Merge branch 'T22423-MachineLearningTractographyPaperExtensions'
8b4a695f731c
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Merge branch 'T22423-MachineLearningTractographyPaperExtensions'

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neher	Authored on Feb 27 2017, 8:27 AM
neher	Pushed on Feb 27 2017, 8:29 AM

Parents

rMITK7ea8b06706e7: Fiberfox parameter save fix
rMITK474abf398fb2: Merge branch 'T22556-adapt-build-configurations'

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neher committed rMITK8b4a695f731c: Merge branch 'T22423-MachineLearningTractographyPaperExtensions' (authored by neher).Feb 27 2017, 8:27 AM

Merged Changes

7ea8b06706e7 Fiberfox parameter save fix
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1001be579d9a adjusted hdf5 version and mitk-data hash
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bb5f1043a45d updated test data. removed dependency of classification on diffusion.
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8290b4c33914 fixed fiber extraction by mask image
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4be0e12fb50a added gradient signal normalization and gradient flip
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f2bfa64231f4 Fixed DF training to work with multiple input datasets again
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4814858c1343 finished GM seeding and gm check
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e0e5a974568a added limit for samples
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f82921316ba0 parametrization of fiber sampling for ml tracking
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9016993cddd2 training fix
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6af77f6d21d0 fixed tracking issue with unnormalized directions
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7b7c9fdec4c8 multithreaded some fiber bundle operations
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45251f1a5757 ml tracking parallelization using open mp
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c7558d462b5d sh features are now possible
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8ac933779079 multiple previous directions possible as ml tracking features
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b72451bb34d7 refactoring
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fc1857fdbb22 added stop voting. avoids tracts that double back.
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bd7c80b64c55 added feature weighting
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Changes (64)

Path

Size

Packages

CMakeExternals/

MITKData.cmake

O1: MITK Reviewer Group I

Modules/

Classification/

DataCollection/

CMakeLists.txt

DataHolder/

mitkDataCollection.h

ReaderWriter/

mitkCollectionReader.cpp

mitkCollectionWriter.cpp

mitkCollectionWriter.h

DiffusionImaging/

DiffusionCore/

include/

Algorithms/

itkDwiNormilzationFilter.h

itkDwiNormilzationFilter.txx

itkFslPeakImageConverter.cpp

itkFslPeakImageConverter.h

itkMrtrixPeakImageConverter.cpp

itkMrtrixPeakImageConverter.h

FiberTracking/

Algorithms/

MLTracking/

itkMLBSTrackingFilter.cpp

itkMLBSTrackingFilter.h

mitkTrackingForestHandler.cpp

mitkTrackingForestHandler.h

itkFiberCurvatureFilter.cpp

itkTractDensityImageFilter.cpp

itkTractDensityImageFilter.h

CMakeLists.txt

Fiberfox/

itkTractsToDWIImageFilter.cpp

IODataStructures/

FiberBundle/

mitkFiberBundle.cpp

mitkFiberBundle.h

Testing/

CMakeLists.txt

mitkFiberExtractionTest.cpp

mitkFiberGenerationTest.cpp

mitkFiberProcessingTest.cpp

mitkFiberTransformationTest.cpp

mitkFiberfoxSignalGenerationTest.cpp

mitkLocalFiberPlausibilityTest.cpp

mitkMachineLearningTrackingTest.cpp

MiniApps/

CMakeLists.txt

DFTracking.cpp

DFTraining.cpp

FiberDirectionExtraction.cpp

FiberProcessing.cpp

TractDensity.cpp

ModuleList.cmake

TumorInvasionAnalysis/

CMakeLists.txt

MiniApps/

TumorInvasionAnalysisTool.cpp

TumorResponseEvaluationTool.cpp

files.cmake

src/

ReaderWriter

test/

mitkClassificationTest.cpp

	TumorInvasionAnalysis/
	Classification/

	include/
	DataCollection/

	mitkDiffusionCollectionReader.h/
	ReaderWriter/


	mitkCollectionReader.h

	mitkDiffusionCollectionWriter.h/
	ReaderWriter/


	mitkCollectionWriter.h

	src/	ReaderWriter/
	DataCollection/	ReaderWriter/

	mitkDiffusionCollectionReader.cpp
	mitkCollectionReader.cpp

	mitkDiffusionCollectionWriter.cpp
	mitkCollectionWriter.cpp

Plugins/

org.mitk.gui.qt.diffusionimaging/

src/

QmitkFreeSurferParcellationHandler.cpp

internal/

QmitkFiberProcessingView.cpp

QmitkFiberProcessingView.h

QmitkFiberProcessingViewControls.ui

QmitkFiberfoxView.cpp

QmitkFiberfoxView.h

QmitkMLBTView.cpp

QmitkMLBTView.h

QmitkMLBTViewControls.ui

QmitkODFDetailsView.cpp

QmitkOdfMaximaExtractionView.cpp

QmitkOdfMaximaExtractionView.h

QmitkOdfMaximaExtractionViewControls.ui

QmitkPreprocessingView.cpp

QmitkPreprocessingView.h

QmitkPreprocessingViewControls.ui

rMITK8b4a695f731c

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CMakeExternals/MITKData.cmake

