├── .gitignore ├── ExperimentalITK ├── Algorithms │ ├── .#itkDMFFDLabeledPointSetRegistrationFilter.txx.1.1 │ ├── README.txt │ ├── itkANTSImageRegistrationOptimizer.cxx │ ├── itkANTSImageRegistrationOptimizer.h │ ├── itkAdaBoost.h │ ├── itkAdaBoost.hxx │ ├── itkAnisotropicDiffusionVesselEnhancementFunction.h │ ├── itkAnisotropicDiffusionVesselEnhancementFunction.hxx │ ├── itkApocritaSegmentationImageFilter.h │ ├── itkApocritaSegmentationImageFilter.hxx │ ├── itkAvantsMutualInformationRegistrationFunction.cxx │ ├── itkAvantsMutualInformationRegistrationFunction.h │ ├── itkAvantsMutualInformationRegistrationFunction.hxx │ ├── itkAvantsPDEDeformableRegistrationFunction.h │ ├── itkBranchDecompositionFilter.h │ ├── itkBranchDecompositionFilter.hxx │ ├── itkCrossCorrelationRegistrationFunction.cxx │ ├── itkCrossCorrelationRegistrationFunction.h │ ├── itkCrossCorrelationRegistrationFunction.hxx │ ├── itkDMFFDLabeledPointSetRegistrationFilter.h │ ├── itkDMFFDLabeledPointSetRegistrationFilter.hxx │ ├── itkDMFFDLabeledPointSetRegistrationICPFilter.h │ ├── itkDMFFDLabeledPointSetRegistrationICPFilter.hxx │ ├── itkDMFFDRegistrationFilter.h │ ├── itkDMFFDRegistrationFilter.hxx │ ├── itkDemonsRegistrationFunction.h │ ├── itkDemonsRegistrationFunction.hxx │ ├── itkDiReCTImageFilter.h │ ├── itkDiReCTImageFilter.hxx │ ├── itkDynamicHistogramWarpingImageFilter.h │ ├── itkDynamicHistogramWarpingImageFilter.hxx │ ├── itkEuclideanDistanceLabeledPointSetMetric.h │ ├── itkEuclideanDistanceLabeledPointSetMetric.hxx │ ├── itkEuclideanDistancePointSetMetric.h │ ├── itkEuclideanDistancePointSetMetric.hxx │ ├── itkExpectationBasedPointSetRegistrationFunction.h │ ├── itkExpectationBasedPointSetRegistrationFunction.hxx │ ├── itkFEMRegistrationFilter.h │ ├── itkFEMRegistrationFilter.h.current │ ├── itkFEMRegistrationFilter.hxx │ ├── itkFEMRegistrationFilter.txx.current │ ├── itkFEMRegistrationFilter.txx.edges │ ├── itkFFD4DRegistrationFilter.h │ ├── itkFFD4DRegistrationFilter.hxx │ ├── itkFFDMultiplePointSetsRegistrationFilter.h │ ├── itkFFDMultiplePointSetsRegistrationFilter.hxx │ ├── itkFFDPointSetRegistrationFilter.h │ ├── itkFFDPointSetRegistrationFilter.hxx │ ├── itkFFDRegistrationFilter.h │ ├── itkFFDRegistrationFilter.hxx │ ├── itkFastMarchingImageFilter.h │ ├── itkFastMarchingImageFilter.hxx │ ├── itkJensenHavrdaCharvatTsallisLabeledPointSetMetric.h │ ├── itkJensenHavrdaCharvatTsallisLabeledPointSetMetric.hxx │ ├── itkJensenHavrdaCharvatTsallisMultiplePointSetMetric.h │ ├── itkJensenHavrdaCharvatTsallisMultiplePointSetMetric.hxx │ ├── itkJensenHavrdaCharvatTsallisPointSetMetric.h │ ├── itkJensenHavrdaCharvatTsallisPointSetMetric.hxx │ ├── itkJensenTsallisBSplineRegistrationFunction.h │ ├── itkJensenTsallisBSplineRegistrationFunction.hxx │ ├── itkJunctionDetectionFilter.h │ ├── itkJunctionDetectionFilter.hxx │ ├── itkMattesCorrelationRatioImageToImageMetric.hxx │ ├── itkMeanSquareRegistrationFunction.h │ ├── itkMeanSquareRegistrationFunction.hxx │ ├── itkMultiLabelSTAPLEImageFilter.h │ ├── itkMultiLabelSTAPLEImageFilter.hxx │ ├── itkMultiResolutionPDEDeformableRegistration.h │ ├── itkMultiResolutionPDEDeformableRegistration.hxx │ ├── itkMultiStencilFastMarchingStopImageFilter.h │ ├── itkMultiStencilFastMarchingStopImageFilter.hxx │ ├── itkMultiplePointSetMetric.h │ ├── itkMultiplePointSetMetric.hxx │ ├── itkOptMeanSquaresImageToImageMetric.h │ ├── itkOptMeanSquaresImageToImageMetric.hxx │ ├── itkParameterizedCurveMatchingPointSetMetric.h │ ├── itkParameterizedCurveMatchingPointSetMetric.hxx │ ├── itkPerfusionRegistrationFilter.h │ ├── itkPerfusionRegistrationFilter.hxx │ ├── itkProbabilisticRegistrationFunction.cxx │ ├── itkProbabilisticRegistrationFunction.h │ ├── itkProbabilisticRegistrationFunction.hxx │ ├── itkRobustDemonsRegistrationFunction.h │ ├── itkRobustDemonsRegistrationFunction.hxx │ ├── itkRobustOpticalFlow.cxx │ ├── itkRobustOpticalFlow.h │ ├── itkSectionMutualInformationRegistrationFunction.cxx │ ├── itkSectionMutualInformationRegistrationFunction.h │ ├── itkSmooth3DSurfaceRepresentationFunction.h │ ├── itkSmooth3DSurfaceRepresentationFunction.hxx │ ├── itkSmoothRepresentationFunction.h │ ├── itkSmoothRepresentationFunction.hxx │ ├── itkSpatialMutualInformationRegistrationFunction.cxx │ ├── itkSpatialMutualInformationRegistrationFunction.h │ ├── itkSyNDemonsRegistrationFunction.cxx │ ├── itkSyNDemonsRegistrationFunction.h │ ├── itkTustisonCorrelationRatioImageToImageMetric.h │ ├── itkTustisonCorrelationRatioImageToImageMetric.hxx │ ├── itkWebSplineWeightFunction.h │ ├── itkWebSplineWeightFunction.hxx │ └── topological_numbers.h ├── BasicFilters │ ├── .#itkLiveWireImageFunction.h.1.2 │ ├── .