Merge commit 'v1.0.20170624-8-g87d2142' into debian

* commit 'v1.0.20170624-8-g87d2142': Fix for neurolabusc/dcm_qa#5 Fix rordenlab#116 [Consistent stdout when generating gradient tables](rordenlab#115) Update CMake files. Update note and warning message on OpenJPEG. Detect images compressed to multiple fragments and warn user Kludges for invalid JPEG2000 files Fix zip working directory in .travis.yml
neurodebian · Jul 24, 2017 · 3c58f65 · 3c58f65
2 parents 4015529 + 87d2142
commit 3c58f65
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diff --git a/.travis.yml b/.travis.yml
@@ -17,7 +17,7 @@ before_install:
 script:
   - mkdir build && cd build && cmake -DBATCH_VERSION=ON -DUSE_OPENJPEG=ON .. && make && cd -
   - export PATH=$PWD/build/bin:$PATH
-  - cd dcm_qa; ./batch.sh
+  - cd dcm_qa && ./batch.sh && cd -
 
 before_deploy:
   - export DATE=`date +%-d-%b-%Y`

diff --git a/COMPILE.md b/COMPILE.md
@@ -12,7 +12,7 @@ The text below generally describes how to build dcm2niix using the [GCC](https:/
 You can also build the software without C-make. The easiest way to do this is to run the function "make" from the "console" folder. Note that this only creates the default version of dcm2niix, not the optional batch version described above. The make command simply calls the g++ compiler, and if you want you can tune this for your build. In essence, the make function simply calls
 
 ```
-g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -DmyDisableJasper
+g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG
 ```
 
 The following sub-sections list how you can modify this basic recipe for your needs.
@@ -37,22 +37,24 @@ g++ -O3 -s -DmyDisableOpenJPEG -DmyDisableZLib -I. main_console.cpp nii_dicom.cp
 DICOM images can be stored as either raw data or compressed using one of many formats as described by the [transfer syntaxes](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Transfer_Syntaxes_and_Compressed_Images). One of the compressed formats is the lossy classic JPEG format (which is separate from and predates the lossy JPEG 2000 format). This software comes with the [NanoJPEG](http://keyj.emphy.de/nanojpeg/) library to handle these images. However, you can use the `myDisableClassicJPEG` compiler switch to remove this dependency. The resulting executable will be smaller but will not be able to convert images stored with this format.
 
 ```
-g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableClassicJPEG -DmyDisableOpenJPEG -DmyDisableJasper
+g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableClassicJPEG -DmyDisableOpenJPEG
 ```
 
 ##### USING LIBJPEG-TURBO TO DECODE CLASSIC JPEG
 
 By default, classic JPEG images will be decoded using the [compact NanoJPEG decoder](http://keyj.emphy.de/nanojpeg/). However, the compiler directive `myTurboJPEG`  will create an executable based on the [libjpeg-turbo](http://www.libjpeg-turbo.org) library. This library is a faster decoder and is the standard for many Linux distributions. On the other hand, the lossy classic JPEG is rarely used for DICOM images, so this compilation has extra dependencies and can result in a larger executable size (for static builds).
 
 ```
-g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -DmyDisableJasper -DmyTurboJPEG -I/opt/libjpeg-turbo/include /opt/libjpeg-turbo/lib/libturbojpeg.a
+g++ -dead_strip -O3 -I. main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -o dcm2niix -DmyDisableOpenJPEG -DmyTurboJPEG -I/opt/libjpeg-turbo/include /opt/libjpeg-turbo/lib/libturbojpeg.a
 ```
 
