itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType > Class Template Reference
[Multithreaded Filters, Objects Related to Tensor Images]

This class takes as input a 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. The class is templated over the pixel type of the reference and gradient images (expected to be scalar images) and the internal representation of the DiffusionTensor3D pixel (double, float etc). More...

#include <itkDiffusionTensor3DReconstructionImageFilter.h>

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

[legend]Collaboration diagram for itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >:

[legend]List of all members.

Public Types
typedef DiffusionTensor3DReconstructionImageFilter	Self
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >	Superclass
typedef TReferenceImagePixelType	ReferencePixelType
typedef TGradientImagePixelType	GradientPixelType
typedef DiffusionTensor3D< TTensorPixelType >	TensorPixelType
typedef Superclass::InputImageType	ReferenceImageType
typedef Image< TensorPixelType, 3 >	TensorImageType
typedef TensorImageType	OutputImageType
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef Image< GradientPixelType, 3 >	GradientImageType
typedef vnl_matrix_fixed< double, 6, 6 >	TensorBasisMatrixType
typedef vnl_matrix< double >	CoefficientMatrixType
typedef vnl_vector_fixed< double, 3 >	GradientDirectionType
typedef VectorContainer< unsigned int, GradientDirectionType >	GradientDirectionContainerType
Public Member Functions
virtual const char *	GetNameOfClass () const
void	AddGradientImage (const GradientDirectionType &, const GradientImageType *image)
void	SetReferenceImage (ReferenceImageType *referenceImage)
virtual ReferenceImageType *	GetReferenceImage ()
virtual GradientImageType *	GetGradientImage (unsigned int idx)
virtual GradientDirectionType	GetGradientDirection (unsigned int idx) const
virtual void	SetThreshold (ReferencePixelType _arg)
virtual ReferencePixelType	GetThreshold ()
Static Public Member Functions
Pointer	New ()
Protected Member Functions
	DiffusionTensor3DReconstructionImageFilter ()
	~DiffusionTensor3DReconstructionImageFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
void	ComputeTensorBasis ()
void	BeforeThreadedGenerateData ()
void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int)

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Detailed Description

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

This class takes as input a 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. The class is templated over the pixel type of the reference and gradient images (expected to be scalar images) and the internal representation of the DiffusionTensor3D pixel (double, float etc).

The funding for creating this class was largely provided by NAMIC (National Alliance for Medical Image Computing) (http://www.na-mic.org).

References:

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.

Author:

Based on code from Xiaodong Tao, GE CRD.

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.

See also:

DiffusionTensor3D SymmetricSecondRankTensor

Definition at line 61 of file itkDiffusionTensor3DReconstructionImageFilter.h.

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Member Typedef Documentation

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

Definition at line 104 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::~DiffusionTensor3DReconstructionImageFilter().

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef SmartPointer<const Self> itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ConstPointer

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 70 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef VectorContainer< unsigned int, GradientDirectionType > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GradientDirectionContainerType

Container to hold gradient directions of the 'n' DW measurements Definition at line 111 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef vnl_vector_fixed< double, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GradientDirectionType

Holds each magnetic field gradient used to acquire one DWImage Definition at line 107 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef Image< GradientPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GradientImageType

Definition at line 99 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetGradientImage().

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

Definition at line 84 of file itkDiffusionTensor3DReconstructionImageFilter.h.

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

Superclass typedefs. Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 97 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::~DiffusionTensor3DReconstructionImageFilter().

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

Some convenient typedefs. Reimplemented from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 94 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef SmartPointer<Self> itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::Pointer

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 69 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef Superclass::InputImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ReferenceImageType

Reference image data, This image is aquired in teh absence of a diffusion sensitizing field gradient Definition at line 90 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetReferenceImage(), and itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::SetReferenceImage().

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

Definition at line 82 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::~DiffusionTensor3DReconstructionImageFilter().

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

Standard class typedefs. Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 68 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>, Image< DiffusionTensor3D< TTensorPixelType >, 3 > > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::Superclass

Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >. Definition at line 73 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef vnl_matrix_fixed< double, 6, 6 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::TensorBasisMatrixType

Holds the tensor basis coefficients G_k Definition at line 102 of file itkDiffusionTensor3DReconstructionImageFilter.h. Referenced by itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::~DiffusionTensor3DReconstructionImageFilter().

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef Image< TensorPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::TensorImageType

Definition at line 92 of file itkDiffusionTensor3DReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> typedef DiffusionTensor3D< TTensorPixelType > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::TensorPixelType

Definition at line 86 of file itkDiffusionTensor3DReconstructionImageFilter.h.

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Constructor & Destructor Documentation

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::DiffusionTensor3DReconstructionImageFilter (   )  [protected]

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::~DiffusionTensor3DReconstructionImageFilter (   )  [inline, protected]

Definition at line 159 of file itkDiffusionTensor3DReconstructionImageFilter.h. References itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::CoefficientMatrixType, itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::OutputImageRegionType, itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ReferencePixelType, and itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::TensorBasisMatrixType.

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Member Function Documentation

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::AddGradientImage (  const GradientDirectionType &  , const GradientImageType *  image )

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

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::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, class TTensorPixelType = double> void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ComputeTensorBasis (   )  [protected]

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

Return the gradient direction. idx is 0 based Definition at line 139 of file itkDiffusionTensor3DReconstructionImageFilter.h. References itkExceptionMacro.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> virtual GradientImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetGradientImage (  unsigned int  idx  )  [inline, virtual]

Return the gradient image. idx is 0 based Definition at line 128 of file itkDiffusionTensor3DReconstructionImageFilter.h. References itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GradientImageType, and NULL.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> virtual const char* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetNameOfClass (   )  const [virtual]

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

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> virtual ReferenceImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetReferenceImage (  void   )  [inline, virtual]

Get reference image Definition at line 124 of file itkDiffusionTensor3DReconstructionImageFilter.h. References itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ReferenceImageType.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> virtual ReferencePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::GetThreshold (   )  [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, class TTensorPixelType = double> Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::New (   )  [static]

Method for creation through the object factory. Reimplemented from itk::Object.

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

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes. Reimplemented from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::SetReferenceImage (  ReferenceImageType *  referenceImage  )  [inline]

Set method to set the reference image. Definition at line 118 of file itkDiffusionTensor3DReconstructionImageFilter.h. References itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ReferenceImageType.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TTensorPixelType = double> virtual void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::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, class TTensorPixelType = double> void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::ThreadedGenerateData (  const OutputImageRegionType &  outputRegionForThread, int  )  [protected, virtual]

If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). This superclass will automatically split the output image into a number of pieces, spawn multiple threads, and call ThreadedGenerateData() in each thread. Prior to spawning threads, the BeforeThreadedGenerateData() method is called. After all the threads have completed, the AfterThreadedGenerateData() method is called. If an image processing filter cannot support threading, that filter should provide an implementation of the GenerateData() method instead of providing an implementation of ThreadedGenerateData(). If a filter provides a GenerateData() method as its implementation, then the filter is responsible for allocating the output data. If a filter provides a ThreadedGenerateData() method as its implementation, then the output memory will allocated automatically by this superclass. The ThreadedGenerateData() method should only produce the output specified by "outputThreadRegion" parameter. ThreadedGenerateData() cannot write to any other portion of the output image (as this is responsibility of a different thread). See also: GenerateData(), SplitRequestedRegion() Reimplemented from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >.

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

• itkDiffusionTensor3DReconstructionImageFilter.h

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