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Modules/Classification/DataCollection/CMakeLists.txt

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Modules/Classification/DataCollection/DataHolder/mitkDataCollection.h

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Modules/Classification/DataCollection/ReaderWriter/mitkCollectionReader.cpp

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Modules/Classification/DataCollection/ReaderWriter/mitkCollectionWriter.cpp

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Modules/Classification/DataCollection/ReaderWriter/mitkCollectionWriter.h

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFslPeakImageConverter.cpp

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFslPeakImageConverter.h

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMrtrixPeakImageConverter.cpp

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Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMrtrixPeakImageConverter.h

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Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/itkMLBSTrackingFilter.cpp

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Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/itkMLBSTrackingFilter.h

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Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/mitkTrackingForestHandler.cpp

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Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/mitkTrackingForestHandler.h

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Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.cpp

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Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp

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Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.h

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Modules/DiffusionImaging/FiberTracking/CMakeLists.txt

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Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp

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Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp

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Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h

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Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt

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Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessingTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp

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Modules/DiffusionImaging/FiberTracking/Testing/mitkMachineLearningTrackingTest.cpp

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Modules/DiffusionImaging/MiniApps/CMakeLists.txt

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Modules/DiffusionImaging/MiniApps/DFTracking.cpp

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Modules/DiffusionImaging/MiniApps/DFTraining.cpp

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Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp

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Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp

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Modules/DiffusionImaging/MiniApps/TractDensity.cpp

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Modules/ModuleList.cmake

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Modules/TumorInvasionAnalysis/CMakeLists.txt

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Modules/TumorInvasionAnalysis/MiniApps/TumorInvasionAnalysisTool.cpp

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Modules/TumorInvasionAnalysis/MiniApps/TumorResponseEvaluationTool.cpp

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Modules/TumorInvasionAnalysis/files.cmake

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Modules/TumorInvasionAnalysis/include/mitkDiffusionCollectionReader.h

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Modules/TumorInvasionAnalysis/include/mitkDiffusionCollectionWriter.h

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Modules/TumorInvasionAnalysis/src/ReaderWriter/mitkDiffusionCollectionReader.cpp

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Modules/TumorInvasionAnalysis/src/ReaderWriter/mitkDiffusionCollectionWriter.cpp

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Modules/TumorInvasionAnalysis/test/mitkClassificationTest.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkFreeSurferParcellationHandler.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTView.h

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTViewControls.ui

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.h

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h

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Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui

Merge branch 'T22423-MachineLearningTractographyPaperExtensions'8b4a695f731cActions

Description

Details

Event Timeline

Merged Changes

Changes (64)

rMITK8b4a695f731c

CMakeExternals/MITKData.cmake

Modules/Classification/DataCollection/CMakeLists.txt

Modules/Classification/DataCollection/DataHolder/mitkDataCollection.h

Modules/Classification/DataCollection/ReaderWriter/mitkCollectionReader.cpp

Modules/Classification/DataCollection/ReaderWriter/mitkCollectionWriter.cpp

Modules/Classification/DataCollection/ReaderWriter/mitkCollectionWriter.h

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFslPeakImageConverter.cpp

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFslPeakImageConverter.h

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMrtrixPeakImageConverter.cpp

Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMrtrixPeakImageConverter.h

Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/itkMLBSTrackingFilter.cpp

Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/itkMLBSTrackingFilter.h

Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/mitkTrackingForestHandler.cpp

Modules/DiffusionImaging/FiberTracking/Algorithms/MLTracking/mitkTrackingForestHandler.h

Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.cpp

Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp

Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.h

Modules/DiffusionImaging/FiberTracking/CMakeLists.txt

Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp

Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp

Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h

Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessingTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp

Modules/DiffusionImaging/FiberTracking/Testing/mitkMachineLearningTrackingTest.cpp

Modules/DiffusionImaging/MiniApps/CMakeLists.txt

Modules/DiffusionImaging/MiniApps/DFTracking.cpp

Modules/DiffusionImaging/MiniApps/DFTraining.cpp

Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp

Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp

Modules/DiffusionImaging/MiniApps/TractDensity.cpp

Modules/ModuleList.cmake

Modules/TumorInvasionAnalysis/CMakeLists.txt

Modules/TumorInvasionAnalysis/MiniApps/TumorInvasionAnalysisTool.cpp

Modules/TumorInvasionAnalysis/MiniApps/TumorResponseEvaluationTool.cpp

Modules/TumorInvasionAnalysis/files.cmake

Modules/TumorInvasionAnalysis/include/mitkDiffusionCollectionReader.h

Modules/TumorInvasionAnalysis/include/mitkDiffusionCollectionWriter.h

Modules/TumorInvasionAnalysis/src/ReaderWriter/mitkDiffusionCollectionReader.cpp

Modules/TumorInvasionAnalysis/src/ReaderWriter/mitkDiffusionCollectionWriter.cpp

Modules/TumorInvasionAnalysis/test/mitkClassificationTest.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkFreeSurferParcellationHandler.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.h

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTView.h

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkMLBTViewControls.ui

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionView.h

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h

Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui

Merge branch 'T22423-MachineLearningTractographyPaperExtensions'
8b4a695f731c
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