R);
+  // Get the first 3 elements of the versor;
+  p[0] = v.GetRight()[0];
+  p[1] = v.GetRight()[1];
+  p[2] = v.GetRight()[2];
+  p[3] = T[0];
+  p[4] = T[1];
+  p[5] = T[2];
+  VT->SetParameters(p);
+  return VT;
+}
+
+itk::Matrix GetMatrixInverse(const itk::Matrix & input)
+{
+  // Hack until enhancemetn fix in ITK is made public for assignment of matrix
+  itk::Matrix::InternalMatrixType temp = input.GetInverse();
+  itk::Matrix                     output;
+  for( unsigned int r = 0; r < 3; r++ )
+    {
+    for( unsigned int c = 0; c < 3; c++ )
+      {
+      output(r, c) = temp(r, c);
+      }
+    }
+  return output;
+}
+
+// Need to use a Pyramid filter here instead of just downsampling to a 32x32
+// image
+typedef itk::MultiResolutionPyramidImageFilter PyramidFilterType;
+
+PyramidFilterType::Pointer MakeThreeLevelPyramid(SImageType::Pointer refImage)
+{
+  PyramidFilterType::ScheduleType pyramidSchedule;
+
+  PyramidFilterType::Pointer MyPyramid = PyramidFilterType::New();
+
+  MyPyramid->SetInput(refImage);
+  MyPyramid->SetNumberOfLevels(3);
+  pyramidSchedule.SetSize(3, 3);
+  // Attempt to set a schedule so that the top of the pyramid
+  // has images of about 8mm, and the next level has resolutions about 4mm
+  // isotropic voxels
+  // these are sizes found to work well for estimating MSP without making the
+  // image too small.
+  SImageType::SpacingType refImageSpacing = refImage->GetSpacing();
+  for( unsigned int c = 0; c < pyramidSchedule.cols(); c++ )
+    {
+    // about 8mm
+    pyramidSchedule[0][c] = static_cast( 2 * round(4.0 / refImageSpacing[c]) );
+    // about 4mm
+    pyramidSchedule[1][c] = static_cast( 2 * round(2.0 / refImageSpacing[c]) );
+    // about 2mm
+    pyramidSchedule[2][c] = static_cast( 2 * round(1.0 / refImageSpacing[c]) );
+    }
+  MyPyramid->SetSchedule(pyramidSchedule);
+  MyPyramid->Update();
+  return MyPyramid;
+}
+
+PyramidFilterType::Pointer MakeOneLevelPyramid(SImageType::Pointer refImage)
+{
+  PyramidFilterType::ScheduleType pyramidSchedule;
+
+  PyramidFilterType::Pointer MyPyramid = PyramidFilterType::New();
+
+  MyPyramid->SetInput(refImage);
+  MyPyramid->SetNumberOfLevels(1);
+  pyramidSchedule.SetSize(1, 3);
+  // Attempt to set a schedule so that the top of the pyramid
+  // has images of about 8mm, and the next level has resolutions about 4mm
+  // isotropic voxels
+  // these are sizes found to work well for estimating MSP without making the
+  // image too small.
+  SImageType::SpacingType refImageSpacing = refImage->GetSpacing();
+  for( unsigned int c = 0; c < pyramidSchedule.cols(); c++ )
+    {
+    pyramidSchedule[0][c] = static_cast( vcl_floor(4.0 / refImageSpacing[c] + 0.5) );
+    }
+  MyPyramid->SetSchedule(pyramidSchedule);
+  MyPyramid->Update();
+  return MyPyramid;
+}
+
+// ////////////////////////////////////////////////////////////////////////
+//  This is a lightweight wrapper for FindCenterOfBrainBasedOnTopOfHead, which
+// evolved from TrimForegroundInDirection.
+SImageType::PointType GetCenterOfHeadMass(SImageType::Pointer volume)
+{
+  // NOTE:   This is a bit of a hack to deal with vastly different sized heads,
+  // note:   or where the field of view is not centered in the brain
+  // note:   or where there is a massive amount of neck.
+
+  // Choose the Inferior/Superior based on maximum dirction cosign
+
+  // Find center of the image space which is where the MSP has been placed.
+  const unsigned int    ISdirectionIndex = 2;
+  SImageType::PointType CenterOfMass =
+    FindCenterOfBrainBasedOnTopOfHead(volume,
+                                      ISdirectionIndex,
+                                      0.01, 7,
+                                      700, 0);
+
+  // IN AN LPS SYSTEM, the INFERIOR/SUPERIOR should be the center of physical
+  // space, rather than the
+  // center of mass because the INFERIOR/SUPERIOR direction depends so much on
+  // the size of the neck.
+
+  return CenterOfMass;
+}
+
+//
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+RigidTransformType::Pointer computeTmspFromPoints(
+  SImageType::PointType RP,
+  SImageType::PointType AC,
+  SImageType::PointType PC,
+  SImageType::PointType DesiredCenter)
+{
+  // a variable to store correlation coefficient values
+  SImageType::PointType::VectorType ACPC = PC - AC;
+
+  ACPC.Normalize();
+  SImageType::PointType::VectorType ACRP = RP - AC;
+
+  vnl_vector_fixed NormalToMSPPlane = vnl_cross_3d( ACPC.GetVnlVector(), ACRP.GetVnlVector() );
+  // --std::cout << ACPC << "=" << PC << " - " << AC << std::endl;
+  // --std::cout << ACRP << "=" << RP << " - " << AC << std::endl;
+  // --std::cout << NormalToMSPPlane << std::endl;
+  SImageType::PointType::VectorType NormalToMSPPlaneVector;
+  NormalToMSPPlaneVector[0] = NormalToMSPPlane[0];
+  NormalToMSPPlaneVector[1] = NormalToMSPPlane[1];
+  NormalToMSPPlaneVector[2] = NormalToMSPPlane[2];
+  NormalToMSPPlaneVector.Normalize();
+  if( NormalToMSPPlaneVector[0] < 0 )
+    {
+    NormalToMSPPlaneVector *= -1.0;
+    }
+
+  // --std::cout << "Norm: " << NormalToMSPPlaneVector << "     NORMACPC: " <<
+  // ACPC << std::endl;
+
+  // double
+  //
+  //
+  // PlaneNormalBank=-vcl_atan2(NormalToMSPPlaneVector[2],NormalToMSPPlaneVector[0]);
+  //  //Rotate the "Y" (i.e. Anterior to Posterior Axis)
+  // double PlaneNormalHeading=-vcl_acos(NormalToMSPPlaneVector[0]);
+  //               //Rotate the "Z" (i.e. Inferior to Superior Axis)
+
+  double PlaneNormalBank = -vcl_atan2(NormalToMSPPlaneVector[2], NormalToMSPPlaneVector[0]);
+  // Rotate the "Y" (i.e. Anterior to Posterior Axis)
+  double PlaneNormalHeading = vcl_sin(NormalToMSPPlaneVector[1]);
+  // Rotate the "Z" (i.e. Inferior to Superior Axis)
+  double PlaneNormalAttitude = vcl_sin(ACPC[2]);
+
+  // --std::cout << "!!!!!!!!!!!!!!!!!!!!! " << PlaneNormalAttitude << " " <<
+  // PlaneNormalBank << " " << PlaneNormalHeading << std::endl;
+  // --std::cout << "!!!!!!!!!!!!!!!!!!!!! " <<
+  // PlaneNormalAttitude*180.9/vnl_math::pi << " " <<
+  // PlaneNormalBank*180.0/vnl_math::pi << " " <<
+  // PlaneNormalHeading*180.0/vnl_math::pi << std::endl;
+  // itk::Matrix
+  //
+  //
+  // BestRotationAlignment=CreateRotationMatrixFromAngles(PlaneNormalAttitude,PlaneNormalBank,PlaneNormalHeading);
+
+  SImageType::PointType::VectorType CenterOffset =
+    AC.GetVectorFromOrigin()
+    - DesiredCenter.GetVectorFromOrigin();
+
+  RigidTransformType::Pointer AlignMSPTransform = RigidTransformType::New();
+  AlignMSPTransform->SetCenter(DesiredCenter);
+  // AlignMSPTransform->SetRotationMatrix(BestRotationAlignment);
+  AlignMSPTransform->SetRotation(PlaneNormalAttitude, PlaneNormalBank, PlaneNormalHeading);
+  AlignMSPTransform->SetTranslation(CenterOffset);
+  if( LMC::globalverboseFlag )
+    {
+    std::cout << "\n============================" << CenterOffset << " \n" << AlignMSPTransform << std::endl;
+    std::cout << " \n" << AlignMSPTransform->GetTranslation() << std::endl;
+    std::cout << "============================\n" << std::endl;
+    }
+  return AlignMSPTransform;
+}
+
+// //
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+int computeTemplateSize(const int r, const int h)
+{
+  const double h_2 = h / 2;
+  const double r2 = r * r;
+  int          size = 0;
+  for( double k = -r; k <= r; k++ )
+    {
+    for( double j = -r; j <= r; j++ )
+      {
+      for( double i = -h_2; i <= h_2; i++ )
+        {
+        if( ( i * i + j * j )  <= r2 )
+          {
+          size++;
+          }
+        }
+      }
+    }
+  return size;
+}
+
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+
+// Use the law of cosines to determine the angle between the RPtoPC vector and
+// the RPtoAC vector.
+void decomposeRPAC(const SImageType::PointType & RP,
+                   const SImageType::PointType & PC,
+                   const SImageType::PointType & AC,
+                   float *const RPPC_to_RPAC_angle, float *const RPAC_over_RPPC)
+{
+  const double RPtoPC = vcl_sqrt( ( ( RP[1] - PC[1] ) * ( RP[1] - PC[1] ) + ( RP[2] - PC[2] ) * ( RP[2] - PC[2] ) ) );
+  const double RPtoAC = vcl_sqrt( ( ( RP[1] - AC[1] ) * ( RP[1] - AC[1] ) + ( RP[2] - AC[2] ) * ( RP[2] - AC[2] ) ) );
+  const double PCtoAC = vcl_sqrt( ( ( PC[1] - AC[1] ) * ( PC[1] - AC[1] ) + ( PC[2] - AC[2] ) * ( PC[2] - AC[2] ) ) );
+
+  const double cos_gamma = ( RPtoPC * RPtoPC + RPtoAC * RPtoAC - PCtoAC * PCtoAC ) / ( 2.0 * RPtoPC * RPtoAC );
+  const double gamma = vcl_acos(cos_gamma);
+
+  // const double sin_gamma = vcl_sqrt( 1.0 - cos_gamma*cos_gamma );
+
+  *RPPC_to_RPAC_angle = gamma;       // The angle between the RP-PC vector and
+                                     // the RP-AC vector
+  *RPAC_over_RPPC = RPtoAC / RPtoPC; // The ratio of lengths between the RP-PC
+                                     // vector and the RP-AC vector
+                                     // std::cout << "----------TEST ANGLE " <<
+                                     //  *RPPC_to_RPAC_angle *180.0/vnl_math::pi
+                                     // << "  RATIO " << *RPAC_over_RPPC <<
+                                     // std::endl;
+}
+
+SImageType::PointType::VectorType initialAC(const SImageType::PointType & RP,  const SImageType::PointType & PC,
+                                            const double RPPC_to_RPAC_angleMean, const double RPAC_over_RPPCMean)
+{
+  const SImageType::PointType::VectorType RPPCVector = PC - RP;
+  SImageType::PointType::VectorType       GuessAC;
+
+  GuessAC[0] = ( RP[0] + RPPCVector[0] * .05 );
+  const double cos_gamma = vcl_cos(RPPC_to_RPAC_angleMean);
+  const double sin_gamma = vcl_sin(RPPC_to_RPAC_angleMean);
+  // First rotate the RPPC vector in the direction of the AC poinnt
+  GuessAC[1] = RP[1] + ( cos_gamma * RPPCVector[1] - sin_gamma * RPPCVector[2] ) * RPAC_over_RPPCMean;
+  GuessAC[2] = RP[2] + ( sin_gamma * RPPCVector[1] + cos_gamma * RPPCVector[2] ) * RPAC_over_RPPCMean;
+  return GuessAC;
+}
+
+void
+extractArray(SImageType::Pointer & image,
+             const SImageType::PointType & CenterPoint,
+             const landmarksConstellationModelIO::IndexLocationVectorType & model,
+             std::vector & result_array)
+{
+  // TODO:  Move the LinearInterpolator to the function parameter, because the
+  // image is never needed.
+  LinearInterpolatorType::Pointer imInterp = LinearInterpolatorType::New();
+
+  imInterp->SetInputImage(image);
+  int q = 0;
+  result_array.resize( model.size() );
+  for( landmarksConstellationModelIO::IndexLocationVectorType::const_iterator it = model.begin();
+       it != model.end(); it++, q++ )
+    {
+    const SImageType::PointType point = CenterPoint + *it;
+    bool                        isin = imInterp->IsInsideBuffer(point);
+    if( isin )
+      {
+      result_array[q] = imInterp->Evaluate(point);
+      }
+    else
+      {
+      result_array[q] = 0.0;
+      }
+    }
+}
+
+void
+extractArrayRemoveVectorMeanNormalize
+  (SImageType::Pointer & image,
+  const SImageType::PointType & CenterPoint,
+  const landmarksConstellationModelIO::IndexLocationVectorType & model,
+  std::vector & result_array)
+{
+  // TODO:  Move the LinearInterpolator to the function parameter, because the
+  // image is never needed.
+  LinearInterpolatorType::Pointer imInterp = LinearInterpolatorType::New();
+
+  imInterp->SetInputImage(image);
+  result_array.resize( model.size() );
+  double mean(0.0);
+  landmarksConstellationModelIO::
+  IndexLocationVectorType::const_iterator it = model.begin();
+  std::vector::iterator            resultIt = result_array.begin();
+  //
+  // interpolate, accumulating mean as you go
+  for( ; it != model.end(); it++, resultIt++ )
+    {
+    const SImageType::PointType point = CenterPoint + *it;
+    bool                        isin = imInterp->IsInsideBuffer(point);
+    if( isin )
+      {
+      ( *resultIt ) = imInterp->Evaluate(point);
+      }
+    else
+      {
+      ( *resultIt ) = 0.0;
+      }
+    mean += ( *resultIt );
+    }
+
+  // remove mean, accumulating norm as you go.
+  mean /= result_array.size();
+  double norm = 0.0;
+  for( resultIt = result_array.begin();
+       resultIt != result_array.end(); ++resultIt )
+    {
+    double v( ( *resultIt ) - mean );
+    *resultIt = v;
+    norm += v * v;
+
+    // debug abnormal behavior of norm!
+    // std::cout << v << " " << norm << std::endl;
+    }
+  norm = vcl_sqrt(norm);
+  if( norm < vcl_numeric_limits::epsilon() )
+    {
+    std::cout << "WARNING:  ZERO NORM VECTOR." << __FILE__ << __LINE__ << std::endl;
+    return;
+    }
+  // normalize array
+  for( resultIt = result_array.begin();
+       resultIt != result_array.end(); ++resultIt )
+    {
+    *resultIt /= norm;
+    }
+}
+
+unsigned char
+ShortToUChar(short in, short min, short max)
+{
+  double x(in);
+
+  x -= static_cast( min );
+  double divisor = max - min;
+  x /= divisor;
+  x *= 255.0;
+  return static_cast( x );
+}
+
+// TODO:  Need to make these pointers const
+SImageType::Pointer CreateTestCenteredRotatedImage2(const RigidTransformType::Pointer ACPC_MSP_AlignedTransform,
+                                                    /* const
+                                                      SImageType::PointType
+                                                      finalPoint_MSP, */
+                                                    const SImageType::PointType PreMSP_Point,
+                                                    /*const*/ SImageType::Pointer & image,
+                                                    const RigidTransformType::Pointer & Point_Rotate)
+{
+  // ////// Compose test rotation with the translated ACPC alignment
+  RigidTransformType::Pointer Point_Centered_TestRotated = RigidTransformType::New();
+
+  Point_Centered_TestRotated->SetParameters( ACPC_MSP_AlignedTransform->GetParameters() );
+  Point_Centered_TestRotated->SetFixedParameters( ACPC_MSP_AlignedTransform->GetFixedParameters() );
+  Point_Centered_TestRotated->Compose(Point_Rotate, true); // TODO:  Perhaps
+                                                           // change sign of
+                                                           // Point_Translate,
+                                                           // and the remove the
+                                                           // true flag.
+
+#if 1
+  SImageType::Pointer image_Point_TestRotated = TransformResample(
+      image, image, /* DEFAULT TO ZERO */ 0,
+      GetInterpolatorFromString("Linear"), Point_Centered_TestRotated.GetPointer() );
+#else
+  SImageType::Pointer image_Point_TestRotated = GenericImageResample(
+      image,
+      Point_Centered_TestRotated,
+      /* DEFAULT TO ZERO */ 0);
+#endif
+
+  RigidTransformType::Pointer invPoint_Centered_TestRotated = RigidTransformType::New();
+  Point_Centered_TestRotated->GetInverse(invPoint_Centered_TestRotated);
+  const SImageType::PointType final_location = invPoint_Centered_TestRotated->TransformPoint(PreMSP_Point);
+  return image_Point_TestRotated;
+}
+
+// typedef landmarksDataSet::PointType PointType;
+
+void MakeLabelImage(SImageType::Pointer in,
+                    const SImageType::PointType & RP,
+                    const SImageType::PointType & AC,
+                    const SImageType::PointType & PC,
+                    const SImageType::PointType & VN4,
+                    const std::string & fname)
+{
+  SImageType::Pointer maskImage = SImageType::New();
+
+  maskImage->CopyInformation(in);
+  maskImage->SetRegions( in->GetLargestPossibleRegion() );
+  maskImage->Allocate();
+  maskImage->FillBuffer(0);
+    {
+    SImageType::IndexType Index;
+    maskImage->TransformPhysicalPointToIndex(RP, Index);
+    maskImage->SetPixel(Index,  250);
+    maskImage->TransformPhysicalPointToIndex(AC, Index);
+    maskImage->SetPixel(Index,  255);
+    maskImage->TransformPhysicalPointToIndex(PC, Index);
+    maskImage->SetPixel(Index,  245);
+    maskImage->TransformPhysicalPointToIndex(VN4, Index);
+    maskImage->SetPixel(Index,  240);
+    }
+  itkUtil::WriteImage(maskImage, fname);
+}
+
+SImageType::PointType GetImageCenterPhysicalPoint(SImageType::Pointer & image)
+{
+  const SImageType::SizeType imageOverallSize = image->GetLargestPossibleRegion().GetSize();
+
+  itk::ContinuousIndex centerIndex;
+  for( int q = 0; q < SImageType::ImageDimension; q++ )
+    {
+    centerIndex[q] = 0.5 * ( imageOverallSize[q] - 1 );
+    }
+  SImageType::PointType centerLocation;
+  image->TransformContinuousIndexToPhysicalPoint(centerIndex,  centerLocation);
+  return centerLocation;
+}
+
+// TODO:  Need to make size and spacing command line arguments that are sent
+// into
+// the ResampleToIsotropicImage filter.
+// HACK:  Currently hard-coded to 1.0^3 isotropic voxels in a 256^3 matrix
+// --outputVolumeSize 256,256,256 --outputVolumeSpacing 1.0,1.0,1.0
+SImageType::Pointer MakeIsoTropicReferenceImage(void)
+{
+  SImageType::DirectionType Ident;
+
+  Ident.SetIdentity();
+  SImageType::PointType Origin;
+  Origin.Fill(-127.5);
+  SImageType::SpacingType Spacing;
+  Spacing.Fill(1.0);
+
+  SImageType::SizeType Size;
+  Size.Fill(256);
+  SImageType::RegionType Region;
+  Region.SetSize(Size);
+
+  SImageType::Pointer isotropicReferenceVolume = SImageType::New();
+  isotropicReferenceVolume->SetDirection(Ident);
+  isotropicReferenceVolume->SetOrigin(Origin);
+  isotropicReferenceVolume->SetSpacing(Spacing);
+  isotropicReferenceVolume->SetRegions(Region);
+  // NOTE:  No need to allocate the image memory, it is just used as a template.
+  return isotropicReferenceVolume;
+}
+
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationCommon.h b/BRAINSConstellationDetector/src/landmarksConstellationCommon.h
new file mode 100644
index 00000000..5bbfe4d9
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationCommon.h
@@ -0,0 +1,685 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+/**
+ * This is a temporary file to be used during refactoring to help consolicate a family of functions into a common library.
+ */
+#ifndef __landmarksConstellationCommon_h
+#define __landmarksConstellationCommon_h
+
+// Use linear interpolation to keep the processing quick.
+#define __QUICK_RUNS_APPROXIMATION__
+
+#include      // This include file should be removed, prefer constructs
+                       // from the std library
+#include     // This include file should be removed, prefer constructs
+                       // from the std library
+#include       // This include file should be removed, use vcl_math
+                       // instead
+#include  // This include file should be removed, unix only
+                       // non-portable
+#include   // This include file should be removed, unix only
+                       // non-portable
+#include     // This include file should be removed, unix only
+                       // non-portable
+#include       // This include file should be removed, unix only
+                       // non-portable
+#include      // This include file should be removed, use vcl_math
+                       // instead
+                       // #include  //This include file should be
+                       // removed
+#include 
+#include 
+#include "itkImage.h"
+#include "itkIO.h"
+
+#include 
+#include 
+#include "itkMultiResolutionPyramidImageFilter.h"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include "itkCylinderSpatialObject.h"
+#include "itkSpatialObjectToImageFilter.h"
+#include "itkRGBPixel.h"
+#include "itkIO.h"
+#include "itkExtractImageFilter.h"
+#include "itkStatisticsImageFilter.h"
+#include "itkFlipImageFilter.h"
+#include "vcl_algorithm.h"
+#include "itkImageDuplicator.h"
+#include "itkEuler3DTransform.h"
+#include 
+
+#include 
+
+extern const unsigned int MAX_ROTATIONS_TESTED;
+extern const unsigned int MAXITER;
+extern const unsigned int DEL;
+extern const unsigned int YES;
+extern const unsigned int NO;
+extern const unsigned int SMAX;
+namespace LMC
+{
+extern bool debug;
+extern bool globalverboseFlag;
+}
+
+//
+//
+// ////////////////////////////////////////////////////////////////////////////////////////////////
+typedef float                 vertexType[4][3];
+typedef itk::Image  SImageType;
+typedef itk::Image DImageType3D;
+typedef itk::Image  FImageType3D;
+// typedef itk::Image SImageType2D;
+typedef itk::Image DImageType2D;
+typedef itk::Image  FImageType2D;
+
+typedef itk::RGBPixel RGBPixelType;
+typedef itk::Image  RGBImageType;
+typedef itk::Image  RGB2DImageType;
+
+// typedef itk::Rigid3DTransform RigidTransformType;
+typedef itk::Euler3DTransform       RigidTransformType;
+typedef itk::VersorRigid3DTransform VersorTransformType;
+
+typedef itk::MultiResolutionPyramidImageFilter PyramidFilterType;
+typedef itk::LinearInterpolateImageFunction        LinearInterpolatorType;
+
+#include "landmarksConstellationModelIO.h"
+
+extern VersorTransformType::Pointer ConvertToVersorRigid3D(RigidTransformType::Pointer RT);
+
+extern std::string globalResultsDir;
+extern int         globalImagedebugLevel;
+extern PyramidFilterType::Pointer MakeThreeLevelPyramid(SImageType::Pointer refImage);
+
+extern PyramidFilterType::Pointer MakeOneLevelPyramid(SImageType::Pointer refImage);
+
+extern SImageType::PointType GetImageCenterPhysicalPoint(SImageType::Pointer & image);
+
+extern unsigned char ShortToUChar(short in, short min, short max);
+
+extern SImageType::Pointer CreateTestCenteredRotatedImage2(
+  const RigidTransformType::Pointer ACPC_MSP_AlignedTransform,
+  /* const
+    SImageType::PointType
+    finalPoint, */
+  const SImageType::PointType PreMSP_Point,
+  /*const*/ SImageType::Pointer & image,
+  const RigidTransformType::Pointer & Point_Rotate);
+
+extern itk::Matrix GetMatrixInverse(const itk::Matrix & input);
+
+// extern itk::Matrix CreateRotationMatrixFromAngles(const double
+// alpha, const double beta, const double gamma);
+extern itk::Versor CreateRotationVersorFromAngles(const double alpha, const double beta, const double gamma);
+
+extern void ComputeEulerAnglesFromRotationMatrix(const itk::Matrix &  m, double & initialAttitudeAngle,
+                                                 double & initialBankAngle,
+                                                 double & initialHeadingAngle);
+
+extern void defineTemplateIndexLocations(const int r, const int h,
+                                         landmarksConstellationModelIO::IndexLocationVectorType & indexLocations,
+                                         std::vector & results_array);
+
+extern int computeTemplateSize(const int r, const int h);
+
+extern void decomposeRPAC(const SImageType::PointType & RP, const SImageType::PointType & PC,
+                          const SImageType::PointType & AC, float *const RPPC_to_RPAC_angle,
+                          float *const RPAC_over_RPPC);
+
+extern void MakeLabelImage(SImageType::Pointer in, const SImageType::PointType & RP, const SImageType::PointType & AC,
+                           const SImageType::PointType & PC, const SImageType::PointType & VN4,
+                           const std::string & fname);
+
+extern SImageType::PointType::VectorType initialAC(const SImageType::PointType & RP, const SImageType::PointType & PC,
+                                                   const double RPPC_to_RPAC_angleMean,
+                                                   const double RPAC_over_RPPCMean);
+
+typedef itk::Statistics::MersenneTwisterRandomVariateGenerator RandomGeneratorType;
+typedef RandomGeneratorType::Pointer                           RandomGeneratorPointer;
+extern RandomGeneratorPointer _RandomGenerator;
+extern double GetRandomZeroOneDouble(void);
+
+extern void InitializeRandomZeroOneDouble(RandomGeneratorType::IntegerType rseed);
+
+extern void ComputeMSP(SImageType::Pointer image, RigidTransformType::Pointer & Tmsp,
+                       SImageType::Pointer & transformedImage, const SImageType::PointType & centerOfHeadMass,
+                       const int qualityLevel);
+
+extern void ComputeMSP(SImageType::Pointer image, RigidTransformType::Pointer & Tmsp, const int qualityLevel);
+
+extern SImageType::Pointer CreatedebugPlaneImage(SImageType::Pointer referenceImage,
+                                                 const RigidTransformType::Pointer MSPTransform,
+                                                 const std::string & debugfilename);
+
+extern void CreatedebugPlaneImage(SImageType::Pointer referenceImage, const std::string & debugfilename);
+
+extern RigidTransformType::Pointer computeTmspFromPoints(SImageType::PointType RP, SImageType::PointType AC,
+                                                         SImageType::PointType PC,
+                                                         SImageType::PointType DesiredCenter);
+
+extern SImageType::PointType GetCenterOfHeadMass(SImageType::Pointer volume);
+
+extern SImageType::Pointer MakeIsoTropicReferenceImage();
+
+#if 0
+// #include 
+#include 
+// TODO:  Replace double precision with single precision math.
+typedef itk::ConstantBoundaryCondition BoundaryConditionType;
+static const unsigned int WindowedSincHammingWindowRadius = 5;
+typedef itk::Function::HammingWindowFunction WindowFunctionType;
+typedef itk::WindowedSincInterpolateImageFunction<
+  SImageType,
+  WindowedSincHammingWindowRadius,
+  WindowFunctionType,
+  BoundaryConditionType,
+  double>    WindowedSincInterpolatorType;
+#endif
+
+/*****************************************************************************/
+template 
+ValuesType vectorNorm(const std::vector & x)
+{
+  ValuesType norm = 0.0;
+  for( typename std::vector::const_iterator it = x.begin();
+       it != x.end(); it++ )
+    {
+    const ValuesType value = *it;
+    norm += value * value;
+    }
+  return vcl_sqrt(norm);
+}
+
+/*
+ This function takes an input array (y) of size n and computes its L2
+ norm.  Then, the array y is modified by dividing each of its elements by
+ the L2 norm.  The resulting array will have an L2 norm of 1.0.
+
+ Example:
+ {
+ float y[3]={0.0, 4.0, 3.0}
+ double mean;
+
+ normalizeVector(y,3);
+
+ printf("y = {%f, %f, %f}\n", y[0],y[1],y[2]);
+ }
+
+ In this example, the L2 norm of y is 5.0.  Array y is replaced by: {0.0,
+ 0.8, 0.6}, which has an L2 norm of 1.0.
+
+ If we run removeVectorMean(y,3) before calling normalizeVector(y,3), we
+ will obtain an array which has a zero mean as well as unit norm.
+ */
+template 
+void normalizeVector(std::vector & x)
+{
+  const ValuesType norm = vectorNorm(x);
+
+  if( norm < vcl_numeric_limits::epsilon() )
+    {
+    std::cout << "WARNING:  ZERO NORM VECTOR." << __FILE__ << __LINE__ << std::endl;
+    return;
+    }
+  for( typename std::vector::iterator it = x.begin();
+       it != x.end(); it++ )
+    {
+    *it /= norm;
+    }
+  return;
+}
+
+// ///////////////////////////////////////////////////////
+// y is a (nxp) matrix.  This function operates on the columns of y.
+// Upon completion, each of the p columns of y will have zero mean.
+/*
+ This function takes an input array (y) of size n, computes and returns
+ the mean of the array.  Also, the input array y is modified by
+ subtracting the computed mean from each of its elements.
+
+ Example:
+
+ {
+ float y[3]={1.0, 5.0, 3.0}
+ double mean;
+
+ mean = removeVectorMean(y,3);
+
+ printf("mean = %lf\n", mean);
+ printf("y = {%f, %f, %f}\n", y[0],y[1],y[2]);
+ }
+
+ This will replace y by: {-2.0, 2.0, 0.0} and return meam=3.0.
+
+ In the particular call:
+
+ removeVectorMean(myModel.AccessRPTemplate()+j*nv_myModel.AccessRPTemplate(), nv_myModel.AccessRPTemplate());
+
+ The array y is represented by: myModel.AccessRPTemplate()+j*nv_myModel.AccessRPTemplate(), and n =
+ nv_myModel.AccessRPTemplate()
+ */
+template 
+ValuesType removeVectorMean(std::vector & x)
+{
+  ValuesType mean = 0.0;
+  for( typename std::vector::const_iterator it = x.begin();
+       it != x.end(); it++ )
+    {
+    mean += *it;
+    }
+  const ValuesType n = x.size();
+  mean /= n;
+  for( typename std::vector::iterator it = x.begin();
+       it != x.end(); it++ )
+    {
+    *it -= mean;
+    }
+  return mean;
+}
+
+/**
+ * This function takes an image and returns an array of type
+ float comprised of an ordered subset of the intensity values
+ stored in 'image'.  The subset of  voxels that is returned is
+ centered around point 'CenterPoint'.  The shape of the subset is
+ specified by a set of point offesets from the 'CenterPoint'
+ given specified by the vector 'model'.
+
+ If any computed voxel location happens to fall outside the
+ memory block 'image', a value of 0.0 is returned in for for that
+ location in 'result_array'.
+ *
+ * @author hjohnson (8/29/2008)
+ *
+ * @param image
+ * @param CenterPoint
+ * @param model
+ * @param result_array
+ */
+extern
+void extractArray(SImageType::Pointer & image, const SImageType::PointType & CenterPoint,
+                  const landmarksConstellationModelIO::IndexLocationVectorType & model,
+                  std::vector & result_array);
+
+extern
+void extractArrayRemoveVectorMeanNormalize(SImageType::Pointer & image, const SImageType::PointType & CenterPoint,
+                                           const landmarksConstellationModelIO::IndexLocationVectorType & model,
+                                           std::vector & result_array);
+
+inline
+static std::string
+PrefixName(const char *prefix, const std::string & name)
+{
+  std::string rval;
+
+  rval += itksys::SystemTools::GetFilenamePath(name);
+  if( rval.size() > 0 )
+    {
+    rval += "/";
+    }
+  //  std::string rval(pathpart);
+  rval += prefix;
+  rval += itksys::SystemTools::GetFilenameName(name);
+  return rval;
+}
+
+#include 
+#include 
+#include 
+template 
+void ImageMinMax(typename SImageType::Pointer image,
+                 typename SImageType::PixelType *imageMin, typename SImageType::PixelType *imageMax)
+{
+  typename itk::MinimumMaximumImageFilter::Pointer minmaxFilter =
+    itk::MinimumMaximumImageFilter::New();
+  minmaxFilter->SetInput(image);
+  minmaxFilter->Update();
+  *imageMax = minmaxFilter->GetMaximum();
+  *imageMin = minmaxFilter->GetMinimum();
+}
+
+/**
+ *
+ *
+ * @author hjohnson (8/12/2008)
+ *
+ * @param SImageType The image type templated over
+ * @param image  the itk image to be used to compute the
+ *               histograms
+ * @param low   The intensity value where "percent" voxels are
+ *              above this threshold
+ * @param high  The intensity value where "1.0-percent" voxels
+ *              are below this threshold
+ * @param percent A value between 0.0 and 100.0 representing the
+ *                Quantile percentages to be eliminated. NOTE:
+ *                This value will be divided by 100.0, so
+ *                100.0=100%, and 1.0=.01%.
+ * @return Background threshold.
+ */
+template 
+typename SImageType::PixelType
+setLowHigh(typename SImageType::Pointer & image,
+           typename SImageType::PixelType & low,
+           typename SImageType::PixelType & high,
+           const float percent)
+{
+  typename SImageType::PixelType imageMin;
+  typename SImageType::PixelType imageMax;
+  ImageMinMax(image, &imageMin, &imageMax);
+
+  typedef itk::Statistics::ScalarImageToHistogramGenerator HistogramGeneratorType;
+  typename HistogramGeneratorType::Pointer histogramGenerator = HistogramGeneratorType::New();
+  histogramGenerator->SetInput(image);
+  histogramGenerator->SetNumberOfBins(imageMax - imageMin + 1);
+  histogramGenerator->SetMarginalScale(1.0);
+#ifndef ITK_USE_REVIEW_STATISTICS
+  histogramGenerator->SetHistogramMin(imageMin);
+  histogramGenerator->SetHistogramMax(imageMax);
+#endif
+  histogramGenerator->Compute();
+  typedef typename HistogramGeneratorType::HistogramType HistogramType;
+  const HistogramType *histogram = histogramGenerator->GetOutput();
+
+  typedef itk::OtsuMultipleThresholdsCalculator OtsuCalcType;
+  typename OtsuCalcType::Pointer OtsuCalc = OtsuCalcType::New();
+  OtsuCalc->SetInputHistogram(histogram);
+  OtsuCalc->SetNumberOfThresholds(1);
+  OtsuCalc->Update();
+  typename OtsuCalcType::OutputType otsuThresholds = OtsuCalc->GetOutput();
+
+  low = static_cast( histogram->Quantile(0, 0.0F + percent) );
+  high = static_cast( histogram->Quantile(0, 1.0F - percent) );
+  return static_cast( otsuThresholds[0] );
+}
+
+// ------------------------------
+// The following should be cleaned up and moved elsewhere
+template 
+double
+removeVectorMean(DType *x, DType *y, int n)
+{
+  double mean = 0.0;
+
+  if( n <= 0 )
+    {
+    return 0.0;
+    }
+  for( int i = 0; i < n; i++ )
+    {
+    mean += static_cast( x[i] );
+    }
+  mean /= n;
+  for( int i = 0; i < n; i++ )
+    {
+    y[i] = static_cast( x[i] - mean );
+    }
+  return mean;
+}
+
+extern void removeVectorMean(double *y, int n, int p);
+
+// ///////////////////////////////////////////////////////
+template 
+DType dot(DType *a, DType *b, int n)
+{
+  float dot = 0.0;
+  for( int i = 0; i < n; i++ )
+    {
+    dot += a[i] * b[i];
+    }
+  return dot;
+}
+
+template 
+double removeVectorMean(DType *y, int n)
+{
+  double mean = 0.0;
+
+  if( n <= 0 )
+    {
+    return 0.0;
+    }
+  for( int i = 0; i < n; i++ )
+    {
+    mean += y[i];
+    }
+  mean /= n;
+  for( int i = 0; i < n; i++ )
+    {
+    y[i] = y[i] - mean;
+    }
+  return mean;
+}
+
+// ///////////////////////////////////////////////////////
+template 
+DType dot(const std::vector & a, const std::vector & b)
+{
+  assert( a.size() == b.size() );
+  DType dot = 0.0;
+  typename std::vector::const_iterator ait = a.begin();
+  typename std::vector::const_iterator bit = b.begin();
+  while( ait != a.end() && bit != b.end() )
+    {
+    dot += ( *ait ) * ( *bit );
+    ait++;
+    bit++;
+    }
+
+  return dot;
+}
+
+// ///////////////////////////////////////////////////////
+// Implements Eq. (2.2.1) of J. Cohen & P. Cohen (2nd ed.)
+template 
+double standardDeviation(DType *x, int n)
+{
+  double sx, sxx;
+  double sd;
+
+  if( n <= 0 )
+    {
+    return 0.0;
+    }
+  sx = sxx = 0.0;
+  for( int i = 0; i < n; i++ )
+    {
+    sx += x[i];
+    sxx += x[i] * x[i];
+    }
+  sd = ( sxx - sx * sx / n ) / n;
+  if( sd > 0.0 )
+    {
+    sd = vcl_sqrt(sd);
+    }
+  else
+    {
+    sd = 0.0;
+    }
+  return sd;
+}
+
+// Computes the Pearson correlation coefficient between x and y.
+// Implements Eq. (2.3.2) of J. Cohen & P. Cohen (2nd ed.)
+template 
+double pearsonCorrelation(DTypeX *x, DTypeY *y, int n)
+{
+  double sx, sy, sxx, syy, sxy;
+  double Sxx, Sxy, Syy;
+  double dum = 0.0;
+
+  sx = sy = sxx = syy = sxy = 0.0;
+  for( int i = 0; i < n; i++ )
+    {
+    sx += x[i];
+    sxx += x[i] * x[i];
+    sy += y[i];
+    syy += y[i] * y[i];
+    sxy += x[i] * y[i];
+    }
+  Sxx = n * sxx - sx * sx;
+  Syy = n * syy - sy * sy;
+  Sxy = n * sxy - sx * sy;
+  if( Sxx * Syy > 0.0 )
+    {
+    dum = vcl_sqrt(Sxx * Syy);
+    }
+  if( dum != 0.0 )
+    {
+    return (double)( Sxy / dum );
+    }
+  else
+    {
+    return 0.0;
+    }
+}
+
+// Implements Eq. (3.3.11) of J. Cohen & P. Cohen (2nd ed.)
+template 
+void partialCorrelation(DTypeY *Y, DTypeX *X1, DTypeX *X2, int n, double *pr1, double *pr2)
+{
+  double rY1, rY2, r12;
+  double dum1, dum2;
+
+  rY1 = pearsonCorrelation(X1, Y, n);
+  rY2 = pearsonCorrelation(X2, Y, n);
+  r12 = pearsonCorrelation(X1, X2, n);
+  dum1 = ( 1.0 - rY2 * rY2 ) * ( 1 - r12 * r12 );
+  dum2 = ( 1.0 - rY1 * rY1 ) * ( 1 - r12 * r12 );
+  if( dum1 > 0.0 )
+    {
+    *pr1 = ( rY1 - rY2 * r12 ) / vcl_sqrt(dum1);
+    }
+  else
+    {
+    *pr1 = 0.0;
+    }
+  if( dum2 > 0.0 )
+    {
+    *pr2 = ( rY2 - rY1 * r12 ) / vcl_sqrt(dum2);
+    }
+  else
+    {
+    *pr2 = 0.0;
+    }
+}
+
+// //////////////////////////////////////////////////////////////
+// Computes the sample mean of a set of n observations {x_1,x_2,...,x_n} from a
+// given distribution.
+// //////////////////////////////////////////////////////////////
+template 
+double
+sample_mean(DType *x, int n)
+{
+  double mean = 0.0;
+
+  if( n <= 0 )
+    {
+    return 0.0;
+    }
+  for( int i = 0; i < n; i++ )
+    {
+    mean += x[i];
+    }
+  mean /= n;
+  return mean;
+}
+
+// //////////////////////////////////////////////////////////////
+// Computes the unbiased sample variance of a set of n observations
+// {x_1,x_2,...,x_n} from a given distribution.