 ##### JPEG2000 BUILD
 
- If you want to build this with JPEG2000 decompression support using OpenJPEG. You will need to have the OpenJPEG 2.1 libraries installed (https://code.google.com/p/openjpeg/wiki/Installation). I suggest building static libraries where you would [download the code](https://github.com/uclouvain/openjpeg) and run
+You can compile dcm2niix to convert DICOM images compressed with the JPEG2000 [transfer syntaxes 1.2.840.10008.1.2.4.90 and 1.2.840.10008.1.2.4.91](https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Transfer_Syntaxes_and_Compressed_Images). This is optional, as JPEG2000 is very rare in DICOMs (usually only created by the proprietary DCMJP2K or OsiriX). Due to the challenges discussed below this is a poor choice for archiving DICOM data. Rather than support conversion with dcm2niix, a better solution would be to use DCMJP2K to do a DICOM-to-DICOM conversion to a more widely supported transfer syntax. Unfortunately, JPEG2000 saw poor adoption as a general image format. This situation is unlikely to change, as JPEG2000 only offered incremental benefits over the simpler classic JPEG, and is outperformed by the more recent HEIF. This has implications for DICOM, as there is little active development on libraries to decode JPEG2000. Indeed, the two popular open-source libraries that decode JPEG2000 have serious limitations for processing these images. Some JPEG2000 DICOM images can not be decoded by the default compilation of OpenJPEG library after version [2.1.0](https://github.com/uclouvain/openjpeg/issues/962). On the other hand, the Jasper library does not handle lossy [16-bit](https://en.wikipedia.org/wiki/JPEG_2000) images with good precision.
+
+You can build dcm2niix with JPEG2000 decompression support using OpenJPEG 2.1.0. You will need to have the OpenJPEG library installed (use the package manager of your linux distribution, Homebrew for macOS, or see [here](https://github.com/uclouvain/openjpeg/blob/master/INSTALL.md) if you want to build it yourself). If you want to use a more recent version of OpenJPEG, it must be custom-compiled with `-DOPJ_DISABLE_TPSOT_FIX` compiler flag. I suggest building static libraries where you would [download the code](https://github.com/uclouvain/openjpeg) and run
 ```
- cmake -DBUILD_SHARED_LIBS:bool=off .
+ cmake -DBUILD_SHARED_LIBS:bool=off -DOPJ_DISABLE_TPSOT_FIX:bool=on .
  make
  sudo make install
 ```
@@ -62,14 +64,19 @@ You should then be able to run then run:
 g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -lopenjp2
 ```
 
-But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these two options:
+But in my experience this works best if you explicitly tell the software how to find the libraries, so your compile will probably look like one of these options:
 
 ```
+#for MacOS
 g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/include/openjpeg-2.1 /usr/local/lib/libopenjp2.a
 ```
-
 ```
-g++ -O3 -dead_strip -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/lib /usr/local/lib/libopenjp2.a
+#For older Linux
+g++ -O3 -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -o dcm2niix -I/usr/local/lib /usr/local/lib/libopenjp2.a
+```
+```
+#For modern Linux
+g++ -O3 -s -I. main_console.cpp nii_dicom.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp jpg_0XC3.cpp ujpeg.cpp nii_foreign.cpp -lpthread -o dcm2niix -I/usr/local/include/openjpeg-2.2 ~/openjpeg-master/build/bin/libopenjp2.a
 ```
 
  If you want to build this with JPEG2000 decompression support using Jasper: You will need to have the Jasper (http://www.ece.uvic.ca/~frodo/jasper/) and libjpeg (http://www.ijg.org) libraries installed which for Linux users may be as easy as running 'sudo apt-get install libjasper-dev' (otherwise, see http://www.ece.uvic.ca/~frodo/jasper/#doc). You can then run:
@@ -84,7 +91,7 @@ This software can be compiled with VisualStudio 2015. This example assumes the c
 