#itkLiveWireImageFunction.txx.1.2 │ ├── WellComposed │ │ ├── CVS │ │ │ ├── Entries │ │ │ ├── Repository │ │ │ └── Root │ │ ├── itkBinaryWellComposed2DImageFilter.h │ │ ├── itkBinaryWellComposed2DImageFilter.hxx │ │ ├── itkBinaryWellComposed3DImageFilter.h │ │ ├── itkBinaryWellComposed3DImageFilter.hxx │ │ ├── itkBinaryWellComposedImageFilter.h │ │ ├── itkBinaryWellComposedImageFilter.hxx │ │ ├── itkWellComposedImageFilter.h │ │ └── itkWellComposedImageFilter.hxx │ ├── itkAdaptiveFiltering3DImageFilter.h │ ├── itkAdaptiveFiltering3DImageFilter.hxx │ ├── itkAdditiveGaussianNoiseImageFilter.h │ ├── itkAdditiveGaussianNoiseImageFilter.hxx │ ├── itkAnisotropicDiffusionVesselEnhancementImageFilter.h │ ├── itkAnisotropicDiffusionVesselEnhancementImageFilter.hxx │ ├── itkArrivalFunctionToPathFilter.h │ ├── itkArrivalFunctionToPathFilter.hxx │ ├── itkBSplineGridTaggingImageFilter.h │ ├── itkBSplineGridTaggingImageFilter.hxx │ ├── itkBSplineRobustPointMethodPointSetFilter.h │ ├── itkBSplineRobustPointMethodPointSetFilter.hxx │ ├── itkBSplineVectorFlowImageFunction.h │ ├── itkBSplineVectorFlowImageFunction.hxx │ ├── itkBiasFieldEstimationBSplineFilter.h │ ├── itkBiasFieldEstimationBSplineFilter.hxx │ ├── itkBinaryBoundedSpaceDilateImageFilter.h │ ├── itkBinaryBoundedSpaceDilateImageFilter.hxx │ ├── itkBinaryBoundedSpaceErodeImageFilter.h │ ├── itkBinaryBoundedSpaceErodeImageFilter.hxx │ ├── itkBinaryPerimeterEstimationCalculator.h │ ├── itkBinaryPerimeterEstimationCalculator.txx │ ├── itkBinaryReinhardtMorphologicalImageFilter.h │ ├── itkBinaryReinhardtMorphologicalImageFilter.hxx │ ├── itkBinaryThinning3DImageFilter.h │ ├── itkBinaryThinning3DImageFilter.hxx │ ├── itkBinaryWellComposedImageFilter.h │ ├── itkBinaryWellComposedImageFilter.hxx │ ├── itkBoykovAlphaExpansionMRFImageFilter.h │ ├── itkBoykovAlphaExpansionMRFImageFilter.hxx │ ├── itkBoykovMinCutGraphFilter.h │ ├── itkBoykovMinCutGraphFilter.hxx │ ├── itkComposeDiffeomorphismsImageFilter.h │ ├── itkComposeDiffeomorphismsImageFilter.hxx │ ├── itkContourDirectedMeanDistanceImageFilter.h │ ├── itkContourDirectedMeanDistanceImageFilter.hxx │ ├── itkContourExtractor2DImageFilter.h │ ├── itkContourExtractor2DImageFilter.hxx │ ├── itkConvolutionImageFilter.nick.h │ ├── itkConvolutionImageFilter.nick.hxx │ ├── itkDecomposeTensorFunction.h │ ├── itkDecomposeTensorFunction.hxx │ ├── itkDecomposeTensorImageFilter.h │ ├── itkDecomposeTensorImageFilter.hxx │ ├── itkDeformationFieldGradientTensorImageFilter.h │ ├── itkDeformationFieldGradientTensorImageFilter.hxx │ ├── itkDeterminantTensorImageFilter.h │ ├── itkDeterminantTensorImageFilter.hxx │ ├── itkDiceMetricImageFilter.h │ ├── itkDiceMetricImageFilter.hxx │ ├── itkDirectedHausdorffDistanceImageFilter.h │ ├── itkDirectedHausdorffDistanceImageFilter.hxx │ ├── itkGaborFilterBankImageFilter.h │ ├── itkGaborFilterBankImageFilter.hxx │ ├── itkGaborFilterBankTagging2DImageFilter.h │ ├── itkGaborFilterBankTagging2DImageFilter.hxx │ ├── itkGaborFilterBankTaggingImageFilter.h │ ├── itkGaborFilterBankTaggingImageFilter.hxx │ ├── itkGeneralToBSplineDeformationFieldFilter.h │ ├── itkGeneralToBSplineDeformationFieldFilter.hxx │ ├── itkGeometricJacobianDeterminantImageFilter.h │ ├── itkGeometricJacobianDeterminantImageFilter.hxx │ ├── itkGeometryUtilities.cxx │ ├── itkGeometryUtilities.h │ ├── itkGraphToGraphFilter.h │ ├── itkGraphToGraphFilter.hxx │ ├── itkGraphToImageFilter.h │ ├── itkGraphToImageFilter.hxx │ ├── itkGridImageSource.old.h │ ├── itkGridImageSource.old.hxx │ ├── itkHessianSmoothed3DToVesselnessMeasureImageFilter.h │ ├── itkHessianSmoothed3DToVesselnessMeasureImageFilter.hxx │ ├── itkHoughTransformRadialVotingImageFilter.h │ ├── itkHoughTransformRadialVotingImageFilter.txx │ ├── itkImageToGraphFilter.h │ ├── itkImageToGraphFilter.hxx │ ├── itkImageToPathFilter.h │ ├── itkImageToPathFilter.hxx │ ├── itkImpulseNoiseImageFilter.h │ ├── itkImpulseNoiseImageFilter.hxx │ ├── itkIterateNeighborhoodOptimizer.h │ ├── itkIterateNeighborhoodOptimizer.hxx │ ├── itkLabelOverlapMeasuresImageFilter.comprehensive.h │ ├── itkLabelOverlapMeasuresImageFilter.comprehensive.hxx │ ├── itkLabelPerimeterEstimationCalculator.h │ ├── itkLabelPerimeterEstimationCalculator.txx │ ├── itkLiveWireImageFunction.h │ ├── itkLiveWireImageFunction.hxx │ ├── itkMinimalPathImageFunction.h │ ├── itkMinimalPathImageFunction.hxx │ ├── itkMultiScaleHessianSmoothed3DToVesselnessMeasureImageFilter.h │ ├── itkMultiScaleHessianSmoothed3DToVesselnessMeasureImageFilter.hxx │ ├── itkMultipleLabelToDistanceMapImageFilter.h │ ├── itkMultipleLabelToDistanceMapImageFilter.hxx │ ├── itkMultiplyByConstantVectorImageFilter.h │ ├── itkN3MRIBiasFieldCorrectionImageFilter.h │ ├── itkN3MRIBiasFieldCorrectionImageFilter.hxx │ ├── itkN4MRIBiasFieldCorrectionImageFilter.h │ ├── itkN4MRIBiasFieldCorrectionImageFilter.hxx │ ├── itkNormalizedCutsSegmentationImageFilter.h │ ├── itkNormalizedCutsSegmentationImageFilter.hxx │ ├── itkPhysicalCentralDifferenceImageFunction.h │ ├── itkPhysicalCentralDifferenceImageFunction.hxx │ ├── itkPointSetToPointSetFilter.h │ ├── itkPointSetToPointSetFilter.hxx │ ├── itkQuadratureFilterImageSource.h │ ├── itkQuadratureFilterImageSource.hxx │ ├── itkScalarToFractalImageFilter.h │ ├── itkScalarToFractalImageFilter.hxx │ ├── itkSingleImageCostFunction.h │ ├── itkSingleImageCostFunction.hxx │ ├── itkSpeedFunctionToPathFilter.h │ ├── itkSpeedFunctionToPathFilter.hxx │ ├── itkSymmetricEigenVectorAnalysisImageFilter.h │ ├── itkThinPlateSplineRobustPointMethodPointSetFilter.h │ ├── itkThinPlateSplineRobustPointMethodPointSetFilter.hxx │ ├── itkTopologyPreservingDigitalSurfaceEvolutionImageFilter.h │ ├── itkTopologyPreservingDigitalSurfaceEvolutionImageFilter.hxx │ ├── itkValuedRegionalMaximaImageFilter.h │ ├── itkValuedRegionalMinimaImageFilter.h │ ├── itkVectorFieldGradientImageFunction.h │ ├── itkVectorFieldGradientImageFunction.hxx │ ├── itkWellComposedImageFilter.h │ └── itkWellComposedImageFilter.hxx ├── Common │ ├── .