+// //////////////////////////////////////////////////////////////
+template 
+double sample_variance(DType *x, int n, double *mean)
+{
+  double sum_of_sq = 0.0;
+  double sum = 0.0;
+  double var;
+
+  if( n < 2 )
+    {
+    *mean = 0.0;
+    return 0.0;
+    }
+  for( int i = 0; i < n; i++ )
+    {
+    sum_of_sq +=
+      static_cast( x[i] )
+      * static_cast( x[i] );
+    sum += static_cast( x[i] );
+    }
+  *mean = sum / n;
+  var = ( sum_of_sq - sum * sum / n ) / ( n - 1.0 );
+  return var;
+}
+
+template 
+double
+independent_samples_t(DType *x1, int n1, DType *x2, int n2, int *df, double *meandiff)
+{
+  double var1, var2;
+  double mean1, mean2;
+  double var, sd;
+  double t;
+
+  *df = n1 + n2 - 2;
+  if( n1 < 2 || n2 < 2 )
+    {
+    return 0.0;
+    }
+  var1 = sample_variance(x1, n1, &mean1);
+  var2 = sample_variance(x2, n2, &mean2);
+  var = ( ( ( n1 - 1 ) * var1 + ( n2 - 1 ) * var2 ) / ( n1 + n2 - 2.0 ) ) * ( 1.0 / n1 + 1.0 / n2 );
+  sd = vcl_sqrt(var);
+  if( sd == 0.0 )
+    {
+    return 0.0;
+    }
+  *meandiff = mean1 - mean2;
+  t = ( mean1 - mean2 ) / sd;
+  return t;
+}
+
+template 
+double
+paired_samples_t(DType *x1, DType *x2, int n, int *df, double *meandiff)
+{
+  double var;
+  double mean;
+  double sd;
+  double t;
+
+  *df = n - 1;
+  if( n < 2 )
+    {
+    return 0.0;
+    }
+  for( int i = 0; i < n; i++ )
+    {
+    x1[i] -= x2[i];
+    }
+  var = sample_variance(x1, n, &mean) / n;
+  sd = vcl_sqrt(var);
+  if( sd == 0.0 )
+    {
+    return 0.0;
+    }
+  *meandiff = mean;
+  t = mean / sd;
+  return t;
+}
+
+#endif
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx b/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx
new file mode 100644
index 00000000..8845dee9
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx
@@ -0,0 +1,793 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#include "landmarksConstellationDetector.h"
+// landmarkIO has to be included after landmarksConstellationDetector
+#include "landmarkIO.h"
+
+SImageType::PointType
+landmarksConstellationDetector::FindCandidatePoints
+  ( SImageType::Pointer volumeMSP,
+  SImageType::Pointer mask_LR,
+  const double LR_restrictions,
+  const double PA_restrictions,
+  const double SI_restrictions,
+  // TODO: restrictions should really be ellipsoidal values
+  const SImageType::PointType::VectorType & CenterOfSearchArea,
+  const std::vector > & TemplateMean,
+  const landmarksConstellationModelIO::IndexLocationVectorType & model,
+  const bool ComputeOutsideSearchRadius,
+  double & cc_Max, const std::string & mapID )
+{
+  cc_Max = -123456789.0;
+  FImageType3D::Pointer ccmap_LR3D;
+  if( globalImagedebugLevel > 8 )
+    {
+    ccmap_LR3D = FImageType3D::New();
+    // NOTE:  The ccmap's are not ever used, and can probably be removed.
+    ccmap_LR3D->CopyInformation( volumeMSP );
+    ccmap_LR3D->SetRegions( volumeMSP->GetLargestPossibleRegion() );
+    ccmap_LR3D->Allocate();
+    ccmap_LR3D->FillBuffer( 0 );
+    }
+
+  // TODO:  Move the LinearInterpolator to the function parameter
+  // because the image is never needed.
+  LinearInterpolatorType::Pointer imInterp = LinearInterpolatorType::New();
+  imInterp->SetInputImage( volumeMSP );
+  LinearInterpolatorType::Pointer maskInterp = LinearInterpolatorType::New();
+  maskInterp->SetInputImage( mask_LR );
+
+  // For all regions within the search radius around the center
+  std::vector    CurrentPoint_test_vec;
+  SImageType::SizeType  imageSize = volumeMSP->GetLargestPossibleRegion().GetSize();
+  SImageType::PointType currentPointLocation;
+  currentPointLocation[0] = CenterOfSearchArea[0];
+  currentPointLocation[1] = CenterOfSearchArea[1];
+  currentPointLocation[2] = CenterOfSearchArea[2];
+
+  const double LeftToRight_END = CenterOfSearchArea[0] + LR_restrictions;
+  const double AnteriorToPostierior_END = CenterOfSearchArea[1] + PA_restrictions;
+  const double InferiorToSuperior_END = CenterOfSearchArea[2] + SI_restrictions;
+  const double deltaLR = 0.5; // in mm
+  const double deltaAP = 0.5;
+  const double deltaIS = 0.5;
+
+  double                cc_insideSearchRadius_max = 0.0;
+  double                cc_outsideSearchRadius_max = 0.0;
+  SImageType::PointType GuessPoint;
+  GuessPoint[0] = CenterOfSearchArea[0];
+  GuessPoint[1] = CenterOfSearchArea[1];
+  GuessPoint[2] = CenterOfSearchArea[2];
+
+  // Boundary check
+    {
+    SImageType::PointType boundaryL( GuessPoint );
+    boundaryL[0] += LR_restrictions;
+    SImageType::PointType boundaryR( GuessPoint );
+    boundaryR[0] -= LR_restrictions;
+    SImageType::PointType boundaryP( GuessPoint );
+    boundaryP[1] += PA_restrictions;
+    SImageType::PointType boundaryA( GuessPoint );
+    boundaryA[1] -= PA_restrictions;
+    SImageType::PointType boundaryS( GuessPoint );
+    boundaryS[2] += SI_restrictions;
+    SImageType::PointType boundaryI( GuessPoint );
+    boundaryI[2] -= SI_restrictions;
+    if( ( !maskInterp->IsInsideBuffer( boundaryL ) ) ||
+        ( !maskInterp->IsInsideBuffer( boundaryR ) ) ||
+        ( !maskInterp->IsInsideBuffer( boundaryP ) ) ||
+        ( !maskInterp->IsInsideBuffer( boundaryA ) ) ||
+        ( !maskInterp->IsInsideBuffer( boundaryS ) ) ||
+        ( !maskInterp->IsInsideBuffer( boundaryI ) ) )
+      {
+      std::cout << "WARNING: search region outside of the image region." << std::endl;
+      std::cout << "The detection has probably large error!" << std::endl;
+      return GuessPoint;
+      }
+    }
+  for( double LeftToRight = CenterOfSearchArea[0] - LR_restrictions;
+       LeftToRight < LeftToRight_END; LeftToRight += deltaLR )
+    {
+    currentPointLocation[0] = LeftToRight;
+    for( double AnteriorToPostierior = CenterOfSearchArea[1] - PA_restrictions;
+         AnteriorToPostierior < AnteriorToPostierior_END; AnteriorToPostierior += deltaAP )
+      {
+      currentPointLocation[1] = AnteriorToPostierior;
+      for( double InferiorToSuperior = CenterOfSearchArea[2] - SI_restrictions;
+           InferiorToSuperior < InferiorToSuperior_END; InferiorToSuperior += deltaIS )
+        {
+        currentPointLocation[2] = InferiorToSuperior;
+        if( maskInterp->Evaluate( currentPointLocation ) > 0.5 )
+          {
+          const SImageType::PointType::VectorType temp =
+            currentPointLocation.GetVectorFromOrigin() - CenterOfSearchArea;
+          const double inclusionDistance = temp.GetNorm();
+          if( ( ComputeOutsideSearchRadius == true )
+              || (
+                ( inclusionDistance < SI_restrictions )
+                && ( vcl_abs( temp[1] ) < PA_restrictions )
+                )
+              )
+            {
+            extractArrayRemoveVectorMeanNormalize
+              ( volumeMSP, currentPointLocation, model, CurrentPoint_test_vec );
+
+            double cc_rotation_max = 0.0;
+            for( unsigned int curr_rotationAngle = 0;
+                 curr_rotationAngle < TemplateMean.size(); curr_rotationAngle++ )
+              {
+              const double cc =
+                dot( CurrentPoint_test_vec, TemplateMean[curr_rotationAngle] );
+              cc_rotation_max = ( cc > cc_rotation_max ) ? cc : cc_rotation_max;
+              if( ( inclusionDistance < SI_restrictions )
+                  && ( vcl_abs( temp[1] ) < PA_restrictions ) )
+                {
+                if( cc > cc_insideSearchRadius_max )
+                  {
+                  cc_insideSearchRadius_max = cc;
+                  GuessPoint = currentPointLocation;
+                  cc_Max = cc;
+                  }
+                }
+              else
+                {
+                if( cc > cc_outsideSearchRadius_max )
+                  {
+                  cc_outsideSearchRadius_max = cc;
+                  }
+                }
+              }
+            if( globalImagedebugLevel > 8 )
+              {
+              FImageType3D::IndexType index3D;
+              ccmap_LR3D->TransformPhysicalPointToIndex
+                ( currentPointLocation, index3D );
+              ccmap_LR3D->SetPixel( index3D, cc_rotation_max );
+              }
+            }
+          }
+        }
+      }
+    }
+  if( globalImagedebugLevel > 8 )
+    {
+    std::string ccmapName( this->m_ResultsDir + "/ccmap_LR3D_"
+                           + itksys::SystemTools::GetFilenameName( mapID ) + ".nii.gz" );
+    itkUtil::WriteImage( ccmap_LR3D, ccmapName );
+    }
+  return GuessPoint;
+}
+
+void landmarksConstellationDetector::Compute( void )
+{
+  std::cout << "\nEstimating MSP..." << std::endl;
+
+  // save the result that whether we are going to process all the landmarks
+  // in light of user-specified eye center info.
+  bool hasUserSpecEyeCenterInfo = true;
+  if( ( this->m_NamedPointEMSP.find( "LE" ) == this->m_NamedPointEMSP.end() )
+      || ( this->m_NamedPointEMSP.find( "RE" ) == this->m_NamedPointEMSP.end() ) )
+    {
+    hasUserSpecEyeCenterInfo = false;
+    }
+
+  // Compute the estimated MSP transform, and aligned image
+  ComputeMSP( this->m_VolOrig, this->m_finalTmsp,
+              this->m_VolumeMSP, this->m_CenterOfHeadMass, this->m_mspQualityLevel );
+
+  // In case hough eye detector failed
+  if( this->m_HoughEyeFailure || ( globalImagedebugLevel > 1 ) )
+    {
+    // write EMSP aligned image
+    itkUtil::WriteImage
+      ( this->m_VolumeMSP, this->m_ResultsDir + "/EMSP.nii.gz" );
+
+    if( this->m_HoughEyeFailure )
+      {
+      std::cout << "EMSP aligned image and zero eye centers "
+                << "landmarks are written to " << std::endl;
+      std::cout << this->m_ResultsDir << ". Use GUI corrector to "
+                << "correct the landmarks on EMSP.fcsv." << std::endl;
+      SImageType::PointType zeroPoint;
+      zeroPoint.Fill( 0 );
+      LandmarksMapType zeroEyeCenters;
+      zeroEyeCenters["LE"] = zeroPoint;
+      zeroEyeCenters["RE"] = zeroPoint;
+      WriteITKtoSlicer3Lmk
+        ( this->m_ResultsDir + "/EMSP.fcsv", zeroEyeCenters );
+      exit( -1 );
+      }
+    }
+
+  if( globalImagedebugLevel > 2 )
+    {
+    const std::string MSP_ImagePlaneForOrig( this->m_ResultsDir + "/MSP_PLANE_For_Orig.nii.gz" );
+    CreatedebugPlaneImage( this->m_VolOrig, MSP_ImagePlaneForOrig );
+    const std::string MSP_ImagePlane( this->m_ResultsDir + "/MSP_PLANE.nii.gz" );
+    CreatedebugPlaneImage( this->m_VolumeMSP, MSP_ImagePlane );
+    }
+
+  // HACK:  TODO:  DEBUG: Need to remove redundant need for volume and mask when
+  // they can be the same image ( perhaps with a threshold );
+  SImageType::Pointer mask_LR = this->m_VolumeMSP;
+
+  VersorTransformType::Pointer InvHoughEyeTransform;
+  if( !hasUserSpecEyeCenterInfo )
+    {
+    InvHoughEyeTransform = VersorTransformType::New();
+    this->m_HoughEyeTransform->GetInverse( InvHoughEyeTransform );
+    }
+
+  VersorTransformType::Pointer InvFinalTmsp = VersorTransformType::New();
+  this->m_finalTmsp->GetInverse( InvFinalTmsp );
+
+  this->m_CenterOfHeadMassEMSP =
+    InvFinalTmsp->TransformPoint( this->m_CenterOfHeadMass );
+  this->m_CenterOfHeadMassEMSP[0] = 0; // Search starts on the estimated MSP
+
+    {
+    SImageType::PointType CandidateRPPoint;
+    SImageType::PointType CandidatePCPoint;
+    SImageType::PointType CandidateVN4Point;
+    SImageType::PointType CandidateACPoint;
+
+    SImageType::PointType::VectorType RPtoCEC;
+    SImageType::PointType::VectorType RPtoVN4;
+    SImageType::PointType::VectorType RPtoAC;
+    SImageType::PointType::VectorType RPtoPC;
+
+    SImageType::PointType mspSpaceCEC;
+
+    if( !hasUserSpecEyeCenterInfo )
+      {
+      m_NamedPointEMSP["LE"] =
+        InvHoughEyeTransform->TransformPoint( this->m_LEPoint );
+      m_NamedPointEMSP["LE"] =
+        InvFinalTmsp->TransformPoint( this->m_NamedPointEMSP["LE"] );
+      m_NamedPointEMSP["RE"] =
+        InvHoughEyeTransform->TransformPoint( this->m_REPoint );
+      m_NamedPointEMSP["RE"] =
+        InvFinalTmsp->TransformPoint( this->m_NamedPointEMSP["RE"] );
+      }
+    mspSpaceCEC.SetToMidPoint( this->m_NamedPointEMSP["LE"],
+                               this->m_NamedPointEMSP["RE"] );
+    mspSpaceCEC[0] = 0; // Search starts on the estimated MSP
+
+    std::cout << "\nPerforming morphmetric search + local search..." << std::endl;
+      {
+      /*
+       * Search for MPJ ( RP )
+       *
+       * Use the knowledge of mean CMtoRP vector + local searching
+       */
+      std::cout << "Processing MPJ..." << std::endl;
+      double searchRadiusLR = 4.; // in mm, and it is only for landmarks near
+                                  // MSP
+      double cc_RP_Max = 0;
+      if( this->m_NamedPointEMSP.find( "RP" ) != this->m_NamedPointEMSP.end() )
+        {
+        CandidateRPPoint = this->m_NamedPointEMSP["RP"];
+        std::cout << "Skip estimation, directly load from file." << std::endl;
+        }
+      else
+        {
+        // The search radius of RP is set to 5 times larger than its template
+        // radius in SI direction.
+        // It's large because some scans have extra contents of neck or shoulder
+        CandidateRPPoint =
+          FindCandidatePoints( this->m_VolumeMSP, mask_LR, searchRadiusLR,
+                               3. * this->m_TemplateRadius["RP"],
+                               5. * this->m_TemplateRadius["RP"],
+                               this->m_CenterOfHeadMassEMSP.GetVectorFromOrigin()
+                               + this->m_InputTemplateModel.GetCMtoRPMean(),
+                               this->m_InputTemplateModel.GetTemplateMeans( "RP" ),
+                               this->m_InputTemplateModel.m_VectorIndexLocations["RP"],
+                               false, cc_RP_Max, "RP" );
+        }
+
+      // Local search radius in LR direction is affected by the
+      // estimated MSP error in LR direction
+      const double err_MSP = vcl_abs( CandidateRPPoint[0]
+                                      - this->m_CenterOfHeadMassEMSP[0] );
+      std::cout << "The estimated MSP error in LR direction: "
+                << err_MSP << " mm" << std::endl;
+
+      if( err_MSP < 1 )
+        {
+        searchRadiusLR = 1.;
+        std::cout << "Local search radius in LR direction is set to 1 mm." << std::endl;
+        }
+      else if( err_MSP < 2 )
+        {
+        searchRadiusLR = 2.;
+        std::cout << "Local search radius in LR direction is set to 2 mm." << std::endl;
+        }
+      else if( err_MSP > 6 )
+        {
+        std::cerr << "Bad MPJ estimation or too large MSP estimation error!" << std::endl;
+        std::cerr << "The estimation result is probably not reliable." << std::endl;
+        exit( -1 );
+        }
+      else // not changed
+        {
+        std::cout << "Local search radius in LR direction is set to 4 mm." << std::endl;
+        }
+
+      /*
+       * Search for 4VN
+       *
+       * we will use RPtoCEC ( RP-to-center of eye centers mean vector ) and RPtoVN4Mean
+       * to determine the search center for VN4
+       *
+       * Assumption:
+       * 1. Human brains share a similar angle from RPtoCEC to RPtoVN4
+       * 2. Human brains share a similar RPtoVN4 norm
+       * 3. The center of eye centers, MPJ, and AC are all very close to the MSP plane
+       * 4. VN4 is always below CEC-MPJ line on MSP plane
+       */
+      std::cout << "Processing 4VN..." << std::endl;
+      RPtoCEC = mspSpaceCEC - CandidateRPPoint;
+
+      // RPtoVN4 = this->m_InputTemplateModel.GetRPtoXMean( "VN4" );
+      RPtoVN4 = FindVectorFromPointAndVectors
+          ( RPtoCEC, this->m_InputTemplateModel.GetRPtoCECMean(),
+          this->m_InputTemplateModel.GetRPtoXMean( "VN4" ), -1 );
+
+      double cc_VN4_Max = 0;
+
+      if( this->m_NamedPointEMSP.find( "VN4" ) != this->m_NamedPointEMSP.end() )
+        {
+        CandidateVN4Point = this->m_NamedPointEMSP["VN4"];
+        std::cout << "Skip estimation, directly load from file." << std::endl;
+        }
+      else
+        {
+        CandidateVN4Point =
+          FindCandidatePoints( this->m_VolumeMSP, mask_LR, searchRadiusLR,
+                               1.6 * this->m_TemplateRadius["VN4"],
+                               1.6 * this->m_TemplateRadius["VN4"],
+                               CandidateRPPoint.GetVectorFromOrigin() + RPtoVN4,
+                               this->m_InputTemplateModel.GetTemplateMeans( "VN4" ),
+                               this->m_InputTemplateModel.m_VectorIndexLocations["VN4"],
+                               false, cc_VN4_Max, "VN4" );
+        }
+
+      /*
+       * Search for AC
+       *
+       * Assumption:
+       * 1. Human brains share a similar angle from RPtoCEC to RPtoAC
+       * 2. Human brains share a similar RPtoAC norm
+       * 3. The center of eye centers, MPJ, and AC are all very close to the MSP plane
+       * 4. AC is always above CEC-MPJ line on MSP plane
+       */
+      std::cout << "Processing AC..." << std::endl;
+
+      // RPtoAC = this->m_InputTemplateModel.GetRPtoXMean( "AC" );
+      RPtoAC = FindVectorFromPointAndVectors
+          ( RPtoCEC, this->m_InputTemplateModel.GetRPtoCECMean(),
+          this->m_InputTemplateModel.GetRPtoXMean( "AC" ), 1 );
+      double cc_AC_Max = 0;
+      if( this->m_NamedPointEMSP.find( "AC" ) != this->m_NamedPointEMSP.end() )
+        {
+        CandidateACPoint = this->m_NamedPointEMSP["AC"];
+        std::cout << "Skip estimation, directly load from file." << std::endl;
+        }
+      else
+        {
+        CandidateACPoint =
+          FindCandidatePoints( this->m_VolumeMSP, mask_LR, searchRadiusLR,
+                               1.6 * this->m_TemplateRadius["AC"],
+                               1.6 * this->m_TemplateRadius["AC"],
+                               CandidateRPPoint.GetVectorFromOrigin() + RPtoAC,
+                               this->m_InputTemplateModel.GetTemplateMeans( "AC" ),
+                               this->m_InputTemplateModel.m_VectorIndexLocations["AC"],
+                               false, cc_AC_Max, "AC" );
+        }
+
+      /*
+       * Search for PC
+       *
+       * Assumption:
+       * 1. Human brains share a similar angle from RPtoCEC to RPtoPC
+       * 2. Human brains share a similar RPtoPC norm
+       * 3. The center of eye centers, MPJ, and PC are all very close to the MSP plane
+       * 4. PC is always above CEC-MPJ line on MSP plane
+       */
+      std::cout << "Processing PC..." << std::endl;
+
+      // RPtoPC = this->m_InputTemplateModel.GetRPtoXMean( "PC" );
+      RPtoPC = FindVectorFromPointAndVectors
+          ( RPtoCEC, this->m_InputTemplateModel.GetRPtoCECMean(),
+          this->m_InputTemplateModel.GetRPtoXMean( "PC" ), 1 );
+      double cc_PC_Max = 0;
+      if( this->m_NamedPointEMSP.find( "PC" ) != this->m_NamedPointEMSP.end() )
+        {
+        CandidatePCPoint = this->m_NamedPointEMSP["PC"];
+        std::cout << "Skip estimation, directly load from file." << std::endl;
+        }
+      else
+        {
+        CandidatePCPoint =
+          FindCandidatePoints( this->m_VolumeMSP, mask_LR, searchRadiusLR,
+                               4 * this->m_TemplateRadius["PC"],
+                               4 * this->m_TemplateRadius["PC"],
+                               CandidateRPPoint.GetVectorFromOrigin() + RPtoPC,
+                               this->m_InputTemplateModel.GetTemplateMeans( "PC" ),
+                               this->m_InputTemplateModel.m_VectorIndexLocations["PC"],
+                               false, cc_PC_Max, "PC" );
+        }
+
+      // A check point for base landmarks
+      if( LMC::globalverboseFlag )
+        {
+        std::cout << cc_RP_Max << " " << cc_PC_Max << " " << cc_VN4_Max
+                  << " " << cc_AC_Max << "\n"
+                  << CandidateRPPoint << " " << CandidatePCPoint << " " << CandidateVN4Point << " "
+                  << CandidateACPoint << std::endl;
+        }
+
+      if( globalImagedebugLevel > 1 )
+        {
+        std::string BrandedImageAName( this->m_ResultsDir + "/BrandedImage.png" );
+
+        MakeBrandeddebugImage( this->m_VolumeMSP.GetPointer(), this->m_InputTemplateModel,
+                               this->m_CenterOfHeadMassEMSP
+                               + this->m_InputTemplateModel.GetCMtoRPMean(),
+                               CandidateRPPoint + RPtoAC,
+                               CandidateRPPoint + RPtoPC,
+                               CandidateRPPoint + RPtoVN4,
+                               BrandedImageAName,
+                               CandidateRPPoint,
+                               CandidateACPoint,
+                               CandidatePCPoint,
+                               CandidateVN4Point
+                               );
+
+        if( globalImagedebugLevel > 3 )
+          {
+          std::string LabelImageAName( this->m_ResultsDir + "/MSP_Mask.nii.gz" );
+          MakeLabelImage( this->m_VolumeMSP, CandidateRPPoint, CandidateACPoint,
+                          CandidatePCPoint, CandidateVN4Point, LabelImageAName );
+          }
+        }
+
+      // After finding RP, AC, PC, we can compute the versor transform for
+      // registration
+      // Also in this stage, we store some results for later use
+      // Save named points in original space
+      this->m_NamedPoint["RP"] =
+        this->m_finalTmsp->TransformPoint( CandidateRPPoint );
+      this->m_NamedPoint["AC"] =
+        this->m_finalTmsp->TransformPoint( CandidateACPoint );
+      this->m_NamedPoint["PC"] =
+        this->m_finalTmsp->TransformPoint( CandidatePCPoint );
+      this->m_NamedPoint["VN4"] =
+        this->m_finalTmsp->TransformPoint( CandidateVN4Point );
+      this->m_NamedPoint["CM"] =
+        this->m_finalTmsp->TransformPoint( this->m_CenterOfHeadMassEMSP );
+
+      if( !hasUserSpecEyeCenterInfo )
+        {
+        this->m_NamedPoint["RP"] =
+          this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint["RP"] );
+        this->m_NamedPoint["AC"] =
+          this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint["AC"] );
+        this->m_NamedPoint["PC"] =
+          this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint["PC"] );
+        this->m_NamedPoint["VN4"] =
+          this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint["VN4"] );
+        this->m_NamedPoint["CM"] =
+          this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint["CM"] );
+        this->m_NamedPoint["LE"] = this->m_LEPoint;
+        this->m_NamedPoint["RE"] = this->m_REPoint;
+        }
+      else
+        {
+        this->m_NamedPoint["LE"] =
+          this->m_finalTmsp->TransformPoint( this->m_NamedPointEMSP["LE"] );
+        this->m_NamedPoint["RE"] =
+          this->m_finalTmsp->TransformPoint( this->m_NamedPointEMSP["RE"] );
+        }
+
+      // Write some debug images
+        {
+        if( globalImagedebugLevel > 3 )
+          {
+          std::string ResampledMaskmageName
+            ( this->m_ResultsDir + "/Resampled_Mask.nii.gz" );
+          MakeLabelImage( this->m_VolOrig, CandidateRPPoint,
+                          CandidateACPoint, CandidatePCPoint,
+                          CandidateVN4Point, ResampledMaskmageName );
+
+          std::string OrigMaskImageName
+            ( this->m_ResultsDir + "/Orig_Mask.nii.gz" );
+          MakeLabelImage( this->m_VolOrig, this->m_NamedPoint["RP"],
+                          this->m_NamedPoint["AC"], this->m_NamedPoint["PC"],
+                          this->m_NamedPoint["VN4"], OrigMaskImageName );
+          }
+        }
+
+      // Save some named points in EMSP space mainly for debug use
+        {
+        this->m_NamedPointEMSP["AC"] = CandidateACPoint;
+        this->m_NamedPointEMSP["PC"] = CandidatePCPoint;
+        this->m_NamedPointEMSP["RP"] = CandidateRPPoint;
+        this->m_NamedPointEMSP["VN4"] = CandidateVN4Point;
+        this->m_NamedPointEMSP["CM"] = this->m_CenterOfHeadMassEMSP;
+        // Eye centers in EMSP have been saved in a earlier time
+        }
+
+      // Compute the AC-PC aligned transform
+      // Note for the sake of EPCA, we need the transform at this stage
+      // so that the method is robust against rotation
+        {
+        RigidTransformType::Pointer ZeroCenteredTransform =
+          this->GetACPCAlignedZeroCenteredTransform();
+        VersorTransformType::Pointer VersorZeroCenteredTransform = VersorTransformType::New();
+        VersorZeroCenteredTransform->SetFixedParameters( ZeroCenteredTransform->GetFixedParameters() );
+        itk::Versor versorRotation;
+        versorRotation.Set( ZeroCenteredTransform->GetRotationMatrix() );
+        VersorZeroCenteredTransform->SetRotation( versorRotation );
+        VersorZeroCenteredTransform->SetTranslation( ZeroCenteredTransform->GetTranslation() );
+        VersorTransformType::Pointer InverseVersorZeroCenteredTransform = VersorTransformType::New();
+        SImageType::PointType        centerPoint = ZeroCenteredTransform->GetCenter();
+        InverseVersorZeroCenteredTransform->SetCenter( centerPoint );
+        InverseVersorZeroCenteredTransform->SetIdentity();
+        ZeroCenteredTransform->GetInverse( InverseVersorZeroCenteredTransform );
+        this->m_VersorTransform = VersorZeroCenteredTransform;
+        this->m_InvVersorTransform = InverseVersorZeroCenteredTransform;
+        }
+
+      // Save some named points in AC-PC aligned space
+        {
+        this->m_NamedPointACPC["AC"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["AC"] );
+        this->m_NamedPointACPC["PC"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["PC"] );
+        this->m_NamedPointACPC["RP"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["RP"] );
+        this->m_NamedPointACPC["VN4"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["VN4"] );
+        this->m_NamedPointACPC["CM"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["CM"] );
+        this->m_NamedPointACPC["LE"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["LE"] );
+        this->m_NamedPointACPC["RE"] =
+          this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint["RE"] );
+        }
+
+      // Get a copy of landmarks on ACPC plane for eliminating accumulative
+      // errors of local search process
+        {
+        this->m_NamedPointACPCRaw["AC"] = this->m_NamedPointACPC["AC"];
+        this->m_NamedPointACPCRaw["PC"] = this->m_NamedPointACPC["PC"];
+        this->m_NamedPointACPCRaw["RP"] = this->m_NamedPointACPC["RP"];
+        this->m_NamedPointACPCRaw["VN4"] = this->m_NamedPointACPC["VN4"];
+        this->m_NamedPointACPCRaw["LE"] = this->m_NamedPointACPC["LE"];
+        this->m_NamedPointACPCRaw["RE"] = this->m_NamedPointACPC["RE"];
+        }
+
+      /*
+     * For the rest of the landmarks
+     *
+     * The search center of the rest of the landmarks will be estimated
+     * by linear model estimation with EPCA
+     * Note The current version use landmarks in acpc-aligned space.
+     */
+        {
+        // Build up an evolutionary processing list
+        // order: RP, AC, PC, VN4, LE, RE, ...
+        // Note this order should comply with the order we defined in LLS model
+        std::vector processingList;
+        processingList.push_back( "RP" );
+        processingList.push_back( "AC" );
+        processingList.push_back( "PC" );
+        processingList.push_back( "VN4" );
+        processingList.push_back( "LE" );
+        processingList.push_back( "RE" );
+        unsigned int numBaseLandmarks = 6;
+        unsigned int dim = 3;
+        for( unsigned int ii = 1; ii <= m_LlsMatrices.size(); ++ii )
+          {
+          // The processing order is indicated by the length of EPCA coefficient
+          std::map::iterator
+            iit = this->m_LlsMatrices.begin();
+          while( iit->second.columns() != ( numBaseLandmarks + ii - 2 ) * dim )
+            {
+            if( iit != this->m_LlsMatrices.end() )
+              {
+              ++iit; // transversal
+              }
+            else
+              {
+              std::cerr << "Error: wrong number of parameters for linear model!" << std::endl;
+              std::cerr << "Some EPCA landmarks may not be detected." << std::endl;
+              return;
+              }
+            }
+
+          std::cout << "Processing " << iit->first << "..." << std::endl;
+          if( this->m_NamedPointEMSP.find( iit->first ) != this->m_NamedPointEMSP.end() )
+            {
+            std::cout << "Skip estimation, directly load from file." << std::endl;
+            this->m_NamedPoint[iit->first] =
+              this->m_finalTmsp->TransformPoint( this->m_NamedPointEMSP[iit->first] );
+            this->m_NamedPointACPC[iit->first] =
+              this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint[iit->first] );
+            this->m_NamedPointACPCRaw[iit->first] = this->m_NamedPointACPC[iit->first];
+            }
+          else
+            {
+            // in every iteration, the last name in the processing list
+            // indicates the landmark to be estimated
+            processingList.push_back( iit->first );
+
+            // Find search center by linear model estimation with
+            // dimension reduction.
+            // The result will be stored into this->m_NamedPointEMSP[iit->first]
+            LinearEstimation( this->m_NamedPointACPCRaw, processingList, numBaseLandmarks );
+
+            // check whether it is midline landmark, set search range
+            // and modify search center accordingly
+            double localSearchRadiusLR = this->m_SearchRadii[iit->first];
+              {
+              std::vector::const_iterator midlineIt =
+                this->m_MidlinePointsList.begin();
+              for( ; midlineIt != this->m_MidlinePointsList.end(); ++midlineIt )
+                {
+                if( ( *midlineIt ).compare( iit->first ) == 0 )
+                  {
+                  localSearchRadiusLR = searchRadiusLR;          // a variable
+                                                                 // changed with
+                                                                 // err_MSP
+                  this->m_NamedPointACPCRaw[iit->first][0] = 0.; // search
+                                                                 // starts
+                                                                 // near EMSP
+                  break;
+                  }
+                }
+              }
+
+            this->m_NamedPointACPC[iit->first][0] = this->m_NamedPointACPCRaw[iit->first][0];
+            this->m_NamedPointACPC[iit->first][1] = this->m_NamedPointACPCRaw[iit->first][1];
+            this->m_NamedPointACPC[iit->first][2] = this->m_NamedPointACPCRaw[iit->first][2];
+
+            // Obtain the position of the current landmark in other spaces
+            this->m_NamedPoint[iit->first] =
+              this->m_VersorTransform->TransformPoint( this->m_NamedPointACPC[iit->first] );
+            if( !hasUserSpecEyeCenterInfo )
+              {
+              this->m_NamedPointEMSP[iit->first] =
+                InvHoughEyeTransform->TransformPoint( this->m_NamedPoint[iit->first] );
+              this->m_NamedPointEMSP[iit->first] =
+                InvFinalTmsp->TransformPoint( this->m_NamedPointEMSP[iit->first] );
+              }
+            else
+              {
+              this->m_NamedPointEMSP[iit->first] =
+                InvFinalTmsp->TransformPoint( this->m_NamedPoint[iit->first] );
+              }
+
+            // Enable local search
+            if( 1 )
+              {
+              // local search
+              double cc_Max = 0;
+              this->m_NamedPointEMSP[iit->first] =
+                FindCandidatePoints( this->m_VolumeMSP, mask_LR, localSearchRadiusLR,
+                                     this->m_SearchRadii[iit->first],
+                                     this->m_SearchRadii[iit->first],
+                                     this->m_NamedPointEMSP[iit->first].GetVectorFromOrigin(),
+                                     this->m_InputTemplateModel.GetTemplateMeans( iit->first ),
+                                     this->m_InputTemplateModel.m_VectorIndexLocations[iit->first],
+                                     false, cc_Max, iit->first );
+
+              // Update landmarks in input and ACPC-aligned space
+              this->m_NamedPoint[iit->first] =
+                this->m_finalTmsp->TransformPoint( this->m_NamedPointEMSP[iit->first] );
+              if( !hasUserSpecEyeCenterInfo )
+                {
+                this->m_NamedPoint[iit->first] =
+                  this->m_HoughEyeTransform->TransformPoint( this->m_NamedPoint[iit->first] );
+                }
+              this->m_NamedPointACPC[iit->first] =
+                this->m_InvVersorTransform->TransformPoint( this->m_NamedPoint[iit->first] );
+              }
+            }
+          } // End of arbitrary landmarks detection for the rest of "new" ones
+        }   // End of arbitrary landmarks detection by linear model estimation
+      if( globalImagedebugLevel > 1 )  // This may be very useful for GUI
+                                       // corrector
+        {
+        WriteITKtoSlicer3Lmk
+          ( this->m_ResultsDir + "/EMSP.fcsv",
+          this->m_NamedPointEMSP );
+        }
+      } // End of local searching kernel
+    }   // End of local searching
+}
+
+void landmarksConstellationDetector::LinearEstimation
+  ( LandmarksMapType & namedPoints,
+  const std::vector & processingList,
+  unsigned numBasePoints )
+{
+  unsigned int dim = namedPoints[processingList[0]].GetPointDimension();
+
+  if( processingList.size() <= numBasePoints )
+    {
+    std::cout << "No EPCA landmarks to be estimated." << std::endl;
+    return;
+    }
+  std::string           newPointName = processingList[processingList.size() - 1];
+  SImageType::PointType newPoint;
+  newPoint.Fill( 0 );
+
+  // Construct Xi_t
+  VectorType Xi_t;
+  Xi_t.set_size( dim * ( processingList.size() - 2 ) );
+  for( unsigned int k = 1; k <= processingList.size() - 2; ++k )
+    {
+    for( unsigned int d = 0; d < dim; ++d )
+      {
+      Xi_t( ( k - 1 ) * dim + d ) = namedPoints[processingList[k]][d]
+        - namedPoints[processingList[0]][d] - this->m_LlsMeans[newPointName][d];
+      }
+    }
+  SImageType::PointType::VectorType tmp;
+  tmp.SetVnlVector( this->m_LlsMatrices[newPointName] * Xi_t );
+  newPoint = namedPoints[processingList[0]] + tmp;
+  namedPoints[newPointName] = newPoint;
+
+  // debug
+  // std::cout << "Mi' = " << this->m_LlsMatrices[newPointName] << std::endl;
+  // std::cout << "Xi_t = " << Xi_t << std::endl;
+  // std::cout << "MPJ = " << namedPoints[processingList[0]] << std::endl;
+  // std::cout << newPointName << " = " << newPoint << std::endl;
+}
+
+SImageType::PointType::VectorType
+landmarksConstellationDetector::FindVectorFromPointAndVectors
+  ( SImageType::PointType::VectorType BA,
+  SImageType::PointType::VectorType BAMean,
+  SImageType::PointType::VectorType BCMean,
+  int sign )
+{
+  SImageType::PointType::VectorType BC;
+
+  double cosTheta; // cosine of the angle from BA to BC
+
+  cosTheta = BAMean * BCMean
+    / BAMean.GetNorm() / BCMean.GetNorm();
+
+  // Start searching on MSP
+  BC[0] = 0;
+  double a = BA * BA;
+  double b = -2. * BA.GetNorm() * BCMean.GetNorm() * BA[2] * cosTheta;
+  double c = BCMean * BCMean
+    * ( BA * BA * cosTheta * cosTheta - BA[1] * BA[1] );
+  double delta = b * b - 4 * a * c;
+  if( delta < 0 )
+    {
+    std::cerr << "Failed to solve a 2rd-order equation!" << std::endl;
+    exit( -1 );
+    }
+  else if( sign == 1 || sign == -1 )
+    {
+    BC[2] = -( b - sign * sqrt( delta ) ) / 2. / a;
+    }
+  else
+    {
+    std::cerr << "Bad parameter! sign = 1 or sign = -1 please" << std::endl;
+    exit( -1 );
+    }
+  BC[1] = ( BA.GetNorm() * BCMean.GetNorm()
+            * cosTheta - BA[2] * BC[2] ) / BA[1];
+  return BC;
+}
+
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationDetector.h b/BRAINSConstellationDetector/src/landmarksConstellationDetector.h
new file mode 100644
index 00000000..7ead9693
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationDetector.h
@@ -0,0 +1,320 @@
+/*
+ * Author: Han J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef __landmarksConstellationDetector__h
+#define __landmarksConstellationDetector__h
+
+#include "landmarksConstellationCommon.h"
+#include "landmarksConstellationModelIO.h"
+#include "itkAffineTransform.h"
+#include "itkOtsuThresholdImageFilter.h"
+#include "Slicer3LandmarkIO.h"
+
+#include 
+
+class landmarksConstellationDetector
+{
+  typedef vnl_matrix                           MatrixType;
+  typedef vnl_vector                           VectorType;
+  typedef std::map LandmarksMapType;
+  typedef std::map                 ValMapType;
+public:
+  landmarksConstellationDetector() :
+      m_mspQualityLevel(1),
+      m_HoughEyeFailure(false)
+  {
+    // Build midline landmarks name list
+    this->m_MidlinePointsList.push_back("AC");
+    this->m_MidlinePointsList.push_back("PC");
+    this->m_MidlinePointsList.push_back("RP");
+    this->m_MidlinePointsList.push_back("VN4");
+    this->m_MidlinePointsList.push_back("aq_4V");
+    this->m_MidlinePointsList.push_back("genu");
+    this->m_MidlinePointsList.push_back("rostrum");
+    this->m_MidlinePointsList.push_back("BPons");
+    this->m_MidlinePointsList.push_back("optic_chiasm");
+    this->m_MidlinePointsList.push_back("mid_ant");
+    this->m_MidlinePointsList.push_back("mid_horiz");
+    this->m_MidlinePointsList.push_back("mid_prim");
+    this->m_MidlinePointsList.push_back("mid_prim_inf");
+    this->m_MidlinePointsList.push_back("mid_prim_sup");
+    this->m_MidlinePointsList.push_back("mid_sup");
+  }
+
+  /**
+   * Returns the named point (AC,PC,VN4,RP) in the space of the
+   * original image.
+   *
+   * @author hjohnson (12/14/2008)
+   *
+   * @param NamedPoint
+   *
+   * @return SImageType::PointType
+   */
+  SImageType::PointType GetOriginalSpaceNamedPoint(const std::string & NamedPoint) const
+  {
+    LandmarksMapType::const_iterator itpair = this->m_NamedPoint.find(NamedPoint);
+
+    if( itpair == this->m_NamedPoint.end() )
+      {
+      std::cout << "ERROR:  " << NamedPoint << " not found in list." << std::endl;
+      return SImageType::PointType();
+      }
+    return itpair->second;
+  }
+
+  // Force the setting of the point values to override those that were
+  // specified.
