├── .azure_BRAINSTools_common.cmake ├── .clang-format ├── .clang-tidy ├── .editorconfig ├── .flake8 ├── .pep8 ├── .pre-commit-config.yaml ├── .toml ├── ARCHIVE ├── BRAINSTalairach │ ├── BRAINSTalairach.cxx │ ├── BRAINSTalairach.xml │ ├── BRAINSTalairachMask.cxx │ ├── BRAINSTalairachMask.xml │ ├── BndToVtk.cxx │ ├── BndToVtk.h │ ├── CMakeLists.txt │ ├── vtkTalairachConversion.cxx │ ├── vtkTalairachConversion.h │ ├── vtkTalairachGrid.cxx │ └── vtkTalairachGrid.h ├── BRAINSTexture │ ├── BRAINSTexture.cxx │ ├── CMakeLists.txt │ └── CenterOfROIInitTest.cxx └── CMAKE │ ├── External_Boost.cmake │ ├── External_Boost_buildboost.cmake │ ├── External_Boost_configureboost.cmake │ ├── External_CTKAPPLAUNCHER.cmake │ ├── External_Cppcheck.cmake │ ├── External_JPEG.cmake │ ├── External_KWStyle.cmake │ ├── External_RTK.cmake │ ├── External_TIFF.cmake │ ├── External_Uncrustify.cmake │ ├── External_qhull.cmake │ └── pcre_configure_step.cmake.in ├── AutoWorkup ├── BAW │ ├── AutoWorkup.py │ ├── BAWScreenShots.py │ ├── BAWantsRegistrationBuildTemplate.py │ ├── BRAINSABCext.py │ ├── BRAINSTalairachext.py │ ├── CreateFreeSufereScripts.py │ ├── CreateT1OnlyTrackOnFreeSufereScripts.py │ ├── DTIPrepext.py │ ├── DWIInACPCTest.py │ ├── DWIProcessingWorkflows │ │ ├── CSWorkflow.py │ │ ├── CorrectionWorkflow.py │ │ ├── DWIWF.py │ │ ├── EstimationWorkflow.py │ │ ├── FS_Extended_Labels_Config.csv │ │ ├── MeasurementWorkflow.py │ │ ├── TractographyWorkflow.py │ │ ├── neuro2012_Labels_Config.csv │ │ └── runCS.m │ ├── DWIWorkflow.py │ ├── DoMiniPigRegistrationPhase1.py │ ├── PipeLineFunctionHelpers.py │ ├── SessionDB.py │ ├── SimpleTestNipype.py │ ├── WorkupT1T2FreeSurfer_custom.py │ ├── WorkupT1T2PERSISTANCE_CHECK.py │ ├── __init__.py │ ├── atlasSmallIslandCleanup.py │ ├── baw_exp.py │ ├── fsscript.py │ ├── fswrap.py │ ├── local_generate_classes.py │ ├── runOneAW.py │ ├── unwrapimage.py │ ├── updateAutoWorkupFile.py │ ├── updateAutoWorkupFile_DWI.py │ ├── utilities │ │ ├── MALFLabel_neuromorphometrics_colortable.txt │ │ ├── __init__.py │ │ ├── bidsUtils.py │ │ ├── bidsUtils_test.py │ │ ├── configFileParser.py │ │ ├── configure_FS.py │ │ ├── configure_env.py │ │ ├── distributed.py │ │ ├── image_processing.py │ │ ├── measureVolumes.py │ │ ├── misc.py │ │ ├── node.sh.template │ │ ├── package_check.py │ │ ├── pathHandling.py │ │ ├── read_fiducial_points.py │ │ └── reportGenerator.py │ └── workflows │ │ ├── FixLabelMapsTools.py │ │ ├── WorkupAddsonBrainStem.py │ │ ├── WorkupAtlasDustCleanup.py │ │ ├── WorkupComputeLabelVolume.py │ │ ├── WorkupJointFusion.py │ │ ├── WorkupT1T2LandmarkInitialization.py │ │ ├── WorkupT1T2TissueClassify.py │ │ ├── __init__.py │ │ ├── atlasNode.py │ │ ├── baseline.py │ │ ├── crossValidate.py │ │ ├── databaseNode.py │ │ └── utils.py ├── CMakeLists.txt ├── README.md ├── Sphinx │ ├── BAW.rst │ ├── Extra.rst │ ├── Makefile │ ├── TestSuite.rst │ ├── bin.rst │ ├── brains.rst │ ├── conf.py │ ├── index.rst │ ├── logismosb.rst │ └── make.bat ├── TestSuite │ ├── CMakeLists.txt │ ├── DoIt.sh.in │ ├── HeliumTestExperiment.config │ ├── OSXTestExperiment.config │ ├── TestDataDescription.csv.in │ ├── TestExperiment.config.in │ ├── __init__.py │ ├── node.sh.template.nomodules │ ├── node.sh.template.test │ └── test_utilities.py ├── __init__.py ├── autorecon1.py ├── autorecon2.py ├── autorecon3.py ├── ba_maps.py ├── bawConfigurationTemplate.ini ├── brains │ ├── __init__.py │ ├── common │ │ ├── __init__.py │ │ └── fileio.py │ ├── config │ │ ├── __init__.py │ │ └── autoworkup.py │ └── metrics │ │ ├── __init__.py │ │ ├── partials.py │ │ └── segmentations.py ├── example │ ├── bawConfigurationTemplate.ini │ └── fixup_bids_BCD_failure.py ├── example_blacklist.csv ├── example_dwi.csv ├── install_python_tools.sh ├── logismosb │ ├── FreeSurferColorLUT.csv │ ├── RunFS.py │ ├── RunLOGISMOSB.py │ ├── __init__.py │ ├── abc_fs_equivelants.json │ ├── config.json │ ├── freesurfer_utils.py │ ├── fs_logb_config.json │ ├── fswm_label_info.xml │ ├── interfaces.py │ ├── maclearn │ │ ├── __init__.py │ │ ├── crossvalidation.py │ │ ├── data_collection.py │ │ ├── data_order.json │ │ ├── logismosb_maclearn_config.json │ │ ├── nipype_interfaces.py │ │ ├── predict.py │ │ ├── preprocess.py │ │ ├── script.py │ │ ├── testing.py │ │ ├── train_all.py │ │ ├── train_classifiers.py │ │ ├── training.py │ │ ├── vesselness.py │ │ └── workflows.py │ ├── utils │ │ ├── __init__.py │ │ ├── fs_thickness_measurements.py │ │ └── mesh2mask.py │ └── workflow.py ├── recon-all.py ├── requirements-dev.txt ├── requirements.txt ├── singleSession.py ├── subject_db.csv ├── template.py └── workflow_reconall.py ├── BRAINSABC ├── CMakeLists.txt ├── TestSuite │ ├── BRAINSABCSmallExtendedAtlasDefinition.xml.in │ ├── BRAINSABCTest.cxx │ ├── BlendImageFilterTest.cxx │ ├── CMakeLists.txt │ ├── TestLinearRegresionInstensityMatching.cxx │ ├── simpleEM.cxx │ └── simpleEM.xml ├── brainseg │ ├── AtlasCropImageSource.h │ ├── AtlasCropImageSource.hxx │ ├── AtlasDefinition.cxx │ ├── AtlasDefinition.h │ ├── AtlasRegistrationMethod.h │ ├── AtlasRegistrationMethod.hxx │ ├── AtlasRegistrationMethod_float+float.cxx │ ├── BRAINSABC.cxx │ ├── BRAINSABC.xml │ ├── BRAINSABCUtilities.cxx │ ├── BRAINSABCUtilities.h │ ├── BRAINSABCUtilities.hxx │ ├── BRAINSCleanMask.cxx │ ├── BRAINSCleanMask.xml │ ├── CMakeLists.txt │ ├── ComputeDistributions.h │ ├── DenoiseFiltering.h │ ├── EMSParameters.cxx │ ├── EMSParameters.h │ ├── EMSegmentationFilter.h │ ├── EMSegmentationFilter.hxx │ ├── EMSegmentationFilter_float+float.cxx │ ├── ESLR.cxx │ ├── ESLR.xml │ ├── GenerateLabelMapFromProbabilityMap.cxx │ ├── GenerateLabelMapFromProbabilityMap.xml │ ├── GeneratePurePlugMask.cxx │ ├── GeneratePurePlugMask.h │ ├── GeneratePurePlugMask.xml │ ├── LLSBiasCorrector.h │ ├── LLSBiasCorrector.hxx │ ├── MSTEdge.h │ ├── QHullMSTClusteringProcess.cxx │ ├── QHullMSTClusteringProcess.h │ ├── StandardizeMaskIntensity.cxx │ ├── filterFloatImages.cxx │ ├── filterFloatImages.h │ ├── itkBlendImageFilter.h │ ├── itkBlendImageFilter.hxx │ ├── itkIntegrityMetricMembershipFunction.h │ ├── itkIntegrityMetricMembershipFunction.hxx │ └── normalA-30.xml ├── common │ ├── Heap.h │ ├── Heap.hxx │ ├── Log.cxx │ ├── Log.h │ ├── mu.h │ ├── muCygwin.h │ ├── muException.h │ ├── muMacros.h │ ├── muUtils.h │ ├── testexc.cxx │ ├── testheap.cxx │ └── testmacro.cxx └── notes.BRAINSABC ├── BRAINSCommonLib ├── ApplicationBase.h ├── ApplicationBase.hxx ├── ApplyField.h ├── ApplyField.hxx ├── BRAINSCommonLib.cxx ├── BRAINSCommonLib.h.in ├── BRAINSCommonLibConfig.cmake ├── BRAINSCommonLibConfig.cmake.in ├── BRAINSCommonLibLauncher.c.in ├── BRAINSCommonLibWin32Header.h ├── BRAINSComputeLabels.cxx ├── BRAINSComputeLabels.h ├── BRAINSFitHelper.cxx ├── BRAINSFitHelper.h ├── BRAINSFitHelperTemplate.h ├── BRAINSFitHelperTemplate.hxx ├── BRAINSFitSyN.h ├── BRAINSFitUtils.h ├── BRAINSIntensityTransform.h ├── BRAINSMacro.h ├── BRAINSThreadControl.cxx ├── BRAINSThreadControl.h ├── BRAINSToolsVersion.cxx ├── BRAINSToolsVersion.h ├── BRAINSToolsVersionConfig.h.in ├── BRAINSTypes.h ├── BuildScripts │ ├── BRAINSLogo.bmp │ ├── BRAINSLogo.h │ ├── BRAINSLogo.ico │ ├── BRAINSLogo.png │ ├── BRAINSSEMCommandLineWrarpperTester.cxx │ ├── CMakeBRAINS3BuildMacros.cmake │ ├── CMakeLists.txt │ ├── License.txt │ ├── Module_Dummy.in │ ├── SEMCommanLineSharedLibraryWrapper.cxx │ ├── ValgrindSuppression.supp │ └── brains.kws.xml ├── CMakeLists.txt ├── CleanBrainLabelMap.h ├── ConvertToRigidAffine.h ├── CreateField.h ├── CreateField.hxx ├── CrossOverAffineSystem.h ├── CrossOverAffineSystem.hxx ├── DWIMetaDataDictionaryValidator.cxx ├── DWIMetaDataDictionaryValidator.h ├── DebugImageViewerClient.h ├── DebugImageWrite.h ├── ExtractSingleLargestRegion.cxx ├── ExtractSingleLargestRegion.h ├── GenericTransformImage.cxx ├── GenericTransformImage.h ├── GenericTransformImage.hxx ├── Imgmath.h ├── LinearRegressionIntensityMatching.h ├── PrettyPrintTable.h ├── ReadMask.h ├── SimpleXMLParserBase.h ├── Slicer3LandmarkIO.cxx ├── Slicer3LandmarkIO.h ├── Slicer3LandmarkWeightIO.cxx ├── Slicer3LandmarkWeightIO.h ├── StandardizeMaskIntensity.h ├── TestLargestForegroundFilledMaskImageFilter │ ├── CMakeLists.txt │ └── TestLargestForegroundFilledMaskImageFilter.cxx ├── TestSuite │ ├── AverageImageFilterTest.cxx │ ├── BRAINSCleanMask.cxx │ ├── CMakeLists.txt │ ├── DWIMetaDataDictionaryValidatorTest.cxx │ ├── DWIMetaDataDictionaryValidatorTests.cxx │ ├── DumpImageInfo.cxx │ ├── FindCenterOfBrain.cxx │ ├── FindCenterOfBrain.xml │ ├── PrettyPrintTableTest.cxx │ ├── Slicer3LandmarkIOTest.cxx │ └── itkResampleInPlaceImageFilterTest.cxx ├── TransformAdaptor.h ├── TransformAdaptor.hxx ├── TransformToDisplacementField.h ├── UseBRAINSCommonLib.cmake.in ├── brainsiaTestingComparisonImageFilter.h ├── brainsiaTestingComparisonImageFilter.hxx ├── genericRegistrationHelper.h ├── genericRegistrationHelper.hxx ├── itkAverageImageFilter.h ├── itkAverageImageFilter.hxx ├── itkBOBFFilter.h ├── itkBOBFFilter.hxx ├── itkBRAINSROIAutoImageFilter.h ├── itkBRAINSROIAutoImageFilter.hxx ├── itkBRAINSToolsTestMain.h ├── itkComputeHistogramQuantileThresholds.h ├── itkComputeHistogramQuantileThresholds.hxx ├── itkDiffusionTensor3DReconstructionWithMaskImageFilter.h ├── itkDiffusionTensor3DReconstructionWithMaskImageFilter.hxx ├── itkFindCenterOfBrainFilter.h ├── itkFindCenterOfBrainFilter.hxx ├── itkIO.h ├── itkInverseConsistentLandmarks.h ├── itkInverseConsistentLandmarks.hxx ├── itkLargestForegroundFilledMaskImageFilter.h ├── itkLargestForegroundFilledMaskImageFilter.hxx ├── itkMultiModeHistogramThresholdBinaryImageFilter.h ├── itkMultiModeHistogramThresholdBinaryImageFilter.hxx ├── itkOppositeImageFilter.h ├── itkOrthogonalize3DRotationMatrix.cxx ├── itkOrthogonalize3DRotationMatrix.h ├── itkOtsuHistogramMatchingImageFilter.h ├── itkOtsuHistogramMatchingImageFilter.hxx ├── itkResampleInPlaceImageFilter.h ├── itkResampleInPlaceImageFilter.hxx ├── itkScalarImagePortionToHistogramGenerator.h ├── itkScalarImagePortionToHistogramGenerator.hxx ├── itkV3TestKernel │ └── include │ │ ├── itkDifferenceImageFilter.h │ │ ├── itkFilterWatcher.h │ │ ├── itkPipelineMonitorImageFilter.h │ │ ├── itkPipelineMonitorImageFilter.hxx │ │ ├── itkRandomImageSource.h │ │ ├── itkRandomImageSource.hxx │ │ ├── itkTestDriverAfterTest.inc │ │ ├── itkTestDriverBeforeTest.inc │ │ ├── itkTestDriverInclude.h │ │ ├── itkTestDriverIncludeBuiltInIOFactories.h │ │ ├── itkTestDriverIncludeRequiredIOFactories.h │ │ ├── itkTestingComparisonImageFilter.h │ │ ├── itkTestingComparisonImageFilter.hxx │ │ ├── itkTestingExtractSliceImageFilter.h │ │ ├── itkTestingExtractSliceImageFilter.hxx │ │ ├── itkTestingMacros.h │ │ ├── itkTestingStretchIntensityImageFilter.h │ │ └── itkTestingStretchIntensityImageFilter.hxx └── vnl_index_sort.h ├── BRAINSConstellationDetector ├── CMakeLists.txt ├── Copyright.txt ├── README.md ├── TestSuite │ ├── BRAINSAlignMSPTest.cxx │ ├── BRAINSClipInferiorTest.cxx │ ├── BRAINSConstellationDetectorTest.cxx │ ├── BRAINSConstellationDetectorTest_outputVerificationScript_standard.sh │ ├── BRAINSConstellationModelerTest.cxx │ ├── BRAINSEyeDetectorTest.cxx │ ├── BRAINSTrimForegroundInDirectionTest.cxx │ ├── CMakeLists.txt │ ├── LandmarksCompare.cxx │ ├── LandmarksCompare.xml │ ├── TestlandmarksConstellationTrainingDefinitionIO.cxx │ ├── VersorTester.cxx │ ├── insertMidACPCpointTest.cxx │ ├── landmarksConstellationAlignerTest.cxx │ ├── landmarksConstellationWeightsTest.cxx │ └── obliq_setup.txt.in ├── buildTool.sh ├── docs │ ├── BCD_FAILED.txt │ ├── EMSP.fcsv │ ├── FAILING_CASES_NOTES.md │ ├── FixBCDFailure.sh │ ├── MANUAL_LANDMARKS_NOT_SET.txt │ ├── input_config_one_subject.config │ ├── newEMSP.fcsv │ └── test_lmks.py ├── gui │ ├── BRAINSConstellationDetectorGUI.cxx │ ├── BRAINSConstellationDetectorGUI.xml │ ├── CMakeLists.txt │ ├── QDelLabelDialogs.cxx │ ├── QFileDialogs.cxx │ ├── QHelpDialog.cxx │ ├── QLabelList.cxx │ ├── QSliceViewer.cxx │ ├── QVTKInteractionCallback.cxx │ └── include │ │ ├── QDelLabelDialogs.h │ │ ├── QFileDialogs.h │ │ ├── QHelpDialog.h │ │ ├── QLabelList.h │ │ ├── QSliceViewer.h │ │ └── QVTKInteractionCallback.h ├── landmarkStatistics │ ├── CMakeLists.txt │ ├── GenerateAverageLmkFile.cxx │ ├── GenerateAverageLmkFile.xml │ └── LmkStatistics.cxx └── src │ ├── BRAINSAlignMSP.cxx │ ├── BRAINSAlignMSP.xml │ ├── BRAINSClipInferior.cxx │ ├── BRAINSClipInferior.xml │ ├── BRAINSConstellationDetector.cxx │ ├── BRAINSConstellationDetector.xml │ ├── BRAINSConstellationDetector2.h │ ├── BRAINSConstellationDetector2.hxx │ ├── BRAINSConstellationDetectorPrimary.cxx │ ├── BRAINSConstellationDetectorPrimary.h │ ├── BRAINSConstellationDetectorVersion.h │ ├── BRAINSConstellationLandmarksTransform.cxx │ ├── BRAINSConstellationLandmarksTransform.xml │ ├── BRAINSConstellationModeler.cxx │ ├── BRAINSConstellationModeler.xml │ ├── BRAINSEyeDetector.cxx │ ├── BRAINSEyeDetector.xml │ ├── BRAINSHoughEyeDetector.h │ ├── BRAINSHoughEyeDetector.hxx │ ├── BRAINSLinearModelerEPCA.cxx │ ├── BRAINSLinearModelerEPCA.h │ ├── BRAINSLinearModelerEPCA.xml │ ├── BRAINSLmkTransform.cxx │ ├── BRAINSLmkTransform.xml │ ├── BRAINSTransformFromFiducials.cxx │ ├── BRAINSTransformFromFiducials.xml │ ├── BRAINSTrimForegroundInDirection.cxx │ ├── BRAINSTrimForegroundInDirection.xml │ ├── BinaryMaskEditorBasedOnLandmarks.cxx │ ├── BinaryMaskEditorBasedOnLandmarks.xml │ ├── CMakeLists.txt │ ├── CTestConfig.cmake │ ├── ChopImageBelowLowerBound.h │ ├── ComputeReflectiveCorrelationMetric.cxx │ ├── ComputeReflectiveCorrelationMetric.xml │ ├── HoughFilterTestProgram.cxx │ ├── LLSModel.cxx │ ├── LLSModel.h │ ├── PrepareOutputImages.cxx │ ├── PrepareOutputImages.h │ ├── TrimForegroundInDirection.cxx │ ├── TrimForegroundInDirection.h │ ├── fcsv_to_hdf5.cxx │ ├── fcsv_to_hdf5.xml │ ├── insertMidACPCpoint.cxx │ ├── insertMidACPCpoint.xml │ ├── itkHoughTransformRadialVotingImageFilter.h │ ├── itkHoughTransformRadialVotingImageFilter.hxx │ ├── itkReflectiveCorrelationCenterToImageMetric.h │ ├── itkReflectiveCorrelationCenterToImageMetric.hxx │ ├── landmarkIO.cxx │ ├── landmarkIO.h │ ├── landmarksConstellationAligner.cxx │ ├── landmarksConstellationAligner.xml │ ├── landmarksConstellationCommon.cxx │ ├── landmarksConstellationCommon.h │ ├── landmarksConstellationDetector.cxx │ ├── landmarksConstellationDetector.h │ ├── landmarksConstellationDetectorCompute.cxx │ ├── landmarksConstellationModelBase.h │ ├── landmarksConstellationModelIO.h │ ├── landmarksConstellationTrainingDefinitionIO.h │ ├── landmarksConstellationWeights.cxx │ ├── landmarksConstellationWeights.xml │ ├── landmarksDataSet.h │ ├── rc_metric_plots.m │ └── tempSphereFromAreaEstimates.cxx ├── BRAINSCreateLabelMapFromProbabilityMaps ├── BRAINSCreateLabelMapFromProbabilityMaps.cxx ├── BRAINSCreateLabelMapFromProbabilityMaps.xml ├── CMakeLists.txt └── TestSuite │ ├── BRAINSCreateLabelMapFromProbabilityMapsTest.cxx │ └── CMakeLists.txt ├── BRAINSDWICleanup ├── BRAINSDWICleanup.cxx ├── BRAINSDWICleanup.xml └── CMakeLists.txt ├── BRAINSDeface ├── BRAINSDeface.cxx ├── BRAINSDeface.xml └── CMakeLists.txt ├── BRAINSFit ├── BRAINSFit.cxx ├── BRAINSFit.xml ├── BRAINSFitCommonLib.h.in ├── BRAINSFitCommonLibLauncher.c.in ├── BRAINSFitCommonLibWin32Header.h ├── CMakeCPackOptions.cmake.in ├── CMakeLists.txt ├── Copyright.txt ├── PerformMetricTest.cxx ├── PerformMetricTest.xml ├── README ├── TestSuite │ ├── BRAINSFitTest.cxx │ ├── CMakeLists.txt │ ├── CenterOfROIInitTest.cxx │ ├── CommandLineWrarpperTester.cxx │ ├── Example.sh │ ├── PerformTestMMI.cxx │ └── makexfrmedImage.cxx ├── Testing │ └── Temporary │ │ ├── CTestCostData.txt │ │ └── LastTest.log └── Transform.notes ├── BRAINSInitializedControlPoints ├── BRAINSInitializedControlPoints.cxx ├── BRAINSInitializedControlPoints.xml ├── CMakeLists.txt ├── README └── RunTests.sh ├── BRAINSIntensityNormalize ├── BRAINSIntensityNormalize.cxx ├── BRAINSIntensityNormalize.xml └── CMakeLists.txt ├── BRAINSLabelStats ├── BRAINSLabelStats.cxx ├── BRAINSLabelStats.xml └── CMakeLists.txt ├── BRAINSLandmarkInitializer ├── BRAINSConstallationLandmarkWeight.csv ├── BRAINSLandmarkInitializer.cxx ├── BRAINSLandmarkInitializer.xml └── CMakeLists.txt ├── BRAINSMultiModeSegment ├── BRAINSMultiModeSegment.cxx ├── BRAINSMultiModeSegment.xml ├── CMakeLists.txt └── README ├── BRAINSMultiSTAPLE ├── BRAINSMultiSTAPLE.cxx ├── BRAINSMultiSTAPLE.xml ├── CMakeLists.txt └── TestSuite │ ├── BRAINSMultiSTAPLETest.cxx │ └── CMakeLists.txt ├── BRAINSMush ├── BRAINSMush.cxx ├── BRAINSMush.xml ├── CMakeLists.txt ├── Copyright.txt ├── README ├── ReadMe.txt ├── TestSuite │ └── CMakeLists.txt ├── itkApplyMaskImageFilter.h ├── itkApplyMaskImageFilter.hxx ├── itkMixtureStatisticCostFunction.h └── itkMixtureStatisticCostFunction.hxx ├── BRAINSPosteriorToContinuousClass ├── BRAINSPosteriorToContinuousClass.cxx ├── BRAINSPosteriorToContinuousClass.xml ├── CMakeLists.txt └── TestSuite │ ├── BRAINSPosteriorToContinuousClassTest.cxx │ └── CMakeLists.txt ├── BRAINSROIAuto ├── BRAINSROIAuto.cxx ├── BRAINSROIAuto.xml ├── BRAINSROIAutoCommonLib.h.in ├── BRAINSROIAutoCommonLibLauncher.c.in ├── BRAINSROIAutoCommonLibWin32Header.h ├── CMakeLists.txt ├── README └── TestSuite │ ├── BRAINSROIAutoTest.cxx │ ├── CMakeLists.txt │ └── TestImage.cxx ├── BRAINSResample ├── BRAINSResample.cxx ├── BRAINSResample.xml ├── BRAINSResampleCommonLib.h.in ├── BRAINSResampleCommonLibLauncher.c.in ├── BRAINSResampleCommonLibWin32Header.h ├── BRAINSResize.cxx ├── BRAINSResize.xml ├── CMakeLists.txt ├── README ├── TestSuite │ ├── BRAINSResampleTest.cxx │ └── CMakeLists.txt ├── itkGridForwardWarpImageFilterNew.h └── itkGridForwardWarpImageFilterNew.hxx ├── BRAINSSnapShotWriter ├── BRAINSSnapShotWriter.cxx ├── BRAINSSnapShotWriter.xml └── CMakeLists.txt ├── BRAINSStripRotation ├── BRAINSStripRotation.cxx ├── BRAINSStripRotation.xml └── CMakeLists.txt ├── BRAINSSuperResolution ├── CMakeLists.txt ├── EdgeBasedWeightedTV │ ├── CMakeLists.txt │ ├── FFTWUpsample.cpp │ ├── FFTWUpsample.h │ ├── FFTWUpsampleTest.cpp │ ├── GradientTest.cpp │ ├── MathUtils.h │ ├── OpWeightedL2.cpp │ ├── OpWeightedL2.h │ ├── SRTypes.h │ ├── SRmain.cpp │ ├── SimpleOpWeightedL2.cpp │ ├── SimpleSR.cpp │ ├── TestFFTW2D.cpp │ ├── itkDivergenceImageFilter.h │ ├── itkDivergenceImageFilter.hxx │ ├── itkIdentityResampleByFFT.h │ └── itkIdentityResampleByFFT.hxx ├── GenerateEdgeMap │ ├── BRAINSSuperResolutionCommonLib.h.in │ ├── CMakeLists.txt │ ├── GenerateEdgeMapImage.cxx │ ├── GenerateEdgeMapImage.xml │ └── GenerateMaxGradientImage.h ├── README.md └── SuperResolutionMatlabExample │ ├── SuperResolution.m │ └── matlab_support_functions │ ├── A_fhp.m │ ├── At_fhp.m │ ├── NormalizeDataComponent.m │ ├── OpWeightedL2.m │ ├── SRdiv.m │ ├── SRgrad.m │ ├── WriteComplex.m │ ├── WriteFile.m │ ├── defAAt_fourier.m │ ├── defDDt.m │ ├── do_SR_estimate.m │ ├── get_kspace_inds.m │ ├── get_kspace_inds_new.m │ ├── get_kspace_inds_pos.m │ ├── get_lowpass_inds.m │ ├── get_lowpass_inds_new.m │ ├── get_lowpass_inds_pos.m │ ├── projInfty.m │ └── shrink.m ├── BRAINSTools.cmake ├── BRAINSTransformConvert ├── BRAINSTransformConvert.cxx ├── BRAINSTransformConvert.xml ├── CMakeLists.txt └── TestSuite │ ├── BRAINSTransformConvertMakeTestFiles.cxx │ ├── BRAINSTransformConvertTest.cxx │ ├── CMakeLists.txt │ └── ImageCompare.cxx ├── CMake ├── BRAINSToolsExternalData.cmake ├── CTestCustom.cmake.in ├── ExternalProjectDependency.cmake ├── ExternalProjectGenerateProjectDescription.cmake ├── FindATLAS.cmake ├── FindDCMTK.cmake ├── FindFFTW.cmake ├── FindITKUtil.cmake ├── FindLAPACKE.cmake ├── FindOpenBLAS.cmake ├── FindVTKUtil.cmake ├── GetGitRevisionDescription.cmake ├── ITKSetStandardCompilerFlags.cmake ├── ITK_CheckCCompilerFlag.cmake ├── ITK_CheckCXXCompilerFlag.cmake ├── InitializeOSXVariables.cmake ├── LinAlgSelector.cmake ├── PreventInBuildInstalls.cmake ├── PreventInSourceBuilds.cmake ├── ProjectSourceVersion.cmake ├── ProjectSourceVersionVars.cmake ├── ProjectSourceVersionVars.cmake.in ├── SlicerBlockOperatingSystemNames.cmake ├── SlicerMacroGetOperatingSystemArchitectureBitness.cmake ├── itkCheckSourceTree.cmake ├── pre-commit └── sparselibSetup.cmake ├── CMakeLists.txt ├── CMakePresets.json ├── CTestConfig.cmake ├── Common.cmake ├── ConvertBetweenFileFormats ├── CMakeLists.txt ├── TestSuite │ ├── CMakeLists.txt │ └── ImageCompareTests.cxx ├── castconvert.cxx ├── castconvertConfigure.h.in ├── castconvertDicomScalar.cxx ├── castconvertDicomScalarA.cxx ├── castconvertScalar.cxx ├── castconvertScalar2D.cxx ├── castconvertScalar2DA.cxx ├── castconvertScalar3D.cxx ├── castconvertScalar3DA.cxx ├── castconvertScalar4D.cxx ├── castconvertScalar4DA.cxx └── castconverthelpers.h ├── DWIConvert ├── CMakeLists.txt ├── Convert4DImageTo3DSeries.cxx ├── DWIConvert.cxx ├── DWIConvert.xml ├── DWIConvertLib.cxx ├── DWIConvertLib.h ├── DWIConvertUtils.cxx ├── DWIConvertUtils.h ├── DWIConvertUtils.hxx ├── DWIConverter.cxx ├── DWIConverter.h ├── DWIConverterFactory.cxx ├── DWIConverterFactory.h ├── DWIDICOMConverterBase.cxx ├── DWIDICOMConverterBase.h ├── FSLDWIConverter.cxx ├── FSLDWIConverter.h ├── FSLToNrrd.cxx ├── FindLIBICONV.cmake ├── GEDWIConverter.cxx ├── GEDWIConverter.h ├── GenericDWIConverter.cxx ├── GenericDWIConverter.h ├── HitachiDWIConverter.cxx ├── HitachiDWIConverter.h ├── NRRDDWIConverter.cxx ├── NRRDDWIConverter.h ├── NrrdToFSL.cxx ├── PhilipsDWIConverter.cxx ├── PhilipsDWIConverter.h ├── README.md ├── SiemensDWIConverter.cxx ├── SiemensDWIConverter.h ├── SiemensDWIConverter.hxx ├── StringContains.h ├── TestSuite │ ├── BFileCompareTool.cpp │ ├── CMakeLists.txt │ ├── CheckNewDWIConvert.py │ ├── ConvertWithdcm2niix.sh │ ├── DWICompare.cxx │ ├── DWICompare.xml │ ├── DWIConvertTest.cxx │ ├── DWISimpleCompare.cxx │ ├── DWISimpleCompare.xml │ ├── DWIVisualizationFixing.pptx │ ├── DWI_ProcessingTest.ipynb │ ├── DicomToNrrdDWICompareTest.cmake │ ├── FSLMultiShellDataTest.cmake │ ├── FSLTextFileCompare.cxx │ ├── FSLToNrrdTest.cmake │ ├── NrrdToFSLTest.cmake │ ├── NrrdToNIfTI.cxx │ ├── SlicerDWIProcessing.sh │ ├── Testing │ │ └── Temporary │ │ │ ├── CTestCostData.txt │ │ │ └── LastTest.log │ ├── ZspaceThicknessDiffDicom.cmake │ ├── checkTagValueInHeader.cxx │ └── tensor.mrml ├── Testing │ ├── CMakeLists.txt │ └── DWIConvertTest.cxx └── WriteProtocolFunction.cxx ├── DebugImageViewer ├── CMakeLists.txt ├── DebugImageViewer.cxx ├── DebugImageViewerClient.h ├── DebugImageViewerClientTest.cxx ├── DebugImageViewerClientTest2.cxx ├── DebugImageViewerVectorClientTest.cxx ├── QDebugImageViewerWindow.cxx ├── QDebugImageViewerWindow.h ├── QImageDisplay.cxx ├── QImageDisplay.h ├── QImageViewerWidget.cxx ├── QImageViewerWidget.h ├── vtkKWImage.cxx └── vtkKWImage.h ├── GTRACT ├── CMakeLists.txt ├── Cmdline │ ├── CMakeLists.txt │ ├── TestSuite │ │ ├── CMakeLists.txt │ │ ├── compareTwoCSVFiles.py.in │ │ ├── gtractAverageBvaluesTests.cxx │ │ ├── gtractCoRegAnatomyTests.cxx │ │ ├── gtractConcatDwiTests.cxx │ │ ├── gtractCoregBvaluesTests.cxx │ │ └── gtractResampleDWIInPlaceTests.cxx │ ├── compareTractInclusion.cxx │ ├── compareTractInclusion.xml │ ├── extractNrrdVectorIndex.cxx │ ├── extractNrrdVectorIndex.xml │ ├── future_work │ │ ├── gtractCoRegAnatomyRigid.cxx │ │ ├── gtractCoRegAnatomyRigid.xml │ │ ├── gtractFreeTracking.cxx │ │ ├── gtractFreeTracking.xml │ │ ├── gtractGraphSearchTracking.cxx │ │ ├── gtractGraphSearchTracking.xml │ │ ├── gtractGuidedTracking.cxx │ │ ├── gtractGuidedTracking.xml │ │ ├── gtractStreamlineTracking.cxx │ │ └── gtractStreamlineTracking.xml │ ├── gtractAnisotropyMap.cxx │ ├── gtractAnisotropyMap.xml │ ├── gtractAverageBvalues.cxx │ ├── gtractAverageBvalues.xml │ ├── gtractClipAnisotropy.cxx │ ├── gtractClipAnisotropy.xml │ ├── gtractCoRegAnatomy.cxx │ ├── gtractCoRegAnatomy.xml │ ├── gtractCoRegAnatomyBspline.cxx │ ├── gtractCoRegAnatomyBspline.xml │ ├── gtractConcatDwi.cxx │ ├── gtractConcatDwi.xml │ ├── gtractCopyImageOrientation.cxx │ ├── gtractCopyImageOrientation.xml │ ├── gtractCoregBvalues.cxx │ ├── gtractCoregBvalues.xml │ ├── gtractCostFastMarching.cxx │ ├── gtractCostFastMarching.xml │ ├── gtractCreateGuideFiber.cxx │ ├── gtractCreateGuideFiber.xml │ ├── gtractFastMarchingTracking.cxx │ ├── gtractFastMarchingTracking.xml │ ├── gtractFiberTracking.cxx │ ├── gtractFiberTracking.xml │ ├── gtractImageConformity.cxx │ ├── gtractImageConformity.xml │ ├── gtractInvertBSplineTransform.cxx │ ├── gtractInvertBSplineTransform.xml │ ├── gtractInvertDisplacementField.cxx │ ├── gtractInvertDisplacementField.xml │ ├── gtractInvertRigidTransform.cxx │ ├── gtractInvertRigidTransform.xml │ ├── gtractResampleAnisotropy.cxx │ ├── gtractResampleAnisotropy.xml │ ├── gtractResampleB0.cxx │ ├── gtractResampleB0.xml │ ├── gtractResampleCodeImage.cxx │ ├── gtractResampleCodeImage.xml │ ├── gtractResampleDWIInPlace.cxx │ ├── gtractResampleDWIInPlace.xml │ ├── gtractResampleFibers.cxx │ ├── gtractResampleFibers.xml │ ├── gtractTensor.cxx │ ├── gtractTensor.xml │ ├── gtractTransformToDisplacementField.cxx │ └── gtractTransformToDisplacementField.xml ├── Common │ ├── CMakeLists.txt │ ├── GtractTypes.h │ ├── algo.cxx │ ├── algo.h │ ├── gtractCommonWin32.h │ ├── gtractDiffusionTensor3D.h │ ├── gtractDiffusionTensor3D.hxx │ ├── itkAnatomicalBSplineFilter.cxx │ ├── itkAnatomicalBSplineFilter.h │ ├── itkAnatomicalVersorRigidFilter.cxx │ ├── itkAnatomicalVersorRigidFilter.h │ ├── itkComputeDiffusionTensorImageFilter.cxx │ ├── itkComputeDiffusionTensorImageFilter.h │ ├── itkCreateSpatialObjectFilter.h │ ├── itkCreateSpatialObjectFilter.hxx │ ├── itkDtiFastMarchingCostFilter.h │ ├── itkDtiFastMarchingCostFilter.hxx │ ├── itkDtiFastMarchingTrackingFilter.cxx │ ├── itkDtiFastMarchingTrackingFilter.h │ ├── itkDtiFastMarchingTrackingFilter.hxx │ ├── itkDtiFreeTrackingFilter.h │ ├── itkDtiFreeTrackingFilter.hxx │ ├── itkDtiGraphSearchTrackingFilter.h │ ├── itkDtiGraphSearchTrackingFilter.hxx │ ├── itkDtiGuidedTrackingFilter.h │ ├── itkDtiGuidedTrackingFilter.hxx │ ├── itkDtiStreamlineTrackingFilter.h │ ├── itkDtiStreamlineTrackingFilter.hxx │ ├── itkDtiTrackingFilterBase.h │ ├── itkDtiTrackingFilterBase.hxx │ ├── itkDtiTrackingFilterFibersAndPoints.cxx │ ├── itkEigenVectorToColorImageFilter.cxx │ ├── itkEigenVectorToColorImageFilter.h │ ├── itkFastMarchingCostFunction.cxx │ ├── itkFastMarchingCostFunction.h │ ├── itkGtractImageIO.cxx │ ├── itkGtractImageIO.h │ ├── itkGtractInverseDeformationFieldImageFilter.hxx │ ├── itkGtractInverseDisplacementFieldImageFilter.h │ ├── itkGtractInverseDisplacementFieldImageFilter.hxx │ ├── itkGtractParameterIO.cxx │ ├── itkGtractParameterIO.h │ ├── itkInvertBSplineFilter.cxx │ ├── itkInvertBSplineFilter.h │ ├── itkTensorInterpolateImageFunction.h │ ├── itkTensorLinearInterpolateImageFunction.h │ ├── itkTensorLinearInterpolateImageFunction.hxx │ ├── itkTensorToAnisotropyImageFilter.cxx │ └── itkTensorToAnisotropyImageFilter.h ├── GTRACT-Copyright.txt ├── README ├── gtractConfigure.h.in ├── parameters │ ├── GE_25dir_1B.txt │ ├── Iowa-GE-DTI.txt │ ├── MGH-60Dir-10B0.txt │ ├── MGH-60Dir.txt │ ├── Siemens-12dir_1B.txt │ ├── Siemens-12dir_2B.txt │ ├── Siemens-20dir_1B.txt │ ├── Siemens-30dir_1B.txt │ ├── Siemens-64dir_1B.txt │ ├── Siemens-6dir_1B.txt │ └── Siemens-6dir_2B.txt └── versionfile ├── ITKMatlabIO ├── CMake │ ├── compilerTestChar16_t.cmake │ ├── compilerTestChar16_t.cxx │ └── mex_stub.cxx ├── CMakeLists.txt ├── GroundTruth │ ├── DontOverWriteMatFileThisDir.txt │ ├── Synthetic-Ground-truth_01.mat │ ├── Synthetic-Ground-truth_01.raw.gz │ ├── Synthetic-Ground-truth_02.mat │ ├── Synthetic-Ground-truth_02.raw.gz │ ├── Synthetic-Ground-truth_03.mat │ ├── Synthetic-Ground-truth_03.raw.gz │ ├── Synthetic-Ground-truth_04.mat │ ├── Synthetic-Test-data_01.mat │ ├── Synthetic-Test-data_01.raw.gz │ ├── Synthetic-Test-data_02.mat │ ├── Synthetic-Test-data_02.raw.gz │ ├── Synthetic-Test-data_03.mat │ ├── Synthetic-Test-data_03.raw.gz │ ├── Synthetic-Test-data_04.mat │ ├── buildGroundTruthMatFile.m │ ├── compareExistMatFiles.m │ ├── mask.mat │ ├── mask.raw.gz │ ├── nrrd_writer_out.mat │ └── nrrd_writer_out.raw.gz ├── LICENSE ├── README.md ├── TestSuite │ ├── ConvertFromMatToVTK.m │ ├── MatlabITKImageObject.m │ ├── Synthetic-Ground-truth_01.nhdr │ ├── Synthetic-Ground-truth_01.raw.gz │ ├── Synthetic-Ground-truth_02.mat │ ├── Synthetic-Ground-truth_02.nhdr │ ├── Synthetic-Ground-truth_02.raw.gz │ ├── Synthetic-Ground-truth_03.nhdr │ ├── Synthetic-Ground-truth_03.raw.gz │ ├── Synthetic-Ground-truth_04.nhdr │ ├── Synthetic-Test-data_01.nhdr │ ├── Synthetic-Test-data_01.raw.gz │ ├── Synthetic-Test-data_02.nhdr │ ├── Synthetic-Test-data_02.raw.gz │ ├── Synthetic-Test-data_03.mat │ ├── Synthetic-Test-data_03.nhdr │ ├── Synthetic-Test-data_03.raw.gz │ ├── Synthetic-Test-data_04.nhdr │ ├── TestITKOO.m │ ├── compareDWIdata.m │ ├── comparevars.m │ ├── cxx_conversion_test.m │ ├── decoratedOutput.vtk │ ├── disp_scale1_numdirs10_1_1_circles.mat │ ├── disp_scale1_numdirs10_1_1_circles.vtk │ ├── disp_scale1_numdirs10_1_1_circles.vtp │ ├── disp_scale1_numdirs10_1_1_rays.mat │ ├── disp_scale1_numdirs10_1_1_rays.vtk │ ├── disp_scale1_numdirs10_1_1_rays.vtp │ ├── disp_scale3_numdirs10_1_1_circles.mat │ ├── disp_scale3_numdirs10_1_1_circles.vtk │ ├── disp_scale3_numdirs10_1_1_circles.vtp │ ├── disp_scale3_numdirs10_1_1_rays.mat │ ├── disp_scale3_numdirs10_1_1_rays.vtk │ ├── disp_scale3_numdirs10_1_1_rays.vtp │ ├── disp_test_circles.mat │ ├── disp_test_circles.vtk │ ├── disp_test_circles.vtp │ ├── disp_test_rays.mat │ ├── disp_test_rays.vtk │ ├── disp_test_rays.vtp │ ├── mask.nhdr │ ├── mask.raw.gz │ ├── matlab_workspace.mat │ ├── minitestITKRW.m │ ├── nrrd_writer_out.nhdr │ ├── nrrd_writer_out.raw.gz │ ├── shortDWITest.m │ ├── testCS.m │ ├── testITKRW.m │ ├── testVTKReading.m │ └── testing_dispersion.m ├── mexFiles │ ├── CMakeLists.txt │ ├── Debug.h │ ├── itkLoadWithMetadata.cxx │ ├── itkLoadWithMetadata1.cxx │ ├── itkSaveWithMetadata.cxx │ ├── itkSaveWithMetadata1.cxx │ ├── myMexPrintf.h │ ├── nrrdCommon.cxx │ ├── nrrdCommon.h │ ├── vtkCommon.h │ ├── vtkErrorObserver.h │ ├── vtkLoadPolyData.cxx │ └── vtkSavePolyData.cxx ├── readItkImage │ ├── CMakeLists.txt │ ├── convertItkImageToMxArray.cpp │ ├── convertItkImageToMxArray.h │ └── itkReadImage.cpp └── utils │ └── Mac10.9_mexopts.sh ├── ImageCalculator ├── CMakeLists.txt ├── ImageCalculator.cxx ├── ImageCalculatorProcess2D.cxx ├── ImageCalculatorProcess3D.cxx ├── ImageCalculatorTemplates.h ├── ImageCalculatorTests.cxx ├── ImageCalculatorUtils.cxx ├── ImageCalculatorUtils.h ├── ImageGenerate.cxx ├── TestSuite │ └── CMakeLists.txt └── doc │ ├── Examples.txt │ ├── ImageCalculator.tex │ ├── InsightArticle.cls │ ├── InsightJournal.ist │ ├── InsightJournal.sty │ ├── Makefile │ ├── algorithm.sty │ ├── algorithmic.sty │ ├── amssymb.sty │ ├── fancyhdr.sty │ ├── figs │ ├── ImageCalculator.dia │ └── ImageCalculator.eps │ ├── floatflt.sty │ ├── fncychap.sty │ └── times.sty ├── LICENSE ├── NOTICE ├── README.md ├── ReferenceAtlas ├── 20141004_BCD │ ├── LLSModel_50Lmks.h5.sha512 │ ├── T1_50Lmks.mdl.sha512 │ ├── template_landmarks_50Lmks.fcsv.sha512 │ └── template_weights_50Lmks.wts.sha512 ├── ALLPVAIR.nii.gz.sha512 ├── ALLPVBASALTISSUE.nii.gz.sha512 ├── ALLPVCRBLGM.nii.gz.sha512 ├── ALLPVCRBLWM.nii.gz.sha512 ├── ALLPVCSF.nii.gz.sha512 ├── ALLPVNOTCSF.nii.gz.sha512 ├── ALLPVNOTGM.nii.gz.sha512 ├── ALLPVNOTVB.nii.gz.sha512 ├── ALLPVNOTWM.nii.gz.sha512 ├── ALLPVSURFGM.nii.gz.sha512 ├── ALLPVVB.nii.gz.sha512 ├── ALLPVWM.nii.gz.sha512 ├── CMake │ └── ReferenceAtlasExternalData.cmake ├── CMakeLists.txt ├── ExtendedAtlasDefinition.xml.in ├── GENERATED_AIR.nii.gz.sha512 ├── GENERATED_BASAL.nii.gz.sha512 ├── GENERATED_CRBLGM.nii.gz.sha512 ├── GENERATED_CRBLWM.nii.gz.sha512 ├── GENERATED_CSF.nii.gz.sha512 ├── GENERATED_GLOBUS.nii.gz.sha512 ├── GENERATED_HIPPOCAMPUS.nii.gz.sha512 ├── GENERATED_NOTCSF.nii.gz.sha512 ├── GENERATED_NOTGM.nii.gz.sha512 ├── GENERATED_NOTVB.nii.gz.sha512 ├── GENERATED_NOTWM.nii.gz.sha512 ├── GENERATED_SURFGM.nii.gz.sha512 ├── GENERATED_THALAMUS.nii.gz.sha512 ├── GENERATED_VB.nii.gz.sha512 ├── GENERATED_WM.nii.gz.sha512 ├── Orig_test.nii.gz.sha512 ├── README.txt.sha512 ├── avg_t1.nii.gz.sha512 ├── avg_t2.nii.gz.sha512 ├── hncma-atlas-lut-mod2.ctbl.sha512 ├── hncma-atlas.nii.gz.sha512 ├── ones.nii.gz.sha512 ├── probabilityMaps │ ├── l_accumben_ProbabilityMap.nii.gz.sha512 │ ├── l_caudate_ProbabilityMap.nii.gz.sha512 │ ├── l_globus_ProbabilityMap.nii.gz.sha512 │ ├── l_hippocampus_ProbabilityMap.nii.gz.sha512 │ ├── l_putamen_ProbabilityMap.nii.gz.sha512 │ ├── l_thalamus_ProbabilityMap.nii.gz.sha512 │ ├── r_accumben_ProbabilityMap.nii.gz.sha512 │ ├── r_caudate_ProbabilityMap.nii.gz.sha512 │ ├── r_globus_ProbabilityMap.nii.gz.sha512 │ ├── r_hippocampus_ProbabilityMap.nii.gz.sha512 │ ├── r_putamen_ProbabilityMap.nii.gz.sha512 │ └── r_thalamus_ProbabilityMap.nii.gz.sha512 ├── tempNOTVBBOX.nii.gz.sha512 ├── template_ABC_labels.nii.gz.sha512 ├── template_WMPM2_labels.nii.gz.sha512 ├── template_WMPM2_labels.txt.sha512 ├── template_brain.nii.gz.sha512 ├── template_cerebellum.nii.gz.sha512 ├── template_class.nii.gz.sha512 ├── template_headregion.nii.gz.sha512 ├── template_leftHemisphere.nii.gz.sha512 ├── template_nac_labels.nii.gz.sha512 ├── template_nac_labels.txt.sha512 ├── template_rightHemisphere.nii.gz.sha512 ├── template_t1.nii.gz.sha512 ├── template_t1_clipped.nii.gz.sha512 ├── template_t1_denoised_gaussian.nii.gz.sha512 ├── template_t2.nii.gz.sha512 ├── template_t2_clipped.nii.gz.sha512 ├── template_t2_denoised_gaussian.nii.gz.sha512 └── template_ventricles.nii.gz.sha512 ├── RunEdgePrediction.py ├── SuperBuild.cmake ├── SuperBuild ├── EP_Autoconf_Utils.cmake ├── External_ANTs.cmake ├── External_DCMTK.cmake ├── External_ITKv5.cmake ├── External_OpenJPEG.cmake ├── External_SlicerExecutionModel.cmake ├── External_VTK.cmake ├── External_tbb.cmake ├── External_teem.cmake └── External_zlib.cmake ├── TestData ├── 0036195-T1T2_ACPC_Talairach_LabelMap.nii.gz.sha512 ├── 0036195-T1T2_leftTissueClass.nii.gz.sha512 ├── 0036195-T1T2_leftTissueClass_genus0.nii.gz.sha512 ├── 0036195-T1T2_left_130_binary.nii.gz.sha512 ├── 0036195_AssignArray.vtk.sha512 ├── 0036195_ClampScalars.vtk.sha512 ├── 0036195_SurfaceGeneration.vtk.sha512 ├── 0036195_leftSurfaceFeatures.vtk.sha512 ├── 0036195_leftTalLabels.vtk.sha512 ├── 0036195_leftTissueClass130.vtk.sha512 ├── 0036195_leftTissueClassGenus0.vtk.sha512 ├── 0036195_left_49Labels.vtk.sha512 ├── 0036195_left_5000_smoothed.vtk.sha512 ├── 0036195_left_5000_sphere0.vtk.sha512 ├── 0036195_left_5000_sphere1.vtk.sha512 ├── 0036195_left_sphere.vtk.sha512 ├── 0036195_left_sphereIC4.vtk.sha512 ├── 0036195_left_sphereIC5.vtk.sha512 ├── 0036195_left_sphereIC6.vtk.sha512 ├── 0036195_left_sphereIC7.vtk.sha512 ├── 0036195_left_sphere_distToHull.vtk.sha512 ├── 0036195_left_transformedLabelMap.nii.gz.sha512 ├── 0036896_left_sphere.vtk.sha512 ├── 0036896_left_sphereIC4.vtk.sha512 ├── 0036896_left_sphereIC5.vtk.sha512 ├── 0036896_left_sphereIC6.vtk.sha512 ├── 0036896_left_sphereIC7.vtk.sha512 ├── 0036896_to_0036195_hmIC4.vtk.sha512 ├── 0436396_left_BRAINSLabels.vtk.sha512 ├── 0436396_left_ManualLabels.vtk.sha512 ├── 2.nii.gz.sha512 ├── 2_EMSP.nrrd.sha512 ├── 62772808_left_surface_tal.vtk.sha512 ├── ANON0006_20_T1_dbg_splayed.nii.gz.sha512 ├── ANON0006_20_T1_sag_twisted.nii.gz.sha512 ├── AllFifties.png.sha512 ├── AllFiveHundreds.png.sha512 ├── AllHundreds.png.sha512 ├── AllTens.png.sha512 ├── AllTwos.hdr.sha512 ├── AllTwos.img.sha512 ├── AllZeroes.png.sha512 ├── AtlasToSubjectScan1.mat.sha512 ├── AtlasToSubjectScan2.mat.sha512 ├── AtlasToSubjectScan3.mat.sha512 ├── AtlasToSubjectScan4.mat.sha512 ├── AverageHullOn0036195.vtk.sha512 ├── BCDTestForLandmarkCompare_standard.nrrd.sha512 ├── BCDTest_T1_outputResampledVolume_standard.nrrd.sha512 ├── BCDTest_T1_outputVolume_standard.nrrd.sha512 ├── BCDTest_acLowerBound_standard.nrrd.sha512 ├── BCDTest_backgroundValue_standard.nrrd.sha512 ├── BCDTest_cutOutHeadInOutputResampledVolume_standard.nrrd.sha512 ├── BCDTest_cutOutHeadInOutputVolume_standard.nrrd.sha512 ├── BCDTest_forceHoughReportFailure_standard.nii.gz.sha512 ├── BCDTest_inputLandmarksEMSP_standard.nrrd.sha512 ├── BCDTest_interpolationMode_standard.nrrd.sha512 ├── BCDTest_mspLevel_standard.nrrd.sha512 ├── BCDTest_otsuThreshold_standard.nrrd.sha512 ├── BCDTest_outputUntransformedClippedVolume_standard.nrrd.sha512 ├── BCDTest_rVN4-rpc-rac-rmpj_standard.nrrd.sha512 ├── BCDTest_rVN4_standard.nrrd.sha512 ├── BCDTest_rac_standard.nrrd.sha512 ├── BCDTest_rescaleIntensityRange_standard.nrrd.sha512 ├── BCDTest_rescaleIntensity_standard.nrrd.sha512 ├── BCDTest_rmpj_standard.nrrd.sha512 ├── BCDTest_rpc_standard.nrrd.sha512 ├── BCDTest_trimRescaledIntensities_standard.nrrd.sha512 ├── BCDTest_writeBranded2DImage_standard.nrrd.sha512 ├── BCDTest_writeBranded2DImage_standard.png.sha512 ├── BRAINSABCSmallExtendedAtlasDefinition.xml.sha512 ├── BRAINSABCSmallLabels.nii.gz.sha512 ├── BRAINSABCSmall_T1.nii.gz.sha512 ├── BRAINSABCSmall_T1_offset.nii.gz.sha512 ├── BRAINSABCSmall_T2.nii.gz.sha512 ├── BRAINSABCSmall_atlas_to_subject_transform.h5.sha512 ├── BRAINSAlignMSPTest_T1_standard.nrrd.sha512 ├── BRAINSContinuousClassTest_baseline.nii.gz.sha512 ├── BRAINSCreateLabelMapFromProbabilityMaps │ ├── CleanLabels.nii.gz.sha512 │ └── DirtyLabels.nii.gz.sha512 ├── BRAINSCutTemplateToScan3.h5.sha512 ├── BRAINSCutcaudate_left_scan3_baseline.nii.gz.sha512 ├── BRAINSCutcaudate_right_scan3_baseline.nii.gz.sha512 ├── BRAINSCutputamen_left_scan3_baseline.nii.gz.sha512 ├── BRAINSCutputamen_right_scan3_baseline.nii.gz.sha512 ├── BRAINSEyeDetectorTest_T1_standard.nii.gz.sha512 ├── BRAINSEyeDetectorTest_T1_standard.nrrd.sha512 ├── BRAINSFitTest_AffineRotationMasks.mat.sha512 ├── BRAINSFitTest_AffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_AffineRotationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_AffineScaleMasks.result.nii.gz.sha512 ├── BRAINSFitTest_AffineScaleNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_AffineTranslationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_AffineTranslationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.sha512 ├── BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineBSplineRescaleHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineOnlyRescaleHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineScaleRotationHeadMasksUShort.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineScaleRotationHistogramHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineScaleRotationHistogramHeadMasksUShort.result.nii.gz.sha512 ├── BRAINSFitTest_BSplineScaleRotationRescaleHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_Initializer_RigidRotationNoMasks.mat.sha512 ├── BRAINSFitTest_KSAffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_KSScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MCAffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MCScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MIHAffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MIHScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MSEAffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_MSEScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_NCAffineRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_NCScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ROIBSpline.result.1.nrrd.sha512 ├── BRAINSFitTest_ROIBSpline.result.nrrd.sha512 ├── BRAINSFitTest_ROIBSpline.test.nrrd.sha512 ├── BRAINSFitTest_RigidAnisotropicMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidMedianRotationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotGeomNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotaRotaRotNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotationHeadMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotationNoMasks.mat.sha512 ├── BRAINSFitTest_RigidRotationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleRotationRescaleHeadMasksNoInit.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleSkewVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleSkewVersorRotationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleSkewVersorScaleMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleSkewVersorScaleNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleTranslationRescaleHeadMasksNoInit.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleVersorRotationMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleVersorRotationNoMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleVersorScaleMasks.result.nii.gz.sha512 ├── BRAINSFitTest_ScaleVersorScaleNoMasks.result.nii.gz.sha512 ├── BRAINSMultiSTAPLE │ ├── AVG_T1.nii.gz.sha512 │ ├── LM_1_seg.nii.gz.sha512 │ ├── LM_2_seg.nii.gz.sha512 │ ├── LM_3_seg.nii.gz.sha512 │ ├── session1composite_1.h5.sha512 │ ├── session1composite_2.h5.sha512 │ └── session1composite_3.h5.sha512 ├── BRAINSPosteriorToContinuousClassTest.result.nii.gz.sha512 ├── BRAINSROIAutoTest_GenerateBrainMask.result.nii.gz.sha512 ├── BRAINSRefacer │ ├── Landmarks.fcsv.sha512 │ ├── README │ ├── float_BrainLabels.nii.gz.sha512 │ ├── float_Landmarks.fcsv.sha512 │ ├── float_Subject.nii.gz.sha512 │ ├── float_SubjectNewImage.nii.gz.sha512 │ ├── short_BrainLabels.nii.gz.sha512 │ ├── short_Landmarks.fcsv.sha512 │ ├── short_Subject.nii.gz.sha512 │ └── short_SubjectNewImage.nii.gz.sha512 ├── BRAINSTrimForegroundInDirectionTest_T1_standard.nrrd.sha512 ├── BigEndian.mhd.sha512 ├── BigEndian.raw.sha512 ├── CombineLabel0036195.vtk.sha512 ├── DWI_TestData_OUTPUTS │ ├── GeSignaHDx.bval.sha512 │ ├── GeSignaHDx.bvec.sha512 │ ├── GeSignaHDx.nii.gz.sha512 │ ├── GeSignaHDx.nrrd.sha512 │ ├── GeSignaHDxt.nrrd.sha512 │ ├── PhilipsAchieva1.nrrd.sha512 │ ├── PhilipsAchieva2.nrrd.sha512 │ ├── PhilipsAchieva3.nrrd.sha512 │ ├── PhilipsAchieva4.nrrd.sha512 │ ├── PhilipsAchieva6.nrrd.sha512 │ ├── PhilipsAchieva7.nrrd.sha512 │ ├── SiemensTrio-Syngo2004A-1.nrrd.sha512 │ ├── SiemensTrio-Syngo2004A-2.nrrd.sha512 │ ├── SiemensTrioTim1.nrrd.sha512 │ ├── SiemensTrioTim2.nrrd.sha512 │ ├── SiemensTrioTim3.nrrd.sha512 │ └── SiemensVerio.nrrd.sha512 ├── DWI_TestData_TARBALLS │ ├── DWIConvertGeSignaHdxBMatrixTest.tar.gz.sha512 │ ├── DWIConvertGeSignaHdxBigEndianTest.tar.gz.sha512 │ ├── DWIConvertGeSignaHdxFSLTest.tar.gz.sha512 │ ├── DWIConvertGeSignaHdxTest.tar.gz.sha512 │ ├── DWIConvertGeSignaHdxtBMatrixTest.tar.gz.sha512 │ ├── DWIConvertGeSignaHdxtTest.tar.gz.sha512 │ ├── DWIConvertMultiShellFSITest.tar.gz.sha512 │ ├── DWIConvertMultiShellFSITestSmallSize.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva2BMatrixTest.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva2Test.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva3Test.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva4Test.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva6Test.tar.gz.sha512 │ ├── DWIConvertPhilipsAchieva7Test.tar.gz.sha512 │ ├── DWIConvertPhilipsAchievaBMatrixTest.tar.gz.sha512 │ ├── DWIConvertPhilipsAchievaBigEndianTest.tar.gz.sha512 │ ├── DWIConvertPhilipsAchievaTest.tar.gz.sha512 │ ├── DWIConvertSiemensTrioSyngo2004A1Test.tar.gz.sha512 │ ├── DWIConvertSiemensTrioSyngo2004A2Test.tar.gz.sha512 │ ├── DWIConvertSiemensTrioTim2Test.tar.gz.sha512 │ ├── DWIConvertSiemensTrioTim3Test.tar.gz.sha512 │ ├── DWIConvertSiemensTrioTimBigEndian1Test.tar.gz.sha512 │ ├── DWIConvertSiemensTrioTimTest.tar.gz.sha512 │ ├── DWIConvertSiemensVerioTest.tar.gz.sha512 │ ├── GeSignaHDx.tar.gz.sha512 │ ├── GeSignaHDxBigEndian.tar.gz.sha512 │ ├── GeSignaHDxt.tar.gz.sha512 │ ├── PhilipsAchieva1.tar.gz.sha512 │ ├── PhilipsAchieva2.tar.gz.sha512 │ ├── PhilipsAchieva3.tar.gz.sha512 │ ├── PhilipsAchieva4.tar.gz.sha512 │ ├── PhilipsAchieva6.tar.gz.sha512 │ ├── PhilipsAchieva7.tar.gz.sha512 │ ├── PhilipsAchievaBigEndian1.tar.gz.sha512 │ ├── SiemensTrio-Syngo2004A-1.tar.gz.sha512 │ ├── SiemensTrio-Syngo2004A-2.tar.gz.sha512 │ ├── SiemensTrioTim1.tar.gz.sha512 │ ├── SiemensTrioTim2.tar.gz.sha512 │ ├── SiemensTrioTim3.tar.gz.sha512 │ ├── SiemensTrioTimBigEndian1.tar.gz.sha512 │ ├── SiemensVerio.tar.gz.sha512 │ └── SpaceThicknessDiffDicom.tar.gz.sha512 ├── DWI_test1.nrrd.sha512 ├── EMSP.fcsv.sha512 ├── FindCenter │ ├── FindCenterAfterGridComputationsForegroundImage.nii.gz.sha512 │ ├── FindCenterClippedImageMask.nii.gz.sha512 │ ├── FindCenterDistanceImage.nii.gz.sha512 │ ├── FindCenterGridImage.nii.gz.sha512 │ └── FindCenterTrimmedImage.nii.gz.sha512 ├── GTRACTTest_gtractAverageBvalues.standard.nrrd.sha512 ├── GTRACTTest_gtractConcatDwi.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_Rot-15z.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_Rot15z.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_Rot30x.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_Rot30y.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_Rot45z.standard.nrrd.sha512 ├── GTRACTTest_gtractResampleDWIInPlace_rigid_transform.mat.sha512 ├── GTRACTTest_rigidTx_Rot-15z.h5.sha512 ├── GTRACTTest_rigidTx_Rot15z.h5.sha512 ├── GTRACTTest_rigidTx_Rot30x.h5.sha512 ├── GTRACTTest_rigidTx_Rot30y.h5.sha512 ├── GTRACTTest_rigidTx_Rot45z.h5.sha512 ├── GaussianIOFilteringTest.png.sha512 ├── Hundred.hdr.sha512 ├── Hundred.img.sha512 ├── InitialDisplacementField.nii.gz.sha512 ├── Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_RigidRotationNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_ScaleSkewVersorRotationNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_ScaleSkewVersorScaleNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_ScaleVersorRotationNoMasks.mat.sha512 ├── Initializer_0.05_BRAINSFitTest_ScaleVersorScaleNoMasks.mat.sha512 ├── Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.mat.sha512 ├── Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.mat.sha512 ├── Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.mat.sha512 ├── LowerHalfHundreds.png.sha512 ├── OutDefField.nii.gz.sha512 ├── OutDefField_orientedImage.nii.gz.sha512 ├── Piecewised_IC4.vtk.sha512 ├── ProbabilityLabels.vtk.sha512 ├── ProstateIntraop.nrrd.sha512 ├── ProstateIntraopMask.nrrd.sha512 ├── ProstatePreop.nrrd.sha512 ├── ProstatePreopMask.nrrd.sha512 ├── RearrangedLabels.vtk.sha512 ├── Removed21And37From49Labels.vtk.sha512 ├── SUBJ_A_small_T1.nii.gz.sha512 ├── SUBJ_A_small_T2.nii.gz.sha512 ├── SUBJ_A_small_T2_mask.nii.gz.sha512 ├── SUBJ_A_small_brain_cut_mask.nii.gz.sha512 ├── SUBJ_B_small_T1.nii.gz.sha512 ├── SUBJ_B_small_T2.nii.gz.sha512 ├── SUBJ_B_small_T2_mask.nii.gz.sha512 ├── SUBJ_B_small_brain_cut_mask.nii.gz.sha512 ├── SimpleSurface1.vtk.sha512 ├── SimpleSurface1_IC4.vtk.sha512 ├── SimpleSurface2.vtk.sha512 ├── SimpleSurface2_IC4.vtk.sha512 ├── SimpleSurfaceIC4.vtk.sha512 ├── SmoothedScalar_IC4.vtk.sha512 ├── SubjectToAtlasScan1.mat.sha512 ├── SubjectToAtlasScan2.mat.sha512 ├── SurfaceColor.vtk.sha512 ├── SurfaceLabelCleanUp.vtk.sha512 ├── T1-2ndVersion.mdl.sha512 ├── T1.mdl.sha512 ├── T1.nii.gz.sha512 ├── T1_50Lmks.mdl.sha512 ├── TrainingCase1.fcsv.sha512 ├── TrainingCase1_T1.nii.gz.sha512 ├── TrainingCase2.fcsv.sha512 ├── TrainingCase2_T1.nii.gz.sha512 ├── TrainingCase3.fcsv.sha512 ├── TrainingCase3_T1.nii.gz.sha512 ├── Transforms_h5 │ ├── AtlasToSubjectScan1.h5.sha512 │ ├── AtlasToSubjectScan2.h5.sha512 │ ├── AtlasToSubjectScan3.h5.sha512 │ ├── AtlasToSubjectScan4.h5.sha512 │ ├── BRAINSFitTest_AffineRotationMasks.h5.sha512 │ ├── BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.h5.sha512 │ ├── BRAINSFitTest_Initializer_RigidRotationNoMasks.h5.sha512 │ ├── BRAINSFitTest_RigidRotationNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_AffineRotationNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_AffineScaleNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_RigidRotationHeadMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_RigidRotationNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_RigidRotationNoMasksRiginInPlaceInterp.