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

#include <itkDiffusionTensor3DReconstructionImageFilter.h>

Inheritance diagram for DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >:

[legend]

Collaboration diagram for DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >:

[legend]

Public Types
typedef vnl_matrix< double >	CoefficientMatrixType

typedef SmartPointer< const Self >	ConstPointer

typedef VectorContainer< unsigned int, GradientDirectionType >	GradientDirectionContainerType
	Container to hold gradient directions of the 'n' DW measurements.

typedef vnl_vector_fixed< double, 3 >	GradientDirectionType
	Holds each magnetic field gradient used to acquire one DWImage.

typedef VectorImage< GradientPixelType, 3 >	GradientImagesType
	An alternative typedef defining one (of the many) gradient images. More...

typedef Image< GradientPixelType, 3 >	GradientImageType
	Typedef defining one (of the many) gradient images. More...

typedef TGradientImagePixelType	GradientPixelType

typedef ImageMaskType::Pointer	ImageMaskPointer

typedef SpatialObject< 3 >	ImageMaskType
	Type for the mask of the fixed image. More...

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef TensorImageType	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef Superclass::InputImageType	ReferenceImageType
	Reference image data, This image is acquired in the absence of a diffusion sensitizing field gradient.

typedef TReferenceImagePixelType	ReferencePixelType

typedef VectorImage< GradientPixelType, 3 >	ResidualImageType
	Typedef defining the residual image. More...

typedef ResidualImageType::PixelType	ResidualPixelType

typedef DiffusionTensor3DReconstructionImageFilter	Self

typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >	Superclass

typedef vnl_matrix_fixed< double, 6, 6 >	TensorBasisInverseMatrixType

typedef vnl_matrix_fixed< double, 6, 6 >	TensorBasisMatrixType
	Holds the tensor basis coefficients G_k.

typedef TensorPixelType::EigenValuesArrayType	TensorEigenValuesType

typedef TensorPixelType::EigenVectorsMatrixType	TensorEigenVectorsType

typedef Image< TensorPixelType, 3 >	TensorImageType

typedef TensorPixelType::MatrixType	TensorMatrixType

typedef DiffusionTensor3D< TTensorPixelType >	TensorPixelType

Public Member Functions
void	AddGradientImage (const GradientDirectionType &, const GradientImageType *image)
	Set method to add a gradient direction and its corresponding image. More...

virtual GradientDirectionType	GetGradientDirection (unsigned int idx) const
	Return the gradient direction. More...

virtual ReferenceImageType *	GetReferenceImage ()
	Get reference image.

	itkGetConstObjectMacro (ImageMask, ImageMaskType)

	itkGetConstObjectMacro (ResidualImage, ResidualImageType)
	Get the Residual image . More...

	itkGetConstReferenceMacro (BValue, TTensorPixelType)

	itkGetMacro (Threshold, ReferencePixelType)

	itkGetMacro (CalculateResidualImage, bool)

	itkNewMacro (Self)
	Method for creation through the object factory. More...

	itkSetMacro (Threshold, ReferencePixelType)
	Threshold on the reference image data. More...

	itkSetMacro (CalculateResidualImage, bool)
	Get/set compute residuals flag. More...

	itkSetMacro (BValue, TTensorPixelType)
	The BValue value used in normalizing the tensors to physically meaningful units. More...

	itkSetObjectMacro (ImageMask, ImageMaskType)
	Set/Get the image mask. More...

	itkTypeMacro (DiffusionTensor3DReconstructionImageFilter, ImageToImageFilter)
	Runtime information support. More...

void	SetGradientImage (GradientDirectionContainerType , const GradientImagesType image)
	Another set method to add a gradient directions and its corresponding image. More...

void	SetReferenceImage (ReferenceImageType *referenceImage)
	Set method to set the reference image. More...

Protected Types
enum	GradientImageTypeEnumeration { GradientIsInASingleImage = 1, GradientIsInManyImages, Else }
	enum to indicate if the gradient image is specified as a single multi- component image or as several separate images

Protected Member Functions
void	BeforeThreadedGenerateData ()

ResidualPixelType	ComputeResidual (vnl_vector< double >, TensorPixelType, double)

void	ComputeTensorBasis ()

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

void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int)

Detailed Description

template<class TReferenceImagePixelType, class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double>
class itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >

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

(with DiffusionTensor3D as the pixel type). Once that is done, you can apply filters on this tensor image to compute FA, ADC, RGB weighted maps etc.

sbia additions to itk DiffusionTensor3DRecon Filter added a spatial Object as a mask. added cludge to fix nonSPD tensors. at the moment only this just takes abs of any negative eigenvalues. Posible future direction is to include spd constrain when this occurs.

