├── .gitignore ├── CMake ├── BuildConfigurations │ ├── DiffusionCmdApps.cmake │ ├── DiffusionDebug.cmake │ ├── DiffusionRelease.cmake │ ├── Fiberfox.cmake │ ├── IVIM.cmake │ ├── Tractography.cmake │ ├── atTRACTive.cmake │ ├── set_always.txt │ └── set_release.txt ├── CTestSubprojectList.cmake └── PackageDepends │ └── MITK_OpenCV_Config.cmake ├── CMakeExternals ├── ExternalProjectList.cmake └── OpenCV.cmake ├── LICENSE.txt ├── Modules ├── DiffusionCmdApps │ ├── CMakeLists.txt │ ├── FiberProcessing │ │ ├── CMakeLists.txt │ │ ├── FiberClustering.cpp │ │ ├── FiberColoring.cpp │ │ ├── FiberDirectionExtraction.cpp │ │ ├── FiberExtraction.cpp │ │ ├── FiberExtractionRoi.cpp │ │ ├── FiberJoin.cpp │ │ ├── FiberModification.cpp │ │ ├── FitFibersToImage.cpp │ │ ├── Sift2WeightCopy.cpp │ │ └── TractDensityFilter.cpp │ ├── FiberQuantification │ │ ├── CMakeLists.txt │ │ ├── PrintFiberStatistics.cpp │ │ └── TractDensity.cpp │ ├── Fiberfox │ │ ├── CMakeLists.txt │ │ ├── Fiberfox.cpp │ │ └── RandomFiberPhantom.cpp │ ├── IVIM │ │ ├── CMakeLists.txt │ │ ├── DiffusionIvimFit.cpp │ │ └── DiffusionKurtosisFit.cpp │ ├── ImageQuantification │ │ ├── CMakeLists.txt │ │ ├── DiffusionIndices.cpp │ │ ├── MultishellMethods.cpp │ │ ├── QballReconstruction.cpp │ │ └── TensorReconstruction.cpp │ ├── Misc │ │ ├── CMakeLists.txt │ │ ├── CopyGeometry.cpp │ │ ├── DImp.cpp │ │ ├── DReg.cpp │ │ ├── DiffusionDICOMLoader.cpp │ │ ├── FiberScreenshot.cpp │ │ ├── FileFormatConverter.cpp │ │ ├── ImageResampler.cpp │ │ ├── PeakExtraction.cpp │ │ └── ShToOdfImage.cpp │ ├── Tractography │ │ ├── CMakeLists.txt │ │ ├── GlobalTractography.cpp │ │ └── StreamlineTractography.cpp │ ├── files.cmake │ ├── mitkDiffusionDataIOHelper.cpp │ └── mitkDiffusionDataIOHelper.h ├── DiffusionImage │ ├── CMakeLists.txt │ ├── IO │ │ ├── DicomImport │ │ │ ├── mitkDicomDiffusionImageHeaderReader.cpp │ │ │ ├── mitkDicomDiffusionImageHeaderReader.h │ │ │ ├── mitkDicomDiffusionImageReader.cpp │ │ │ ├── mitkDicomDiffusionImageReader.h │ │ │ ├── mitkDiffusionDICOMFileReader.cpp │ │ │ ├── mitkDiffusionDICOMFileReader.h │ │ │ ├── mitkDiffusionDICOMFileReaderHelper.h │ │ │ ├── mitkDiffusionHeaderDICOMFileReader.cpp │ │ │ ├── mitkDiffusionHeaderDICOMFileReader.h │ │ │ ├── mitkDiffusionHeaderGEDICOMFileReader.cpp │ │ │ ├── mitkDiffusionHeaderGEDICOMFileReader.h │ │ │ ├── mitkDiffusionHeaderPhilipsDICOMFileReader.cpp │ │ │ ├── mitkDiffusionHeaderPhilipsDICOMFileReader.h │ │ │ ├── mitkDiffusionHeaderSiemensDICOMFileHelper.cpp │ │ │ ├── mitkDiffusionHeaderSiemensDICOMFileHelper.h │ │ │ ├── mitkDiffusionHeaderSiemensDICOMFileReader.cpp │ │ │ ├── mitkDiffusionHeaderSiemensDICOMFileReader.h │ │ │ ├── mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp │ │ │ ├── mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h │ │ │ ├── mitkGEDicomDiffusionImageHeaderReader.cpp │ │ │ ├── mitkGEDicomDiffusionImageHeaderReader.h │ │ │ ├── mitkGroupDiffusionHeadersFilter.cpp │ │ │ ├── mitkGroupDiffusionHeadersFilter.h │ │ │ ├── mitkPhilipsDicomDiffusionImageHeaderReader.cpp │ │ │ ├── mitkPhilipsDicomDiffusionImageHeaderReader.h │ │ │ ├── mitkSiemensDicomDiffusionImageHeaderReader.cpp │ │ │ ├── mitkSiemensDicomDiffusionImageHeaderReader.h │ │ │ ├── mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp │ │ │ └── mitkSiemensMosaicDicomDiffusionImageHeaderReader.h │ │ ├── mitkDiffusionImageDicomReader.cpp │ │ ├── mitkDiffusionImageDicomReader.h │ │ ├── mitkDiffusionImageMimeTypes.cpp │ │ ├── mitkDiffusionImageMimeTypes.h │ │ ├── mitkDiffusionImageNiftiReader.cpp │ │ ├── mitkDiffusionImageNiftiReader.h │ │ ├── mitkDiffusionImageNiftiWriter.cpp │ │ ├── mitkDiffusionImageNiftiWriter.h │ │ ├── mitkDiffusionImageNrrdReader.cpp │ │ ├── mitkDiffusionImageNrrdReader.h │ │ ├── mitkDiffusionImageNrrdWriter.cpp │ │ ├── mitkDiffusionImageNrrdWriter.h │ │ ├── mitkDiffusionImageObjectFactory.cpp │ │ ├── mitkDiffusionImageObjectFactory.h │ │ └── mitkDiffusionImageServiceActivator.cpp │ ├── Properties │ │ ├── mitkBValueMapProperty.cpp │ │ ├── mitkBValueMapProperty.h │ │ ├── mitkBValueMapPropertySerializer.cpp │ │ ├── mitkDiffusionPropertyHelper.cpp │ │ ├── mitkDiffusionPropertyHelper.h │ │ ├── mitkGradientDirectionsProperty.cpp │ │ ├── mitkGradientDirectionsProperty.h │ │ ├── mitkGradientDirectionsPropertySerializer.cpp │ │ ├── mitkMeasurementFrameProperty.cpp │ │ ├── mitkMeasurementFrameProperty.h │ │ ├── mitkMeasurementFramePropertySerializer.cpp │ │ ├── mitkNodePredicateIsDWI.cpp │ │ └── mitkNodePredicateIsDWI.h │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ └── mitkDiffusionPropertySerializerTest.cpp │ ├── files.cmake │ ├── mitkDiffusionImageHeaderInformation.cpp │ ├── mitkDiffusionImageHeaderInformation.h │ ├── mitkDiffusionImageHelperFunctions.cpp │ └── mitkDiffusionImageHelperFunctions.h ├── DiffusionModelling │ ├── Algorithms │ │ ├── Reconstruction │ │ │ ├── MultishellProcessing │ │ │ │ ├── itkADCAverageFunctor.cpp │ │ │ │ ├── itkADCAverageFunctor.h │ │ │ │ ├── itkADCFitFunctor.cpp │ │ │ │ ├── itkADCFitFunctor.h │ │ │ │ ├── itkBiExpFitFunctor.cpp │ │ │ │ ├── itkBiExpFitFunctor.h │ │ │ │ ├── itkDWIVoxelFunctor.h │ │ │ │ ├── itkKurtosisFitFunctor.cpp │ │ │ │ ├── itkKurtosisFitFunctor.h │ │ │ │ ├── itkRadialMultishellToSingleshellImageFilter.cpp │ │ │ │ └── itkRadialMultishellToSingleshellImageFilter.h │ │ │ ├── itkAnalyticalDiffusionQballReconstructionImageFilter.cpp │ │ │ ├── itkAnalyticalDiffusionQballReconstructionImageFilter.h │ │ │ ├── itkDiffusionMultiShellQballReconstructionImageFilter.cpp │ │ │ ├── itkDiffusionMultiShellQballReconstructionImageFilter.h │ │ │ ├── itkDiffusionQballReconstructionImageFilter.h │ │ │ ├── itkDiffusionQballReconstructionImageFilter.txx │ │ │ ├── itkOrientationDistributionFunction.h │ │ │ ├── itkOrientationDistributionFunction.txx │ │ │ ├── itkPointShell.h │ │ │ ├── itkPointShell.txx │ │ │ ├── mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp │ │ │ └── mitkTeemDiffusionTensor3DReconstructionImageFilter.h │ │ ├── itkAdcImageFilter.h │ │ ├── itkAdcImageFilter.txx │ │ ├── itkDiffusionOdfGeneralizedFaImageFilter.h │ │ ├── itkDiffusionOdfGeneralizedFaImageFilter.txx │ │ ├── itkDiffusionTensorPrincipalDirectionImageFilter.h │ │ ├── itkDiffusionTensorPrincipalDirectionImageFilter.txx │ │ ├── itkFlipPeaksFilter.cpp │ │ ├── itkFlipPeaksFilter.h │ │ ├── itkGaussianInterpolateImageFunction.h │ │ ├── itkGaussianInterpolateImageFunction.txx │ │ ├── itkOdfMaximaExtractionFilter.cpp │ │ ├── itkOdfMaximaExtractionFilter.h │ │ ├── itkOdfToRgbImageFilter.h │ │ ├── itkShCoefficientImageExporter.cpp │ │ ├── itkShCoefficientImageExporter.h │ │ ├── itkShCoefficientImageImporter.cpp │ │ ├── itkShCoefficientImageImporter.h │ │ ├── itkShToOdfImageFilter.cpp │ │ ├── itkShToOdfImageFilter.h │ │ ├── itkShToRgbImageFilter.h │ │ ├── itkTensorDerivedMeasurementsFilter.h │ │ ├── itkTensorDerivedMeasurementsFilter.txx │ │ ├── itkTensorImageToDiffusionImageFilter.h │ │ ├── itkTensorImageToDiffusionImageFilter.txx │ │ ├── itkTensorImageToOdfImageFilter.h │ │ ├── itkTensorImageToOdfImageFilter.txx │ │ ├── itkTensorReconstructionWithEigenvalueCorrectionFilter.h │ │ ├── itkTensorReconstructionWithEigenvalueCorrectionFilter.txx │ │ ├── itkTensorToL2NormImageFilter.h │ │ ├── itkTensorToL2NormImageFilter.txx │ │ └── itkTensorToRgbImageFilter.h │ ├── CMakeLists.txt │ ├── IO │ │ ├── mitkDiffusionCoreObjectFactory.cpp │ │ ├── mitkDiffusionCoreObjectFactory.h │ │ ├── mitkDiffusionIOMimeTypes.cpp │ │ ├── mitkDiffusionIOMimeTypes.h │ │ ├── mitkDiffusionServiceActivator.cpp │ │ ├── mitkNrrdOdfImageReader.cpp │ │ ├── mitkNrrdOdfImageReader.h │ │ ├── mitkNrrdOdfImageWriter.cpp │ │ ├── mitkNrrdOdfImageWriter.h │ │ ├── mitkNrrdTensorImageReader.cpp │ │ ├── mitkNrrdTensorImageReader.h │ │ ├── mitkNrrdTensorImageWriter.cpp │ │ ├── mitkNrrdTensorImageWriter.h │ │ ├── mitkOdfImage.cpp │ │ ├── mitkOdfImage.h │ │ ├── mitkOdfImageSerializer.cpp │ │ ├── mitkOdfImageSerializer.h │ │ ├── mitkPeakImage.cpp │ │ ├── mitkPeakImage.h │ │ ├── mitkPeakImageReader.cpp │ │ ├── mitkPeakImageReader.h │ │ ├── mitkPeakImageSerializer.cpp │ │ ├── mitkPeakImageSerializer.h │ │ ├── mitkShImage.cpp │ │ ├── mitkShImage.h │ │ ├── mitkShImageReader.cpp │ │ ├── mitkShImageReader.h │ │ ├── mitkShImageSerializer.cpp │ │ ├── mitkShImageSerializer.h │ │ ├── mitkShImageWriter.cpp │ │ ├── mitkShImageWriter.h │ │ ├── mitkTensorImage.cpp │ │ ├── mitkTensorImage.h │ │ ├── mitkTensorImageSerializer.cpp │ │ └── mitkTensorImageSerializer.h │ ├── Rendering │ │ ├── mitkCompositeMapper.cpp │ │ ├── mitkCompositeMapper.h │ │ ├── mitkOdfNormalizationMethodProperty.cpp │ │ ├── mitkOdfNormalizationMethodProperty.h │ │ ├── mitkOdfScaleByProperty.cpp │ │ ├── mitkOdfScaleByProperty.h │ │ ├── mitkOdfVtkMapper2D.h │ │ ├── mitkOdfVtkMapper2D.txx │ │ ├── mitkPeakImageMapper2D.cpp │ │ ├── mitkPeakImageMapper2D.h │ │ ├── mitkPeakImageMapper3D.cpp │ │ ├── mitkPeakImageMapper3D.h │ │ ├── mitkVectorImageVtkGlyphMapper3D.cpp │ │ ├── mitkVectorImageVtkGlyphMapper3D.h │ │ ├── vtkMaskedProgrammableGlyphFilter.cpp │ │ ├── vtkMaskedProgrammableGlyphFilter.h │ │ ├── vtkOdfSource.cxx │ │ ├── vtkOdfSource.h │ │ ├── vtkThickPlane.cxx │ │ └── vtkThickPlane.h │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ ├── mitkExtractSingleShellTest.cpp │ │ ├── mitkImageReconstructionTest.cpp │ │ └── mitkPeakShImageReaderTest.cpp │ ├── files.cmake │ ├── mitkDiffusionModellingHelperFunctions.cpp │ └── mitkDiffusionModellingHelperFunctions.h ├── DiffusionPreprocessing │ ├── CMakeLists.txt │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ └── mitkNonLocalMeansDenoisingTest.cpp │ ├── files.cmake │ ├── itkB0ImageExtractionImageFilter.h │ ├── itkB0ImageExtractionImageFilter.txx │ ├── itkB0ImageExtractionToSeparateImageFilter.h │ ├── itkB0ImageExtractionToSeparateImageFilter.txx │ ├── itkDwiGradientLengthCorrectionFilter.cpp │ ├── itkDwiGradientLengthCorrectionFilter.h │ ├── itkDwiNormilzationFilter.h │ ├── itkDwiNormilzationFilter.txx │ ├── itkElectrostaticRepulsionDiffusionGradientReductionFilter.h │ ├── itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx │ ├── itkExtractDwiChannelFilter.h │ ├── itkExtractDwiChannelFilter.txx │ ├── itkMergeDiffusionImagesFilter.h │ ├── itkMergeDiffusionImagesFilter.txx │ ├── itkNonLocalMeansDenoisingFilter.h │ ├── itkNonLocalMeansDenoisingFilter.txx │ ├── itkRemoveDwiChannelFilter.h │ ├── itkRemoveDwiChannelFilter.txx │ ├── itkResampleDwiImageFilter.h │ ├── itkResampleDwiImageFilter.txx │ ├── itkVectorImageToImageFilter.h │ └── itkVectorImageToImageFilter.txx ├── DiffusionRegistration │ ├── CMakeLists.txt │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ ├── mitkDWHeadMotionCorrectionTest.cpp │ │ └── mitkPyramidImageRegistrationMethodTest.cpp │ ├── files.cmake │ ├── itkSplitDWImageFilter.h │ ├── itkSplitDWImageFilter.txx │ ├── mitkDWIHeadMotionCorrectionFilter.cpp │ ├── mitkDWIHeadMotionCorrectionFilter.h │ ├── mitkDiffusionImageCorrectionFilter.cpp │ ├── mitkDiffusionImageCorrectionFilter.h │ ├── mitkPyramidImageRegistrationMethod.cpp │ ├── mitkPyramidImageRegistrationMethod.h │ ├── mitkPyramidRegistrationMethodHelper.h │ ├── mitkRegistrationWrapper.cpp │ └── mitkRegistrationWrapper.h ├── FiberBundle │ ├── CMakeLists.txt │ ├── IO │ │ ├── mitkFiberBundleDicomReader.cpp │ │ ├── mitkFiberBundleDicomReader.h │ │ ├── mitkFiberBundleDicomWriter.cpp │ │ ├── mitkFiberBundleDicomWriter.h │ │ ├── mitkFiberBundleIOHelper.cpp │ │ ├── mitkFiberBundleIOHelper.h │ │ ├── mitkFiberBundleMimeTypes.cpp │ │ ├── mitkFiberBundleMimeTypes.h │ │ ├── mitkFiberBundleObjectFactory.cpp │ │ ├── mitkFiberBundleObjectFactory.h │ │ ├── mitkFiberBundleSerializer.cpp │ │ ├── mitkFiberBundleSerializer.h │ │ ├── mitkFiberBundleServiceActivator.cpp │ │ ├── mitkFiberBundleTckReader.cpp │ │ ├── mitkFiberBundleTckReader.h │ │ ├── mitkFiberBundleTrackVisReader.cpp │ │ ├── mitkFiberBundleTrackVisReader.h │ │ ├── mitkFiberBundleTrackVisWriter.cpp │ │ ├── mitkFiberBundleTrackVisWriter.h │ │ ├── mitkFiberBundleVtkReader.cpp │ │ ├── mitkFiberBundleVtkReader.h │ │ ├── mitkFiberBundleVtkWriter.cpp │ │ ├── mitkFiberBundleVtkWriter.h │ │ ├── mitkPlanarFigureCompositeReader.cpp │ │ ├── mitkPlanarFigureCompositeReader.h │ │ ├── mitkPlanarFigureCompositeSerializer.cpp │ │ ├── mitkPlanarFigureCompositeSerializer.h │ │ ├── mitkPlanarFigureCompositeWriter.cpp │ │ ├── mitkPlanarFigureCompositeWriter.h │ │ ├── mitkTrackvis.cpp │ │ └── mitkTrackvis.h │ ├── Rendering │ │ ├── mitkFiberBundleMapper2D.cpp │ │ ├── mitkFiberBundleMapper2D.h │ │ ├── mitkFiberBundleMapper3D.cpp │ │ └── mitkFiberBundleMapper3D.h │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ ├── mitkFiberBundleReaderWriterTest.cpp │ │ └── mitkFiberMapper3DTest.cpp │ ├── files.cmake │ ├── mitkFiberBundle.cpp │ ├── mitkFiberBundle.h │ ├── mitkPlanarFigureComposite.cpp │ └── mitkPlanarFigureComposite.h ├── FiberDissection │ ├── CMakeLists.txt │ ├── CMakeLists.txt.user │ ├── Interactor │ │ ├── mitkSphereInteractor.cpp │ │ ├── mitkSphereInteractor.h │ │ ├── mitkSphereSegmentationInteractor.cpp │ │ ├── mitkSphereSegmentationInteractor.h │ │ ├── mitkStreamlineInteractor.cpp │ │ ├── mitkStreamlineInteractor.h │ │ ├── mitkStreamlineInteractorBrush.cpp │ │ └── mitkStreamlineInteractorBrush.h │ ├── MachineLearning │ │ ├── mitkStatisticModel.cpp │ │ ├── mitkStatisticModel.h │ │ ├── mitkStreamlineFeatureExtractor.cpp │ │ └── mitkStreamlineFeatureExtractor.h │ ├── files.cmake │ └── resource │ │ └── Interactions │ │ ├── SphereInteractionsConfig.xml │ │ ├── SphereInteractionsStates.xml │ │ ├── SphereSegmentationInteractionsConfig.xml │ │ ├── SphereSegmentationInteractionsStates.xml │ │ ├── Streamline3DConfig.xml │ │ ├── Streamline3DStates.xml │ │ ├── StreamlineBrush3DConfig.xml │ │ └── StreamlineBrush3DStates.xml ├── FiberProcessing │ ├── CMakeLists.txt │ ├── FiberClustering │ │ ├── mitkClusteringMetric.h │ │ ├── mitkClusteringMetricAnatomic.h │ │ ├── mitkClusteringMetricEuclideanMax.h │ │ ├── mitkClusteringMetricEuclideanMean.h │ │ ├── mitkClusteringMetricEuclideanStd.h │ │ ├── mitkClusteringMetricInnerAngles.h │ │ ├── mitkClusteringMetricLength.h │ │ ├── mitkClusteringMetricScalarMap.h │ │ ├── mitkTractClusteringFilter.cpp │ │ └── mitkTractClusteringFilter.h │ ├── FiberDerivedImages │ │ ├── itkTractDensityImageFilter.cpp │ │ ├── itkTractDensityImageFilter.h │ │ ├── itkTractsToFiberEndingsImageFilter.cpp │ │ ├── itkTractsToFiberEndingsImageFilter.h │ │ ├── itkTractsToRgbaImageFilter.cpp │ │ ├── itkTractsToRgbaImageFilter.h │ │ ├── itkTractsToVectorImageFilter.cpp │ │ └── itkTractsToVectorImageFilter.h │ ├── FiberModification │ │ ├── itkFiberCurvatureFilter.cpp │ │ ├── itkFiberCurvatureFilter.h │ │ ├── itkFiberExtractionFilter.cpp │ │ └── itkFiberExtractionFilter.h │ ├── FiberQuantification │ │ ├── itkDistanceFromSegmentationImageFilter.cpp │ │ └── itkDistanceFromSegmentationImageFilter.h │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ ├── mitkFiberExtractionTest.cpp │ │ ├── mitkFiberProcessingTest.cpp │ │ └── mitkFiberTransformationTest.cpp │ └── files.cmake ├── FiberTracking │ ├── Algorithms │ │ ├── GibbsTracking │ │ │ ├── mitkEnergyComputer.cpp │ │ │ ├── mitkEnergyComputer.h │ │ │ ├── mitkFiberBuilder.cpp │ │ │ ├── mitkFiberBuilder.h │ │ │ ├── mitkGibbsEnergyComputer.cpp │ │ │ ├── mitkGibbsEnergyComputer.h │ │ │ ├── mitkMetropolisHastingsSampler.cpp │ │ │ ├── mitkMetropolisHastingsSampler.h │ │ │ ├── mitkParticle.h │ │ │ ├── mitkParticleGrid.cpp │ │ │ ├── mitkParticleGrid.h │ │ │ ├── mitkSimpSamp.h │ │ │ ├── mitkSphereInterpolator.cpp │ │ │ └── mitkSphereInterpolator.h │ │ ├── TrackingHandlers │ │ │ ├── mitkTrackingDataHandler.cpp │ │ │ ├── mitkTrackingDataHandler.h │ │ │ ├── mitkTrackingHandlerOdf.cpp │ │ │ ├── mitkTrackingHandlerOdf.h │ │ │ ├── mitkTrackingHandlerPeaks.cpp │ │ │ ├── mitkTrackingHandlerPeaks.h │ │ │ ├── mitkTrackingHandlerTensor.cpp │ │ │ └── mitkTrackingHandlerTensor.h │ │ ├── itkGibbsTrackingFilter.cpp │ │ ├── itkGibbsTrackingFilter.h │ │ ├── itkStreamlineTrackingFilter.cpp │ │ └── itkStreamlineTrackingFilter.h │ ├── CMakeLists.txt │ ├── Resources │ │ └── empty │ ├── Testing │ │ ├── CMakeLists.txt │ │ ├── files.cmake │ │ ├── mitkGlobalTractographyTest.cpp │ │ └── mitkStreamlineTractographyTest.cpp │ ├── files.cmake │ ├── mitkStreamlineTractographyParameters.cpp │ └── mitkStreamlineTractographyParameters.h ├── IVIM │ ├── CMakeLists.txt │ ├── files.cmake │ ├── itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp │ ├── itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h │ ├── itkDiffusionKurtosisReconstructionImageFilter.cpp │ ├── itkDiffusionKurtosisReconstructionImageFilter.h │ ├── itkRegularizedIVIMLocalVariationImageFilter.h │ ├── itkRegularizedIVIMLocalVariationImageFilter.txx │ ├── itkRegularizedIVIMReconstructionFilter.h │ ├── itkRegularizedIVIMReconstructionFilter.txx │ ├── itkRegularizedIVIMReconstructionSingleIteration.h │ └── itkRegularizedIVIMReconstructionSingleIteration.txx ├── ModuleList.cmake └── MriSimulation │ ├── Algorithms │ ├── itkDftImageFilter.cpp │ ├── itkDftImageFilter.h │ ├── itkFibersFromPlanarFiguresFilter.cpp │ ├── itkFibersFromPlanarFiguresFilter.h │ ├── itkFieldmapGeneratorFilter.cpp │ ├── itkFieldmapGeneratorFilter.h │ ├── itkFitFibersToImageFilter.cpp │ ├── itkFitFibersToImageFilter.h │ ├── itkKspaceImageFilter.cpp │ ├── itkKspaceImageFilter.h │ ├── itkRandomPhantomFilter.cpp │ ├── itkRandomPhantomFilter.h │ ├── itkTractsToDWIImageFilter.cpp │ └── itkTractsToDWIImageFilter.h │ ├── CMakeLists.txt │ ├── Sequences │ ├── mitkAcquisitionType.h │ ├── mitkConventionalSpinEcho.h │ ├── mitkFastSpinEcho.h │ └── mitkSingleShotEpi.h │ ├── SignalModels │ ├── mitkAstroStickModel.cpp │ ├── mitkAstroStickModel.h │ ├── mitkBallModel.cpp │ ├── mitkBallModel.h │ ├── mitkChiSquareNoiseModel.cpp │ ├── mitkChiSquareNoiseModel.h │ ├── mitkDiffusionNoiseModel.h │ ├── mitkDiffusionSignalModel.h │ ├── mitkDotModel.cpp │ ├── mitkDotModel.h │ ├── mitkRawShModel.cpp │ ├── mitkRawShModel.h │ ├── mitkRicianNoiseModel.cpp │ ├── mitkRicianNoiseModel.h │ ├── mitkStickModel.cpp │ ├── mitkStickModel.h │ ├── mitkTensorModel.cpp │ └── mitkTensorModel.h │ ├── Testing │ ├── CMakeLists.txt │ ├── files.cmake │ ├── mitkFiberFitTest.cpp │ ├── mitkFiberGenerationTest.cpp │ ├── mitkFiberfoxSignalGenerationBrainSliceTest.cpp │ └── mitkFiberfoxSignalGenerationTest.cpp │ ├── files.cmake │ ├── mitkFiberfoxParameters.cpp │ └── mitkFiberfoxParameters.h ├── Plugins ├── PluginList.cmake ├── org.mitk.gui.qt.diffusionimaging.controls │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── Data_CSD.png │ │ │ ├── Data_Tensors.png │ │ │ ├── QmitkDiffusionImagingDataImportPage.dox │ │ │ ├── QmitkDiffusionImagingVisualization.dox │ │ │ ├── dicom1.png │ │ │ └── tract_visualization.png │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── ConnectomicsNetwork.png │ │ ├── DiffData24.png │ │ ├── DiffData48.png │ │ ├── MapperEfx2D.png │ │ ├── QmitkDiffusionImaging.qrc │ │ ├── Refresh_48.png │ │ ├── arrow.png │ │ ├── color64.png │ │ ├── crosshair.png │ │ ├── diffusion_2.gif │ │ ├── dwi.png │ │ ├── dwiimport.png │ │ ├── glyphsoff_C.png │ │ ├── glyphsoff_S.png │ │ ├── glyphsoff_T.png │ │ ├── glyphson.png │ │ ├── glyphson_C.png │ │ ├── glyphson_S.png │ │ ├── glyphson_T.png │ │ ├── ml_tractogram.png │ │ ├── odf.png │ │ ├── odf_peaks.png │ │ ├── paint2.png │ │ ├── refresh.xpm │ │ ├── reset.png │ │ ├── segmentation.svg │ │ ├── sh.png │ │ ├── source │ │ │ ├── 1002diffusion.cpt │ │ │ ├── 1002odf.cpt │ │ │ ├── Generator.cpt │ │ │ ├── dwiimport.cpt │ │ │ ├── gear_wheel.png │ │ │ ├── one_eye_close.png │ │ │ ├── one_eye_open.jpeg │ │ │ ├── one_eye_open.png │ │ │ ├── pfeil.png │ │ │ ├── quantification.cpt │ │ │ ├── reconodf (+Generator.cpt).cpt │ │ │ ├── recontensor (+Generator.cpt).cpt │ │ │ ├── stats.cpt │ │ │ ├── texIntOFF.png │ │ │ └── texIntON.png │ │ ├── stats.png │ │ ├── tensor.png │ │ ├── texIntOFFIcon.png │ │ ├── texIntONIcon.png │ │ ├── tractogram.png │ │ └── vizControls.png │ └── src │ │ └── internal │ │ ├── Perspectives │ │ ├── QmitkDiffusionDefaultPerspective.cpp │ │ ├── QmitkDiffusionDefaultPerspective.h │ │ ├── QmitkSegmentationPerspective.cpp │ │ └── QmitkSegmentationPerspective.h │ │ ├── QmitkControlVisualizationPropertiesView.cpp │ │ ├── QmitkControlVisualizationPropertiesView.h │ │ ├── QmitkControlVisualizationPropertiesViewControls.ui │ │ ├── QmitkDicomTractogramTagEditorView.cpp │ │ ├── QmitkDicomTractogramTagEditorView.h │ │ ├── QmitkDicomTractogramTagEditorViewControls.ui │ │ ├── QmitkDiffusionDicomImportView.cpp │ │ ├── QmitkDiffusionDicomImportView.h │ │ ├── QmitkDiffusionDicomImportViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.denoising │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── GaussianFilter.png │ │ │ ├── NLM.png │ │ │ └── QmitkDenoisingViewUserManual.dox │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ └── denoisingicon.png │ └── src │ │ └── internal │ │ ├── QmitkDenoisingView.cpp │ │ ├── QmitkDenoisingView.h │ │ ├── QmitkDenoisingViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.fiberfit │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ └── QmitkFiberFitViewUserManual.dox │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ └── FiberFit.png │ └── src │ │ └── internal │ │ ├── QmitkFiberFitView.cpp │ │ ├── QmitkFiberFitView.h │ │ ├── QmitkFiberFitViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.fiberfox │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── Fiberfox-Fiducial.png │ │ │ ├── Fiberfox.png │ │ │ ├── FiberfoxExamples.png │ │ │ ├── FiberfoxWholebrain.png │ │ │ ├── QmitkFiberGenerationViewUserManual.dox │ │ │ ├── QmitkFiberfoxViewUserManual.dox │ │ │ ├── QmitkFieldmapGeneratorViewUserManual.dox │ │ │ ├── fieldmapGenerator.png │ │ │ └── random_phantom.png │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── QmitkFiberfox.qrc │ │ ├── circle.png │ │ ├── download.png │ │ ├── fieldmap.png │ │ ├── models.png │ │ ├── phantom.png │ │ ├── refresh.xpm │ │ ├── right.png │ │ ├── stop.png │ │ ├── syntheticdata.png │ │ └── upload.png │ └── src │ │ ├── QmitkAstrosticksModelParametersWidget.cpp │ │ ├── QmitkAstrosticksModelParametersWidget.h │ │ ├── QmitkAstrosticksModelParametersWidgetControls.ui │ │ ├── QmitkBallModelParametersWidget.cpp │ │ ├── QmitkBallModelParametersWidget.h │ │ ├── QmitkBallModelParametersWidgetControls.ui │ │ ├── QmitkDotModelParametersWidget.cpp │ │ ├── QmitkDotModelParametersWidget.h │ │ ├── QmitkDotModelParametersWidgetControls.ui │ │ ├── QmitkPrototypeSignalParametersWidget.cpp │ │ ├── QmitkPrototypeSignalParametersWidget.h │ │ ├── QmitkPrototypeSignalParametersWidgetControls.ui │ │ ├── QmitkStickModelParametersWidget.cpp │ │ ├── QmitkStickModelParametersWidget.h │ │ ├── QmitkStickModelParametersWidgetControls.ui │ │ ├── QmitkTensorModelParametersWidget.cpp │ │ ├── QmitkTensorModelParametersWidget.h │ │ ├── QmitkTensorModelParametersWidgetControls.ui │ │ ├── QmitkZeppelinModelParametersWidget.cpp │ │ ├── QmitkZeppelinModelParametersWidget.h │ │ ├── QmitkZeppelinModelParametersWidgetControls.ui │ │ └── internal │ │ ├── Perspectives │ │ ├── QmitkDIAppSyntheticDataGenerationPerspective.cpp │ │ └── QmitkDIAppSyntheticDataGenerationPerspective.h │ │ ├── QmitkFiberGenerationView.cpp │ │ ├── QmitkFiberGenerationView.h │ │ ├── QmitkFiberGenerationViewControls.ui │ │ ├── QmitkFiberfoxView.cpp │ │ ├── QmitkFiberfoxView.h │ │ ├── QmitkFiberfoxViewControls.ui │ │ ├── QmitkFieldmapGeneratorView.cpp │ │ ├── QmitkFieldmapGeneratorView.h │ │ ├── QmitkFieldmapGeneratorViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.fiberprocessing │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── DirectionExtractionFib.png │ │ │ ├── DirectionExtractionPeaks.png │ │ │ ├── QmitkFiberClusteringViewUserManual.dox │ │ │ ├── QmitkFiberProcessingViewUserManual.dox │ │ │ ├── QmitkFiberQuantificationViewUserManual.dox │ │ │ └── QmitkInteractiveFiberDissectionView.dox │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── FiberBundle.png │ │ ├── FiberBundleOperations.png │ │ ├── FiberClustering.png │ │ ├── FiberFit.png │ │ ├── FiberQuantification.png │ │ ├── QmitkFiberprocessing.qrc │ │ ├── QmitkInteractiveFiberDissection.qrc │ │ ├── atTRACTive.png │ │ ├── brush.png │ │ ├── circle.png │ │ ├── eraze.png │ │ ├── highlighter.png │ │ └── polygon.png │ └── src │ │ └── internal │ │ ├── Perspectives │ │ ├── QmitkFiberProcessingPerspective.cpp │ │ └── QmitkFiberProcessingPerspective.h │ │ ├── QmitkFiberClusteringView.cpp │ │ ├── QmitkFiberClusteringView.h │ │ ├── QmitkFiberClusteringViewControls.ui │ │ ├── QmitkFiberProcessingView.cpp │ │ ├── QmitkFiberProcessingView.h │ │ ├── QmitkFiberProcessingViewControls.ui │ │ ├── QmitkFiberQuantificationView.cpp │ │ ├── QmitkFiberQuantificationView.h │ │ ├── QmitkFiberQuantificationViewControls.ui │ │ ├── QmitkInteractiveFiberDissectionView.cpp │ │ ├── QmitkInteractiveFiberDissectionView.h │ │ ├── QmitkInteractiveFiberDissectionViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.ivim │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── QmitkUserIVIMViewManual.dox │ │ │ └── ivimview.png │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── IVIM_48.png │ │ └── ivim.png │ └── src │ │ └── internal │ │ ├── Perspectives │ │ ├── QmitkDIAppIVIMPerspective.cpp │ │ └── QmitkDIAppIVIMPerspective.h │ │ ├── QmitkIVIMView.cpp │ │ ├── QmitkIVIMView.h │ │ ├── QmitkIVIMViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.preprocessing │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── PreprocessingGUI_1.png │ │ │ ├── PreprocessingGUI_2.png │ │ │ ├── PreprocessingGUI_3.png │ │ │ ├── PreprocessingGUI_4.png │ │ │ └── QmitkDiffusionImagingPreprocessingPage.dox │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── dwi2.png │ │ └── prprocessing.svg │ └── src │ │ └── internal │ │ ├── QmitkPreprocessingView.cpp │ │ ├── QmitkPreprocessingView.h │ │ ├── QmitkPreprocessingViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.reconstruction │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── QmitkDiffusionImagingQuantificationPage.dox │ │ │ ├── QmitkOdfDetailsViewUserManual.dox │ │ │ ├── QmitkOdfMaximaExtractionViewUserManual.dox │ │ │ ├── QmitkQBallReconstructionViewUserManual.dox │ │ │ ├── QmitkTensorReconstructionViewUserManual.dox │ │ │ ├── ScalarIndicesGUI.png │ │ │ ├── odfdetails.png │ │ │ ├── qballs1.png │ │ │ ├── qballs2.png │ │ │ ├── qballs3.png │ │ │ ├── residuals.png │ │ │ ├── tensor1.png │ │ │ └── tensor4.png │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ ├── OdfDetails.png │ │ ├── odf.png │ │ ├── odf_peaks.png │ │ ├── quantification.png │ │ └── tensor.png │ └── src │ │ └── internal │ │ ├── Perspectives │ │ ├── QmitkQuantificationPerspective.cpp │ │ ├── QmitkQuantificationPerspective.h │ │ ├── QmitkReconstructionPerspective.cpp │ │ └── QmitkReconstructionPerspective.h │ │ ├── QmitkDiffusionQuantificationView.cpp │ │ ├── QmitkDiffusionQuantificationView.h │ │ ├── QmitkDiffusionQuantificationViewControls.ui │ │ ├── QmitkOdfMaximaExtractionView.cpp │ │ ├── QmitkOdfMaximaExtractionView.h │ │ ├── QmitkOdfMaximaExtractionViewControls.ui │ │ ├── QmitkQBallReconstructionView.cpp │ │ ├── QmitkQBallReconstructionView.h │ │ ├── QmitkQBallReconstructionViewControls.ui │ │ ├── QmitkTensorReconstructionView.cpp │ │ ├── QmitkTensorReconstructionView.h │ │ ├── QmitkTensorReconstructionViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h ├── org.mitk.gui.qt.diffusionimaging.registration │ ├── CMakeLists.txt │ ├── documentation │ │ ├── UserManual │ │ │ ├── QmitkHeadMotionCorrection.dox │ │ │ ├── QmitkSimpleRegistration.dox │ │ │ ├── registration_basic.png │ │ │ └── registration_batch.png │ │ └── doxygen │ │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ │ └── diffusionregistration.png │ └── src │ │ └── internal │ │ ├── QmitkHeadMotionCorrectionView.cpp │ │ ├── QmitkHeadMotionCorrectionView.h │ │ ├── QmitkHeadMotionCorrectionViewControls.ui │ │ ├── QmitkSimpleRegistrationView.cpp │ │ ├── QmitkSimpleRegistrationView.h │ │ ├── QmitkSimpleRegistrationViewControls.ui │ │ ├── mitkPluginActivator.cpp │ │ └── mitkPluginActivator.h └── org.mitk.gui.qt.diffusionimaging.tractography │ ├── CMakeLists.txt │ ├── documentation │ ├── UserManual │ │ ├── QmitkGibbsTrackingViewUserManual.dox │ │ └── QmitkStreamlineTrackingViewUserManual.dox │ └── doxygen │ │ └── modules.dox │ ├── files.cmake │ ├── manifest_headers.cmake │ ├── plugin.xml │ ├── resources │ ├── GibbsTracking.png │ ├── QmitkTractography.qrc │ ├── download.png │ ├── ml_tractography.png │ ├── right.png │ ├── stop.png │ ├── tract.png │ ├── tractogram.png │ └── upload.png │ └── src │ └── internal │ ├── Perspectives │ ├── QmitkGibbsTractographyPerspective.cpp │ ├── QmitkGibbsTractographyPerspective.h │ ├── QmitkStreamlineTractographyPerspective.cpp │ └── QmitkStreamlineTractographyPerspective.h │ ├── QmitkGibbsTrackingView.cpp │ ├── QmitkGibbsTrackingView.h │ ├── QmitkGibbsTrackingViewControls.ui │ ├── QmitkStreamlineTrackingView.cpp │ ├── QmitkStreamlineTrackingView.h │ ├── QmitkStreamlineTrackingViewControls.ui │ ├── mitkPluginActivator.cpp │ └── mitkPluginActivator.h └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/.gitignore -------------------------------------------------------------------------------- /CMake/BuildConfigurations/DiffusionRelease.cmake: -------------------------------------------------------------------------------- 1 | include(${CMAKE_CURRENT_LIST_DIR}/DiffusionDebug.cmake) 2 | include(${CMAKE_CURRENT_LIST_DIR}/set_release.txt) 3 | set(BUILD_TESTING ON CACHE BOOL "Build the MITK tests" FORCE) 4 | -------------------------------------------------------------------------------- /CMake/BuildConfigurations/set_release.txt: -------------------------------------------------------------------------------- 1 | 2 | set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE) 3 | set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE) 4 | set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) 5 | 6 | -------------------------------------------------------------------------------- /CMake/CTestSubprojectList.cmake: -------------------------------------------------------------------------------- 1 | list(APPEND MITK_CTEST_SUBPROJECTS 2 | MITK-Diffusion 3 | ) 4 | -------------------------------------------------------------------------------- /CMake/PackageDepends/MITK_OpenCV_Config.cmake: -------------------------------------------------------------------------------- 1 | foreach(opencv_module ${OpenCV_REQUIRED_COMPONENTS_BY_MODULE}) 2 | if(NOT opencv_module MATCHES "^opencv_") 3 | set(opencv_module "opencv_${opencv_module}") 4 | endif() 5 | list(APPEND _opencv_required_components_by_module ${opencv_module}) 6 | endforeach() 7 | 8 | find_package(OpenCV COMPONENTS ${_opencv_required_components_by_module} REQUIRED) 9 | 10 | foreach(opencv_module ${_opencv_required_components_by_module}) 11 | list(APPEND ALL_LIBRARIES ${opencv_module}) 12 | endforeach() 13 | 14 | if(WIN32) 15 | if (EXISTS ${OpenCV_LIB_PATH}) 16 | list(APPEND opencv_path "${OpenCV_LIB_PATH}/../bin") # OpenCV is built in superbuild 17 | else() 18 | list(APPEND opencv_path "${OpenCV_DIR}/bin") # External OpenCV build is used 19 | endif() 20 | 21 | get_property(library_search_paths GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS) 22 | 23 | if(NOT opencv_path IN_LIST library_search_paths) 24 | set_property(GLOBAL APPEND PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS "${opencv_path}") 25 | endif() 26 | endif() 27 | -------------------------------------------------------------------------------- /CMakeExternals/ExternalProjectList.cmake: -------------------------------------------------------------------------------- 1 | mitkFunctionAddExternalProject(NAME OpenCV ON) 2 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE( 2 | SUBPROJECTS MITK-Diffusion 3 | # INCLUDE_DIRS Helpers 4 | DEPENDS MitkCommandLine 5 | PACKAGE_DEPENDS PUBLIC ITK 6 | ) 7 | 8 | if(MODULE_IS_ENABLED) 9 | add_subdirectory(Fiberfox) 10 | add_subdirectory(FiberProcessing) 11 | add_subdirectory(Tractography) 12 | add_subdirectory(Misc) 13 | add_subdirectory(ImageQuantification) 14 | add_subdirectory(FiberQuantification) 15 | add_subdirectory(IVIM) 16 | endif() 17 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/FiberQuantification/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionFiberQuantificationCmdApps "Build commandline tools for diffusion fiber processing" OFF) 2 | 3 | if(BUILD_DiffusionFiberQuantificationCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusionFiberProcessingcmdapps 15 | TractDensity^^ 16 | PrintFiberStatistics^^ 17 | ) 18 | 19 | foreach(diffusionFiberProcessingcmdapp ${diffusionFiberProcessingcmdapps}) 20 | # extract cmd app name and dependencies 21 | string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberProcessingcmdapp}) 22 | set(cmdapp_info_list ${cmdapp_info}) 23 | list(GET cmdapp_info_list 0 appname) 24 | list(GET cmdapp_info_list 1 raw_dependencies) 25 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 26 | set(dependencies_list ${dependencies}) 27 | 28 | mitkFunctionCreateCommandLineApp( 29 | NAME ${appname} 30 | DEPENDS