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_ScaleSkewVersorRotationNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_ScaleSkewVersorScaleNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_ScaleVersorRotationNoMasks.h5.sha512 │ ├── Initializer_0.05_BRAINSFitTest_ScaleVersorScaleNoMasks.h5.sha512 │ ├── Initializer_BRAINSFitTest_BSplineAnteScaleRotationRescaleHeadMasks.h5.sha512 │ ├── Initializer_BRAINSFitTest_BSplineOnlyRescaleHeadMasks.h5.sha512 │ ├── Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.h5.sha512 │ ├── LLSModel-2ndVersion.h5.sha512 │ ├── LLSModel-30Landmarks.h5.sha512 │ ├── LLSModel.h5.sha512 │ ├── LLSModel_50Lmks.h5.sha512 │ ├── SubjectToAtlasScan1.h5.sha512 │ ├── SubjectToAtlasScan2.h5.sha512 │ ├── applyWarp_BSpline.h5.sha512 │ └── syn.benchmark.transform.h5.sha512 ├── TwoHundred.hdr.sha512 ├── TwoHundred.img.sha512 ├── UpperHalfHundreds.png.sha512 ├── ValidateBRAINSResampleTest7.result.nii.gz.sha512 ├── ValidateInitialTransform_Test.nii.gz.sha512 ├── ValidateOrientedImagesTest5.nii.gz.sha512 ├── ValidateVectorOrientedImagesTest6.nii.gz.sha512 ├── ValidateVectorOrientedImagesTest7.nii.gz.sha512 ├── affine_t1.nrrd.sha512 ├── affine_t2.nrrd.sha512 ├── applyWarp1.nii.gz.sha512 ├── applyWarp2.nii.gz.sha512 ├── applyWarp_BSpline.mat.sha512 ├── benchmark │ ├── BRAINSFit_SyNScale.benchmark.nii.gz.sha512 │ └── BRAINSFit_SyNScaleSkew.benchmark.nii.gz.sha512 ├── chk_BCDTest_ForceACPoint_standard.fcsv.sha512 ├── chk_BCDTest_ForcePCPoint_standard.fcsv.sha512 ├── chk_BCDTest_ForceRPPoint_standard.fcsv.sha512 ├── chk_BCDTest_ForceVN4Point_standard.fcsv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_Rot-15z_metaData.standard.csv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_Rot15z_metaData.standard.csv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_Rot30x_metaData.standard.csv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_Rot30y_metaData.standard.csv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_Rot45z_metaData.standard.csv.sha512 ├── chk_GTRACTTest_gtractResampleDWIInPlace_referenceMetaData.csv.sha512 ├── chk_a_BCDTestForLandmarkCompare_standard.fcsv.sha512 ├── chk_i_BCDTestForLandmarkCompare_standard.fcsv.sha512 ├── chk_insertMidACPCpointTest_standard.fcsv.sha512 ├── chk_landmarksConstellationAlignerTest_standard.fcsv.sha512 ├── deformed0036195.vtk.sha512 ├── deformedMovingImage.nii.gz.sha512 ├── diffeomorphicDemons1.nii.gz.sha512 ├── diffeomorphicDemons2.nii.gz.sha512 ├── diffeomorphicDemons3.nii.gz.sha512 ├── diffeomorphicDemons4.nii.gz.sha512 ├── diffeomorphicDemons5.nii.gz.sha512 ├── diffeomorphicDemonsWithMask.nii.gz.sha512 ├── diffeomorphicDemons_AutoMask.nii.gz.sha512 ├── fastSymmetricForcesDemons.nii.gz.sha512 ├── fixedImage.nii.gz.sha512 ├── fixedlk.lnd.sha512 ├── histeq2D.png.sha512 ├── histeq_input1.png.sha512 ├── histeq_input2.png.sha512 ├── iccdef_result1.nii.gz.sha512 ├── iccdef_result2.nii.gz.sha512 ├── image1.nii.gz.sha512 ├── image2.nii.gz.sha512 ├── image_in.mhd.sha512 ├── image_in.raw.sha512 ├── insertMidACPCpointTest_input.fcsv.sha512 ├── labels.nii.gz.sha512 ├── landmarksConstellationAlignerTest_input.fcsv.sha512 ├── landmarksWeightsCompareTest_standard.wts.sha512 ├── movingImage.nii.gz.sha512 ├── movinglk.lnd.sha512 ├── optdigits.test.sha512 ├── optdigits.train.sha512 ├── orientedImagesDemons_test.nii.gz.sha512 ├── rho.nii.gz.sha512 ├── rotation.geom.test.nii.gz.sha512 ├── rotation.rescale.rigid.nii.gz.sha512 ├── rotation.rescale.test.nii.gz.sha512 ├── rotation.test.nii.gz.sha512 ├── rotation.test_mask.nii.gz.sha512 ├── rotationUShort.rescale.rigid.nii.gz.sha512 ├── scale.test.nii.gz.sha512 ├── scale.test_mask.nii.gz.sha512 ├── scan1Mask1.nii.gz.sha512 ├── scan1T1.nii.gz.sha512 ├── scan1T2.nii.gz.sha512 ├── scan2Mask1.nii.gz.sha512 ├── scan2T1.nii.gz.sha512 ├── scan2T2.nii.gz.sha512 ├── scan3Mask1.nii.gz.sha512 ├── scan3SG.nii.gz.sha512 ├── scan3T1.nii.gz.sha512 ├── scan3T2.nii.gz.sha512 ├── scan4Mask1.nii.gz.sha512 ├── scan4T1.nii.gz.sha512 ├── scan4T2.nii.gz.sha512 ├── small_ISO_T1_REP0.nii.gz.sha512 ├── small_ISO_T2_REP0.nii.gz.sha512 ├── smoothed.benchmark.test.nii.gz.sha512 ├── template_t1.nii.gz.sha512 ├── template_t1_denoised_gaussian.nii.gz.sha512 ├── template_t2_denoised_gaussian.nii.gz.sha512 ├── test.nii.gz.sha512 ├── testMask.nii.gz.sha512 ├── test_mask.nii.gz.sha512 ├── thirionDemons.nii.gz.sha512 ├── translation.rescale.test.nii.gz.sha512 ├── translation.test.nii.gz.sha512 ├── translation.test_mask.nii.gz.sha512 ├── update-to-sha512.sh ├── warped0036896Hull.vtk.sha512 └── weight_tolerance.wts ├── Utilities ├── BRAINSMakeMD5SigFileAndMoveData.py ├── DevelopmentSetupScripts │ └── SetupHooks.sh ├── FindCTestMatchingWarnings.py ├── Hooks │ ├── commit-msg │ ├── pre-commit │ ├── pre-commit-style │ └── prepare-commit-msg ├── KWStyle │ └── kws.xml.in ├── Maintenance │ ├── clang-format.bash │ ├── replace_atoi_atof.sh │ └── uncrustify.cfg ├── PushDataDirctoryToMidas.py ├── SetupForDevelopment.sh ├── UpdateCopyrightStatementsInBRAINSTools.py ├── UploadBinaryData.sh ├── build_configs │ ├── Darwin │ │ ├── BRAINSTools-llvm10-Debug.cmake │ │ ├── BRAINSTools-llvm10-RelWithDebInfo.cmake │ │ ├── BRAINSTools-llvm10-Release.cmake │ │ └── BRAINSTools-sysclang-RelWithDebInfo.cmake │ ├── README.md │ └── nightly.sh ├── createClionConfigFromSuperbuild.py └── push_new_reference_data.sh ├── Version.cmake ├── azure-pipelines.yml ├── cpack_brainstools.cmake ├── docs ├── BRAINSToolsInClion.md ├── _config.yml ├── build_20220126 │ ├── CMakeUserPresets.json │ └── build_20220126.sh ├── images │ ├── CMake_refresh.png │ ├── CMake_settings_window.png │ ├── CTest_menu.png │ ├── CTest_parallel_field_entry.png │ ├── bg_hr.png │ ├── blacktocat.png │ ├── component_selection.png │ ├── edit_configurations.png │ ├── hammer_icon.png │ ├── icon_download.png │ ├── refresh_icon.png │ ├── run_icon.png │ ├── run_single_test.png │ ├── sprite_download.png │ └── stop_icon.png ├── index.md └── stylesheets │ ├── pygment_trac.css │ └── stylesheet.css ├── github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE.md └── 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