anima::GcStremMsLesionsSegmentationFilter< TInputImage > Class Template Reference

Class performing lesion segmentation. More...

#include <animaGcStremMsLesionsSegmentationFilter.h>

Inheritance diagram for anima::GcStremMsLesionsSegmentationFilter< TInputImage >:

Collaboration diagram for anima::GcStremMsLesionsSegmentationFilter< TInputImage >:

Public Types
typedef itk::BinaryThresholdImageFilter< ImageTypeD, ImageTypeUC >	BinaryThresholdImageFilterType_F_UC
typedef itk::BinaryThresholdImageFilter< ImageTypeUC, ImageTypeUC >	BinaryThresholdImageFilterType_UC_UC
typedef anima::CheckStructureNeighborFilter< ImageTypeUC, ImageTypeUC >	CheckStructureNeighborFilterFilterType
typedef anima::ComputeMahalanobisImagesFilter< ImageTypeUC, ImageTypeUC, ImageTypeD >	ComputeMahalanobisImagesFilterType
typedef anima::ComputeSolution< ImageTypeUC, ImageTypeUC, ImageTypeD >	ComputeSolutionType
typedef itk::ConnectedComponentImageFilter< ImageTypeUC, ImageTypeInt >	ConnectedComponentType
typedef itk::SmartPointer< const Self >	ConstPointer
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType >	GaussianFunctionType
typedef anima::GraphCutFilter< TInputImage, ImageTypeUC >	GraphCutFilterType
typedef itk::ImageRegionConstIterator< InputImageType >	ImageIteratorTypeConstInput
typedef itk::ImageRegionConstIterator< ImageTypeUC >	ImageIteratorTypeConstUC
typedef itk::ImageRegionIterator< ImageTypeD >	ImageIteratorTypeD
typedef itk::ImageRegionIterator< ImageTypeInt >	ImageIteratorTypeInt
typedef itk::ImageRegionIterator< ImageTypeUC >	ImageIteratorTypeUC
typedef itk::Image< PixelTypeD, 3 >	ImageTypeD
typedef itk::Image< PixelTypeInt, 3 >	ImageTypeInt
typedef itk::Image< PixelTypeUC, 3 >	ImageTypeUC
typedef TInputImage	InputImageType
typedef itk::IntensityWindowingImageFilter< ImageTypeUC, ImageTypeD >	IntensityWindowingImageFilterType
typedef itk::MaskImageFilter< ImageTypeD, ImageTypeUC >	MaskFilterType_F_UC
typedef itk::MaskImageFilter< ImageTypeUC, ImageTypeUC >	MaskFilterType_UC_UC
typedef itk::MaximumImageFilter< ImageTypeD, ImageTypeD, ImageTypeD >	MaximumFilterType
typedef itk::VariableLengthVector< double >	MeasurementVectorType
typedef itk::MinimumImageFilter< ImageTypeD, ImageTypeD, ImageTypeD >	MinimumFilterTypeF
typedef itk::MinimumImageFilter< ImageTypeUC, ImageTypeUC, ImageTypeUC >	MinimumFilterTypeUC
typedef OutputImageType::Pointer	OutputImagePointer
typedef TOutputImage	OutputImageType
typedef itk::ImageRegionIterator< OutputImageType >	OutputIteratorType
typedef OutputImageType::PixelType	OutputPixelType
typedef double	PixelTypeD
typedef int	PixelTypeInt
typedef unsigned char	PixelTypeUC
typedef itk::SmartPointer< Self >	Pointer
typedef itk::RelabelComponentImageFilter< ImageTypeInt, ImageTypeInt >	RelabelComponentType
typedef anima::RemoveTouchingBorderFilter< ImageTypeUC, ImageTypeUC, ImageTypeUC >	RemoveTouchingBorderFilterType
typedef itk::RescaleIntensityImageFilter< TInputImage, ImageTypeUC >	RescaleFilterType
typedef GcStremMsLesionsSegmentationFilter	Self
typedef itk::ImageToImageFilter< TInputImage, TOutputImage >	Superclass
typedef anima::TLinksFilter< TInputImage, ImageTypeD >	TLinksFilterType
typedef itk::Image< unsigned char, 3 >	TOutputImage