MitkDiffusionCmdApps MitkFiberProcessing ${dependencies_list} 31 | PACKAGE_DEPENDS 32 | ) 33 | endforeach() 34 | 35 | if(EXECUTABLE_IS_ENABLED) 36 | MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) 37 | endif() 38 | 39 | endif() 40 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/Fiberfox/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionFiberfoxCmdApps "Build commandline tools for diffusion data simulation (Fiberfox)" OFF) 2 | 3 | if(BUILD_DiffusionFiberfoxCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusionFiberfoxcmdapps 15 | Fiberfox^^ 16 | RandomFiberPhantom^^ 17 | ) 18 | 19 | foreach(diffusionFiberfoxcmdapp ${diffusionFiberfoxcmdapps}) 20 | # extract cmd app name and dependencies 21 | string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberfoxcmdapp}) 22 | set(cmdapp_info_list ${cmdapp_info}) 23 | list(GET cmdapp_info_list 0 appname) 24 | list(GET cmdapp_info_list 1 raw_dependencies) 25 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 26 | set(dependencies_list ${dependencies}) 27 | 28 | mitkFunctionCreateCommandLineApp( 29 | NAME ${appname} 30 | DEPENDS MitkDiffusionCmdApps MitkMriSimulation ${dependencies_list} 31 | PACKAGE_DEPENDS 32 | ) 33 | endforeach() 34 | 35 | if(EXECUTABLE_IS_ENABLED) 36 | MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) 37 | endif() 38 | 39 | endif() 40 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/IVIM/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionIVIMCmdApps "Build commandline tools for diffusion IVIM and Kurtosis" OFF) 2 | 3 | if(BUILD_DiffusionIVIMCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusionIVIMcmdapps 15 | DiffusionKurtosisFit^^ 16 | DiffusionIvimFit^^ 17 | ) 18 | 19 | foreach(app ${diffusionIVIMcmdapps}) 20 | # extract cmd app name and dependencies 21 | string(REPLACE "^^" "\\;" cmdapp_info ${app}) 22 | set(cmdapp_info_list ${cmdapp_info}) 23 | list(GET cmdapp_info_list 0 appname) 24 | list(GET cmdapp_info_list 1 raw_dependencies) 25 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 26 | set(dependencies_list ${dependencies}) 27 | 28 | mitkFunctionCreateCommandLineApp( 29 | NAME ${appname} 30 | DEPENDS MitkDiffusionCmdApps MitkIVIM ${dependencies_list} 31 | PACKAGE_DEPENDS 32 | ) 33 | endforeach() 34 | 35 | endif() 36 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/ImageQuantification/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionQuantificationCmdApps "Build commandline tools for diffusion quantification (FA, ADC, ...)" OFF) 2 | 3 | if(BUILD_DiffusionQuantificationCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusionQuantificationcmdapps 15 | DiffusionIndices^^ 16 | QballReconstruction^^ 17 | TensorReconstruction^^ 18 | MultishellMethods^^ 19 | ) 20 | 21 | foreach(diffusionQuantificationcmdapp ${diffusionQuantificationcmdapps}) 22 | # extract cmd app name and dependencies 23 | string(REPLACE "^^" "\\;" cmdapp_info ${diffusionQuantificationcmdapp}) 24 | set(cmdapp_info_list ${cmdapp_info}) 25 | list(GET cmdapp_info_list 0 appname) 26 | list(GET cmdapp_info_list 1 raw_dependencies) 27 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 28 | set(dependencies_list ${dependencies}) 29 | 30 | mitkFunctionCreateCommandLineApp( 31 | NAME ${appname} 32 | DEPENDS MitkDiffusionCmdApps MitkDiffusionModelling MitkDiffusionPreprocessing ${dependencies_list} 33 | PACKAGE_DEPENDS 34 | ITK|ITKIONRRD+ITKIONIFTI 35 | ) 36 | endforeach() 37 | 38 | endif() 39 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/Misc/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionMiscCmdApps "Build miscellaneous commandline tools for diffusion" OFF) 2 | 3 | if(BUILD_DiffusionMiscCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusionMisccmdapps 15 | FileFormatConverter^^ 16 | ImageResampler^^ 17 | CopyGeometry^^ 18 | DiffusionDICOMLoader^^ 19 | ShToOdfImage^^ 20 | DImp^^ 21 | DReg^^ 22 | FiberScreenshot^^ 23 | PeakExtraction^^ 24 | ) 25 | 26 | foreach(diffusionMisccmdapp ${diffusionMisccmdapps}) 27 | # extract cmd app name and dependencies 28 | string(REPLACE "^^" "\\;" cmdapp_info ${diffusionMisccmdapp}) 29 | set(cmdapp_info_list ${cmdapp_info}) 30 | list(GET cmdapp_info_list 0 appname) 31 | list(GET cmdapp_info_list 1 raw_dependencies) 32 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 33 | set(dependencies_list ${dependencies}) 34 | 35 | mitkFunctionCreateCommandLineApp( 36 | NAME ${appname} 37 | DEPENDS MitkDiffusionCmdApps MitkDiffusionRegistration MitkDiffusionModelling MitkFiberBundle MitkTestingHelper ${dependencies_list} 38 | PACKAGE_DEPENDS 39 | ) 40 | endforeach() 41 | 42 | endif() 43 | 44 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/Tractography/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_DiffusionTractographyCmdApps "Build commandline tools for diffusion fiber tractography" OFF) 2 | 3 | if(BUILD_DiffusionTractographyCmdApps OR MITK_BUILD_ALL_APPS) 4 | 5 | # needed include directories 6 | include_directories( 7 | ${CMAKE_CURRENT_SOURCE_DIR} 8 | ${CMAKE_CURRENT_BINARY_DIR} 9 | ) 10 | 11 | # list of diffusion cmdapps 12 | # if an app requires additional dependencies 13 | # they are added after a "^^" and separated by "_" 14 | set( diffusiontractographycmdapps 15 | StreamlineTractography^^ 16 | GlobalTractography^^ 17 | ) 18 | 19 | foreach(diffusiontractographycmdapp ${diffusiontractographycmdapps}) 20 | # extract cmd app name and dependencies 21 | string(REPLACE "^^" "\\;" cmdapp_info ${diffusiontractographycmdapp}) 22 | set(cmdapp_info_list ${cmdapp_info}) 23 | list(GET cmdapp_info_list 0 appname) 24 | list(GET cmdapp_info_list 1 raw_dependencies) 25 | string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") 26 | set(dependencies_list ${dependencies}) 27 | 28 | mitkFunctionCreateCommandLineApp( 29 | NAME ${appname} 30 | DEPENDS MitkDiffusionCmdApps MitkFiberTracking ${dependencies_list} 31 | PACKAGE_DEPENDS 32 | ) 33 | endforeach() 34 | 35 | if(EXECUTABLE_IS_ENABLED) 36 | MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) 37 | endif() 38 | 39 | endif() 40 | -------------------------------------------------------------------------------- /Modules/DiffusionCmdApps/files.cmake: -------------------------------------------------------------------------------- 1 | set(CPP_FILES 2 | mitkDiffusionDataIOHelper.cpp 3 | ) 4 | 5 | set(H_FILES 6 | mitkDiffusionDataIOHelper.h 7 | ) 8 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE( 2 | SUBPROJECTS MITK-Diffusion 3 | INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} Properties IO IO/DicomImport Modification 4 | DEPENDS MitkCore MitkSceneSerializationBase MitkDICOM 5 | PACKAGE_DEPENDS 6 | ITK|ITKIONRRD+ITKIOGDCM+ITKIOBruker+ITKIONIFTI 7 | ) 8 | 9 | # if(TARGET ${MODULE_TARGET} AND MITK_USE_OpenMP) 10 | # target_link_libraries(${MODULE_TARGET} PUBLIC OpenMP::OpenMP_CXX) 11 | # endif() 12 | 13 | add_subdirectory(Testing) 14 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h: -------------------------------------------------------------------------------- 1 | #ifndef MITKDIFFUSIONHEADERGEDICOMFILEREADER_H 2 | #define MITKDIFFUSIONHEADERGEDICOMFILEREADER_H 3 | 4 | #include 5 | #include "mitkDiffusionHeaderDICOMFileReader.h" 6 | 7 | namespace mitk 8 | { 9 | 10 | class MITKDIFFUSIONIMAGE_EXPORT DiffusionHeaderGEDICOMFileReader 11 | : public DiffusionHeaderDICOMFileReader 12 | { 13 | public: 14 | 15 | mitkClassMacro( DiffusionHeaderGEDICOMFileReader, DiffusionHeaderDICOMFileReader ) 16 | itkNewMacro( Self ) 17 | 18 | bool ReadDiffusionHeader(std::string filename) override; 19 | 20 | protected: 21 | DiffusionHeaderGEDICOMFileReader(); 22 | 23 | ~DiffusionHeaderGEDICOMFileReader() override; 24 | }; 25 | 26 | } 27 | 28 | #endif // MITKDIFFUSIONHEADERGEDICOMFILEREADER_H 29 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H 18 | #define MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H 19 | 20 | #include 21 | #include "mitkDiffusionHeaderDICOMFileReader.h" 22 | 23 | namespace mitk 24 | { 25 | 26 | class MITKDIFFUSIONIMAGE_EXPORT DiffusionHeaderPhilipsDICOMFileReader 27 | : public DiffusionHeaderDICOMFileReader 28 | { 29 | public: 30 | 31 | mitkClassMacro( DiffusionHeaderPhilipsDICOMFileReader, DiffusionHeaderDICOMFileReader ) 32 | itkNewMacro( Self ) 33 | 34 | bool ReadDiffusionHeader(std::string filename) override; 35 | 36 | protected: 37 | DiffusionHeaderPhilipsDICOMFileReader(); 38 | 39 | ~DiffusionHeaderPhilipsDICOMFileReader() override; 40 | }; 41 | 42 | } 43 | 44 | #endif // MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H 45 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp: -------------------------------------------------------------------------------- 1 | #include "mitkDiffusionHeaderSiemensDICOMFileHelper.h" 2 | 3 | #include 4 | #include 5 | 6 | mitk::SiemensDiffusionHeaderType mitk::GetHeaderType( std::string header ) 7 | { 8 | // The CSA2 format begins with the string ‘SV10’, the CSA1 format does not. 9 | if( header.find("SV10") != std::string::npos ) 10 | { 11 | return mitk::SIEMENS_CSA2; 12 | } 13 | else 14 | { 15 | return mitk::SIEMENS_CSA1; 16 | } 17 | } 18 | 19 | bool mitk::ParseInputString( std::string input, std::vector& values, Siemens_Header_Format format_specs ) 20 | { 21 | // TODO : Compute offset based on the format_specs, where does the 84 come from??? 22 | int offset = 84; 23 | int vm = *(input.c_str() + format_specs.NameLength ); 24 | 25 | for (int k = 0; k < vm; k++) 26 | { 27 | int itemLength = *(input.c_str() + offset + 4); 28 | 29 | int strideSize = static_cast (ceil(static_cast(itemLength)/4) * 4); 30 | std::string valueString = input.substr( offset+16, itemLength ); 31 | 32 | double value = atof( valueString.c_str() ); 33 | values.push_back( value ); 34 | 35 | offset += 16+strideSize; 36 | } 37 | 38 | // If there are no values it is invalid 39 | return (values.size() > 0 ); 40 | } 41 | 42 | 43 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h: -------------------------------------------------------------------------------- 1 | #ifndef MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H 2 | #define MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H 3 | 4 | #include 5 | #include 6 | 7 | namespace mitk 8 | { 9 | 10 | enum SiemensDiffusionHeaderType { 11 | SIEMENS_CSA1 = 0, 12 | SIEMENS_CSA2 13 | }; 14 | 15 | SiemensDiffusionHeaderType GetHeaderType( std::string header ); 16 | 17 | struct Siemens_Header_Format 18 | { 19 | Siemens_Header_Format( size_t nlen, 20 | size_t vm, 21 | size_t vr, 22 | size_t syngodt, 23 | size_t nitems ) 24 | : NameLength( nlen ), 25 | Delimiter( "\0" ), 26 | VM( vm ), 27 | VR( vr ), 28 | Syngodt( syngodt ), 29 | NumItems( nitems ) 30 | { 31 | 32 | } 33 | 34 | size_t NameLength; 35 | std::string Delimiter; 36 | size_t VM; 37 | size_t VR; 38 | size_t Syngodt; 39 | size_t NumItems; 40 | }; 41 | 42 | bool ParseInputString( std::string input, std::vector& values, Siemens_Header_Format format_specs ); 43 | 44 | } //end namespace 45 | #endif // MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H 46 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H 18 | #define MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H 19 | 20 | #include 21 | 22 | #include "mitkDiffusionHeaderDICOMFileReader.h" 23 | #include "mitkDiffusionHeaderSiemensDICOMFileHelper.h" 24 | 25 | namespace mitk 26 | { 27 | 28 | class MITKDIFFUSIONIMAGE_EXPORT DiffusionHeaderSiemensDICOMFileReader 29 | : public DiffusionHeaderDICOMFileReader 30 | { 31 | public: 32 | 33 | mitkClassMacro( DiffusionHeaderSiemensDICOMFileReader, DiffusionHeaderDICOMFileReader ) 34 | itkNewMacro( Self ) 35 | 36 | bool ReadDiffusionHeader(std::string filename) override; 37 | 38 | protected: 39 | DiffusionHeaderSiemensDICOMFileReader(); 40 | 41 | ~DiffusionHeaderSiemensDICOMFileReader() override; 42 | 43 | bool ExtractSiemensDiffusionTagInformation( std::string tag_value, mitk::DiffusionImageDICOMHeaderInformation& values ); 44 | 45 | std::vector< Siemens_Header_Format > m_SiemensFormatsCollection; 46 | }; 47 | 48 | } 49 | #endif // MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H 50 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef __mitkGEDicomDiffusionImageHeaderReader_h__ 19 | #define __mitkGEDicomDiffusionImageHeaderReader_h__ 20 | 21 | #include "mitkDicomDiffusionImageHeaderReader.h" 22 | 23 | namespace mitk 24 | { 25 | 26 | class GEDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader 27 | { 28 | public: 29 | 30 | mitkClassMacro( GEDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | 34 | void Update() override; 35 | 36 | protected: 37 | 38 | GEDicomDiffusionImageHeaderReader(); 39 | ~GEDicomDiffusionImageHeaderReader() override; 40 | 41 | }; 42 | 43 | } 44 | 45 | #endif 46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #include "mitkPhilipsDicomDiffusionImageHeaderReader.h" 19 | 20 | mitk::PhilipsDicomDiffusionImageHeaderReader::PhilipsDicomDiffusionImageHeaderReader() 21 | { 22 | } 23 | 24 | mitk::PhilipsDicomDiffusionImageHeaderReader::~PhilipsDicomDiffusionImageHeaderReader() 25 | { 26 | } 27 | 28 | // do the work 29 | void mitk::PhilipsDicomDiffusionImageHeaderReader::Update() 30 | { 31 | 32 | // check if there are filenames 33 | if(m_DicomFilenames.size()) 34 | { 35 | ReadPublicTags(); 36 | 37 | ReadPublicTags2(); 38 | 39 | TransformGradients(); 40 | 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/IO/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef __mitkPhilipsDicomDiffusionImageHeaderReader_h__ 19 | #define __mitkPhilipsDicomDiffusionImageHeaderReader_h__ 20 | 21 | #include "mitkDicomDiffusionImageHeaderReader.h" 22 | 23 | namespace mitk 24 | { 25 | /** 26 | @brief The PhilipsDicomDiffusionImageHeaderReader class reads in the image header information for the Philips DICOM Format */ 27 | class PhilipsDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader 28 | { 29 | public: 30 | 31 | mitkClassMacro( PhilipsDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader ); 32 | itkFactorylessNewMacro(Self) 33 | itkCloneMacro(Self) 34 | 35 | /** read in the data */ 36 | void Update() override; 37 | 38 | protected: 39 | 40 | /** Default c'tor */ 41 | PhilipsDicomDiffusionImageHeaderReader(); 42 | 43 | /** Default d'tor */ 44 | ~PhilipsDicomDiffusionImageHeaderReader() override; 45 | 46 | }; 47 | 48 | } 49 | 50 | #endif 51 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/Properties/mitkNodePredicateIsDWI.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkNodePredicateIsDWI.h" 18 | #include "mitkDataNode.h" 19 | #include 20 | 21 | mitk::NodePredicateIsDWI::NodePredicateIsDWI() 22 | : NodePredicateBase() 23 | { 24 | } 25 | 26 | mitk::NodePredicateIsDWI::~NodePredicateIsDWI() 27 | { 28 | } 29 | 30 | 31 | bool mitk::NodePredicateIsDWI::CheckNode(const mitk::DataNode* node) const 32 | { 33 | if (node == nullptr) 34 | throw std::invalid_argument("NodePredicateIsDWI: invalid node"); 35 | 36 | mitk::Image* image = dynamic_cast(node->GetData()); 37 | 38 | return mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( image ); 39 | } 40 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkDiffusionPropertySerializerTest mitkDiffusionPropertySerializerTest) 4 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | set(MODULE_CUSTOM_TESTS 2 | mitkDiffusionPropertySerializerTest.cpp 3 | ) 4 | 5 | -------------------------------------------------------------------------------- /Modules/DiffusionImage/mitkDiffusionImageHeaderInformation.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkDiffusionImageHeaderInformation.h" 18 | 19 | mitk::DiffusionImageHeaderInformation::DiffusionImageHeaderInformation() 20 | { 21 | 22 | } 23 | 24 | mitk::DiffusionImageHeaderInformation::~DiffusionImageHeaderInformation() 25 | { 26 | 27 | } 28 | 29 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/Algorithms/Reconstruction/itkPointShell.