├── .clang-format ├── .dockerignore ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── build_errors.md │ ├── config.yml │ ├── feature_request.md │ └── other_questions.md ├── pull_request_template.md ├── stale.yml └── workflows │ ├── ci-docker.yml │ ├── github-repo-stats.yml │ ├── release-binaries.yml │ ├── release-docker-binaries.yml │ └── release-win-binaries.yml ├── .gitignore ├── .htaccess ├── .mailmap ├── .travis.yml ├── ANTS.cmake ├── ANTSCopyright.txt ├── ANTSnightly.sh ├── ANTsVersionConfig.h.in ├── CITATION.bib ├── CMake ├── ANTSExternalData.cmake ├── CCache.cmake ├── ExternalData_config.cmake.in ├── GetGitRevisionDescription.cmake ├── ITKSetStandardCompilerFlags.cmake ├── ITK_CheckCCompilerFlag.cmake ├── ITK_CheckCXXCompilerFlag.cmake ├── PreventInBuildInstalls.cmake ├── PreventInSourceBuilds.cmake ├── ProjectSourceVersion.cmake ├── SlicerMacroCheckExternalProjectDependency.cmake ├── SlicerMacroEmptyExternalProject.cmake ├── itkCheckSourceTree.cmake └── pre-commit ├── CMakeLists.txt ├── CONTRIBUTING.md ├── COPYING.txt ├── CTestConfig.cmake ├── CTestCustom.cmake ├── Common.cmake ├── Dockerfile ├── Examples ├── ANTS.cxx ├── ANTSConformalMapping.cxx ├── ANTSIntegrateVectorField.cxx ├── ANTSIntegrateVelocityField.cxx ├── ANTSJacobian.cxx ├── ANTSUseDeformationFieldToGetAffineTransform.cxx ├── ANTSUseLandmarkImagesToGetAffineTransform.cxx ├── ANTSUseLandmarkImagesToGetBSplineDisplacementField.cxx ├── ANTsVersion.cxx ├── ANTsVersion.h ├── AddNoiseToImage.cxx ├── Atropos.cxx ├── AverageAffineTransform.cxx ├── AverageAffineTransformNoRigid.cxx ├── AverageImages.cxx ├── AverageTensorImages.cxx ├── CMakeLists.txt ├── CheckTopology.cxx ├── ClusterImageStatistics.cxx ├── ComposeMultiTransform.cxx ├── CompositeTransformUtil.cxx ├── ComputeSimilarityMetric.cxx ├── ConformalMapping.cxx ├── ConvertImage.cxx ├── ConvertImagePixelType.cxx ├── ConvertInputImagePixelTypeToFloat.cxx ├── ConvertScalarImageToRGB.cxx ├── ConvertToJpg.cxx ├── ConvertTransformFile.cxx ├── ConvertVectorFieldToVTK.cxx ├── CopyImageHeaderInformation.cxx ├── CreateDTICohort.cxx ├── CreateDisplacementField.cxx ├── CreateImage.cxx ├── CreateJacobianDeterminantImage.cxx ├── CreateTiledMosaic.cxx ├── CreateWarpedGridImage.cxx ├── CustomColormaps │ ├── bone.txt │ ├── christmas.txt │ ├── christmas2.txt │ ├── colorcube.txt │ ├── cool.txt │ ├── flag.txt │ ├── itkSnap.txt │ ├── itkSnap255.txt │ ├── itkSnap_BRATS.txt │ ├── lines.txt │ ├── pink.txt │ ├── prism.txt │ └── vga.txt ├── DeNrrd.cxx ├── DenoiseImage.cxx ├── ExtractRegionFromImage.cxx ├── ExtractRegionFromImageByMask.cxx ├── ExtractSliceFromImage.cxx ├── FitBSplineToPoints.cxx ├── GetConnectedComponentsFeatureImages.cxx ├── GetMeshAndTopology.cxx ├── ImageCompare.cxx ├── ImageIntensityStatistics.cxx ├── ImageMath.cxx ├── ImageMathHelper2D.cxx ├── ImageMathHelper3D.cxx ├── ImageMathHelper4D.cxx ├── ImageMath_Templates.hxx ├── ImageSetStatistics.cxx ├── KellyKapowski.cxx ├── KellySlater.cxx ├── LabelClustersUniquely.cxx ├── LabelGeometryMeasures.cxx ├── LabelOverlapMeasures.cxx ├── LaplacianThickness.cxx ├── LesionFilling.cxx ├── MeasureImageSimilarity.cxx ├── MeasureMinMaxMean.cxx ├── MemoryTest.cxx ├── MultiplyImages.cxx ├── N3BiasFieldCorrection.cxx ├── N4BiasFieldCorrection.cxx ├── NonLocalSuperResolution.cxx ├── PasteImageIntoImage.cxx ├── PermuteFlipImageOrientationAxes.cxx ├── PrintHeader.cxx ├── RebaseTensorImage.cxx ├── ReorientTensorImage.cxx ├── ResampleImage.cxx ├── ResampleImageBySpacing.cxx ├── ResetDirection.cxx ├── SetDirectionByMatrix.cxx ├── SetOrigin.cxx ├── SetSpacing.cxx ├── SimulateDisplacementField.cxx ├── SmoothDisplacementField.cxx ├── SmoothImage.cxx ├── StackSlices.cxx ├── StudentsTestOnImages.cxx ├── SuperResolution.cxx ├── SurfaceBasedSmoothing.cxx ├── SurfaceCurvature.cxx ├── TensorDerivedImage.cxx ├── TestSuite │ ├── ANTS_CC_1_test.cmake │ ├── ANTS_CC_2_test.cmake │ ├── ANTS_CC_3_test.cmake │ ├── ANTS_ELASTIC_test.cmake │ ├── ANTS_EXP_test.cmake │ ├── ANTS_GSYN_test.cmake │ ├── ANTS_MI_1_test.cmake │ ├── ANTS_MI_2_test.cmake │ ├── ANTS_MSQ_test.cmake │ ├── ANTS_PSE_MSQ_IMG_test.cmake │ ├── ANTS_PSE_MSQ_TXT_test.cmake │ ├── ANTS_PSE_MSQ_VTK_test.cmake │ ├── ANTS_ROT_EXP_test.cmake │ ├── ANTS_ROT_GSYN_test.cmake │ ├── ANTS_SYN_WITH_TIME_test.cmake │ ├── ANTS_SYN_test.cmake │ ├── APOC_OTSU_INIT_test.cmake │ ├── CMakeLists.txt │ └── template_for_executableTestWrapper.cxx.in ├── Testing │ └── Temporary │ │ ├── CTestCostData.txt │ │ └── LastTest.log ├── TextureCooccurrenceFeatures.cxx ├── TextureRunLengthFeatures.cxx ├── ThresholdImage.cxx ├── TileImages.cxx ├── TimeSCCAN.cxx ├── WarpImageMultiTransform.cxx ├── WarpTensorImageMultiTransform.cxx ├── WarpTimeSeriesImageMultiTransform.cxx ├── WarpVTKPolyDataMultiTransform.cxx ├── antsAI.cxx ├── antsAffineInitializer.cxx ├── antsAlignOrigin.cxx ├── antsApplyTransforms.cxx ├── antsApplyTransformsToPoints.cxx ├── antsCommandIterationUpdate.h ├── antsDisplacementAndVelocityFieldRegistrationCommandIterationUpdate.h ├── antsJointFusion.cxx ├── antsJointTensorFusion.cxx ├── antsLandmarkBasedTransformInitializer.cxx ├── antsMotionCorr.cxx ├── antsMotionCorrDiffusionDirection.cxx ├── antsMotionCorrStats.cxx ├── antsRegistration.cxx ├── antsRegistration2DDouble.cxx ├── antsRegistration2DFloat.cxx ├── antsRegistration3DDouble.cxx ├── antsRegistration3DFloat.cxx ├── antsRegistration4DDouble.cxx ├── antsRegistration4DFloat.cxx ├── antsRegistrationCommandIterationUpdate.h ├── antsRegistrationOptimizerCommandIterationUpdate.h ├── antsRegistrationTemplateHeader.cxx ├── antsRegistrationTemplateHeader.h ├── antsSliceRegularizedRegistration.cxx ├── antsSurf.cxx ├── antsTransformInfo.cxx ├── antsUtilities.cxx ├── antsUtilities.h ├── antsUtilitiesTesting.cxx ├── antsVol.cxx ├── compareTwoTransforms.cxx ├── iMath.cxx ├── iMathFunctions.h ├── iMathFunctions.hxx ├── iMathFunctions1.h ├── iMathFunctions1.hxx ├── iMathFunctions2.h ├── iMathFunctions2.hxx ├── include │ ├── ANTSConformalMapping.h │ ├── ANTSIntegrateVectorField.h │ ├── ANTSIntegrateVelocityField.h │ ├── ANTSJacobian.h │ ├── ANTSUseDeformationFieldToGetAffineTransform.h │ ├── ANTSUseLandmarkImagesToGetAffineTransform.h │ ├── ANTSUseLandmarkImagesToGetBSplineDisplacementField.h │ ├── ANTS_.h │ ├── AddNoiseToImage.h │ ├── Atropos.h │ ├── AverageAffineTransform.h │ ├── AverageAffineTransformNoRigid.h │ ├── AverageImages.h │ ├── AverageTensorImages.h │ ├── CheckTopology.h │ ├── ClusterImageStatistics.h │ ├── ComposeMultiTransform.h │ ├── CompositeTransformUtil.h │ ├── ComputeSimilarityMetric.h │ ├── ConformalMapping.h │ ├── ConvertImage.h │ ├── ConvertImagePixelType.h │ ├── ConvertInputImagePixelTypeToFloat.h │ ├── ConvertScalarImageToRGB.h │ ├── ConvertToJpg.h │ ├── ConvertTransformFile.h │ ├── ConvertVectorFieldToVTK.h │ ├── CopyImageHeaderInformation.h │ ├── CreateDTICohort.h │ ├── CreateDisplacementField.h │ ├── CreateImage.h │ ├── CreateJacobianDeterminantImage.h │ ├── CreateTiledMosaic.h │ ├── CreateWarpedGridImage.h │ ├── DeNrrd.h │ ├── DenoiseImage.h │ ├── ExtractRegionFromImage.h │ ├── ExtractRegionFromImageByMask.h │ ├── ExtractSliceFromImage.h │ ├── FitBSplineToPoints.h │ ├── GetConnectedComponentsFeatureImages.h │ ├── GetMeshAndTopology.h │ ├── ImageCompare.h │ ├── ImageIntensityStatistics.h │ ├── ImageMath.h │ ├── ImageSetStatistics.h │ ├── KellyKapowski.h │ ├── KellySlater.h │ ├── LabelClustersUniquely.h │ ├── LabelGeometryMeasures.h │ ├── LabelOverlapMeasures.h │ ├── LaplacianThickness.h │ ├── LesionFilling.h │ ├── MeasureImageSimilarity.h │ ├── MeasureMinMaxMean.h │ ├── MemoryTest.h │ ├── MultiplyImages.h │ ├── N3BiasFieldCorrection.h │ ├── N4BiasFieldCorrection.h │ ├── NonLocalSuperResolution.h │ ├── PasteImageIntoImage.h │ ├── PermuteFlipImageOrientationAxes.h │ ├── PrintHeader.h │ ├── RebaseTensorImage.h │ ├── ReorientTensorImage.h │ ├── ResampleImage.h │ ├── ResampleImageBySpacing.h │ ├── ResetDirection.h │ ├── SetDirectionByMatrix.h │ ├── SetOrigin.h │ ├── SetSpacing.h │ ├── SimulateDisplacementField.h │ ├── SmoothDisplacementField.h │ ├── SmoothImage.h │ ├── StackSlices.h │ ├── StudentsTestOnImages.h │ ├── SuperResolution.h │ ├── SurfaceBasedSmoothing.h │ ├── SurfaceCurvature.h │ ├── TensorDerivedImage.h │ ├── TextureCooccurrenceFeatures.h │ ├── TextureRunLengthFeatures.h │ ├── ThresholdImage.h │ ├── TileImages.h │ ├── TimeSCCAN.h │ ├── WarpImageMultiTransform.h │ ├── WarpTensorImageMultiTransform.h │ ├── WarpTimeSeriesImageMultiTransform.h │ ├── WarpVTKPolyDataMultiTransform.h │ ├── ants.h │ ├── antsAI.h │ ├── antsAffineInitializer.h │ ├── antsAlignOrigin.h │ ├── antsApplyTransforms.h │ ├── antsApplyTransformsToPoints.h │ ├── antsImageRead.h │ ├── antsImageWrite.h │ ├── antsJointFusion.h │ ├── antsJointTensorFusion.h │ ├── antsLandmarkBasedTransformInitializer.h │ ├── antsMotionCorr.h │ ├── antsMotionCorrDiffusionDirection.h │ ├── antsMotionCorrStats.h │ ├── antsRegistration.h │ ├── antsSliceRegularizedRegistration.h │ ├── antsSurf.h │ ├── antsTransformInfo.h │ ├── antsUtilitiesTesting.h │ ├── antsVol.h │ ├── ants_moco.h │ ├── compareTwoTransforms.h │ ├── iMath.h │ ├── itkCommandLineParserTest.h │ ├── sccan.h │ └── simpleSynRegistration.h ├── itkCommandLineParserTest.cxx ├── itkTestMain.h ├── itkantsRegistrationHelper.h ├── itkantsRegistrationHelper.hxx ├── make_interpolator_snip.tmpl ├── sccan.cxx ├── simpleSynRegistration.cxx └── template_for_executables.cxx.in ├── ImageRegistration ├── ANTS_affine_registration.h ├── ANTS_affine_registration2.h ├── itkANTSAffine3DTransform.h ├── itkANTSAffine3DTransform.hxx ├── itkANTSCenteredAffine2DTransform.h ├── itkANTSCenteredAffine2DTransform.hxx ├── itkANTSImageRegistrationOptimizer.cxx ├── itkANTSImageRegistrationOptimizer.h ├── itkANTSImageTransformation.cxx ├── itkANTSImageTransformation.h ├── itkANTSLabeledPointSet.h ├── itkANTSSimilarityMetric.h ├── itkAvantsMutualInformationRegistrationFunction.cxx ├── itkAvantsMutualInformationRegistrationFunction.h ├── itkAvantsPDEDeformableRegistrationFunction.h ├── itkCrossCorrelationRegistrationFunction.cxx ├── itkCrossCorrelationRegistrationFunction.h ├── itkExpectationBasedPointSetRegistrationFunction.h ├── itkExpectationBasedPointSetRegistrationFunction.hxx ├── itkJensenHavrdaCharvatTsallisLabeledPointSetMetric.h ├── itkJensenHavrdaCharvatTsallisLabeledPointSetMetric.hxx ├── itkJensenHavrdaCharvatTsallisPointSetMetric.h ├── itkJensenHavrdaCharvatTsallisPointSetMetric.hxx ├── itkJensenTsallisBSplineRegistrationFunction.h ├── itkJensenTsallisBSplineRegistrationFunction.hxx ├── itkPICSLAdvancedNormalizationToolKit.h ├── itkPICSLAdvancedNormalizationToolKit.hxx ├── itkProbabilisticRegistrationFunction.cxx ├── itkProbabilisticRegistrationFunction.h ├── itkSpatialMutualInformationRegistrationFunction.cxx ├── itkSpatialMutualInformationRegistrationFunction.h ├── itkSyNDemonsRegistrationFunction.cxx ├── itkSyNDemonsRegistrationFunction.h ├── itkVectorParameterizedNeighborhoodOperatorImageFilter.h └── itkVectorParameterizedNeighborhoodOperatorImageFilter.hxx ├── ImageSegmentation ├── antsAtroposSegmentationImageFilter.h ├── antsAtroposSegmentationImageFilter.hxx ├── antsBoxPlotQuantileListSampleFilter.h ├── antsBoxPlotQuantileListSampleFilter.hxx ├── antsGaussianListSampleFunction.h ├── antsGaussianListSampleFunction.hxx ├── antsGrubbsRosnerListSampleFilter.h ├── antsGrubbsRosnerListSampleFilter.hxx ├── antsHistogramParzenWindowsListSampleFunction.h ├── antsHistogramParzenWindowsListSampleFunction.hxx ├── antsJointHistogramParzenShapeAndOrientationListSampleFunction.h ├── antsJointHistogramParzenShapeAndOrientationListSampleFunction.hxx ├── antsJointHistogramParzenWindowsListSampleFunction.h ├── antsJointHistogramParzenWindowsListSampleFunction.hxx ├── antsListSampleFunction.h ├── antsListSampleFunction.hxx ├── antsListSampleToListSampleFilter.h ├── antsListSampleToListSampleFilter.hxx ├── antsLogEuclideanGaussianListSampleFunction.h ├── antsLogEuclideanGaussianListSampleFunction.hxx ├── antsManifoldParzenWindowsListSampleFunction.h ├── antsManifoldParzenWindowsListSampleFunction.hxx ├── antsPartialVolumeGaussianListSampleFunction.h ├── antsPartialVolumeGaussianListSampleFunction.hxx ├── antsPassThroughListSampleFilter.h ├── antsPassThroughListSampleFilter.hxx ├── itkWeightedVotingFusionImageFilter.h └── itkWeightedVotingFusionImageFilter.hxx ├── README.md ├── Scripts ├── ANTSAverage2DAffine.sh ├── ANTSAverage3DAffine.sh ├── ANTSpexec.sh ├── ants.sh ├── antsASLProcessing.R ├── antsASLProcessing.sh ├── antsAtroposN4.sh ├── antsBOLDNetworkAnalysis.R ├── antsBrainExtraction.sh ├── antsCookTemplatePriors.sh ├── antsCorticalThickness.sh ├── antsIntermodalityIntrasubject.sh ├── antsIntroduction.sh ├── antsJointLabelFusion.sh ├── antsJointLabelFusion2.sh ├── antsLaplacianBoundaryCondition.R ├── antsLongitudinalCorticalThickness.sh ├── antsLongitudinalJointLabelFusion.sh ├── antsMotionCorrExample ├── antsMultivariateTemplateConstruction.sh ├── antsMultivariateTemplateConstruction2.sh ├── antsNetworkAnalysis.R ├── antsNeuroimagingBattery ├── antsRegistrationSpaceTime.sh ├── antsRegistrationSyN.sh ├── antsRegistrationSyNQuick.sh ├── antsaffine.sh ├── antsbashstats.sh ├── antsdeformationmag.sh ├── antsqsub.sh ├── antswithdt.sh ├── asymmetry.sh ├── basic_ants_example.sh ├── buildtemplateparallel.sh ├── cbf_pasl_robust_batch.R ├── cbf_pcasl_robust_batch.R ├── directlabels.sh ├── geodesicinterpolation.sh ├── guidedregistration.sh ├── landmarkmatch.sh ├── lohmann.sh ├── multi_template_script.sh ├── newAntsExample.sh ├── optimalsmooth.sh ├── phantomstudy.sh ├── registerimages.pl ├── runprogramonimageset.pl ├── sccan_tests ├── shapeupdatetotemplate.sh ├── skel.sh ├── sliceBySliceOperation.sh ├── submitexperimentalbuild.sh ├── sygnccavg.sh ├── thickstudy.sh ├── unbiased_longitudinal_map ├── unbiased_pairwise_registration.sh ├── unbiased_pairwise_registration_with_aux_images.sh ├── waitForPBSQJobs.pl ├── waitForSGEQJobs.pl ├── waitForSlurmJobs.pl ├── waitForXGridJobs.pl ├── warpimages.pl ├── weightedaverage.pl └── weightedaverage.sh ├── SuperBuild.cmake ├── SuperBuild ├── External_Cppcheck.cmake ├── External_ITKv5.cmake ├── External_KWStyle.cmake ├── External_SlicerExecutionModel.cmake ├── External_Uncrustify.cmake ├── External_VTK.cmake ├── External_VTK_build_step.cmake.in └── External_VTK_patch.cmake ├── Temporary ├── antsFastMarchingImageFilter.h ├── antsFastMarchingImageFilter.hxx ├── deprecate_itkFEMElement3DC0LinearTriangular.cxx ├── deprecate_itkFEMElement3DC0LinearTriangular.h ├── deprecate_itkFEMElement3DC0LinearTriangularLaplaceBeltrami.cxx ├── deprecate_itkFEMElement3DC0LinearTriangularLaplaceBeltrami.h ├── deprecate_itkFEMElement3DC0LinearTriangularMembrane.cxx ├── deprecate_itkFEMElement3DC0LinearTriangularMembrane.h ├── itkAddConstantToImageFilter.h ├── itkDijkstrasAlgorithm.cxx ├── itkDijkstrasAlgorithm.h ├── itkFEMConformalMap.cxx ├── itkFEMConformalMap.h ├── itkFEMDiscConformalMap.cxx ├── itkFEMDiscConformalMap.h ├── itkFEMElement3DMembrane1DOF.h ├── itkFEMElement3DMembrane1DOF.hxx ├── itkManifoldIntegrationAlgorithm.cxx ├── itkManifoldIntegrationAlgorithm.h ├── itkMeanSquaresPointSetToPointSetIntensityMetricv4.h ├── itkMeanSquaresPointSetToPointSetIntensityMetricv4.hxx ├── itkMultiplyByConstantImageFilter.h └── topological_numbers.h ├── Tensor ├── TensorFunctions.h ├── itkDecomposeTensorFunction2.h ├── itkDecomposeTensorFunction2.hxx ├── itkExpTensorImageFilter.h ├── itkExpTensorImageFilter.hxx ├── itkLogTensorImageFilter.h ├── itkLogTensorImageFilter.hxx ├── itkPreservationOfPrincipalDirectionTensorReorientationImageFilter.cxx ├── itkPreservationOfPrincipalDirectionTensorReorientationImageFilter.h ├── itkRotationMatrixFromVectors.h ├── itkWarpTensorImageMultiTransformFilter.h └── itkWarpTensorImageMultiTransformFilter.hxx ├── TestData ├── ANON0006_20_T1_dbg_splayed.nii.gz.sha512 ├── ANON0006_20_T1_sag_twisted.nii.gz.sha512 ├── CompositeTransformUtilTest.result.h5.sha512 ├── CompositeTransformUtilTest_AffineTransform.mat.sha512 ├── CompositeTransformUtilTest_RigidTransform.mat.sha512 ├── CompositeTransformUtilTest_SyNTransform.nii.gz.sha512 ├── Data │ ├── B1.tiff.md5 │ ├── B2.tiff.md5 │ ├── B3.tiff.md5 │ ├── B4.tiff.md5 │ ├── B5.tiff.md5 │ ├── Frown.nii.sha512 │ ├── Frown.txt.sha512 │ ├── Frown.vtk.sha512 │ ├── README.md5 │ ├── Smile.nii.sha512 │ ├── Smile.txt.sha512 │ ├── Smile.vtk.sha512 │ ├── beetlerot.jpg.md5 │ ├── c.nii.gz.sha512 │ ├── ch2brainmask.nii.gz.md5 │ ├── chalf.nii.gz.sha512 │ ├── ford.jpg.md5 │ ├── functional.nii.md5 │ ├── listPriorWolk_nirepDemo.txt.md5 │ ├── mov2.nii.gz.md5 │ ├── myview1.csv.md5 │ ├── myview2.csv.md5 │ ├── myview3.csv.md5 │ ├── myview4.csv.md5 │ ├── myview_mismatch.csv.md5 │ ├── phantomAwmgm.jpg.md5 │ ├── phantomBwmgm.jpg.md5 │ ├── phantomCwmgm.jpg.md5 │ ├── phantomDwmgm.jpg.md5 │ ├── phantomEwmgm.jpg.md5 │ ├── phantomFwmgm.jpg.md5 │ ├── phantomGwmgm.jpg.md5 │ ├── phantomHwmgm.jpg.md5 │ ├── phantomtemplate.jpg.md5 │ ├── priorScaleListWolk_nirep0p1Demo.csv.md5 │ ├── r16mask.nii.gz.md5 │ ├── r16priors.nii.gz.md5 │ ├── r16roth.nii.gz.sha512 │ ├── r16slice.nii.gz.sha512 │ ├── r27slice.nii.gz.md5 │ ├── r30slice.nii.gz.md5 │ ├── r62slice.nii.gz.md5 │ ├── r64roth.nii.gz.sha512 │ ├── r64slice.nii.gz.sha512 │ ├── r85slice.nii.gz.md5 │ ├── ref2.nii.gz.md5 │ ├── test_DiReCT.sh.md5 │ ├── test_image_ground_truth.nii.gz.md5 │ ├── test_image_seg.nii.gz.md5 │ ├── wolk_dataMCINormalDemo.mhd.md5 │ ├── wolk_dataMCINormalDemo.raw.md5 │ └── wolk_mask.nii.gz.md5 ├── Initializer_0.05_antsRegistrationTest_AffineRotationMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_AffineRotationNoMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_AffineScaleMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_AffineScaleMasks_Float.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_RigidRotationHeadMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_RigidRotationNoMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_RigidRotationNoMasks_Float.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_SimilarityRotationNoMasks.mat.sha512 ├── Initializer_0.05_antsRegistrationTest_SimilarityScaleNoMasks.mat.sha512 ├── Initializer_antsRegistrationTest_AffineTranslationMasks.mat.sha512 ├── Initializer_antsRegistrationTest_RigidAnisotropicMasks.mat.sha512 ├── Initializer_antsRegistrationTest_RigidRotGeomNoMasks.mat.sha512 ├── Initializer_antsRegistrationTest_ScaleRotationRescaleHeadMasks.mat.sha512 ├── Initializer_antsRegistrationTest_ScaleRotationRescaleHeadMasks_Float.mat.sha512 ├── Initializer_antsRegistrationTest_TranslationRescaleHeadMasks.mat.sha512 ├── Initializer_antsRegistrationTest_TranslationRescaleHeadMasks_Float.mat.sha512 ├── antsApplyTransformsTesting.result.nii.gz.sha512 ├── antsApplyTransformsTesting_InputWarpTransform.nii.gz.sha512 ├── antsRegistrationTest_AffineRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_AffineRotationNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_AffineScaleMasks.result.nii.gz.sha512 ├── antsRegistrationTest_AffineScaleNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_AffineTranslationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_AffineTranslationNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_CCSimilarityRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_MSEAffineRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_MSESimilarityRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_MSESimilarityRotationMasks_Float.result.nii.gz.sha512 ├── antsRegistrationTest_RigidAnisotropicMasks.