+  void SetOriginalSpaceNamedPoint(const std::string & NamedPoint, const SImageType::PointType & PointValue)
+  {
+    this->m_NamedPoint[NamedPoint] = PointValue;
+    return;
+  }
+
+  const LandmarksMapType & GetNamedPoints()
+  {
+    return this->m_NamedPoint;
+  }
+
+  void SetMSPQualityLevel(const int newLevel)
+  {
+    this->m_mspQualityLevel = newLevel;
+  }
+
+  void SetTemplateRadius(const ValMapType & NewTemplateRadius)
+  {
+    m_TemplateRadius = NewTemplateRadius;
+  }
+
+  void SetVolOrig(SImageType::Pointer image)
+  {
+    m_VolOrig = image;
+  }
+
+  void SetInputTemplateModel(landmarksConstellationModelIO & myModel)
+  {
+    m_InputTemplateModel = myModel;
+  }
+
+  double GetModelHeight(std::string PointName)
+  {
+    return m_InputTemplateModel.GetHeight(PointName);
+  }
+
+  double GetModelRadius(std::string PointName)
+  {
+    return m_InputTemplateModel.GetRadius(PointName);
+  }
+
+  RigidTransformType::Pointer GetTransformToMSP(void) const
+  {
+    RigidTransformType::Pointer value = RigidTransformType::New();
+
+    value->SetFixedParameters( this->m_finalTmsp->GetFixedParameters() );
+    value->SetParameters( this->m_finalTmsp->GetParameters() );
+    return value;
+  }
+
+  SImageType::PointType GetCenterOfHeadMassMSP(void) const
+  {
+    return this->m_CenterOfHeadMassEMSP;
+  }
+
+  void SetResultsDir(std::string resultsDir)
+  {
+    this->m_ResultsDir = resultsDir;
+  }
+
+  void SetHoughEyeTransform(VersorTransformType::Pointer houghEyeTransform)
+  {
+    this->m_HoughEyeTransform = houghEyeTransform;
+  }
+
+  void SetHoughEyeFailure(bool failure)
+  {
+    m_HoughEyeFailure = failure;
+  }
+
+  void SetLEPoint(const SImageType::PointType & LEPoint)
+  {
+    this->m_LEPoint = LEPoint;
+  }
+
+  const SImageType::PointType & GetLEPoint() const
+  {
+    return this->m_LEPoint;
+  }
+
+  void SetREPoint(const SImageType::PointType & REPoint)
+  {
+    this->m_REPoint = REPoint;
+  }
+
+  const SImageType::PointType & GetREPoint() const
+  {
+    return this->m_REPoint;
+  }
+
+  void SetCenterOfHeadMass(const SImageType::PointType & centerOfHeadMass)
+  {
+    m_CenterOfHeadMass = centerOfHeadMass;
+  }
+
+  void SetLlsMeans(std::map > & llsMeans)
+  {
+    this->m_LlsMeans = llsMeans;
+  }
+
+  void SetLlsMatrices(std::map & llsMatrices)
+  {
+    this->m_LlsMatrices = llsMatrices;
+  }
+
+  /** Set search radii for corresponding landmarks **/
+  void SetSearchRadii(const std::map & radii)
+  {
+    this->m_SearchRadii = radii;
+  }
+
+  void SetLandmarksEMSP(LandmarksMapType landmarks)
+  {
+    m_NamedPointEMSP.clear();
+    m_NamedPointEMSP.insert( landmarks.begin(), landmarks.end() );
+  }
+
+  void Compute(void);
+
+  SImageType::Pointer GetTaggedImage(void) const
+  {
+    itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New();
+    duplicator->SetInputImage(this->m_VolOrig);
+    duplicator->Update();
+    SImageType::Pointer taggedImage = duplicator->GetOutput();
+
+    SImageType::PixelType low, high;
+    setLowHigh(taggedImage, low, high, 0.01F);
+
+    SImageType::IndexType PTIndex;
+    taggedImage->TransformPhysicalPointToIndex(this->GetOriginalSpaceNamedPoint("AC"), PTIndex);
+    taggedImage->SetPixel(PTIndex, high);
+    taggedImage->TransformPhysicalPointToIndex(this->GetOriginalSpaceNamedPoint("PC"), PTIndex);
+    taggedImage->SetPixel(PTIndex, high);
+    taggedImage->TransformPhysicalPointToIndex(this->GetOriginalSpaceNamedPoint("VN4"), PTIndex);
+    taggedImage->SetPixel(PTIndex, high);
+    taggedImage->TransformPhysicalPointToIndex(this->GetOriginalSpaceNamedPoint("RP"), PTIndex);
+    taggedImage->SetPixel(PTIndex, high);
+    return taggedImage;
+  }
+
+  RigidTransformType::Pointer GetACPCAlignedZeroCenteredTransform(void) const
+  {
+    SImageType::PointType ZeroCenter;
+
+    ZeroCenter.Fill(0.0);
+    RigidTransformType::Pointer
+      landmarkDefinedACPCAlignedToZeroTransform =
+      computeTmspFromPoints(this->GetOriginalSpaceNamedPoint("RP"),
+                            this->GetOriginalSpaceNamedPoint("AC"),
+                            this->GetOriginalSpaceNamedPoint("PC"),
+                            ZeroCenter);
+    return landmarkDefinedACPCAlignedToZeroTransform;
+  }
+
+  SImageType::Pointer GetVolumeMSP()
+  {
+    return this->m_VolumeMSP;
+  }
+
+private:
+
+  // Linear model estimation using EPCA
+  void LinearEstimation( LandmarksMapType & namedPoints, const std::vector & processingList,
+                         unsigned int numBasePoints );
+
+  /*
+   * Mainly designed for estimating the search center of
+   * 4VN, ac, pc points in a morphometric way.
+   *
+   * Solve 2rd-order equations for BC.
+   * Given:
+   * BC.GetNorm() = BCMean.GetNorm();
+   * angle(ABC) = angle(ABCMean);
+   * BA[0] = BC[0] = 0.
+   *
+   * Then, we have
+   * BA * BC = BA.GetNorm() * BC.GetNorm() * cosTheta;
+   * Rearrange to solve a*BC[2]^2 + b*BC[2] + c = 0
+   */
+  SImageType::PointType::VectorType FindVectorFromPointAndVectors(SImageType::PointType::VectorType BA,
+                                                                  SImageType::PointType::VectorType BAMean,
+                                                                  SImageType::PointType::VectorType BCMean,
+                                                                  int sign);
+
+  SImageType::PointType FindCandidatePoints(
+    SImageType::Pointer volumeMSP, SImageType::Pointer mask_LR, const double LR_restrictions,
+    const double PA_restrictions,
+    const double SI_restrictions,
+    // TODO: restrictions should really be ellipsoidal values
+    const SImageType::PointType::VectorType & CenterOfSearchArea,
+    const std::vector > & TemplateMean,
+    const landmarksConstellationModelIO::IndexLocationVectorType & model, const bool ComputeOutsideSearchRadius,
+    double & cc_Max, const std::string & mapID);
+
+private:
+  RigidTransformType::Pointer   m_TmspBasedOnReflectionCrossCorrelation;
+  SImageType::PointType         m_CenterOfHeadMassEMSP;
+  SImageType::PointType         m_BestCenter;
+  SImageType::Pointer           m_VolOrig;
+  SImageType::Pointer           m_VolumeMSP;
+  landmarksConstellationModelIO m_InputTemplateModel;
+  ValMapType                    m_TemplateRadius;
+  int                           m_mspQualityLevel;
+  std::string                   m_ResultsDir;
+
+  LandmarksMapType m_NamedPoint;                  // named points in the
+                                                  // original space
+                                                  // even before the Hough eye
+                                                  // detector
+  LandmarksMapType m_NamedPointEMSP;              // named points in EMSP space
+  LandmarksMapType m_NamedPointACPC;              // named points in
+                                                  // ACPC-aligned space
+  LandmarksMapType m_NamedPointACPCRaw;           // reserve this map to avoid
+                                                  // the
+                                                  // accumulation of local
+                                                  // search
+                                                  // errors
+  std::vector m_MidlinePointsList;   // name list of the landmarks
+                                                  // that
+                                                  // should be treated as
+                                                  // midline landmarks
+
+  RigidTransformType::Pointer  m_finalTmsp;
+  VersorTransformType::Pointer m_VersorTransform;
+  VersorTransformType::Pointer m_InvVersorTransform;
+
+  // Wei: Read in LE, RE value for linear model estimation
+  VersorTransformType::Pointer m_HoughEyeTransform;
+  bool                         m_HoughEyeFailure;
+  SImageType::PointType        m_LEPoint;    // in input space
+  SImageType::PointType        m_REPoint;
+
+  SImageType::PointType m_ReferencePointAC;
+  SImageType::PointType m_ReferencePointPC;
+  SImageType::PointType m_CenterOfHeadMass;
+
+  // Store linear model parameters
+  // Note each matrix of m_LlsMatrices is actually cascaded by two mapping:
+  // input space -> principal components space, and the coefs minimize their
+  // least squares
+  std::map m_LlsMatrices;              // parameter
+                                                                // matricess
+  std::map > m_LlsMeans;       // means to be
+                                                                // subtracted by
+                                                                // PCA
+  std::map m_SearchRadii;
+};
+
+#endif // __landmarksConstellationDetector__h
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationModelBase.h b/BRAINSConstellationDetector/src/landmarksConstellationModelBase.h
new file mode 100644
index 00000000..1ccd24d8
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationModelBase.h
@@ -0,0 +1,131 @@
+#ifndef _landmarksConstellationModelBase_h
+#define  _landmarksConstellationModelBase_h
+
+class landmarksConstellationModelBase
+{
+protected:
+  typedef std::map ValMapType;
+  typedef ValMapType::const_iterator   ValMapConstIterator;
+  typedef ValMapType::iterator         ValMapIterator;
+public:
+  landmarksConstellationModelBase() : m_NumDataSets(0),
+    m_SearchboxDims(0),
+    m_ResolutionUnits(1.0),
+    m_InitialRotationAngle(0.0),
+    m_InitialRotationStep(0.0),
+    m_NumRotationSteps(0)
+  {
+  }
+
+  virtual ~landmarksConstellationModelBase()
+  {
+  }
+  virtual unsigned int GetNumDataSets() const
+  {
+    return m_NumDataSets;
+  }
+
+  virtual unsigned int GetSearchboxDims() const
+  {
+    return m_SearchboxDims;
+  }
+
+  virtual float GetResolutionUnits() const
+  {
+    return m_ResolutionUnits;
+  }
+
+  virtual const ValMapType & GetRadii() const
+  {
+    return this->m_Radius;
+  }
+
+  virtual float GetRadius(const std::string & PointName) const
+  {
+    ValMapConstIterator it( m_Radius.find(PointName) );
+
+    if( it == m_Radius.end() )
+      {
+      throw;
+      }
+    return it->second;
+  }
+
+  virtual float GetHeight(const std::string & PointName) const
+  {
+    ValMapConstIterator it( m_Height.find(PointName) );
+
+    if( it == m_Height.end() )
+      {
+      throw;
+      }
+    return it->second;
+  }
+
+  virtual void SetRadius(const std::string & PointName, float x)
+  {
+    m_Radius[PointName] = x;
+  }
+
+  virtual void SetHeight(const std::string & PointName, float x)
+  {
+    m_Height[PointName] = x;
+  }
+
+  virtual float GetInitialRotationAngle() const
+  {
+    return m_InitialRotationAngle;
+  }
+
+  virtual float GetInitialRotationStep() const
+  {
+    return m_InitialRotationStep;
+  }
+
+  virtual unsigned int GetNumRotationSteps() const
+  {
+    return m_NumRotationSteps;
+  }
+
+  virtual void SetNumDataSets(unsigned int x)
+  {
+    m_NumDataSets = x;
+  }
+
+  virtual void SetSearchboxDims(unsigned int x)
+  {
+    m_SearchboxDims = x;
+  }
+
+  virtual void SetResolutionUnits(float x)
+  {
+    m_ResolutionUnits = x;
+  }
+
+  virtual void SetInitialRotationAngle(float x)
+  {
+    m_InitialRotationAngle = x;
+  }
+
+  virtual void SetInitialRotationStep(float x)
+  {
+    m_InitialRotationStep = x;
+  }
+
+  virtual void SetNumRotationSteps(unsigned int x)
+  {
+    m_NumRotationSteps = x;
+  }
+
+protected:
+  unsigned int m_NumDataSets;
+  unsigned int m_SearchboxDims;
+  float        m_ResolutionUnits;
+  ValMapType   m_Height;
+  ValMapType   m_Radius;
+  float        m_InitialRotationAngle;
+  float        m_InitialRotationStep;
+  unsigned int m_NumRotationSteps;
+};
+
+#endif // _landmarksConstellationModelBase_h
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationModelIO.h b/BRAINSConstellationDetector/src/landmarksConstellationModelIO.h
new file mode 100644
index 00000000..af063b26
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationModelIO.h
@@ -0,0 +1,771 @@
+/*
+ * Author: Hans J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef landmarksConstellationModelIO_h
+#define landmarksConstellationModelIO_h
+
+#include "landmarksConstellationCommon.h"
+#include "landmarksConstellationTrainingDefinitionIO.h"
+#include "landmarksConstellationModelBase.h"
+
+#include "itkByteSwapper.h"
+#include "itkIO.h"
+
+#include 
+#include 
+#include 
+#include "math.h"
+#include "string.h"
+#include 
+
+inline void
+defineTemplateIndexLocations
+  (const float r,
+  const float h,
+  std::vector & indexLocations)
+{
+  typedef SImageType::PointType::VectorType::ComponentType CoordType;
+
+  // Reserve space that will be needed
+  indexLocations.reserve( static_cast( ( r + 1.0 ) * ( h + 1.0 ) ) );
+
+  const CoordType h_2 = h / 2;
+  const CoordType r2 = r * r;
+  for( CoordType SI = -r; SI <= r; SI += 1.0F )
+    {
+    for( CoordType PA = -r; PA <= r; PA += 1.0F )
+      {
+      for( CoordType LR = -h_2; LR <= h_2; LR += 1.0F )
+        {
+        if( ( LR * LR + PA * PA )  <= r2 )  // a suspicious place
+          {
+          SImageType::PointType::VectorType temp;
+          temp[0] = LR;
+          temp[1] = PA;
+          temp[2] = SI;
+          indexLocations.push_back(temp);
+          }
+        }
+      }
+    }
+}
+
+class landmarksConstellationModelIO : public landmarksConstellationModelBase
+{
+private:
+  typedef landmarksConstellationModelIO Self;
+  typedef enum { readFail, writeFail }  ioErr;
+  typedef enum { file_signature = 0x12345678,
+                 swapped_file_signature = 0x78563412 } fileSig;
+public:
+  typedef std::vector IndexLocationVectorType;
+  typedef std::vector                             FloatVectorType;
+  typedef std::vector                   Float2DVectorType;
+  typedef std::vector                 Float3DVectorType;
+
+  typedef FloatVectorType::iterator       FloatVectorIterator;
+  typedef FloatVectorType::const_iterator ConstFloatVectorIterator;
+
+  typedef Float2DVectorType::iterator       Float2DVectorIterator;
+  typedef Float2DVectorType::const_iterator ConstFloat2DVectorIterator;
+
+  typedef Float3DVectorType::iterator       Float3DVectorIterator;
+  typedef Float3DVectorType::const_iterator ConstFloat3DVectorIterator;
+public:
+
+  landmarksConstellationModelIO()
+  {
+    m_Swapped = false;
+    m_RPPC_to_RPAC_angleMean = 0;
+    m_RPAC_over_RPPCMean = 0;
+  }
+
+  virtual ~landmarksConstellationModelIO()
+  {
+  }
+
+  void SetCMtoRPMean(const SImageType::PointType::VectorType & CMtoRPMean)
+  {
+    this->m_CMtoRPMean = CMtoRPMean;
+  }
+
+  void SetRPtoXMean(std::string name, const SImageType::PointType::VectorType & RPtoXMean)
+  {
+    this->m_RPtoXMean[name] = RPtoXMean;
+  }
+
+  void SetRPtoCECMean(const SImageType::PointType::VectorType & RPtoCECMean)
+  {
+    this->m_RPtoCECMean = RPtoCECMean;
+  }
+
+  void SetRPPC_to_RPAC_angleMean(float RPPC_to_RPAC_angleMean)
+  {
+    this->m_RPPC_to_RPAC_angleMean = RPPC_to_RPAC_angleMean;
+  }
+
+  void SetRPAC_over_RPPCMean(float RPAC_over_RPPCMean)
+  {
+    this->m_RPAC_over_RPPCMean = RPAC_over_RPPCMean;
+  }
+
+  const SImageType::PointType::VectorType & GetCMtoRPMean() const
+  {
+    return this->m_CMtoRPMean;
+  }
+
+  const SImageType::PointType::VectorType & GetRPtoXMean(std::string name)
+  {
+    return this->m_RPtoXMean[name];
+  }
+
+  const SImageType::PointType::VectorType & GetRPtoCECMean() const
+  {
+    return this->m_RPtoCECMean;
+  }
+
+  float GetRPPC_to_RPAC_angleMean() const
+  {
+    return this->m_RPPC_to_RPAC_angleMean;
+  }
+
+  float GetRPAC_over_RPPCMean() const
+  {
+    return this->m_RPAC_over_RPPCMean;
+  }
+
+  /**
+   * Creates a mean for each of the angles by collapsing the image
+   * dimensions.
+   *
+   * @author hjohnson (9/6/2008)
+   *
+   * @param output
+   * @param input
+   */
+  void ComputeAllMeans(Float2DVectorType & output, const Float3DVectorType & input)
+  {
+    // First allocate the output mememory
+    output.resize( input[0].size() );
+    for( unsigned int q = 0; q < output.size(); q++ )
+      {
+      output[q].resize( input[0][0].size() );
+      for( FloatVectorIterator oit = output[q].begin(); oit != output[q].end(); ++oit )
+        {
+        *oit = 0;
+        }
+      }
+    for( ConstFloat3DVectorIterator curr_dataset = input.begin(); curr_dataset != input.end(); ++curr_dataset )
+      {
+      ConstFloat2DVectorIterator input_angleit = curr_dataset->begin();
+      Float2DVectorIterator      output_angleit = output.begin();
+      while( input_angleit != curr_dataset->end() && output_angleit != output.end() )
+        {
+        ConstFloatVectorIterator init = input_angleit->begin();
+        FloatVectorIterator      outit = output_angleit->begin();
+        while( init != input_angleit->end() && outit != output_angleit->end() )
+          {
+          *outit += *init;
+          ++outit;
+          ++init;
+          }
+
+        ++input_angleit;
+        ++output_angleit;
+        }
+      }
+    // Now divide by number of data sets
+    const float inv_size = 1.0 / input.size();
+    for( unsigned int q = 0; q < output.size(); q++ )
+      {
+      for( FloatVectorIterator oit = output[q].begin(); oit != output[q].end(); ++oit )
+        {
+        *oit *= inv_size;
+        }
+      }
+  }
+
+  // Access the internal memory locations for modification.
+  FloatVectorType & AccessTemplate(std::string name, const unsigned int indexDataSet, const unsigned int indexAngle)
+  {
+    if( this->m_Templates.find(name) == this->m_Templates.end() )
+      {
+      std::cerr << "Attempt to access an undifined landmark template for " << name << "! Abort." << std::endl;
+      exit(-1);
+      }
+    return this->m_Templates[name][indexDataSet][indexAngle];
+  }
+
+  // Access the mean vectors of templates
+  const FloatVectorType & AccessTemplateMean(std::string name, const unsigned int indexAngle)
+  {
+    if( this->m_TemplateMeansComputed.find(name) == this->m_TemplateMeansComputed.end()
+        || this->m_Templates.find(name) == this->m_Templates.end() )
+      {
+      std::cerr << "Attempt to access an undifined landmark template (mean)! Abort." << std::endl;
+      exit(-1);
+      }
+    ComputeAllMeans(this->m_TemplateMeans[name], this->m_Templates[name]);
+    return this->m_TemplateMeans[name][indexAngle];
+  }
+
+  const Float2DVectorType & AccessAllTemplateMeans(std::string name)
+  {
+    if( this->m_TemplateMeansComputed.find(name) == this->m_TemplateMeansComputed.end()
+        && this->m_Templates.find(name) == this->m_Templates.end() )
+      {
+      std::cerr << "Attempt to access an undefined landmark template (mean)! Abort." << std::endl;
+      exit(-1);
+      }
+    ComputeAllMeans(this->m_TemplateMeans[name], this->m_Templates[name]);
+    return this->m_TemplateMeans[name];
+  }
+
+  const Float2DVectorType & GetTemplateMeans(const std::string& name)
+  {
+    return this->m_TemplateMeans[name];
+  }
+
+  void WriteModelFile(const std::string & filename)
+  {
+    //
+    //
+    // //////////////////////////////////////////////////////////////////////////
+
+    std::ofstream output( filename.c_str() ); // open setup file for reading
+
+    if( !output.is_open() )
+      {
+      std::cerr << "Can't write " << filename << std::endl;
+      std::cerr.flush();
+      }
+    try
+      {
+      this->Write(output, file_signature);   // Write out the
+                                                           // signature first
+
+      /*
+       * WEI: As the new model deals with arbitrary landmarks, we need to
+       * write the landmark names to the model file in order to
+       * differentiate for example the search radius of each landmark.
+       * That means ofstream::write() alone is not sufficient for reading
+       * landmark names with variable length.
+       */
+      this->Write(output, '\n');
+
+      std::map::const_iterator it2;
+      for( it2 = this->m_TemplateMeansComputed.begin();
+           it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+        {
+        output << it2->first.c_str() << std::endl;
+        output << this->GetRadius(it2->first) << std::endl;
+        output << this->GetHeight(it2->first) << std::endl;
+        }
+      output << "END" << std::endl;
+
+      this->Write( output, this->GetSearchboxDims() );
+      this->Write( output, this->GetResolutionUnits() );
+      this->Write( output, this->GetNumDataSets() );
+      this->Write( output, this->GetNumRotationSteps() );
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&output, "before vectors", -1);
+#endif
+      for( it2 = this->m_TemplateMeansComputed.begin();
+           it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+        {
+        ComputeAllMeans(this->m_TemplateMeans[it2->first],
+                        this->m_Templates[it2->first]);
+        this->Write(output, this->m_TemplateMeans[it2->first]);
+        this->WritedebugMeanImages(it2->first);
+        }
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&output, "after vectors", -1);
+#endif
+
+      // We only need those RPtoXMeans
+      this->Write(output, this->m_RPtoXMean["PC"][0]);
+      this->Write(output, this->m_RPtoXMean["PC"][1]);
+      this->Write(output, this->m_RPtoXMean["PC"][2]);
+      this->Write(output, this->m_CMtoRPMean[0]);
+      this->Write(output, this->m_CMtoRPMean[1]);
+      this->Write(output, this->m_CMtoRPMean[2]);
+      this->Write(output, this->m_RPtoXMean["VN4"][0]);
+      this->Write(output, this->m_RPtoXMean["VN4"][1]);
+      this->Write(output, this->m_RPtoXMean["VN4"][2]);
+      this->Write(output, this->m_RPtoCECMean[0]);
+      this->Write(output, this->m_RPtoCECMean[1]);
+      this->Write(output, this->m_RPtoCECMean[2]);
+      this->Write(output, this->m_RPtoXMean["AC"][0]);
+      this->Write(output, this->m_RPtoXMean["AC"][1]);
+      this->Write(output, this->m_RPtoXMean["AC"][2]);
+      this->Write(output, this->m_RPPC_to_RPAC_angleMean);
+      this->Write(output, this->m_RPAC_over_RPPCMean);
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&output, "end of file", -1);
+#endif
+      }
+    catch( ioErr e )
+      {
+      std::cerr << "Write failed for " << filename << std::endl;
+      }
+    output.close();
+  }
+
+  void PrintHeaderInfo(void)
+  {
+    //
+    //
+    // //////////////////////////////////////////////////////////////////////////
+    std::cout << "SearchboxDims"    << ": " << this->GetSearchboxDims() << std::endl;
+    std::cout << "ResolutionUnits"  << ": " << this->GetResolutionUnits() << std::endl;
+    std::cout << "NumDataSets"      << ": " << this->GetNumDataSets() << std::endl;
+    std::cout << "NumRotationSteps" << ": " << this->GetNumRotationSteps() << std::endl;
+
+    std::map::const_iterator it2;
+    for( it2 = this->m_TemplateMeansComputed.begin();
+         it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+      {
+      std::cout << it2->first << "Radius: " << this->GetRadius(it2->first) << std::endl;
+      std::cout << it2->first << "Height: " << this->GetHeight(it2->first) << std::endl;
+      }
+
+    std::cout << "CMtoRPMean: " << this->m_CMtoRPMean << std::endl;
+    std::cout << "RPtoECEMean: " << this->m_RPtoCECMean << std::endl;
+    std::cout << "RPtoACMean: " << this->m_RPtoXMean["AC"] << std::endl;
+    std::cout << "RPtoPCMean: " << this->m_RPtoXMean["PC"] << std::endl;
+    std::cout << "RPtoVN4Mean: " << this->m_RPtoXMean["VN4"] << std::endl;
+    std::cout << "RPPC_to_RPAC_angleMean: " << this->m_RPPC_to_RPAC_angleMean << std::endl;
+    std::cout << "RPAC_over_RPPCMean: " << this->m_RPAC_over_RPPCMean << std::endl;
+  }
+
+  void ReadModelFile(const std::string & filename)
+  {
+    //
+    //
+    // //////////////////////////////////////////////////////////////////////////
+
+    std::ifstream input( filename.c_str() ); // open setup file for reading
+
+    if( !input.is_open() )
+      {
+      std::cerr << "Can't read " << filename << std::endl;
+      std::cerr.flush();
+      exit(-1);
+      }
+    try
+      {
+      unsigned int sig = 0;
+      this->Read(input, sig);
+      if( sig != file_signature && sig != swapped_file_signature )
+        {
+        this->m_Swapped = false;
+        }
+      else if( sig == swapped_file_signature )
+        {
+        this->m_Swapped = true;
+        }
+
+      /*
+       * WEI: As the new model deals with arbitrary landmarks, we need to
+       * write the landmark names to the model file in order to
+       * differentiate for example the search radius of each landmark.
+       * That means ofstream::write() alone is not sufficient for reading
+       * landmark names with variable length.
+       */
+      std::string name;
+      input >> name;
+      while( name.compare("END") != 0 )
+        {
+        input >> this->m_Radius[name];
+        input >> this->m_Height[name];
+        this->m_TemplateMeansComputed[name] = false;
+        input >> name;
+        }
+
+        {
+        char tmp = '\0';
+        this->Read(input, tmp);
+        }
+
+      this->Read(input, this->m_SearchboxDims);
+      this->Read(input, this->m_ResolutionUnits);
+      this->Read(input, this->m_NumDataSets);
+      this->Read(input, this->m_NumRotationSteps);
+
+      // initalize the size of m_VectorIndexLocations and m_TemplateMeans
+      InitializeModel(false);
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&input, "before vectors", -1);
+#endif
+
+        {
+        std::map::const_iterator it2;
+        for( it2 = this->m_TemplateMeansComputed.begin();
+             it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+          {
+          this->Read(input, this->m_TemplateMeans[it2->first]);
+          this->m_TemplateMeansComputed[it2->first] = true;
+          }
+        }
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&input, "after vectors", -1);
+#endif
+
+      this->Read(input, this->m_RPtoXMean["PC"][0]);
+      this->Read(input, this->m_RPtoXMean["PC"][1]);
+      this->Read(input, this->m_RPtoXMean["PC"][2]);
+      this->Read(input, this->m_CMtoRPMean[0]);
+      this->Read(input, this->m_CMtoRPMean[1]);
+      this->Read(input, this->m_CMtoRPMean[2]);
+      this->Read(input, this->m_RPtoXMean["VN4"][0]);
+      this->Read(input, this->m_RPtoXMean["VN4"][1]);
+      this->Read(input, this->m_RPtoXMean["VN4"][2]);
+      this->Read(input, this->m_RPtoCECMean[0]);
+      this->Read(input, this->m_RPtoCECMean[1]);
+      this->Read(input, this->m_RPtoCECMean[2]);
+      this->Read(input, this->m_RPtoXMean["AC"][0]);
+      this->Read(input, this->m_RPtoXMean["AC"][1]);
+      this->Read(input, this->m_RPtoXMean["AC"][2]);
+      this->Read(input, this->m_RPPC_to_RPAC_angleMean);
+      this->Read(input, this->m_RPAC_over_RPPCMean);
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&input, "end of file", -1);
+#endif
+      }
+    catch( ioErr e )
+      {
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+      this->debugOffset(&input, "end of file", -1);
+#endif
+      std::cerr << "Read failed for " << filename << std::endl;
+      std::cerr << e << std::endl;
+      exit(-1);
+      }
+    input.close();
+  }
+
+  class debugImageDescriptor
+  {
+public:
+    Float2DVectorType &     mean;
+    IndexLocationVectorType locations;
+    float                   r;
+    float                   h;
+    const char *            debugImageName;
+
+    debugImageDescriptor(Float2DVectorType & _mean, float _r, float _h, const char *_debugImageName) :
+      mean(_mean), r(_r), h(_h), debugImageName(_debugImageName)
+    {
+      defineTemplateIndexLocations(_r, _h, this->locations);
+    }
+
+  };
+
+  void WritedebugMeanImages(std::string name)
+  {
+    debugImageDescriptor DID(this->m_TemplateMeans[name],
+                             this->GetRadius(name),
+                             this->GetHeight(name),
+                             "");
+
+    Float2DVectorType::iterator meanIt = DID.mean.begin();
+    for( int j = 0; meanIt != DID.mean.end(); ++meanIt, j++ )
+      {
+      typedef itk::Image        FloatImageType;
+      typedef FloatImageType::RegionType  FloatImageRegion;
+      typedef FloatImageType::SpacingType FloatImageSpacing;
+      FloatImageSpacing spacing;
+      spacing[0] = spacing[1] = spacing[2] = 1.0;
+      FloatImageRegion region;
+      region.SetSize
+        ( 0, static_cast( DID.h + 1 ) );
+      region.SetSize
+        (1, static_cast( 2.0 * DID.r ) + 1);
+      region.SetSize
+        (2, static_cast( 2.0 * DID.r ) + 1);
+      FloatImageRegion::IndexType _index;
+      _index[0] = _index[1] = _index[2] = 0;
+      region.SetIndex(_index);
+      FloatImageType::Pointer debugImage = FloatImageType::New();
+      debugImage->SetSpacing(spacing);
+      // Just use defaults debugImage->SetOrigin(in->GetOrigin());
+      // Just use defaults debugImage->SetDirection(in->GetDirection());
+      debugImage->SetRegions(region);
+      debugImage->Allocate();
+      debugImage->FillBuffer(0.0);
+      float center[3];
+
+      center[0] = ( DID.h + 1 ) / 2.0;
+      center[1] =
+        center[2] = ( DID.r + 0.5 );
+
+      IndexLocationVectorType::iterator locIt = DID.locations.begin();
+      FloatVectorType::iterator         floatIt = ( *meanIt ).begin();
+      for( ; locIt != DID.locations.end(); ++floatIt, ++locIt )
+        {
+        FloatImageType::IndexType ind;
+        for( unsigned k = 0; k < 3; k++ )
+          {
+          ind[k] = static_cast( center[k] + ( *locIt )[k] );
+          }
+        //          std::cerr << ind<< std::endl;
+        debugImage->SetPixel( ind, ( *floatIt ) );
+        }
+      char buf[512];
+      sprintf( buf, "%d%s", j, name.c_str() );
+      std::string fname(buf);
+      fname += "Mean.nii.gz";
+      itkUtil::WriteImage(debugImage, fname);
+      }
+  }
+
+  void InitializeModel(bool CreatingModel)
+  {
+    //
+    //
+    // ///////////////////////////////////////////////////////////////////////////////
+    // NOTE:  THIS IS NOW AT FULL RESOLUTION, but there was an optimization that
+    // had reduced
+    //       the resolution in the IS/RP direction to gain some speed
+    // efficiency.
+    std::map::const_iterator it2;
+    for( it2 = this->m_TemplateMeansComputed.begin(); it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+      {
+      defineTemplateIndexLocations(this->GetRadius(it2->first), this->GetHeight(it2->first),
+                                   this->m_VectorIndexLocations[it2->first]);
+      printf( "%s template size = %d voxels\n", it2->first.c_str(),
+              static_cast( this->m_VectorIndexLocations[it2->first].size() ) );
+      if( CreatingModel )
+        {
+        // Allocate the outter dim for all datasets
+        this->m_Templates[it2->first].resize( this->GetNumDataSets() );
+        for( unsigned int currdataset = 0; currdataset < this->GetNumDataSets(); ++currdataset )
+          {
+          // Allocate for number of angles
+          this->m_Templates[it2->first][currdataset].resize( this->GetNumRotationSteps() );
+          for( unsigned int currrotstep = 0; currrotstep < this->GetNumRotationSteps(); ++currrotstep )
+            {
+            // Allocate for number of intensity values
+            this->m_Templates[it2->first][currdataset][currrotstep].resize
+              ( this->m_VectorIndexLocations[it2->first].size() );
+            }
+          }
+        }
+      else // make room for reading in template means result
+        {
+        this->m_TemplateMeans[it2->first].resize( this->GetNumRotationSteps() );
+        for( unsigned i = 0; i < this->GetNumRotationSteps(); ++i )
+          {
+          this->m_TemplateMeans[it2->first][i].resize
+            ( this->m_VectorIndexLocations[it2->first].size() );
+          }
+        }
+      }
+  }
+
+  void CopyFromModelDefinition(const landmarksConstellationTrainingDefinitionIO & mDef)
+  {
+    this->SetNumDataSets( mDef.GetNumDataSets() );
+    this->SetSearchboxDims( mDef.GetSearchboxDims() );
+    this->SetResolutionUnits( mDef.GetResolutionUnits() );
+    this->SetInitialRotationAngle( mDef.GetInitialRotationAngle() );
+    this->SetInitialRotationStep( mDef.GetInitialRotationStep() );
+    this->SetNumRotationSteps( mDef.GetNumRotationSteps() );
+
+      {
+      ValMapConstIterator it2;
+      for( it2 = mDef.GetRadii().begin(); it2 != mDef.GetRadii().end(); ++it2 )
+        {
+        this->SetRadius(it2->first, it2->second);
+        this->SetHeight( it2->first, mDef.GetHeight(it2->first) );
+        this->m_TemplateMeansComputed[it2->first] = false;
+        }
+      }
+  }
+
+  bool NE(double const a, double const b)
+  {
+    if( ( a < 0.0 && b >= 0.0 )
+        || ( b < 0.0 && a >= 0.0 ) )
+      {
+      return true;
+      }
+    double absa( fabs(a) ),
+    absb( fabs(b) );
+    double absdiff( fabs(absa - absb) );
+    double avg( ( absa + absb ) / 2.0 );
+    if( absdiff > ( avg / 1000.0 ) )
+      {
+      return true;
+      }
+    return false;
+  }
+
+  bool NE(const std::string & label,
+          const Float2DVectorType & a,
+          const Float2DVectorType & b)
+  {
+    for( unsigned i = 0; i < a.size(); i++ )
+      {
+      for( unsigned j = 0; j < a[i].size(); j++ )
+        {
+        if( NE(a[i][j], b[i][j]) )
+          {
+          std::cerr << label << " a[" << i
+                    << "] = " << a[i][j]
+                    << "b[" << j << "] = "
+                    << b[i][j] << std::endl;
+          return true;
+          }
+        }
+      }
+    return false;
+  }
+
+  bool operator==(Self & other)
+  {
+    if( ( NE(this->m_SearchboxDims, other.m_SearchboxDims) )
+        || ( NE(this->m_ResolutionUnits, other.m_ResolutionUnits) )
+        || ( NE(this->m_NumDataSets, other.m_NumDataSets) )
+        || ( NE(this->m_NumRotationSteps, other.m_NumRotationSteps) )
+        || ( NE(this->m_RPPC_to_RPAC_angleMean, other.m_RPPC_to_RPAC_angleMean) )
+        || ( NE(this->m_RPAC_over_RPPCMean, other.m_RPAC_over_RPPCMean) )
+        || ( NE(this->m_CMtoRPMean[0], other.m_CMtoRPMean[0]) )
+        || ( NE(this->m_CMtoRPMean[1], other.m_CMtoRPMean[1]) )
+        || ( NE(this->m_CMtoRPMean[2], other.m_CMtoRPMean[2]) ) )
+      {
+      return false;
+      }
+
+    std::map::const_iterator it2;
+    for( it2 = this->m_TemplateMeansComputed.begin(); it2 != this->m_TemplateMeansComputed.end(); ++it2 )
+      {
+      if( ( NE( this->GetRadius(it2->first), other.GetRadius(it2->first) ) )
+          || ( NE( this->GetHeight(it2->first), other.GetHeight(it2->first) ) )
+          || ( NE(it2->first + " template mean",
+                  this->m_TemplateMeans[it2->first], other.m_TemplateMeans[it2->first]) ) )
+        {
+        return false;
+        }
+      }
+
+    if( ( NE(this->m_RPtoXMean["AC"][0], other.m_RPtoXMean["AC"][0]) )
+        || ( NE(this->m_RPtoXMean["AC"][1], other.m_RPtoXMean["AC"][1]) )
+        || ( NE(this->m_RPtoXMean["PC"][0], other.m_RPtoXMean["PC"][0]) )
+        || ( NE(this->m_RPtoXMean["PC"][1], other.m_RPtoXMean["PC"][1]) )
+        || ( NE(this->m_RPtoXMean["VN4"][0], other.m_RPtoXMean["VN4"][0]) )
+        || ( NE(this->m_RPtoXMean["VN4"][1], other.m_RPtoXMean["VN4"][1]) ) )
+      {
+      return false;
+      }
+
+    return true;
+  }
+
+  // HACK:  Kent please wrap these in member variables
+  std::map m_VectorIndexLocations;
+private:
+  bool m_Swapped;
+
+  template 
+  void Write(std::ofstream & f, T var)
+  {
+    if( f.bad() || f.eof() )
+      {
+      throw writeFail;
+      }
+    f.write( reinterpret_cast( &var ), sizeof( T ) );
+  }
+
+  template 
+  void Read(std::ifstream & f, T & var)
+  {
+    if( f.bad() || f.eof() )
+      {
+      throw readFail;
+      }
+    f.read( reinterpret_cast( &var ), sizeof( T ) );
+    if( this->m_Swapped )
+      {
+      if( itk::ByteSwapper::SystemIsBigEndian() )
+        {
+        itk::ByteSwapper::SwapFromSystemToLittleEndian(&var);
+        }
+      else
+        {
+        itk::ByteSwapper::SwapFromSystemToBigEndian(&var);
+        }
+      }
+  }
+
+  void Write(std::ofstream & f, const Float2DVectorType & vec)
+  {
+    for( ConstFloat2DVectorIterator it1 = vec.begin();
+         it1 != vec.end(); ++it1 )
+      {
+      for( ConstFloatVectorIterator it2 = it1->begin();
+           it2 != it1->end(); ++it2 )
+        {
+        this->Write(f, *it2);
+        }
+      }
+  }
+
+  void Read(std::ifstream & f, Float2DVectorType & vec)
+  {
+    for( Float2DVectorIterator it1 = vec.begin();
+         it1 != vec.end(); ++it1 )
+      {
+      for( FloatVectorIterator it2 = it1->begin();
+           it2 != it1->end(); ++it2 )
+        {
+        this->Read(f, *it2);
+        }
+      }
+  }
+
+#ifdef __USE_OFFSET_DEBUGGING_CODE__
+  void debugOffset(std::ifstream *f, const std::string & msg, long int x)
+  {
+    std::ostream::pos_type offset(-1);
+
+    offset = f->tellg();
+    std::cerr << msg << " " << x << " offset " << offset << std::endl;
+    std::cerr.flush();
+  }
+
+  void debugOffset(std::ofstream *f, const std::string & msg, long int x)
+  {
+    std::ostream::pos_type offset(-1);
+
+    offset = f->tellp();
+    std::cerr << msg << " " << x << " offset " << offset << std::endl;
+    std::cerr.flush();
+  }
+
+#endif
+  // The templates are arrays of data sets, arrayed by number of angles, and a
+  // vector of model intensity values.
+  std::map m_Templates;
+  std::map m_TemplateMeans;
+  std::map              m_TemplateMeansComputed;
+  std::map m_RPtoXMean;
+
+  SImageType::PointType::VectorType m_RPtoCECMean;           // CEC is a little
+                                                             // different
+  SImageType::PointType::VectorType m_CMtoRPMean;
+  float                             m_RPPC_to_RPAC_angleMean;
+  float                             m_RPAC_over_RPPCMean;
+};
+
+#endif // landmarksConstellationModelIO_h
diff --git a/BRAINSConstellationDetector/src/landmarksConstellationTrainingDefinitionIO.h b/BRAINSConstellationDetector/src/landmarksConstellationTrainingDefinitionIO.h
new file mode 100644
index 00000000..a6329053
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksConstellationTrainingDefinitionIO.h
@@ -0,0 +1,160 @@
+/*
+ * Author: Hans J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef landmarksConstellationTrainingDefinitionIO_h
+#define landmarksConstellationTrainingDefinitionIO_h
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "landmarksDataSet.h"
+#include "landmarksConstellationModelBase.h"
+
+// HACK:  Remove the multiple inheritance here.
+class landmarksConstellationTrainingDefinitionIO : public landmarksConstellationModelBase,
+  public std::vector   // This should be a private member
+                                         // variable
+{
+private:
+  typedef enum { eof, bad } err_flags;
+public:
+  landmarksConstellationTrainingDefinitionIO()
+  {
+  }
+
+  landmarksConstellationTrainingDefinitionIO(const std::string & filename)
+  {
+    this->ReadFile(filename);
+  }
+
+  const ValMapType & GetRadii() const
+  {
+    return landmarksConstellationModelBase::GetRadii();
+  }
+
+  template 
+  void Read(std::ifstream & s, type & var)
+  {
+    if( s.bad() )
+      {
+      throw bad;
+      }
+    if( s.eof() )
+      {
+      throw eof;
+      }
+    s >> var;
+  }
+
+  int ReadFile(const std::string & filename)
+  {
+    std::ifstream input( filename.c_str() );
+
+    if( input.bad() )
+      {
+      return -1;
+      }
+    try
+      {
+      this->Read(input, this->m_NumDataSets);
+      // Note, more than 2 datasets are needed in order to get valid sample
+      // means and variances.
+      if( m_NumDataSets < 2 )
+        {
+        std::cerr << "NumberOfDatasets must be greater than 2" << std::endl;
+        exit(-1);
+        }
+      this->Read(input, this->m_SearchboxDims);
+      if( m_SearchboxDims % 2 == 0 )
+        {
+        std::cerr << "SearchBoxDims must be odd" << std::endl;
+        exit(-1);
+        }
+      this->Read(input, this->m_ResolutionUnits);
+      if( m_ResolutionUnits <= 0 )
+        {
+        std::cerr << "m_ResolutionUnits must be greater than zero" << std::endl;
+        exit(-1);
+        }
+      this->Read(input, this->m_InitialRotationAngle);
+      this->Read(input, this->m_InitialRotationStep);
+      this->Read(input, this->m_NumRotationSteps);
+
+      // Read in template size for each landmark
+      std::string name;
+      float       val = 0;
+      this->Read(input, name);
+
+      while( name.compare("END") != 0 )
+        {
+        this->Read(input, val);
+        this->m_Radius[name] = val;
+        this->Read(input, val);
+        this->m_Height[name] = val;
+        this->Read(input, name);
+        }
+      // Read in landmarks
+      for( unsigned int i = 0; i < this->m_NumDataSets; i++ )
+        {
+        std::string TrainingImageFilename;
+        this->Read(input, TrainingImageFilename);
+
+        std::string LandmarksFilename;
+        this->Read(input, LandmarksFilename);
+
+        landmarksDataSet DataSet(TrainingImageFilename, LandmarksFilename);
+        this->push_back(DataSet);
+
+        std::string Finished;
+        this->Read(input, Finished);
+        // This separator line says 'END'
+        }
+      input.close();
+      }
+    catch( err_flags f )
+      {
+      std::cerr << "File read error "
+                << ( f == eof ?