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __itkPointShell_h__ 18 | #define __itkPointShell_h__ 19 | 20 | 21 | namespace itk 22 | { 23 | // generate by n-fold subdivisions of an icosahedron 24 | template 25 | class PointShell 26 | { 27 | public: 28 | static TMatrixType *DistributePointShell(); 29 | }; 30 | 31 | template 32 | class ThreeLayerPointShell 33 | { 34 | public: 35 | static TMatrixTypeshell1 *DistributePointShell1(); 36 | static TMatrixTypeshell2 *DistributePointShell2(); 37 | static TMatrixTypeshell3 *DistributePointShell3(); 38 | }; 39 | 40 | } 41 | 42 | #ifndef ITK_MANUAL_INSTANTIATION 43 | #include "itkPointShell.txx" 44 | #endif 45 | 46 | #endif //__itkPointShell_h__ 47 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_DiffusionModelling "" OFF) 2 | 3 | if(BUILD_MODULE_DiffusionModelling) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS Algorithms Algorithms/Reconstruction Algorithms/Reconstruction/MultishellProcessing IO Rendering ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkDiffusionImage MitkMapperExt 9 | PACKAGE_DEPENDS 10 | VTK|FiltersProgrammable ITK|ITKIONRRD+ITKIONIFTI 11 | ) 12 | 13 | #if(MSVC) 14 | # mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) 15 | #endif() 16 | 17 | add_subdirectory(Testing) 18 | 19 | endif() 20 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkNrrdOdfImageReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkNrrdOdfImageReader_h 18 | #define __mitkNrrdOdfImageReader_h 19 | 20 | #include "mitkCommon.h" 21 | #include "itkVectorContainer.h" 22 | #include "vnl/vnl_vector_fixed.h" 23 | #include "mitkOdfImage.h" 24 | #include "itkVectorImage.h" 25 | #include 26 | #include 27 | #include 28 | 29 | namespace mitk 30 | { 31 | 32 | /** \brief 33 | */ 34 | 35 | class NrrdOdfImageReader : public mitk::AbstractFileReader 36 | { 37 | public: 38 | 39 | typedef mitk::OdfImage OutputType; 40 | 41 | NrrdOdfImageReader(const NrrdOdfImageReader& other); 42 | NrrdOdfImageReader(); 43 | ~NrrdOdfImageReader() override; 44 | 45 | using AbstractFileReader::DoRead; 46 | std::vector > DoRead() override; 47 | 48 | protected: 49 | 50 | 51 | private: 52 | private: 53 | NrrdOdfImageReader* Clone() const override; 54 | 55 | us::ServiceRegistration m_ServiceReg; 56 | }; 57 | 58 | } //namespace MITK 59 | 60 | #endif // __mitkNrrdOdfImageReader_h 61 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkNrrdOdfImageWriter.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef _MITK_NRRDODF_WRITER__H_ 18 | #define _MITK_NRRDODF_WRITER__H_ 19 | 20 | #include 21 | #include 22 | 23 | 24 | namespace mitk 25 | { 26 | 27 | /** 28 | * Writes diffusion volumes to a file 29 | * @ingroup Process 30 | */ 31 | class NrrdOdfImageWriter : public mitk::AbstractFileWriter 32 | { 33 | public: 34 | 35 | typedef mitk::OdfImage InputType; 36 | 37 | NrrdOdfImageWriter(); 38 | ~NrrdOdfImageWriter() override; 39 | 40 | using AbstractFileWriter::Write; 41 | void Write() override; 42 | 43 | ConfidenceLevel GetConfidenceLevel() const override; 44 | 45 | protected: 46 | 47 | NrrdOdfImageWriter(const NrrdOdfImageWriter& other); 48 | mitk::NrrdOdfImageWriter* Clone() const override; 49 | }; 50 | 51 | 52 | } // end of namespace mitk 53 | 54 | #endif //_MITK_NRRDODF_WRITER__H_ 55 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkNrrdTensorImageWriter.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef _MITK_NRRDDTI_WRITER__H_ 18 | #define _MITK_NRRDDTI_WRITER__H_ 19 | 20 | #include 21 | #include 22 | 23 | 24 | namespace mitk 25 | { 26 | 27 | /** 28 | * Writes diffusion volumes to a file 29 | * @ingroup Process 30 | */ 31 | class NrrdTensorImageWriter : public mitk::AbstractFileWriter 32 | { 33 | public: 34 | 35 | typedef mitk::TensorImage InputType; 36 | 37 | NrrdTensorImageWriter(); 38 | ~NrrdTensorImageWriter() override; 39 | 40 | using AbstractFileWriter::Write; 41 | void Write() override; 42 | 43 | ConfidenceLevel GetConfidenceLevel() const override; 44 | 45 | protected: 46 | 47 | NrrdTensorImageWriter(const NrrdTensorImageWriter& other); 48 | mitk::NrrdTensorImageWriter* Clone() const override; 49 | }; 50 | 51 | 52 | } // end of namespace mitk 53 | 54 | #endif //_MITK_NRRDDTI_WRITER__H_ 55 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkOdfImageSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkOdfImageSerializer_h_included 18 | #define mitkOdfImageSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::Surface for mitk::SceneIO 26 | */ 27 | class OdfImageSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( OdfImageSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | OdfImageSerializer(); 36 | ~OdfImageSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkPeakImageReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkPeakImageReader_h 18 | #define __mitkPeakImageReader_h 19 | 20 | #include "mitkCommon.h" 21 | #include 22 | #include 23 | #include 24 | 25 | namespace mitk 26 | { 27 | 28 | /** \brief 29 | */ 30 | 31 | class PeakImageReader : public mitk::AbstractFileReader 32 | { 33 | public: 34 | 35 | PeakImageReader(const PeakImageReader& other); 36 | PeakImageReader(); 37 | ~PeakImageReader() override; 38 | 39 | using AbstractFileReader::DoRead; 40 | std::vector > DoRead() override; 41 | 42 | protected: 43 | 44 | 45 | private: 46 | PeakImageReader* Clone() const override; 47 | 48 | us::ServiceRegistration m_ServiceReg; 49 | }; 50 | 51 | } //namespace MITK 52 | 53 | #endif // __mitkPeakImageReader_h 54 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkPeakImageSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkPeakImageSerializer_h_included 18 | #define mitkPeakImageSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::Surface for mitk::SceneIO 26 | */ 27 | class PeakImageSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( PeakImageSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | PeakImageSerializer(); 36 | ~PeakImageSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkShImageSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkShImageSerializer_h_included 18 | #define mitkShImageSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::Surface for mitk::SceneIO 26 | */ 27 | class ShImageSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( ShImageSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | ShImageSerializer(); 36 | ~ShImageSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkShImageWriter.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef _MITK_SH_WRITER__H_ 18 | #define _MITK_SH_WRITER__H_ 19 | 20 | #include 21 | #include 22 | 23 | 24 | namespace mitk 25 | { 26 | 27 | /** 28 | * Writes diffusion volumes to a file 29 | * @ingroup Process 30 | */ 31 | class ShImageWriter : public mitk::AbstractFileWriter 32 | { 33 | public: 34 | 35 | typedef itk::VectorImage VecImgType; 36 | typedef mitk::ShImage InputType; 37 | 38 | ShImageWriter(); 39 | ~ShImageWriter() override; 40 | 41 | using AbstractFileWriter::Write; 42 | void Write() override; 43 | 44 | ConfidenceLevel GetConfidenceLevel() const override; 45 | 46 | protected: 47 | 48 | ShImageWriter(const ShImageWriter& other); 49 | mitk::ShImageWriter* Clone() const override; 50 | 51 | template 52 | void WriteShImage(InputType::ConstPointer input); 53 | }; 54 | 55 | 56 | } // end of namespace mitk 57 | 58 | #endif //_MITK_NRRDODF_WRITER__H_ 59 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/IO/mitkTensorImageSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkTensorImageSerializer_h_included 18 | #define mitkTensorImageSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::Surface for mitk::SceneIO 26 | */ 27 | class TensorImageSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( TensorImageSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | TensorImageSerializer(); 36 | ~TensorImageSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/Rendering/mitkCompositeMapper.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | 19 | #include "mitkCompositeMapper.h" 20 | 21 | 22 | mitk::CompositeMapper::CompositeMapper() 23 | { 24 | m_OdfMapper = mitk::OdfVtkMapper2D::New(); 25 | m_ImgMapper = mitk::CopyImageMapper2D::New(); 26 | } 27 | 28 | mitk::CompositeMapper::~CompositeMapper() 29 | { 30 | } 31 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkPeakShImageReaderTest mitkPeakShImageReaderTest) 4 | mitkAddCustomModuleTest(mitkImageReconstructionTest mitkImageReconstructionTest) 5 | -------------------------------------------------------------------------------- /Modules/DiffusionModelling/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | set(MODULE_CUSTOM_TESTS 2 | mitkImageReconstructionTest.cpp 3 | mitkPeakShImageReaderTest.cpp 4 | ) 5 | 6 | -------------------------------------------------------------------------------- /Modules/DiffusionPreprocessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_DiffusionPreprocessing "" OFF) 2 | 3 | if(BUILD_MODULE_DiffusionPreprocessing) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkDiffusionImage 9 | ) 10 | 11 | add_subdirectory(Testing) 12 | 13 | endif() 14 | -------------------------------------------------------------------------------- /Modules/DiffusionPreprocessing/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkNonLocalMeansDenoisingTest mitkNonLocalMeansDenoisingTest) 4 | -------------------------------------------------------------------------------- /Modules/DiffusionPreprocessing/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | set(MODULE_CUSTOM_TESTS 2 | mitkNonLocalMeansDenoisingTest.cpp 3 | ) 4 | 5 | -------------------------------------------------------------------------------- /Modules/DiffusionPreprocessing/files.cmake: -------------------------------------------------------------------------------- 1 | set(H_FILES 2 | 3 | itkB0ImageExtractionImageFilter.h 4 | itkB0ImageExtractionToSeparateImageFilter.h 5 | itkExtractDwiChannelFilter.h 6 | 7 | itkElectrostaticRepulsionDiffusionGradientReductionFilter.h 8 | itkMergeDiffusionImagesFilter.h 9 | itkResampleDwiImageFilter.h 10 | itkDwiGradientLengthCorrectionFilter.h 11 | itkDwiNormilzationFilter.h 12 | itkRemoveDwiChannelFilter.h 13 | itkNonLocalMeansDenoisingFilter.h 14 | itkVectorImageToImageFilter.h 15 | ) 16 | 17 | set(CPP_FILES 18 | 19 | itkB0ImageExtractionImageFilter.txx 20 | itkB0ImageExtractionToSeparateImageFilter.txx 21 | itkExtractDwiChannelFilter.txx 22 | 23 | itkDwiGradientLengthCorrectionFilter.cpp 24 | ) 25 | 26 | set(RESOURCE_FILES 27 | 28 | ) 29 | -------------------------------------------------------------------------------- /Modules/DiffusionRegistration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_DiffusionRegistration "" OFF) 2 | 3 | if(BUILD_MODULE_DiffusionRegistration) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkDiffusionPreprocessing MitkMatchPointRegistration 9 | ) 10 | 11 | add_subdirectory(Testing) 12 | 13 | endif() 14 | -------------------------------------------------------------------------------- /Modules/DiffusionRegistration/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | -------------------------------------------------------------------------------- /Modules/DiffusionRegistration/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | SET(MODULE_CUSTOM_TESTS 2 | mitkDWHeadMotionCorrectionTest.cpp 3 | mitkPyramidImageRegistrationMethodTest.cpp 4 | ) 5 | 6 | 7 | -------------------------------------------------------------------------------- /Modules/DiffusionRegistration/files.cmake: -------------------------------------------------------------------------------- 1 | set(H_FILES 2 | mitkRegistrationWrapper.h 3 | mitkPyramidImageRegistrationMethod.h 4 | mitkDWIHeadMotionCorrectionFilter.h 5 | mitkDiffusionImageCorrectionFilter.h 6 | mitkPyramidRegistrationMethodHelper.h 7 | itkSplitDWImageFilter.h 8 | ) 9 | 10 | set(CPP_FILES 11 | mitkRegistrationWrapper.cpp 12 | mitkPyramidImageRegistrationMethod.cpp 13 | mitkDWIHeadMotionCorrectionFilter.cpp 14 | mitkDiffusionImageCorrectionFilter.cpp 15 | itkSplitDWImageFilter.txx 16 | ) 17 | 18 | set(RESOURCE_FILES 19 | 20 | ) 21 | -------------------------------------------------------------------------------- /Modules/FiberBundle/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_FiberBundle "" OFF) 2 | 3 | if(BUILD_MODULE_FiberBundle) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} IO Rendering 8 | DEPENDS MitkPlanarFigure MitkDICOM MitkDiffusionModelling 9 | PACKAGE_DEPENDS 10 | DCMTK|dcmtract VTK|CommonComputationalGeometry ITK|ITKIONRRD+ITKIONIFTI 11 | ) 12 | 13 | add_subdirectory(Testing) 14 | 15 | endif() 16 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleDicomReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleDicomReader_h 18 | #define __mitkFiberBundleDicomReader_h 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | 25 | #include 26 | 27 | namespace mitk 28 | { 29 | 30 | /** \brief 31 | */ 32 | 33 | class FiberBundleDicomReader : public AbstractFileReader 34 | { 35 | public: 36 | 37 | FiberBundleDicomReader(); 38 | ~FiberBundleDicomReader() override{} 39 | FiberBundleDicomReader(const FiberBundleDicomReader& other); 40 | FiberBundleDicomReader * Clone() const override; 41 | 42 | using mitk::AbstractFileReader::DoRead; 43 | std::vector > DoRead() override; 44 | 45 | private: 46 | 47 | us::ServiceRegistration m_ServiceReg; 48 | }; 49 | 50 | } //namespace MITK 51 | 52 | #endif // __mitkFiberBundleReader_h 53 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleDicomWriter.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleDicomWriter_h 18 | #define __mitkFiberBundleDicomWriter_h 19 | 20 | #include 21 | #include "mitkFiberBundle.h" 22 | 23 | namespace mitk 24 | { 25 | 26 | /** 27 | * Writes fiber bundles to a DICOM file 28 | * @ingroup Process 29 | */ 30 | class FiberBundleDicomWriter : public mitk::AbstractFileWriter 31 | { 32 | public: 33 | 34 | 35 | FiberBundleDicomWriter(); 36 | FiberBundleDicomWriter(const FiberBundleDicomWriter & other); 37 | FiberBundleDicomWriter * Clone() const override; 38 | ~FiberBundleDicomWriter() override; 39 | 40 | using mitk::AbstractFileWriter::Write; 41 | void Write() override; 42 | }; 43 | 44 | 45 | } // end of namespace mitk 46 | 47 | #endif //__mitkFiberBundleWriter_h 48 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleIOHelper.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleIOHelper_h_ 18 | #define __mitkFiberBundleIOHelper_h_ 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | #include 25 | #include 26 | 27 | #include 28 | #include 29 | #include 30 | 31 | typedef itksys::SystemTools ist; 32 | 33 | namespace mitk{ 34 | 35 | class MITKFIBERBUNDLE_EXPORT FiberBundleIOHelper 36 | { 37 | public: 38 | 39 | static std::vector< std::string > get_file_list(const std::string& path, const std::vector< std::string > extensions={".fib", ".trk"}); 40 | 41 | static std::vector< mitk::FiberBundle::Pointer > load_fibs(const std::vector files, std::vector* filenames=nullptr); 42 | }; 43 | 44 | } 45 | 46 | #endif //__mitkFiberBundleIOHelper_h_ 47 | 48 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkFiberBundleSerializer_h_included 18 | #define mitkFiberBundleSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::Surface for mitk::SceneIO 26 | */ 27 | class FiberBundleSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( FiberBundleSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | FiberBundleSerializer(); 36 | ~FiberBundleSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleTckReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleTckReader_h 18 | #define __mitkFiberBundleTckReader_h 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | 25 | #include 26 | 27 | namespace mitk 28 | { 29 | 30 | /** \brief 31 | */ 32 | 33 | class FiberBundleTckReader : public AbstractFileReader 34 | { 35 | public: 36 | 37 | FiberBundleTckReader(); 38 | ~FiberBundleTckReader() override{} 39 | FiberBundleTckReader(const FiberBundleTckReader& other); 40 | FiberBundleTckReader * Clone() const override; 41 | 42 | using mitk::AbstractFileReader::DoRead; 43 | std::vector > DoRead() override; 44 | 45 | private: 46 | 47 | us::ServiceRegistration m_ServiceReg; 48 | }; 49 | 50 | } //namespace MITK 51 | 52 | #endif // __mitkFiberBundleReader_h 53 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleTrackVisReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleTrackVisReader_h 18 | #define __mitkFiberBundleTrackVisReader_h 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | 25 | #include 26 | 27 | namespace mitk 28 | { 29 | 30 | /** \brief 31 | */ 32 | 33 | class FiberBundleTrackVisReader : public AbstractFileReader 34 | { 35 | public: 36 | 37 | FiberBundleTrackVisReader(); 38 | ~FiberBundleTrackVisReader() override{} 39 | FiberBundleTrackVisReader(const FiberBundleTrackVisReader& other); 40 | FiberBundleTrackVisReader * Clone() const override; 41 | 42 | using mitk::AbstractFileReader::DoRead; 43 | std::vector > DoRead() override; 44 | 45 | private: 46 | 47 | us::ServiceRegistration m_ServiceReg; 48 | }; 49 | 50 | } //namespace MITK 51 | 52 | #endif // __mitkFiberBundleReader_h 53 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkFiberBundleVtkReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkFiberBundleVtkReader_h 18 | #define __mitkFiberBundleVtkReader_h 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | 25 | #include 26 | 27 | namespace mitk 28 | { 29 | 30 | /** \brief 31 | */ 32 | 33 | class FiberBundleVtkReader : public AbstractFileReader 34 | { 35 | public: 36 | 37 | FiberBundleVtkReader(); 38 | ~FiberBundleVtkReader() override{} 39 | FiberBundleVtkReader(const FiberBundleVtkReader& other); 40 | FiberBundleVtkReader * Clone() const override; 41 | 42 | using mitk::AbstractFileReader::DoRead; 43 | std::vector > DoRead() override; 44 | 45 | private: 46 | 47 | us::ServiceRegistration m_ServiceReg; 48 | }; 49 | 50 | } //namespace MITK 51 | 52 | #endif // __mitkFiberBundleReader_h 53 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkPlanarFigureCompositeReader.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkPlanarFigureCompositeReader_h 18 | #define __mitkPlanarFigureCompositeReader_h 19 | 20 | #include 21 | #include 22 | #include 23 | 24 | #include 25 | 26 | namespace mitk 27 | { 28 | 29 | /** \brief 30 | */ 31 | 32 | class PlanarFigureCompositeReader : public AbstractFileReader 33 | { 34 | public: 35 | 36 | PlanarFigureCompositeReader(); 37 | ~PlanarFigureCompositeReader() override{} 38 | PlanarFigureCompositeReader(const PlanarFigureCompositeReader& other); 39 | PlanarFigureCompositeReader * Clone() const override; 40 | 41 | using mitk::AbstractFileReader::DoRead; 42 | std::vector > DoRead() override; 43 | 44 | private: 45 | 46 | us::ServiceRegistration m_ServiceReg; 47 | }; 48 | 49 | } //namespace MITK 50 | 51 | #endif // __mitkFiberBundleReader_h 52 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkPlanarFigureCompositeSerializer.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef mitkPlanarFigureCompositeSerializer_h_included 18 | #define mitkPlanarFigureCompositeSerializer_h_included 19 | 20 | #include "mitkBaseDataSerializer.h" 21 | 22 | namespace mitk 23 | { 24 | /** 25 | \brief Serializes mitk::PlanarFigureComposite for mitk::SceneIO 26 | */ 27 | class PlanarFigureCompositeSerializer : public BaseDataSerializer 28 | { 29 | public: 30 | mitkClassMacro( PlanarFigureCompositeSerializer, BaseDataSerializer ); 31 | itkFactorylessNewMacro(Self) 32 | itkCloneMacro(Self) 33 | std::string Serialize() override; 34 | protected: 35 | PlanarFigureCompositeSerializer(); 36 | ~PlanarFigureCompositeSerializer() override; 37 | }; 38 | } // namespace 39 | #endif 40 | -------------------------------------------------------------------------------- /Modules/FiberBundle/IO/mitkPlanarFigureCompositeWriter.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef __mitkPlanarFigureCompositeWriter_h 18 | #define __mitkPlanarFigureCompositeWriter_h 19 | 20 | #include 21 | 22 | namespace mitk 23 | { 24 | 25 | /** 26 | * Writes fiber bundles to a file 27 | * @ingroup Process 28 | */ 29 | class PlanarFigureCompositeWriter : public mitk::AbstractFileWriter 30 | { 31 | public: 32 | 33 | 34 | PlanarFigureCompositeWriter(); 35 | PlanarFigureCompositeWriter(const PlanarFigureCompositeWriter & other); 36 | PlanarFigureCompositeWriter * Clone() const override; 37 | ~PlanarFigureCompositeWriter() override; 38 | 39 | using mitk::AbstractFileWriter::Write; 40 | void Write() override; 41 | 42 | }; 43 | 44 | 45 | } // end of namespace mitk 46 | 47 | #endif //__mitkFiberBundleWriter_h 48 | -------------------------------------------------------------------------------- /Modules/FiberBundle/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkFiberBundleReaderWriterTest mitkFiberBundleReaderWriterTest) 4 | 5 | # does not work reliably 6 | # mitkAddCustomModuleTest(mitkFiberMapper3DTest mitkFiberMapper3DTest) 7 | -------------------------------------------------------------------------------- /Modules/FiberBundle/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | SET(MODULE_CUSTOM_TESTS 2 | mitkFiberBundleReaderWriterTest.cpp 3 | mitkFiberMapper3DTest.cpp 4 | ) 5 | 6 | 7 | -------------------------------------------------------------------------------- /Modules/FiberBundle/mitkPlanarFigureComposite.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPlanarFigureComposite.h" 18 | 19 | 20 | mitk::PlanarFigureComposite::PlanarFigureComposite() 21 | { 22 | mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); 23 | this->SetGeometry(geometry); 24 | } 25 | 26 | mitk::PlanarFigureComposite::~PlanarFigureComposite() 27 | { 28 | 29 | } 30 | 31 | void mitk::PlanarFigureComposite::setOperationType(OperationType pfcOp) 32 | { 33 | this->m_compOperation = pfcOp; 34 | } 35 | 36 | 37 | mitk::PlanarFigureComposite::OperationType mitk::PlanarFigureComposite::getOperationType() const 38 | { 39 | return this->m_compOperation; 40 | } 41 | 42 | /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ 43 | 44 | void mitk::PlanarFigureComposite::SetRequestedRegionToLargestPossibleRegion() 45 | { 46 | 47 | } 48 | bool mitk::PlanarFigureComposite::RequestedRegionIsOutsideOfTheBufferedRegion() 49 | { 50 | return false; 51 | } 52 | bool mitk::PlanarFigureComposite::VerifyRequestedRegion() 53 | { 54 | return true; 55 | } 56 | void mitk::PlanarFigureComposite::SetRequestedRegion(const itk::DataObject* ) 57 | { 58 | 59 | } 60 | 61 | -------------------------------------------------------------------------------- /Modules/FiberDissection/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_FiberDissection "" OFF) 2 | 3 | if(BUILD_MODULE_FiberDissection) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS Interactor MachineLearning ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkMultilabel MitkFiberProcessing 9 | PACKAGE_DEPENDS 10 | PUBLIC OpenCV|opencv_ml 11 | ) 12 | 13 | endif() 14 | -------------------------------------------------------------------------------- /Modules/FiberDissection/MachineLearning/mitkStatisticModel.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkStatisticModel.h" 18 | 19 | 20 | 21 | 22 | mitk::StatisticModel::StatisticModel() 23 | { 24 | 25 | } 26 | 27 | mitk::StatisticModel::~StatisticModel() 28 | { 29 | 30 | } -------------------------------------------------------------------------------- /Modules/FiberDissection/MachineLearning/mitkStatisticModel.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef _MITK_StatisticModel_H 19 | #define _MITK_StatisticModel_H 20 | 21 | //includes for MITK datastructure 22 | #include 23 | #include 24 | #include 25 | 26 | //includes storing fiberdata 27 | #include 28 | 29 | // OpenCV 30 | #include 31 | #include 32 | #include 33 | 34 | 35 | namespace mitk { 36 | 37 | /** 38 | * \brief Base Class for Fiber Bundles; */ 39 | class MITKFIBERDISSECTION_EXPORT StatisticModel : public BaseData 40 | { 41 | public: 42 | 43 | 44 | // mitkClassMacro( StatisticModel, BaseData ) 45 | // itkFactorylessNewMacro(Self) 46 | // itkCloneMacro(Self) 47 | 48 | StatisticModel(); 49 | virtual ~StatisticModel(); 50 | 51 | // Member variable that represents the statistical model 52 | cv::Ptr m_StatModel; 53 | 54 | protected: 55 | 56 | 57 | private: 58 | 59 | }; 60 | 61 | } // namespace mitk 62 | 63 | #endif /* _MITK_StatisticModel_H */ 64 | -------------------------------------------------------------------------------- /Modules/FiberDissection/files.cmake: -------------------------------------------------------------------------------- 1 | set(H_FILES 2 | 3 | #Interactor 4 | Interactor/mitkSphereInteractor.h 5 | Interactor/mitkSphereSegmentationInteractor.h 6 | Interactor/mitkStreamlineInteractor.h 7 | Interactor/mitkStreamlineInteractorBrush.h 8 | 9 | #MachineLearning 10 | MachineLearning/mitkStreamlineFeatureExtractor.h 11 | 12 | MachineLearning/mitkStatisticModel.h 13 | ) 14 | 15 | set(CPP_FILES 16 | 17 | #Interactor 18 | Interactor/mitkSphereInteractor.cpp 19 | Interactor/mitkSphereSegmentationInteractor.cpp 20 | Interactor/mitkStreamlineInteractor.cpp 21 | Interactor/mitkStreamlineInteractorBrush.cpp 22 | 23 | #MachineLearning 24 | MachineLearning/mitkStreamlineFeatureExtractor.cpp 25 | 26 | MachineLearning/mitkStatisticModel.cpp 27 | ) 28 | 29 | set(RESOURCE_FILES 30 | # "Interactions" prefix forced by mitk::StateMachine 31 | 32 | Interactions/SphereSegmentationInteractionsStates.xml 33 | Interactions/SphereSegmentationInteractionsConfig.xml 34 | Interactions/SphereInteractionsStates.xml 35 | Interactions/SphereInteractionsConfig.xml 36 | Interactions/Streamline3DStates.xml 37 | Interactions/Streamline3DConfig.xml 38 | Interactions/StreamlineBrush3DStates.xml 39 | Interactions/StreamlineBrush3DConfig.xml 40 | ) 41 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/SphereInteractionsConfig.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 17 | 18 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/SphereInteractionsStates.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/SphereSegmentationInteractionsConfig.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 17 | 18 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/SphereSegmentationInteractionsStates.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/Streamline3DConfig.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/Streamline3DStates.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/StreamlineBrush3DConfig.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | addtolabelstreamline 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | -------------------------------------------------------------------------------- /Modules/FiberDissection/resource/Interactions/StreamlineBrush3DStates.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /Modules/FiberProcessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_FiberProcessing "" OFF) 2 | 3 | if(BUILD_MODULE_FiberProcessing) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS FiberClustering FiberDerivedImages FiberModification FiberQuantification ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkFiberBundle 9 | ) 10 | 11 | add_subdirectory(Testing) 12 | 13 | endif() 14 | -------------------------------------------------------------------------------- /Modules/FiberProcessing/FiberClustering/mitkClusteringMetric.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #ifndef _ClusteringMetric 18 | #define _ClusteringMetric 19 | 20 | #include 21 | 22 | namespace mitk 23 | { 24 | 25 | /** 26 | * \brief Base class for fiber clustering metrics */ 27 | 28 | class ClusteringMetric 29 | { 30 | 31 | public: 32 | 33 | ClusteringMetric() 34 | : m_Scale(1.0) 35 | {} 36 | virtual ~ClusteringMetric(){} 37 | 38 | virtual float CalculateDistance(vnl_matrix& s, vnl_matrix& t, bool &flipped) = 0; 39 | 40 | float GetScale() const 41 | { 42 | return m_Scale; 43 | } 44 | void SetScale(float Scale) 45 | { 46 | m_Scale = Scale; 47 | } 48 | 49 | protected: 50 | 51 | float m_Scale; 52 | 53 | }; 54 | 55 | } 56 | 57 | #endif 58 | -------------------------------------------------------------------------------- /Modules/FiberProcessing/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib) 4 | mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_subtracted.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_added.fib) 5 | mitkAddCustomModuleTest(mitkFiberProcessingTest mitkFiberProcessingTest) 6 | -------------------------------------------------------------------------------- /Modules/FiberProcessing/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | SET(MODULE_CUSTOM_TESTS 2 | mitkFiberTransformationTest.cpp 3 | mitkFiberExtractionTest.cpp 4 | mitkFiberProcessingTest.cpp 5 | ) 6 | 7 | 8 | -------------------------------------------------------------------------------- /Modules/FiberProcessing/files.cmake: -------------------------------------------------------------------------------- 1 | set(H_FILES 2 | FiberDerivedImages/itkTractDensityImageFilter.h 3 | FiberDerivedImages/itkTractsToVectorImageFilter.h 4 | FiberDerivedImages/itkTractsToFiberEndingsImageFilter.h 5 | FiberDerivedImages/itkTractsToRgbaImageFilter.h 6 | 7 | FiberModification/itkFiberCurvatureFilter.h 8 | FiberModification/itkFiberExtractionFilter.h 9 | 10 | FiberQuantification/itkDistanceFromSegmentationImageFilter.h 11 | 12 | # Clustering 13 | FiberClustering/mitkTractClusteringFilter.h 14 | FiberClustering/mitkClusteringMetric.h 15 | FiberClustering/mitkClusteringMetricEuclideanMean.h 16 | FiberClustering/mitkClusteringMetricEuclideanMax.h 17 | FiberClustering/mitkClusteringMetricEuclideanStd.h 18 | FiberClustering/mitkClusteringMetricAnatomic.h 19 | FiberClustering/mitkClusteringMetricScalarMap.h 20 | FiberClustering/mitkClusteringMetricInnerAngles.h 21 | FiberClustering/mitkClusteringMetricLength.h 22 | ) 23 | 24 | set(CPP_FILES 25 | FiberClustering/mitkTractClusteringFilter.cpp 26 | ) 27 | 28 | set(RESOURCE_FILES 29 | 30 | ) 31 | -------------------------------------------------------------------------------- /Modules/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkTrackingDataHandler.h" 18 | 19 | namespace mitk 20 | { 21 | TrackingDataHandler::TrackingDataHandler() 22 | : m_RngItk(ItkRngType::New()) 23 | , m_NeedsDataInit(true) 24 | { 25 | 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /Modules/FiberTracking/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_FiberTracking "" OFF) 2 | 3 | if(BUILD_MODULE_FiberTracking) 4 | 5 | set(_module_deps MitkFiberBundle) 6 | 7 | mitk_check_module_dependencies( 8 | MODULES ${_module_deps} 9 | MISSING_DEPENDENCIES_VAR _missing_deps 10 | ) 11 | 12 | if(NOT _missing_deps) 13 | 14 | set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz) 15 | set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz) 16 | file(DOWNLOAD ${lut_url} ${lut_tarball} 17 | EXPECTED_MD5 38ecb6d4a826c9ebb0f4965eb9aeee44 18 | TIMEOUT 60 19 | STATUS status 20 | SHOW_PROGRESS 21 | ) 22 | 23 | list(GET status 0 status_code) 24 | list(GET status 1 status_msg) 25 | 26 | if(NOT status_code EQUAL 0) 27 | message(SEND_ERROR "${status_msg} (error code ${status_code})") 28 | endif() 29 | 30 | file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources) 31 | execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ../FibertrackingLUT.tar.gz 32 | WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources 33 | RESULT_VARIABLE result 34 | ERROR_VARIABLE err_msg) 35 | if(result) 36 | message(SEND_ERROR "Unpacking FibertrackingLUT.tar.gz failed: ${err_msg}") 37 | endif() 38 | 39 | endif() 40 | 41 | MITK_CREATE_MODULE( 42 | SUBPROJECTS MITK-Diffusion 43 | INCLUDE_DIRS Algorithms Algorithms/TrackingHandlers Algorithms/GibbsTracking ${CMAKE_CURRENT_BINARY_DIR} 44 | DEPENDS ${_module_deps} 45 | ) 46 | 47 | add_subdirectory(Testing) 48 | 49 | endif() 50 | -------------------------------------------------------------------------------- /Modules/FiberTracking/Resources/empty: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Modules/FiberTracking/Resources/empty -------------------------------------------------------------------------------- /Modules/FiberTracking/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkStreamlineTractographyTest mitkStreamlineTractographyTest) 4 | mitkAddCustomModuleTest(mitkGlobalTractographyTest mitkGlobalTractographyTest) 5 | 6 | -------------------------------------------------------------------------------- /Modules/FiberTracking/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | SET(MODULE_CUSTOM_TESTS 2 | mitkGlobalTractographyTest.cpp 3 | mitkStreamlineTractographyTest.cpp 4 | ) 5 | 6 | 7 | -------------------------------------------------------------------------------- /Modules/IVIM/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_IVIM "" OFF) 2 | 3 | if(BUILD_MODULE_IVIM) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkDiffusionImage 9 | ) 10 | 11 | endif() 12 | -------------------------------------------------------------------------------- /Modules/IVIM/files.cmake: -------------------------------------------------------------------------------- 1 | set(H_FILES 2 | 3 | itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h 4 | itkDiffusionKurtosisReconstructionImageFilter.h 5 | itkRegularizedIVIMLocalVariationImageFilter.h 6 | itkRegularizedIVIMReconstructionFilter.h 7 | itkRegularizedIVIMReconstructionSingleIteration.h 8 | ) 9 | 10 | set(CPP_FILES 11 | itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp 12 | itkDiffusionKurtosisReconstructionImageFilter.cpp 13 | itkRegularizedIVIMLocalVariationImageFilter.txx 14 | itkRegularizedIVIMReconstructionFilter.txx 15 | itkRegularizedIVIMReconstructionSingleIteration.txx 16 | ) 17 | 18 | set(RESOURCE_FILES 19 | 20 | ) 21 | -------------------------------------------------------------------------------- /Modules/ModuleList.cmake: -------------------------------------------------------------------------------- 1 | set(MITK_MODULES 2 | DiffusionImage 3 | DiffusionPreprocessing 4 | DiffusionModelling 5 | DiffusionRegistration 6 | FiberBundle 7 | FiberProcessing 8 | FiberTracking 9 | MriSimulation 10 | FiberDissection 11 | IVIM 12 | DiffusionCmdApps 13 | ) 14 | -------------------------------------------------------------------------------- /Modules/MriSimulation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | option(BUILD_MODULE_MriSimulation "" OFF) 2 | 3 | if(BUILD_MODULE_MriSimulation) 4 | 5 | MITK_CREATE_MODULE( 6 | SUBPROJECTS MITK-Diffusion 7 | INCLUDE_DIRS SignalModels Sequences Algorithms ${CMAKE_CURRENT_BINARY_DIR} 8 | DEPENDS MitkFiberProcessing MitkDiffusionPreprocessing 9 | ) 10 | 11 | add_subdirectory(Testing) 12 | 13 | endif() 14 | -------------------------------------------------------------------------------- /Modules/MriSimulation/SignalModels/mitkChiSquareNoiseModel.