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotGeomNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotaRotaRotNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotaRotaRotNoMasks_Float.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotationHeadMasks.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_RigidRotationNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_ScaleRotationRescaleHeadMasks.result.nii.gz.sha512 ├── antsRegistrationTest_ScaleRotationRescaleHeadMasks_Float.result.nii.gz.sha512 ├── antsRegistrationTest_ScaleTranslationRescaleHeadMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityRotationMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityRotationNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityScaleMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityScaleNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityTranslationRescaleNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SimilarityTranslationRescaleNoMasks_Float.result.nii.gz.sha512 ├── antsRegistrationTest_SyNScaleNoMasks.result.nii.gz.sha512 ├── antsRegistrationTest_SyNScaleNoMasks_Float.result.nii.gz.sha512 ├── antsRegistrationTest_initialize_transforms_per_stageComposite.result.h5.sha512 ├── rotation.geom.test.nii.gz.sha512 ├── rotation.rescale.test.nii.gz.sha512 ├── rotation.test.nii.gz.sha512 ├── rotation.test_mask.nii.gz.sha512 ├── scale.test.nii.gz.sha512 ├── scale.test_mask.nii.gz.sha512 ├── test.nii.gz.sha512 ├── test_mask.nii.gz.sha512 ├── translation.rescale.test.nii.gz.sha512 ├── translation.test.nii.gz.sha512 └── translation.test_mask.nii.gz.sha512 ├── Utilities ├── ANTSMakeMD5SigFileAndMoveData.py ├── BinaryImageToMeshFilter.h ├── DevelopmentSetupScripts │ └── SetupHooks.sh ├── Hooks │ ├── commit-msg │ ├── pre-commit │ ├── pre-commit-style │ └── prepare-commit-msg ├── ReadWriteData.cxx ├── ReadWriteData.h ├── SetupForDevelopment.sh ├── antsAllocImage.h ├── antsCommandLineOption.cxx ├── antsCommandLineOption.h ├── antsCommandLineParser.cxx ├── antsCommandLineParser.h ├── antsMatrixUtilities.h ├── antsMatrixUtilities.hxx ├── antsSCCANObject.h ├── antsSCCANObject.hxx ├── itkAlternatingValueDifferenceImageFilter.h ├── itkAlternatingValueDifferenceImageFilter.hxx ├── itkAlternatingValueSimpleSubtractionImageFilter.h ├── itkAlternatingValueSimpleSubtractionImageFilter.hxx ├── itkAverageAffineTransformFunction.h ├── itkAverageAffineTransformFunction.hxx ├── itkAverageOverDimensionImageFilter.h ├── itkAverageOverDimensionImageFilter.hxx ├── itkComposeDiffeomorphismsImageFilter.h ├── itkComposeDiffeomorphismsImageFilter.hxx ├── itkDecomposeTensorFunction.h ├── itkDecomposeTensorFunction.hxx ├── itkDeformationFieldGradientTensorImageFilter.h ├── itkDeformationFieldGradientTensorImageFilter.hxx ├── itkDeterminantTensorImageFilter.h ├── itkDeterminantTensorImageFilter.hxx ├── itkDiReCTImageFilter.h ├── itkDiReCTImageFilter.hxx ├── itkDisplacementFieldFromMultiTransformFilter.h ├── itkGeneralToBSplineDisplacementFieldFilter.h ├── itkGeneralToBSplineDisplacementFieldFilter.hxx ├── itkGeometricJacobianDeterminantImageFilter.h ├── itkGeometricJacobianDeterminantImageFilter.hxx ├── itkImageIntensityAndGradientToPointSetFilter.h ├── itkImageIntensityAndGradientToPointSetFilter.hxx ├── itkLabeledPointSetFileReader.h ├── itkLabeledPointSetFileReader.hxx ├── itkLabeledPointSetFileWriter.h ├── itkLabeledPointSetFileWriter.hxx ├── itkManifoldParzenWindowsPointSetFunction.h ├── itkManifoldParzenWindowsPointSetFunction.hxx ├── itkMaskedSmoothingImageFilter.h ├── itkMaskedSmoothingImageFilter.hxx ├── itkMultiScaleLaplacianBlobDetectorImageFilter.h ├── itkMultiScaleLaplacianBlobDetectorImageFilter.hxx ├── itkMultiplyByConstantVectorImageFilter.h ├── itkN3BiasFieldCorrectionImageFilter.h ├── itkN3BiasFieldCorrectionImageFilter.hxx ├── itkN3MRIBiasFieldCorrectionImageFilter.h ├── itkN3MRIBiasFieldCorrectionImageFilter.hxx ├── itkNeighborhoodFirstOrderStatisticsImageFilter.h ├── itkNonLocalSuperresolutionImageFilter.h ├── itkNonLocalSuperresolutionImageFilter.hxx ├── itkOptimalSharpeningImageFilter.h ├── itkOptimalSharpeningImageFilter.hxx ├── itkPointSetFunction.h ├── itkPointSetFunction.hxx ├── itkPreservationOfVectorDirectionImageFilter.cxx ├── itkPreservationOfVectorDirectionImageFilter.h ├── itkPseudoContinuousArterialSpinLabeledCerebralBloodFlowImageFilter.h ├── itkPseudoContinuousArterialSpinLabeledCerebralBloodFlowImageFilter.hxx ├── itkPulsedArterialSpinLabeledCerebralBloodFlowImageFilter.h ├── itkPulsedArterialSpinLabeledCerebralBloodFlowImageFilter.hxx ├── itkSimulatedBSplineDisplacementFieldSource.h ├── itkSimulatedBSplineDisplacementFieldSource.hxx ├── itkSimulatedDisplacementFieldSource.h ├── itkSimulatedDisplacementFieldSource.hxx ├── itkSimulatedExponentialDisplacementFieldSource.h ├── itkSimulatedExponentialDisplacementFieldSource.hxx ├── itkSliceTimingCorrectionImageFilter.h ├── itkSliceTimingCorrectionImageFilter.hxx ├── itkSplitAlternatingTimeSeriesImageFilter.h ├── itkSplitAlternatingTimeSeriesImageFilter.hxx ├── itkSurfaceCurvatureBase.h ├── itkSurfaceCurvatureBase.hxx ├── itkSurfaceImageCurvature.h ├── itkSurfaceImageCurvature.hxx ├── itkSurfaceMeshCurvature.h ├── itkTextureHistogram.h ├── itkVectorFieldGradientImageFunction.h ├── itkVectorFieldGradientImageFunction.hxx ├── itkVectorGaussianInterpolateImageFunction.h ├── itkVectorImageFileReader.h ├── itkVectorImageFileReader.hxx ├── itkVectorImageFileWriter.h ├── itkVectorImageFileWriter.hxx ├── itkWarpImageMultiTransformFilter.h ├── itkWarpImageMultiTransformFilter.hxx ├── itkWarpImageWAffineFilter.h ├── itkWarpImageWAffineFilter.hxx ├── itkWarpTensorImageMultiTransformFilter.h ├── itkWarpTensorImageMultiTransformFilter.hxx ├── itkantsReadWriteTransform.h └── tagRelease.pl ├── Version.cmake ├── _config.yml ├── antsRegistrationCLP ├── CMakeLists.txt ├── antsRegistrationCLP.cxx └── antsRegistrationCLP.xml ├── appveyor.yml ├── code_of_conduct.md ├── forhtml ├── README ├── ants.bib ├── 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