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. More...

#include <itkDiffusionTensor3DReconstructionImageFilter.h>

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

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

List of all members.

Public Types
typedef vnl_matrix< double >	CoefficientMatrixType
typedef SmartPointer< const Self >	ConstPointer
typedef VectorContainer < unsigned int, GradientDirectionType >	GradientDirectionContainerType
typedef vnl_vector_fixed < double, 3 >	GradientDirectionType
typedef VectorImage < GradientPixelType, 3 >	GradientImagesType
typedef Image < GradientPixelType, 3 >	GradientImageType
typedef TGradientImagePixelType	GradientPixelType
typedef TMaskImageType	MaskImageType
typedef SpatialObject< 3 >	MaskSpatialObjectType
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef TensorImageType	OutputImageType
typedef SmartPointer< Self >	Pointer
typedef Superclass::InputImageType	ReferenceImageType
typedef TReferenceImagePixelType	ReferencePixelType
typedef DiffusionTensor3DReconstructionImageFilter	Self
typedef ImageToImageFilter < Image < TReferenceImagePixelType, 3 > , Image< DiffusionTensor3D < TTensorPixelType >, 3 > >	Superclass
typedef vnl_matrix_fixed < double, 6, 6 >	TensorBasisMatrixType
typedef Image< TensorPixelType, 3 >	TensorImageType
typedef DiffusionTensor3D < TTensorPixelType >	TensorPixelType
Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual const char *	GetNameOfClass () const
virtual ReferenceImageType *	GetReferenceImage ()
void	SetGradientImage (GradientDirectionContainerType , const GradientImagesType image)
void	SetMaskImage (MaskImageType *maskImage)
void	SetMaskSpatialObject (MaskSpatialObjectType *maskSpatialObject)
void	SetReferenceImage (ReferenceImageType *referenceImage)
	typedef (Concept::OStreamWritable< TensorPixelType >) TensorOStreamWritableCheck
	typedef (Concept::OStreamWritable< ReferencePixelType >) ReferenceOStreamWritableCheck

void	AddGradientImage (const GradientDirectionType &, const GradientImageType *image)
const GradientImageType *	GetGradientImage (unsigned index) const

virtual GradientDirectionType	GetGradientDirection (unsigned int idx) const

virtual void	SetThreshold (ReferencePixelType _arg)
virtual ReferencePixelType	GetThreshold () const

virtual void	SetBValue (TTensorPixelType _arg)
virtual const TTensorPixelType &	GetBValue ()

	typedef (Concept::EqualityComparable< ReferencePixelType >) ReferenceEqualityComparableCheck
	typedef (Concept::EqualityComparable< TensorPixelType >) TensorEqualityComparableCheck
	typedef (Concept::Convertible< GradientPixelType, double >) GradientConvertibleToDoubleCheck
	typedef (Concept::Convertible< double, TensorPixelType >) DoubleConvertibleToTensorCheck
	typedef (Concept::AdditiveOperators< GradientPixelType, GradientPixelType, ReferencePixelType >) GradientReferenceAdditiveOperatorsCheck
	typedef (Concept::AdditiveAndAssignOperators< GradientPixelType, ReferencePixelType >) GradientReferenceAdditiveAndAssignOperatorsCheck
Static Public Member Functions
static Pointer	New ()
Protected Types
enum	GradientImageTypeEnumeration { GradientIsInASingleImage = 1, GradientIsInManyImages, Else }
Protected Member Functions
void	BeforeThreadedGenerateData ()
void	ComputeTensorBasis ()
void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType)

	DiffusionTensor3DReconstructionImageFilter ()
	~DiffusionTensor3DReconstructionImageFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
Private Attributes
CoefficientMatrixType	m_BMatrix
TTensorPixelType	m_BValue
GradientDirectionContainerType::Pointer	m_GradientDirectionContainer
GradientImageTypeEnumeration	m_GradientImageTypeEnumeration
bool	m_MaskImagePresent
unsigned int	m_NumberOfBaselineImages
unsigned int	m_NumberOfGradientDirections
TensorBasisMatrixType	m_TensorBasis
ReferencePixelType	m_Threshold

Detailed Description

template<class TReferenceImagePixelType, class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>
class itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >

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.