Public Member Functions
void	ApplyHeuristicRules ()
void	CheckInputImages ()
void	ComputeAutomaticInitialization ()
void	ComputeNABT ()
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
void	CreateFuzzyRuleImage ()
void	GenerateData () ITK_OVERRIDE
virtual double	GetAlpha ()
virtual bool	GetEM_before_concentration ()
virtual int	GetEmIter ()
virtual int	GetEmIter_concentration ()
std::string	GetFuzzyOutputObjectFilename ()
virtual double	GetFuzzyRuleMax ()
virtual double	GetFuzzyRuleMin ()
virtual unsigned int	GetInitMethodType ()
virtual double	GetIntensityDPFactor ()
virtual double	GetIntensityFLAIRFactor ()
virtual double	GetIntensityT2Factor ()
virtual double	GetLesionPriorProportion ()
LesionSegmentationType	GetLesionSegmentationType ()
virtual double	GetMahalanobisThCSF ()
virtual double	GetMahalanobisThGM ()
virtual double	GetMahalanobisThWM ()
std::string	GetMatrixGradFilename ()
virtual double	GetMinDistance ()
virtual double	GetMinLesionsSize ()
virtual double	GetMultiVarSinks ()
virtual double	GetMultiVarSources ()
virtual const char *	GetNameOfClass () const
TOutputImage *	GetOutputCSF ()
std::string	GetOutputCSFFilename ()
itk::Image< double, 3 > *	GetOutputFuzzyObjectImage ()
std::string	GetOutputGCFilename ()
TOutputImage *	GetOutputGM ()
std::string	GetOutputGMFilename ()
TOutputImage *	GetOutputGraphCut ()
TOutputImage *	GetOutputIntensityImage1 ()
std::string	GetOutputIntensityImage1Filename ()
TOutputImage *	GetOutputIntensityImage2 ()
std::string	GetOutputIntensityImage2Filename ()
std::string	GetOutputLesionFile ()
TOutputImage *	GetOutputLesions ()
std::string	GetOutputMahaCSFFilename ()
itk::Image< double, 3 > *	GetOutputMahaCSFImage ()
std::string	GetOutputMahaGMFilename ()
itk::Image< double, 3 > *	GetOutputMahaGMImage ()
std::string	GetOutputMahaMaximumFilename ()
itk::Image< double, 3 > *	GetOutputMahaMaximumImage ()
std::string	GetOutputMahaMinimumFilename ()
itk::Image< double, 3 > *	GetOutputMahaMinimumImage ()
std::string	GetOutputMahaWMFilename ()
itk::Image< double, 3 > *	GetOutputMahaWMImage ()
TOutputImage *	GetOutputStrem ()
TOutputImage *	GetOutputStremCSF ()
std::string	GetOutputStremCSFFilename ()
std::string	GetOutputStremFilename ()
TOutputImage *	GetOutputStremGM ()
std::string	GetOutputStremGMFilename ()
TOutputImage *	GetOutputStremWM ()
std::string	GetOutputStremWMFilename ()
std::string	GetOutputWholeFilename ()
TOutputImage *	GetOutputWholeSeg ()
TOutputImage *	GetOutputWM ()
std::string	GetOutputWMFilename ()
virtual double	GetRatioContourWM ()
virtual double	GetRejRatio ()
virtual double	GetRejRatioHierar ()
virtual bool	GetRemoveBorder ()
virtual double	GetSigma ()
std::vector< GaussianFunctionType::Pointer >	GetSolution ()
virtual double	GetThresoldWMmap ()
virtual bool	GetUseDP ()
virtual bool	GetUseFLAIR ()
virtual bool	GetUseSpecGrad ()
virtual bool	GetUseT2 ()
virtual bool	GetVerbose ()
void	GraphCut ()
void	RescaleImages ()
virtual void	SetAlpha (double _arg)
virtual void	SetEM_before_concentration (bool _arg)
virtual void	SetEmIter (int _arg)
virtual void	SetEmIter_concentration (int _arg)
virtual void	SetFuzzyRuleMax (double _arg)
virtual void	SetFuzzyRuleMin (double _arg)
void	SetGaussianModel (std::vector< GaussianFunctionType::Pointer > solution)
virtual void	SetInitMethodType (unsigned int _arg)
void	SetInputCSFAtlas (const ImageTypeD *image)
void	SetInputGMAtlas (const ImageTypeD *image)
void	SetInputImageDP (const InputImageType *image)
void	SetInputImageFLAIR (const InputImageType *image)
void	SetInputImageT1 (const InputImageType *image)
void	SetInputImageT1Gd (const InputImageType *image)
void	SetInputImageT2 (const InputImageType *image)
void	SetInputLesionPrior (const ImageTypeD *image)
void	SetInputWMAtlas (const ImageTypeD *image)
virtual void	SetIntensityDPFactor (double _arg)
virtual void	SetIntensityFLAIRFactor (double _arg)
virtual void	SetIntensityT2Factor (double _arg)
virtual void	SetLesionPriorProportion (double _arg)
void	SetLesionSegmentationType (LesionSegmentationType type)
virtual void	SetMahalanobisThCSF (double _arg)
virtual void	SetMahalanobisThGM (double _arg)
virtual void	SetMahalanobisThWM (double _arg)
void	SetMask (const TInputImage *MaskImage)
void	SetMatrixGradFilename (std::string fn)
virtual void	SetMinDistance (double _arg)
virtual void	SetMinLesionsSize (double _arg)
virtual void	SetMultiVarSinks (double _arg)
virtual void	SetMultiVarSources (double _arg)
void	SetOutputCSFFilename (std::string fn)
void	SetOutputFuzzyObjectFilename (std::string fn)
void	SetOutputGCFilename (std::string fn)
void	SetOutputGMFilename (std::string fn)
void	SetOutputIntensityImage1Filename (std::string fn)
void	SetOutputIntensityImage2Filename (std::string fn)
void	SetOutputLesionFilename (std::string fn)
void	SetOutputMahaCSFFilename (std::string fn)
void	SetOutputMahaGMFilename (std::string fn)
void	SetOutputMahaMaximumFilename (std::string fn)
void	SetOutputMahaMinimumFilename (std::string fn)
void	SetOutputMahaWMFilename (std::string fn)
void	SetOutputStremCSFFilename (std::string fn)
void	SetOutputStremFilename (std::string fn)
void	SetOutputStremGMFilename (std::string fn)
void	SetOutputStremWMFilename (std::string fn)
void	SetOutputWholeFilename (std::string fn)
void	SetOutputWMFilename (std::string fn)
virtual void	SetRatioContourWM (double _arg)
virtual void	SetRejRatio (double _arg)
virtual void	SetRejRatioHierar (double _arg)
virtual void	SetRemoveBorder (bool _arg)
virtual void	SetSigma (double _arg)
void	SetSinksMask (const ImageTypeUC *MaskImage)
void	SetSolutionReadFilename (std::string fn)
void	SetSolutionWriteFilename (std::string fn)
void	SetSourcesMask (const ImageTypeUC *MaskImage)
virtual void	SetThresoldWMmap (double _arg)
void	SetTol (const double tol)
virtual void	SetUseDP (bool _arg)
virtual void	SetUseFLAIR (bool _arg)
virtual void	SetUseSpecGrad (bool _arg)
virtual void	SetUseT2 (bool _arg)
virtual void	SetVerbose (bool _arg)
void	StremThreshold ()
void	WriteOutputs ()

