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Update Utilities.cxx #1418

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Jul 21, 2021
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Update Utilities.cxx #1418

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63477bc
Update Utilities.cxx
chiharusako Jun 17, 2021
707388f
Dummy edit to Chiharu's PR to re-trigger azure
AlexanderGetka-cbica Jun 17, 2021
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4 changes: 2 additions & 2 deletions src/applications/Utilities/src/Utilities.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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");
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