ANIMA
4.0
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Class performing lesion segmentation. More...
#include <animaGcStremMsLesionsSegmentationFilter.h>
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 |
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 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:
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.
typedef itk::BinaryThresholdImageFilter<ImageTypeD, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_F_UC |
Definition at line 126 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::BinaryThresholdImageFilter<ImageTypeUC, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_UC_UC |
Definition at line 127 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::CheckStructureNeighborFilter< ImageTypeUC,ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CheckStructureNeighborFilterFilterType |
Definition at line 116 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::ComputeMahalanobisImagesFilter<ImageTypeUC,ImageTypeUC,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeMahalanobisImagesFilterType |
Definition at line 119 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::ComputeSolution<ImageTypeUC,ImageTypeUC, ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeSolutionType |
Definition at line 120 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ConnectedComponentImageFilter<ImageTypeUC,ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConnectedComponentType |
Definition at line 131 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::SmartPointer<const Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConstPointer |
Definition at line 80 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GaussianFunctionType |
Definition at line 112 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::GraphCutFilter< TInputImage, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCutFilterType |
Define filters.
Definition at line 115 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionConstIterator<InputImageType> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstInput |
Definition at line 90 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionConstIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstUC |
Definition at line 101 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionIterator<ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeD |
Definition at line 105 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionIterator<ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeInt |
Definition at line 109 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeUC |
Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::Image<PixelTypeD,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeD |
Definition at line 104 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::Image<PixelTypeInt,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeInt |
Definition at line 108 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::Image<PixelTypeUC,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeUC |
Definition at line 99 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef TInputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::InputImageType |
Type of the input images.
Definition at line 89 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::IntensityWindowingImageFilter<ImageTypeUC, ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::IntensityWindowingImageFilterType |
Definition at line 128 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::MaskImageFilter< ImageTypeD, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_F_UC |
Definition at line 130 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::MaskImageFilter< ImageTypeUC, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_UC_UC |
Definition at line 129 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::MaximumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaximumFilterType |
Definition at line 123 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::VariableLengthVector<double> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MeasurementVectorType |
Definition at line 111 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::MinimumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeF |
Definition at line 124 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::MinimumImageFilter<ImageTypeUC,ImageTypeUC,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeUC |
Definition at line 125 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef OutputImageType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImagePointer |
Definition at line 94 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef TOutputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImageType |
Type of the output images.
Definition at line 93 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageRegionIterator< OutputImageType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputIteratorType |
Definition at line 95 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef OutputImageType::PixelType anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputPixelType |
Definition at line 96 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeD |
Definition at line 103 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeInt |
Definition at line 107 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef unsigned char anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeUC |
Definition at line 98 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::SmartPointer<Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Pointer |
Definition at line 79 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::RelabelComponentImageFilter< ImageTypeInt, ImageTypeInt > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RelabelComponentType |
Definition at line 132 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::RemoveTouchingBorderFilter<ImageTypeUC,ImageTypeUC,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RemoveTouchingBorderFilterType |
Definition at line 117 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::RescaleIntensityImageFilter<TInputImage,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleFilterType |
Definition at line 122 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef GcStremMsLesionsSegmentationFilter anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Self |
Standard class typedefs.
Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::ImageToImageFilter< TInputImage, TOutputImage > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Superclass |
Definition at line 78 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef anima::TLinksFilter<TInputImage,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TLinksFilterType |
Definition at line 118 of file animaGcStremMsLesionsSegmentationFilter.h.
typedef itk::Image<unsigned char, 3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TOutputImage |
Definition at line 77 of file animaGcStremMsLesionsSegmentationFilter.h.
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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.
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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().
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.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CheckInputImages | ( | ) |
Definition at line 391 of file animaGcStremMsLesionsSegmentationFilter.hxx.
References manualGC.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeAutomaticInitialization | ( | ) |
Definition at line 534 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeNABT | ( | ) |
Definition at line 1127 of file animaGcStremMsLesionsSegmentationFilter.hxx.