+           "unexpected end of file" :
+           "file read error" )
+      << std::endl;
+      std::cerr.flush();
+      input.close();
+      return -1;
+      }
+    return 0;
+  }
+
+private:
+};
+
+inline
+std::ostream & operator<<(std::ostream & os, const landmarksConstellationTrainingDefinitionIO & def)
+{
+  os << def.GetNumDataSets() << std::endl;
+  os << def.GetSearchboxDims() << " "
+  << def.GetResolutionUnits() << std::endl;
+  os << def.GetRadius("RP") << " "
+  << def.GetHeight("RP") << std::endl;
+  os << def.GetRadius("AC") << " "
+  << def.GetHeight("AC") << std::endl;
+  os << def.GetRadius("PC") << " "
+  << def.GetHeight("PC") << std::endl;
+  os << def.GetRadius("VN4") << " "
+  << def.GetHeight("VN4") << std::endl;
+  os << def.GetInitialRotationAngle() << " "
+  << def.GetInitialRotationStep() << " "
+  << def.GetNumRotationSteps() << std::endl << std::endl;
+  for( unsigned int i = 0; i < def.GetNumDataSets(); i++ )
+    {
+    os << def[i] << std::endl;
+    }
+  return os;
+}
+
+#endif // landmarksConstellationTrainingDefinitionIO_h
diff --git a/BRAINSConstellationDetector/src/landmarksDataSet.h b/BRAINSConstellationDetector/src/landmarksDataSet.h
new file mode 100644
index 00000000..a6fff38e
--- /dev/null
+++ b/BRAINSConstellationDetector/src/landmarksDataSet.h
@@ -0,0 +1,166 @@
+/*
+ * Author: Hans J. Johnson, Wei Lu
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2010
+ */
+
+#ifndef _landmarksDataSet_h
+#define _landmarksDataSet_h
+#include 
+#include 
+#include 
+#include 
+#include 
+
+/*
+ * This class contains a single set of landmarks and it's associated intensity image file.
+ * This is usually used to hold information like the following:
+ @TEST_DATA_DIR@/A.nii.gz
+ RP 128.25 -105.341 115.861
+ AC 128.25 -127.356 127.553
+ PC 128.25 -97.3915 127.251
+ END
+ * that is read in from a different class.
+ */
+
+class landmarksDataSet :  // public PointMapType
+  public std::map >
+{
+private:
+  typedef enum { eof, bad, shortLine } err_flags;
+public:
+  typedef itk::Point            PointType;
+  typedef std::map Superclass;
+
+  landmarksDataSet()
+  {
+  }
+
+  // Constructor for use by
+  // landmarksConstellationTrainingDefinitionIO::ReadFile(const std::string)
+  //
+  landmarksDataSet(const std::string & TrainingImageFilename, const std::string & LandmarksFilename)
+  {
+    this->SetImageFilename(TrainingImageFilename);
+    this->SetLandmarkFilename(LandmarksFilename);
+
+    std::ifstream singleLandmarkFile( LandmarksFilename.c_str() );
+    if( !singleLandmarkFile.is_open() )
+      {
+      std::cerr << "Input model file cannot open! :" << LandmarksFilename << ":" << std::endl;
+      exit(-1);
+      }
+    landmarksDataSet::PointType tempPoint;
+    char                        linebuf[300];
+
+    // Read in RP, AC, PC, VN4, and LE, RE, and other "new" landmarks
+    while( singleLandmarkFile.getline(linebuf, 300) )
+      {
+      // skip comment lines and newlines
+      while( linebuf[0] == '#' || linebuf[0] == '\0' )
+        {
+        singleLandmarkFile.getline(linebuf, 300);
+        }
+
+      std::string            CSVs(linebuf);
+      std::string::size_type posA = CSVs.find(',');
+      if( posA == std::string::npos )
+        {
+        throw shortLine;
+        }
+      std::string            PointName( CSVs.substr(0, posA - 0) );
+      std::string::size_type posB = 0;
+      for( unsigned int j = 0; j < 3; ++j )  // Image Dimension = 3
+        {
+        posB = CSVs.find(',', posA + 1);
+        if( posB == std::string::npos )
+          {
+          throw shortLine;
+          }
+        std::string datum = CSVs.substr( posA + 1, posB - ( posA + 1 ) );
+        tempPoint[j] = atof( datum.c_str() );
+        posA = posB;
+        }
+      // NOTE:  RAS is was slicer requires, but ITK is internall LPS, so we need
+      // to negate the first two landmark points
+      tempPoint[0] *= -1;
+      tempPoint[1] *= -1;
+      this->SetNamedPoint(PointName, tempPoint);
+      }
+
+    // RP, AC, PC, VN4, LE and RE are six "must-have" landmarks
+    if( ( this->find("RP") == this->end() )
+        || ( this->find("AC") == this->end() )
+        || ( this->find("PC") == this->end() )
+        || ( this->find("VN4") == this->end() )
+        || ( this->find("LE") == this->end() )
+        || ( this->find("RE") == this->end() ) )
+      {
+      std::cerr << "Essential landmarks are missing!" << std::endl;
+      std::cerr << "Make sure the RP (MPJ), AC, PC, 4VN (4th ventricle notch), "
+                << "LE (left eye centers), and RE (right eye centers) are all defined." << std::endl;
+      exit(-1);
+      }
+
+    singleLandmarkFile.close();
+  }
+
+  PointType GetNamedPoint(const std::string & NamedPoint) const
+  {
+    landmarksDataSet::const_iterator it = this->find(NamedPoint);
+
+    //
+    // originally, no check at all for missing points.  Next best thing,
+    // throw an exception
+    if( it == this->end() )
+      {
+      throw;
+      }
+    return it->second;
+  }
+
+  void SetNamedPoint(const std::string & NamedPoint, const PointType & NewPoint)
+  {
+    ( *this )[NamedPoint] = NewPoint;
+  }
+
+  void SetImageFilename(const std::string & NewImageFilename)
+  {
+    m_ImageFilename = NewImageFilename;
+  }
+
+  std::string GetImageFilename(void) const
+  {
+    return m_ImageFilename;
+  }
+
+  void SetLandmarkFilename(const std::string & NewImageFilename)
+  {
+    m_LandmarkFilename = NewImageFilename;
+  }
+
+  std::string GetLandmarkFilename(void) const
+  {
+    return m_LandmarkFilename;
+  }
+
+private:
+  std::string m_ImageFilename;
+  std::string m_LandmarkFilename;
+};
+
+inline
+std::ostream & operator<<(std::ostream & os, const landmarksDataSet & ds)
+{
+  os << ds.GetImageFilename() << " "
+  << ds.GetNamedPoint("RP") << std::endl
+  << ds.GetNamedPoint("AC") << std::endl
+  << ds.GetNamedPoint("PC") << std::endl
+  << ds.GetNamedPoint("VN4") << std::endl
+  << ds.GetNamedPoint("LE") << std::endl
+  << ds.GetNamedPoint("RE") << std::endl
+  << std::endl;
+  return os;
+}
+
+#endif // #ifndef _landmarksDataSet_h
diff --git a/BRAINSConstellationDetector/src/load_landmarks.m b/BRAINSConstellationDetector/src/load_landmarks.m
new file mode 100644
index 00000000..56b4ef34
--- /dev/null
+++ b/BRAINSConstellationDetector/src/load_landmarks.m
@@ -0,0 +1,1215 @@
+% NOTE THE LANDMARKS ARE ACPC-ALIGNED
+
+
+%% Variables & constants declaration
+dim = 3; %3D points
+numBaseLandmarks = 6; % number of base landmarks for LME-EPCA
+numNewLandmarks = 35; % number of new landmarks to be processed
+numMidBrainNewLandmarks = 11; % number of midbrain landmarks
+newLandmarks = cell(numNewLandmarks,1); % new landmarks cell
+newLandmarksName = cell(numNewLandmarks,1);
+
+
+%% Initialization
+AC = [];
+PC = [];
+RP = [];
+VN4 = [];
+LE = [];
+RE = [];
+aq_4V = [];
+genu = [];
+rostrum = [];
+BPons = [];
+optic_chiasm = [];
+mid_ant = [];
+mid_horiz = [];
+mid_prim = [];
+mid_prim_inf = [];
+mid_prim_sup = [];
+mid_sup = [];
+l_corp = [];
+l_ext = [];
+l_horiz_ant = [];
+l_horiz_corp = [];
+l_horiz_corp_post = [];
+l_horiz_ext = [];
+l_horiz_post = [];
+l_inf_prim = [];
+l_prim_ext = [];
+l_sup = [];
+l_sup_prim = [];
+r_corp = [];
+r_ext = [];
+r_horiz_ant = [];
+r_horiz_corp = [];
+r_horiz_corp_post = [];
+r_horiz_ext = [];
+r_horiz_post = [];
+r_inf_prim = [];
+r_prim_ext = [];
+r_sup = [];
+r_sup_prim = [];
+left_ventricular_head = [];
+right_ventricular_head = [];
+left_frontal_pole = [];
+right_frontal_pole = [];
+left_temporal_pole = [];
+right_temporal_pole = [];
+left_occipital_pole = [];
+right_occipital_pole = [];
+
+
+%% Add landmarks info from training datasets
+% Note The following landmarks are acpc-aligned
+AC = [AC; -0.0336909,-0.313266,0.287061];
+BPons = [BPons; 0.903665,-32.9569,-35.5206];
+LE = [LE; -30.131,51.0004,-34.6347];
+PC = [PC; 0.198296,-27.783,-0.681221];
+RE = [RE; 31.8639,50.2806,-33.5829];
+RP = [RP; 0.249947,-24.2403,-12.6831];
+VN4 = [VN4; 0.140815,-54.777,-19.3358];
+aq_4V = [aq_4V; 0.0130941,-42.5077,-12.0045];
+genu = [genu; 0.0843674,15.8192,6.52063];
+l_corp = [l_corp; -31.4458,-52.0194,-31.4431];
+l_ext = [l_ext; -48.5144,-55.8271,-31.0374];
+l_horiz_ant = [l_horiz_ant; -31.2417,-40.0057,-33.348];
+l_horiz_corp = [l_horiz_corp; -12.8528,-72.2776,-25.9739];
+l_horiz_corp_post = [l_horiz_corp_post; -13.2482,-92.3129,-21.1333];
+l_horiz_ext = [l_horiz_ext; -45.261,-53.8104,-37.9184];
+l_horiz_post = [l_horiz_post; -31.8793,-84.0312,-29.6947];
+l_inf_prim = [l_inf_prim; -12.9805,-60.3383,-17.8846];
+l_prim_ext = [l_prim_ext; -27.4981,-39.1123,-25.2125];
+l_sup = [l_sup; -32.0683,-60.1377,-15.5149];
+l_sup_prim = [l_sup_prim; -13.3454,-60.4201,-6.89096];
+left_ventricular_head = [left_ventricular_head; -13.9334,24.0379,3.18086];
+left_frontal_pole = [left_frontal_pole; -9.64876,65.9373,7.12407];
+left_occipital_pole = [left_occipital_pole; -13.7027,-105.899,4.6154];
+left_temporal_pole = [left_temporal_pole; -36.4603,20.8931,-29.5194];
+mid_ant = [mid_ant; 0.00753544,-43.537,-11.3249];
+mid_horiz = [mid_horiz; -0.159405,-72.497,-16.549];
+mid_prim = [mid_prim; -0.255156,-63.5425,-10.482];
+mid_prim_inf = [mid_prim_inf; 0.0344307,-58.4909,-17.4389];
+mid_prim_sup = [mid_prim_sup; -0.621308,-66.6167,-0.511294];
+mid_sup = [mid_sup; -0.649459,-54.655,4.57973];
+optic_chiasm = [optic_chiasm; 0.572682,0.0252848,-13.8295];
+r_corp = [r_corp; 31.5818,-52.7435,-31.3576];
+r_ext = [r_ext; 48.3583,-59.972,-26.8523];
+r_horiz_ant = [r_horiz_ant; 31.8075,-41.7222,-34.2698];
+r_horiz_corp = [r_horiz_corp; 13.1311,-72.5825,-25.1137];
+r_horiz_corp_post = [r_horiz_corp_post; 12.6579,-93.6326,-18.2821];
+r_horiz_ext = [r_horiz_ext; 43.6484,-60.8463,-36.0203];
+r_horiz_post = [r_horiz_post; 31.138,-82.7629,-28.5941];
+r_inf_prim = [r_inf_prim; 15.0698,-57.6595,-17.9342];
+r_prim_ext = [r_prim_ext; 30.4432,-41.7924,-23.3093];
+r_sup = [r_sup; 30.8699,-62.8765,-13.4463];
+r_sup_prim = [r_sup_prim; 14.682,-59.7412,-6.95621];
+right_ventricular_head = [right_ventricular_head; 14.5277,22.9765,2.63777];
+right_frontal_pole = [right_frontal_pole; 12.9493,65.7076,8.0065];
+right_occipital_pole = [right_occipital_pole; 15.1205,-105.879,5.18202];
+right_temporal_pole = [right_temporal_pole; 35.8595,19.989,-27.4651];
+rostrum = [rostrum; 0.171115,10.1508,1.89065];
+AC = [AC; -0.154282,-0.655781,0.348864];
+BPons = [BPons; -0.604093,-37.4336,-35.7089];
+LE = [LE; -34.0295,52.1546,-28.0395];
+PC = [PC; 0.138453,-28.2923,-0.47455];
+RE = [RE; 33.9418,50.328,-28.7858];
+RP = [RP; -0.0129349,-24.7651,-12.873];
+VN4 = [VN4; -1.85327,-56.8309,-19.8189];
+aq_4V = [aq_4V; -0.541167,-44.4072,-12.9092];
+genu = [genu; 1.31011,16.5317,6.55403];
+l_corp = [l_corp; -30.7529,-47.9212,-31.3707];
+l_ext = [l_ext; -53.929,-55.3673,-28.3005];
+l_horiz_ant = [l_horiz_ant; -30.5193,-38.9039,-32.1665];
+l_horiz_corp = [l_horiz_corp; -16.2623,-70.5169,-23.0366];
+l_horiz_corp_post = [l_horiz_corp_post; -16.5381,-84.7377,-13.357];
+l_horiz_ext = [l_horiz_ext; -47.9873,-54.3455,-36.3412];
+l_horiz_post = [l_horiz_post; -31.6147,-84.1512,-21.1899];
+l_inf_prim = [l_inf_prim; -12.8116,-56.7669,-15.7546];
+l_prim_ext = [l_prim_ext; -23.3541,-37.3456,-21.2015];
+l_sup = [l_sup; -30.7729,-56.3522,-12.558];
+l_sup_prim = [l_sup_prim; -12.704,-58.0645,-2.78137];
+left_ventricular_head = [left_ventricular_head; -12.7885,21.521,4.03476];
+left_frontal_pole = [left_frontal_pole; -8.55082,66.1087,9.97281];
+left_occipital_pole = [left_occipital_pole; -13.8377,-107.173,4.95604];
+left_temporal_pole = [left_temporal_pole; -37.9763,23.2209,-26.1156];
+mid_ant = [mid_ant; -1.41203,-44.1852,-10.5824];
+mid_horiz = [mid_horiz; -2.16457,-71.1224,-13.1935];
+mid_prim = [mid_prim; -1.93979,-65.2639,-7.05942];
+mid_prim_inf = [mid_prim_inf; -1.90786,-60.0375,-16.943];
+mid_prim_sup = [mid_prim_sup; -1.92787,-68.4685,1.86976];
+mid_sup = [mid_sup; -1.51336,-55.6143,8.1624];
+optic_chiasm = [optic_chiasm; 0.737441,4.0055,-14.9463];
+r_corp = [r_corp; 29.1031,-53.5075,-33.1195];
+r_ext = [r_ext; 47.9133,-63.1499,-27.5338];
+r_horiz_ant = [r_horiz_ant; 29.343,-43.4449,-35.892];
+r_horiz_corp = [r_horiz_corp; 15.6597,-73.3523,-24.4328];
+r_horiz_corp_post = [r_horiz_corp_post; 15.2547,-91.5246,-16.8432];
+r_horiz_ext = [r_horiz_ext; 43.8488,-61.8366,-36.4644];
+r_horiz_post = [r_horiz_post; 28.2955,-87.7387,-22.8933];
+r_inf_prim = [r_inf_prim; 11.1951,-56.3892,-16.995];
+r_prim_ext = [r_prim_ext; 21.5791,-39.5078,-23.7174];
+r_sup = [r_sup; 29.1102,-60.9391,-14.2841];
+r_sup_prim = [r_sup_prim; 11.2923,-57.6639,-5.02147];
+right_ventricular_head = [right_ventricular_head; 15.6915,20.6377,8.92501];
+right_frontal_pole = [right_frontal_pole; 14.058,65.5347,9.85939];
+right_occipital_pole = [right_occipital_pole; 9.5666,-107.824,4.30845];
+right_temporal_pole = [right_temporal_pole; 38.6323,21.4979,-27.2883];
+rostrum = [rostrum; 1.12374,10.3561,1.77874];
+AC = [AC; 0.216767,-0.570647,-0.337442];
+BPons = [BPons; 0.59508,-36.4257,-34.5962];
+LE = [LE; -33.9148,45.7088,-35.6022];
+PC = [PC; -0.180831,-27.1458,0.456217];
+RE = [RE; 30.0867,47.1819,-37.2268];
+RP = [RP; 0.315418,-24.9635,-13.0245];
+VN4 = [VN4; -0.782553,-52.5834,-19.84];
+aq_4V = [aq_4V; 0.509573,-41.9308,-13.1375];
+genu = [genu; -0.0648855,19.499,6.62101];
+l_corp = [l_corp; -34.1911,-56.2836,-29.4003];
+l_ext = [l_ext; -52.1544,-64.4096,-25.4902];
+l_horiz_ant = [l_horiz_ant; -34.2506,-48.2839,-29.4166];
+l_horiz_corp = [l_horiz_corp; -15.104,-71.1336,-25.2578];
+l_horiz_corp_post = [l_horiz_corp_post; -15.0188,-88.1191,-18.2233];
+l_horiz_ext = [l_horiz_ext; -49.1132,-64.4012,-32.4724];
+l_horiz_post = [l_horiz_post; -34.0048,-85.2728,-24.3413];
+l_inf_prim = [l_inf_prim; -15.2421,-58.12,-18.2844];
+l_prim_ext = [l_prim_ext; -31.3189,-46.2436,-20.4032];
+l_sup = [l_sup; -34.2187,-65.2514,-13.3823];
+l_sup_prim = [l_sup_prim; -15.2907,-61.096,-6.27854];
+left_ventricular_head = [left_ventricular_head; -18.0748,23.5769,4.53936];
+left_frontal_pole = [left_frontal_pole; -19.5339,62.2336,7.3947];
+left_occipital_pole = [left_occipital_pole; -15.8326,-100.714,6.64751];
+left_temporal_pole = [left_temporal_pole; -38.448,16.3727,-28.0241];
+mid_ant = [mid_ant; -0.420983,-41.9887,-8.22877];
+mid_horiz = [mid_horiz; -0.146033,-71.0078,-18.1695];
+mid_prim = [mid_prim; -0.233602,-63.996,-12.1839];
+mid_prim_inf = [mid_prim_inf; -0.244316,-57.0102,-19.198];
+mid_prim_sup = [mid_prim_sup; -0.277836,-65.976,-2.17997];
+mid_sup = [mid_sup; -0.429325,-51.9605,5.79134];
+optic_chiasm = [optic_chiasm; 0.179892,2.22425,-13.0495];
+r_corp = [r_corp; 33.7909,-53.7768,-29.0034];
+r_ext = [r_ext; 50.786,-58.636,-21.8931];
+r_horiz_ant = [r_horiz_ant; 33.7491,-45.783,-32.0197];
+r_horiz_corp = [r_horiz_corp; 17.8827,-70.8836,-23.0632];
+r_horiz_corp_post = [r_horiz_corp_post; 17.9368,-86.8612,-12.0308];
+r_horiz_ext = [r_horiz_ext; 47.8453,-58.6783,-31.9106];
+r_horiz_post = [r_horiz_post; 33.9669,-83.7599,-20.9424];
+r_inf_prim = [r_inf_prim; 14.7283,-54.8945,-17.1136];
+r_prim_ext = [r_prim_ext; 29.6576,-43.787,-19.0476];
+r_sup = [r_sup; 33.7441,-61.7406,-10.9875];
+r_sup_prim = [r_sup_prim; 14.6648,-55.8705,-5.11184];
+right_ventricular_head = [right_ventricular_head; 16.9841,24.5421,6.14573];
+right_frontal_pole = [right_frontal_pole; 14.143,65.6893,7.72091];
+right_occipital_pole = [right_occipital_pole; 15.4659,-97.4732,6.43608];
+right_temporal_pole = [right_temporal_pole; 37.6801,20.1596,-27.9207];
+rostrum = [rostrum; 0.0307465,9.82633,2.63178];
+AC = [AC; -0.29003,-0.560839,-0.697978];
+BPons = [BPons; -0.434819,-36.5007,-36.3852];
+LE = [LE; -33.1151,57.9228,-34.7659];
+PC = [PC; -0.0320543,-28.5721,-0.224761];
+RE = [RE; 32.8828,56.7568,-35.7232];
+RP = [RP; -0.0618849,-27.0639,-12.6872];
+VN4 = [VN4; -0.59965,-53.8586,-19.9364];
+aq_4V = [aq_4V; 0.250734,-42.3144,-12.4493];
+genu = [genu; 0.971067,16.3252,8.26186];
+l_corp = [l_corp; -35.1839,-52.3197,-29.5408];
+l_ext = [l_ext; -53.1593,-56.3162,-28.1569];
+l_horiz_ant = [l_horiz_ant; -35.0377,-42.4652,-25.1973];
+l_horiz_corp = [l_horiz_corp; -16.1301,-70.486,-26.7238];
+l_horiz_corp_post = [l_horiz_corp_post; -15.946,-86.755,-19.2883];
+l_horiz_ext = [l_horiz_ext; -50.3287,-54.1144,-34.1685];
+l_horiz_post = [l_horiz_post; -35.132,-83.475,-25.6236];
+l_inf_prim = [l_inf_prim; -13.8596,-57.7766,-18.3384];
+l_prim_ext = [l_prim_ext; -27.8805,-37.6564,-20.2324];
+l_sup = [l_sup; -34.7436,-60.8722,-13.8354];
+l_sup_prim = [l_sup_prim; -13.5203,-61.1928,-6.455];
+left_ventricular_head = [left_ventricular_head; -18.929,24.1188,7.57128];
+left_frontal_pole = [left_frontal_pole; -12.7167,64.2919,9.85375];
+left_occipital_pole = [left_occipital_pole; -11.2464,-108.479,2.69116];
+left_temporal_pole = [left_temporal_pole; -36.0191,20.6009,-26.4269];
+mid_ant = [mid_ant; -0.555758,-42.1258,-9.16991];
+mid_horiz = [mid_horiz; -0.904236,-70.7947,-19.1688];
+mid_prim = [mid_prim; -0.653973,-65.077,-10.9684];
+mid_prim_inf = [mid_prim_inf; -0.833095,-56.838,-17.6831];
+mid_prim_sup = [mid_prim_sup; -0.4368,-70.3526,-3.15046];
+mid_sup = [mid_sup; -0.153448,-53.6417,5.43228];
+optic_chiasm = [optic_chiasm; 0.304959,3.17685,-13.7064];
+r_corp = [r_corp; 32.8972,-54.5936,-27.5942];
+r_ext = [r_ext; 48.9884,-60.7612,-24.2727];
+r_horiz_ant = [r_horiz_ant; 32.9853,-44.6694,-25.2486];
+r_horiz_corp = [r_horiz_corp; 15.9634,-73.6874,-23.7639];
+r_horiz_corp_post = [r_horiz_corp_post; 16.2025,-91.0254,-14.3651];
+r_horiz_ext = [r_horiz_ext; 46.8091,-62.547,-30.2778];
+r_horiz_post = [r_horiz_post; 33.0011,-87.8173,-21.7486];
+r_inf_prim = [r_inf_prim; 12.2284,-53.9355,-15.9594];
+r_prim_ext = [r_prim_ext; 24.1263,-37.795,-20.7474];
+r_sup = [r_sup; 33.3376,-63.1461,-11.8888];
+r_sup_prim = [r_sup_prim; 12.5417,-56.3174,-5.04021];
+right_ventricular_head = [right_ventricular_head; 18.0354,27.407,6.61188];
+right_frontal_pole = [right_frontal_pole; 15.0859,63.749,9.1611];
+right_occipital_pole = [right_occipital_pole; 12.2766,-101.515,5.44282];
+right_temporal_pole = [right_temporal_pole; 34.345,21.8384,-28.7678];
+rostrum = [rostrum; 0.818802,10.4327,3.43806];
+AC = [AC; 0.0229883,0.0665653,-0.198352];
+BPons = [BPons; -0.762957,-30.6847,-38.23];
+LE = [LE; -33.5517,45.2355,-36.6215];
+PC = [PC; -0.00454655,-28.8052,0.572258];
+RE = [RE; 29.4326,44.2166,-38.3363];
+RP = [RP; -0.492736,-23.5942,-13.9343];
+VN4 = [VN4; -1.00201,-49.4277,-22.9822];
+aq_4V = [aq_4V; -0.513151,-39.4457,-14.7024];
+genu = [genu; -0.238081,19.4615,6.42682];
+l_corp = [l_corp; -31.5764,-48.9277,-32.3319];
+l_ext = [l_ext; -49.5327,-60.0524,-27.4522];
+l_horiz_ant = [l_horiz_ant; -31.5646,-37.9322,-32.0176];
+l_horiz_corp = [l_horiz_corp; -13.5771,-68.9903,-31.1003];
+l_horiz_corp_post = [l_horiz_corp_post; -13.5529,-87.0973,-27.6164];
+l_horiz_ext = [l_horiz_ext; -47.6134,-53.8278,-35.2989];
+l_horiz_post = [l_horiz_post; -31.6575,-73.7746,-38.0437];
+l_inf_prim = [l_inf_prim; -15.4641,-55.2517,-21.6828];
+l_prim_ext = [l_prim_ext; -30.5124,-40.075,-27.088];
+l_sup = [l_sup; -31.4022,-59.4094,-15.6255];
+l_sup_prim = [l_sup_prim; -15.3379,-59.593,-9.80266];
+left_ventricular_head = [left_ventricular_head; -13.4089,25.921,4.96594];
+left_frontal_pole = [left_frontal_pole; -14.569,62.7003,8.63629];
+left_occipital_pole = [left_occipital_pole; -13.2453,-95.8015,1.20602];
+left_temporal_pole = [left_temporal_pole; -37.5786,16.0193,-24.2819];
+mid_ant = [mid_ant; 0.659708,-40.5558,-11.4334];
+mid_horiz = [mid_horiz; 0.519919,-69.2582,-22.2571];
+mid_prim = [mid_prim; 0.589444,-65.4313,-16.1457];
+mid_prim_inf = [mid_prim_inf; 0.53598,-54.2643,-21.8286];
+mid_prim_sup = [mid_prim_sup; 0.693897,-69.7154,-6.2646];
+mid_sup = [mid_sup; 0.833852,-51.0375,5.27302];
+optic_chiasm = [optic_chiasm; -0.493211,-0.0143385,-15.6213];
+r_corp = [r_corp; 29.3993,-47.9173,-34.9672];
+r_ext = [r_ext; 49.4396,-60.0705,-30.5304];
+r_horiz_ant = [r_horiz_ant; 29.409,-38.921,-34.7101];
+r_horiz_corp = [r_horiz_corp; 13.443,-69.068,-29.3955];
+r_horiz_corp_post = [r_horiz_corp_post; 13.5129,-85.2901,-21.8563];
+r_horiz_ext = [r_horiz_ext; 43.3257,-54.7536,-41.317];
+r_horiz_post = [r_horiz_post; 29.3661,-78.9046,-35.8528];
+r_inf_prim = [r_inf_prim; 15.5329,-56.2749,-22.0492];
+r_prim_ext = [r_prim_ext; 30.4959,-39.1503,-26.7248];
+r_sup = [r_sup; 29.6061,-58.4847,-15.2623];
+r_sup_prim = [r_sup_prim; 15.6483,-60.5876,-11.1687];
+right_ventricular_head = [right_ventricular_head; 13.1184,24.8356,3.54881];
+right_frontal_pole = [right_frontal_pole; 14.8737,62.7107,8.45035];
+right_occipital_pole = [right_occipital_pole; 10.9329,-93.8488,2.78866];
+right_temporal_pole = [right_temporal_pole; 34.3329,16.2767,-24.5006];
+rostrum = [rostrum; -0.314562,11.93,-0.0646071];
+AC = [AC; 0.0164792,0.936004,-0.130689];
+BPons = [BPons; -0.895707,-37.0501,-38.1548];
+LE = [LE; -31.0245,52.0937,-37.9811];
+PC = [PC; 0.0137149,-27.0868,-1.0078];
+RE = [RE; 30.9728,52.5436,-40.2476];
+RP = [RP; -0.208139,-26.4037,-15.9041];
+VN4 = [VN4; -1.23148,-55.1477,-22.6331];
+aq_4V = [aq_4V; -0.580112,-43.5132,-13.5553];
+genu = [genu; 1.29048,18.5947,4.9696];
+l_corp = [l_corp; -31.4464,-52.7392,-31.0622];
+l_ext = [l_ext; -49.5935,-62.1417,-26.3426];
+l_horiz_ant = [l_horiz_ant; -31.1261,-41.6384,-28.4798];
+l_horiz_corp = [l_horiz_corp; -14.8668,-73.022,-27.6375];
+l_horiz_corp_post = [l_horiz_corp_post; -15.0839,-88.7082,-19.0412];
+l_horiz_ext = [l_horiz_ext; -48.6841,-59.467,-34.4678];
+l_horiz_post = [l_horiz_post; -32.2936,-87.7418,-30.7413];
+l_inf_prim = [l_inf_prim; -14.3312,-57.7017,-19.2113];
+l_prim_ext = [l_prim_ext; -27.963,-40.4518,-21.5814];
+l_sup = [l_sup; -31.3371,-61.1344,-14.7371];
+l_sup_prim = [l_sup_prim; -14.1405,-60.2145,-6.10977];
+left_ventricular_head = [left_ventricular_head; -13.154,25.0988,4.49866];
+left_frontal_pole = [left_frontal_pole; -11.7632,70.2892,2.93429];
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+r_sup_prim = [r_sup_prim; 11.2596,-55.453,-0.698348];
+right_ventricular_head = [right_ventricular_head; 13.9405,20.2144,2.07933];
+right_frontal_pole = [right_frontal_pole; 13.3065,56.2927,6.91307];
+right_occipital_pole = [right_occipital_pole; 13.1487,-94.036,11.7238];
+right_temporal_pole = [right_temporal_pole; 36.5142,14.2825,-28.5948];
+rostrum = [rostrum; -0.178864,8.78135,2.56463];
+AC = [AC; -0.103286,-0.954265,0.331673];
+BPons = [BPons; -0.597635,-26.0888,-35.8948];
+LE = [LE; -28.3788,48.2224,-31.6075];
+PC = [PC; -0.175547,-26.9327,0.145477];
+RE = [RE; 29.6041,46.3966,-32.4194];
+RP = [RP; -0.192421,-21.2514,-13.2554];
+VN4 = [VN4; -0.0497113,-46.7041,-21.6138];
+aq_4V = [aq_4V; -0.0618162,-36.7487,-13.6081];
+genu = [genu; 1.31865,15.8362,8.29629];
+l_corp = [l_corp; -30.6048,-42.8434,-31.3619];
+l_ext = [l_ext; -48.6379,-53.757,-27.2751];
+l_horiz_ant = [l_horiz_ant; -30.5463,-34.7673,-33.027];
+l_horiz_corp = [l_horiz_corp; -13.7902,-65.2619,-27.8008];
+l_horiz_corp_post = [l_horiz_corp_post; -13.6532,-80.7508,-16.4398];
+l_horiz_ext = [l_horiz_ext; -45.8344,-50.4648,-35.2313];
+l_horiz_post = [l_horiz_post; -30.8685,-77.146,-24.7847];
+l_inf_prim = [l_inf_prim; -14.388,-52.5547,-20.2397];
+l_prim_ext = [l_prim_ext; -28.2486,-33.1739,-24.0169];
+l_sup = [l_sup; -30.2591,-54.5461,-14.8414];
+l_sup_prim = [l_sup_prim; -14.0589,-53.0163,-9.25429];
+left_ventricular_head = [left_ventricular_head; -12.941,23.3854,3.21982];
+left_frontal_pole = [left_frontal_pole; -9.15483,66.7005,10.593];
+left_occipital_pole = [left_occipital_pole; -12.1021,-96.7876,5.40392];
+left_temporal_pole = [left_temporal_pole; -35.1891,18.4015,-26.1015];
+mid_ant = [mid_ant; 0.214985,-38.3042,-7.06095];
+mid_horiz = [mid_horiz; -0.588071,-65.7315,-21.2066];
+mid_prim = [mid_prim; -0.215327,-59.116,-11.9279];
+mid_prim_inf = [mid_prim_inf; -0.321458,-49.789,-19.5434];
+mid_prim_sup = [mid_prim_sup; -0.0352269,-63.4478,-4.10461];
+mid_sup = [mid_sup; 0.470663,-47.841,5.54797];
+optic_chiasm = [optic_chiasm; 0.425796,0.719307,-14.2533];
+r_corp = [r_corp; 29.3621,-45.6953,-32.2764];
+r_ext = [r_ext; 48.3981,-57.2355,-26.3221];
+r_horiz_ant = [r_horiz_ant; 29.4653,-36.6621,-32.9012];
+r_horiz_corp = [r_horiz_corp; 15.2236,-65.6963,-27.6867];
+r_horiz_corp_post = [r_horiz_corp_post; 15.286,-82.1003,-18.3645];
+r_horiz_ext = [r_horiz_ext; 44.1013,-56.7617,-36.1868];
+r_horiz_post = [r_horiz_post; 29.1286,-82.08,-23.7849];
+r_inf_prim = [r_inf_prim; 12.6864,-51.0059,-18.9828];
+r_prim_ext = [r_prim_ext; 24.7817,-33.975,-23.6361];
+r_sup = [r_sup; 29.7525,-56.4409,-14.7156];
+r_sup_prim = [r_sup_prim; 13.0154,-51.4675,-7.99741];
+right_ventricular_head = [right_ventricular_head; 12.6155,21.4706,2.37396];
+right_frontal_pole = [right_frontal_pole; 14.5993,65.8625,9.84634];
+right_occipital_pole = [right_occipital_pole; 11.2653,-98.9064,4.22454];
+right_temporal_pole = [right_temporal_pole; 36.7493,17.7693,-28.6223];
+rostrum = [rostrum; 1.126,12.9564,3.26152];
+AC = [AC; 0.288221,-0.967423,-0.255533];
+BPons = [BPons; 0.581372,-41.1164,-34.2074];
+LE = [LE; -27.9099,40.0476,-44.8834];
+PC = [PC; -0.0513956,-32.2888,0.380645];
+RE = [RE; 30.0559,41.0026,-42.6355];
+RP = [RP; 0.0947442,-27.4916,-11.7177];
+VN4 = [VN4; -0.384157,-58.3176,-17.8541];
+aq_4V = [aq_4V; 0.0697299,-45.9461,-12.2475];
+genu = [genu; -0.173926,15.8776,3.85385];
+l_corp = [l_corp; -34.4263,-56.1502,-30.8293];
+l_ext = [l_ext; -52.5528,-66.7858,-26.4348];
+l_horiz_ant = [l_horiz_ant; -34.3402,-45.3296,-33.6412];
+l_horiz_corp = [l_horiz_corp; -15.6223,-76.7581,-23.8488];
+l_horiz_corp_post = [l_horiz_corp_post; -15.7984,-93.3388,-17.6];
+l_horiz_ext = [l_horiz_ext; -49.3729,-61.3295,-33.7912];
+l_horiz_post = [l_horiz_post; -34.6539,-92.7499,-24.0903];
+l_inf_prim = [l_inf_prim; -10.817,-60.9911,-13.8833];
+l_prim_ext = [l_prim_ext; -24.596,-39.4705,-21.8208];
+l_sup = [l_sup; -34.8782,-66.7774,-11.9916];
+l_sup_prim = [l_sup_prim; -11.036,-58.2525,-4.06226];
+left_ventricular_head = [left_ventricular_head; -18.915,25.0212,-1.46098];
+left_frontal_pole = [left_frontal_pole; -12.2396,62.553,-3.13305];
+left_occipital_pole = [left_occipital_pole; -11.3241,-108.386,8.55035];
+left_temporal_pole = [left_temporal_pole; -36.3145,14.5681,-35.6031];
+mid_ant = [mid_ant; 0.0961438,-46.6056,-8.69104];
+mid_horiz = [mid_horiz; 0.147147,-76.046,-13.5135];
+mid_prim = [mid_prim; 0.0862404,-67.7706,-10.1205];
+mid_prim_inf = [mid_prim_inf; 0.195318,-63.0821,-14.4802];
+mid_prim_sup = [mid_prim_sup; -0.185411,-66.8775,1.84314];
+mid_sup = [mid_sup; -0.291996,-52.3954,7.78096];
+optic_chiasm = [optic_chiasm; 0.248343,0.16087,-16.0041];
+r_corp = [r_corp; 34.5255,-58.209,-28.1069];
+r_ext = [r_ext; 50.3596,-64.7753,-21.239];
+r_horiz_ant = [r_horiz_ant; 34.6416,-45.4684,-32.0645];
+r_horiz_corp = [r_horiz_corp; 15.3243,-76.6716,-21.1465];
+r_horiz_corp_post = [r_horiz_corp_post; 15.016,-91.8086,-8.99019];
+r_horiz_ext = [r_horiz_ext; 49.5446,-64.3714,-29.312];
+r_horiz_post = [r_horiz_post; 34.2184,-91.5193,-17.6031];
+r_inf_prim = [r_inf_prim; 12.1843,-59.0429,-13.5064];
+r_prim_ext = [r_prim_ext; 24.3611,-41.4891,-19.5554];
+r_sup = [r_sup; 34.0658,-64.7728,-8.56968];
+r_sup_prim = [r_sup_prim; 11.9164,-57.1527,-1.61711];
+right_ventricular_head = [right_ventricular_head; 18.993,24.945,-0.594531];
+right_frontal_pole = [right_frontal_pole; 12.4758,64.6445,-2.59357];
+right_occipital_pole = [right_occipital_pole; 12.0736,-103.898,10.1499];
+right_temporal_pole = [right_temporal_pole; 37.685,14.7211,-34.2745];
+rostrum = [rostrum; -0.0996603,11.3515,0.206308];
+AC = [AC; 0.111918,0.586374,0.535452];
+BPons = [BPons; 0.911263,-35.6741,-34.4211];
+LE = [LE; -30.9229,48.6175,-39.7511];
+PC = [PC; -0.345331,-28.0287,-1.05174];
+RE = [RE; 35.0961,47.5662,-39.1338];
+RP = [RP; 0.221865,-24.8389,-13.1395];
+VN4 = [VN4; -0.417862,-50.7275,-18.719];
+aq_4V = [aq_4V; -0.0625509,-42.6889,-12.3536];
+genu = [genu; 0.15395,20.3126,4.74583];
+l_corp = [l_corp; -32.7044,-49.9757,-30.0966];
+l_ext = [l_ext; -49.9592,-56.491,-26.3788];
+l_horiz_ant = [l_horiz_ant; -32.5342,-42.0477,-31.5519];
+l_horiz_corp = [l_horiz_corp; -14.1718,-67.9819,-24.3244];
+l_horiz_corp_post = [l_horiz_corp_post; -14.7056,-83.5488,-16.4259];
+l_horiz_ext = [l_horiz_ext; -45.598,-56.0698,-35.2558];
+l_horiz_post = [l_horiz_post; -33.3134,-79.749,-25.3875];
+l_inf_prim = [l_inf_prim; -11.3643,-55.4675,-14.9164];
+l_prim_ext = [l_prim_ext; -23.8799,-38.6024,-21.3916];
+l_sup = [l_sup; -33.4551,-57.0365,-13.6777];
+l_sup_prim = [l_sup_prim; -11.79,-54.8316,-3.9431];
+left_ventricular_head = [left_ventricular_head; -15.9259,26.2731,-0.37951];
+left_frontal_pole = [left_frontal_pole; -12.5372,62.6818,3.19537];
+left_occipital_pole = [left_occipital_pole; -12.8321,-93.3214,11.1283];
+left_temporal_pole = [left_temporal_pole; -36.4205,13.7842,-30.3811];
+mid_ant = [mid_ant; -0.353895,-42.3575,-10.2369];
+mid_horiz = [mid_horiz; -0.416351,-67.8334,-17.7848];
+mid_prim = [mid_prim; -0.633221,-59.3273,-9.26429];
+mid_prim_inf = [mid_prim_inf; -0.263721,-53.7426,-16.5906];
+mid_prim_sup = [mid_prim_sup; -1.03083,-61.8017,-0.114454];
+mid_sup = [mid_sup; -1.12101,-50.4165,6.23923];
+optic_chiasm = [optic_chiasm; 0.730162,-0.819534,-17.3667];
+r_corp = [r_corp; 32.3707,-50.0724,-30.5737];
+r_ext = [r_ext; 51.2272,-53.2208,-27.6548];
+r_horiz_ant = [r_horiz_ant; 32.5408,-42.1444,-32.029];
+r_horiz_corp = [r_horiz_corp; 14.8413,-68.4508,-24.1741];
+r_horiz_corp_post = [r_horiz_corp_post; 14.3462,-84.0755,-17.2732];
+r_horiz_ext = [r_horiz_ext; 43.6107,-56.738,-38.7732];
+r_horiz_post = [r_horiz_post; 31.7781,-78.8475,-25.9217];
+r_inf_prim = [r_inf_prim; 12.7741,-50.9323,-16.2477];
+r_prim_ext = [r_prim_ext; 25.2034,-36.4181,-21.6188];
+r_sup = [r_sup; 31.5977,-56.0771,-13.2144];
+r_sup_prim = [r_sup_prim; 12.3319,-51.2945,-5.21711];
+right_ventricular_head = [right_ventricular_head; 16.2756,25.8162,0.896262];
+right_frontal_pole = [right_frontal_pole; 14.5402,62.3418,4.3999];
+right_occipital_pole = [right_occipital_pole; 10.6101,-91.9211,11.5657];
+right_temporal_pole = [right_temporal_pole; 38.5021,14.1494,-27.8355];
+rostrum = [rostrum; 0.229879,11.8298,-0.208812];
+
+
+%% RAS -> LPS
+RP(:,1) = -RP(:,1);
+RP(:,2) = -RP(:,2);
+AC(:,1) = -AC(:,1);
+AC(:,2) = -AC(:,2);
+PC(:,1) = -PC(:,1);
+PC(:,2) = -PC(:,2);
+VN4(:,1) = -VN4(:,1);
+VN4(:,2) = -VN4(:,2);
+LE(:,1) = -LE(:,1);
+LE(:,2) = -LE(:,2);
+RE(:,1) = -RE(:,1);
+RE(:,2) = -RE(:,2);
+aq_4V(:,1) = -aq_4V(:,1);
+aq_4V(:,2) = -aq_4V(:,2);
+genu(:,1) = -genu(:,1);
+genu(:,2) = -genu(:,2);
+rostrum(:,1) = -rostrum(:,1);
+rostrum(:,2) = -rostrum(:,2);
+BPons(:,1) = -BPons(:,1);
+BPons(:,2) = -BPons(:,2);
+optic_chiasm(:,1) = -optic_chiasm(:,1);
+optic_chiasm(:,2) = -optic_chiasm(:,2);
+left_ventricular_head(:,1) = -left_ventricular_head(:,1);
+left_ventricular_head(:,2) = -left_ventricular_head(:,2);
+right_ventricular_head(:,1) = -right_ventricular_head(:,1);
+right_ventricular_head(:,2) = -right_ventricular_head(:,2);
+left_frontal_pole(:,1) = -left_frontal_pole(:,1);
+left_frontal_pole(:,2) = -left_frontal_pole(:,2);
+right_frontal_pole(:,1) = -right_frontal_pole(:,1);
+right_frontal_pole(:,2) = -right_frontal_pole(:,2);
+left_temporal_pole(:,1) = -left_temporal_pole(:,1);
+left_temporal_pole(:,2) = -left_temporal_pole(:,2);
+right_temporal_pole(:,1) = -right_temporal_pole(:,1);
+right_temporal_pole(:,2) = -right_temporal_pole(:,2);
+left_occipital_pole(:,1) = -left_occipital_pole(:,1);
+left_occipital_pole(:,2) = -left_occipital_pole(:,2);
+right_occipital_pole(:,1) = -right_occipital_pole(:,1);
+right_occipital_pole(:,2) = -right_occipital_pole(:,2);
+l_corp(:,1) = -l_corp(:,1);
+l_ext(:,1) = -l_ext(:,1);
+l_horiz_ant(:,1) = -l_horiz_ant(:,1);
+l_horiz_corp(:,1) = -l_horiz_corp(:,1);
+l_horiz_corp_post(:,1) = -l_horiz_corp_post(:,1);
+l_horiz_ext(:,1) = -l_horiz_ext(:,1);
+l_horiz_post(:,1) = -l_horiz_post(:,1);
+l_inf_prim(:,1) = -l_inf_prim(:,1);
+l_prim_ext(:,1) = -l_prim_ext(:,1);
+l_sup(:,1) = -l_sup(:,1);
+l_sup_prim(:,1) = -l_sup_prim(:,1);
+mid_ant(:,1) = -mid_ant(:,1);
+mid_horiz(:,1) = -mid_horiz(:,1);
+mid_prim(:,1) = -mid_prim(:,1);
+mid_prim_inf(:,1) = -mid_prim_inf(:,1);
+mid_prim_sup(:,1) = -mid_prim_sup(:,1);
+mid_sup(:,1) = -mid_sup(:,1);
+r_corp(:,1) = -r_corp(:,1);
+r_ext(:,1) = -r_ext(:,1);
+r_horiz_ant(:,1) = -r_horiz_ant(:,1);
+r_horiz_corp(:,1) = -r_horiz_corp(:,1);
+r_horiz_corp_post(:,1) = -r_horiz_corp_post(:,1);
+r_horiz_ext(:,1) = -r_horiz_ext(:,1);
+r_horiz_post(:,1) = -r_horiz_post(:,1);
+r_inf_prim(:,1) = -r_inf_prim(:,1);
+r_prim_ext(:,1) = -r_prim_ext(:,1);
+r_sup(:,1) = -r_sup(:,1);
+r_sup_prim(:,1) = -r_sup_prim(:,1);
+l_corp(:,2) = -l_corp(:,2);
+l_ext(:,2) = -l_ext(:,2);
+l_horiz_ant(:,2) = -l_horiz_ant(:,2);
+l_horiz_corp(:,2) = -l_horiz_corp(:,2);
+l_horiz_corp_post(:,2) = -l_horiz_corp_post(:,2);
+l_horiz_ext(:,2) = -l_horiz_ext(:,2);
+l_horiz_post(:,2) = -l_horiz_post(:,2);
+l_inf_prim(:,2) = -l_inf_prim(:,2);
+l_prim_ext(:,2) = -l_prim_ext(:,2);
+l_sup(:,2) = -l_sup(:,2);
+l_sup_prim(:,2) = -l_sup_prim(:,2);
+mid_ant(:,2) = -mid_ant(:,2);
+mid_horiz(:,2) = -mid_horiz(:,2);
+mid_prim(:,2) = -mid_prim(:,2);
+mid_prim_inf(:,2) = -mid_prim_inf(:,2);
+mid_prim_sup(:,2) = -mid_prim_sup(:,2);
+mid_sup(:,2) = -mid_sup(:,2);
+r_corp(:,2) = -r_corp(:,2);
+r_ext(:,2) = -r_ext(:,2);
+r_horiz_ant(:,2) = -r_horiz_ant(:,2);
+r_horiz_corp(:,2) = -r_horiz_corp(:,2);
+r_horiz_corp_post(:,2) = -r_horiz_corp_post(:,2);
+r_horiz_ext(:,2) = -r_horiz_ext(:,2);
+r_horiz_post(:,2) = -r_horiz_post(:,2);
+r_inf_prim(:,2) = -r_inf_prim(:,2);
+r_prim_ext(:,2) = -r_prim_ext(:,2);
+r_sup(:,2) = -r_sup(:,2);
+r_sup_prim(:,2) = -r_sup_prim(:,2);
+
+
+%% Register landmarks
+numDatasets = size(AC,1); % number of datasets
+
+% base landmarks
+baseLandmarks = {RP, AC, PC, VN4, LE, RE};
+baseLandmarksName = {'MPJ', 'AC', 'PC', '4VN', 'LE', 'RE'};
+
+% Midbrain landmarks
+newLandmarks{1} = aq_4V;
+newLandmarks{2} = genu;
+newLandmarks{3} = rostrum;
+newLandmarks{4} = BPons;
+newLandmarks{5} = optic_chiasm;
+newLandmarks{6} = mid_ant;
+newLandmarks{7} = mid_horiz;
+newLandmarks{8} = mid_prim;
+newLandmarks{9} = mid_prim_inf;
+newLandmarks{10} = mid_prim_sup;
+newLandmarks{11} = mid_sup;
+
+% Cerebellum landmarks
+newLandmarks{12} = l_corp;
+newLandmarks{13} = r_corp;
+newLandmarks{14} = l_horiz_ant;
+newLandmarks{15} = r_horiz_ant;
+newLandmarks{16} = l_sup;
+newLandmarks{17} = r_sup;
+newLandmarks{18} = l_horiz_ext;
+newLandmarks{19} = r_horiz_ext;
+newLandmarks{20} = l_horiz_corp;
+newLandmarks{21} = r_horiz_corp;
+
+% The following quasi-landmarks may be less reliable
+newLandmarks{22} = l_inf_prim;
+newLandmarks{23} = r_inf_prim;
+newLandmarks{24} = l_prim_ext;
+newLandmarks{25} = r_prim_ext;
+newLandmarks{26} = l_sup_prim;
+newLandmarks{27} = r_sup_prim;
+newLandmarks{28} = l_ext;
+newLandmarks{29} = r_ext;
+newLandmarks{30} = left_ventricular_head;
+newLandmarks{31} = right_ventricular_head;
+newLandmarks{32} = left_frontal_pole;
+newLandmarks{33} = right_frontal_pole;
+newLandmarks{34} = left_occipital_pole;
+newLandmarks{35} = right_occipital_pole;
+
+% The following quasi-landmarks may be much less reliable
+newLandmarks{36} = left_temporal_pole;
+newLandmarks{37} = right_temporal_pole;
+newLandmarks{38} = l_horiz_post;
+newLandmarks{39} = r_horiz_post;
+newLandmarks{40} = l_horiz_corp_post;
+newLandmarks{41} = r_horiz_corp_post;
+
+% Midbrain landmarks
+newLandmarksName{1} = 'aq_4V';
+newLandmarksName{2} = 'genu';
+newLandmarksName{3} = 'rostrum';
+newLandmarksName{4} = 'BPons';
+newLandmarksName{5} = 'optic_chiasm';
+newLandmarksName{6} = 'mid_ant';
+newLandmarksName{7} = 'mid_horiz';
+newLandmarksName{8} = 'mid_prim';
+newLandmarksName{9} = 'mid_prim_inf';
+newLandmarksName{10} = 'mid_prim_sup';
+newLandmarksName{11} = 'mid_sup';
+
+% Cerebellum landmarks
+newLandmarksName{12} = 'l_corp';
+newLandmarksName{13} = 'r_corp';
+newLandmarksName{14} = 'l_horiz_ant';
+newLandmarksName{15} = 'r_horiz_ant';
+newLandmarksName{16} = 'l_sup';
+newLandmarksName{17} = 'r_sup';
+newLandmarksName{18} = 'l_horiz_ext';
+newLandmarksName{19} = 'r_horiz_ext';
+newLandmarksName{20} = 'l_horiz_corp';
+newLandmarksName{21} = 'r_horiz_corp';
+
+% The following quasi-landmarks may be less reliable
+newLandmarksName{22} = 'l_inf_prim';
+newLandmarksName{23} = 'r_inf_prim';
+newLandmarksName{24} = 'l_prim_ext';
+newLandmarksName{25} = 'r_prim_ext';