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
void	EmitProgress (int prog)
	GcStremMsLesionsSegmentationFilter ()
ImageTypeD::ConstPointer	GetInputCSFAtlas ()
ImageTypeD::ConstPointer	GetInputGMAtlas ()
InputImageType::ConstPointer	GetInputImageDP ()
InputImageType::ConstPointer	GetInputImageFLAIR ()
InputImageType::ConstPointer	GetInputImageT1 ()
InputImageType::ConstPointer	GetInputImageT1Gd ()
InputImageType::ConstPointer	GetInputImageT2 ()
ImageTypeD::ConstPointer	GetInputLesionPrior ()
ImageTypeD::ConstPointer	GetInputWMAtlas ()
InputImageType::ConstPointer	GetMask ()
ImageTypeUC::ConstPointer	GetSinksMask ()
ImageTypeUC::ConstPointer	GetSourcesMask ()
itk::DataObject::Pointer	MakeOutput (unsigned int idx)
	~GcStremMsLesionsSegmentationFilter ()

Static Protected Member Functions
static void	ManageProgress (itk::Object *caller, const itk::EventObject &event, void *clientData)

Protected Attributes
MaximumFilterType::Pointer	m_FilterMaxSinks
MaximumFilterType::Pointer	m_FilterMaxSources
GraphCutFilterType::Pointer	m_GraphCutFilter
ComputeMahalanobisImagesFilterType::Pointer	m_MahalanobisFilter
TLinksFilterType::Pointer	m_TLinksFilter

Detailed Description

template<typename TInputImage>
class anima::GcStremMsLesionsSegmentationFilter< TInputImage >

Class performing lesion segmentation.

The segmentation method has three steps:

1) Estimation of the NABT model: The NABT model computation requires strictly 3 sequences: T1-w and two sequences among T2-w, DP and FLAIR.

2) Detection of candidate lesions: The lesion detection can be done two different ways:

• applying a simple threshold after computing the mahalanobis distances on each one of the healthy tissues. (LesionSegmentationType == strem)

• applying a graph cut segmentation. (LesionSegmentationType == gcem) The automatic graph cut segmentation requires a sources and a sink probabilities maps that are computed from the mahalanobis images. The sources map is computed using also fuzzy weights between 0 and 1, based on T2-w, DP and FLAIR hyper-intensities. Additionally, binary sources and sinks masks can be added as entries of the graph cut.(LesionSegmentationType == gcemAndManualGC) Their information will be mixed with the automatic sources and sinks probabilities map. This option simulates the lesion segmentation correction done by a user that adds/removes seeds for the graph cut computation.

  The last segmentation type option (LesionSegmentationType == manualGC) just uses manual binary sources and sinks masks as entries of the graph cut. This option does not perform the estimation of the NABT model.

3) Application of a priori heuristic rules to extract the MS lesions from others outliers: The heuritic rules that can be used to refine the segmentation are:

• the size rule to remove small lesions
• the border rule to remove lesions touching the border of the brain mask if the NABT model has being computed, the following rules can be applied:
• hyper-intensity rule to remove voxels that are not hyper-intense comparing to the white matter in T2, DP and FLAIR sequence.
• white matter neighbor rule to remove lesions that are not in white matter.

Additionally to the lesions segmentation, the filter provides a segmentation of the healthy tissues based on the NABT estimation.

Definition at line 71 of file animaGcStremMsLesionsSegmentationFilter.h.

Member Typedef Documentation

BinaryThresholdImageFilterType_F_UC

template<typename TInputImage >

typedef itk::BinaryThresholdImageFilter<ImageTypeD, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_F_UC

Definition at line 126 of file animaGcStremMsLesionsSegmentationFilter.h.

BinaryThresholdImageFilterType_UC_UC

template<typename TInputImage >

typedef itk::BinaryThresholdImageFilter<ImageTypeUC, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_UC_UC

Definition at line 127 of file animaGcStremMsLesionsSegmentationFilter.h.