References manualGC.
virtual::itk::LightObject::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateAnother | ( | void | ) | const |
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateFuzzyRuleImage | ( | ) |
Definition at line 695 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GenerateData | ( | ) |
Definition at line 1230 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 314 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 152 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 159 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 131 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 138 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 117 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 144 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 124 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 173 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 166 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 281 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 110 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 344 of file animaGcStremMsLesionsSegmentationFilter.h.
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Run-time type information (and related methods)
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputCSF | ( | ) |
Definition at line 219 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 287 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputFuzzyObjectImage | ( | ) |
Definition at line 269 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGM | ( | ) |
Definition at line 224 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 290 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGraphCut | ( | ) |
Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.hxx.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage1 | ( | ) |
Definition at line 259 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 332 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage2 | ( | ) |
Definition at line 264 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 335 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputLesions | ( | ) |
Definition at line 214 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 317 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaCSFImage | ( | ) |
Definition at line 274 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 320 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaGMImage | ( | ) |
Definition at line 279 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 326 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMaximumImage | ( | ) |
Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 329 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMinimumImage | ( | ) |
Definition at line 289 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 323 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaWMImage | ( | ) |
Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.hxx.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStrem | ( | ) |
Definition at line 239 of file animaGcStremMsLesionsSegmentationFilter.hxx.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremCSF | ( | ) |
Definition at line 244 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 305 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 302 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremGM | ( | ) |
Definition at line 249 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 308 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremWM | ( | ) |
Definition at line 254 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 311 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 296 of file animaGcStremMsLesionsSegmentationFilter.h.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWholeSeg | ( | ) |
Definition at line 234 of file animaGcStremMsLesionsSegmentationFilter.hxx.
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWM | ( | ) |
Definition at line 229 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 293 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 185 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Definition at line 339 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 179 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCut | ( | ) |
Definition at line 784 of file animaGcStremMsLesionsSegmentationFilter.hxx.
References gcemAndManualGC, manualGC, anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetAlpha(), singleGaussianTLink, and stremTLink.
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Create the Output
Definition at line 193 of file animaGcStremMsLesionsSegmentationFilter.hxx.
Referenced by anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GcStremMsLesionsSegmentationFilter(), and anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter().
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Method for creation through the object factory.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleImages | ( | void | ) |
Definition at line 427 of file animaGcStremMsLesionsSegmentationFilter.hxx.
References manualGC.
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Definition at line 338 of file animaGcStremMsLesionsSegmentationFilter.h.
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Setter/Getter for parameters
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputCSFAtlas | ( | const ImageTypeD * | image | ) |
Definition at line 60 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputGMAtlas | ( | const ImageTypeD * | image | ) |
Definition at line 68 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageDP | ( | const InputImageType * | image | ) |
Definition at line 33 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageFLAIR | ( | const InputImageType * | image | ) |
Definition at line 42 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1 | ( | const InputImageType * | image | ) |
Setter for images
Definition at line 15 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1Gd | ( | const InputImageType * | image | ) |
Definition at line 51 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT2 | ( | const InputImageType * | image | ) |
Definition at line 24 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputLesionPrior | ( | const ImageTypeD * | image | ) |
Definition at line 84 of file animaGcStremMsLesionsSegmentationFilter.hxx.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputWMAtlas | ( | const ImageTypeD * | image | ) |
Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 282 of file animaGcStremMsLesionsSegmentationFilter.h.
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void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMask | ( | const TInputImage * | MaskImage | ) |
Definition at line 7 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 345 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 288 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 315 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 300 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 291 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 333 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 336 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 285 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 318 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 321 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 327 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 330 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 324 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 306 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 303 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 309 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 312 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 297 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.h.
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void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSinksMask | ( | const ImageTypeUC * | MaskImage | ) |
Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 341 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 342 of file animaGcStremMsLesionsSegmentationFilter.h.
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSourcesMask | ( | const ImageTypeUC * | MaskImage | ) |
Definition at line 92 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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Definition at line 184 of file animaGcStremMsLesionsSegmentationFilter.h.
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void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::StremThreshold | ( | ) |
Definition at line 610 of file animaGcStremMsLesionsSegmentationFilter.hxx.
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().
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Definition at line 351 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 350 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 348 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 352 of file animaGcStremMsLesionsSegmentationFilter.h.
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Definition at line 349 of file animaGcStremMsLesionsSegmentationFilter.h.