+newLandmarksName{26} = 'l_sup_prim';
+newLandmarksName{27} = 'r_sup_prim';
+newLandmarksName{28} = 'l_ext';
+newLandmarksName{29} = 'r_ext';
+newLandmarksName{30} = 'left_ventricular_head';
+newLandmarksName{31} = 'right_ventricular_head';
+newLandmarksName{32} = 'left_frontal_pole';
+newLandmarksName{33} = 'right_frontal_pole';
+newLandmarksName{34} = 'left_occipital_pole';
+newLandmarksName{35} = 'right_occipital_pole';
+
+% The following quasi-landmarks may be much less reliable
+newLandmarksName{36} = 'left_temporal_pole';
+newLandmarksName{37} = 'right_temporal_pole';
+newLandmarksName{38} = 'l_horiz_post';
+newLandmarksName{39} = 'r_horiz_post';
+newLandmarksName{40} = 'l_horiz_corp_post';
+newLandmarksName{41} = 'r_horiz_corp_post';
+
+
+%% Further classify landmarks
+midBrainNewLandmarks = {aq_4V, genu, rostrum, BPons, optic_chiasm, ...
+    mid_ant, mid_horiz, mid_prim, mid_prim_inf, mid_prim_sup, mid_sup};
+midBrainNewLandmarksName = {'aq_4V', 'genu', 'rostrum', 'BPons', ...
+    'optic_chiasm', 'mid_ant', 'mid_horiz', 'mid_prim', 'mid_prim_inf', ...
+    'mid_prim_sup', 'mid_sup'};
diff --git a/BRAINSConstellationDetector/src/newT1LLSModel.hdf5 b/BRAINSConstellationDetector/src/newT1LLSModel.hdf5
new file mode 100644
index 00000000..bfa1c450
Binary files /dev/null and b/BRAINSConstellationDetector/src/newT1LLSModel.hdf5 differ
diff --git a/BRAINSConstellationDetector/src/tempSphereFromAreaEstimates.cxx b/BRAINSConstellationDetector/src/tempSphereFromAreaEstimates.cxx
new file mode 100644
index 00000000..31ddf5e5
--- /dev/null
+++ b/BRAINSConstellationDetector/src/tempSphereFromAreaEstimates.cxx
@@ -0,0 +1,593 @@
+/*
+ * Copyright (c) 2009, Hans J. Johnson
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * Neither the name of the Nathan Kline Institute nor the names of its
+ * contributors may be used to endorse or promote products derived from this
+ * software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "itkIO.h"
+#include "TrimForegroundInDirection.h"
+#include "itkLargestForegroundFilledMaskImageFilter.h"
+#include 
+#include 
+#include 
+#include 
+
+double FindCenterOfBrainBasedOnTopOfHead(SImageType::Pointer & foreground,  SImageType::Pointer & volOrig,
+                                         bool maximize, unsigned int axis,
+                                         double otsuPercentileThreshold, unsigned int closingSize,
+                                         double headSizeLimit, SImageType::PixelType BackgroundFillValue)
+{
+  double SI_CenterBasedOnTopOfHead = 0; // This is the return value for the
+
+  // estimated SI location of the center
+  // of the brain.
+
+  //   TrimForeground follows these steps:
+  //
+  //   largest region filled mask for head and neck tissue outline
+  //   find maximum Z location of the corner voxels (superior-inferior Z), maxZ
+  //   for each voxel in the tissue mask, compute the distance of that voxel
+  // PhysicalPoint Z-level to maxZ and store it in a similar code image
+  //   make a histogram of the distance map image
+  //   count out 2200 CCs to determine a threshold T for too far from the top.
+  //   edit the image with the rule, if not in tissue outline or distance map is
+  // greater than T, set the source image voxel to zero.
+
+  // ////////////////////////////////////////////////////////////////////////
+  //  foreground = FindLargestForgroundFilledMask(volOrig,
+  // otsuPercentileThreshold, closingSize);
+  typedef itk::LargestForegroundFilledMaskImageFilter LFFMaskFilterType;
+  LFFMaskFilterType::Pointer LFF = LFFMaskFilterType::New();
+  LFF->SetInput(volOrig);
+  LFF->SetOtsuPercentileThreshold(otsuPercentileThreshold);
+  LFF->SetClosingSize(closingSize);
+  LFF->Update();
+  foreground = LFF->GetOutput();
+
+  //  foreground will initially hold just a tissue outline (a so-called integer
+  // mask),
+  //  then it will code for the integer distance to the top of physical space,
+  // only within the outline,
+  //  then we will convert the zeros and distance codes to input image signal
+  // and the assigned background value
+  //  in conformity with the assigned volume-distance thresholding from a
+  // histogram.
+
+  // ////////////////////////////////////////////////////////////////////////
+  //  This will find maximum Superior/Inferior location of the corner voxels.
+  double extremum;
+    {
+    SImageType::SizeType  volOrigSize = volOrig->GetLargestPossibleRegion().GetSize();
+    SImageType::IndexType U, V;
+    SImageType::PointType limitU, limitV;
+    V.Fill(0);
+    volOrig->TransformIndexToPhysicalPoint(V, limitV);
+    extremum = limitV[axis];
+    for( unsigned int i = 0; i < volOrigSize[0]; i += volOrigSize[0] - 1 )
+      {
+      U[0] = i;
+      for( unsigned int j = 0; j < volOrigSize[1]; j += volOrigSize[1] - 1 )
+        {
+        U[1] = j;
+        for( unsigned int k = 0; k < volOrigSize[2]; k += volOrigSize[2] - 1 )
+          {
+          U[2] = k;
+          volOrig->TransformIndexToPhysicalPoint(U, limitU);
+          if( maximize ? limitU[axis] > limitV[axis] : limitU[axis] < limitV[axis] )
+            {
+            extremum = limitU[axis];
+            limitV = limitU;
+            V = U;
+            }
+          }
+        }
+      }
+    //  Now extremum is the level of the highest subspace plane in the voxel
+    // array.
+    }
+  std::cout << "extremum = " << extremum << std::endl;
+
+  // ////////////////////////////////////////////////////////////////////////
+  //  This will produce ForegroundLevel representing where to threshold the head
+  // from the neck.
+  double ForegroundLevel = 1;
+    {
+    typedef itk::ImageRegionIteratorWithIndex SImageIteratorType;
+    SImageIteratorType ItPixel( foreground, foreground->GetLargestPossibleRegion() );
+
+    SImageType::PointType PixelPhysicalPoint;
+    PixelPhysicalPoint.Fill(0.0);
+
+    ItPixel.Begin();
+    for( ; !ItPixel.IsAtEnd(); ++ItPixel )
+      {
+      if( ItPixel.Get() != 0 )
+        {
+        volOrig->TransformIndexToPhysicalPoint(ItPixel.GetIndex(), PixelPhysicalPoint);
+        ItPixel.Set( static_cast( vnl_math_rnd( vnl_math_abs(extremum
+                                                                                    - PixelPhysicalPoint[axis]) ) ) );
+        }
+      // else, leave the foreground coded zero, not some positive distance from
+      // the top.
+      }
+    // Now foreground holds both the silouette information and the
+    // distance-from-extermum information.
+    }
+#if 0
+  return true;
+#endif
+
+  // ////////////////////////////////////////////////////////////////////////
+  //  This will populate a histogram to make an increasing volume distribution.
+    {
+    typedef itk::Statistics::Histogram HistogramType;
+
+    typedef itk::ImageRegionIteratorWithIndex Iterator;
+
+#if 0
+    typedef itk::MinimumMaximumImageCalculator minMaxCalcType;
+    minMaxCalcType::Pointer minMaxCalc = minMaxCalcType::New();
+    minMaxCalc->SetImage(foreground);
+    minMaxCalc->Compute();
+#endif
+
+    double maxval = 0;
+    double minval = vcl_numeric_limits::max();
+    typedef itk::ImageRegionIteratorWithIndex SImageIteratorType;
+    SImageIteratorType imIter( foreground, foreground->GetLargestPossibleRegion() );
+    while( !imIter.IsAtEnd() )
+      {
+      const double curr_val = imIter.Value();
+      if( curr_val > 1 )  // Need to find min that is greater than zero.
+        {
+        maxval = ( curr_val > maxval ) ? curr_val : maxval;
+        minval = ( curr_val < minval ) ? curr_val : minval;
+        }
+      ++imIter;
+      }
+
+    const SImageType::SpacingType origSpacing = volOrig->GetSpacing();
+    const double                  voxelSize = origSpacing[0] * origSpacing[1] * origSpacing[2] * 0.001; //
+    // Cubic
+    // CC.
+    std::cout << "voxelSize = " << voxelSize << " cubic CC"  << std::endl;
+    std::cout << "MIN MAX " << minval << "  " << maxval << std::endl;
+
+    // Make sure that bin width is smaller than the minimum voxel width.  A
+    // single layer cannot have more than one row of voxels accumulated in a
+    // single bin.
+    int numBins =
+      (int)( ( maxval - minval ) / ( vnl_math_min( origSpacing[0], vnl_math_min(origSpacing[1], origSpacing[2]) ) ) );
+
+    // Histogram computation
+    HistogramType::SizeType size;
+    size[0] = numBins;
+    std::cout << "Histo values " << minval << " ...  " << maxval << " -> " << numBins << std::endl;
+
+#if 0
+    itk::ImageFileWriter::Pointer dbgWriter = itk::ImageFileWriter::New();
+    dbgWriter->UseCompressionOn();
+    dbgWriter->SetFileName("distmap.nii.gz");
+    dbgWriter->SetInput(foreground);
+    dbgWriter->Update();
+#endif
+
+    HistogramType::MeasurementVectorType minValVector, maxValVector;
+    minValVector[0] = minval;
+    maxValVector[0] = maxval;
+
+    HistogramType::Pointer histogram = HistogramType::New();
+    histogram->Initialize(size, minValVector, maxValVector);
+
+    // put each image pixel into the histogram
+    HistogramType::MeasurementVectorType measurement;
+    Iterator                             iter( foreground, foreground->GetLargestPossibleRegion() );
+    iter.Begin();
+    while( !iter.IsAtEnd() )
+      {
+      const float value = iter.Get();
+      measurement[0] = value;
+      histogram->IncreaseFrequency(measurement, 1);
+
+      ++iter;
+      }
+
+    // ////////////////////////////////////////////////////////////////////////
+    //  This will use the histogram to find the desired ForegroundLevel.
+
+    //   SImageType::RegionType imageRegion =
+    // foreground->GetLargestPossibleRegion();
+    //   int numVoxels = imageRegion.GetSize(0) * imageRegion.GetSize(1) *
+    // imageRegion.GetSize(2);
+    std::cout << "headSizeLimit = " << headSizeLimit << " CCs" << std::endl;
+    double DesiredVolumeToIncludeBeforeClipping = vcl_numeric_limits::max();   //
+    // headSizeLimit
+    // is
+    // initialized
+    // to
+    // the
+    // smallest
+    // possible
+    // adult
+    // head
+    // in
+    // cubic
+    // cm.
+
+    HistogramType::Iterator           histoIter;
+    HistogramType::IndexType          index;
+    HistogramType::InstanceIdentifier instance;
+
+    double CummulativeVolume = 0;  //  We need to skip over the zero bin.
+    bool   exitLoop = false;
+
+    histoIter = histogram->Begin();
+    ++histoIter; // Skip the zero bins.
+
+    instance =  histoIter.GetInstanceIdentifier();
+    index =  histogram->GetIndex(instance);
+    maxValVector = histogram->GetHistogramMaxFromIndex(index);
+    double SupInf_thickness = 0;
+    double RLbyAP_area = 0;
+      {
+      SImageType::PointType physOrigin;
+        {
+        SImageType::IndexType origin;
+        origin[0] = 0;
+        origin[1] = 0;
+        origin[2] = 0;
+        volOrig->TransformIndexToPhysicalPoint(origin, physOrigin);
+        }
+      SImageType::PointType           physOriginPlusOne;
+      itk::ContinuousIndex originPlusOne;
+      originPlusOne[0] = volOrig->GetSpacing()[0];
+      originPlusOne[1] = volOrig->GetSpacing()[1];
+      originPlusOne[2] = volOrig->GetSpacing()[2];
+      volOrig->TransformContinuousIndexToPhysicalPoint(originPlusOne, physOriginPlusOne);
+      // std::cout << "physOrigin         " << physOrigin        << std::endl;
+      // std::cout << "physOriginPlusOne  " << physOriginPlusOne << std::endl;
+      const double RL_thickness = vnl_math_abs(physOrigin[0] - physOriginPlusOne[0]) * 0.1;
+      const double AP_thickness = vnl_math_abs(physOrigin[1] - physOriginPlusOne[1]) * 0.1;
+      SupInf_thickness         = vnl_math_abs(physOrigin[2] - physOriginPlusOne[2]) * 0.1; //
+      // Convert
+      // to
+      // cm
+      // std::cout << "TEST RL:  " << RL_thickness << " AP " << AP_thickness <<
+      // std::endl;
+      RLbyAP_area = RL_thickness * AP_thickness; // Convert to cm^2
+      if( RLbyAP_area < 1e-5 || SupInf_thickness < 1e-5 )
+        {
+        // std::cout << "  " << SupInf_thickness << std::endl;
+        // std::cout << "  " << RL_thickness << std::endl;
+        // std::cout << "  " << AP_thickness << std::endl;
+        // std::cout << "  " << vnl_math_abs(physOrigin[1]-physOriginPlusOne[1])
+        // << std::endl;
+
+        std::cout << "ERROR:  Can not have zero area, or zero thickness." << std::endl;
+        std::cout << volOrig << std::endl;
+        exit(-1);
+        }
+      }
+
+    double topOfHeadDistFromExtremeSI = -1;
+    double CurrentDistanceFromTopOfHead = 0;
+    double largestAreaRadius = 0;
+    double MaxCrossSectionalArea = 0.0;
+    std::cout << "zero bin count to be skipped = " << histoIter.GetFrequency() << std::endl;
+    for( ; ( histoIter != histogram->End() && !exitLoop ); ++histoIter )
+      {
+      instance =  histoIter.GetInstanceIdentifier();
+      index =  histogram->GetIndex(instance);
+      maxValVector = histogram->GetHistogramMaxFromIndex(index);
+      minValVector = histogram->GetHistogramMinFromIndex(index);
+      if( histoIter.GetFrequency() < 50 )
+        {
+        continue;
+        }
+      const double CurrentCrossSectionalArea = histoIter.GetFrequency() * RLbyAP_area;
+      if( topOfHeadDistFromExtremeSI < 0 && CurrentCrossSectionalArea > 10.0 )
+        {
+        topOfHeadDistFromExtremeSI = maxValVector[0];
+        }
+      CurrentDistanceFromTopOfHead = ( maxValVector[0] - topOfHeadDistFromExtremeSI );
+      ForegroundLevel = maxValVector[0];
+
+      if(
+        ( CurrentDistanceFromTopOfHead > 70.0 ) // Require at least 70mm from
+                                                // top  of head before
+                                                // considering stoping.
+        &&
+        (
+          ( CurrentCrossSectionalArea > MaxCrossSectionalArea )
+          && (
+            ( MaxCrossSectionalArea < 10 )
+            || ( CurrentCrossSectionalArea < MaxCrossSectionalArea * 1.20 ) //
+                                                                            //
+                                                                            // Sometimes
+                                                                            //
+                                                                            //
+                                                                            // histogram
+                                                                            //
+                                                                            //
+                                                                            // bins
+                                                                            //
+                                                                            //
+                                                                            // are
+                                                                            //
+                                                                            //
+                                                                            // filled
+                                                                            //
+                                                                            //
+                                                                            // with
+                                                                            // 2
+                                                                            //
+                                                                            //
+                                                                            // slices,
+                                                                            //
+                                                                            //
+                                                                            // and
+                                                                            //
+                                                                            //
+                                                                            // that
+                                                                            //
+                                                                            //
+                                                                            // needs
+                                                                            //
+                                                                            //
+                                                                            // to
+                                                                            //
+                                                                            //
+                                                                            // be
+                                                                            //
+                                                                            //
+                                                                            // avoided.
+            )
+        )
+        )
+        {
+        MaxCrossSectionalArea = CurrentCrossSectionalArea;
+        const double estimated_radius = vcl_sqrt(MaxCrossSectionalArea / vnl_math::pi); //
+        // Estimate
+        // the
+        // radis
+        // of
+        // a
+        // circle
+        // filling
+        // this
+        // much
+        // space
+        // Now compute 1.5 times the size of a sphere with this estimated
+        // radius.
+        const double ScaleFactor = 1.1; // Add 10% for safety
+        //  //5+(MaxCrossSectionalArea-200)/100;
+        // //Larger brains need more scaling
+        const double CurentVolumeBasedOnArea = ScaleFactor
+          * ( 1.33333333333333333 * vnl_math::pi * estimated_radius
+              * estimated_radius * estimated_radius );
+        DesiredVolumeToIncludeBeforeClipping = CurentVolumeBasedOnArea;
+        // std::cout << "TESTING:  Radius: " << estimated_radius << "
+        // DesiredVolume " << DesiredVolumeToIncludeBeforeClipping << std::endl;
+        }
+      const double CurrentCrossSectionalVolume = histoIter.GetFrequency() * voxelSize;
+      CummulativeVolume += CurrentCrossSectionalVolume;
+      largestAreaRadius = vcl_pow(0.75 * vnl_math::one_over_pi * CummulativeVolume, 0.33333333333333333); //
+      // Assuming
+      // Sphere,
+      // what
+      // is
+      // radius.
+#if 0
+      std::cout << "HISTOGRAM: " << index << "," << histoIter.GetFrequency() << "," << minValVector[0] << ","
+                << maxValVector[0] << std::endl;
+      // std::cout << " SupInf_thickness " << SupInf_thickness;
+      // std::cout << " RLbyAP_area " << RLbyAP_area;
+      std::cout << "ForegroundLevel = " << ForegroundLevel;
+      std::cout << " CUMULATIVEVolume: " << CummulativeVolume;
+      std::cout << " MAXCrossSectonalArea: " << MaxCrossSectionalArea << "  CurrentCrossSectionalArea: "
+                << CurrentCrossSectionalArea << " DesiredVolumeToIncludeBeforeClipping: "
+                << DesiredVolumeToIncludeBeforeClipping << std::endl;
+#endif
+      if( ( CurrentDistanceFromTopOfHead > 100.0 )                          //
+                                                                            //
+                                                                            //
+                                                                            // Can
+                                                                            //
+                                                                            //
+                                                                            // not
+                                                                            //
+                                                                            //
+                                                                            // stop
+                                                                            //
+                                                                            //
+                                                                            // before
+                                                                            //
+                                                                            //
+                                                                            // 100
+                                                                            //
+                                                                            //
+                                                                            // mm
+                                                                            //
+                                                                            //
+                                                                            // from
+                                                                            //
+                                                                            //
+                                                                            // top
+                                                                            //
+                                                                            //
+                                                                            // of
+                                                                            //
+                                                                            //
+                                                                            // head
+                                                                            //
+                                                                            //
+                                                                            // are
+                                                                            //
+                                                                            //
+                                                                            // reached.
+          && ( CummulativeVolume >= DesiredVolumeToIncludeBeforeClipping )  //
+                                                                            //
+                                                                            //
+                                                                            // Maximum
+                                                                            //
+                                                                            //
+                                                                            // sustainable
+                                                                            //
+                                                                            //
+                                                                            // volume
+                                                                            //
+                                                                            //
+                                                                            // based
+                                                                            //
+                                                                            //
+                                                                            // on
+                                                                            //
+                                                                            //
+                                                                            // max
+                                                                            //
+                                                                            //
+                                                                            // area
+                                                                            //
+                                                                            //
+                                                                            // of
+                                                                            //
+                                                                            //
+                                                                            // any
+                                                                            //
+                                                                            //
+                                                                            // slice.
+          )
+        {
+        std::cout << "VOLUME CRITERIA MET, so exiting. " << CummulativeVolume << " >= "
+                  << DesiredVolumeToIncludeBeforeClipping  << std::endl;
+        exitLoop = true;
+        }
+#if 0 // This just does not work in many cases.
+      if( ( ( CurrentCrossSectionalArea  > MaxCrossSectionalArea * .25 )
+            && ( CurrentCrossSectionalArea < 0.65 * MaxCrossSectionalArea ) )  //
+                                                                               //
+                                                                               //
+                                                                               // If
+                                                                               //
+                                                                               //
+                                                                               // a
+                                                                               //
+                                                                               //
+                                                                               // constriction
+                                                                               //
+                                                                               //
+                                                                               // of
+                                                                               //
+                                                                               //
+                                                                               // 75%
+                                                                               //
+                                                                               //
+                                                                               // max
+                                                                               //
+                                                                               //
+                                                                               // occurs,
+                                                                               //
+                                                                               //
+                                                                               // then
+                                                                               //
+                                                                               //
+                                                                               // assume
+                                                                               //
+                                                                               //
+                                                                               // that
+                                                                               //
+                                                                               //
+                                                                               // the
+                                                                               //
+                                                                               //
+                                                                               // neck
+                                                                               //
+                                                                               //
+                                                                               // area
+                                                                               //
+                                                                               //
+                                                                               // has
+                                                                               //
+                                                                               //
+                                                                               // been
+                                                                               //
+                                                                               //
+                                                                               // entered.
+          )
+        {
+        std::cout << "NECK CONSTRICTION CRITERIA MET, so exiting." << std::endl;
+        exitLoop = true;
+        }
+#endif
+      // Now ForegroundLevel represents where to threshold the head from the
+      // neck.
+      }
+    // NOTE:  1 radius was based on some empircal work done by Hans on 100's of
+    // data sets.
+    SI_CenterBasedOnTopOfHead = extremum - ( topOfHeadDistFromExtremeSI + largestAreaRadius * 10.0 );
+    std::cout << "ForegroundLevel = " << ForegroundLevel << " topOfHeadDistFromExtremeSI "
+              << topOfHeadDistFromExtremeSI
+              << " Y_Location_from_Top_of_Head: = "  << SI_CenterBasedOnTopOfHead <<  std::endl;
+    }
+
+  // ////////////////////////////////////////////////////////////////////////
+  //  This will convert the foreground code image with the rule, foreach voxel,
+  //  if not in tissue outline or distance map is greater than T, set the result
+  // image voxel to Background;
+  //  otherwise set the result image voxel to the source image pixel value.
+    {
+    typedef itk::ImageRegionIteratorWithIndex SImageIteratorType;
+    SImageIteratorType ClippedImagePixel( foreground, foreground->GetLargestPossibleRegion() );
+    SImageIteratorType OriginalImagePixel( volOrig, volOrig->GetLargestPossibleRegion() );
+
+    ClippedImagePixel.Begin();
+    for( ; !ClippedImagePixel.IsAtEnd(); ++ClippedImagePixel )
+      {
+      if( ClippedImagePixel.Get() != 0 )
+        {
+        if( ClippedImagePixel.Get() <= ForegroundLevel )
+          {
+          OriginalImagePixel.SetIndex( ClippedImagePixel.GetIndex() );
+          ClippedImagePixel.Set( OriginalImagePixel.Get() );
+          }
+        else
+          {
+          ClippedImagePixel.Set(BackgroundFillValue);
+          }
+        }
+      else
+        {
+        ClippedImagePixel.Set(BackgroundFillValue);
+        }
+      }
+    // Now foreground holds the clipped image.
+    }
+
+  return SI_CenterBasedOnTopOfHead;
+}
+
diff --git a/BRAINSConstellationDetector/src/train_LM_EPCA.m b/BRAINSConstellationDetector/src/train_LM_EPCA.m
new file mode 100644
index 00000000..ba25bb0b
--- /dev/null
+++ b/BRAINSConstellationDetector/src/train_LM_EPCA.m
@@ -0,0 +1,202 @@
+% Author: Wei Lu
+% at Psychiatry Imaging Lab, University of Iowa Health Care, 2010
+%
+% This is the implementation of the two training phases for the proposed
+% LME-EPCA algorithm (Section 3.3 in my MS thesis).
+%
+% Objective:
+% Train a linear model that can evolutionary estimate new landmarks from
+% already known landmarks.
+%
+% Input:
+% baselandmarks     - Base landmarks in training datasets
+% newLandmarks      - EPCA landmarks in training datasets
+% numBaseLandmarks  - Number of base landmarks
+% numNewLandmarks   - Number of EPCA landmarks
+% numDatasets       - Number of training datasets
+% dim               - Dimension of the landmarks
+%
+% Output: (variables stored in files)
+% M                 - Optimal linear combination of principal components
+%                     in each iteration
+% s                 - The 3-by-1 mean of landmark vector space in each
+%                     iteration
+% search_radius     - Search radius of each EPCA landmark
+% newLandmarksNames  - A name list of all EPCA landmarks
+
+
+%% Dependencies
+load_landmarks % load all landmarks and other input parameters
+
+
+%% Init
+W = cell(numNewLandmarks, 1);
+s = zeros(dim, numNewLandmarks);
+M = cell(numNewLandmarks, 1);
+lmk_est = zeros(dim,numNewLandmarks,numDatasets);
+err = zeros(dim,numNewLandmarks,numDatasets); % to find search_radius
+
+% Initialize the landmark vector space
+Xi = zeros(dim*(numBaseLandmarks-1), numDatasets);
+for k = 2:numBaseLandmarks
+    lmkVec = (baseLandmarks{k} - baseLandmarks{1})';
+   Xi((k-2)*dim + 1 : (k-1)*dim, :) = lmkVec;
+end
+
+% Compute all principal components
+
+% Test stuff
+ratioPC1 = zeros(numNewLandmarks, 1);
+ratioPC = zeros(numNewLandmarks, 1);
+
+for i = 1:numNewLandmarks
+    %% Training phase-1
+    % Train principal components for landmark vector space associated with the
+    % EPCA landmarks in each iteration.
+    if i > 1
+        lmkVec = (newLandmarks{i-1} - baseLandmarks{1})';
+        Xi = [Xi; lmkVec];
+    end
+
+    % Remove Xi mean
+    Xi_mean = zeros(dim, 1);
+    mean_stacked = mean(Xi, 2);
+    for d = 1:dim
+        Xi_mean(d) = sum(mean_stacked(...
+            d:dim:end-dim+d))/(numBaseLandmarks+i-2);
+    end
+    s(:, i) = Xi_mean;
+    I_si = repmat(s(:, i), numBaseLandmarks+i-2, numDatasets);
+    Xi_demeaned = Xi - I_si;
+    [V, D] = eig(Xi_demeaned*Xi_demeaned');
+
+    ratioPC1(i) = sum(sum(D(:, end))) / sum(D(:));
+
+    % Number of PCs should be chosen so that the following condition is
+    % met:
+    % sum(sum(D(:, end-numPCs+1))) / sum(D(:)) > 99%;
+    % in this case, numPCs >= 1 will meet the requirement
+    % or we can use as must PCs as possible
+    % tol argument of the rank func is set conservatively
+    % Adjust the tol argument for different training datasets
+    %tolXi = 100;
+    %numPCs = rank(Xi_demeaned, tolXi);
+
+    numPCs = 10;
+    W{i} = V(:, end-numPCs+1 : end);
+
+    %% Training phase-2
+    % Train optimal linear relationship between already known landmark
+    % vector space and the EPCA landmark to be estimated in each iteration.
+    Zi = W{i}'*Xi_demeaned; % PCA mapped space
+    Yi = newLandmarks{i} - baseLandmarks{1};
+    Ci = (Zi*Zi')\Zi*Yi;
+    M{i} = W{i}*Ci;
+
+    %% Compute the estimation errors for training datasets
+    Xi_t = zeros((numBaseLandmarks+i-2)*dim, 1);
+    x1_t = baseLandmarks{1};
+    I_si_t = repmat(s(:, i), numBaseLandmarks+i-2, 1);
+    for j = 1:numDatasets
+        for k = 2:numBaseLandmarks+i-1
+            if k <= numBaseLandmarks
+                xk_t = baseLandmarks{k};
+            else
+                xk_t = newLandmarks{k - numBaseLandmarks};
+            end
+            Xi_t((k-2)*dim+1:(k-1)*dim, 1) = xk_t(j, :)' - x1_t(j, :)';
+        end
+        Xi_demeaned_t = Xi_t - I_si_t;
+        lmk_est(:, i, j) = x1_t(j, :)' + M{i}'*Xi_demeaned_t;
+        lmk_groundTruth = newLandmarks{i};
+        err(:, i, j) = lmk_est(:, i, j) - lmk_groundTruth(j, :)';
+    end
+end
+
+
+%% Determine search radii
+err_dist = zeros(numNewLandmarks,numDatasets); % Euclidean err distance
+for j = 1:numNewLandmarks
+    for k = 1:numDatasets
+        err_dist(j,k) = sqrt(sum(err(:,j,k).^2));
+    end
+end
+err_mean = mean(err_dist, 2);
+err_std = sqrt(sum((err_dist - repmat(err_mean,1,numDatasets)).^2, ...
+    2)/numDatasets);
+err_max = max(err_dist,[],2);
+err_min = min(err_dist,[],2);
+err_median = median(err_dist,2);
+
+% Aim for 99.7% coverage of anotomical variation (assuming normal distr.)
+search_radius = err_mean + 3*err_std;
+search_radius_max = 1.2*err_max;
+search_radius_min = 1.6*ones(numNewLandmarks, 1); % if max < min, take min
+search_radius(search_radius > search_radius_max) = ...
+    search_radius_max(search_radius > search_radius_max);
+search_radius(search_radius < search_radius_min) = ...