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #include 17 | #include 18 | #include 19 | 20 | using namespace mitk; 21 | 22 | template< class ScalarType > 23 | ChiSquareNoiseModel< ScalarType >::ChiSquareNoiseModel() 24 | { 25 | m_RandGen.seed(); 26 | } 27 | 28 | template< class ScalarType > 29 | ChiSquareNoiseModel< ScalarType >::~ChiSquareNoiseModel() 30 | { 31 | 32 | } 33 | 34 | template< class ScalarType > 35 | void ChiSquareNoiseModel< ScalarType >::SetSeed(int seed) 36 | { 37 | if (seed>=0) 38 | m_RandGen.seed(seed); 39 | else 40 | m_RandGen.seed(); 41 | } 42 | 43 | template< class ScalarType > 44 | void ChiSquareNoiseModel< ScalarType >::AddNoise(PixelType& pixel) 45 | { 46 | for( unsigned int i=0; i 21 | #include 22 | #include 23 | #include 24 | 25 | namespace mitk { 26 | 27 | /** 28 | * \brief Abstract class for diffusion noise models 29 | * 30 | */ 31 | 32 | template< class ScalarType = double > 33 | class DiffusionNoiseModel 34 | { 35 | public: 36 | 37 | DiffusionNoiseModel(){} 38 | virtual ~DiffusionNoiseModel(){} 39 | 40 | typedef itk::VariableLengthVector< ScalarType > PixelType; 41 | 42 | /** Adds noise according to model to the input pixel. Has to be implemented in subclass. **/ 43 | virtual void AddNoise(PixelType& pixel) = 0; 44 | 45 | /** Seed for random generator. Has to be implemented in subclass. **/ 46 | virtual void SetSeed(int seed) = 0; 47 | 48 | virtual double GetNoiseVariance() = 0; 49 | virtual void SetNoiseVariance(double var) = 0; 50 | 51 | protected: 52 | 53 | }; 54 | 55 | } 56 | 57 | #endif 58 | 59 | -------------------------------------------------------------------------------- /Modules/MriSimulation/SignalModels/mitkDotModel.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #include 17 | #include 18 | #include 19 | 20 | using namespace mitk; 21 | 22 | template< class ScalarType > 23 | DotModel< ScalarType >::DotModel() 24 | { 25 | 26 | } 27 | 28 | template< class ScalarType > 29 | DotModel< ScalarType >::~DotModel() 30 | { 31 | 32 | } 33 | 34 | template< class ScalarType > 35 | ScalarType DotModel< ScalarType >::SimulateMeasurement(unsigned int /*dir*/, GradientType& ) 36 | { 37 | return 1; 38 | } 39 | 40 | template< class ScalarType > 41 | typename DotModel< ScalarType >::PixelType DotModel< ScalarType >::SimulateMeasurement(GradientType& ) 42 | { 43 | PixelType signal; 44 | signal.SetSize(this->m_GradientList.size()); 45 | signal.Fill(1); 46 | return signal; 47 | } 48 | -------------------------------------------------------------------------------- /Modules/MriSimulation/Testing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | MITK_CREATE_MODULE_TESTS() 2 | 3 | mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib) 4 | 5 | mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationBrainSliceTest mitkFiberfoxSignalGenerationBrainSliceTest) 6 | mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest) 7 | mitkAddCustomModuleTest(mitkFiberFitTest mitkFiberFitTest) 8 | -------------------------------------------------------------------------------- /Modules/MriSimulation/Testing/files.cmake: -------------------------------------------------------------------------------- 1 | SET(MODULE_CUSTOM_TESTS 2 | mitkFiberGenerationTest.cpp 3 | mitkFiberfoxSignalGenerationTest.cpp 4 | mitkFiberfoxSignalGenerationBrainSliceTest.cpp 5 | mitkFiberFitTest.cpp 6 | ) 7 | 8 | 9 | -------------------------------------------------------------------------------- /Modules/MriSimulation/files.cmake: -------------------------------------------------------------------------------- 1 | set(CPP_FILES 2 | 3 | mitkFiberfoxParameters.cpp 4 | ) 5 | 6 | set(H_FILES 7 | mitkFiberfoxParameters.h 8 | 9 | Algorithms/itkFitFibersToImageFilter.h 10 | Algorithms/itkFibersFromPlanarFiguresFilter.h 11 | Algorithms/itkTractsToDWIImageFilter.h 12 | Algorithms/itkKspaceImageFilter.h 13 | Algorithms/itkDftImageFilter.h 14 | Algorithms/itkFieldmapGeneratorFilter.h 15 | Algorithms/itkRandomPhantomFilter.h 16 | 17 | SignalModels/mitkDiffusionSignalModel.h 18 | SignalModels/mitkTensorModel.h 19 | SignalModels/mitkBallModel.h 20 | SignalModels/mitkDotModel.h 21 | SignalModels/mitkAstroStickModel.h 22 | SignalModels/mitkStickModel.h 23 | SignalModels/mitkRawShModel.h 24 | SignalModels/mitkDiffusionNoiseModel.h 25 | SignalModels/mitkRicianNoiseModel.h 26 | SignalModels/mitkChiSquareNoiseModel.h 27 | 28 | Sequences/mitkAcquisitionType.h 29 | Sequences/mitkSingleShotEpi.h 30 | Sequences/mitkConventionalSpinEcho.h 31 | Sequences/mitkFastSpinEcho.h 32 | ) 33 | -------------------------------------------------------------------------------- /Plugins/PluginList.cmake: -------------------------------------------------------------------------------- 1 | set(MITK_PLUGINS 2 | org.mitk.gui.qt.diffusionimaging.controls:OFF 3 | org.mitk.gui.qt.diffusionimaging.denoising:OFF 4 | org.mitk.gui.qt.diffusionimaging.fiberfox:OFF 5 | org.mitk.gui.qt.diffusionimaging.fiberprocessing:OFF 6 | org.mitk.gui.qt.diffusionimaging.fiberfit:OFF 7 | org.mitk.gui.qt.diffusionimaging.ivim:OFF 8 | org.mitk.gui.qt.diffusionimaging.preprocessing:OFF 9 | org.mitk.gui.qt.diffusionimaging.reconstruction:OFF 10 | org.mitk.gui.qt.diffusionimaging.registration:OFF 11 | org.mitk.gui.qt.diffusionimaging.tractography:OFF 12 | ) 13 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | project(org_mitk_gui_qt_diffusionimaging_controls) 2 | 3 | mitk_create_plugin( 4 | SUBPROJECTS MITK-Diffusion 5 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_EXPORT 6 | EXPORTED_INCLUDE_SUFFIXES src 7 | MODULE_DEPENDS MitkFiberBundle 8 | ) 9 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/documentation/UserManual/Data_CSD.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.controls/documentation/UserManual/Data_CSD.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/documentation/UserManual/Data_Tensors.png: 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Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Diffusion Imaging") 2 | set(Plugin-Version "0.1") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.common) 6 | #set(Plugin-ActivationPolicy eager) 7 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/resources/ConnectomicsNetwork.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.controls/resources/ConnectomicsNetwork.png 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===================================================================*/ 16 | 17 | 18 | #ifndef QmitkDiffusionDefaultPerspective_H_ 19 | #define QmitkDiffusionDefaultPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkDiffusionDefaultPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkDiffusionDefaultPerspective() {} 31 | ~QmitkDiffusionDefaultPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkDiffusionDefaultPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/src/internal/Perspectives/QmitkSegmentationPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkSegmentationPerspective_H_ 19 | #define QmitkSegmentationPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkSegmentationPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkSegmentationPerspective() {} 31 | ~QmitkSegmentationPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkSegmentationPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.controls/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk { 22 | 23 | class PluginActivator : 24 | public QObject, public ctkPluginActivator 25 | { 26 | Q_OBJECT 27 | Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_diffusionimaging_controls") 28 | Q_INTERFACES(ctkPluginActivator) 29 | 30 | public: 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | }; // PluginActivator 36 | 37 | } 38 | 39 | #endif // MITKPLUGINACTIVATOR_H 40 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_denoising) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_DENOISING_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkDiffusionPreprocessing MitkImageDenoising 10 | PACKAGE_DEPENDS 11 | PUBLIC ITK|ITKDenoising 12 | ) 13 | 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/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/QmitkDenoisingViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_denoisingview DWI Denoising 3 | 4 | This view provides several methods to denoise diffusion-weighted images. Simply select the image to denoise and press the start button. The default parameters should work relatively well. The NLM method is by far the slowest. 5 | 6 | */ 7 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_denoising org.mitk.gui.qt.diffusionimaging.denoising 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.denoising plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_denoising_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_denoising 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.denoising plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | 4 | ) 5 | 6 | set(INTERNAL_CPP_FILES 7 | mitkPluginActivator.cpp 8 | 9 | QmitkDenoisingView.cpp 10 | ) 11 | 12 | set(UI_FILES 13 | src/internal/QmitkDenoisingViewControls.ui 14 | ) 15 | 16 | set(MOC_H_FILES 17 | src/internal/mitkPluginActivator.h 18 | 19 | src/internal/QmitkDenoisingView.h 20 | ) 21 | 22 | set(CACHED_RESOURCE_FILES 23 | plugin.xml 24 | 25 | resources/denoisingicon.png 26 | ) 27 | 28 | set(QRC_FILES 29 | 30 | ) 31 | 32 | 33 | set(CPP_FILES ) 34 | 35 | foreach(file ${SRC_CPP_FILES}) 36 | set(CPP_FILES ${CPP_FILES} src/${file}) 37 | endforeach(file ${SRC_CPP_FILES}) 38 | 39 | foreach(file ${INTERNAL_CPP_FILES}) 40 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 41 | endforeach(file ${INTERNAL_CPP_FILES}) 42 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK DWI Denoising") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/plugin.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/resources/denoisingicon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/resources/denoisingicon.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/QmitkDenoisingView.h" 20 | 21 | 22 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 23 | 24 | ctkPluginContext* mitk::PluginActivator::GetContext() 25 | { 26 | return m_Context; 27 | } 28 | 29 | void mitk::PluginActivator::start(ctkPluginContext* context) 30 | { 31 | BERRY_REGISTER_EXTENSION_CLASS(QmitkDenoisingView, context) 32 | m_Context = context; 33 | } 34 | 35 | void mitk::PluginActivator::stop(ctkPluginContext* context) 36 | { 37 | Q_UNUSED(context) 38 | m_Context = nullptr; 39 | } 40 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.denoising") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_fiberfit) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERFIT_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkMriSimulation 10 | PACKAGE_DEPENDS 11 | ) 12 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing org.mitk.gui.qt.diffusionimaging.fiberprocessing 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.fiberprocessing plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_fiberprocessing 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.fiberprocessing plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | 4 | ) 5 | 6 | set(INTERNAL_CPP_FILES 7 | mitkPluginActivator.cpp 8 | QmitkFiberFitView.cpp 9 | ) 10 | 11 | set(UI_FILES 12 | src/internal/QmitkFiberFitViewControls.ui 13 | ) 14 | 15 | set(MOC_H_FILES 16 | src/internal/mitkPluginActivator.h 17 | src/internal/QmitkFiberFitView.h 18 | ) 19 | 20 | set(CACHED_RESOURCE_FILES 21 | plugin.xml 22 | 23 | resources/FiberFit.png 24 | ) 25 | 26 | set(QRC_FILES 27 | 28 | ) 29 | 30 | 31 | set(CPP_FILES ) 32 | 33 | foreach(file ${SRC_CPP_FILES}) 34 | set(CPP_FILES ${CPP_FILES} src/${file}) 35 | endforeach(file ${SRC_CPP_FILES}) 36 | 37 | foreach(file ${INTERNAL_CPP_FILES}) 38 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 39 | endforeach(file ${INTERNAL_CPP_FILES}) 40 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Fiber Fitting") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/plugin.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/resources/FiberFit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/resources/FiberFit.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/QmitkFiberFitView.h" 20 | 21 | 22 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 23 | 24 | ctkPluginContext* mitk::PluginActivator::GetContext() 25 | { 26 | return m_Context; 27 | } 28 | 29 | void mitk::PluginActivator::start(ctkPluginContext* context) 30 | { 31 | BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberFitView, context) 32 | m_Context = context; 33 | } 34 | 35 | void mitk::PluginActivator::stop(ctkPluginContext* context) 36 | { 37 | Q_UNUSED(context) 38 | m_Context = nullptr; 39 | } 40 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfit/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.fiberprocessing") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_fiberfox) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERFOX_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkMriSimulation 10 | ) 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox-Fiducial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox-Fiducial.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxExamples.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxExamples.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxWholebrain.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxWholebrain.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFieldmapGeneratorViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_fieldmapgenerator Fieldmap Generator 3 | 4 | This view allows the creation of artificial frequency maps used by Fiberfox to introduce distortions into diffusion weighted images. The generated images can contain a linear frequency gradient and/or multiple 3D gaussian shaped field inhomogeneities. 5 | 6 | Example: 7 | \li Select a reference image with the combo box. The generated fieldmap will feature the same geometry as the selected image. 8 | \li Move the crosshair to the any position in the image and click "Place Field Source". 9 | \li A position marker will appear in the render windows and in the datamanager, which indicates the position of a 3D gaussian field distortion that will be introduced upon clicking "Generate Fieldmap". 10 | \li The strength and variance of the placed sources can be modified by selecting the corresponding data node in the data manager and adjusting the parameters in the lower part of the view (below "Edit Selected Source"). 11 | \li To introduce an (additional) linear frequency gradient, specify the gradient below "Add Gradient". 12 | \li To finally generate the fieldmap, press "Generate Fieldmap". 13 | 14 | \imageMacro{fieldmapGenerator.png,"The Fieldmap Generator View. The render window shows a diffusion weighted image of the brain superimposed by a frequency map with two 3D gaussian field inhomogeneities (red).",16.00} 15 | 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/fieldmapGenerator.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/fieldmapGenerator.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/random_phantom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/random_phantom.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberfox org.mitk.gui.qt.diffusionimaging.fiberfox 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.fiberfox plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberfox_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_fiberfox 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.fiberfox plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Fiberfox") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc: -------------------------------------------------------------------------------- 1 | 2 | 3 | circle.png 4 | refresh.xpm 5 | download.png 6 | right.png 7 | stop.png 8 | upload.png 9 | 10 | 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/circle.