CheckStructureNeighborFilterFilterType

template<typename TInputImage >

typedef anima::CheckStructureNeighborFilter< ImageTypeUC,ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CheckStructureNeighborFilterFilterType

Definition at line 116 of file animaGcStremMsLesionsSegmentationFilter.h.

ComputeMahalanobisImagesFilterType

template<typename TInputImage >

typedef anima::ComputeMahalanobisImagesFilter<ImageTypeUC,ImageTypeUC,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeMahalanobisImagesFilterType

Definition at line 119 of file animaGcStremMsLesionsSegmentationFilter.h.

ComputeSolutionType

template<typename TInputImage >

typedef anima::ComputeSolution<ImageTypeUC,ImageTypeUC, ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeSolutionType

Definition at line 120 of file animaGcStremMsLesionsSegmentationFilter.h.

ConnectedComponentType

template<typename TInputImage >

typedef itk::ConnectedComponentImageFilter<ImageTypeUC,ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConnectedComponentType

Definition at line 131 of file animaGcStremMsLesionsSegmentationFilter.h.

ConstPointer

template<typename TInputImage >

typedef itk::SmartPointer<const Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConstPointer

Definition at line 80 of file animaGcStremMsLesionsSegmentationFilter.h.

GaussianFunctionType

template<typename TInputImage >

typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GaussianFunctionType

Definition at line 112 of file animaGcStremMsLesionsSegmentationFilter.h.

GraphCutFilterType

template<typename TInputImage >

typedef anima::GraphCutFilter< TInputImage, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCutFilterType

Define filters.

Definition at line 115 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageIteratorTypeConstInput

template<typename TInputImage >

typedef itk::ImageRegionConstIterator<InputImageType> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstInput

Definition at line 90 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageIteratorTypeConstUC

template<typename TInputImage >

typedef itk::ImageRegionConstIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstUC

Definition at line 101 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageIteratorTypeD

template<typename TInputImage >

typedef itk::ImageRegionIterator<ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeD

Definition at line 105 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageIteratorTypeInt

template<typename TInputImage >

typedef itk::ImageRegionIterator<ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeInt

Definition at line 109 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageIteratorTypeUC

template<typename TInputImage >

typedef itk::ImageRegionIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeUC

Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageTypeD

template<typename TInputImage >

typedef itk::Image<PixelTypeD,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeD

Definition at line 104 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageTypeInt

template<typename TInputImage >

typedef itk::Image<PixelTypeInt,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeInt

Definition at line 108 of file animaGcStremMsLesionsSegmentationFilter.h.

ImageTypeUC

template<typename TInputImage >

typedef itk::Image<PixelTypeUC,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeUC

Definition at line 99 of file animaGcStremMsLesionsSegmentationFilter.h.

InputImageType

template<typename TInputImage >

typedef TInputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::InputImageType

Type of the input images.

Definition at line 89 of file animaGcStremMsLesionsSegmentationFilter.h.

IntensityWindowingImageFilterType

template<typename TInputImage >

typedef itk::IntensityWindowingImageFilter<ImageTypeUC, ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::IntensityWindowingImageFilterType

Definition at line 128 of file animaGcStremMsLesionsSegmentationFilter.h.

MaskFilterType_F_UC

template<typename TInputImage >

typedef itk::MaskImageFilter< ImageTypeD, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_F_UC

Definition at line 130 of file animaGcStremMsLesionsSegmentationFilter.h.

MaskFilterType_UC_UC

template<typename TInputImage >

typedef itk::MaskImageFilter< ImageTypeUC, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_UC_UC

Definition at line 129 of file animaGcStremMsLesionsSegmentationFilter.h.

MaximumFilterType

template<typename TInputImage >

typedef itk::MaximumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaximumFilterType

Definition at line 123 of file animaGcStremMsLesionsSegmentationFilter.h.

MeasurementVectorType

template<typename TInputImage >

typedef itk::VariableLengthVector<double> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MeasurementVectorType

Definition at line 111 of file animaGcStremMsLesionsSegmentationFilter.h.

MinimumFilterTypeF

template<typename TInputImage >

typedef itk::MinimumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeF

Definition at line 124 of file animaGcStremMsLesionsSegmentationFilter.h.

MinimumFilterTypeUC

template<typename TInputImage >

typedef itk::MinimumImageFilter<ImageTypeUC,ImageTypeUC,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeUC

Definition at line 125 of file animaGcStremMsLesionsSegmentationFilter.h.

OutputImagePointer

template<typename TInputImage >

typedef OutputImageType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImagePointer

Definition at line 94 of file animaGcStremMsLesionsSegmentationFilter.h.

OutputImageType

template<typename TInputImage >

typedef TOutputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImageType

Type of the output images.

Definition at line 93 of file animaGcStremMsLesionsSegmentationFilter.h.

OutputIteratorType

template<typename TInputImage >

typedef itk::ImageRegionIterator< OutputImageType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputIteratorType

Definition at line 95 of file animaGcStremMsLesionsSegmentationFilter.h.