+    search_radius_min(search_radius < search_radius_min);
+
+
+%% Write model parameters to file
+% txt version
+fid = fopen('LME_EPCA.txt','w');
+for i = 1:numNewLandmarks
+    fprintf(fid, '%s\n', newLandmarksNames{i});
+    for d = 1:dim
+        fprintf(fid, '%6.32f ', s(d,i));
+    end
+    fprintf(fid, '\n');
+    fprintf(fid, '%6.32f\n', search_radius(i));
+    fprintf(fid, '%d\n', size(M{i},1));
+    tmp = M{i};
+    for d = 1:dim
+        fprintf(fid, '%6.32f ', tmp(:,d));
+        fprintf(fid, '\n');
+    end
+    fprintf(fid, '\n');
+end
+fclose(fid);
+
+% mat version
+fid = fopen('processingList.txt','w');
+for i = 1:numNewLandmarks
+    name = newLandmarksNames{i};
+    fprintf(fid, '%s\n', name);
+    fprintf(fid, '%6.32f\n', search_radius(i));
+end
+fclose(fid);
+
+fid = fopen('LME_EPCA.m','w');
+fprintf(fid, 'clear\n');
+for i = 1:numNewLandmarks
+    name = newLandmarksNames{i};
+
+    % write s
+    if size(name, 2) > 16
+      fprintf(fid, '%s__s = [', name(1:16));
+    else
+        fprintf(fid, '%s__s = [', name);
+    end
+    for d = 1:dim
+        fprintf(fid, '%6.32f ', s(d,i));
+    end
+    fprintf(fid, '];\n');
+
+    % write M
+    if size(name, 2) > 16
+      fprintf(fid, '%s__M = [', name(1:16));
+    else
+        fprintf(fid, '%s__M = [', name);
+    end
+    tmp = M{i};
+    for d = 1:dim
+        fprintf(fid, '%6.32f ', tmp(:,d));
+        fprintf(fid, ';\n');
+    end
+    fprintf(fid, '];\n');
+end
+fclose(fid);
+
+
+disp('LME-EPCA coefficients have been written to disk.');
diff --git a/BRAINSCut/README b/BRAINSCut/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSCut/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSDemonWarp/README b/BRAINSDemonWarp/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSDemonWarp/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSFit/BRAINSFit.cxx b/BRAINSFit/BRAINSFit.cxx
new file mode 100644
index 00000000..19f1ffdc
--- /dev/null
+++ b/BRAINSFit/BRAINSFit.cxx
@@ -0,0 +1,758 @@
+/*=========================================================================
+
+Program:   Insight Segmentation & Registration Toolkit
+Module:    $RCSfile$
+Language:  C++
+Date:      $Date: 2007-08-31 11:20:20 -0500 (Fri, 31 Aug 2007) $
+Version:   $Revision: 10358 $
+
+Copyright (c) Insight Software Consortium. All rights reserved.
+See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+#if defined( _MSC_VER )
+#pragma warning ( disable : 4786 )
+#endif
+#include 
+#include "itkMedianImageFilter.h"
+#include "itkExtractImageFilter.h"
+#include "BRAINSThreadControl.h"
+#include "BRAINSFitHelper.h"
+#include "BRAINSFitCLP.h"
+
+// This program was modified from
+// Insight/Examples/Registration/ImageRegistration8.cxx
+// and is an improved replacement for the old (and defective)
+
+typedef float                            PixelType;
+typedef itk::Image FixedVolumeType;
+typedef itk::Image MovingVolumeType;
+
+typedef itk::Image InputImageType;
+typedef itk::ImageFileReader     FixedVolumeReaderType;
+typedef itk::ImageFileReader     MovingVolumeReaderType;
+typedef AffineTransformType::Pointer             AffineTransformPointer;
+typedef itk::Vector           VectorType;
+
+// This function deciphers the BackgroundFillValueString and returns a double
+// precision number based on the requested value
+double GetBackgroundFillValueFromString(
+  const std::string & BackgroundFillValueString)
+{
+  const std::string BIGNEGText("BIGNEG");
+  const std::string NaNText("NaN");
+  double            BackgroundFillValue = 0.0;
+
+  if( BackgroundFillValueString == BIGNEGText )
+    {
+    union
+      {
+      unsigned int i_val[2];
+      double d_val;
+      } FourByteHolder;
+    FourByteHolder.i_val[0] = 0xF000F000;
+    FourByteHolder.i_val[1] = 0xF000F000;
+    BackgroundFillValue = FourByteHolder.d_val;
+    }
+  else if( BackgroundFillValueString == NaNText )
+    {
+    union
+      {
+      unsigned int i_val[2];
+      double d_val;
+      } FourByteHolder;
+    FourByteHolder.i_val[0] = 0xFFFFFFFF;
+    FourByteHolder.i_val[1] = 0xFFFFFFFF;
+    BackgroundFillValue = FourByteHolder.d_val;
+    }
+  else
+    {
+    BackgroundFillValue =
+      static_cast( atof( BackgroundFillValueString.c_str() ) );
+    }
+  return BackgroundFillValue;
+}
+
+template 
+typename ImageType::Pointer ExtractImage(
+  typename InputImageType::Pointer & inputImage,
+  unsigned int InputImageTimeIndex)
+{
+  typedef typename itk::ExtractImageFilter ExtractImageFilterType;
+  typename ExtractImageFilterType::Pointer extractImageFilter = ExtractImageFilterType::New();
+#if  ITK_VERSION_MAJOR >= 4
+  extractImageFilter->SetDirectionCollapseToSubmatrix();
+#endif
+
+  // fixedVolumeReader->GetOutput();
+  InputImageType::RegionType inputRegion = inputImage->GetLargestPossibleRegion();
+  InputImageType::SizeType   inputSize = inputRegion.GetSize();
+  inputSize[3] = 0;
+  inputRegion.SetSize(inputSize);
+
+  InputImageType::IndexType inputIndex = inputRegion.GetIndex();
+  inputIndex[0] = 0;
+  inputIndex[1] = 0;
+  inputIndex[2] = 0;
+  inputIndex[3] = InputImageTimeIndex;
+  inputRegion.SetIndex(inputIndex);
+  extractImageFilter->SetExtractionRegion(inputRegion);
+  extractImageFilter->SetInput(inputImage);
+
+  try
+    {
+    extractImageFilter->Update();
+    }
+  catch( ... )
+    {
+    std::cout << "Error while extracting a time indexed fixed image."
+              << std::endl;
+    throw;
+    }
+
+  typename ImageType::Pointer extractImage = extractImageFilter->GetOutput();
+  //  std::cerr << "Extract fixed image origin" << extractImage->GetOrigin() <<
+  // std::endl;
+
+  return extractImage;
+}
+
+template 
+typename ImageType::Pointer DoMedian(typename ImageType::Pointer & input,
+                                     typename ImageType::SizeType indexRadius)
+{
+  typedef typename itk::MedianImageFilter MedianFilterType;
+  typename MedianFilterType::Pointer medianFilter = MedianFilterType::New();
+
+  medianFilter->SetRadius(indexRadius);
+  medianFilter->SetInput(input);
+  medianFilter->Update();
+  typename ImageType::Pointer result = medianFilter->GetOutput();
+  return result;
+}
+
+#ifdef USE_DEBUG_IMAGE_VIEWER
+/*************************
+ * Have a global variable to
+ * add debugging information.
+ */
+DebugImageViewerClient DebugImageDisplaySender;
+#endif
+
+int main(int argc, char *argv[])
+{
+  PARSE_ARGS;
+#if ( ITK_VERSION_MAJOR < 4  ) // These are all defaults in ITKv4
+  itk::ObjectFactoryBase::RegisterFactory( itk::Brains2MaskImageIOFactory::New() );
+#endif
+
+  itk::AddExtraTransformRegister();
+  // Apparently when you register one transform, you need to register all your
+  // transforms.
+  //
+  itk::TransformFactory::RegisterTransform();
+  itk::TransformFactory::RegisterTransform();
+  itk::TransformFactory::RegisterTransform();
+  itk::TransformFactory::RegisterTransform();
+  itk::TransformFactory::RegisterTransform();
+
+#ifdef USE_DEBUG_IMAGE_VIEWER
+  if( UseDebugImageViewer )
+    {
+    DebugImageDisplaySender.SetEnabled(UseDebugImageViewer);
+    }
+#endif
+
+  BRAINSUtils::SetThreadCount(numberOfThreads);
+
+  std::string localInitializeTransformMode = initializeTransformMode;
+  // Intially set using the string enumeration
+    {
+    // For backwards compatibility, allow old flags to overwrite setting of the new flag.
+    if( ( 0
+          + ( initialTransform.size() > 0 )
+          + ( useCenterOfHeadAlign == true )
+          + ( useGeometryAlign == true )
+          + ( useMomentsAlign == true )
+          + ( initializeTransformMode != "Off" ) // This is the default value,
+                                                 // so don't count it.
+          ) > 1 )
+      {
+      std::cout
+      <<
+      "ERROR:  Can only specify one of [initialTransform | useCenterOfHeadAlign | useGeometryAlign | useMomentsAlign | initializeTransformMode ]"
+      << std::endl;
+      exit(-1);
+      }
+    if( useCenterOfHeadAlign == true )
+      {
+      localInitializeTransformMode = "useCenterOfHeadAlign";
+      }
+    if( useGeometryAlign == true )
+      {
+      localInitializeTransformMode = "useGeometryAlign";
+      }
+    if( useMomentsAlign == true )
+      {
+      localInitializeTransformMode = "useMomentsAlign";
+      }
+    }
+
+  // std::vector zeroOrigin(3, 0);
+
+  // Verify that the spline grid sizes are greater than 3
+    {
+//    bool validGridSize = true;
+    for( unsigned int sgs = 0; sgs < splineGridSize.size(); sgs++ )
+      {
+      if( splineGridSize[sgs] < 3 )
+        {
+//        validGridSize = false;
+        std::cout << "splineGridSize[" << sgs << "]= " << splineGridSize[sgs]
+                  << " is invalid.  There must be at lest 3 divisions in each dimension of the image." << std::endl;
+        exit(-1);
+        }
+      }
+    }
+  std::vector localTransformType;
+  // See if the individual boolean registration options are being used.  If any
+  // of these are set, then transformType is not used.
+  if( ( useRigid == true ) || ( useScaleVersor3D == true ) || ( useScaleSkewVersor3D == true )
+      || ( useAffine == true ) || ( useBSpline == true ) )
+    {
+    localTransformType.resize(0); // Set to zero lenght;
+    if( useRigid == true )
+      {
+      localTransformType.push_back("Rigid");
+      }
+    if( useScaleVersor3D == true )
+      {
+      localTransformType.push_back("ScaleVersor3D");
+      }
+    if( useScaleSkewVersor3D == true )
+      {
+      localTransformType.push_back("ScaleSkewVersor3D");
+      }
+    if( useAffine == true )
+      {
+      localTransformType.push_back("Affine");
+      }
+    if( useBSpline == true )
+      {
+      localTransformType.push_back("BSpline");
+      }
+    }
+  else if( transformType.size() > 0 )
+    {
+    localTransformType = transformType;
+    }
+  else if( ( ( initialTransform.size() > 0 ) + ( initializeTransformMode != "Off" ) ) > 0 )
+    {
+    // Only do the initialization phase;
+    }
+  else
+    {
+    std::cerr << "ERROR: No registration phases specified to perform!" << std::endl;
+    exit(-1);
+    }
+
+  // In order to make the Slicer interface work, a few alternate command line
+  // options need to available
+  std::string localOutputTransform;
+  if( ( linearTransform.size() > 0 && bsplineTransform.size() > 0 )
+      || ( linearTransform.size() > 0 && outputTransform.size() > 0 )
+      || ( outputTransform.size() > 0 && bsplineTransform.size() > 0 ) )
+    {
+    std::cout << "Error:  user can only specify one output transform type." << std::endl;
+    exit(-1);
+    }
+  if( linearTransform.size() > 0 )
+    {
+    localOutputTransform = linearTransform;
+    if( ( !localTransformType.empty() ) && ( localTransformType[localTransformType.size() - 1] == "BSpline" ) )
+      {
+      std::cout << "Error:  Linear transforms can not be used for BSpline registration!" << std::endl;
+      exit(-1);
+      }
+    }
+  else if( !bsplineTransform.empty() )
+    {
+    localOutputTransform = bsplineTransform;
+    if( ( !localTransformType.empty() ) && ( localTransformType[localTransformType.size() - 1] != "BSpline" ) )
+      {
+      std::cout << "Error:  BSpline registrations require output transform to be of type BSpline!" << std::endl;
+      exit(-1);
+      }
+    else if( localTransformType.empty() )
+      {
+      std::cout << "Error:  Initializer only registrations require output transform to be of type Linear!" << std::endl;
+      exit(-1);
+      }
+    }
+  else if( !outputTransform.empty() )
+    {
+    localOutputTransform = outputTransform;
+    }
+
+  if( localOutputTransform.empty()
+      && strippedOutputTransform.empty()
+      && outputVolume.empty() )
+    {
+    std::cout << "Error:  user requested neither localOutputTransform,"
+              << " nor strippedOutputTransform,"
+              << " nor outputVolume." << std::endl;
+    return 2;
+    }
+
+  if( numberOfIterations.size() != localTransformType.size() )
+    {
+    if( numberOfIterations.size() != 1 )
+      {
+      std::cerr << "The numberOfIterations array must match the length of the transformType"
+                << "length, or have a single value that is used for all registration phases." << std::endl;
+      exit(-1);
+      }
+    else
+      {
+      // replicate throughout
+      numberOfIterations.resize( localTransformType.size() );
+      const int numberOf = numberOfIterations[0];
+      for( unsigned int i = 1; i < localTransformType.size(); i++ )
+        {
+        numberOfIterations[i] = ( numberOf );
+        }
+      }
+    }
+  if( minimumStepLength.size() != localTransformType.size() )
+    {
+    if( minimumStepLength.size() != 1 )
+      {
+      std::cerr << "The minimumStepLength array must match the localTransformType length" << std::endl;
+      exit(-1);
+      }
+    else
+      {
+      // replicate throughout
+      const double stepSize = minimumStepLength[0];
+      for( unsigned int i = 1; i < localTransformType.size(); i++ )
+        {
+        minimumStepLength.push_back(stepSize);
+        }
+      }
+    }
+
+  // Need to ensure that the order of transforms is from smallest to largest.
+  itk::ValidateTransformRankOrdering(localTransformType);
+
+  // Extracting a timeIndex cube from the fixed image goes here....
+  // Also MedianFilter
+  FixedVolumeType::Pointer  extractFixedVolume;
+  MovingVolumeType::Pointer extractMovingVolume;
+  InputImageType::Pointer
+  OriginalFixedVolume( itkUtil::ReadImage(fixedVolume) );
+
+  std::cerr << "Original Fixed image origin"
+            << OriginalFixedVolume->GetOrigin() << std::endl;
+  // fixedVolumeTimeIndex lets lets us treat 3D as 4D.
+  /***********************
+   * Acquire Fixed Image Index
+   **********************/
+  extractFixedVolume = ExtractImage(OriginalFixedVolume,
+                                                     fixedVolumeTimeIndex);
+  // Extracting a timeIndex cube from the moving image goes here....
+
+  InputImageType::Pointer OriginalMovingVolume(
+    itkUtil::ReadImage(movingVolume) );
+  // This default lets us treat 3D as 4D.
+  // const unsigned int movingVolumeTimeIndex;
+
+  /***********************
+   * Acquire Moving Image Index
+   **********************/
+  extractMovingVolume = ExtractImage(OriginalMovingVolume,
+                                                       movingVolumeTimeIndex);
+
+#ifdef USE_DEBUG_IMAGE_VIEWER
+  if( DebugImageDisplaySender.Enabled() )
+    {
+    DebugImageDisplaySender.SendImage >(extractFixedVolume, 0);
+    DebugImageDisplaySender.SendImage >(extractMovingVolume, 1);
+    }
+#endif
+
+  // get median filter radius.
+  // const unsigned int MedianFilterRadius =
+  // command.GetValueAsInt(MedianFilterRadiusText, IntegerText);
+  // Median Filter images if requested.
+  if( medianFilterSize[0] > 0 || medianFilterSize[1] > 0
+      || medianFilterSize[2] > 0 )
+    {
+    FixedVolumeType::SizeType indexRadius;
+    indexRadius[0] = static_cast( medianFilterSize[0] );   // radius
+                                                                     // along x
+    indexRadius[1] = static_cast( medianFilterSize[1] );   // radius
+                                                                     // along y
+    indexRadius[2] = static_cast( medianFilterSize[2] );   // radius
+                                                                     // along z
+    // DEBUG
+    std::cout << "Median radius  " << indexRadius << std::endl;
+    std::cout << "Fixed Image size     "  << extractFixedVolume->GetLargestPossibleRegion().GetSize() << std::endl;
+    std::cout << "Moving Image size     " << extractMovingVolume->GetLargestPossibleRegion().GetSize() << std::endl;
+    extractFixedVolume = DoMedian(extractFixedVolume,
+                                                   indexRadius);
+    extractMovingVolume = DoMedian(extractMovingVolume,
+                                                     indexRadius);
+    }
+
+  //
+  // If masks are associated with the images, then read them into the correct
+  // orientation.
+  // if they've been defined assign the masks...
+  //
+  ImageMaskPointer fixedMask = NULL;
+  ImageMaskPointer movingMask = NULL;
+    {
+    if( maskProcessingMode == "NOMASK" )
+      {
+      if( ( fixedBinaryVolume != "" )
+          || ( movingBinaryVolume != "" ) )
+        {
+        std::cout
+        << "ERROR:  Can not specify mask file names when the default of NOMASK is used for the maskProcessingMode"
+        << std::endl;
+        exit(-1);
+        }
+      }
+    else if( maskProcessingMode == "ROIAUTO" )
+      {
+      if( ( fixedBinaryVolume != "" )
+          || ( movingBinaryVolume != "" ) )
+        {
+        std::cout
+        << "ERROR:  Can not specify mask file names when ROIAUTO is used for the maskProcessingMode"
+        << std::endl;
+        exit(-1);
+        }
+        {
+        typedef itk::BRAINSROIAutoImageFilter > ROIAutoType;
+        ROIAutoType::Pointer ROIFilter = ROIAutoType::New();
+        ROIFilter->SetInput(extractFixedVolume);
+        ROIFilter->SetClosingSize(ROIAutoClosingSize);
+        ROIFilter->SetDilateSize(ROIAutoDilateSize);
+        ROIFilter->Update();
+        fixedMask = ROIFilter->GetSpatialObjectROI();
+        }
+        {
+        typedef itk::BRAINSROIAutoImageFilter > ROIAutoType;
+        ROIAutoType::Pointer ROIFilter = ROIAutoType::New();
+        ROIFilter->SetInput(extractMovingVolume);
+        ROIFilter->SetClosingSize(ROIAutoClosingSize);
+        ROIFilter->SetDilateSize(ROIAutoDilateSize);
+        ROIFilter->Update();
+        movingMask = ROIFilter->GetSpatialObjectROI();
+        }
+      }
+    else if( maskProcessingMode == "ROI" )
+      {
+      if( ( fixedBinaryVolume == "" )
+          || ( movingBinaryVolume == "" ) )
+        {
+        std::cout
+        <<
+        "ERROR:  Must specify mask file names when ROI is used for the maskProcessingMode"
+        << std::endl;
+        exit(-1);
+        }
+      fixedMask = ReadImageMask(
+          fixedBinaryVolume,
+          extractFixedVolume.GetPointer() );
+      movingMask = ReadImageMask(
+          movingBinaryVolume,
+          extractMovingVolume.GetPointer() );
+      }
+    }
+  /* This default fills the background with zeros
+   *  const double BackgroundFillValue =
+   * GetBackgroundFillValueFromString(command.GetValueAsString(BackgroundFillValueText,
+   *  FloatCodeText));
+   * Note itk::ReadTransformFromDisk returns NULL if file name does not exist.
+   */
+  GenericTransformType::Pointer currentGenericTransform = itk::ReadTransformFromDisk(initialTransform);
+
+  FixedVolumeType::Pointer resampledImage;
+  /*
+   *  Everything prior to this point is preprocessing
+   *  Start Processing
+   *
+   */
+//  int actualIterations = 0;
+//  int permittedIterations = 0;
+  // int allLevelsIterations=0;
+
+    {
+    typedef itk::BRAINSFitHelper HelperType;
+    HelperType::Pointer myHelper = HelperType::New();
+    myHelper->SetTransformType(localTransformType);
+    myHelper->SetFixedVolume(extractFixedVolume);
+    myHelper->SetMovingVolume(extractMovingVolume);
+    myHelper->SetHistogramMatch(histogramMatch);
+    myHelper->SetRemoveIntensityOutliers(removeIntensityOutliers);
+    myHelper->SetNumberOfMatchPoints(numberOfMatchPoints);
+    myHelper->SetFixedBinaryVolume(fixedMask);
+    myHelper->SetMovingBinaryVolume(movingMask);
+    myHelper->SetOutputFixedVolumeROI(outputFixedVolumeROI);
+    myHelper->SetOutputMovingVolumeROI(outputMovingVolumeROI);
+    myHelper->SetPermitParameterVariation(permitParameterVariation);
+    myHelper->SetNumberOfSamples(numberOfSamples);
+    myHelper->SetNumberOfHistogramBins(numberOfHistogramBins);
+    myHelper->SetNumberOfIterations(numberOfIterations);
+    myHelper->SetMaximumStepLength(maximumStepLength);
+    myHelper->SetMinimumStepLength(minimumStepLength);
+    myHelper->SetRelaxationFactor(relaxationFactor);
+    myHelper->SetTranslationScale(translationScale);
+    myHelper->SetReproportionScale(reproportionScale);
+    myHelper->SetSkewScale(skewScale);
+    myHelper->SetUseExplicitPDFDerivativesMode(useExplicitPDFDerivativesMode);
+    myHelper->SetUseCachingOfBSplineWeightsMode(useCachingOfBSplineWeightsMode);
+    myHelper->SetBackgroundFillValue(backgroundFillValue);
+    myHelper->SetInitializeTransformMode(localInitializeTransformMode);
+    myHelper->SetMaskInferiorCutOffFromCenter(maskInferiorCutOffFromCenter);
+    myHelper->SetCurrentGenericTransform(currentGenericTransform);
+    myHelper->SetSplineGridSize(splineGridSize);
+    myHelper->SetCostFunctionConvergenceFactor(costFunctionConvergenceFactor);
+    myHelper->SetProjectedGradientTolerance(projectedGradientTolerance);
+    myHelper->SetMaxBSplineDisplacement(maxBSplineDisplacement);
+    myHelper->SetDisplayDeformedImage(UseDebugImageViewer);
+    myHelper->SetPromptUserAfterDisplay(PromptAfterImageSend);
+    myHelper->SetDebugLevel(debugLevel);
+    myHelper->SetCostMetric(costMetric);
+    if( debugLevel > 7 )
+      {
+      myHelper->PrintCommandLine(true, "BF");
+      }
+    myHelper->StartRegistration();
+    currentGenericTransform = myHelper->GetCurrentGenericTransform();
+    MovingVolumeType::ConstPointer preprocessedMovingVolume = myHelper->GetPreprocessedMovingVolume();
+#if 0
+    if( interpolationMode == "ResampleInPlace" )
+      {
+      % {
+        VersorRigid3DTransformType::ConstPointer versor3D =
+          dynamic_cast(currentGenericTransform.GetPointer() );
+        if( versor3D.IsNotNull() )
+          {
+          FixedVolumeType::Pointer tempInPlaceResample = itk::SetRigidTransformInPlace(
+              versor3D.GetPointer(), extractMovingVolume.GetPointer() );
+          resampledImage = itkUtil::TypeCast(tempInPlaceResample);
+          }
+        else
+          {
+          // This should be an exception thow instead of exit.
+          std::cout << "could not convert to rigid versor type" << std::endl;
+          exit(-1);
+          }
+        }
+      else
+        {
+        // Remember:  the Data is Moving's, the shape is Fixed's.
+        resampledImage = TransformResample(
+            preprocessedMovingVolume,
+            extractFixedVolume,
+            backgroundFillValue,
+            GetInterpolatorFromString(interpolationMode),
+            currentGenericTransform);
+        }
+      }
+#else
+      {
+      typedef float                                                                     VectorComponentType;
+      typedef itk::Vector VectorPixelType;
+      typedef itk::Image     DeformationFieldType;
+      resampledImage = GenericTransformImage(
+          preprocessedMovingVolume,
+          extractFixedVolume,
+          NULL,
+          currentGenericTransform,
+          backgroundFillValue,
+          interpolationMode,
+          false);
+      }
+#endif
+//    actualIterations = myHelper->GetActualNumberOfIterations();
+//    permittedIterations = myHelper->GetPermittedNumberOfIterations();
+    /*
+      allLevelsIterations=myHelper->GetAccumulatedNumberOfIterationsForAllLevels();
+      */
+    }
+  /*
+   *  At this point we can save the resampled image.
+   */
+
+  if( outputVolume.size() > 0 )
+    {
+    //      std::cout << "=========== resampledImage :\n" <<
+    // resampledImage->GetDirection() << std::endl;
+    // Set in PARSEARGS const bool scaleOutputValues=false;//TODO: Make this a
+    // command line parameter
+    if( outputVolumePixelType == "float" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+    else if( outputVolumePixelType == "short" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+    else if( outputVolumePixelType == "ushort" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+    else if( outputVolumePixelType == "int" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+    else if( outputVolumePixelType == "uint" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+#if 0
+    else if( outputVolumePixelType == "char" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+#endif
+    else if( outputVolumePixelType == "uchar" )
+      {
+      // itkUtil::WriteCastImage,
+      // FixedVolumeType>(resampledImage,outputVolume);
+      typedef itk::Image WriteOutImageType;
+      WriteOutImageType::Pointer CastImage =
+        ( scaleOutputValues == true ) ?
+        ( itkUtil::PreserveCast(resampledImage) ) :
+        ( itkUtil::TypeCast(resampledImage) );
+      itkUtil::WriteImage(CastImage, outputVolume);
+      }
+    }
+
+#if 0  // HACK:  This does not work properly when only an initializer transform
+       // is used, or if the final transform is BSpline.
+       // GREG:  BRAINSFit currently does not determine if the registrations
+       // have not
+       // converged before reaching their maximum number of iterations.
+       //  Currently
+       // transforms are always written out, under the assumption that the
+       // registraiton converged.  We need to figure out how to determine if the
+       // registrations did not converge (i.e. maximum number of iterations were
+       // reached), and then not write out the transforms, unless explicitly
+       // demanded
+       // to write them out from a command line flag.
+       // GREG:  We should write a test, and document what the expected
+       // behaviors are
+       // when a multi-level registration is requested (Rigid,ScaleSkew,Affine),
+       // and
+       // one of the first types does not converge.
+       // HACK  This does not work properly until BSpline reports iterations
+       // correctly
+  if( actualIterations + 1 >= permittedIterations )
+    {
+    if( writeTransformOnFailure == false )    // taken right off the command
+                                              // line.
+      {
+      std::cout << "actualIterations: " << actualIterations << std::endl;
+      std::cout << "permittedIterations: " << permittedIterations << std::endl;
+      return failureExitCode;   // taken right off the command line.
+      }
+    }
+#endif
+
+  /*const int write_status=*/
+  itk::WriteBothTransformsToDisk(currentGenericTransform.GetPointer(),
+                                 localOutputTransform, strippedOutputTransform);
+
+#if 0  // HACK:  This does not work properly when only an initializer transform
+       // is used, or if the final transform is BSpline.
+  if( actualIterations + 1 >= permittedIterations )
+    {
+    std::cout << "actualIterations: " << actualIterations << std::endl;
+    std::cout << "permittedIterations: " << permittedIterations << std::endl;
+    return failureExitCode;   // taken right off the command line.
+    }
+#endif
+
+  return 0;
+}
+
diff --git a/BRAINSFit/BRAINSFit.xml b/BRAINSFit/BRAINSFit.xml
new file mode 100644
index 00000000..fcf0b755
--- /dev/null
+++ b/BRAINSFit/BRAINSFit.xml
@@ -0,0 +1,564 @@
+
+
+  Registration
+  BRAINSFit
+  Uses the Mattes Mutual Registration algorithm to register a three-dimensional volume to a reference volume. Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291
+  http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit
+  https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt 
+  Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu
+  Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3);  Andriy Fedorov(5), fedorov -at- bwh.harvard.edu (Slicer integration); (1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard)  
+  3.0.0
+  
+    
+
+    
+      fixedVolume
+      fixedVolume
+      
+      The fixed image for registration by mutual information optimization.
+      input
+      
+    
+
+    
+      movingVolume
+      movingVolume
+      
+      The moving image for registration by mutual information optimization.
+      
+      input
+    
+
+
+  
+  
+  
+    
+    Parameters that define which registration steps to use.
+
+    
+      initialTransform
+      initialTransform
+      
+      Filename of transform used to initialize the registration.  This CAN NOT be used with either CenterOfHeadLAlign, MomentsAlign, GeometryAlign, or initialTransform file.
+      input
+    
+
+    
+      initializeTransformMode
+      initializeTransformMode
+      
+      Determine how to initialize the transform center.  GeometryAlign on assumes that the center of the voxel lattice of the images represent similar structures.  MomentsAlign assumes that the center of mass of the images represent similar structures.  useCenterOfHeadAlign attempts to use the top of head and shape of neck to drive a center of mass estimate.  Off assumes that the physical space of the images are close, and that centering in terms of the image Origins is a good starting point.  This flag is mutually exclusive with the initialTransform flag.
+      Off
+      Off
+      useMomentsAlign
+      useCenterOfHeadAlign
+      useGeometryAlign
+    
+
+    
+       useRigid
+       useRigid
+       
+       Perform a rigid registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.
+       false
+    
+    
+       useScaleVersor3D
+       useScaleVersor3D
+       
+       Perform a ScaleVersor3D registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.
+       false
+    
+    
+       useScaleSkewVersor3D
+       useScaleSkewVersor3D
+       
+       Perform a ScaleSkewVersor3D registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.
+       false
+    
+    
+       useAffine
+       useAffine
+       
+       Perform an Affine registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.
+       false
+    
+    
+       useBSpline
+       useBSpline
+       
+       Perform a BSpline registration as part of the sequential registration steps.  This family of options superceeds the use of transformType if any of them are set.
+       false
+    
+    
+  
+
+  
+    
+    
+      bsplineTransform
+      bsplineTransform
+      
+      (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform.  NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS BSpline
+      output
+    
+
+    
+      linearTransform
+      linearTransform
+      
+      (optional) Filename to which save the estimated transform. NOTE: You must set at least one output object (either a deformed image or a transform.  NOTE: USE THIS ONLY IF THE FINAL TRANSFORM IS ---NOT--- BSpline
+      output
+    
+
+    
+      outputTransform
+      outputTransform
+      
+      (optional) Filename to which save the (optional) estimated transform. NOTE: You must select either the outputTransform or the outputVolume option.
+      output
+    
+
+
+    
+      outputVolume
+      outputVolume
+      
+      (optional) Output image for registration. NOTE: You must select either the outputTransform or the outputVolume option.
+      output
+      
+    
+
+    
+      outputVolumePixelType
+      outputVolumePixelType
+      
+      The output image Pixel Type is the scalar datatype for representation of the Output Volume.
+      float
+      float
+      short
+      ushort
+      int
+      uint
+      uchar
+    
+
+ 
+  
+  
+    
+
+    
+      transformType
+      transformType
+      
+      Specifies a list of registration types to be used.  The valid types are, Rigid, ScaleVersor3D, ScaleSkewVersor3D, Affine, and BSpline.  Specifiying more than one in a comma separated list will initialize the next stage with the previous results. If registrationClass flag is used, it overrides this parameter setting.
+      
+    
+
+
+    
+      numberOfIterations
+      numberOfIterations
+      
+      The maximum number of iterations to try before failing to converge.  Use an explicit limit like 500 or 1000 to manage risk of divergence
+      1500
+    
+
+    
+      numberOfSamples
+      numberOfSamples
+      
+      The number of voxels sampled for mutual information computation.  Increase this for a slower, more careful fit.  You can also limit the sampling focus with ROI masks and ROIAUTO mask generation.
+      100000
+    
+
+    
+      minimumStepLength
+      minimumStepLength
+      
+      Each step in the optimization takes steps at least this big.  When none are possible, registration is complete.
+      0.005
+    
+
+    
+      translationScale
+      translationScale
+      
+      How much to scale up changes in position compared to unit rotational changes in radians -- decrease this to put more rotation in the search pattern.
+      1000.0
+    
+
+    
+      reproportionScale
+      reproportionScale
+      
+      ScaleVersor3D 'Scale' compensation factor.  Increase this to put more rescaling in a ScaleVersor3D or ScaleSkewVersor3D search pattern.  1.0 works well with a translationScale of 1000.0
+      1.0
+    
+
+    
+      skewScale
+      skewScale
+      
+      ScaleSkewVersor3D Skew compensation factor.  Increase this to put more skew in a ScaleSkewVersor3D search pattern.  1.0 works well with a translationScale of 1000.0
+      1.0
+    
+
+    
+      splineGridSize
+      splineGridSize
+      
+      The number of subdivisions of the BSpline Grid to be centered on the image space.  Each dimension must have at least 3 subdivisions for the BSpline to be correctly computed. 
+      14,10,12
+    
+
+    
+      maxBSplineDisplacement
+      maxBSplineDisplacement
+      
+       Sets the maximum allowed displacements in image physical coordinates for BSpline control grid along each axis.  A value of 0.0 indicates that the problem should be unbounded.  NOTE:  This only constrains the BSpline portion, and does not limit the displacement from the associated bulk transform.  This can lead to a substantial reduction in computation time in the BSpline optimizer.
+      
+      0.0
+    
+
+  
+  
+
+  
+    
+
+    
+      strippedOutputTransform
+      strippedOutputTransform
+      
+      File name for the rigid component of the estimated affine transform. Can be used to rigidly register the moving image to the fixed image. NOTE:  This value is overwritten if either bsplineTransform or linearTransform is set.
+      output
+    
+
+    
+      backgroundFillValue
+      backgroundFillValue
+      
+      Background fill value for output image.
+      0.0
+    
+
+    
+      maskInferiorCutOffFromCenter
+      maskInferiorCutOffFromCenter
+      
+      For use with --useCenterOfHeadAlign (and --maskProcessingMode ROIAUTO): the cut-off below the image centers, in millimeters, 
+      1000.0
+    
+
+    
+      scaleOutputValues
+      scaleOutputValues
+      
+      If true, and the voxel values do not fit within the minimum and maximum values of the desired outputVolumePixelType, then linearly scale the min/max output image voxel values to fit within the min/max range of the outputVolumePixelType.
+      false
+    
+
+    
+      interpolationMode
+      interpolationMode
+      
+      Type of interpolation to be used when applying transform to moving volume.  Options are Linear, NearestNeighbor, BSpline, WindowedSinc, or ResampleInPlace.  The ResampleInPlace option will create an image with the same discrete voxel values and will adjust the origin and direction of the physical space interpretation.
+      Linear
+      NearestNeighbor
+      Linear
+      ResampleInPlace
+      BSpline
+      WindowedSinc
+    
+  
+  
+  
+    
+
+    
+      maskProcessingMode
+      maskProcessingMode
+      What mode to use for using the masks.  If ROIAUTO is choosen, then the mask is implicitly defined using a otsu forground and hole filling algorithm. The Region Of Interest mode (choose ROI) uses the masks to define what parts of the image should be used for computing the transform.
+      
+      NOMASK
+      NOMASK
+      ROIAUTO
+      ROI
+    
+
+    
+      outputFixedVolumeROI
+      outputFixedVolumeROI
+      
+      The ROI automatically found in fixed image.
+      output
+    
+
+    
+      outputMovingVolumeROI
+      outputMovingVolumeROI
+      
+      The ROI automatically found in moving image.
+      output
+    
+
+    
+      fixedBinaryVolume
+      fixedBinaryVolume
+      
+      Fixed Image binary mask volume.
+      
+      input
+    
+
+    
+      movingBinaryVolume
+      movingBinaryVolume
+      
+      Moving Image binary mask volume.
+      
+      input
+    
+
+  
+  
+    
+
+    
+      fixedVolumeTimeIndex
+      fixedVolumeTimeIndex
+      
+      The index in the time series for the 3D fixed image to fit, if 4-dimensional.
+      0
+    
+
+    
+      movingVolumeTimeIndex
+      movingVolumeTimeIndex
+      
+      The index in the time series for the 3D moving image to fit, if 4-dimensional.
+      0
+    
+
+    
+      medianFilterSize
+      medianFilterSize
+      
+      The radius for the optional MedianImageFilter preprocessing in all 3 directions.
+      0,0,0
+    
+
+    
+      removeIntensityOutliers
+      removeIntensityOutliers
+      
+      The half percentage to decide outliers of image intensities. The default value is zero, which means no outlier removal. If the value of 0.005 is given, the moduel will throw away 0.005 % of both tails, so 0.01% of intensities in total would be ignored in its statistic calculation. 
+      0.0F
+    
+
+    
+       histogramMatch
+       e
+       histogramMatch
+       Histogram Match the input images.  This is suitable for images of the same modality that may have different absolute scales, but the same overall intensity profile. Do NOT use if registering images from different modailties.
+       
+       false
+    
+    
+    
+      numberOfHistogramBins
+      numberOfHistogramBins
+      The number of histogram levels
+      
+      50
+    
+    
+      numberOfMatchPoints
+      numberOfMatchPoints
+      the number of match points
+      
+      10
+    
+  
+  
+  
+  
+    
+
+    
+      useCachingOfBSplineWeightsMode
+      useCachingOfBSplineWeightsMode
+      This is a 5x speed advantage at the expense of requiring much more memory.  Only relevant when transformType is BSpline.
+      
+      ON
+      ON
+      OFF
+    
+
+    
+      useExplicitPDFDerivativesMode
+      useExplicitPDFDerivativesMode
+      Using mode AUTO means OFF for BSplineDeformableTransforms and ON for the linear transforms.  The ON alternative uses more memory to sometimes do a better job.
+      
+      AUTO
+      AUTO
+      ON
+      OFF
+    
+
+    
+      ROIAutoDilateSize
+      ROIAutoDilateSize
+      
+      This flag is only relavent when using ROIAUTO mode for initializing masks.  It defines the final dilation size to capture a bit of background outside the tissue region.  At setting of 10mm has been shown to help regularize a BSpline registration type so that there is some background constraints to match the edges of the head better.
+      0.0
+    
+
+    
+      ROIAutoClosingSize
+      ROIAutoClosingSize
+      
+      This flag is only relavent when using ROIAUTO mode for initializing masks.  It defines the hole closing size in mm.  It is rounded up to the nearest whole pixel size in each direction. The default is to use a closing size of 9mm.  For mouse data this value may need to be reset to 0.9 or smaller.
+      9.0
+    
+
+    
+      relaxationFactor
+      relaxationFactor
+      
+      Internal debugging parameter, and should probably never be used from the command line.  This will be removed in the future.
+      0.5
+    
+
+    
+      maximumStepLength
+      maximumStepLength
+      
+      Internal debugging parameter, and should probably never be used from the command line.  This will be removed in the future.
+      0.2
+    
+
+    
+      failureExitCode
+      failureExitCode
+      
+      If the fit fails, exit with this status code.  (It can be used to force a successfult exit status of (0) if the registration fails due to reaching the maximum number of iterations.
+      -1
+    
+
+    
+      writeTransformOnFailure
+      writeTransformOnFailure
+      
+      Flag to save the final transform even if the numberOfIterations are reached without convergence. (Intended for use when --failureExitCode 0 )
+      0
+    
+
+    
+      numberOfThreads
+      numberOfThreads
+      
+      Explicitly specify the maximum number of threads to use.
+      -1
+    
+
+    
+      debugLevel
+      
+      Display debug messages, and produce debug intermediate results.  0=OFF, 1=Minimal, 10=Maximum debugging.
+      debugLevel
+      0
+    
+    
+      costFunctionConvergenceFactor
+      costFunctionConvergenceFactor
+       From itkLBFGSBOptimizer.h: Set/Get the CostFunctionConvergenceFactor. Algorithm terminates when the reduction in cost function is less than (factor * epsmcj) where epsmch is the machine precision. Typical values for factor: 1e+12 for low accuracy; 1e+7 for moderate accuracy and 1e+1 for extremely high accuracy.  1e+9 seems to work well.
+      
+      1e+9
+    
+    
+      projectedGradientTolerance
+      projectedGradientTolerance
+       From itkLBFGSBOptimizer.h: Set/Get the ProjectedGradientTolerance. Algorithm terminates when the project gradient is below the tolerance. Default lbfgsb value is 1e-5, but 1e-4 seems to work well.
+      
+      1e-5
+    
+
+    
+      UseDebugImageViewer
+      G
+      gui
+      Display intermediate image volumes for debugging.  NOTE:  This is not part of the standard build sytem, and probably does nothing on your installation.
+      false
+    
+    
+      PromptAfterImageSend
+      p
+      promptUser
+      Prompt the user to hit enter each time an image is sent to the DebugImageViewer
+      false
+    
+  
+  
+    
+
+    
+       useMomentsAlign
+       NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00
+       
+       DO NOT USE THIS FLAG
+       false
+    
+    
+       useGeometryAlign
+       NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01
+       
+       DO NOT USE THIS FLAG
+       false
+    
+    
+       useCenterOfHeadAlign
+       NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02
+       
+       DO NOT USE THIS FLAG
+       false
+    
+
+    
+      permitParameterVariation
+      permitParameterVariation
+      
+      A bit vector to permit linear transform parameters to vary under optimization.  The vector order corresponds with transform parameters, and beyond the end ones fill in as a default.  For instance, you can choose to rotate only in x (pitch) with 1,0,0;  this is mostly for expert use in turning on and off individual degrees of freedom in rotation, translation or scaling without multiplying the number of transform representations; this trick is probably meaningless when tried with the general affine transform.
+      
+    
+    
+        costMetric
+        costMetric
+        
+	The cost metric to be used during fitting. Defaults to MMI. Options are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC (Normalized Correlation), MC (Match Cardinality for binary images)
+        MMI
+        MMI
+        MSE
+        NC
+        MC
+    
+  
+
+
diff --git a/BRAINSFit/BRAINSFitCommonLib.h.in b/BRAINSFit/BRAINSFitCommonLib.h.in
new file mode 100755
index 00000000..44f78c22
--- /dev/null
+++ b/BRAINSFit/BRAINSFitCommonLib.h.in
@@ -0,0 +1,13 @@
+/* 
+ * Here is where system computed values get stored.