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/circle.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/fieldmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/fieldmap.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/models.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/models.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/phantom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/phantom.png 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/syntheticdata.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | //Qmitk headers 18 | #include "QmitkAstrosticksModelParametersWidget.h" 19 | #include 20 | 21 | const std::string QmitkAstrosticksModelParametersWidget::VIEW_ID = "org.mitk.views.AstrosticksModelParametersWidget"; 22 | 23 | QmitkAstrosticksModelParametersWidget::QmitkAstrosticksModelParametersWidget( QWidget * parent, Qt::WindowFlags ) 24 | : QWidget(parent) 25 | { 26 | m_Controls = nullptr; 27 | this->CreateQtPartControl(this); 28 | } 29 | 30 | QmitkAstrosticksModelParametersWidget::~QmitkAstrosticksModelParametersWidget() 31 | { 32 | } 33 | 34 | void QmitkAstrosticksModelParametersWidget::CreateQtPartControl(QWidget *parent) 35 | { 36 | if (!m_Controls) 37 | { 38 | // create GUI widgets 39 | m_Controls = new Ui::QmitkAstrosticksModelParametersWidgetControls; 40 | m_Controls->setupUi(parent); 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | //Qmitk headers 18 | #include "QmitkBallModelParametersWidget.h" 19 | #include 20 | 21 | const std::string QmitkBallModelParametersWidget::VIEW_ID = "org.mitk.views.BallModelParametersWidget"; 22 | 23 | QmitkBallModelParametersWidget::QmitkBallModelParametersWidget( QWidget * parent, Qt::WindowFlags ) 24 | : QWidget(parent) 25 | { 26 | m_Controls = nullptr; 27 | this->CreateQtPartControl(this); 28 | } 29 | 30 | QmitkBallModelParametersWidget::~QmitkBallModelParametersWidget() 31 | { 32 | } 33 | 34 | void QmitkBallModelParametersWidget::CreateQtPartControl(QWidget *parent) 35 | { 36 | if (!m_Controls) 37 | { 38 | // create GUI widgets 39 | m_Controls = new Ui::QmitkBallModelParametersWidgetControls; 40 | m_Controls->setupUi(parent); 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | //Qmitk headers 18 | #include "QmitkDotModelParametersWidget.h" 19 | #include 20 | 21 | const std::string QmitkDotModelParametersWidget::VIEW_ID = "org.mitk.views.DotModelParametersWidget"; 22 | 23 | QmitkDotModelParametersWidget::QmitkDotModelParametersWidget( QWidget * parent, Qt::WindowFlags ) 24 | : QWidget(parent) 25 | { 26 | m_Controls = nullptr; 27 | this->CreateQtPartControl(this); 28 | } 29 | 30 | QmitkDotModelParametersWidget::~QmitkDotModelParametersWidget() 31 | { 32 | } 33 | 34 | void QmitkDotModelParametersWidget::CreateQtPartControl(QWidget *parent) 35 | { 36 | if (!m_Controls) 37 | { 38 | // create GUI widgets 39 | m_Controls = new Ui::QmitkDotModelParametersWidgetControls; 40 | m_Controls->setupUi(parent); 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | //Qmitk headers 18 | #include "QmitkPrototypeSignalParametersWidget.h" 19 | #include 20 | 21 | const std::string QmitkPrototypeSignalParametersWidget::VIEW_ID = "org.mitk.views.prototypesignalparameterswidget"; 22 | 23 | QmitkPrototypeSignalParametersWidget::QmitkPrototypeSignalParametersWidget( QWidget * parent, Qt::WindowFlags ) 24 | : QWidget(parent) 25 | { 26 | m_Controls = nullptr; 27 | this->CreateQtPartControl(this); 28 | } 29 | 30 | QmitkPrototypeSignalParametersWidget::~QmitkPrototypeSignalParametersWidget() 31 | { 32 | } 33 | 34 | void QmitkPrototypeSignalParametersWidget::CreateQtPartControl(QWidget *parent) 35 | { 36 | if (!m_Controls) 37 | { 38 | // create GUI widgets 39 | m_Controls = new Ui::QmitkPrototypeSignalParametersWidgetControls; 40 | m_Controls->setupUi(parent); 41 | 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | //Qmitk headers 18 | #include "QmitkStickModelParametersWidget.h" 19 | #include 20 | 21 | const std::string QmitkStickModelParametersWidget::VIEW_ID = "org.mitk.views.StickModelParametersWidget"; 22 | 23 | QmitkStickModelParametersWidget::QmitkStickModelParametersWidget( QWidget * parent, Qt::WindowFlags ) 24 | : QWidget(parent) 25 | { 26 | m_Controls = nullptr; 27 | this->CreateQtPartControl(this); 28 | } 29 | 30 | QmitkStickModelParametersWidget::~QmitkStickModelParametersWidget() 31 | { 32 | } 33 | 34 | void QmitkStickModelParametersWidget::CreateQtPartControl(QWidget *parent) 35 | { 36 | if (!m_Controls) 37 | { 38 | // create GUI widgets 39 | m_Controls = new Ui::QmitkStickModelParametersWidgetControls; 40 | m_Controls->setupUi(parent); 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkDIAppSyntheticDataGenerationPerspective_H_ 19 | #define QmitkDIAppSyntheticDataGenerationPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkDIAppSyntheticDataGenerationPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkDIAppSyntheticDataGenerationPerspective() {} 31 | ~QmitkDIAppSyntheticDataGenerationPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkDIAppSyntheticDataGenerationPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h" 20 | 21 | #include "src/internal/QmitkFiberfoxView.h" 22 | #include "src/internal/QmitkFiberGenerationView.h" 23 | #include "src/internal/QmitkFieldmapGeneratorView.h" 24 | 25 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 26 | 27 | ctkPluginContext* mitk::PluginActivator::GetContext() 28 | { 29 | return m_Context; 30 | } 31 | 32 | void mitk::PluginActivator::start(ctkPluginContext* context) 33 | { 34 | BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppSyntheticDataGenerationPerspective, context) 35 | 36 | BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberfoxView, context) 37 | BERRY_REGISTER_EXTENSION_CLASS(QmitkFieldmapGeneratorView, context) 38 | BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberGenerationView, context) 39 | m_Context = context; 40 | } 41 | 42 | void mitk::PluginActivator::stop(ctkPluginContext* context) 43 | { 44 | Q_UNUSED(context) 45 | m_Context = nullptr; 46 | } 47 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.fiberfox") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_fiberprocessing) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERPROCESSING_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkFiberProcessing MitkQtWidgets MitkFiberDissection 10 | PACKAGE_DEPENDS 11 | PRIVATE ITK|ITKVTK 12 | ) 13 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionFib.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionFib.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionPeaks.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionPeaks.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_fiberprocessing Fiber Processing 3 | 4 | This view provides tools to extract subbundles from a given fiber bundle, to remove unwanted fibers (e.g. via length, curvature, directional and fiber weight constraints) and to modify the properties of a fiber bundles such as coloring, fiber weights or fiber sampling. 5 | 6 | Fiber Extraction: 7 | Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. The extraction can also be performed using 3D ROIs represented as binary mask images. In this extraction method, the logical operations are not implemented at the moment. 8 | 9 | */ 10 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing org.mitk.gui.qt.diffusionimaging.fiberprocessing 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.fiberprocessing plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_fiberprocessing 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.fiberprocessing plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Fiber Processing") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundle.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundle.png 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-------------------------------------------------------------------------------- 1 | 2 | 3 | FiberBundle.png 4 | circle.png 5 | polygon.png 6 | 7 | 8 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkInteractiveFiberDissection.qrc: -------------------------------------------------------------------------------- 1 | 2 | 3 | FiberBundle.png 4 | circle.png 5 | polygon.png 6 | eraze.png 7 | highlighter.png 8 | atTRACTive.png 9 | 10 | 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/atTRACTive.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/atTRACTive.png 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https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkFiberProcessingPerspective_H_ 19 | #define QmitkFiberProcessingPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkFiberProcessingPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkFiberProcessingPerspective() {} 31 | ~QmitkFiberProcessingPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkFiberProcessingPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.fiberprocessing") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_ivim) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_IVIM_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkQtWidgetsExt MitkChart MitkIVIM 10 | ) 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/ivimview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/ivimview.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_ivim org.mitk.gui.qt.diffusionimaging.ivim 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.ivim plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_ivim_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_ivim 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.ivim plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | ) 4 | 5 | set(INTERNAL_CPP_FILES 6 | mitkPluginActivator.cpp 7 | 8 | QmitkIVIMView.cpp 9 | 10 | Perspectives/QmitkDIAppIVIMPerspective.cpp 11 | ) 12 | 13 | set(UI_FILES 14 | src/internal/QmitkIVIMViewControls.ui 15 | ) 16 | 17 | set(MOC_H_FILES 18 | src/internal/mitkPluginActivator.h 19 | 20 | src/internal/QmitkIVIMView.h 21 | 22 | src/internal/Perspectives/QmitkDIAppIVIMPerspective.h 23 | ) 24 | 25 | set(CACHED_RESOURCE_FILES 26 | plugin.xml 27 | 28 | resources/IVIM_48.png 29 | resources/ivim.png 30 | ) 31 | 32 | set(QRC_FILES 33 | 34 | ) 35 | 36 | 37 | set(CPP_FILES ) 38 | 39 | foreach(file ${SRC_CPP_FILES}) 40 | set(CPP_FILES ${CPP_FILES} src/${file}) 41 | endforeach(file ${SRC_CPP_FILES}) 42 | 43 | foreach(file ${INTERNAL_CPP_FILES}) 44 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 45 | endforeach(file ${INTERNAL_CPP_FILES}) 46 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK IVIM") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/IVIM_48.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/IVIM_48.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/ivim.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/ivim.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkDIAppIVIMPerspective_H_ 19 | #define QmitkDIAppIVIMPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkDIAppIVIMPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkDIAppIVIMPerspective() {} 31 | ~QmitkDIAppIVIMPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkDIAppIVIMPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/Perspectives/QmitkDIAppIVIMPerspective.h" 20 | 21 | #include "src/internal/QmitkIVIMView.h" 22 | 23 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 24 | 25 | ctkPluginContext* mitk::PluginActivator::GetContext() 26 | { 27 | 28 | return m_Context; 29 | } 30 | 31 | void mitk::PluginActivator::start(ctkPluginContext* context) 32 | { 33 | BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppIVIMPerspective, context) 34 | 35 | BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context) 36 | m_Context = context; 37 | } 38 | 39 | void mitk::PluginActivator::stop(ctkPluginContext* context) 40 | { 41 | Q_UNUSED(context) 42 | m_Context = nullptr; 43 | } 44 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.ivim") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_preprocessing) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkDiffusionPreprocessing 10 | PACKAGE_DEPENDS 11 | ITK|ITKDenoising 12 | ) 13 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_1.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_2.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_3.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_4.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing org.mitk.gui.qt.diffusionimaging.preprocessing 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.preprocessing plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_preprocessing 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.preprocessing plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | 4 | ) 5 | 6 | set(INTERNAL_CPP_FILES 7 | mitkPluginActivator.cpp 8 | 9 | QmitkPreprocessingView.cpp 10 | ) 11 | 12 | set(UI_FILES 13 | src/internal/QmitkPreprocessingViewControls.ui 14 | ) 15 | 16 | set(MOC_H_FILES 17 | src/internal/mitkPluginActivator.h 18 | 19 | src/internal/QmitkPreprocessingView.h 20 | ) 21 | 22 | set(CACHED_RESOURCE_FILES 23 | plugin.xml 24 | 25 | resources/dwi2.png 26 | ) 27 | 28 | set(QRC_FILES 29 | 30 | ) 31 | 32 | 33 | set(CPP_FILES ) 34 | 35 | foreach(file ${SRC_CPP_FILES}) 36 | set(CPP_FILES ${CPP_FILES} src/${file}) 37 | endforeach(file ${SRC_CPP_FILES}) 38 | 39 | foreach(file ${INTERNAL_CPP_FILES}) 40 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 41 | endforeach(file ${INTERNAL_CPP_FILES}) 42 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Preprocessing") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/dwi2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/dwi2.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/QmitkPreprocessingView.h" 20 | #include 21 | 22 | 23 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 24 | 25 | US_INITIALIZE_MODULE 26 | 27 | ctkPluginContext* mitk::PluginActivator::GetContext() 28 | { 29 | return m_Context; 30 | } 31 | 32 | void mitk::PluginActivator::start(ctkPluginContext* context) 33 | { 34 | BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) 35 | m_Context = context; 36 | } 37 | 38 | void mitk::PluginActivator::stop(ctkPluginContext* context) 39 | { 40 | Q_UNUSED(context) 41 | m_Context = nullptr; 42 | } 43 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.preprocessing") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_reconstruction) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkQtWidgetsExt MitkDiffusionPreprocessing 10 | ) 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkDiffusionImagingQuantificationPage.dox: -------------------------------------------------------------------------------- 1 | /** 2 | 3 | \page org_mitk_views_diffusionquantification Scalar Indices 4 | 5 | The scalar indices view allows the calculation of different scalar measures for raw diffusion-weighted images (MD, ADC), tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or ODFs (Generalized Fractional Anisotropy). 6 | 7 | */ 8 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_odfdetails ODF Details 3 | 4 | This view provides detailed information about the orentation distribution function at the current crosshair position (if a Tensor/ODF image is selected). A visualization of the ODF as well as statistical information are displayed. 5 | 6 | \imageMacro{odfdetails.png,"The ODF Details View",10.01} 7 | 8 | */ 9 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_odfmaximaextraction ODF Peak Extraction 3 | 4 | This view provides the user interface to extract the principal diffusion direction of tensors and the peaks of spherical harmonic ODFs using gradient descent optimization. 5 | 6 | The output peaks can for example be used for streamline tractography. 7 | 8 | 9 | */ 10 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkQBallReconstructionViewUserManual.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_qballreconstruction Q-Ball Reconstruction 3 | 4 | The q-ball reonstruction view implements a variety of reconstruction methods. The different reconstruction methods are described in the following: 5 | \li Numerical: The original, numerical q-ball reconstruction presented by Tuch et al. [5] 6 | \li Standard (SH): Descoteaux's reconstruction based on spherical harmonic basis functions [6] 7 | \li Solid Angle (SH): Aganj's reconstruction with solid angle consideration [7] 8 | \li ADC-profile only: The ADC-profile reconstructed with spherical harmonic basis functions 9 | \li Raw signal only: The raw signal reconstructed with spherical harmonic basis functions 10 | 11 | \imageMacro{qballs1.png,"The q-ball resonstruction view",9.99} 12 | 13 | B0 threshold works the same as in tensor reconstruction. The maximum l-level configures the size of the spherical harmonics basis. Larger l-values (e.g. l=8) allow higher levels of detail, lower levels are more stable against noise (e.g. l=4). Lambda is a regularisation parameter. Set it to 0 for no regularisation. lambda = 0.006 has proven to be a stable choice under various settings. 14 | 15 | \imageMacro{qballs2.png,"Advanced q-ball reconstruction settings",8.00} 16 | 17 | This is how a q-ball image should initially look after reconstruction. Standard q-balls feature a relatively low GFA and thus appear rather dark. Adjust the level-window to solve this. 18 | 19 | \imageMacro{qballs3.png,"q-ball image after reconstruction",16.00} 20 | 21 | */ 22 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/ScalarIndicesGUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/ScalarIndicesGUI.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/odfdetails.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/odfdetails.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs1.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs2.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs3.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/residuals.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/residuals.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor1.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor4.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_reconstruction org.mitk.gui.qt.diffusionimaging.reconstruction 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.reconstruction plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_reconstruction_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_reconstruction 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.reconstruction plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | ) 4 | 5 | set(INTERNAL_CPP_FILES 6 | mitkPluginActivator.cpp 7 | 8 | Perspectives/QmitkReconstructionPerspective.cpp 9 | Perspectives/QmitkQuantificationPerspective.cpp 10 | 11 | QmitkQBallReconstructionView.cpp 12 | QmitkDiffusionQuantificationView.cpp 13 | QmitkTensorReconstructionView.cpp 14 | QmitkOdfMaximaExtractionView.cpp 15 | ) 16 | 17 | set(UI_FILES 18 | src/internal/QmitkQBallReconstructionViewControls.ui 19 | src/internal/QmitkDiffusionQuantificationViewControls.ui 20 | src/internal/QmitkTensorReconstructionViewControls.ui 21 | src/internal/QmitkOdfMaximaExtractionViewControls.ui 22 | ) 23 | 24 | set(MOC_H_FILES 25 | src/internal/mitkPluginActivator.h 26 | 27 | src/internal/Perspectives/QmitkReconstructionPerspective.h 28 | src/internal/Perspectives/QmitkQuantificationPerspective.h 29 | 30 | src/internal/QmitkQBallReconstructionView.h 31 | src/internal/QmitkDiffusionQuantificationView.h 32 | src/internal/QmitkTensorReconstructionView.h 33 | src/internal/QmitkOdfMaximaExtractionView.h 34 | ) 35 | 36 | set(CACHED_RESOURCE_FILES 37 | plugin.xml 38 | 39 | resources/quantification.png 40 | resources/tensor.png 41 | resources/odf.png 42 | resources/odf_peaks.png 43 | ) 44 | 45 | set(QRC_FILES 46 | 47 | ) 48 | 49 | 50 | set(CPP_FILES ) 51 | 52 | foreach(file ${SRC_CPP_FILES}) 53 | set(CPP_FILES ${CPP_FILES} src/${file}) 54 | endforeach(file ${SRC_CPP_FILES}) 55 | 56 | foreach(file ${INTERNAL_CPP_FILES}) 57 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 58 | endforeach(file ${INTERNAL_CPP_FILES}) 59 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Reconstruction") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/OdfDetails.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/OdfDetails.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf_peaks.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf_peaks.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/quantification.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/quantification.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/tensor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/tensor.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkQuantificationPerspective_H_ 19 | #define QmitkQuantificationPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkQuantificationPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkQuantificationPerspective() {} 31 | ~QmitkQuantificationPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkQuantificationPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkReconstructionPerspective_H_ 19 | #define QmitkReconstructionPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkReconstructionPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkReconstructionPerspective() {} 31 | ~QmitkReconstructionPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkReconstructionPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.reconstruction") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_registration) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_REGISTRATION_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkDiffusionRegistration MitkMatchPointRegistrationUI 10 | ) 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkHeadMotionCorrection.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_headmotioncorrectionview Head-Motion Correction 3 | 4 | This view allows head-motion and eddy-current correction by affinely registering all volumes to the first unweighted volume of the complete diffusion-weighted image. The individual gradient directions are roated accordingly. 5 | */ 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRegistration.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \page org_mitk_views_simpleregistrationview Registration 3 | 4 | This view enables the simple rigid or affine registration of two images. It is also possible to transform a tractogram with a registration object obtained from a previous registration of two images. 5 | 6 | */ 7 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_basic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_basic.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_batch.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_batch.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_registration org.mitk.gui.qt.diffusionimaging.registration 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.registration plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_registration_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_registration 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.registration plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ 17 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake: -------------------------------------------------------------------------------- 1 | set(SRC_CPP_FILES 2 | 3 | 4 | ) 5 | 6 | set(INTERNAL_CPP_FILES 7 | mitkPluginActivator.cpp 8 | 9 | QmitkHeadMotionCorrectionView.cpp 10 | QmitkSimpleRegistrationView.cpp 11 | ) 12 | 13 | set(UI_FILES 14 | src/internal/QmitkHeadMotionCorrectionViewControls.ui 15 | src/internal/QmitkSimpleRegistrationViewControls.ui 16 | ) 17 | 18 | set(MOC_H_FILES 19 | src/internal/mitkPluginActivator.h 20 | 21 | src/internal/QmitkHeadMotionCorrectionView.h 22 | src/internal/QmitkSimpleRegistrationView.h 23 | ) 24 | 25 | set(CACHED_RESOURCE_FILES 26 | plugin.xml 27 | 28 | resources/diffusionregistration.png 29 | ) 30 | 31 | set(QRC_FILES 32 | 33 | ) 34 | 35 | 36 | set(CPP_FILES ) 37 | 38 | foreach(file ${SRC_CPP_FILES}) 39 | set(CPP_FILES ${CPP_FILES} src/${file}) 40 | endforeach(file ${SRC_CPP_FILES}) 41 | 42 | foreach(file ${INTERNAL_CPP_FILES}) 43 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 44 | endforeach(file ${INTERNAL_CPP_FILES}) 45 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK dMRI Registration") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.diffusionimaging.controls org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/resources/diffusionregistration.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.registration/resources/diffusionregistration.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/QmitkHeadMotionCorrectionView.h" 20 | #include "src/internal/QmitkSimpleRegistrationView.h" 21 | 22 | 23 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 24 | 25 | ctkPluginContext* mitk::PluginActivator::GetContext() 26 | { 27 | return m_Context; 28 | } 29 | 30 | void mitk::PluginActivator::start(ctkPluginContext* context) 31 | { 32 | BERRY_REGISTER_EXTENSION_CLASS(QmitkHeadMotionCorrectionView, context) 33 | BERRY_REGISTER_EXTENSION_CLASS(QmitkSimpleRegistrationView, context) 34 | m_Context = context; 35 | } 36 | 37 | void mitk::PluginActivator::stop(ctkPluginContext* context) 38 | { 39 | Q_UNUSED(context) 40 | m_Context = nullptr; 41 | } 42 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.registration") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # The project name must correspond to the directory name of your plug-in 2 | # and must not contain periods. 3 | project(org_mitk_gui_qt_diffusionimaging_tractography) 4 | 5 | mitk_create_plugin( 6 | SUBPROJECTS MITK-Diffusion 7 | EXPORT_DIRECTIVE DIFFUSIONIMAGING_TRACTOGRAPHY_EXPORT 8 | EXPORTED_INCLUDE_SUFFIXES src 9 | MODULE_DEPENDS MitkFiberTracking 10 | ) 11 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/doxygen/modules.dox: -------------------------------------------------------------------------------- 1 | /** 2 | \defgroup org_mitk_gui_qt_diffusionimaging_tractography org.mitk.gui.qt.diffusionimaging.tractography 3 | \ingroup MITKPlugins 4 | 5 | \brief This is the diffusionimaging.tractography plugin. 6 | 7 | */ 8 | 9 | /** 10 | \defgroup org_mitk_gui_qt_diffusionimaging_tractography_internal Internal 11 | \ingroup org_mitk_gui_qt_diffusionimaging_tractography 12 | 13 | \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.tractography plugin. Other 14 | plugins must not rely on these classes. They contain implementation details and their interface 15 | may change at any time. We mean it. 16 | */ -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake: -------------------------------------------------------------------------------- 1 | set(INTERNAL_CPP_FILES 2 | QmitkGibbsTrackingView.cpp 3 | QmitkStreamlineTrackingView.cpp 4 | 5 | Perspectives/QmitkGibbsTractographyPerspective.cpp 6 | Perspectives/QmitkStreamlineTractographyPerspective.cpp 7 | 8 | mitkPluginActivator.cpp 9 | ) 10 | 11 | set(UI_FILES 12 | src/internal/QmitkGibbsTrackingViewControls.ui 13 | src/internal/QmitkStreamlineTrackingViewControls.ui 14 | ) 15 | 16 | set(MOC_H_FILES 17 | src/internal/mitkPluginActivator.h 18 | 19 | src/internal/QmitkGibbsTrackingView.h 20 | src/internal/QmitkStreamlineTrackingView.h 21 | 22 | src/internal/Perspectives/QmitkGibbsTractographyPerspective.h 23 | src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h 24 | ) 25 | 26 | set(CACHED_RESOURCE_FILES 27 | plugin.xml 28 | 29 | resources/tract.png 30 | resources/tractogram.png 31 | resources/ml_tractography.png 32 | resources/download.png 33 | resources/right.png 34 | resources/stop.png 35 | resources/upload.png 36 | ) 37 | 38 | set(QRC_FILES 39 | resources/QmitkTractography.qrc 40 | ) 41 | 42 | 43 | set(CPP_FILES ) 44 | 45 | foreach(file ${SRC_CPP_FILES}) 46 | set(CPP_FILES ${CPP_FILES} src/${file}) 47 | endforeach(file ${SRC_CPP_FILES}) 48 | 49 | foreach(file ${INTERNAL_CPP_FILES}) 50 | set(CPP_FILES ${CPP_FILES} src/internal/${file}) 51 | endforeach(file ${INTERNAL_CPP_FILES}) 52 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/manifest_headers.cmake: -------------------------------------------------------------------------------- 1 | set(Plugin-Name "MITK Tractography") 2 | set(Plugin-Version "1.0.0") 3 | set(Plugin-Vendor "DKFZ, Medical Image Computing") 4 | set(Plugin-ContactAddress "http://www.mitk.org") 5 | set(Require-Plugin org.mitk.gui.qt.common) 6 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/GibbsTracking.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/GibbsTracking.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc: -------------------------------------------------------------------------------- 1 | 2 | 3 | upload.png 4 | download.png 5 | right.png 6 | stop.png 7 | 8 | 9 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png: 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https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tract.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tract.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tractogram.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tractogram.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MITK-Diffusion/566f934072380358e808db00b0a44dbb96ac9142/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkGibbsTractographyPerspective_H_ 19 | #define QmitkGibbsTractographyPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkGibbsTractographyPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkGibbsTractographyPerspective() {} 31 | ~QmitkGibbsTractographyPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkGibbsTractographyPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | 18 | #ifndef QmitkStreamlineTractographyPerspective_H_ 19 | #define QmitkStreamlineTractographyPerspective_H_ 20 | 21 | #include 22 | 23 | class QmitkStreamlineTractographyPerspective : public QObject, public berry::IPerspectiveFactory 24 | { 25 | Q_OBJECT 26 | Q_INTERFACES(berry::IPerspectiveFactory) 27 | 28 | public: 29 | 30 | QmitkStreamlineTractographyPerspective() {} 31 | ~QmitkStreamlineTractographyPerspective() {} 32 | 33 | void CreateInitialLayout(berry::IPageLayout::Pointer layout) override; 34 | }; 35 | 36 | #endif /* QmitkStreamlineTractographyPerspective_H_ */ 37 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.cpp: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | 17 | #include "mitkPluginActivator.h" 18 | 19 | #include "src/internal/Perspectives/QmitkGibbsTractographyPerspective.h" 20 | #include "src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h" 21 | 22 | #include "src/internal/QmitkGibbsTrackingView.h" 23 | #include "src/internal/QmitkStreamlineTrackingView.h" 24 | 25 | ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; 26 | 27 | ctkPluginContext* mitk::PluginActivator::GetContext() 28 | { 29 | return m_Context; 30 | } 31 | 32 | void mitk::PluginActivator::start(ctkPluginContext* context) 33 | { 34 | BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTractographyPerspective, context) 35 | BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTractographyPerspective, context) 36 | 37 | BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context) 38 | BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTrackingView, context) 39 | 40 | m_Context = context; 41 | } 42 | 43 | void mitk::PluginActivator::stop(ctkPluginContext* context) 44 | { 45 | Q_UNUSED(context) 46 | m_Context = nullptr; 47 | } 48 | -------------------------------------------------------------------------------- /Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.h: -------------------------------------------------------------------------------- 1 | /*=================================================================== 2 | 3 | The Medical Imaging Interaction Toolkit (MITK) 4 | 5 | Copyright (c) German Cancer Research Center. 6 | 7 | All rights reserved. 8 | 9 | This software is distributed WITHOUT ANY WARRANTY; without 10 | even the implied warranty of MERCHANTABILITY or FITNESS FOR 11 | A PARTICULAR PURPOSE. 12 | 13 | See LICENSE.txt or http://www.mitk.org for details. 14 | 15 | ===================================================================*/ 16 | #ifndef MITKPLUGINACTIVATOR_H 17 | #define MITKPLUGINACTIVATOR_H 18 | 19 | #include 20 | 21 | namespace mitk 22 | { 23 | class PluginActivator : public QObject, public ctkPluginActivator 24 | { 25 | Q_OBJECT 26 | Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.tractography") 27 | Q_INTERFACES(ctkPluginActivator) 28 | 29 | public: 30 | static ctkPluginContext* GetContext(); 31 | 32 | void start(ctkPluginContext* context) override; 33 | void stop(ctkPluginContext* context) override; 34 | 35 | private: 36 | static ctkPluginContext* m_Context; 37 | }; 38 | } 39 | 40 | #endif 41 | 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