 ```
 vcvarsall amd64
-cl /EHsc main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -DmyDisableOpenJPEG -DmyDisableJasper /odcm2niix
+cl /EHsc main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp nii_foreign.cpp -DmyDisableOpenJPEG /o dcm2niix
 ```
 
 ##### OSX BUILD WITH BOTH 32 AND 64-BIT SUPPORT
@@ -140,4 +147,4 @@ CXXFLAGS = -DmyUseCOut -DWX_PRECOMP ....
  i.) For a full refresh
 rm clipboard
 rm *.o
-make
+make
diff --git a/SuperBuild/External-OPENJPEG.cmake b/SuperBuild/External-OPENJPEG.cmake
@@ -12,4 +12,4 @@ ExternalProject_Add(openjpeg
         -DCMAKE_INSTALL_PREFIX=${DEP_INSTALL_DIR}
 )
 
-set(OPENJPEG_DIR ${DEP_INSTALL_DIR}/lib/openjpeg-2.1)
+set(OpenJPEG_DIR ${DEP_INSTALL_DIR}/lib/openjpeg-2.1)
diff --git a/SuperBuild/SuperBuild.cmake b/SuperBuild/SuperBuild.cmake
@@ -21,10 +21,10 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 option(USE_STATIC_RUNTIME "Use static runtime" ON)
 
 option(USE_SYSTEM_ZLIB "Use the system zlib" OFF)
-option(USE_SYSTEM_TURBOJPEG "Use the system TurboJPEG" OFF)
-option(USE_JASPER "Compile with Jasper support" OFF)
+option(USE_TURBOJPEG "Use TurboJPEG to decode classic JPEG" OFF)
+option(USE_JASPER "Build with JPEG2000 support using Jasper" OFF)
 
-option(USE_OPENJPEG "Build with OpenJPEG support" OFF)
+option(USE_OPENJPEG "Build with JPEG2000 support using OpenJPEG" OFF)
 option(BATCH_VERSION "Build dcm2niibatch for multiple conversions" OFF)
 
 include(ExternalProject)
@@ -42,38 +42,48 @@ endif()
 if(USE_OPENJPEG)
     message("-- Build with OpenJPEG: ${USE_OPENJPEG}")
 
-    find_package(PkgConfig)
-    if(PKG_CONFIG_FOUND)
-        pkg_check_modules(OPENJPEG libopenjp2)
-    endif()
-
-    if(OPENJPEG_FOUND)
-        set(OPENJPEG_DIR ${OPENJPEG_LIBDIR}/openjepg-2.1)
-        message("--     Using the system OpenJPEG")
+    if(OpenJPEG_DIR OR OPENJPEG_DIR)
+        set(OpenJPEG_DIR "${OpenJPEG_DIR}${OPENJPEG_DIR}" CACHE PATH "Path to OpenJPEG configuration file"  FORCE)
+        message("--     Using OpenJPEG library from ${OpenJPEG_DIR}")
     else()
-        include(${CMAKE_SOURCE_DIR}/SuperBuild/External-OPENJPEG.cmake)
-        list(APPEND DEPENDENCIES openjpeg)
-        set(BUILD_OPENJPEG TRUE)
-        message("--     Will build OpenJPEG from github")
+        find_package(PkgConfig)
+        if(PKG_CONFIG_FOUND)
+            pkg_check_modules(OPENJPEG libopenjp2)
+        endif()
+
+        if(OPENJPEG_FOUND)
+            set(OpenJPEG_DIR ${OPENJPEG_LIBDIR}/openjepg-2.1 CACHE PATH "Path to OpenJPEG configuration file" FORCE)
+            message("--     Using OpenJPEG library from ${OpenJPEG_DIR}")
+        else()
+            include(${CMAKE_SOURCE_DIR}/SuperBuild/External-OPENJPEG.cmake)
+            list(APPEND DEPENDENCIES openjpeg)
+            set(BUILD_OPENJPEG TRUE)
+            message("--     Will build OpenJPEG library from github")
+        endif()
     endif()
 endif()
 
 if(BATCH_VERSION)
     message("-- Build dcm2niibatch: ${BATCH_VERSION}")
 
-    find_package(PkgConfig)
-    if(PKG_CONFIG_FOUND)
-        pkg_check_modules(YAML-CPP yaml-cpp)
-    endif()
-
-    if(YAML-CPP_FOUND)
-        set(YAML-CPP_DIR ${YAML-CPP_LIBDIR}/cmake/yaml-cpp)
-        message("--     Using the system yaml-cpp")
+    if(YAML-CPP_DIR)
+        set(YAML-CPP_DIR ${YAML-CPP_DIR} CACHE PATH "Path to yaml-cpp configuration file"  FORCE)
+        message("--     Using yaml-cpp library from ${YAML-CPP_DIR}")
     else()
-        include(${CMAKE_SOURCE_DIR}/SuperBuild/External-YAML-CPP.cmake)
-        list(APPEND DEPENDENCIES yaml-cpp)
-        set(BUILD_YAML-CPP TRUE)
-        message("--     Will build yaml-cpp from github")
+        find_package(PkgConfig)
+        if(PKG_CONFIG_FOUND)
+            pkg_check_modules(YAML-CPP yaml-cpp)
+        endif()
+
+        if(YAML-CPP_FOUND)