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 applying the Stejskal-Tanner equations.

Outputs: The output image is an image of Tensors:
Image< DiffusionTensor3D< TTensorPixelType >, 3 >

Parameters

Threshold - Threshold on the reference image data. The output tensor will be a null tensor 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.

Template parameters: The class is templated over the pixel type of the reference and gradient images (expected to be scalar data types) and the internal representation of the DiffusionTensor3D pixel (double, float etc).

References:

[1] C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis, "Processing and visualization for Diffusion tensor MRI", Medical image Analysis, 2002, pp 93-108.
[2] A Dual Tensor Basis Solution to the Stejskal-Tanner Equations for DT-MRI

WARNING:: Although this filter has been written to support multiple threads, please set the number of threads to 1.
filter->SetNumberOfThreads(1);
This is due to buggy code in netlib/dsvdc, that is called by vnl_svd. (used to compute the psudo-inverse to find the dual tensor basis).

Author: Thanks to Xiaodong Tao, GE, for contributing parts of this class. Also thanks to Casey Goodlet, UNC for patches to support multiple baseline images and other improvements.

Note: This work is part of the National Alliance for Medical image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.

Examples and Datasets: See Examples/Filtering/DiffusionTensor3DReconstructionImageFilter.cxx Sample DTI datasets may be obtained from \begin verbatim ftp://public.kitware.com/pub/namic/DTI/Data/dwi.nhdr ftp://public.kitware.com/pub/namic/DTI/Data/dwi.img.gz ( gunzip this ) \end verbatim

See also: DiffusionTensor3D SymmetricSecondRankTensor

Member Typedef Documentation

◆ GradientImagesType

typedef VectorImage< GradientPixelType, 3 > GradientImagesType

An alternative typedef defining one (of the many) gradient images.

It will be assumed that the vectorImage has the same dimension as the Reference image and a vector length parameter of n (number of gradient directions)

◆ GradientImageType

typedef Image< GradientPixelType, 3 > GradientImageType

Typedef defining one (of the many) gradient images.

◆ ImageMaskType

typedef SpatialObject< 3 > ImageMaskType

Type for the mask of the fixed image.

Only pixels that are "inside" this mask will be considered for the computation of the metric

◆ ResidualImageType

typedef VectorImage< GradientPixelType, 3 > ResidualImageType

Typedef defining the residual image.

Member Function Documentation

◆ AddGradientImage()

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

Set method to add a gradient direction and its corresponding image.

◆ GetGradientDirection()

virtual GradientDirectionType GetGradientDirection ( unsigned int idx ) const

inlinevirtual

Return the gradient direction.

idx is 0 based

◆ itkGetConstObjectMacro()

itkGetConstObjectMacro	(	ResidualImage	,
		ResidualImageType
	)

Get the Residual image .

◆ itkNewMacro()

itkNewMacro ( Self )

Method for creation through the object factory.

◆ itkSetMacro() [1/3]

itkSetMacro	(	Threshold	,
		ReferencePixelType
	)

Threshold on the reference image data.

The output tensor will be a null tensor for pixels in the reference image that have a value less than this threshold.

◆ itkSetMacro() [2/3]

itkSetMacro	(	CalculateResidualImage	,
		bool
	)

Get/set compute residuals flag.

◆ itkSetMacro() [3/3]

itkSetMacro	(	BValue	,
		TTensorPixelType
	)

The BValue $ (s/mm^2) $ value used in normalizing the tensors to physically meaningful units.

See equation (24) of the first reference for a description of how this is applied to the tensor estimation. Equation (1) of the same reference describes the physical significance.

◆ itkSetObjectMacro()

itkSetObjectMacro	(	ImageMask	,
		ImageMaskType
	)

Set/Get the image mask.

◆ itkTypeMacro()

itkTypeMacro	(	DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >	,
		ImageToImageFilter
	)

Runtime information support.

◆ SetGradientImage()

void SetGradientImage	(	GradientDirectionContainerType *	,
		const GradientImagesType *	image
	)

Another set method to add a gradient directions and its corresponding image.

The image here is a VectorImage. The user is expected to pass the gradient directions in a container. The ith element of the container corresponds to the gradient direction of the ith component image the VectorImage. For the baseline image, a vector of all zeros should be set.

◆ SetReferenceImage()

void SetReferenceImage ( ReferenceImageType * referenceImage )

inline

Set method to set the reference image.

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

src/classes/itk/itkDiffusionTensor3DReconstructionImageFilter.h

Public Types

Public Member Functions

Protected Types

Protected Member Functions