OutputPixelType

template<typename TInputImage >

typedef OutputImageType::PixelType anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputPixelType

Definition at line 96 of file animaGcStremMsLesionsSegmentationFilter.h.

PixelTypeD

template<typename TInputImage >

typedef double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeD

Definition at line 103 of file animaGcStremMsLesionsSegmentationFilter.h.

PixelTypeInt

template<typename TInputImage >

typedef int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeInt

Definition at line 107 of file animaGcStremMsLesionsSegmentationFilter.h.

PixelTypeUC

template<typename TInputImage >

typedef unsigned char anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeUC

Definition at line 98 of file animaGcStremMsLesionsSegmentationFilter.h.

Pointer

template<typename TInputImage >

typedef itk::SmartPointer<Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Pointer

Definition at line 79 of file animaGcStremMsLesionsSegmentationFilter.h.

RelabelComponentType

template<typename TInputImage >

typedef itk::RelabelComponentImageFilter< ImageTypeInt, ImageTypeInt > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RelabelComponentType

Definition at line 132 of file animaGcStremMsLesionsSegmentationFilter.h.

RemoveTouchingBorderFilterType

template<typename TInputImage >

typedef anima::RemoveTouchingBorderFilter<ImageTypeUC,ImageTypeUC,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RemoveTouchingBorderFilterType

Definition at line 117 of file animaGcStremMsLesionsSegmentationFilter.h.

RescaleFilterType

template<typename TInputImage >

typedef itk::RescaleIntensityImageFilter<TInputImage,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleFilterType

Definition at line 122 of file animaGcStremMsLesionsSegmentationFilter.h.

Self

template<typename TInputImage >

typedef GcStremMsLesionsSegmentationFilter anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Self

Standard class typedefs.

Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.h.

Superclass

template<typename TInputImage >

typedef itk::ImageToImageFilter< TInputImage, TOutputImage > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Superclass

Definition at line 78 of file animaGcStremMsLesionsSegmentationFilter.h.

TLinksFilterType

template<typename TInputImage >

typedef anima::TLinksFilter<TInputImage,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TLinksFilterType

Definition at line 118 of file animaGcStremMsLesionsSegmentationFilter.h.

TOutputImage

template<typename TInputImage >

typedef itk::Image<unsigned char, 3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TOutputImage

Definition at line 77 of file animaGcStremMsLesionsSegmentationFilter.h.

Constructor & Destructor Documentation

GcStremMsLesionsSegmentationFilter()

template<typename TInputImage >

anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GcStremMsLesionsSegmentationFilter ( )

inlineprotected

Definition at line 354 of file animaGcStremMsLesionsSegmentationFilter.h.

References anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MakeOutput(), anima::GraphCutFilter< TInput, TOutput >::New(), anima::ComputeMahalanobisImagesFilter< TInputImage, TMaskImage, TOutput >::New(), anima::TLinksFilter< TInput, TOutput >::New(), and strem.

~GcStremMsLesionsSegmentationFilter()

template<typename TInputImage >

anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter ( )

inlineprotected

Definition at line 459 of file animaGcStremMsLesionsSegmentationFilter.h.

References anima::GcStremMsLesionsSegmentationFilter< TInputImage >::EmitProgress(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputCSFAtlas(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputGMAtlas(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageDP(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageFLAIR(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1Gd(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT2(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputLesionPrior(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputWMAtlas(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMask(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSinksMask(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSourcesMask(), anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MakeOutput(), and anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ManageProgress().

Member Function Documentation

ApplyHeuristicRules()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ApplyHeuristicRules

(

)

Intensity Rule: MS lesions are known to be hyperintense compared to the WM intensity on T2-w and PD-w and FLAIR sequences. We use the information given by the NABT model to define hyper-intensity. A voxel is considered to be hyper-intense for a given sequence if its intensity y is greater than a threshold T that is defined by the probability of the Gaussian distribution and an intensity factor intensityFactor: For example the hyperintensity threshold T in T2 is defined as: T = meanT2 + intensityFactor * stdT2 meanT2 and stdT2 being the mean and standard deviation of the white matter in the sequence T2. If the voxel is not considered hyper-intense on T2-w, PD and FLAIR, it is discarded as a lesion voxel.

Size Rule: In order to avoid false positives, candidate lesions smaller than 9 mm3 in size are rejected. These small candidate lesions are usually produced by noise or flow artifacts. In clinical practice, lesions must have a radius of 3 mm on one image slice to be considered as such.

Definition at line 897 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References HierarchicalDP, and manualGC.

CheckInputImages()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CheckInputImages

(

)

Definition at line 391 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

ComputeAutomaticInitialization()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeAutomaticInitialization

(

)

Definition at line 534 of file animaGcStremMsLesionsSegmentationFilter.hxx.

ComputeNABT()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeNABT

(

)

Definition at line 1127 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

CreateAnother()

template<typename TInputImage >

virtual::itk::LightObject::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateAnother

(

void

)

const

CreateFuzzyRuleImage()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateFuzzyRuleImage

(

)

Definition at line 695 of file animaGcStremMsLesionsSegmentationFilter.hxx.

EmitProgress()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::EmitProgress ( int  prog )

protected

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GenerateData()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GenerateData

(

)

Definition at line 1230 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC, and strem.