+            set(YAML-CPP_DIR ${YAML-CPP_LIBDIR}/cmake/yaml-cpp CACHE PATH "Path to yaml-cpp configuration file"  FORCE)
+            message("--     Using yaml-cpp library from ${YAML-CPP_DIR}")
+        else()
+            include(${CMAKE_SOURCE_DIR}/SuperBuild/External-YAML-CPP.cmake)
+            list(APPEND DEPENDENCIES yaml-cpp)
+            set(BUILD_YAML-CPP TRUE)
+            message("--     Will build yaml-cpp library from github")
+        endif()
     endif()
 endif()
 
@@ -89,11 +99,11 @@ ExternalProject_Add(console
         -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}
         -DUSE_STATIC_RUNTIME:BOOL=${USE_STATIC_RUNTIME}
         -DUSE_SYSTEM_ZLIB:BOOL=${USE_SYSTEM_ZLIB}
-        -DUSE_SYSTEM_TURBOJPEG:BOOL=${USE_SYSTEM_TURBOJPEG}
-        -DUSE_SYSTEM_JASPER:BOOL=${USE_SYSTEM_JASPER}
+        -DUSE_TURBOJPEG:BOOL=${USE_TURBOJPEG}
+        -DUSE_JASPER:BOOL=${USE_JASPER}
          # OpenJPEG
         -DUSE_OPENJPEG:BOOL=${USE_OPENJPEG}
-        -DOpenJPEG_DIR:PATH=${OPENJPEG_DIR}
+        -DOpenJPEG_DIR:PATH=${OpenJPEG_DIR}
         # yaml-cpp
         -DBATCH_VERSION:BOOL=${BATCH_VERSION}
         -DYAML-CPP_DIR:PATH=${YAML-CPP_DIR}

diff --git a/console/CMakeLists.txt b/console/CMakeLists.txt
@@ -11,15 +11,24 @@ else()
     ucm_set_runtime(DYNAMIC)
 endif()
 
+# Basic CMake build settings
+set(CMAKE_BUILD_TYPE "Release" CACHE STRING
+    "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
+set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS  "Debug;Release;RelWithDebInfo;MinSizeRel")
+
 set(PROGRAMS dcm2niix)
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
     # using Clang
     add_definitions(-Wno-deprecated-register)
+    add_definitions(-fno-caret-diagnostics)
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-dead_strip")
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     # using GCC
     add_definitions(-Wno-unused-result)
+    if (${CMAKE_CXX_COMPILER_VERSION} VERSION_GREATER 4.7)
+        add_definitions(-fno-diagnostics-show-caret)
+    endif()
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
     # using Intel C++
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
@@ -56,30 +65,28 @@ if(USE_SYSTEM_ZLIB)
     target_link_libraries(dcm2niix ${ZLIB_LIBRARIES})
 endif()
 
-option(USE_SYSTEM_TURBOJPEG "Use the system TurboJPEG" OFF)
-if(USE_SYSTEM_TURBOJPEG)
+option(USE_TURBOJPEG "Use TurboJPEG to decode classic JPEG" OFF)
+if(USE_TURBOJPEG)
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(TurboJPEG REQUIRED libturbojpeg)
+    pkg_check_modules(TURBOJPEG REQUIRED libturbojpeg)
     add_definitions(-DmyTurboJPEG)
-    target_include_directories(dcm2niix PRIVATE ${TurboJPEG_INCLUDE_DIRS})
-    target_link_libraries(dcm2niix ${TurboJPEG_LIBRARIES})
+    target_include_directories(dcm2niix PRIVATE ${TURBOJPEG_INCLUDEDIR})
+    target_link_libraries(dcm2niix ${TURBOJPEG_LIBRARIES})
 endif()
 
-option(USE_JASPER "Compile with Jasper support" OFF)
+option(USE_JASPER "Build with JPEG2000 support using Jasper" OFF)
 if(USE_JASPER)
     find_package(Jasper REQUIRED)
     add_definitions(-DmyEnableJasper)
     target_include_directories(dcm2niix PRIVATE ${JASPER_INCLUDE_DIR})
     target_link_libraries(dcm2niix ${JASPER_LIBRARIES})
-else ()
-    add_definitions(-DmyDisableJASPER)
 endif()
 
-option(USE_OPENJPEG "Build with OpenJPEG support" OFF)
+option(USE_OPENJPEG "Build with JPEG2000 support using OpenJPEG" OFF)
 if(USE_OPENJPEG)
-    option(OpenJPEG_DIR "Path to OpenJPEG configuration file" "")
+    set(OpenJPEG_DIR "${OpenJPEG_DIR}${OPENJPEG_DIR}" CACHE PATH "Path to yaml-cpp configuration file" FORCE)
 
-    find_package(OpenJPEG)
+    find_package(OpenJPEG REQUIRED)
 
     if(WIN32)
         if(BUILD_SHARED_LIBS)
@@ -109,29 +116,31 @@ if(BATCH_VERSION)
         nii_ortho.cpp