+ * These values should only change when the target compile platform changes.
+ */
+
+#if defined(WIN32) && !defined(BRAINSFITCOMMONLIB_STATIC)
+#pragma warning ( disable : 4275 )
+#endif
+
+#cmakedefine BUILD_SHARED_LIBS
+#ifndef BUILD_SHARED_LIBS
+#define BRAINSFITCOMMONLIB_STATIC
+#endif
diff --git a/BRAINSFit/BRAINSFitCommonLibLauncher.c.in b/BRAINSFit/BRAINSFitCommonLibLauncher.c.in
new file mode 100644
index 00000000..1b0c2cb0
--- /dev/null
+++ b/BRAINSFit/BRAINSFitCommonLibLauncher.c.in
@@ -0,0 +1,30 @@
+#if defined(_WIN32)
+#if defined(CMAKE_INTDIR)
+#define itksys_SHARED_FORWARD_CONFIG_NAME CMAKE_INTDIR
+#define CONFIG_DIR_PRE CMAKE_INTDIR "/"
+#define CONFIG_DIR_POST "/" CMAKE_INTDIR
+#else
+#define CONFIG_DIR_PRE ""
+#define CONFIG_DIR_POST ""
+#endif
+#endif
+
+#define itksys_SHARED_FORWARD_DIR_BUILD "@BRAINSFitCommonLib_FORWARD_DIR_BUILD@"
+#define itksys_SHARED_FORWARD_PATH_BUILD @BRAINSFitCommonLib_FORWARD_PATH_BUILD@
+#define itksys_SHARED_FORWARD_PATH_INSTALL @BRAINSFitCommonLib_FORWARD_PATH_INSTALL@
+#if defined(_WIN32)
+#define itksys_SHARED_FORWARD_EXE_BUILD CONFIG_DIR_PRE "@BRAINSFitCommonLib_FORWARD_EXE@"
+#else
+#define itksys_SHARED_FORWARD_EXE_BUILD "@BRAINSFitCommonLib_FORWARD_DIR_BUILD@/@BRAINSFitCommonLib_FORWARD_EXE@"
+#endif
+#define itksys_SHARED_FORWARD_EXE_INSTALL "@BRAINSFitCommonLib_FORWARD_DIR_INSTALL@/@BRAINSFitCommonLib_FORWARD_EXE@"
+#define itksys_SHARED_FORWARD_OPTION_PRINT "--print"
+#define itksys_SHARED_FORWARD_OPTION_LDD "--ldd"
+
+#include 
+
+int main(int argc, char *argv[])
+{
+  return itksys_shared_forward_to_real(argc, argv);
+}
+
diff --git a/BRAINSFit/BRAINSFitCommonLibWin32Header.h b/BRAINSFit/BRAINSFitCommonLibWin32Header.h
new file mode 100755
index 00000000..8fc07529
--- /dev/null
+++ b/BRAINSFit/BRAINSFitCommonLibWin32Header.h
@@ -0,0 +1,22 @@
+// /  BRAINSFitCommonLibWin32Header - manage Windows system differences
+// /
+// / The BRAINSFitCommonLibWin32Header captures some system differences between
+// Unix
+// / and Windows operating systems.
+
+#ifndef __BRAINSFitCommonLibWin32Header_h
+#define __BRAINSFitCommonLibWin32Header_h
+
+#include 
+
+#if defined( WIN32 ) && !defined( BRAINSFitCommonLib_STATIC )
+#if defined( BRAINSFitCommonLib_EXPORTS )
+#define BRAINSFitCommonLib_EXPORT __declspec(dllexport)
+#else
+#define BRAINSFitCommonLib_EXPORT __declspec(dllimport)
+#endif
+#else
+#define BRAINSFitCommonLib_EXPORT
+#endif
+
+#endif
diff --git a/BRAINSFit/CMakeCPackOptions.cmake.in b/BRAINSFit/CMakeCPackOptions.cmake.in
new file mode 100644
index 00000000..96e43850
--- /dev/null
+++ b/BRAINSFit/CMakeCPackOptions.cmake.in
@@ -0,0 +1,44 @@
+# This file is configured at cmake time, and loaded at cpack time.
+# To pass variables to cpack from cmake, they must be configured
+# in this file.
+
+if(CPACK_GENERATOR MATCHES "NSIS")
+  # set the install/unistall icon used for the installer itself
+  # There is a bug in NSI that does not handle full unix paths properly.
+  set(CPACK_NSIS_MUI_ICON "@BRAINSCommonLib_BUILDSCRIPTS_DIR@/BRAINSLogo.ico")
+  set(CPACK_NSIS_MUI_UNIICON "@BRAINSCommonLib_BUILDSCRIPTS_DIR@/BRAINSLogo.ico")
+  # set the package header icon for MUI
+  set(CPACK_PACKAGE_ICON "@BRAINSFit_SOURCE_DIR@/BRAINSLogo.bmp")
+  # tell cpack to create links to the doc files
+  set(CPACK_NSIS_MENU_LINKS
+    "http://www.nitrc.org" "Neuroinformatics Tools and Resources Clearinghouse"
+    )
+  # Use the icond from cmake-gui for add-remove programs
+#  set(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\cmake-gui.exe")
+  set(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\\\MyExecutable.exe")
+
+  set(CPACK_NSIS_DISPLAY_NAME "CMake @BRAINSFit_VERSION_MAJOR@.@BRAINSFit_VERSION_MINOR@ a cross-platform, open-source build system")
+  set(CPACK_NSIS_PACKAGE_NAME "CMake @BRAINSFit_VERSION_MAJOR@.@BRAINSFit_VERSION_MINOR@")
+  set(CPACK_NSIS_HELP_LINK "http://www.nitrc.org")
+  set(CPACK_NSIS_URL_INFO_ABOUT "http://www.nitrc.com")
+  set(CPACK_NSIS_CONTACT @CPACK_PACKAGE_CONTACT@)
+  set(CPACK_NSIS_MODIFY_PATH ON)
+endif(CPACK_GENERATOR MATCHES "NSIS")
+
+# include the cpack options for qt dialog if they exisit
+# they might not if qt was not enabled for the build
+include("@QT_DIALOG_CPACK_OPTIONS_FILE@" OPTIONAL)
+
+if(CPACK_GENERATOR MATCHES "CygwinSource")
+  # when packaging source make sure the .build directory is not included
+    set(CPACK_SOURCE_IGNORE_FILES
+      "/CVS/" "/\\.build/" "/\\.svn/" "\\.swp$" "\\.#" "/#" "~$")
+endif(CPACK_GENERATOR MATCHES "CygwinSource")
+
+if("${CPACK_GENERATOR}" STREQUAL "PackageMaker")
+  if(CMAKE_PACKAGE_QTGUI)
+    set(CPACK_PACKAGE_DEFAULT_LOCATION "/Applications")
+  else(CMAKE_PACKAGE_QTGUI)
+    set(CPACK_PACKAGE_DEFAULT_LOCATION "/usr")
+  endif(CMAKE_PACKAGE_QTGUI)
+endif("${CPACK_GENERATOR}" STREQUAL "PackageMaker")
diff --git a/BRAINSFit/CMakeLists.txt b/BRAINSFit/CMakeLists.txt
new file mode 100644
index 00000000..3065e59b
--- /dev/null
+++ b/BRAINSFit/CMakeLists.txt
@@ -0,0 +1,68 @@
+project(BRAINSFit)
+set(LOCAL_PROJECT_NAME BRAINSFit)
+cmake_minimum_required(VERSION 2.8)
+cmake_policy(VERSION 2.8)
+
+enable_testing()
+include(CTest)
+
+find_package(BRAINSCommonLib NO_MODULE REQUIRED)
+include(${BRAINSCommonLib_USE_FILE})
+
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/PreventInSourceBuilds.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMMacroBuildCLI.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/CMakeBRAINS3BuildMacros.cmake)
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/IJMacros.txt)
+
+###
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_BINARY_DIR}/bin)
+link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+if(NOT ITK_FOUND)
+    find_package(ITK REQUIRED)
+    include(${ITK_USE_FILE})
+endif(NOT ITK_FOUND)
+
+#-----------------------------------------------------------------------------
+# Output directories.
+#
+#SETOPTIONALDEBUGIMAGEVIEWER()
+
+
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/BRAINSFitCommonLib.h.in
+  ${CMAKE_CURRENT_BINARY_DIR}/BRAINSFitCommonLib.h
+  )
+
+## ITKv4 requires that ITKReview is explicitly linked against
+if(ITK_VERSION_MAJOR EQUAL 4 )
+  set(ITKREVIEWLIB ITKReview)
+endif(ITK_VERSION_MAJOR EQUAL 4 )
+
+###
+if(0) # Build against Slicer
+  ## Include the Slicer macro for setting up default locations!
+  SlicerMacroBuildCLI(
+    NAME BRAINSFit
+    LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+    TARGET_LIBRARIES BRAINSCommonLib ${ITK_LIBRARIES} ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+    CLI_SHARED_LIBRARY_WRAPPER_CXX  ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+    VERBOSE
+  )
+else()
+  SEMMacroBuildCLI(
+    NAME BRAINSFit
+    LOGO_HEADER ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/BRAINSLogo.h
+    TARGET_LIBRARIES BRAINSCommonLib ${ITK_LIBRARIES} ${OPTIONAL_DEBUG_LINK_LIBRARIES}
+    CLI_SHARED_LIBRARY_WRAPPER_CXX ${BRAINSCommonLib_BUILDSCRIPTS_DIR}/SEMCommanLineSharedLibraryWrapper.cxx
+    VERBOSE
+    )
+endif()
+
+if(BUILD_TESTING)
+    add_subdirectory(TestSuite)
+endif(BUILD_TESTING)
diff --git a/BRAINSFit/CTestConfig.cmake b/BRAINSFit/CTestConfig.cmake
new file mode 100644
index 00000000..e143ad88
--- /dev/null
+++ b/BRAINSFit/CTestConfig.cmake
@@ -0,0 +1,14 @@
+## This file should be placed in the root directory of your project.
+## Then modify the CMakeLists.txt file in the root directory of your
+## project to incorporate the testing dashboard.
+## # The following are required to uses Dart and the Cdash dashboard
+##   enable_testing()
+##   include(Dart)
+site_name(SITE)
+set(CTEST_PROJECT_NAME "BRAINSFit")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
+
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "testing.psychiatry.uiowa.edu")
+set(CTEST_DROP_LOCATION "/CDash/submit.php?project=BRAINSFit")
+set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/BRAINSFit/CTestCustom.ctest b/BRAINSFit/CTestCustom.ctest
new file mode 100644
index 00000000..b35239ef
--- /dev/null
+++ b/BRAINSFit/CTestCustom.ctest
@@ -0,0 +1,52 @@
+#-- #NOTES from http: // www.cmake.org/Wiki/CMake_Testing_With_CTest
+set(CTEST_CUSTOM_MEMCHECK_IGNORE
+    $ {CTEST_CUSTOM_MEMCHECK_IGNORE}
+    DummyExcludeMemcheckIgnoreTestSetGet
+    )
+
+#-- #set(CTEST_CUSTOM_WARNING_MATCH
+#-- #${CTEST_CUSTOM_WARNING_MATCH}
+#-- #"{standard input}:[0-9][0-9]*: Warning: "
+#-- #)
+
+#-- #IF("@CMAKE_SYSTEM@" MATCHES "OSF")
+set(CTEST_CUSTOM_WARNING_EXCEPTION
+    $ {CTEST_CUSTOM_WARNING_EXCEPTION}
+    "fltk"
+    "xforms"
+    "vtkKWApplication"
+    "vtkKWObject"
+    )
+#-- #ENDIF("@CMAKE_SYSTEM@" MATCHES "OSF")
+
+#-- #The following are brains2 warnings that just need to be suppressed because they are caused
+#-- #by third parties, and will never be fixed.
+set(CTEST_CUSTOM_WARNING_EXCEPTION
+    $ {CTEST_CUSTOM_WARNING_EXCEPTION}
+    "tcl8.4.5/[^/]+/../[^/]+/[^.]+.c[:\"]"
+    "tk8.4.5/[^/]+/[^/]+.c[:\"]"
+    "SlicerExecutionModel"
+    "VTK/Utilities/vtktiff/"
+    "Utilities/vtkmpeg2/"
+    "Utilities/hdf5/"
+    "xtree.[0-9]+. : warning C4702: unreachable code"
+    "warning LNK4221"
+    "variable .var_args[2]*. is used before its value is set"
+    "qHullLib"
+    "/FL/"
+    "bkHull.cxx:[0-9]+: warning: dereferencing type-punned pointer will break strict-aliasing rules"
+    "warning #1170: invalid redeclaration of nested class"
+    )
+##Intel compiler does not like itkLegacyMacro warning #1170
+
+#-- #Reset maximum number of warnings so that they all show up.
+set(CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS 1000)
+
+set(CTEST_CUSTOM_COVERAGE_EXCLUDE $ {CTEST_CUSTOM_COVERAGE_EXCLUDE}
+    "./SlicerExecutionModel/"
+    "./SlicerExecutionModel/.*"
+    "./SlicerExecutionModel/.*/.*"
+    ".*SlicerExecutionModel.*"
+    "SlicerExecutionModel"
+    )
+
diff --git a/BRAINSFit/Copyright.txt b/BRAINSFit/Copyright.txt
new file mode 100644
index 00000000..1bbc630a
--- /dev/null
+++ b/BRAINSFit/Copyright.txt
@@ -0,0 +1 @@
+Need to fill in copyright files.
diff --git a/BRAINSFit/README b/BRAINSFit/README
new file mode 100644
index 00000000..4f691e5b
--- /dev/null
+++ b/BRAINSFit/README
@@ -0,0 +1,5 @@
+## TODO:  Need to fill in the readme
+see www.nitrc.org under BRAINSFit for more complete information.
+
+## Documentation has been moved to a branch:
+svn co https://www.nitrc.org/svn/multimodereg/branches/BRAINSFitDocs
diff --git a/BRAINSFit/TestSuite/BRAINSFitTest.cxx b/BRAINSFit/TestSuite/BRAINSFitTest.cxx
new file mode 100644
index 00000000..d0bd8ddf
--- /dev/null
+++ b/BRAINSFit/TestSuite/BRAINSFitTest.cxx
@@ -0,0 +1,23 @@
+//
+//A test driver to append the
+//itk image processing test
+//commands to an
+//the SEM compatibile program
+//
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int BRAINSFitTest(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
+
diff --git a/BRAINSFit/TestSuite/CMakeLists.txt b/BRAINSFit/TestSuite/CMakeLists.txt
new file mode 100644
index 00000000..3f076880
--- /dev/null
+++ b/BRAINSFit/TestSuite/CMakeLists.txt
@@ -0,0 +1,1442 @@
+
+MakeTestDriverFromSEMTool(BRAINSFit BRAINSFitTest.cxx)
+
+if(COMPILE_TEST_GENERATION_PROGRAMS)  ## These were programs needed to create the test suite, but are not needed for actual testing!
+  # The following program was used to generate TestData/test2.nii.gz
+  # from test.nii.gz
+  if(MakeMakeXfrmImage)
+    add_executable(makexfrmedImage makexfrmedImage.cxx)
+    target_link_libraries(makexfrmedImage ${ITK_LIBRARIES})
+  endif(MakeMakeXfrmImage)
+
+  if(BRAINSFitTestDriver)
+    # The test driver is only needed to help generate new testcases
+    add_executable(BRAINSFitTestDriver BRAINSFitTestDriver.cxx)
+    target_link_libraries(BRAINSFitTestDriver ${ITK_LIBRARIES}
+      ${OPTIONAL_DEBUG_LINK_LIBRARIES} )
+    set_target_properties(BRAINSFitTestDriver PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${BRAINSFit_BINARY_DIR})
+  endif()
+endif(COMPILE_TEST_GENERATION_PROGRAMS)
+
+if (WIN32)
+  set(BUILD_SUBDIR ${CMAKE_BUILD_TYPE}/)
+endif (WIN32)
+
+configure_file(${BRAINSFit_SOURCE_DIR}/CTestCustom.ctest ${BRAINSFit_BINARY_DIR}/CTestCustom.ctest COPYONLY)
+
+include(${BRAINSCommonLib_BUILDSCRIPTS_DIR}/ExternalData.cmake)
+list(APPEND ExternalData_URL_TEMPLATES
+  # Local data store populated by the ITK pre-commit hook
+  "file:///${CMAKE_SOURCE_DIR}/.ExternalData/%(algo)/%(hash)"
+  # Data published by Iowa Psychiatry web interface
+  "http://www.psychiatry.uiowa.edu/users/brainstestdata/ctestdata/%(algo)/%(hash)"
+
+  # Data published by MIDAS
+  "http://midas.kitware.com/api/rest/midas.bitstream.by.hash?hash=%(hash)&algorithm=%(algo)"
+
+  # Data published by developers using git-gerrit-push.
+  "http://www.itk.org/files/ExternalData/%(algo)/%(hash)"
+)
+
+
+
+# Tell ExternalData commands to transform raw files to content links.
+set(ExternalData_LINK_CONTENT MD5)
+
+#SETIFEMPTY(MIDAS_REST_URL "http://midas.kitware.com/api/rest" CACHE STRING "The MIDAS server where testing data resides")
+#
+## Needed to set this for Slicer3 to find the test data directory
+#set(BRAINSCommonLib_DATA_DIRS "${PROJECT_SOURCE_DIR}/../BRAINSCommonLib/TestData")
+
+set(BRAINSFitTestName BRAINSFitTest_AffineRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --debugLevel 50
+)
+
+set(BRAINSFitTestName BRAINSFitTest_AffineRotationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_AffineScaleMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initializeTransformMode useMomentsAlign
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/scale.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_AffineScaleNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_AffineTranslationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MSE
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initializeTransformMode useMomentsAlign
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/translation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/translation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_AffineTranslationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MSE
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initializeTransformMode useMomentsAlign
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/translation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500,2500,500
+  --numberOfHistogramBins 200
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003,0.001,0.001
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D,Affine,BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineOnlyRescaleHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 1500
+  --numberOfHistogramBins 200
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initialTransform DATA{./TestData/Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat}
+  --transformType BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --debugLevel 10
+  --maxBSplineDisplacement 7.3
+  --projectedGradientTolerance 1e-4
+  --costFunctionConvergenceFactor 1e+9
+)
+## NOTE: 7.3 above was computed explicitly through testing.
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineBSplineRescaleHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 1500
+  --numberOfHistogramBins 200
+  --splineGridSize 7,5,6
+  --numberOfSamples 288000
+  --translationScale 250
+  --minimumStepLength 0.005
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initialTransform DATA{./TestData/Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.mat}
+  --transformType BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500,500
+  --numberOfHistogramBins 200
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003,0.01
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D,BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 1
+  --compareNumberOfPixelsTolerance 1500
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500,500
+  --numberOfHistogramBins 50
+  --numberOfMatchPoints 10
+  --histogramMatch
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003,0.01
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D,BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+
+set(BRAINSFitTestName BRAINSFitTest_RigidAnisotropicMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 1
+  --compareNumberOfPixelsTolerance 1500
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --fixedVolume DATA{./TestData/ANON0006_20_T1_dbg_splayed.nii.gz}
+  --movingVolume DATA{./TestData/ANON0006_20_T1_sag_twisted.nii.gz}
+  --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0
+  --minimumStepLength 0.001 --numberOfSamples 100000 --numberOfIterations 1500
+  --numberOfHistogramBins 200
+  --transformType Rigid --initializeTransformMode useMomentsAlign --translationScale 1000
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  )
+
+set(BRAINSFitTestName BRAINSFitTest_RigidMedianRotationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid
+  --initializeTransformMode useMomentsAlign
+  --medianFilterSize 1,1,1
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_RigidRotGeomNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 144000
+  --translationScale 500
+  --minimumStepLength 0.05,0.0050
+  --outputVolumePixelType short
+  --transformType Rigid,Rigid
+  --initializeTransformMode useGeometryAlign
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.geom.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_RigidRotaRotaRotNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.05,0.001,0.00075
+  --outputVolumePixelType uchar
+  --transformType Rigid,Rigid,Rigid
+  --initializeTransformMode useCenterOfHeadAlign
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_RigidRotationHeadMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --maskProcessingMode ROIAUTO
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_RigidRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid
+  --initializeTransformMode useMomentsAlign
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_RigidRotationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid
+  --interpolationMode WindowedSinc
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+set(BRAINSFitTestName BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid
+  --interpolationMode ResampleInPlace
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003
+  --outputVolumePixelType uchar
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --useRigid --useScaleVersor3D
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.rescale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleSkewVersorRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleSkewVersorRotationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleSkewVersorScaleMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1200
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initializeTransformMode useMomentsAlign
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/scale.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleSkewVersorScaleNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001,0.0001
+  --outputVolumePixelType uchar
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D
+  --permitParameterVariation 0,0,0,1,1,1
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/translation.rescale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --maskProcessingMode ROIAUTO
+  --initialTransform DATA{./TestData/Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.mat}
+  --transformType ScaleVersor3D
+  --permitParameterVariation 0,0,0,1,1,1,1,1,1
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/translation.rescale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleVersorRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleVersorRotationNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleVersorScaleMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --initializeTransformMode useMomentsAlign
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/scale.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_ScaleVersorScaleNoMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --initialTransform DATA{./TestData/Initializer_0.05_${BRAINSFitTestName}.mat}
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/scale.test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+if(Test_SignedDistanceData)
+ExternalData_add_test( FetchData NAME BRAINSFitTest_SignedDistanceData COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/TEST_output.nii.gz} ${BRAINSFit_BINARY_DIR}/Testing/TEST_output.nii.gz
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode 1
+  --fixedVolume DATA{./TestData/AtlasBrain_SignedDistance.nii.gz}
+  --movingVolume DATA{./TestData/Unoriented_RawBrain_SignedDistance.nii.gz}
+  --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0
+  --minimumStepLength 0.001 --numberOfSamples 75000 --numberOfIterations 1500
+  --numberOfHistogramBins 200
+  --transformType Rigid --initializeTransformMode useMomentsAlign --translationScale 1000
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/TEST.mat
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/TEST_output.nii.gz
+  )
+endif(Test_SignedDistanceData)
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineScaleRotationHeadMasksUShort)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 2505
+  --compareRadiusTolerance 1
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MMI
+  --backgroundFillValue 10000
+  --scaleOutputValues
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500,500
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003,0.01
+  --outputVolumePixelType ushort
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D,BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotationUShort.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+set(BRAINSFitTestName BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 1
+  --compareNumberOfPixelsTolerance 1900
+  BRAINSFitTest
+  --costMetric MMI
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500,2500,500
+  --numberOfHistogramBins 50
+  --numberOfMatchPoints 10
+  --histogramMatch
+  --splineGridSize 7,5,6
+  --numberOfSamples 144000
+  --translationScale 250
+  --minimumStepLength 0.01,0.003,0.01
+  --outputVolumePixelType short
+  --maskProcessingMode ROIAUTO
+  --initializeTransformMode useCenterOfHeadAlign
+  --transformType Rigid,ScaleVersor3D,BSpline
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/rotationUShort.rescale.rigid.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --maxBSplineDisplacement 7.3
+)
+
+set(BRAINSFitTestName BRAINSFitTest_NCMetricBrainToItself)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/test.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric NC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 25
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_NCAffineRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric NC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --debugLevel 50
+)
+
+set(BRAINSFitTestName BRAINSFitTest_NCScaleSkewVersorRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric NC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+
+set(BRAINSFitTestName BRAINSFitTest_MSEMetricBrainToItself)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/test.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MSE
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 25
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleVersor3D
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MSEAffineRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MSE
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --debugLevel 50
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MSEScaleSkewVersorRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MSE
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MCMetricBrainToItself)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/test.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 25
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid --initializeTransformMode useMomentsAlign
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --movingVolume DATA{./TestData/test.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MCMetricMaskBrainToItself)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/testMask.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.testMask.nii.gz
+  --compareIntensityTolerance 9
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 25
+  --numberOfHistogramBins 200
+  --numberOfSamples 72000
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Rigid --initializeTransformMode useMomentsAlign
+  --fixedVolume DATA{./TestData/testMask.nii.gz}
+  --movingVolume DATA{./TestData/testMask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.testMask.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MCAffineRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 7
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 777
+  BRAINSFitTest
+  --costMetric MC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType Affine
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  --debugLevel 50
+)
+
+set(BRAINSFitTestName BRAINSFitTest_MCScaleSkewVersorRotationMasks)
+ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --compareIntensityTolerance 11
+  --compareRadiusTolerance 0
+  --compareNumberOfPixelsTolerance 1000
+  BRAINSFitTest
+  --costMetric MC
+  --failureExitCode -1 --writeTransformOnFailure
+  --numberOfIterations 2500
+  --numberOfHistogramBins 200
+  --numberOfSamples 131072
+  --translationScale 250
+  --minimumStepLength 0.001
+  --outputVolumePixelType uchar
+  --transformType ScaleSkewVersor3D
+  --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+  --maskProcessingMode ROI
+  --fixedVolume DATA{./TestData/test.nii.gz}
+  --fixedBinaryVolume DATA{./TestData/test_mask.nii.gz}
+  --movingVolume DATA{./TestData/rotation.test.nii.gz}
+  --movingBinaryVolume DATA{./TestData/rotation.test_mask.nii.gz}
+  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+)
+
+# Start of broken metric tests
+# Add ", KS (Kappa Statistic for binary images with voxel value=255), MRSD (Mean Reciprocal Square Difference), MIH (Mutual Information Histogram), GD (Gradient Difference), CCH (Correlation Coefficient Histogram), MSEH (Mean Squared Error Histogram), NMIH (Normalized Mutual Information Histogram)" to the end of the description for costMetric in BRAINSFitPrimary.xml then add KS, MRSD, MIH, GD, CCH, MSEH, and NMIH as enumeration elements.
+set(RUN_EXTRA_METRIC_TESTS OFF)
+if(RUN_EXTRA_METRIC_TESTS)
+  # KullbackLeiblerCompareHistogramImageToImageMetric requires training images / infrastructure
+  # which is different from the other metrics, making it much harder to incorporate into the
+  # BRAINSFIT framework.  This test and the relevant code has been commented out for now.
+  #set(BRAINSFitTestName BRAINSFitTest_KLMetricBrainToItself)
+  #add_test(NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+  #  --compare ${BRAINSCommonLib_DATA_DIRS}/test.nii.gz
+  #            ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  #  --compareIntensityTolerance 9
+  #  --compareRadiusTolerance 0
+  #  --compareNumberOfPixelsTolerance 1000
+  #  BRAINSFitTest
+  #  --costMetric KL
+  #  --failureExitCode -1 --writeTransformOnFailure
+  #  --numberOfIterations 25
+  #  --numberOfHistogramBins 200
+  #  --numberOfSamples 72000
+  #  --translationScale 250
+  #  --minimumStepLength 0.001
+  #  --outputVolumePixelType uchar
+  #  --transformType ScaleVersor3D
+  #  --fixedVolume ${BRAINSCommonLib_DATA_DIRS}/test.nii.gz
+  #  --movingVolume ${BRAINSCommonLib_DATA_DIRS}/test.nii.gz
+  #  --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+  #  --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  #)
+
+  # The Kappa Statistic metric is meant for binary images which is why
+  # the fixed and moving images are binarized before the tranfsorm is calculated
+  # then the transform is applied to the input image.  This produces somethign
+  # close for gray scale images but in the next test using binary images it fails
+  # to converge even when given many iterations (which it shouldn't need, since
+  # it's registering the same image to itself).
+  set(BRAINSFitTestName BRAINSFitTest_KSMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric KS
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  set(BRAINSFitTestName BRAINSFitTest_KSMetricBrainMaskToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/testMask.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.testMask.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric KS
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid
+    #--initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/testMask.nii.gz}
+    --movingVolume DATA{./TestData/testMask.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.testMask.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+
+  set(BRAINSFitTestName BRAINSFitTest_KSAffineRotationMasks)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 7
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 777
+    BRAINSFitTest
+    --costMetric KS
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 2500
+    --numberOfHistogramBins 200
+    --numberOfSamples 131072
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Affine
+    --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+    --maskProcessingMode ROI
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --fixedBinaryVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/rotation.test.nii.gz}
+    --movingBinaryVolume DATA{./TestData/rotation.test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+    --debugLevel 50
+  )
+
+  set(BRAINSFitTestName BRAINSFitTest_KSScaleSkewVersorRotationMasks)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/${BRAINSFitTestName}.result.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 11
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric KS
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 2500
+    --numberOfHistogramBins 200
+    --numberOfSamples 131072
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType ScaleSkewVersor3D
+    --initialTransform DATA{./TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat}
+    --maskProcessingMode ROI
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --fixedBinaryVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/rotation.test.nii.gz}
+    --movingBinaryVolume DATA{./TestData/rotation.test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Fails to converge when registering a brain to itself.
+  set(BRAINSFitTestName BRAINSFitTest_MRSDMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric MRSD
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Segfault when running this test
+  set(BRAINSFitTestName BRAINSFitTest_MIHMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric MIH
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Fails to converge when registering a brain to itself.
+  set(BRAINSFitTestName BRAINSFitTest_GDMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric GD
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Segfault when running this test
+  set(BRAINSFitTestName BRAINSFitTest_CCHMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric CCH
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Segfault when running this test
+  set(BRAINSFitTestName BRAINSFitTest_MSEHMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric MSEH
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+
+  # Segfault when running this test
+  set(BRAINSFitTestName BRAINSFitTest_NMIHMetricBrainToItself)
+  ExternalData_add_test( FetchData NAME ${BRAINSFitTestName} COMMAND ${LAUNCH_EXE} $
+    --compare DATA{./TestData/test.nii.gz}
+              ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --compareIntensityTolerance 9
+    --compareRadiusTolerance 0
+    --compareNumberOfPixelsTolerance 1000
+    BRAINSFitTest
+    --costMetric NMIH
+    --failureExitCode -1 --writeTransformOnFailure
+    --numberOfIterations 25
+    --numberOfHistogramBins 200
+    --numberOfSamples 72000
+    --translationScale 250
+    --minimumStepLength 0.001
+    --outputVolumePixelType uchar
+    --transformType Rigid --initializeTransformMode useMomentsAlign
+    --fixedVolume DATA{./TestData/test.nii.gz}
+    --movingVolume DATA{./TestData/test.nii.gz}
+    --outputVolume ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.test.nii.gz
+    --outputTransform ${BRAINSFit_BINARY_DIR}/Testing/${BRAINSFitTestName}.mat
+  )
+endif(RUN_EXTRA_METRIC_TESTS)
+
+ExternalData_Add_Target( FetchData )  # Name of data management target
+
diff --git a/BRAINSFit/TestSuite/CommandLineWrarpperTester.cxx b/BRAINSFit/TestSuite/CommandLineWrarpperTester.cxx
new file mode 100644
index 00000000..52cd75f6
--- /dev/null
+++ b/BRAINSFit/TestSuite/CommandLineWrarpperTester.cxx
@@ -0,0 +1,36 @@
+/*=========================================================================
+
+  Program:   Insight Segmentation & Registration Toolkit
+  Module:    $HeadURL$
+  Language:  C++
+  Date:      $Date$
+  Version:   $Revision$
+
+  Copyright (c) Insight Software Consortium. All rights reserved.
+  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even 
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+     PURPOSE.  See the above copyright notices for more information.
+
+=========================================================================*/
+
+// This file is intended to be compiled and linked against a shared
+// library CLP to prevent the need to compile twice.
+
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifdef WIN32
+#define MODULE_IMPORT __declspec(dllimport)
+#else
+#define MODULE_IMPORT
+#endif
+
+extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char* []);
+
+int main(int argc, char** argv)
+{
+  return ModuleEntryPoint(argc, argv);
+}
diff --git a/BRAINSFit/TestSuite/Example.sh b/BRAINSFit/TestSuite/Example.sh
new file mode 100644
index 00000000..a3056a0e
--- /dev/null
+++ b/BRAINSFit/TestSuite/Example.sh
@@ -0,0 +1,6 @@
+#
+# Example run for BRAINSFit
+echo Registering test2.nii.gz to test.nii.gz.
+echo Using Affine transform type
+echo Output image registered.nii.gz
+BRAINSFit --FixedImage test.nii.gz --MovingImage test2.nii.gz --OutputImage registered.nii.gz --FitTransformType Affine
diff --git a/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5
new file mode 100644
index 00000000..65b24026
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_splayed.nii.gz.md5
@@ -0,0 +1 @@
+c34916939b720607bb5e288c14cf8b65
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5
new file mode 100644
index 00000000..320f6c3b
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_dbg_twisted.nii.gz.md5
@@ -0,0 +1 @@
+37a7b73290fc6811bd54239861fb24b1
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5
new file mode 100644
index 00000000..52b695fd
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/ANON0006_20_T1_sag_twisted.nii.gz.md5
@@ -0,0 +1 @@
+dda9fde8ee4fa034a6a56f4cc22f2f55
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/AtlasBrain_SignedDistance.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/AtlasBrain_SignedDistance.nii.gz.md5
new file mode 100644
index 00000000..1738bce2
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/AtlasBrain_SignedDistance.nii.gz.md5
@@ -0,0 +1 @@
+fbbd51cf6e360a5325d55434c61e4e3e
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5
new file mode 100644
index 00000000..cc7b9bd4
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.mask.md5
@@ -0,0 +1 @@
+e19a0452f8b647d05300906abb470fab
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5
new file mode 100644
index 00000000..49ce602f
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineExplicitOrigins_moving.nii.gz.md5
@@ -0,0 +1 @@
+3273a81d72e662100363dd182c54b47e
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5
new file mode 100644
index 00000000..7c8dad23
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.mat.md5
@@ -0,0 +1 @@
+19e4481a52fe3dc64c37e92fff751aac
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..8c04c046
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+5f96a6bb32258268ec6023e635cd92b9
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b8a5c384
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+9b6ab30aa97e6f2331a78fcec5b041b5
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5
new file mode 100644
index 00000000..62b2c5c8
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+2be56a4f3a852777fde1b49bd237ecf5
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..fb10ac56
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+05c6c173327d8351a0e5a62cc174ef91
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..5944f422
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+50070308caef3b2cac1a415d655673c9
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..53a730e8
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+723874386daa4e702ed360d796aa29c2
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
new file mode 100644
index 00000000..1de5149d
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.md5
@@ -0,0 +1 @@
+138d28d14b99e2fcab20b7d69b9aa353
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..937e25f3
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+03483aa7c3fb11844b96cab1ab8bb045
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7a92baca
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+85a4d6fbf1dba3aebdfec02de8141d15
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..abf6af46
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
+a756ebb4df7155221597b0923dc0177f
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5
new file mode 100644
index 00000000..0d936fea
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..14f9cbea
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5
new file mode 100644
index 00000000..ac55549b
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b80a5609
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5
new file mode 100644
index 00000000..dc63b0ae
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_KSAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
index 00000000..470257eb
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MCAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..7ce7c62d
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..4f272fc3
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..920ec378
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidMedianRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..4a46ef3e
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5
new file mode 100644
index 00000000..a88e0267
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5
new file mode 100644
index 00000000..b6ac08a2
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5
new file mode 100644
index 00000000..4b69b994
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.mat.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5
new file mode 100644
index 00000000..0eeda98f
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.output.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5
new file mode 100644
index 00000000..bbd9895e
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5
new file mode 100644
index 00000000..4fc26e4f
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
index 00000000..7184f50c
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_ScaleVersorScaleNoMasks.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSFitTest_rotation.input.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
index 00000000..582134f8
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/BRAINSROIAutoTest_GenerateBrainMask.result.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/FCOB-aftergridcomp.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
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@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/FCOB-grid.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/FCOB-trimmed.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/FCOB-trimmed.nii.gz.md5
new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/FCOB-trimmed.nii.gz.md5
@@ -0,0 +1 @@
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new file mode 100644
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--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/InitialDeformationField.nii.gz.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5
new file mode 100644
index 00000000..582e8ca5
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5
new file mode 100644
index 00000000..9ac3c221
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.md5
@@ -0,0 +1 @@
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diff --git a/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5 b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5
new file mode 100644
index 00000000..817f8c74
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.md5
@@ -0,0 +1 @@
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/rotation.rescale.test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/rotation.rescale.test.nii.gz.md5
new file mode 100644
index 00000000..1696efe4
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/rotation.rescale.test.nii.gz.md5
@@ -0,0 +1 @@
+3705b9d451b1eb52eb7c15d4d5650dd3
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/rotation.test.mask.md5 b/BRAINSFit/TestSuite/TestData/rotation.test.mask.md5
new file mode 100644
index 00000000..76739b82
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/rotation.test.mask.md5
@@ -0,0 +1 @@
+dd929140569763fdc31692061edd5595
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/rotation.test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/rotation.test.nii.gz.md5
new file mode 100644
index 00000000..060ecdef
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/rotation.test.nii.gz.md5
@@ -0,0 +1 @@
+e4891faada07461571c27c477e6d736d
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/rotation.test_mask.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/rotation.test_mask.nii.gz.md5
new file mode 100644
index 00000000..f3c10f78
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/rotation.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+989827131b94b75a201a7c4a946ca95b
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/rotationUShort.rescale.rigid.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/rotationUShort.rescale.rigid.nii.gz.md5
new file mode 100644
index 00000000..bc4abdab
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/rotationUShort.rescale.rigid.nii.gz.md5
@@ -0,0 +1 @@
+6eebd8c70081692ec757fed104333db3
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/scale.test.mask.md5 b/BRAINSFit/TestSuite/TestData/scale.test.mask.md5
new file mode 100644
index 00000000..cf52ccf4
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/scale.test.mask.md5
@@ -0,0 +1 @@
+da905ca3300899a672840bd7cc0261b4
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/scale.test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/scale.test.nii.gz.md5
new file mode 100644
index 00000000..7da1d1ea
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/scale.test.nii.gz.md5
@@ -0,0 +1 @@
+1fa2661a07130796300f23b66d7b5149
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/scale.test_mask.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/scale.test_mask.nii.gz.md5
new file mode 100644
index 00000000..7bea3b70
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/scale.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+5c57ed69a6dfbab1875ec00879aa6fe2
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/standard.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/standard.nii.gz.md5
new file mode 100644
index 00000000..06497ce7
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/standard.nii.gz.md5
@@ -0,0 +1 @@
+871ffb8f546e670f8cf2c53924728ae5
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/symmetricLogDemons1.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/symmetricLogDemons1.nii.gz.md5
new file mode 100644
index 00000000..9269895c
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/symmetricLogDemons1.nii.gz.md5
@@ -0,0 +1 @@
+753676d3bccf159980e4d8888f71047a
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/symmetricLogDemons2.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/symmetricLogDemons2.nii.gz.md5
new file mode 100644
index 00000000..162f858c
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/symmetricLogDemons2.nii.gz.md5
@@ -0,0 +1 @@
+9106e002e822398d1f9ee8a445b00c4e
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/test.mask.md5 b/BRAINSFit/TestSuite/TestData/test.mask.md5
new file mode 100644
index 00000000..670c239b
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/test.mask.md5
@@ -0,0 +1 @@
+befa5b791b4d8c63c667b3bcab1783ae
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/test.nii.gz.md5
new file mode 100644
index 00000000..dac50682
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/test.nii.gz.md5
@@ -0,0 +1 @@
+70518dc3306838ebf1a6b187d61a28e9
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/test2.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/test2.nii.gz.md5
new file mode 100644
index 00000000..f4204447
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/test2.nii.gz.md5
@@ -0,0 +1 @@
+fb295d462eba7b231de4dd31dbc7ae3a
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/testMask.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/testMask.nii.gz.md5
new file mode 100644
index 00000000..086eb819
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/testMask.nii.gz.md5
@@ -0,0 +1 @@
+9e82cbc341ff59b2b2fb38d071ba6ba9
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/test_mask.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/test_mask.nii.gz.md5
new file mode 100644
index 00000000..d3c10773
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/test_mask.nii.gz.md5
@@ -0,0 +1 @@
+5baf8e5fbcc414f3f4e84afd3de2f18a
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/thirionDemons.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/thirionDemons.nii.gz.md5
new file mode 100644
index 00000000..a313626a
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/thirionDemons.nii.gz.md5
@@ -0,0 +1 @@
+63ad8f465b46ce9e654fce1d6a2d294a
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/translation.rescale.test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/translation.rescale.test.nii.gz.md5
new file mode 100644
index 00000000..af6ca9e1
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/translation.rescale.test.nii.gz.md5
@@ -0,0 +1 @@
+cba09d76112bb66e183b6abcd5b7ec00
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/translation.test.mask.md5 b/BRAINSFit/TestSuite/TestData/translation.test.mask.md5
new file mode 100644
index 00000000..08e33e62
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/translation.test.mask.md5
@@ -0,0 +1 @@
+327b2c70900870ed68627c80af2426f5
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/translation.test.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/translation.test.nii.gz.md5
new file mode 100644
index 00000000..b99f87d5
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/translation.test.nii.gz.md5
@@ -0,0 +1 @@
+0acc2a5a1f20ed373c49103e189ba549
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/TestData/translation.test_mask.nii.gz.md5 b/BRAINSFit/TestSuite/TestData/translation.test_mask.nii.gz.md5
new file mode 100644
index 00000000..bfb95dd9
--- /dev/null
+++ b/BRAINSFit/TestSuite/TestData/translation.test_mask.nii.gz.md5
@@ -0,0 +1 @@
+bf6514195fffb4c61cc1f1894b24f59e
\ No newline at end of file
diff --git a/BRAINSFit/TestSuite/makexfrmedImage.cxx b/BRAINSFit/TestSuite/makexfrmedImage.cxx
new file mode 100644
index 00000000..6bb8fbbe
--- /dev/null
+++ b/BRAINSFit/TestSuite/makexfrmedImage.cxx
@@ -0,0 +1,127 @@
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include "itkIO.h"
+#include "ReadMask.h"
+#include 
+
+#ifndef M_PI
+#define M_PI 3.1415926
+#endif
+#ifndef M_TWOPI
+#define M_TWOPI ( 2.0 * M_PI )
+#endif
+inline double DEGREES(double x)
+{
+  double rval = x * ( M_PI / 180 );
+
+  return rval;
+}
+
+bool keepOutputs(false);
+
+//
+// typedefs
+typedef itk::Image ImageType;
+typedef itk::AffineTransform                        AffineTransformType;
+typedef itk::LinearInterpolateImageFunction InterpolatorType;
+typedef itk::ResampleImageFilter         ResampleImageFilter;
+
+//
+// apply an affine transform to an image, and
+// return the transformed image
+ImageType::Pointer
+Resample(ImageType::Pointer & inputImage,
+         AffineTransformType::Pointer & transform)
+{
+  ImageType::IndexType index = { { 0, 0, 0}};
+  ImageType::PointType origin;
+  ImageType::SizeType  size = inputImage->GetLargestPossibleRegion().GetSize();
+
+  InterpolatorType::Pointer interp = InterpolatorType::New();
+
+  interp->SetInputImage(inputImage);
+
+  ResampleImageFilter::Pointer resample =
+    ResampleImageFilter::New();
+  resample->SetInput(inputImage);
+  resample->SetSize(size);
+  resample->SetTransform(transform);
+  resample->SetInterpolator(interp);
+  resample->SetOutputStartIndex(index);
+  resample->SetOutputOrigin( inputImage->GetOrigin() );
+  resample->SetOutputSpacing( inputImage->GetSpacing() );
+  resample->Update();
+  ImageType::Pointer returnval = resample->GetOutput();
+  returnval->SetDirection( inputImage->GetDirection() );
+  return returnval;
+}
+
+int main(int argc, char * *argv)
+{
+  std::string startImageName( itksys::SystemTools::CollapseFullPath(argv[1]) );
+  std::string xfrmImageName( itksys::SystemTools::CollapseFullPath(argv[2]) );
+
+  // read input image
+  ImageType::Pointer startImage =
+    itkUtil::ReadImageCoronal(startImageName);
+
+  if( startImage.IsNull() )
+    {
+    std::cerr << "Can't read test image "
+              << startImageName << std::endl;
+    exit(3);
+    }
+
+  AffineTransformType::Pointer transform = AffineTransformType::New();
+
+  ImageType::SpacingType spacing = startImage->GetSpacing();
+  ImageType::PointType   origin = startImage->GetOrigin();
+  ImageType::SizeType    size = startImage->GetLargestPossibleRegion().GetSize();
+
+  // do rotation around image center;
+  double imageCenter[3];
+  imageCenter[0] = -1 * ( origin[0] + spacing[0] * size[0] / 2.0 );
+  imageCenter[1] = -1 * ( origin[1] + spacing[1] * size[1] / 2.0 );
+  imageCenter[2] = -1 * ( origin[2] + spacing[1] * size[2] / 2.0 );
+  transform->Translate(imageCenter);
+
+  AffineTransformType::OutputVectorType scale;
+  scale[0] = 1.2;
+  scale[1] = 1.3;
+  scale[2] = 1.15;
+  transform->Scale(scale);
+
+  AffineTransformType::OutputVectorType rotationAxis;
+  rotationAxis[0] = 0.0; rotationAxis[1] = 0.0; rotationAxis[2] = 1.0;
+  transform->Rotate3D( rotationAxis, DEGREES(6.0) );
+  rotationAxis[0] = 1.0;                        rotationAxis[2] = 0.0;
+  transform->Rotate3D( rotationAxis, DEGREES(-5.0) );
+  rotationAxis[0] = 0.0; rotationAxis[1] = 1.0;
+  transform->Rotate3D( rotationAxis, DEGREES(4.0) );
+
+  AffineTransformType::OutputVectorType offset;
+  offset[0] = 4.0;
+  offset[1] = -3.0;
+  offset[2] = 2.0;
+  transform->Translate(offset);
+
+  imageCenter[0] *= -1;
+  imageCenter[1] *= -1;
+  imageCenter[2] *= -1;
+  transform->Translate(imageCenter);
+
+  ImageType::Pointer xfrmImage = Resample(startImage, transform);
+  itkUtil::WriteImage(xfrmImage, xfrmImageName);
+  exit(0);
+}
+
diff --git a/BRAINSFit/Transform.notes b/BRAINSFit/Transform.notes
new file mode 100644
index 00000000..79669943
--- /dev/null
+++ b/BRAINSFit/Transform.notes
@@ -0,0 +1,88 @@
+Notes:
+
+ITK transforms are centered based and take one from mm to mm
+
+AIR transforms appear to be center based and take one
+from isotropic voxels to isotropic voxels
+
+Here is what I expect to need:
+
+Moving                                      Fixed
+Result = S2 B+ Inv B-  Xfrm  A+ Inv A- S1   [orig]
+
+BPlus=[1 0 0 0; 0 255/2*1.015625  0 0; 0 0 1 0; 0 0 0 1]
+INV=[1 0 0 0; 0 -1 0 0; 0 0 0 1; 0 0 0 1]
+
+Where:
+  S1 is scaling from voxels to mm
+  S2 is scalling from mm to voxels
+  Inv is a conversion from right handed to left handed coordinate system (y axis)
+  A- is a negative shift in fixed image space (y axis)
+  A+ is a positive shift in fixed image space (y axis)
+
+  B- is a negative shift in moving image space (y axis)
+  B+ is a positive shift in moving image space (y axis)
+
+There sould also be an additional V2 and V1 matrices at the two
+ends of this equation that would map in the case of non-isotropic
+in either the fixed or moving image. The current solution is a
+multiplication of the air matrix to account for the non-istropic
+voxels in the moving image, but it would be nicer to make this part
+of our matrix multiplications.