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:: Xiaodong Tao, GE, for contributing parts of this class.; 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

Examples:: Examples/Filtering/DiffusionTensor3DReconstructionImageFilter.cxx.

Definition at line 127 of file itkDiffusionTensor3DReconstructionImageFilter.h.

Member Typedef Documentation

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef vnl_matrix< double > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::CoefficientMatrixType

Definition at line 182 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef SmartPointer< const Self > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ConstPointer

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 135 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef VectorContainer< unsigned int, GradientDirectionType > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GradientDirectionContainerType

Container to hold gradient directions of the 'n' DW measurements

Definition at line 189 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef vnl_vector_fixed< double, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GradientDirectionType

Holds each magnetic field gradient used to acquire one DWImage

Definition at line 185 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef VectorImage< GradientPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::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)

Definition at line 171 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef Image< GradientPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GradientImageType

Typedef defining one (of the many) gradient images.

Definition at line 165 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef TGradientImagePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GradientPixelType

Definition at line 149 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef TMaskImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::MaskImageType

The type for the optional mask image

Definition at line 177 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef SpatialObject<3> itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::MaskSpatialObjectType

The type for the optional SpatialObject for masking

Definition at line 174 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef Superclass::OutputImageRegionType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::OutputImageRegionType

Superclass typedefs.

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 162 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef TensorImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::OutputImageType

Some convenient typedefs.

Reimplemented from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 159 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef SmartPointer< Self > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::Pointer

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 134 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef Superclass::InputImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ReferenceImageType

Reference image data, This image is aquired in the absence of a diffusion sensitizing field gradient

Definition at line 155 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef TReferenceImagePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ReferencePixelType

Definition at line 145 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef DiffusionTensor3DReconstructionImageFilter itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::Self

Standard class typedefs.

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 133 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::Superclass

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

Definition at line 138 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef vnl_matrix_fixed< double, 6, 6 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::TensorBasisMatrixType

Holds the tensor basis coefficients G_k

Definition at line 180 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef Image< TensorPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::TensorImageType

Definition at line 157 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

typedef DiffusionTensor3D< TTensorPixelType > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::TensorPixelType

Definition at line 151 of file itkDiffusionTensor3DReconstructionImageFilter.h.

Member Enumeration Documentation

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

enum itk::DiffusionTensor3DReconstructionImageFilter::GradientImageTypeEnumeration [protected]

enum to indicate if the gradient image is specified as a single multi- component image or as several separate images

Enumerator:

GradientIsInASingleImage
GradientIsInManyImages
Else

Definition at line 300 of file itkDiffusionTensor3DReconstructionImageFilter.h.

Constructor & Destructor Documentation

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::DiffusionTensor3DReconstructionImageFilter ( ) [protected]

End concept checking

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::~DiffusionTensor3DReconstructionImageFilter ( ) [inline, protected]

End concept checking

Definition at line 287 of file itkDiffusionTensor3DReconstructionImageFilter.h.

Member Function Documentation

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::AddGradientImage	(	const GradientDirectionType &	,
		const GradientImageType *	image
	)

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

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::BeforeThreadedGenerateData ( void ) [protected, virtual]

If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.

Reimplemented from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ComputeTensorBasis ( ) [protected]

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual::itk::LightObject::Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::CreateAnother ( void ) const [virtual]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual const TTensorPixelType& itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetBValue ( ) [virtual]

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.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual GradientDirectionType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetGradientDirection ( unsigned int idx ) const [inline, virtual]

Return the gradient direction. idx is 0 based

Definition at line 224 of file itkDiffusionTensor3DReconstructionImageFilter.h.