#itkBinaryDiamondStructuringElement.txx.1.1.1.1 │ ├── CMakeLists.txt │ ├── README.txt │ ├── antsCommandLineOption.cxx │ ├── antsCommandLineOption.h │ ├── antsCommandLineParser.cxx │ ├── antsCommandLineParser.h │ ├── itkBSplineKernelFunction.h.nick │ ├── itkBSplineKernelFunction.txx.nick │ ├── itkBSplineKernelTransform.h │ ├── itkBSplineKernelTransform.hxx │ ├── itkBinaryBoxStructuringElement.h │ ├── itkBinaryBoxStructuringElement.hxx │ ├── itkBinaryDiamondStructuringElement.h │ ├── itkBinaryDiamondStructuringElement.hxx │ ├── itkBoykovGraphTraits.h │ ├── itkBoykovImageToGraphFunctor.h │ ├── itkBoykovImageToGraphFunctor.hxx │ ├── itkCommandLineOption.cxx │ ├── itkCommandLineOption.h │ ├── itkCommandLineParser.cxx │ ├── itkCommandLineParser.h │ ├── itkConstantScalarOperator.h │ ├── itkConstantScalarOperator.hxx │ ├── itkDefaultGraphTraits.h │ ├── itkDefaultImageToGraphFunctor.h │ ├── itkDefaultImageToGraphFunctor.hxx │ ├── itkDenseFiniteDifferenceImageFilter.h │ ├── itkDenseFiniteDifferenceImageFilter.hxx │ ├── itkGaborKernelFunction.cxx │ ├── itkGaborKernelFunction.h │ ├── itkGaussianInterpolateImageFunction.h │ ├── itkGaussianInterpolateImageFunction.hxx │ ├── itkGaussianInterpolateImageFunction2.h │ ├── itkGraph.h │ ├── itkGraph.hxx │ ├── itkGraphDuplicator.h │ ├── itkGraphDuplicator.hxx │ ├── itkGraphSource.h │ ├── itkGraphSource.hxx │ ├── itkImageGraphTraits.h │ ├── itkImageKernelOperator.nick.h │ ├── itkImageKernelOperator.nick.hxx │ ├── itkImageToPathFilter.h │ ├── itkImageToPathFilter.hxx │ ├── itkInPlaceGraphFilter.h │ ├── itkInPlaceGraphFilter.hxx │ ├── itkInverseImageFilter.h │ ├── itkManifoldParzenWindowsPointSetFunction.h │ ├── itkManifoldParzenWindowsPointSetFunction.hxx │ ├── itkMultiplyPixelAccessor.h │ ├── itkPointSetFunction.h │ ├── itkPointSetFunction.hxx │ ├── itkPointSetSource.h │ ├── itkPointSetSource.hxx │ ├── itkSparseMatrixEigenAnalysis.h │ ├── itkSparseMatrixEigenAnalysis.hxx │ ├── itkSparseSymmetricMatrixEigenAnalysis.h │ ├── itkSparseSymmetricMatrixEigenAnalysis.hxx │ └── topological_numbers.h ├── ESMTransforms │ ├── CMakeLists.txt │ ├── ESMImageRegistration.cxx │ ├── itkESMDogLegOptimizer.h │ ├── itkESMDogLegOptimizer.hxx │ ├── itkESMImageToImageMetric.h │ ├── itkESMImageToImageMetric.hxx │ ├── itkESMMatrixOffsetTransformBase.h │ ├── itkESMMatrixOffsetTransformBase.hxx │ ├── itkESMMeanSquaresImageToImageMetric.h │ ├── itkESMMeanSquaresImageToImageMetric.hxx │ ├── itkESMOptimizer.h │ ├── itkESMOptimizer.hxx │ ├── itkESMOptimizerBase.h │ ├── itkESMOptimizerBase.hxx │ ├── itkESMRegistrationTest.cxx │ ├── itkESMRigid2DTransform.h │ ├── itkESMRigid2DTransform.hxx │ ├── itkESMTransform.h │ ├── vnl_sd_matrix_tools.h │ └── vnl_sd_matrix_tools.hxx ├── IO │ ├── .#itkLabeledPointSetFileWriter.h.1.1.1.1 │ ├── .#itkLabeledPointSetFileWriter.txx.1.1.1.1 │ ├── CMakeLists.txt │ ├── itkDeformationFieldReader.h │ ├── itkDeformationFieldReader.hxx │ ├── itkDeformationFieldWriter.h │ ├── itkDeformationFieldWriter.hxx │ ├── itkFDFCommonImageIO.cxx │ ├── itkFDFCommonImageIO.h │ ├── itkFDFImageIO.cxx │ ├── itkFDFImageIO.h │ ├── itkFDFImageIOFactory.cxx │ ├── itkFDFImageIOFactory.h │ ├── itkImageIOFactory.cxx │ ├── itkLabeledPointSetFileReader.h │ ├── itkLabeledPointSetFileReader.hxx │ ├── itkLabeledPointSetFileWriter.h │ ├── itkLabeledPointSetFileWriter.hxx │ ├── itkVectorImageFileReader.h │ ├── itkVectorImageFileReader.hxx │ ├── itkVectorImageFileWriter.h │ ├── itkVectorImageFileWriter.hxx │ ├── itkVoxBoCUBImageIO.cxx │ ├── itkVoxBoCUBImageIO.h │ ├── itkVoxBoCUBImageIOFactory.cxx │ └── itkVoxBoCUBImageIOFactory.h └── Numerics │ ├── FEM │ ├── CMakeCCompiler.cmake │ ├── CMakeCXXCompiler.cmake │ ├── CMakeCache.txt │ ├── CMakeLists.txt │ ├── CMakeOutput.log │ ├── CMakeSystem.cmake │ ├── DartTestfile.txt │ ├── ReadMe.txt │ ├── ToDo.txt │ ├── itkFEM.h │ ├── itkFEMBSplineShapeFunctions.cxx │ ├── itkFEMBSplineShapeFunctions.h │ ├── itkFEMElement1DStress.h │ ├── itkFEMElement1DStress.hxx │ ├── itkFEMElement2DBSplinePatch.cxx │ ├── itkFEMElement2DBSplinePatch.h │ ├── itkFEMElement2DBSplinePatchLinearElasticity.cxx │ ├── itkFEMElement2DBSplinePatchLinearElasticity.h │ ├── itkFEMElement2DBSplinePatchMembrane.cxx │ ├── itkFEMElement2DBSplinePatchMembrane.h │ ├── itkFEMElement2DBSplinePatchStrain.cxx │ ├── itkFEMElement2DBSplinePatchStrain.h │ ├── itkFEMElement2DBSplinePatchStress.cxx │ ├── itkFEMElement2DBSplinePatchStress.h │ ├── itkFEMElement2DC0LinearLine.cxx │ ├── itkFEMElement2DC0LinearLine.h │ ├── itkFEMElement2DC0LinearLineStress.cxx │ ├── itkFEMElement2DC0LinearLineStress.h │ ├── itkFEMElement2DC0LinearQuadrilateral.cxx │ ├── itkFEMElement2DC0LinearQuadrilateral.h │ ├── itkFEMElement2DC0LinearQuadrilateralLinearElasticity.cxx │ ├── itkFEMElement2DC0LinearQuadrilateralLinearElasticity.h │ ├── itkFEMElement2DC0LinearQuadrilateralMembrane.cxx │ ├── itkFEMElement2DC0LinearQuadrilateralMembrane.h │ ├── itkFEMElement2DC0LinearQuadrilateralStrain.cxx │ ├── itkFEMElement2DC0LinearQuadrilateralStrain.h │ ├── itkFEMElement2DC0LinearQuadrilateralStress.cxx │ ├── itkFEMElement2DC0LinearQuadrilateralStress.h │ ├── itkFEMElement2DC0LinearTriangular.cxx │ ├── itkFEMElement2DC0LinearTriangular.h │ ├── itkFEMElement2DC0LinearTriangularMembrane.cxx │ ├── itkFEMElement2DC0LinearTriangularMembrane.h │ ├── itkFEMElement2DC0LinearTriangularStrain.cxx │ ├── itkFEMElement2DC0LinearTriangularStrain.h │ ├── itkFEMElement2DC0LinearTriangularStress.cxx │ ├── itkFEMElement2DC0LinearTriangularStress.h │ ├── itkFEMElement2DC0QuadraticTriangular.cxx │ ├── itkFEMElement2DC0QuadraticTriangular.h │ ├── itkFEMElement2DC0QuadraticTriangularStrain.cxx │ ├── itkFEMElement2DC0QuadraticTriangularStrain.h │ ├── itkFEMElement2DC0QuadraticTriangularStress.cxx │ ├── itkFEMElement2DC0QuadraticTriangularStress.h │ ├── itkFEMElement2DC1Beam.cxx │ ├── itkFEMElement2DC1Beam.h │ ├── itkFEMElement2DLinearElasticity.h │ ├── itkFEMElement2DLinearElasticity.hxx │ ├── itkFEMElement2DMembrane.h │ ├── itkFEMElement2DMembrane.hxx │ ├── itkFEMElement2DStrain.h │ ├── itkFEMElement2DStrain.hxx │ ├── itkFEMElement2DStress.h │ ├── itkFEMElement2DStress.hxx │ ├── itkFEMElement2DThinPlate.h │ ├── itkFEMElement2DThinPlate.hxx │ ├── itkFEMElement3DBSplinePatch.cxx │ ├── itkFEMElement3DBSplinePatch.h │ ├── itkFEMElement3DBSplinePatchLinearElasticity.cxx │ ├── itkFEMElement3DBSplinePatchLinearElasticity.h │ ├── itkFEMElement3DBSplinePatchMembrane.cxx │ ├── itkFEMElement3DBSplinePatchMembrane.h │ ├── itkFEMElement3DBSplinePatchStrain.cxx │ ├── itkFEMElement3DBSplinePatchStrain.h │ ├── itkFEMElement3DBSplinePatchStress.cxx │ ├── itkFEMElement3DBSplinePatchStress.h │ ├── itkFEMElement3DC0LinearHexahedron.cxx │ ├── itkFEMElement3DC0LinearHexahedron.h │ ├── itkFEMElement3DC0LinearHexahedronLinearElasticity.cxx │ ├── itkFEMElement3DC0LinearHexahedronLinearElasticity.h │ ├── itkFEMElement3DC0LinearHexahedronMembrane.cxx │ ├── itkFEMElement3DC0LinearHexahedronMembrane.h │ ├── itkFEMElement3DC0LinearHexahedronStrain.cxx │ ├── itkFEMElement3DC0LinearHexahedronStrain.h │ ├── itkFEMElement3DC0LinearTetrahedron.cxx │ ├── itkFEMElement3DC0LinearTetrahedron.h │ ├── itkFEMElement3DC0LinearTetrahedronMembrane.cxx │ ├── itkFEMElement3DC0LinearTetrahedronMembrane.h │ ├── itkFEMElement3DC0LinearTetrahedronStrain.cxx │ ├── itkFEMElement3DC0LinearTetrahedronStrain.h │ ├── itkFEMElement3DLinearElasticity.h │ ├── itkFEMElement3DLinearElasticity.hxx │ ├── itkFEMElement3DMembrane.h │ ├── itkFEMElement3DMembrane.hxx │ ├── itkFEMElement3DStrain.h │ ├── itkFEMElement3DStrain.hxx │ ├── itkFEMElementBase.cxx │ ├── itkFEMElementBase.h │ ├── itkFEMElementStd.h │ ├── itkFEMElementStd.hxx │ ├── itkFEMElements.h │ ├── itkFEMException.cxx │ ├── itkFEMException.h │ ├── itkFEMFiniteDifferenceFunctionLoad.h │ ├── itkFEMFiniteDifferenceFunctionLoad.hxx │ ├── itkFEMGenerateBSplineMesh.cxx │ ├── itkFEMGenerateBSplineMesh.h │ ├── itkFEMGenerateMesh.cxx │ ├── itkFEMGenerateMesh.h │ ├── itkFEMImageMetricLoad.h │ ├── itkFEMImageMetricLoad.h.new │ ├── itkFEMImageMetricLoad.hxx │ ├── itkFEMImageMetricLoad.txx.new │ ├── itkFEMImageMetricLoadImplementation.h │ ├── itkFEMInitialization.cxx │ ├── itkFEMInitialization.h │ ├── itkFEMItpackSparseMatrix.cxx │ ├── itkFEMItpackSparseMatrix.h │ ├── itkFEMLightObject.cxx │ ├── itkFEMLightObject.h │ ├── itkFEMLinearSystemWrapper.cxx │ ├── itkFEMLinearSystemWrapper.h │ ├── itkFEMLinearSystemWrapperDenseVNL.cxx │ ├── itkFEMLinearSystemWrapperDenseVNL.h │ ├── itkFEMLinearSystemWrapperItpack.cxx │ ├── itkFEMLinearSystemWrapperItpack.h │ ├── itkFEMLinearSystemWrapperVNL.cxx │ ├── itkFEMLinearSystemWrapperVNL.h │ ├── itkFEMLinearSystemWrappers.h │ ├── itkFEMLoadBC.cxx │ ├── itkFEMLoadBC.h │ ├── itkFEMLoadBCMFC.cxx │ ├── itkFEMLoadBCMFC.h │ ├── itkFEMLoadBase.cxx │ ├── itkFEMLoadBase.h │ ├── itkFEMLoadEdge.cxx │ ├── itkFEMLoadEdge.h │ ├── itkFEMLoadElementBase.cxx │ ├── itkFEMLoadElementBase.h │ ├── itkFEMLoadGrav.cxx │ ├── itkFEMLoadGrav.h │ ├── itkFEMLoadImplementationGenericBodyLoad.cxx │ ├── itkFEMLoadImplementationGenericBodyLoad.h │ ├── itkFEMLoadImplementationGenericLandmarkLoad.cxx │ ├── itkFEMLoadImplementationGenericLandmarkLoad.h │ ├── itkFEMLoadImplementationTest.h │ ├── itkFEMLoadImplementationsRegister.cxx │ ├── itkFEMLoadLandmark.cxx │ ├── itkFEMLoadLandmark.h │ ├── itkFEMLoadNode.cxx │ ├── itkFEMLoadNode.h │ ├── itkFEMLoadPoint.cxx │ ├── itkFEMLoadPoint.h │ ├── itkFEMLoadTest.h │ ├── itkFEMLoads.h │ ├── itkFEMMacro.h │ ├── itkFEMMaterialBase.cxx │ ├── itkFEMMaterialBase.h │ ├── itkFEMMaterialLinearElasticity.cxx │ ├── itkFEMMaterialLinearElasticity.h │ ├── itkFEMMaterials.h │ ├── itkFEMObjectFactory.h │ ├── itkFEMP.h │ ├── itkFEMPArray.h │ ├── itkFEMSolution.h │ ├── itkFEMSolver.cxx │ ├── itkFEMSolver.h │ ├── itkFEMSolverCrankNicolson.cxx │ ├── itkFEMSolverCrankNicolson.h │ ├── itkFEMSolverHyperbolic.cxx │ ├── itkFEMSolverHyperbolic.h │ ├── itkFEMUtility.cxx │ ├── itkFEMUtility.h │ ├── itkVisitorDispatcher.h │ └── itpack.h │ ├── FEMBSpline │ ├── CMakeLists.txt │ ├── DeformableRegistration1.cxx │ ├── FEM.tar.gz │ ├── FEMBSpline.tar.gz │ ├── itkFEMRegistrationFilter.h │ └── itkFEMRegistrationFilter.hxx │ └── Statistics │ ├── CVS │ ├── Entries │ ├── Repository │ └── Root │ ├── itkBoxPlotQuantileListSampleFilter.h │ ├── itkBoxPlotQuantileListSampleFilter.hxx │ ├── itkDensityFunction.h │ ├── itkGaussianClassDensityFunction.h │ ├── itkGaussianClassDensityFunction.hxx │ ├── itkGaussianListSampleFunction.h │ ├── itkGaussianListSampleFunction.hxx │ ├── itkGaussianMembershipFunction.h │ ├── itkGaussianMembershipFunction.hxx │ ├── itkGaussianMixtureModelComponent.h │ ├── itkGaussianMixtureModelComponent.hxx │ ├── itkGaussianProbabilityDensityFunction.h │ ├── itkGaussianProbabilityDensityFunction.hxx │ ├── itkGreyLevelRunLengthMatrixTextureCoefficientsCalculator.h │ ├── itkGreyLevelRunLengthMatrixTextureCoefficientsCalculator.hxx │ ├── itkGrubbsRosnerListSampleFilter.h │ ├── itkGrubbsRosnerListSampleFilter.hxx │ ├── itkHistogramParzenWindowsListSampleFunction.h │ ├── itkHistogramParzenWindowsListSampleFunction.hxx │ ├── itkHistogramToRunLengthFeaturesFilter.h │ ├── itkHistogramToRunLengthFeaturesFilter.hxx │ ├── itkImageToListSampleFilter.h │ ├── itkImageToListSampleFilter.hxx │ ├── itkListSampleDAgostinoPearsonNormalityTest.h │ ├── itkListSampleDAgostinoPearsonNormalityTest.hxx │ ├── itkListSampleFunction.h │ ├── itkListSampleFunction.hxx │ ├── itkListSampleMomentCalculator.h │ ├── itkListSampleMomentCalculator.hxx │ ├── itkListSampleToListSampleFilter.h │ ├── itkListSampleToListSampleFilter.hxx │ ├── itkManifoldParzenWindowsListSampleFunction.h │ ├── itkManifoldParzenWindowsListSampleFunction.hxx │ ├── itkMaskedScalarImageToGreyLevelRunLengthMatrixGenerator.h │ ├── itkMaskedScalarImageToGreyLevelRunLengthMatrixGenerator.hxx │ ├── itkMeasurementVectorTraits.h │ ├── itkMixtureModelComponentBase.h │ ├── itkMixtureModelComponentBase.hxx │ ├── itkNeighborhoodFirstOrderStatisticsImageFilter.h │ ├── itkPassThroughListSampleFilter.h │ ├── itkPassThroughListSampleFilter.hxx │ ├── itkScalarImageToGreyLevelRunLengthMatrixGenerator.h │ ├── itkScalarImageToGreyLevelRunLengthMatrixGenerator.hxx │ ├── itkScalarImageToRunLengthMatrixFilter.h │ ├── itkScalarImageToRunLengthMatrixFilter.hxx │ ├── itkTextureFeaturesImageFilter.h │ ├── itkTextureFeaturesImageFilter.hxx │ ├── itkTextureHistogram.h │ ├── itkWatsonDistributionListSampleFilter.h │ └── itkWatsonDistributionListSampleFilter.hxx ├── README ├── scripts ├── General │ ├── SyMMN.pl │ ├── Testing │ │ └── Temporary │ │ │ └── LastTest.log │ ├── antsMedIATest.pl │ ├── antsMedIATest.sh │ ├── buildTemplate.pl │ ├── buildTemplate.sh │ ├── convertFLIRTtoITK.pl │ ├── convertFiles.pl │ ├── convertImages.pl │ ├── cputime.sh │ ├── extractSlices.pl │ ├── extractTagLines.pl │ ├── imageRegistration.pl │ ├── imageRegistration.sh │ ├── keyhole.pl │ ├── pointSetRegistration.pl │ ├── pointSetRegistration.sh │ ├── recursiveDirectory.pl │ ├── rename_txx_to_hxx.pl │ ├── segmentHeliumLungs.pl │ ├── segmentLungs.pl │ ├── taggedImagePipeline.pl │ ├── updateANTScvs.output │ ├── updateANTScvs.sh │ ├── updateITKcvs.output │ ├── updateITKcvs.sh │ ├── updateUtilitiescvs.output │ └── updateUtilitiescvs.sh ├── HeliumLungStudies │ ├── DataSet01_RepeatabilityExperiment │ │ ├── ImageVolumes │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── pointSetRegistration.pl │ │ │ ├── pointSetRegistration.sh │ │ │ ├── recursiveDirectory.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ ├── recursiveInspectImages.sh │ │ │ ├── recursivePointSetRegistration.pl │ │ │ ├── recursivePointSetRegistration.sh │ │ │ ├── recursivePrepareImagesForPCA.pl │ │ │ ├── recursivePrepareImagesForPCA.sh │ │ │ ├── recursiveWarpImages.pl │ │ │ ├── recursiveWarpImages.sh │ │ │ ├── renameFiles.sh │ │ │ ├── stopJobs.sh │ │ │ └── warpImages.sh │ │ ├── recursivePrepareImagesForPCA.pl │ │ └── recursivePrepareImagesForPCA.sh │ ├── DataSet02_ExerciseMethacholineChallenge │ │ ├── Data_1.7.09 │ │ │ └── ImageVolumes │ │ │ │ ├── heliumLungAnalysis.sh │ │ │ │ ├── pointSetRegistration.pl │ │ │ │ ├── pointSetRegistration.sh │ │ │ │ ├── recursiveDirectory.pl │ │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ │ ├── recursiveInspectImages.pl │ │ │ │ ├── recursiveInspectImages.sh │ │ │ │ ├── recursivePointSetRegistration.pl │ │ │ │ ├── recursivePointSetRegistration.sh │ │ │ │ ├── recursiveWarpImages.pl │ │ │ │ ├── recursiveWarpImages.sh │ │ │ │ └── warpImages.sh │ │ └── Data_2.12.09 │ │ │ └── ImageVolumes │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── pointSetRegistration.pl │ │ │ ├── pointSetRegistration.sh │ │ │ ├── recursiveDirectory.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ ├── recursiveInspectImages.sh │ │ │ ├── recursivePointSetRegistration.pl │ │ │ ├── recursivePointSetRegistration.sh │ │ │ ├── recursiveWarpImages.pl │ │ │ ├── recursiveWarpImages.sh │ │ │ ├── stopJobs.sh │ │ │ └── warpImages.sh │ ├── DataSet03_PrePostAlbuterol │ │ └── ImageVolumes │ │ │ ├── antsRegistration.pl │ │ │ ├── antsRegistration.sh │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── pointSetRegistration.pl │ │ │ ├── pointSetRegistration.sh │ │ │ ├── recursiveAntsRegistration.pl │ │ │ ├── recursiveAntsRegistration.sh │ │ │ ├── recursiveDirectory.