         nii_dicom_batch.cpp)
 
-    option(YAML-CPP_DIR "Path to yaml-cpp configuration file" "")
+    set(YAML-CPP_DIR ${YAML-CPP_DIR} CACHE PATH "Path to yaml-cpp configuration file" FORCE)
 
-    find_package(YAML-CPP)
+    find_package(YAML-CPP REQUIRED)
     target_include_directories(dcm2niibatch PRIVATE ${YAML_CPP_INCLUDE_DIR})
     target_link_libraries(dcm2niibatch ${YAML_CPP_LIBRARIES})
 
     if(ZLIB_FOUND)
         add_definitions(-DmyDisableMiniZ)
+        target_include_directories(dcm2niibatch PRIVATE ${ZLIB_INCLUDE_DIRS})
         target_link_libraries(dcm2niibatch z)
     endif()
 
-    if(TurboJPEG_FOUND)
-        target_include_directories(dcm2niibatch PRIVATE ${TurboJPEG_INCLUDE_DIRS})
-        target_link_libraries(dcm2niibatch ${TurboJPEG_LIBRARIES})
+    if(TURBOJPEG_FOUND)
+        add_definitions(-DmyTurboJPEG)
+        target_include_directories(dcm2niibatch PRIVATE ${TURBOJPEG_INCLUDEDIR})
+        target_link_libraries(dcm2niibatch ${TURBOJPEG_LIBRARIES})
     endif()
 
     if(JASPER_FOUND)
+        add_definitions(-DmyEnableJasper)
+        target_include_directories(dcm2niibatch PRIVATE ${JASPER_INCLUDE_DIR})
         target_link_libraries(dcm2niibatch ${JASPER_LIBRARIES})
-    else()
-        add_definitions(-DmyDisableJASPER)
     endif()
 
-    if(USE_OPENJPEG)
+    if(OPENJPEG_FOUND)
         target_include_directories(dcm2niibatch PRIVATE ${OPENJPEG_INCLUDE_DIRS})
         target_link_libraries(dcm2niibatch ${OPENJPEG_LIBRARIES})
     else()

diff --git a/console/main_console.cpp b/console/main_console.cpp
@@ -23,7 +23,7 @@
 
 //Alternatively, windows users with VisualStudio can compile this project
 // vcvarsall amd64
-// cl /EHsc main_console.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -DmyDisableOpenJPEG -DmyDisableJasper /odcm2niix
+// cl /EHsc main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp -DmyDisableOpenJPEG /o dcm2niix
 
 
 //#define mydebugtest //automatically process directory specified in main, ignore input arguments
@@ -82,10 +82,9 @@ void showHelp(const char * argv[], struct TDCMopts opts) {
     #else
      #define kQstr ""
     #endif
-    printf("  -f : filename (%%a=antenna  (coil) number, %%c=comments, %%d=description, %%e echo number, %%f=folder name, %%i ID of patient, %%j seriesInstanceUID, %%k studyInstanceUID, %%m=manufacturer, %%n=name of patient, %%p=protocol,%s %%s=series number, %%t=time, %%u=acquisition number, %%x study ID; %%z sequence name; default '%s')\n", kQstr, opts.filename);
+    printf("  -f : filename (%%a=antenna  (coil) number, %%c=comments, %%d=description, %%e echo number, %%f=folder name, %%i ID of patient, %%j seriesInstanceUID, %%k studyInstanceUID, %%m=manufacturer, %%n=name of patient, %%p=protocol,%s %%s=series number, %%t=time, %%u=acquisition number, %%v=vendor, %%x=study ID; %%z sequence name; default '%s')\n", kQstr, opts.filename);
     printf("  -h : show help\n");
     printf("  -i : ignore derived, localizer and 2D images (y/n, default n)\n");
-    printf("  -t : text notes includes private patient details (y/n, default n)\n");
     printf("  -m : merge 2D slices from same series regardless of study time, echo, coil, orientation, etc. (y/n, default n)\n");
     printf("  -o : output directory (omit to save to input folder)\n");
     printf("  -p : Philips precise float (not display) scaling (y/n, default y)\n");

diff --git a/console/makefile b/console/makefile
@@ -6,4 +6,4 @@ ifneq ($(OS),Windows_NT)
 	endif
 endif
 all:
-	g++ $(CFLAGS) -O3 -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  -o dcm2niix -DmyDisableOpenJPEG -DmyDisableJasper
+	g++ $(CFLAGS) -O3 -I. main_console.cpp nii_foreign.cpp nii_dicom.cpp jpg_0XC3.cpp ujpeg.cpp nifti1_io_core.cpp nii_ortho.cpp nii_dicom_batch.cpp  -o dcm2niix -DmyDisableOpenJPEG