+
+
+Here is what seems to work but is off by less than a pixel in (x, y, and z)
+
+Moving                                Fixed
+Result =  B- Inv B+  Xfrm  A- Inv A+ [orig]
+
+
+The result of this set of matrix multiplications is an affine
+transformation with one rotation in the
+opposite direction. The transpose of this matrix is used to correct this
+issue.
+
+The transform is then scaled to voxelDimension/pixel_size_r to
+account for non-isotropic voxels.
+
+Issues that are currently unresolved:
+  1) slight shift in x, y, z
+  2) why the conversion from voxel to mm is not needed
+
+
+Ways to cheat and make this run fast for debugging
+
+1. Run once and save the resulting transform using the the -otxfm option
+2. Rerun all future cases with the -itxfm option
+
+
+Standard parameters that seem to work well in general:
+-n 5
+-l 0.0001 0.00005 0.00001 0.000005 0.000001
+-i 2500 2500 2500 2500 2500
+
+
+1st Run
+--------
+export PathToRegressionTest=~/src/regressiontest
+MutualRegistration -type ushort -s $PathToRegressionTest/SGI/MR/5x-B2/TEST/10_ACPC/14831300_10_T1_strict.img \
+           -r $PathToRegressionTest/SGI/MR/5x-B2/TEST/31_003/T2_axial.img \
+           -o test.img \
+           -n 5 \
+           -l 0.0001 0.00005 0.00001 0.000005 0.000001 \
+           -i 2500 2500 2500 2500 2500 \
+           -otxfm test.dat
+
+
+Subsequent Runs
+---------------
+MutualRegistration -type ushort -s $PathToRegressionTest/SGI/MR/5x-B2/TEST/10_ACPC/14831300_10_T1_strict.img \
+           -r $PathToRegressionTest/SGI/MR/5x-B2/TEST/31_003/T2_axial.img \
+           -o test.img \
+           -n 5 \
+           -l 0.0001 0.00005 0.00001 0.000005 0.000001 \
+           -i 2500 2500 2500 2500 2500 \
+           -itxfm test.dat
+
+
+By default it will save an air16 file called  temp.air16 in the present working directory
diff --git a/BRAINSInitializedControlPoints/README b/BRAINSInitializedControlPoints/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSInitializedControlPoints/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSMultiModeSegment/README b/BRAINSMultiModeSegment/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSMultiModeSegment/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSMush/README b/BRAINSMush/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSMush/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSROIAuto/README b/BRAINSROIAuto/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSROIAuto/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSResample/README b/BRAINSResample/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/BRAINSResample/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/BRAINSStandAlone.cmake b/BRAINSStandAlone.cmake
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/BRAINSStandAlone.cmake
@@ -0,0 +1 @@
+
diff --git a/CMake/CompilerFlagSettings.cmake b/CMake/CompilerFlagSettings.cmake
new file mode 100644
index 00000000..1953b2cc
--- /dev/null
+++ b/CMake/CompilerFlagSettings.cmake
@@ -0,0 +1,60 @@
+# To create a portable build system, it is best to not
+# test for platforms, but to test for features.
+#
+# Instead of testing "if Windows then do this", test for
+# "if the -Wno-invalid-offsetof flag works then use it".
+# You can do that with the CheckCCompilerFlag module,
+# for example:
+
+include(CheckCCompilerFlag)
+include(CheckCXXCompilerFlag)
+
+#
+# this functions loops through the list to add the flags
+# supported by the current compiler
+function(test_cc_flags c_flag_var flag_list)
+  set(local_c_flags "")
+  foreach(flag IN LISTS ${flag_list})
+    check_c_compiler_flag(${flag} C_HAS${flag})
+    if(${C_HAS${flag}})
+      set(local_c_flags "${local_c_flags} ${flag}")
+    endif()
+  endforeach(flag)
+  set(${c_flag_var} "${local_c_flags}" PARENT_SCOPE)
+endfunction(test_cc_flags)
+
+#
+# this functions loops through the list to add the flags
+# supported by the current compiler
+function(test_cxx_flags cxx_flag_var flag_list)
+  set(local_cxx_flags "")
+  foreach(flag IN LISTS ${flag_list})
+    check_cxx_compiler_flag(${flag} CXX_HAS${flag})
+    if(${CXX_HAS${flag}})
+      set(local_cxx_flags "${local_cxx_flags} ${flag}")
+    endif()
+  endforeach(flag)
+  set(${cxx_flag_var} "${local_cxx_flags}" PARENT_SCOPE)
+endfunction(test_cxx_flags)
+
+#-pedantic
+set(common_flags_to_test
+-Wall
+-Wextra
+#-Wshadow
+-Wlong-long
+-fopenmp
+)
+
+set(cc_flags_to_test ${common_flags_to_test})
+
+test_cc_flags(C_RELEASE_DESIRED_FLAGS cc_flags_to_test)
+test_cc_flags(C_DEBUG_DESIRED_FLAGS cc_flags_to_test)
+
+set(cxx_flags_to_test ${common_flags_to_test} -Wno-invalid-offsetof )
+test_cxx_flags(CXX_RELEASE_DESIRED_FLAGS cxx_flags_to_test)
+test_cxx_flags(CXX_DEBUG_DESIRED_FLAGS cxx_flags_to_test)
+# message("C_DEBUG_DESIRED_FLAGS ${C_DEBUG_DESIRED_FLAGS}")
+# message("CXX_DEBUG_DESIRED_FLAGS ${CXX_DEBUG_DESIRED_FLAGS}")
+# message("C_RELEASE_DESIRED_FLAGS ${C_RELEASE_DESIRED_FLAGS}")
+# message("CXX_RELEASE_DESIRED_FLAGS ${CXX_RELEASE_DESIRED_FLAGS}")
diff --git a/CMake/SlicerMacroEmptyExternalProject.cmake b/CMake/SlicerMacroEmptyExternalProject.cmake
new file mode 100644
index 00000000..122a3403
--- /dev/null
+++ b/CMake/SlicerMacroEmptyExternalProject.cmake
@@ -0,0 +1,40 @@
+###########################################################################
+#
+#  Library:   CTK
+#
+#  Copyright (c) Kitware Inc.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.commontk.org/LICENSE
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+###########################################################################
+
+# See http://github.com/commontk/CTK/blob/master/CMake/ctkMacroEmptyExternalProject.cmake
+
+#
+# Convenient macro allowing to define a "empty" project in case an external one is provided
+# using for example _DIR.
+# Doing so allows to keep the external project dependency system happy.
+#
+macro(SlicerMacroEmptyExternalProject proj dependencies)
+
+  ExternalProject_Add(${proj}
+    SOURCE_DIR ${CMAKE_BINARY_DIR}/EMPTY_${proj}
+    BINARY_DIR EMPTY_${proj}-build
+    DOWNLOAD_COMMAND ""
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ""
+    DEPENDS
+      ${dependencies}
+    )
+endmacro()
diff --git a/CMake/sparselibSetup.cmake b/CMake/sparselibSetup.cmake
new file mode 100644
index 00000000..a4dc4be6
--- /dev/null
+++ b/CMake/sparselibSetup.cmake
@@ -0,0 +1,27 @@
+
+include_directories(${SPHARMPDM_SOURCE_DIR}/Libraries/SparseLibMVIml)
+link_directories(${SPHARMP_BINARY_DIR}/bin)
+
+# here prepared only for ISO C++ compatibles compilers
+
+# IBM xlC  v. 1.1
+# CCCFLAGS        = -DCOMPLEX=complex
+# LDFLAGS         = -lm -lcomplex
+
+# Sun C++ 4.0.1
+# CCCFLAGS        = -DMV_VECTOR_BOUNDS_CHECK -g -DCOMPLEX_OSTREAM -DCOMPLEX=complex
+# LDFLAGS         =   -lm -lcomplex
+
+# g++ v. 2.6.3
+# CCCFLAGS                =   -O5 '-DCOMPLEX=std::complex'
+# LDFLAGS                 =   -lm
+
+
+if(WIN32)
+add_definitions("-DCOMPLEX=std::complex")
+else(WIN32)
+add_definitions('-DCOMPLEX=std::complex')
+endif(WIN32)
+
+link_libraries(SparseMatrixLib)
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 00000000..e0c87698
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,27 @@
+project(BRAINSStandAlone)
+cmake_minimum_required(VERSION 2.8)
+
+#-----------------------------------------------------------------------------
+# Set a default build type if none was specified
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to 'Release' as none was specified.")
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+#-----------------------------------------------------------------------------
+# Superbuild Option - Enabled by default
+#-----------------------------------------------------------------------------
+option(BRAINSStandAlone_SUPERBUILD "Build Slicer and the projects it depends on via SuperBuild.cmake." ON)
+mark_as_advanced(BRAINSStandAlone_SUPERBUILD)
+#-----------------------------------------------------------------------------
+# Superbuild script
+#-----------------------------------------------------------------------------
+if(BRAINSStandAlone_SUPERBUILD)
+  include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
+  return()
+else()
+  include("${CMAKE_CURRENT_SOURCE_DIR}/BRAINSStandAlone.cmake")
+endif()
+
diff --git a/GTRACT/README b/GTRACT/README
new file mode 100644
index 00000000..0534a354
--- /dev/null
+++ b/GTRACT/README
@@ -0,0 +1 @@
+TODO: http:www.nitrc.org is the primary home of managing this project.
diff --git a/README b/README
index bb416ae1..d4d3548d 100644
--- a/README
+++ b/README
@@ -1,2 +1,20 @@
-This is a place for holding the StandAlone applications for building BRAINSTools.
+The BRAINSStandAlone is a harness to assist in building the many
+BRAINSTools under development.
+
+Developers should run the "GitSetupEnvironmnet.sh" script to get started.
+
+
+Example session for a clean build:
+mkdir ~/src/mytester
+cd ~/src/mytester
+git clone git://github.com/BRAINSia/BRAINSStandAlone.git
+cd BRAINSStandAlone/
+bash GitSetupEnvironmnet.sh
+mkdir -p ../BRAINSStandAlone-build
+cd ../BRAINSStandAlone-build/
+CC=/usr/bin/gcc-4.2 CXX=/usr/bin/g++-4.2 ccmake ../BRAINSStandAlone -DUSE_BRAINSFit:BOOL=ON -DUSE_BRAINSConstellationDetector:BOOL=ON -DUSE_BRAINSABC:BOOL=ON
+make -j24 -k ; ## NOTE:  The fetching of data still has problems with parallel builds, so we need to restart it a efw times
+make
+make
+make
 
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
new file mode 100644
index 00000000..321d47f8
--- /dev/null
+++ b/SuperBuild.cmake
@@ -0,0 +1,171 @@
+find_package(Git REQUIRED)
+include(ExternalProject)
+enable_language(C)
+enable_language(CXX)
+
+if(NOT SETIFEMPTY)
+macro(SETIFEMPTY)
+  set(KEY ${ARGV0})
+  set(VALUE ${ARGV1})
+  if(NOT ${KEY})
+    set(${ARGV})
+  endif(NOT ${KEY})
+endmacro(SETIFEMPTY KEY VALUE)
+endif(NOT SETIFEMPTY)
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
+SETIFEMPTY(CMAKE_BUNDLE_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_BINARY_DIR}/bin)
+link_directories(${CMAKE_LIBRARY_OUTPUT_DIRECTORY} ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+#-----------------------------------------------------------------------------
+# Update CMake module path
+#------------------------------------------------------------------------------
+
+set(CMAKE_MODULE_PATH
+  ${CMAKE_SOURCE_DIR}/CMake
+  ${CMAKE_SOURCE_DIR}/SuperBuild
+  ${CMAKE_BINARY_DIR}/CMake
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  ${CMAKE_CURRENT_SOURCE_DIR}/CMake #  CMake directory
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/CMake # CMake directory
+  ${CMAKE_MODULE_PATH}
+  )
+
+#-----------------------------------------------------------------------------
+# Platform check
+#-----------------------------------------------------------------------------
+
+set(PLATFORM_CHECK true)
+
+if(PLATFORM_CHECK)
+  # See CMake/Modules/Platform/Darwin.cmake)
+  #   6.x == Mac OSX 10.2 (Jaguar)
+  #   7.x == Mac OSX 10.3 (Panther)
+  #   8.x == Mac OSX 10.4 (Tiger)
+  #   9.x == Mac OSX 10.5 (Leopard)
+  #  10.x == Mac OSX 10.6 (Snow Leopard)
+  if (DARWIN_MAJOR_VERSION LESS "9")
+    message(FATAL_ERROR "Only Mac OSX >= 10.5 are supported !")
+  endif()
+endif()
+
+#-----------------------------------------------------------------------------
+# Prerequisites
+#------------------------------------------------------------------------------
+#
+# BRAINS4 Addition: install to the common library
+# directory, so that all libs/include etc ends up
+# in one common tree
+set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "Where all the prerequisite libraries go" FORCE)
+set(${CMAKE_PROJECT_NAME}_BUILD_TESTING ON CACHE BOOL "Turn on Testing for BRAINS")
+
+# Compute -G arg for configuring external projects with the same CMake generator:
+if(CMAKE_EXTRA_GENERATOR)
+  set(gen "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
+else()
+  set(gen "${CMAKE_GENERATOR}")
+endif()
+
+
+#-------------------------------------------------------------------------
+# augment compiler flags
+#-------------------------------------------------------------------------
+include(CompilerFlagSettings)
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_DEBUG_DESIRED_FLAGS}" )
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_DEBUG_DESIRED_FLAGS}" )
+else() # Release, or anything else
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_RELEASE_DESIRED_FLAGS}" )
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_RELEASE_DESIRED_FLAGS}" )
+endif()
+
+#------------------------------------------------------------------------------
+# Conditionnaly include ExternalProject Target
+#------------------------------------------------------------------------------
+
+set(ep_common_args
+  --no-warn-unused-cli
+  -DMAKECOMMAND:STRING=${MAKECOMMAND}
+  -DCMAKE_SKIP_RPATH:BOOL=ON
+  -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+  -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
+  -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
+  -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+  -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
+  -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
+  -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+  -DBUILD_EXAMPLES:BOOL=OFF
+  -DBUILD_TESTING:BOOL=${BUILD_TESTING}
+  -DCMAKE_GENERATOR:STRING=${CMAKE_GENERATOR}
+  -DCMAKE_EXTRA_GENERATOR:STRING=${CMAKE_EXTRA_GENERATOR}
+  -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
+  -DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
+  -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
+  -DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
+  -DCMAKE_BUNDLE_OUTPUT_DIRECTORY:PATH=${CMAKE_BUNDLE_OUTPUT_DIRECTORY}
+  -DCTEST_NEW_FORMAT:BOOL=ON
+  -DMEMORYCHECK_COMMAND_OPTIONS:STRING=${MEMORYCHECK_COMMAND_OPTIONS}
+  -DMEMORYCHECK_COMMAND:PATH=${MEMORYCHECK_COMMAND}
+  -DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS}
+  -DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS}
+  -DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
+  -DSITE:STRING=${SITE}
+  -DBUILDNAME:STRING=${BUILDNAME}
+)
+
+
+#------------------------------------------------------------------------------
+# Determine if building stand-alone, or using external versions of ITKv4
+# and SEM (i.e. for tight integration with Slicer)
+#------------------------------------------------------------------------------
+include(SlicerMacroEmptyExternalProject)
+option(USE_SYSTEM_ITKv4             "Build using an externally defined version of ITKv4" OFF)
+if(USE_SYSTEM_ITKv4)
+  find_package(ITK 4 REQUIRED)
+  include(${ITK_USE_FILE})
+  SlicerMacroEmptyExternalProject("ITKv4" "")
+else()
+  include(External_ITKv4)
+endif()
+
+option(USE_SYSTEM_SEM               "Build using an externally defined version of SEM"  OFF)
+if(USE_SYSTEM_SEM)
+  find_package(SlicerExecutionModel NO_MODULE REQUIRED GenerateCLP)
+  if(GenerateCLP_DIR)
+    include(${GenerateCLP_USE_FILE})
+  else(GenerateCLP_DIR)
+    message(FATAL_ERROR "Can't build without GenerateCLP. Please set GenerateCLP_DIR")
+  endif(GenerateCLP_DIR)
+  SlicerMacroEmptyExternalProject("SlicerExecutionModel" "")
+else()
+  set(SlicerExecutionModel_DEPENDENCIES ITKv4)
+  include(External_SlicerExecutionModel)
+endif()
+
+include(External_BRAINSTools)
+
+set(BRAINSStandAlone_DEPENDENCIES ${BRAINSTools_PROVIDES})
+#------------------------------------------------------------------------------
+# Configure and build
+#------------------------------------------------------------------------------
+set(proj BRAINSStandAlone)
+ExternalProject_Add(${proj}
+  DEPENDS ${BRAINSStandAlone_DEPENDENCIES}
+  DOWNLOAD_COMMAND ""
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
+  BINARY_DIR BRAINSStandAlone-build
+  CMAKE_GENERATOR ${gen}
+  CMAKE_ARGS
+    ${ep_common_args}
+    -DBRAINSStandAlone_SUPERBUILD:BOOL=OFF
+    -DADDITIONAL_CXX_FLAGS:STRING=${ADDITIONAL_CXX_FLAGS}
+    -DGIT_EXECUTABLE:FILEPATH=${GIT_EXECUTABLE}
+    # ITK
+    -DITK_DIR:PATH=${ITK_DIR}
+    # VTK
+    -DVTK_DIR:PATH=${VTK_DIR}
+    # SlicerExecutionModel_DIR
+    -DSlicerExecutionModel_DIR:PATH=${SlicerExecutionModel_DIR}
+  INSTALL_COMMAND ""
+  )
diff --git a/SuperBuild/External_BRAINSTools.cmake b/SuperBuild/External_BRAINSTools.cmake
new file mode 100644
index 00000000..336d3df3
--- /dev/null
+++ b/SuperBuild/External_BRAINSTools.cmake
@@ -0,0 +1,147 @@
+## The purpose of this file is to provide a common way
+## to build all the BRAINSTools for distribution in
+## various build environments.
+
+
+## This macro builds each of the BRAINSTools Components.
+macro(BuildExtPackage PackageName PACKAGE_DEPENDANCIES)
+  ## The following assumes that each PackageName
+  ## is a git submodule of the current ${CMAKE_CURRENT_SOURCE_DIR}
+  ## that was created with a command similar to:
+  ## cd ${CMAKE_CURRENT_SOURCE_DIR} 
+  ## git submodule add -b master -- git://github.com/BRAINSia/BRAINSABC.git
+  ## git submodule init
+  ## git submodule update
+  set(SRCCMDS SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${PackageName} )
+  if(0) ## TODO:  if PACKAGE_DEPENDANCIES contains VTK, then add -DVTK_DIR:
+    set(VTK_BUILD_FLAGS
+                 -DVTK_DIR:PATH=${VTK_DIR}
+                 )
+  elseif()
+    set(VTK_BUILD_FLAGS "")
+  endif()
+  if(0) ## TODO:  if PACKAGE_DEPENDANCIES contains OpenCV, then add -DVTK_DIR:
+    set(OpenCV_BUILD_FLAGS
+                 -DOpenCV_DIR:PATH=${OpenCV_DIR}
+                 )
+  elseif()
+    set(OpenCV_BUILD_FLAGS "")
+  endif()
+  if(0) ## TODO:  if PACKAGE_DEPENDANCIES contains Qt, then add -DVTK_DIR:
+    set(QT_BUILD_FLAGS
+                -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE}
+                -D${CMAKE_PROJECT_NAME}_USE_QT:BOOL=${${CMAKE_PROJECT_NAME}_USE_QT}
+                )
+  elseif()
+    set(QT_BUILD_FLAGS "")
+  endif()
+
+  if(NOT INTEGRATE_WITH_SLICER)
+    set(INTEGRATE_WITH_SLICER OFF)
+  endif()
+
+  message(STATUS "                                    CONFIGUREING PROJECT ${PackageName} WITH : ${SlicerExecutionModel_DIR}")
+  message(STATUS " -DSlicerExecutionModel_DIR:PATH=${SlicerExecutionModel_DIR}")
+## Configure and build the package.
+  ExternalProject_Add(${PackageName}
+    ${SRCCMDS}
+    BINARY_DIR ${PackageName}-build
+    CMAKE_GENERATOR ${gen}
+    DEPENDS ${PACKAGE_DEPENDANCIES}
+    CMAKE_ARGS
+    ${ep_common_args}
+    -DSlicerExecutionModel_DIR:PATH=${SlicerExecutionModel_DIR}
+    -DITK_DIR:PATH=${ITK_DIR}
+    -DINTEGRATE_WITH_SLICER:BOOL=${INTEGRATE_WITH_SLICER}
+    -DSlicer_SOURCE_DIR:PATH=${Slicer_SOURCE_DIR}
+    -DBRAINSCommonLib_DIR:PATH=${BRAINSCommonLib_DIR}
+    -DBUILD_TESTING:BOOL=ON
+    -D${CMAKE_PROJECT_NAME}_USE_ITK4:BOOL=ON
+    ${VTK_BUILD_FLAGS}
+    ${OpenCV_BUILD_FLAGS}
+    ${QT_BUILD_FLAGS}
+    #INSTALL_COMMAND ""
+    #INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}
+    )
+
+## Force building the package every time (i.e. look for code changes).i
+## Without this step, after the first successful build, the
+## the package is never built again.  This means that source code
+## changes do not trigger rebuilds
+  ExternalProject_Add_Step(${PackageName} forcebuild
+    COMMAND ${CMAKE_COMMAND} -E remove
+    ${CMAKE_CURRENT_BUILD_DIR}/${PackageName}-prefix/src/${PackageName}-stamp/${PackageName}-build
+    DEPENDEES configure
+    DEPENDERS build
+    ALWAYS 1
+    )
+
+## Setup some common variables for each package.
+  set(${PackageName}_DEPEND "${proj}")
+  set(${PackageName}_DIR ${CMAKE_INSTALL_PREFIX}/lib/${PackageName})
+  set(${PackageName}_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${PackageName} )
+  message(STATUS "${CMAKE_PROJECT_NAME}")
+  message(STATUS "${PackageName}_DIR = ${CMAKE_INSTALL_PREFIX}/lib/${PackageName})
+  message(STATUS "${PackageName}_DIR = ${${PackageName}_DIR}})
+  list(APPEND BRAINSTools_PROVIDES ${PackageName})
+endmacro(BuildExtPackage)
+
+
+option(USE_BRAINSCommonLib             "Build BRAINSCommonLib"             ON)
+option(USE_BRAINSFit                   "Build BRAINSFit"                   OFF)
+#option(USE_BRAINSCut                   "Build BRAINSCut"                   OFF)
+option(USE_BRAINSABC                   "Build BRAINSABC"                   OFF)
+option(USE_BRAINSConstellationDetector "Build BRAINSConstellationDetector" OFF)
+
+#-----------------------------------------------------------------------------
+# BRAINSCommonLib
+#-----------------------------------------------------------------------------
+if(USE_BRAINSCommonLib)
+  ## This is required option(USE_BRAINSCommonLib "Build BRAINSCommonLib" ON)
+  BuildExtPackage(BRAINSCommonLib "SlicerExecutionModel")
+endif()
+
+#-----------------------------------------------------------------------------
+# BRAINSFit
+#-----------------------------------------------------------------------------
+if(USE_BRAINSFit)
+  BuildExtPackage(BRAINSFit "BRAINSCommonLib" )
+endif()
+
+#-----------------------------------------------------------------------------
+# BRAINSConstellationDetector
+#-----------------------------------------------------------------------------
+if(USE_BRAINSConstellationDetector)
+  BuildExtPackage(BRAINSConstellationDetector "BRAINSCommonLib" )
+endif()
+
+#-----------------------------------------------------------------------------
+# ReferenceAtlas
+#-----------------------------------------------------------------------------
+if(USE_BRAINSABC) # OR USE_BRAINSCut)
+  # Define the atlas subdirectory in one place
+  set(${CMAKE_PROJECT_NAME}_RUNTIME_DIR ${CMAKE_CURRENT_BINARY_DIR}/src/bin)
+  include(External_ReferenceAtlas)
+  list(APPEND ${CMAKE_PROJECT_NAME}_DEPENDENCIES ${ReferenceAtlas_DEPEND})
+endif()
+
+#-----------------------------------------------------------------------------
+# BRAINSABC
+#-----------------------------------------------------------------------------
+if(USE_BRAINSABC)
+  BuildExtPackage(BRAINSABC "BRAINSCommonLib;${ReferenceAtlas_DEPEND}" )
+endif()
+
+
+if(0)
+  BuildExtPackage(BRAINSResample "BRAINSCommonLib" )
+  BuildExtPackage(BRAINSROIAuto "BRAINSCommonLib" )
+  BuildExtPackage(GTRACT "BRAINSCommonLib" )
+  BuildExtPackage(BRAINSCut "BRAINSCommonLib;${OpenCV_DEPEND}" )
+  BuildExtPackage(BRAINSMush "BRAINSCommonLib" )
+  BuildExtPackage(BRAINSDemonWarp "BRAINSCommonLib" )
+  BuildExtPackage(BRAINSMultiModeSegment "BRAINSCommonLib" )
+  BuildExtPackage(BRAINSInitializedControlPoints "BRAINSCommonLib" )
+endif() ## Comment out things that are not yet ready
+
+
diff --git a/SuperBuild/External_ITKv4.cmake b/SuperBuild/External_ITKv4.cmake
new file mode 100644
index 00000000..b1e29325
--- /dev/null
+++ b/SuperBuild/External_ITKv4.cmake
@@ -0,0 +1,82 @@
+
+#-----------------------------------------------------------------------------
+# Get and build itk
+
+set(ITK_PYTHON_ARGS
+      -DPYTHON_EXECUTABLE:PATH=${${CMAKE_PROJECT_NAME}_PYTHON_EXECUTABLE}
+      -DPYTHON_INCLUDE_DIR:PATH=${${CMAKE_PROJECT_NAME}_PYTHON_INCLUDE}
+      -DPYTHON_LIBRARY:FILEPATH=${${CMAKE_PROJECT_NAME}_PYTHON_LIBRARY}
+      )
+
+# Sanity checks
+if(DEFINED ITK_DIR AND NOT EXISTS ${ITK_DIR})
+  message(FATAL_ERROR "ITK_DIR variable is defined but corresponds to non-existing directory")
+endif()
+
+
+if(NOT DEFINED ITK_DIR)
+  #
+  # this code fixes a loony problem with HDF5 -- it doesn't
+  # link properly if -fopenmp is used.
+  string(REPLACE "-fopenmp" "" ITK_CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
+  string(REPLACE "-fopenmp" "" ITK_CMAKE_CXX_FLAGS "${CMAKE_CX_FLAGS}")
+
+  set(proj ITKv4)  ## Use ITKv4 convention of calling it ITK
+  set(ITK_REPOSITORY git://itk.org/ITK.git)
+  #set(ITK_DIR ${CMAKE_INSTALL_PREFIX}/lib/cmake/ITK-4.0)
+  set(ITK_DIR ${CMAKE_BINARY_DIR}/${proj}-build)
+  #set(ITK_TAG_COMMAND GIT_TAG v4.0a08)
+  set(ITK_TAG_COMMAND GIT_TAG 096ef1c344960449d0f82cba8c22206a470412c1)
+  set(WrapITK_DIR ${CMAKE_INSTALL_PREFIX}/lib/cmake/ITK-4.0/WrapITK)
+  message(STATUS "ITK_WRAPPING=${ITK_WRAPPING}")
+  ExternalProject_Add(${proj}
+    GIT_REPOSITORY ${ITK_REPOSITORY}
+    ${ITK_TAG_COMMAND}
+    UPDATE_COMMAND ""
+    SOURCE_DIR ${proj}
+    BINARY_DIR ${proj}-build
+    CMAKE_GENERATOR ${gen}
+    CMAKE_ARGS
+      ${ep_common_args}
+    -DBUILD_EXAMPLES:BOOL=OFF
+    -DBUILD_TESTING:BOOL=OFF
+    -DITK_LEGACY_REMOVE:BOOL=ON
+    -DITK_BUILD_ALL_MODULES:BOOL=ON
+    -DITK_USE_REVIEW:BOOL=ON
+    -DUSE_WRAP_ITK:BOOL=${BUILD_SHARED_LIBS} ## HACK:  QUICK CHANGE
+    -DINSTALL_WRAP_ITK_COMPATIBILITY:BOOL=OFF
+    -DWRAP_float:BOOL=ON
+    -DWRAP_unsigned_char:BOOL=ON
+    -DWRAP_signed_short:BOOL=ON
+    -DWRAP_unsigned_short:BOOL=ON
+    -DWRAP_complex_float:BOOL=ON
+    -DWRAP_vector_float:BOOL=ON
+    -DWRAP_covariant_vector_float:BOOL=ON
+    -DWRAP_rgb_signed_short:BOOL=ON
+    -DWRAP_rgb_unsigned_char:BOOL=ON
+    -DWRAP_rgb_unsigned_short:BOOL=ON
+    -DWRAP_ITK_TCL:BOOL=OFF
+    -DWRAP_ITK_JAVA:BOOL=OFF
+    -DWRAP_ITK_PYTHON:BOOL=ON
+    ${ITK_PYTHON_ARGS}
+    ${FFTW_FLAGS}
+    #    ${CableSwig_FLAGS}
+    BUILD_COMMAND ${BUILD_COMMAND_STRING}
+    INSTALL_COMMAND ""
+    DEPENDS
+    ${Insight_DEPENDENCIES}
+    )
+else()
+  # The project is provided using ITK_DIR, nevertheless since other project may depend on ITK,
+  # let's add an 'empty' one
+  ExternalProject_Add(${proj}
+    SOURCE_DIR ${proj}
+    BINARY_DIR ${proj}-build
+    DOWNLOAD_COMMAND ""
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ""
+    DEPENDS
+    ${Insight_DEPENDENCIES}
+    )
+endif()
diff --git a/SuperBuild/External_ReferenceAtlas.cmake b/SuperBuild/External_ReferenceAtlas.cmake
new file mode 100644
index 00000000..b9600b59
--- /dev/null
+++ b/SuperBuild/External_ReferenceAtlas.cmake
@@ -0,0 +1,46 @@
+#
+# ReferenceAtlas is a reference set of prior-probabilities and atlas images.
+#
+if(DEFINED ReferenceAtlas_DIR AND NOT EXISTS ${ReferenceAtlas_DIR})
+  message(FATAL_ERROR "ReferenceAtlas_DIR variable is defined but corresponds to non-existing directory")
+endif()
+
+
+if(NOT DEFINED ReferenceAtlas_DIR)
+
+  set(ATLAS_VERSION 20110607)
+  set(ATLAS_URL http://www.psychiatry.uiowa.edu/users/hjohnson/ftp/Atlas_${ATLAS_VERSION}.tar.gz)
+  set(ATLAS_NAME Atlas/Atlas_${ATLAS_VERSION})
+
+  set(ReferenceAtlas_DEPEND ReferenceAtlas_${ATLAS_VERSION} )
+  set(proj ReferenceAtlas_${ATLAS_VERSION})
+  ExternalProject_add(${proj}
+    URL ${ATLAS_URL}
+    SOURCE_DIR ${proj}
+    BINARY_DIR ${proj}-build
+    UPDATE_COMMAND ""
+    CMAKE_GENERATOR ${gen}
+    CMAKE_ARGS  ${LOCAL_CMAKE_BUILD_OPTIONS}
+    --no-warn-unused-cli
+    -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
+    -DCMAKE_CXX_COMPILER:STRING=${CMAKE_CXX_COMPILER}
+    -DCMAKE_CXX_COMPILER_ARG1:STRING=${CMAKE_CXX_COMPILER_ARG1}
+    -DCMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
+    -DCMAKE_C_COMPILER_ARG1:STRING=${CMAKE_C_COMPILER_ARG1}
+    -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+    -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+    -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
+    -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
+    -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+    -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
+    -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
+    -DBUILD_EXAMPLES:BOOL=OFF
+    -DBUILD_TESTING:BOOL=OFF
+    -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
+    -DReferenceAtlas_XML_DIR:PATH=${${CMAKE_PROJECT_NAME}_RUNTIME_DIR}
+    -DATLAS_VERSION:STRING=${ATLAS_VERSION}
+    INSTALL_COMMAND ""
+    )
+  set(ReferenceAtlas_DIR ${proj}-build)
+
+endif(NOT DEFINED ReferenceAtlas_DIR)
diff --git a/SuperBuild/External_SlicerExecutionModel.cmake b/SuperBuild/External_SlicerExecutionModel.cmake
new file mode 100644
index 00000000..2f028cfb
--- /dev/null
+++ b/SuperBuild/External_SlicerExecutionModel.cmake
@@ -0,0 +1,63 @@
+if(NOT DEFINED git_protocol)
+set(git_protocol "git")
+endif()
+
+# Make sure this file is included only once
+get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE)
+if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
+  return()
+endif()
+set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)
+
+# Sanity checks
+if(DEFINED SlicerExecutionModel_DIR AND NOT EXISTS ${SlicerExecutionModel_DIR})
+  message(FATAL_ERROR "SlicerExecutionModel_DIR variable is defined but corresponds to non-existing directory")
+endif()
+
+# Set dependency list
+set(SlicerExecutionModel_DEPENDENCIES ${ITK_EXTERNAL_NAME})
+
+# Include dependent projects if any
+# SlicerMacroCheckExternalProjectDependency(SlicerExecutionModel)
+set(proj SlicerExecutionModel)
+
+# Set CMake OSX variable to pass down the external project
+set(CMAKE_OSX_EXTERNAL_PROJECT_ARGS)
+if(APPLE)
+  list(APPEND CMAKE_OSX_EXTERNAL_PROJECT_ARGS
+    -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
+    -DCMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}
+    -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET})
+endif()
+
+if(NOT DEFINED SlicerExecutionModel_DIR)
+  #message(STATUS "${__indent}Adding project ${proj}")
+  ExternalProject_Add(${proj}
+    GIT_REPOSITORY "${git_protocol}://github.com/Slicer/SlicerExecutionModel.git"
+    GIT_TAG "origin/master"
+    SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}
+    BINARY_DIR ${proj}-build
+    CMAKE_GENERATOR ${gen}
+    CMAKE_ARGS
+      ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
+      -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+      -DCMAKE_CXX_FLAGS:STRING=${ep_common_cxx_flags}
+      -DCMAKE_C_FLAGS:STRING=${ep_common_c_flags} # Unused
+      -DBUILD_TESTING:BOOL=OFF
+      -DITK_DIR:PATH=${ITK_DIR}
+      -DSlicerExecutionModel_LIBRARY_PROPERTIES:STRING=${Slicer_LIBRARY_PROPERTIES}
+      -DSlicerExecutionModel_INSTALL_BIN_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
+      -DSlicerExecutionModel_INSTALL_LIB_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
+      #-DSlicerExecutionModel_INSTALL_SHARE_DIR:PATH=${Slicer_INSTALL_ROOT}share/${SlicerExecutionModel}
+      -DSlicerExecutionModel_INSTALL_NO_DEVELOPMENT:BOOL=${Slicer_INSTALL_NO_DEVELOPMENT}
+    INSTALL_COMMAND ""
+    DEPENDS
+      ${SlicerExecutionModel_DEPENDENCIES}
+    )
+  set(SlicerExecutionModel_DIR ${CMAKE_BINARY_DIR}/${proj}-build)
+else()
+  # The project is provided using SlicerExecutionModel_DIR, nevertheless since other project may depend on SlicerExecutionModel,
+  # let's add an 'empty' one
+  #  SlicerMacroEmptyExternalProject(${proj} "${SlicerExecutionModel_DEPENDENCIES}")
+endif()
+