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ ├── recursiveInspectImages.sh │ │ │ ├── recursivePointSetRegistration.pl │ │ │ ├── recursivePointSetRegistration.sh │ │ │ ├── recursivePrepareImagesForPCA.pl │ │ │ ├── recursivePrepareImagesForPCA.sh │ │ │ ├── recursiveWarpImages.pl │ │ │ ├── recursiveWarpImages.sh │ │ │ ├── renameFiles.sh │ │ │ ├── stopJobs.sh │ │ │ └── warpImages.sh │ ├── DataSet05_HeliumvsCT │ │ └── ImageVolumes │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── recursiveDirectory.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ └── recursiveInspectImages.sh │ ├── DataSet06_SingleCaseSevereAsthma │ │ └── ImageVolumes │ │ │ └── RegistrationResults │ │ │ ├── alterJobs.sh │ │ │ ├── antsMI.sh │ │ │ ├── antsPR.sh │ │ │ └── stopJobs.sh │ ├── DataSet07_SpecialCase │ │ └── IBVData │ │ │ └── ImageVolumes │ │ │ ├── antsPR.sh │ │ │ └── antsRegistrations.sh │ ├── DataSet08_TwoImagingSites │ │ └── ImageVolumes │ │ │ ├── antsRegistration.pl │ │ │ ├── antsRegistration.sh │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── pointSetRegistration.pl │ │ │ ├── pointSetRegistration.sh │ │ │ ├── recursiveAntsRegistration.pl │ │ │ ├── recursiveAntsRegistration.sh │ │ │ ├── recursiveDirectory.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ ├── recursiveInspectImages.sh │ │ │ ├── recursiveWarpImages.pl │ │ │ ├── recursiveWarpImages.sh │ │ │ ├── renameFiles.sh │ │ │ ├── splitSite1Images.pl │ │ │ ├── stopJobs.sh │ │ │ ├── ventilationAnalysis.pl │ │ │ └── ventilationAnalysis.sh │ ├── DataSet09_ChengboAsthmaData │ │ └── ImageVolumes │ │ │ ├── recursiveDirectory.pl │ │ │ └── recursiveDirectory.sh │ ├── DataSet10_MethMeth │ │ └── ImageVolumes │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ └── recursiveHeliumLungAnalysis.sh │ ├── DataSet11_deLangeBaselineAsthma │ │ ├── ImageVolumes │ │ │ ├── calculateMNDS.pl │ │ │ ├── heliumLungAnalysis.pl │ │ │ ├── heliumLungAnalysis.sh │ │ │ ├── heliumSlice.pl │ │ │ ├── hessianTest.pl │ │ │ ├── hessianTest.sh │ │ │ ├── makeLatexOutput.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── recursiveInspectImages.pl │ │ │ ├── recursiveInspectImages.sh │ │ │ ├── registerToTemplate.pl │ │ │ ├── registerToTemplate.sh │ │ │ ├── ventilationDefectSegmentation.pl │ │ │ └── ventilationDefectSegmentation.sh │ │ └── heliumLungAnalysis.pl │ ├── DataSet_Proposal │ │ └── He3_1151 │ │ │ ├── heliumSlice.pl │ │ │ ├── recursiveHeliumLungAnalysis.pl │ │ │ ├── recursiveHeliumLungAnalysis.sh │ │ │ ├── segmentProtonLungs.pl │ │ │ ├── ventilationDefectSegmentation.pl │ │ │ └── ventilationDefectSegmentation.sh │ ├── ParragaImages_Oct72009 │ │ └── antsqsub.sh │ └── Templates │ │ ├── ANTSShapeIntensityTemplate │ │ ├── Axial │ │ │ └── buildtemplate.sh │ │ ├── Coronal │ │ │ └── buildtemplate.sh │ │ └── Coronal_Site2 │ │ │ └── buildtemplate.sh │ │ └── PCAShapeTemplate │ │ ├── calculateModes.pl │ │ ├── copyImages.pl │ │ └── warpImages.pl ├── R │ ├── Bland.Altman.R │ ├── blandAltman.R │ ├── boxPlot2.R │ ├── boxPlotResults.R │ ├── iccScript.R │ ├── plotResults.R │ ├── randomForestExample.R │ ├── similarity.R │ └── voronoi_image.R ├── T1MappingMotionCorrection.pl ├── antsr_cbf.R ├── appendSuffix.pl ├── applyModel.R ├── applyTumorSegmentationModel.sh ├── coordinate_apb_pbs_jobs.pl ├── createCSVFileFromModel.R ├── createFeatureImages.sh ├── createModel.R ├── delete_range_of_jobs.pl ├── extract_brain_20100719.sh ├── ncaaBracket.R ├── ncaaBracket2.R ├── pbs_test.sh ├── pipedream_t1_brain_extraction.sh ├── plotVariableImportance.R └── snap2paraviewLabelColor.pl └── src ├── AdaBoostTest.cxx ├── AdaptiveHistogramEqualizeImage.cxx ├── AddGaussianNoiseToImage.cxx ├── AddImpulseNoiseToImage.cxx ├── AlignImageCenters.cxx ├── ApproximateImageWithBSplines.cxx ├── AtroposSegmentation.cxx ├── AttachDicomHeaderToImage.cxx ├── BSplineBasisFunctions.cxx ├── BSplineCalc.cxx ├── BSplineExample.cxx ├── BSplineTest.cxx ├── BinaryMorphology.cxx ├── BinaryOperateImages.cxx ├── BoykovGraphCutFilter.cxx ├── CMakeCache.txt ├── CMakeFiles ├── CMakeCCompiler.cmake ├── CMakeCXXCompiler.cmake ├── CMakeDetermineCompilerABI_C.bin ├── CMakeDetermineCompilerABI_CXX.bin ├── CMakeOutput.log ├── CMakeSystem.cmake ├── CompilerIdC │ ├── CMakeCCompilerId.c │ └── a.out ├── CompilerIdCXX │ ├── CMakeCXXCompilerId.cpp │ └── a.out └── cmake.check_cache ├── CMakeLists.txt ├── CVS ├── Entries ├── Repository └── Root ├── CalculateFirstOrderStatisticsFromImage.cxx ├── CalculateHausdorffDistance.cxx ├── CalculateStatisticsFromImagePair.cxx ├── CalculateStatisticsImage.cxx ├── CalculateVolumeFromBinaryImage.cxx ├── ChangeImageInformation.cxx ├── Check3TissueLabeling.cxx ├── CollidingFronts.cxx ├── ColorPolyDataByImage.cxx ├── Common.h ├── CompareLandmarks.cxx ├── ConcatenateAvantsLandmarks.cxx ├── ConnectedSegmentImage.cxx ├── ConnectedSegmentImageSliceBySlice.cxx ├── ConvertAvantsLandmarkFileToImageLines.cxx ├── ConvertAvantsLandmarkFileToVTK.cxx ├── ConvertAvantsLandmarkFileToVTKLines.cxx ├── ConvertDICOMImageSeries.cxx ├── ConvertDeformationFieldToAvantsLandmarkFiles.cxx ├── ConvertImage.cxx ├── ConvertImageSeries.cxx ├── ConvertImageSeriesToDicom.cxx ├── ConvertImageToDicom.cxx ├── ConvertImageToDicomRGB.cxx ├── ConvertImageToVTKSurface.cxx ├── ConvertLabeledPointSet.cxx ├── ConvertScalarImageToRGB.cxx ├── ConvertScalarImageToVTKSurface.cxx ├── ConvertUnlabeledPointSet.cxx ├── ConvolveImage.cxx ├── CopyDicomHeader.cxx ├── CreateADCImage.cxx ├── CreateBSplineDeformationFieldFromPoints.cxx ├── CreateBoundingBoxMask.cxx ├── CreateColoredLabeledImage.cxx ├── CreateDeformedGrid.cxx ├── CreateDirectionalStrainImages.cxx ├── CreateImage.cxx ├── CreateImageSource.cxx ├── CreateJacobianDeterminantImage.cxx ├── CreatePrincipalStrainImages.cxx ├── CreateRidgeMap.cxx ├── CreateSampledBSplineSurface.cxx ├── CreateTopologicalNumberMapFromBinaryImage.cxx ├── CreateVirtualCT.cxx ├── CustomColormaps ├── CVS │ ├── Entries │ ├── Repository │ └── Root ├── bone.txt ├── colorcube.txt ├── cool.txt ├── flag.txt ├── itksnap_colormap.txt ├── lines.txt ├── pink.txt ├── prism.txt └── vga.txt ├── DenoiseImage.cxx ├── DiceMetric.cxx ├── DirectionalBiasCorrection.cxx ├── DivideLungs.cxx ├── DrawBresenhamLinesFromMaskToPoint.cxx ├── DynamicProgrammingForSkullLayers.cxx ├── EstimateDiffeomorphism.cxx ├── EstimateVesselCurve.cxx ├── EvaluatePointSetMetric.cxx ├── ExtractContours.cxx ├── ExtractLungs.cxx ├── ExtractMaskImage.cxx ├── ExtractRGBComponent.cxx ├── ExtractRegionFromImage.cxx ├── ExtractSliceFromImage.cxx ├── ExtractTagLinePoints.cxx ├── FastMarching.cxx ├── FindClosestPointsBetweenTwoObjects.cxx ├── FindOverlappingLabels.cxx ├── FitBSplineCurveToAvantsLandmarks.cxx ├── FitBSplineCurveToPoints.cxx ├── FlipImage.cxx ├── FloodFill.cxx ├── FourierTransformImage.cxx ├── GaborFeatureImage.cxx ├── GenerateAttenuationMask.cxx ├── GenerateCooccurrenceImage.cxx ├── GenerateCooccurrenceMeasures.cxx ├── GenerateDeformationFieldMagnitudeImage.cxx ├── GenerateDistanceImage.cxx ├── GenerateDomainImage.cxx ├── GenerateFractalImage.cxx ├── GenerateImageFromControlPointLattice.cxx ├── GenerateImageFromIndexFile.cxx ├── GenerateInterpolationMeasures.cxx ├── GenerateOEFImages.cxx ├── GeneratePercentileAttenuationMask.cxx ├── GenerateRunLengthMeasures.cxx ├── GenerateStatisticsFromImage.cxx ├── GenerateTPSDeformationField.cxx ├── GenerateVectorFieldFromControlPointLattice.cxx ├── GetCaminoToPhysicalSpaceAffine.cxx ├── GetConnectedComponents.cxx ├── GetConnectedComponentsFeatureImages.cxx ├── GetDicomTagValue.cxx ├── GetImageInformation.cxx ├── GetJointSamples.cxx ├── GetPhysicalSpaceToParaviewAffine.cxx ├── GetPhysicalToImageAffineTransform.cxx ├── GetSkullTop.cxx ├── GradientAnisotropicDiffusionImageFilter.cxx ├── GradientImage.cxx ├── GradientMagnitudeImageFilter.cxx ├── GrayscaleMorphology.cxx ├── HessianBasedFeatures.cxx ├── HessianImage.cxx ├── HistogramMatchImages.cxx ├── HoughTransform.cxx ├── ICP.cxx ├── ImageReadDicomSeriesWrite.cxx ├── InvertDisplacementField.cxx ├── InvertImageIntensity.cxx ├── JHCT.cxx ├── JunctionAndBranch.cxx ├── KellyKapowski.cxx ├── LabelGeometryMeasures.cxx ├── LabelIntensityStatistics.cxx ├── LabelOverlapMeasures.cxx ├── LaplacianForSkullLayers.cxx ├── LevelSets.cxx ├── LungAffineInitializer.cxx ├── MSQ.cxx ├── MakeCheckerBoardImage.cxx ├── MakeHilbertPath.cxx ├── MakePDFImageFromPointSet.cxx ├── MinimalPath.cxx ├── MultipleOperateImages.cxx ├── OldCode ├── 2D │ ├── AdaptiveHistogramEqualizeImage.cxx │ ├── AddGaussianNoiseToImage.cxx │ ├── AddImage.cxx │ ├── AddImpulseNoiseToImage.cxx │ ├── AlignImageCenters.cxx │ ├── BinaryMorphologicalCloseImage.cxx │ ├── BoundedSpaceDilateImage.cxx │ ├── BoykovGraphCutFilter.cxx │ ├── CMakeLists.txt │ ├── CVS │ │ ├── Entries │ │ ├── Repository │ │ └── Root │ ├── CalculateFirstOrderStatisticsFromImage.cxx │ ├── CalculateGradientImage.cxx │ ├── CalculateHausdorffDistance.cxx │ ├── CalculateHessianImage.cxx │ ├── CalculateMetricImages.cxx │ ├── CalculateVolumeFromBinaryImage.cxx │ ├── CommensurateImages.cxx │ ├── ConcatenateAvantsLandmarks.cxx │ ├── ContourExtractor.cxx │ ├── ConvertAvantsLandmarkFileToVTK.cxx │ ├── ConvertAvantsLandmarkFileToVTKLines.cxx │ ├── ConvertDICOMImageSeries.cxx │ ├── ConvertDeformationFieldToAvantsLandmarkFiles.cxx │ ├── ConvertImage.cxx │ ├── ConvertImageSeries.cxx │ ├── ConvertImageToVTKSurface.cxx │ ├── ConvertScalarImageToRGB.cxx │ ├── ConvertScalarImageToVTKSurface.cxx │ ├── ConvertSegmentedImageToAvantsLandmarkFile.cxx │ ├── ConvertTensorFieldToVTK.cxx │ ├── ConvertVectorFieldToVTK.cxx │ ├── CreateDeformedGrid.cxx │ ├── CreateDifferenceImage.cxx │ ├── CreateDirectionalStrainImages.cxx │ ├── CreateGaussianImage.cxx │ ├── CreateGridImage.cxx │ ├── CreateImageVolumeFromImageSlices.cxx │ ├── CreateJacobianDeterminantImage.cxx │ ├── CreatePrincipalStrainImages.cxx │ ├── CreateRandomImage.cxx │ ├── CreateStrainTensorComponentImages.cxx │ ├── CreateWarpedGridImage.cxx │ ├── CreateZeroImage.cxx │ ├── CropImage.cxx │ ├── CurvatureAnisotropicDiffusionImageFilter.cxx │ ├── DiceMetric.cxx │ ├── DilateImage.cxx │ ├── DivideLungs.cxx │ ├── ErodeImage.cxx │ ├── EvaluateImageAtAvantsPoints.cxx │ ├── ExtractLungs.cxx │ ├── ExtractMaskImage.cxx │ ├── ExtractRegionFromImage.cxx │ ├── ExtractSliceFromImage.cxx │ ├── ExtractTagLinePoints.cxx │ ├── ExtractTagLinePointsSliceBySlice.cxx │ ├── FillHoles.cxx │ ├── FitBSplineCurveToAvantsLandmarks.cxx │ ├── FlipImage.cxx │ ├── FourierTransformImage.cxx │ ├── GaussianSmoothImage.cxx │ ├── GeneralToBSplineDeformationField.cxx │ ├── GenerateADFMFeatures.cxx │ ├── GenerateAttenuationMask.cxx │ ├── GenerateCooccurrenceMeasures.cxx │ ├── GenerateDeformationFieldDerivatives.cxx │ ├── GenerateDeformationFieldFromAvantsLandmarks.cxx │ ├── GenerateDeformationFieldMagnitudeImage.cxx │ ├── GenerateDistanceImage.cxx │ ├── GenerateFractalImage.cxx │ ├── GenerateHistogram.cxx │ ├── GenerateHistogramFromBoxMask.cxx │ ├── GenerateImageFromControlPointLattice.cxx │ ├── GenerateInverseBSplineDeformationField.cxx │ ├── GenerateLikelihoodImages.cxx │ ├── GeneratePercentileAttenuationMask.cxx │ ├── GenerateRunLengthMeasures.cxx │ ├── GenerateStatisticsFromImage.cxx │ ├── GetConnectedComponents.cxx │ ├── GradientAnisotropicDiffusionImageFilter.cxx │ ├── GrayscaleDilateImage.cxx │ ├── GrayscaleErodeImage.cxx │ ├── HistogramMatchImages.cxx │ ├── Hough2DTransform.cxx │ ├── ImageSeriesReadWrite.cxx │ ├── InhomogeneityCorrectImage.cxx │ ├── JHCT.cxx │ ├── JHCTMulti.cxx │ ├── LabelAndCloseImage.cxx │ ├── LevelSets.cxx │ ├── LiveWire.cxx │ ├── MakeCheckerBoardImage.cxx │ ├── MakePDFImageFromPointSet.cxx │ ├── MarceloImageConversion.cxx │ ├── MultiplyImages.cxx │ ├── OtsuThresholdImage.cxx │ ├── PadImage.cxx │ ├── PermuteAxesImage.cxx │ ├── PointSetToPointSetRegistration.cxx │ ├── PrunePointSet.cxx │ ├── RegionalMaximaImage.cxx │ ├── RegionalMinimaImage.cxx │ ├── RegisterImagesFFD.cxx │ ├── RegisterMultiplePointSetsFFD.cxx │ ├── RegisterPointSetsFFD.cxx │ ├── RegisterWithMultiResDemons.cxx │ ├── ResampleImage.cxx │ ├── RescaleImageIntensity.cxx │ ├── ResizeHeliumImage.cxx │ ├── Rigid3DTransformImage.cxx │ ├── RigidVersor3DRegistration.cxx │ ├── STAPLEAnalysis.cxx │ ├── SegmentAirways.cxx │ ├── SeparateLungs.cxx │ ├── ShapeMorphology.cxx │ ├── SmoothLungs.cxx │ ├── SubtractImage.cxx │ ├── ThinTagLines.cxx │ ├── ThresholdImage.cxx │ ├── TileImages.cxx │ ├── TranslateImage.cxx │ ├── TranslationRegistration.cxx │ ├── WarpAvantsPoints.cxx │ ├── WarpImage.cxx │ ├── WellComposeImage.cxx │ ├── ZeroCrossingsImage.cxx │ └── global.h ├── ApocritaSegmentation.cxx ├── BinaryMorphologicalCloseImage.cxx ├── CalculateGradientImage.cxx ├── CalculateHessianImage.cxx ├── CalculateMetricImages.cxx ├── CommensurateImages.cxx ├── ConvertTensorFieldToVTK.cxx ├── ConvertVectorFieldToVTK.cxx ├── CreateDifferenceImage.cxx ├── CreateGridImage.cxx ├── CreateImageVolumeFromImageSlices.cxx ├── CreateJacobianDeterminantImage.cxx ├── CreateRandomImage.cxx ├── CreateStrainTensorComponentImages.cxx ├── CreateWarpedGridImage.cxx ├── CropImage.cxx ├── CurvatureAnisotropicDiffusionImageFilter.cxx ├── DilateImage.cxx ├── ErodeImage.cxx ├── EvaluateImageAtAvantsPoints.cxx ├── ExtractTagLinePointsSliceBySlice.cxx ├── FillHoles.cxx ├── FlipImage.cxx ├── GaborFilterBank.cxx ├── GaussianSmoothImage.cxx ├── GenerateADFMFeatures.cxx ├── GenerateDeformationFieldDerivatives.cxx ├── GenerateDeformationFieldFromAvantsLandmarks.cxx ├── GenerateHistogram.cxx ├── GenerateHistogramFromBoxMask.cxx ├── GenerateInverseBSplineDeformationField.cxx ├── GenerateLikelihoodImages.cxx ├── ImageSeriesReadWrite.cxx ├── JHCT.cxx ├── JHCTMulti.cxx ├── LiveWire.cxx ├── MarceloImageConversion.cxx ├── MultiplyImages.cxx ├── PadImage.cxx ├── PointSetToPointSetRegistration.cxx ├── PrunePointSet.cxx ├── RegionalMinimaImage.cxx ├── RegisterImagesDMFFD.cxx ├── RegisterImagesFFD.old.cxx ├── RegisterWithMultiResDemons.cxx ├── ResizeHeliumImage.cxx ├── RigidVersor3DRegistration.cxx ├── STAPLEAnalysis.cxx ├── ThinTagLines.cxx ├── TranslateImage.cxx ├── TranslationRegistration.cxx ├── WarpAvantsPoints.cxx ├── WarpImage.cxx ├── WellComposeImage.cxx ├── ZeroCrossingsImage.cxx └── global.h ├── OrderDicomSeries.cxx ├── OtsuThresholdImage.cxx ├── PCAImageDecomposition.cxx ├── PadImage.cxx ├── PadImageForIsotropicBSplineMesh.cxx ├── PasteImageIntoImage.cxx ├── PermuteAxesImage.cxx ├── PointSetPairStatistics.cxx ├── PropagateLabels.cxx ├── RegionalMinMax.cxx ├── RegisterPointSetsDMFFD.cxx ├── ResampleImage.cxx ├── RescaleImageIntensity.cxx ├── RigidTransformImage.cxx ├── SSI.cxx ├── STAPLEAnalysis.cxx ├── SalernoFitVoxelwise3ParameterModel.cxx ├── SalernoGenerateSignalImage.cxx ├── SalernoSyntheticImageEstimation.cxx ├── SampleFeatureImages.cxx ├── SegmentAirways.cxx ├── SegmentHeliumLungs.cxx ├── SeparateLungs.cxx ├── ShapeMorphology.cxx ├── ShapePriorLevelSet.cxx ├── SimpleRegistration.cxx ├── SmoothDisplacementField.cxx ├── SmoothLongitudinalDisplacementFields.cxx ├── SmoothLungs.cxx ├── SplitHeliumLungs.cxx ├── SsdHelper.cxx ├── Statistics ├── CMakeLists.txt ├── PermutationTests.cxx ├── controls.txt ├── csf.txt ├── spd.txt ├── subjects.txt ├── ttest │ ├── CMakeLists.txt │ ├── CVS │ │ ├── Entries │ │ ├── Repository │ │ └── Root │ ├── controls.txt │ ├── csf.txt │ ├── histogram1.dat │ ├── histogram2.dat │ ├── histogram_controls.dat │ ├── histogram_csf.dat │ ├── histogram_spd.dat │ ├── histogram_wt.dat │ ├── spd.txt │ ├── ttest.cxx │ └── wt.txt └── wt.txt ├── StatsForSkullThickness.cxx ├── SuperResolution.cxx ├── Test.cxx ├── Thickness.cxx ├── ThresholdImage.cxx ├── ThresholdPlane.cxx ├── TileImages.cxx ├── Tortuosity.cxx ├── TruncateImageIntensity.cxx ├── UnaryOperateImage.cxx ├── WarpPoints.cxx ├── WarpVTKPolyData.cxx ├── WellComposeImage.cxx ├── ZeroCrossingImage.cxx ├── itkTimeAndMemoryProbeTest.cxx ├── testRegulItkBspline.cxx ├── topological_numbers.h └── volumeRender.cxx /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | bin 3 | 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