This class takes as input one or more reference images (acquired in the absence of diffusion sensitizing gradients) and 'n' diffusion weighted images and their gradient directions and computes an image of orientation distribution functions (ODFs). More...

#include <itkDiffusionQballReconstructionImageFilter.h>

Inheritance diagram for itk::DiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters >:

[legend]

Collaboration diagram for itk::DiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters >:

[legend]

Public Types
enum	Normalization { QBR_STANDARD, QBR_B_ZERO_B_VALUE, QBR_B_ZERO, QBR_NONE }

typedef DiffusionQballReconstructionImageFilter	Self

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >	Superclass

typedef TReferenceImagePixelType	ReferencePixelType

typedef TGradientImagePixelType	GradientPixelType

typedef Vector< TOdfPixelType, NrOdfDirections >	OdfPixelType

typedef Superclass::InputImageType	ReferenceImageType

typedef Image< OdfPixelType, 3 >	OdfImageType

typedef OdfImageType	OutputImageType

typedef TOdfPixelType	BZeroPixelType

typedef Image< BZeroPixelType, 3 >	BZeroImageType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef Image< GradientPixelType, 3 >	GradientImageType

typedef VectorImage< GradientPixelType, 3 >	GradientImagesType

typedef vnl_matrix< TOdfPixelType > *	OdfReconstructionMatrixType

typedef vnl_vector_fixed< double, 3 >	GradientDirectionType

typedef VectorContainer< unsigned int, GradientDirectionType >	GradientDirectionContainerType

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

	itkStaticConstMacro (NOdfDirections, int, NrOdfDirections)

	itkStaticConstMacro (NBasisFunctionCenters, int, NrBasisFunctionCenters)

void	AddGradientImage (const GradientDirectionType &, const GradientImageType *image)

void	SetGradientImage (const GradientDirectionContainerType , const GradientImagesType image)

void	SetReferenceImage (ReferenceImageType *referenceImage)

virtual ReferenceImageType *	GetReferenceImage ()

virtual GradientDirectionType	GetGradientDirection (unsigned int idx) const

OdfPixelType	Normalize (OdfPixelType odf, typename NumericTraits< ReferencePixelType >::AccumulateType b0)

vnl_vector< TOdfPixelType >	PreNormalize (vnl_vector< TOdfPixelType > vec)

virtual void	SetThreshold (ReferencePixelType _arg)

virtual ReferencePixelType	GetThreshold ()

virtual void	SetNormalizationMethod (Normalization _arg)

virtual Normalization	GetNormalizationMethod ()

virtual BZeroImageType::Pointer	GetBZeroImage ()

virtual void	SetBValue (TOdfPixelType _arg)

virtual const TOdfPixelType &	GetBValue ()

Static Public Member Functions
static Pointer	New ()

Protected Types
enum	GradientImageTypeEnumeration { GradientIsInASingleImage, GradientIsInManyImages, Else }

Protected Member Functions
	DiffusionQballReconstructionImageFilter ()

	~DiffusionQballReconstructionImageFilter ()

void	PrintSelf (std::ostream &os, Indent indent) const

void	ComputeReconstructionMatrix ()

void	BeforeThreadedGenerateData ()

void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType)

Detailed Description

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NrOdfDirections, int NrBasisFunctionCenters = NrOdfDirections>
class itk::DiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters >

This class takes as input one or more reference images (acquired in the absence of diffusion sensitizing gradients) and 'n' diffusion weighted images and their gradient directions and computes an image of orientation distribution functions (ODFs).

Inputs and Usage: There are two ways to use this class. When you have one reference image and n gradient images, you would use the class as
filter->SetReferenceImage( image0 );

filter->AddGradientImage( direction1, image1 );

filter->AddGradientImage( direction2, image2 );

...

: When you have the 'n' gradient and one or more reference images in a single multi-component image (VectorImage), you can specify the images simply as
filter->SetGradientImage( directionsContainer, vectorImage );

Note that this method is used to specify both the reference and gradient images. This is convenient when the DWI images are read in using the NRRD format. Like the Nrrd format, the reference images are those components of the vectorImage whose gradient direction is (0,0,0). If more than one reference image is present, they are averaged prior to the reconstruction.

Outputs: The output image is an image of vectors that must be understood as ODFs:
Image< Vector< TPixelType, OdfNrDirections >, 3 >

Parameters

Threshold - Threshold on the reference image data. The output ODF will be a null pdf for pixels in the reference image that have a value less than this.
BValue - See the documentation of SetBValue().
At least 6 gradient images must be specified for the filter to be able to run. If the input gradient directions g_i are majorly sampled on one half of the sqhere, then each input image I_i will be duplicated and assign -g_i in order to guarantee stability of the Tuch-Algorithm.
OdfDirections - directions of resulting orientation distribution function
EquatorNrSamplingPoints - number of sampling points on equator when performing Funk Radeon Transform (FRT)
BasisFunctionCenters - the centers of the basis functions are used for the sRBF (spherical radial basis functions interpolation). If not set, they will be defaulted to equal m_EquatorNrSamplingPoints

Template parameters

The class is templated over

the pixel type of the reference and gradient images (expected to be scalar data types)
the internal representation of the ODF pixels (double, float etc).
the number of OdfDirections
the number of basis function centers for the sRBF

References:

[1] Tuch DS, "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72.

Definition at line 100 of file itkDiffusionQballReconstructionImageFilter.h.