GetAlpha()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetAlpha ( )

virtual

GetEM_before_concentration()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEM_before_concentration ( )

virtual

GetEmIter()

template<typename TInputImage >

virtual int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEmIter ( )

virtual

GetEmIter_concentration()

template<typename TInputImage >

virtual int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEmIter_concentration ( )

virtual

GetFuzzyOutputObjectFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyOutputObjectFilename ( )

inline

Definition at line 314 of file animaGcStremMsLesionsSegmentationFilter.h.

GetFuzzyRuleMax()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyRuleMax ( )

virtual

GetFuzzyRuleMin()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyRuleMin ( )

virtual

GetInitMethodType()

template<typename TInputImage >

virtual unsigned int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInitMethodType ( )

virtual

GetInputCSFAtlas()

template<typename TInputImage >

itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputCSFAtlas ( )

protected

Definition at line 152 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputGMAtlas()

template<typename TInputImage >

itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputGMAtlas ( )

protected

Definition at line 159 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputImageDP()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageDP ( )

protected

Definition at line 131 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputImageFLAIR()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageFLAIR ( )

protected

Definition at line 138 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputImageT1()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1 ( )

protected

Definition at line 117 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputImageT1Gd()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1Gd ( )

protected

Definition at line 144 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputImageT2()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT2 ( )

protected

Definition at line 124 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputLesionPrior()

template<typename TInputImage >

itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputLesionPrior ( )

protected

Definition at line 173 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetInputWMAtlas()

template<typename TInputImage >

itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputWMAtlas ( )

protected

Definition at line 166 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetIntensityDPFactor()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityDPFactor ( )

virtual

GetIntensityFLAIRFactor()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityFLAIRFactor ( )

virtual

GetIntensityT2Factor()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityT2Factor ( )

virtual

GetLesionPriorProportion()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetLesionPriorProportion ( )

virtual

GetLesionSegmentationType()

template<typename TInputImage >

LesionSegmentationType anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetLesionSegmentationType ( )

inline

Definition at line 281 of file animaGcStremMsLesionsSegmentationFilter.h.

GetMahalanobisThCSF()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThCSF ( )

virtual

GetMahalanobisThGM()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThGM ( )

virtual

GetMahalanobisThWM()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThWM ( )

virtual

GetMask()

template<typename TInputImage >

TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMask ( )

protected

Definition at line 110 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetMatrixGradFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMatrixGradFilename ( )

inline

Definition at line 344 of file animaGcStremMsLesionsSegmentationFilter.h.

GetMinDistance()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMinDistance ( )

virtual

GetMinLesionsSize()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMinLesionsSize ( )

virtual

GetMultiVarSinks()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMultiVarSinks ( )

virtual

GetMultiVarSources()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMultiVarSources ( )

virtual

GetNameOfClass()

template<typename TInputImage >

virtual const char* anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods)

GetOutputCSF()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputCSF

(

)

Definition at line 219 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputCSFFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputCSFFilename ( )

inline

Definition at line 287 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputFuzzyObjectImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputFuzzyObjectImage

(

)

Definition at line 269 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputGCFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGCFilename ( )

inline

Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputGM()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGM

(

)

Definition at line 224 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputGMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGMFilename ( )

inline

Definition at line 290 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputGraphCut()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGraphCut

(

)

Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputIntensityImage1()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage1

(

)

Definition at line 259 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputIntensityImage1Filename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage1Filename ( )

inline

Definition at line 332 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputIntensityImage2()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage2

(

)

Definition at line 264 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputIntensityImage2Filename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage2Filename ( )

inline

Definition at line 335 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputLesionFile()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputLesionFile ( )

inline

Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputLesions()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputLesions

(

)

Definition at line 214 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputMahaCSFFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaCSFFilename ( )

inline

Definition at line 317 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputMahaCSFImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaCSFImage

(

)

Definition at line 274 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputMahaGMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaGMFilename ( )

inline

Definition at line 320 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputMahaGMImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaGMImage

(

)

Definition at line 279 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputMahaMaximumFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMaximumFilename ( )

inline

Definition at line 326 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputMahaMaximumImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMaximumImage

(

)

Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputMahaMinimumFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMinimumFilename ( )

inline

Definition at line 329 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputMahaMinimumImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMinimumImage

(

)

Definition at line 289 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputMahaWMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaWMFilename ( )

inline

Definition at line 323 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputMahaWMImage()

template<typename TInputImage >

itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaWMImage

(

)

Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputStrem()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStrem

(

)

Definition at line 239 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputStremCSF()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremCSF

(

)

Definition at line 244 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputStremCSFFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremCSFFilename ( )

inline

Definition at line 305 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputStremFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremFilename ( )

inline

Definition at line 302 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputStremGM()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremGM

(

)

Definition at line 249 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputStremGMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremGMFilename ( )

inline

Definition at line 308 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputStremWM()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremWM

(

)

Definition at line 254 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputStremWMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremWMFilename ( )

inline

Definition at line 311 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputWholeFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWholeFilename ( )

inline

Definition at line 296 of file animaGcStremMsLesionsSegmentationFilter.h.

