Testing CS's PR from my fork

Readme.md

@@ -12,7 +12,7 @@
     <img src="https://img.shields.io/badge/language-c%2B%2B11-blue.svg" />
 </p>
 
-CaPTk is a software platform, written in C++, for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer. CaPTk integrates advanced, validated tools performing various aspects of medical image analysis, that have been developed in the context of active clinical research studies and collaborations toward addressing real clinical needs. With emphasis given in its use as a very lightweight and efficient viewer, and with no prerequisites for substantial computational background, CaPTk aims to facilitate the swift translation of advanced computational algorithms into routine clinical quantification, analysis, decision making, and reporting workflow.
+CaPTk is a software platform, written in C++, for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer. CaPTk integrates advanced, validated tools performing various aspects of medical image analysis, that have been developed in the context of active clinical research studies and collaborations toward addressing real clinical needs. With emphasis given in its use as a very lightweight and efficient viewer, and with no prerequisites for substantial computational background, CaPTk aims to facilitate the swift translation of advanced computational algorithms into routine clinical quantification, analysis, decision making, and reporting workflow. 
 
 Its long-term goal is to provide widely used technology that leverages the value of advanced imaging analytics in cancer prediction, diagnosis, and prognosis, as well as in better understanding the biological mechanisms of cancer development.
 

azure-pipelines.yml

@@ -573,6 +573,7 @@ jobs:
 
     # submodule 
     - bash: |
+        export GIT_LFS_SKIP_SMUDGE=1
         git submodule update --init --recursive
 
       displayName: 'Git Submodule Init and Update'

src/applications/Utilities/src/Utilities.cxx

@@ -3,7 +3,7 @@
 #include "cbicaITKSafeImageIO.h"
 #include "cbicaUtilities.h"
 #include "cbicaITKUtilities.h"
-#include "DicomMetadataReader.h"
+#include "DicomMetadataReader.h" 
 
 #include "itkBoundingBox.h"
 #include "itkPointSet.h"
@@ -1264,7 +1264,7 @@ int main(int argc, char** argv)
   parser.addOptionalParameter("e2j", "extracted2joined", cbica::Parameter::FLOAT, "0-10", "The spacing in the new direction", "Pass the folder containing all images in '-i'");
   parser.addOptionalParameter("ejT", "extrac2joinToler", cbica::Parameter::FLOAT, "0-10", "The spacing tolerance in the original axes", "Only used of 'e2j' is passed", "Defaults to " + std::to_string(nifti2dicomSpacingTolerance));
   parser.addOptionalParameter("ls", "labelSimilarity", cbica::Parameter::FILE, "NIfTI Reference", "Calculate similarity measures for 2 label maps", "Pass the reference map after '-ls' and the comparison will be done with '-i'", "For images with more than 2 labels, individual label stats are also presented");
-  parser.addOptionalParameter("lsb", "lSimilarityBrats", cbica::Parameter::FILE, "NIfTI Reference", "Calculate BraTS similarity measures for 2 brain labels", "Pass the reference map after '-lsb' and the comparison will be done with '-i'", "Assumed labels in image are '1,2,4' and missing labels will be populate with '0'");
+  parser.addOptionalParameter("lsb", "lSimilarityBrats", cbica::Parameter::FILE, "NIfTI Reference", "Calculate BraTS similarity measures for 2 brain labels", "Pass the reference map (such as the ground truth labels that you would like to compare)", "after '-i' and the comparison will be done with '-lsb'", "Assumed labels in image are '1,2,4' and missing labels will be populate with '0'");
   parser.addOptionalParameter("hd", "hausdorffDist", cbica::Parameter::FILE, "NIfTI Reference", "Calculate the Hausdorff Distance for the input image and", "the one passed after '-hd'");
   parser.addOptionalParameter("co", "collectInfo", cbica::Parameter::BOOLEAN, "Dir with read", "Collects information about all images in input directory", "Input directory passed using '-i'", "Recursion defined using '-co 1'", "Output CSV passed using '-o'");
   parser.addOptionalParameter("cF", "collectFileName", cbica::Parameter::STRING, "File pattern", "The file pattern to check for in every file when collecting information", "Defaults to check all");