Extract ODF peaks by searching all local maxima on a densely sampled ODF und clustering these maxima to get the underlying fiber direction. NrOdfDirections: number of sampling points on the ODF surface (about 20000 is a good value) More...

#include <itkFiniteDiffOdfMaximaExtractionFilter.h>

Inheritance diagram for itk::FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections >:

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Collaboration diagram for itk::FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections >:

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Public Types
enum	Toolkit { FSL, MRTRIX }

enum	NormalizationMethods { NO_NORM, SINGLE_VEC_NORM, MAX_VEC_NORM }

typedef FiniteDiffOdfMaximaExtractionFilter	Self

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef ImageToImageFilter< Image< Vector< PixelType,(ShOrder *ShOrder+ShOrder+2)/2+ShOrder >, 3 >, Image< Vector< PixelType, 3 >, 3 > >	Superclass

typedef Superclass::InputImageType	CoefficientImageType

typedef CoefficientImageType::RegionType	CoefficientImageRegionType

typedef CoefficientImageType::PixelType	CoefficientPixelType

typedef Superclass::OutputImageType	OutputImageType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef OrientationDistributionFunction< PixelType, NrOdfDirections >	OdfType

typedef itk::Image< unsigned char, 3 >	ItkUcharImgType

typedef vnl_vector_fixed< double, 3 >	DirectionType

typedef Image< Vector< float, 3 >, 3 >	ItkDirectionImage

typedef VectorContainer< unsigned int, ItkDirectionImage::Pointer >	ItkDirectionImageContainer

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

virtual void	SetMaxNumPeaks (unsigned int _arg)
	maximum number of peaks per voxel. if more peaks are detected, only the largest are kept. More...

virtual void	SetPeakThreshold (double _arg)
	threshold on the peak length relative to the largest peak inside the current voxel More...

virtual void	SetAbsolutePeakThreshold (double _arg)
	hard threshold on the peak length of all local maxima More...

virtual void	SetClusteringThreshold (double _arg)
	directions closer together than the specified angular threshold will be clustered (in rad) More...

virtual void	SetAngularThreshold (double _arg)
	directions closer together than the specified threshold that remain after clustering are discarded (largest is kept) (in rad) More...

virtual void	SetMaskImage (ItkUcharImgType::Pointer _arg)
	only voxels inside the binary mask are processed More...

virtual void	SetNormalizationMethod (NormalizationMethods _arg)
	normalization method of ODF peaks More...

virtual void	SetFlipX (bool _arg)
	flip peaks in x direction More...

virtual void	SetFlipY (bool _arg)
	flip peaks in y direction More...

virtual void	SetFlipZ (bool _arg)
	flip peaks in z direction More...

virtual mitk::FiberBundle::Pointer	GetOutputFiberBundle ()
	vector field (peak sizes rescaled for visualization purposes) More...

virtual ItkDirectionImageContainer::Pointer	GetDirectionImageContainer ()
	container for output peaks More...

virtual ItkUcharImgType::Pointer	GetNumDirectionsImage ()
	number of peaks per voxel More...

virtual void	SetToolkit (Toolkit _arg)
	define SH coefficient convention (depends on toolkit) More...

virtual Toolkit	GetToolkit ()
	SH coefficient convention (depends on toolkit) More...

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	FiniteDiffOdfMaximaExtractionFilter ()

	~FiniteDiffOdfMaximaExtractionFilter ()

void	BeforeThreadedGenerateData ()

void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadID)

void	AfterThreadedGenerateData ()

void	FindCandidatePeaks (OdfType &odf, double odfMax, std::vector< DirectionType > &inDirs)

std::vector< DirectionType >	MeanShiftClustering (std::vector< DirectionType > &inDirs)

void	Cart2Sph (const std::vector< DirectionType > &dir, vnl_matrix< double > &sphCoords)

vnl_matrix< double >	CalcShBasis (vnl_matrix< double > &sphCoords)

Detailed Description

template<class PixelType, int ShOrder, int NrOdfDirections>
class itk::FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections >

Extract ODF peaks by searching all local maxima on a densely sampled ODF und clustering these maxima to get the underlying fiber direction. NrOdfDirections: number of sampling points on the ODF surface (about 20000 is a good value)

Definition at line 37 of file itkFiniteDiffOdfMaximaExtractionFilter.h.