GetOutputWholeSeg()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWholeSeg

(

)

Definition at line 234 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputWM()

template<typename TInputImage >

itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWM

(

)

Definition at line 229 of file animaGcStremMsLesionsSegmentationFilter.hxx.

GetOutputWMFilename()

template<typename TInputImage >

std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWMFilename ( )

inline

Definition at line 293 of file animaGcStremMsLesionsSegmentationFilter.h.

GetRatioContourWM()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRatioContourWM ( )

virtual

GetRejRatio()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRejRatio ( )

virtual

GetRejRatioHierar()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRejRatioHierar ( )

virtual

GetRemoveBorder()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRemoveBorder ( )

virtual

GetSigma()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSigma ( )

virtual

GetSinksMask()

template<typename TInputImage >

itk::Image< unsigned char, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSinksMask ( )

protected

Definition at line 185 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetSolution()

template<typename TInputImage >

std::vector<GaussianFunctionType::Pointer> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSolution ( )

inline

Definition at line 339 of file animaGcStremMsLesionsSegmentationFilter.h.

GetSourcesMask()

template<typename TInputImage >

itk::Image< unsigned char, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSourcesMask ( )

protected

Definition at line 179 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

GetThresoldWMmap()

template<typename TInputImage >

virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetThresoldWMmap ( )

virtual

GetUseDP()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseDP ( )

virtual

GetUseFLAIR()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseFLAIR ( )

virtual

GetUseSpecGrad()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseSpecGrad ( )

virtual

GetUseT2()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseT2 ( )

virtual

GetVerbose()

template<typename TInputImage >

virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetVerbose ( )

virtual

GraphCut()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCut

(

)

Definition at line 784 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References gcemAndManualGC, manualGC, anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetAlpha(), singleGaussianTLink, and stremTLink.

MakeOutput()

template<typename TInputImage >

itk::DataObject::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MakeOutput ( unsigned int  idx )

protected

Create the Output

Definition at line 193 of file animaGcStremMsLesionsSegmentationFilter.hxx.

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GcStremMsLesionsSegmentationFilter(), and anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

ManageProgress()

template<typename TInputImage >

static void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ManageProgress ( itk::Object *  caller, const itk::EventObject &  event, void *  clientData  )

staticprotected

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().

New()

template<typename TInputImage >

static Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::New ( )

static

Method for creation through the object factory.

RescaleImages()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleImages

(

void

)

Definition at line 427 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

SetAlpha()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetAlpha ( double  _arg )

virtual

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCut().

SetEM_before_concentration()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEM_before_concentration ( bool  _arg )

virtual

SetEmIter()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEmIter ( int  _arg )

virtual

SetEmIter_concentration()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEmIter_concentration ( int  _arg )

virtual

SetFuzzyRuleMax()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetFuzzyRuleMax ( double  _arg )

virtual

SetFuzzyRuleMin()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetFuzzyRuleMin ( double  _arg )

virtual

SetGaussianModel()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetGaussianModel ( std::vector< GaussianFunctionType::Pointer >  solution )

inline

Definition at line 338 of file animaGcStremMsLesionsSegmentationFilter.h.

SetInitMethodType()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInitMethodType ( unsigned int  _arg )

virtual

Setter/Getter for parameters

SetInputCSFAtlas()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputCSFAtlas

(

const ImageTypeD *

image

)

Definition at line 60 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputGMAtlas()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputGMAtlas

(

const ImageTypeD *

image

)

Definition at line 68 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputImageDP()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageDP

(

const InputImageType *

image

)

Definition at line 33 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputImageFLAIR()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageFLAIR

(

const InputImageType *

image

)

Definition at line 42 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputImageT1()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1

(

const InputImageType *

image

)

Setter for images

Definition at line 15 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputImageT1Gd()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1Gd

(

const InputImageType *

image

)

Definition at line 51 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputImageT2()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT2

(

const InputImageType *

image

)

Definition at line 24 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputLesionPrior()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputLesionPrior

(

const ImageTypeD *

image

)

Definition at line 84 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetInputWMAtlas()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputWMAtlas

(

const ImageTypeD *

image

)

Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetIntensityDPFactor()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityDPFactor ( double  _arg )

virtual

SetIntensityFLAIRFactor()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityFLAIRFactor ( double  _arg )

virtual

SetIntensityT2Factor()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityT2Factor ( double  _arg )

virtual

SetLesionPriorProportion()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetLesionPriorProportion ( double  _arg )

virtual

SetLesionSegmentationType()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetLesionSegmentationType ( LesionSegmentationType  type )

inline

Definition at line 282 of file animaGcStremMsLesionsSegmentationFilter.h.

SetMahalanobisThCSF()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThCSF ( double  _arg )

virtual

SetMahalanobisThGM()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThGM ( double  _arg )

virtual

SetMahalanobisThWM()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThWM ( double  _arg )

virtual

SetMask()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMask

(

const TInputImage *

MaskImage

)

Definition at line 7 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetMatrixGradFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMatrixGradFilename ( std::string  fn )

inline

Definition at line 345 of file animaGcStremMsLesionsSegmentationFilter.h.