References itkExceptionMacro.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

const GradientImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetGradientImage ( unsigned index ) const

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

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual const char* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetNameOfClass ( ) const [virtual]

Runtime information support.

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual ReferenceImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetReferenceImage ( ) [inline, virtual]

Get reference image

Definition at line 220 of file itkDiffusionTensor3DReconstructionImageFilter.h.

References itk::ProcessObject::GetInput().

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual ReferencePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetThreshold ( ) const [virtual]

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.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

static Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const `[protected, virtual]`

End concept checking

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetBValue ( TTensorPixelType _arg ) [virtual]

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.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::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.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetMaskImage ( MaskImageType * maskImage )

set an image mask

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetMaskSpatialObject ( MaskSpatialObjectType * maskSpatialObject )

set a spatial object mask

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetReferenceImage ( ReferenceImageType * referenceImage ) [inline]

Set method to set the reference image.

Definition at line 206 of file itkDiffusionTensor3DReconstructionImageFilter.h.

References itkExceptionMacro, and itk::ProcessObject::SetNthInput().

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

virtual void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetThreshold ( ReferencePixelType _arg ) [virtual]

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.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ThreadedGenerateData	(	const OutputImageRegionType &	outputRegionForThread,
		ThreadIdType
	)		`[protected]`

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::AdditiveOperators< GradientPixelType, GradientPixelType, ReferencePixelType > )

This class requires GradientReferenceAdditiveOperatorsCheck in the form of ( Concept::AdditiveOperators< GradientPixelType, GradientPixelType, ReferencePixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::OStreamWritable< ReferencePixelType > )

This class requires ReferenceOStreamWritableCheck in the form of ( Concept::OStreamWritable< ReferencePixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::AdditiveAndAssignOperators< GradientPixelType, ReferencePixelType > )

This class requires GradientReferenceAdditiveAndAssignOperatorsCheck in the form of ( Concept::AdditiveAndAssignOperators< GradientPixelType, ReferencePixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::EqualityComparable< ReferencePixelType > )

Begin concept checking This class requires ReferenceEqualityComparableCheck in the form of ( Concept::EqualityComparable< ReferencePixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::EqualityComparable< TensorPixelType > )

This class requires TensorEqualityComparableCheck in the form of ( Concept::EqualityComparable< TensorPixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::Convertible< double, TensorPixelType > )

This class requires DoubleConvertibleToTensorCheck in the form of ( Concept::Convertible< double, TensorPixelType > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::Convertible< GradientPixelType, double > )

This class requires GradientConvertibleToDoubleCheck in the form of ( Concept::Convertible< GradientPixelType, double > )

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef ( Concept::OStreamWritable< TensorPixelType > )

This class requires TensorOStreamWritableCheck in the form of ( Concept::OStreamWritable< TensorPixelType > )

Member Data Documentation

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

CoefficientMatrixType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_BMatrix [private]

Definition at line 310 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

TTensorPixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_BValue [private]

LeBihan's b-value for normalizing tensors

Definition at line 325 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

GradientDirectionContainerType::Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_GradientDirectionContainer [private]

container to hold gradient directions

Definition at line 313 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

GradientImageTypeEnumeration itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_GradientImageTypeEnumeration [private]

Gradient image was specified in a single image or in multiple images

Definition at line 328 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

bool itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_MaskImagePresent [private]

Mask Image Present

Definition at line 331 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

unsigned int itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_NumberOfBaselineImages [private]

Number of baseline images

Definition at line 319 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

unsigned int itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_NumberOfGradientDirections [private]

Number of gradient measurements

Definition at line 316 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

TensorBasisMatrixType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_TensorBasis [private]

Definition at line 308 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>

ReferencePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_Threshold [private]

Threshold on the reference image data

Definition at line 322 of file itkDiffusionTensor3DReconstructionImageFilter.h.

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