SetMinDistance()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMinDistance ( double  _arg )

virtual

SetMinLesionsSize()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMinLesionsSize ( double  _arg )

virtual

SetMultiVarSinks()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMultiVarSinks ( double  _arg )

virtual

SetMultiVarSources()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMultiVarSources ( double  _arg )

virtual

SetOutputCSFFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputCSFFilename ( std::string  fn )

inline

Definition at line 288 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputFuzzyObjectFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputFuzzyObjectFilename ( std::string  fn )

inline

Definition at line 315 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputGCFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputGCFilename ( std::string  fn )

inline

Definition at line 300 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputGMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputGMFilename ( std::string  fn )

inline

Definition at line 291 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputIntensityImage1Filename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputIntensityImage1Filename ( std::string  fn )

inline

Definition at line 333 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputIntensityImage2Filename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputIntensityImage2Filename ( std::string  fn )

inline

Definition at line 336 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputLesionFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputLesionFilename ( std::string  fn )

inline

Definition at line 285 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputMahaCSFFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaCSFFilename ( std::string  fn )

inline

Definition at line 318 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputMahaGMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaGMFilename ( std::string  fn )

inline

Definition at line 321 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputMahaMaximumFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaMaximumFilename ( std::string  fn )

inline

Definition at line 327 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputMahaMinimumFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaMinimumFilename ( std::string  fn )

inline

Definition at line 330 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputMahaWMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaWMFilename ( std::string  fn )

inline

Definition at line 324 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputStremCSFFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremCSFFilename ( std::string  fn )

inline

Definition at line 306 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputStremFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremFilename ( std::string  fn )

inline

Definition at line 303 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputStremGMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremGMFilename ( std::string  fn )

inline

Definition at line 309 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputStremWMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremWMFilename ( std::string  fn )

inline

Definition at line 312 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputWholeFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputWholeFilename ( std::string  fn )

inline

Definition at line 297 of file animaGcStremMsLesionsSegmentationFilter.h.

SetOutputWMFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputWMFilename ( std::string  fn )

inline

Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.h.

SetRatioContourWM()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRatioContourWM ( double  _arg )

virtual

SetRejRatio()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRejRatio ( double  _arg )

virtual

SetRejRatioHierar()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRejRatioHierar ( double  _arg )

virtual

SetRemoveBorder()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRemoveBorder ( bool  _arg )

virtual

SetSigma()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSigma ( double  _arg )

virtual

SetSinksMask()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSinksMask

(

const ImageTypeUC *

MaskImage

)

Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetSolutionReadFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSolutionReadFilename ( std::string  fn )

inline

Definition at line 341 of file animaGcStremMsLesionsSegmentationFilter.h.

SetSolutionWriteFilename()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSolutionWriteFilename ( std::string  fn )

inline

Definition at line 342 of file animaGcStremMsLesionsSegmentationFilter.h.

SetSourcesMask()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSourcesMask

(

const ImageTypeUC *

MaskImage

)

Definition at line 92 of file animaGcStremMsLesionsSegmentationFilter.hxx.

SetThresoldWMmap()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetThresoldWMmap ( double  _arg )

virtual

SetTol()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetTol ( const double  tol )

inline

Definition at line 184 of file animaGcStremMsLesionsSegmentationFilter.h.

SetUseDP()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseDP ( bool  _arg )

virtual

SetUseFLAIR()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseFLAIR ( bool  _arg )

virtual

SetUseSpecGrad()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseSpecGrad ( bool  _arg )

virtual

SetUseT2()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseT2 ( bool  _arg )

virtual

SetVerbose()

template<typename TInputImage >

virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetVerbose ( bool  _arg )

virtual

StremThreshold()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::StremThreshold

(

)

Definition at line 610 of file animaGcStremMsLesionsSegmentationFilter.hxx.

WriteOutputs()

template<typename TInputImage >

void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::WriteOutputs

(

)

Definition at line 307 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References gcem, gcemAndManualGC, manualGC, strem, and anima::GcStremMsLesionsSegmentationFilter< TInputImage >::WriteOutputs().

Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::WriteOutputs().

Member Data Documentation

m_FilterMaxSinks

template<typename TInputImage >

MaximumFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_FilterMaxSinks

protected

Definition at line 351 of file animaGcStremMsLesionsSegmentationFilter.h.

m_FilterMaxSources

template<typename TInputImage >

MaximumFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_FilterMaxSources

protected

Definition at line 350 of file animaGcStremMsLesionsSegmentationFilter.h.

m_GraphCutFilter

template<typename TInputImage >

GraphCutFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_GraphCutFilter

protected

Definition at line 348 of file animaGcStremMsLesionsSegmentationFilter.h.

m_MahalanobisFilter

template<typename TInputImage >

ComputeMahalanobisImagesFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_MahalanobisFilter

protected

Definition at line 352 of file animaGcStremMsLesionsSegmentationFilter.h.

m_TLinksFilter

template<typename TInputImage >

TLinksFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_TLinksFilter

protected

Definition at line 349 of file animaGcStremMsLesionsSegmentationFilter.h.

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The documentation for this class was generated from the following files:

• animaGcStremMsLesionsSegmentationFilter.h
• animaGcStremMsLesionsSegmentationFilter.hxx