ITK
4.1.0
Insight Segmentation and Registration Toolkit
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#include <itkDiffusionTensor3DReconstructionImageFilter.h>
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.
n
gradient images, you would use the class as filter->SetReferenceImage( image0 ); filter->AddGradientImage( direction1, image1 ); filter->AddGradientImage( direction2, image2 ); ...
filter->SetGradientImage( directionsContainer, vectorImage );
Image< DiffusionTensor3D< TTensorPixelType >, 3 >
filter->SetNumberOfThreads(1);
Definition at line 127 of file itkDiffusionTensor3DReconstructionImageFilter.h.
typedef vnl_matrix< double > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::CoefficientMatrixType |
Definition at line 182 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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.
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.
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.
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.
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.
typedef TGradientImagePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GradientPixelType |
Definition at line 149 of file itkDiffusionTensor3DReconstructionImageFilter.h.
typedef TMaskImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::MaskImageType |
The type for the optional mask image
Definition at line 177 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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.
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.
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.
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.
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.
typedef TReferenceImagePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ReferencePixelType |
Definition at line 145 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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.
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.
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.
typedef Image< TensorPixelType, 3 > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::TensorImageType |
Definition at line 157 of file itkDiffusionTensor3DReconstructionImageFilter.h.
typedef DiffusionTensor3D< TTensorPixelType > itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::TensorPixelType |
Definition at line 151 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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
Definition at line 300 of file itkDiffusionTensor3DReconstructionImageFilter.h.
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::DiffusionTensor3DReconstructionImageFilter | ( | ) | [protected] |
End concept checking
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::~DiffusionTensor3DReconstructionImageFilter | ( | ) | [inline, protected] |
End concept checking
Definition at line 287 of file itkDiffusionTensor3DReconstructionImageFilter.h.
void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::AddGradientImage | ( | const GradientDirectionType & | , |
const GradientImageType * | image | ||
) |
Set method to add a gradient direction and its corresponding image.
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 > >.
void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ComputeTensorBasis | ( | ) | [protected] |
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.
virtual const TTensorPixelType& itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetBValue | ( | ) | [virtual] |
The BValue 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.
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.
const GradientImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetGradientImage | ( | unsigned | index | ) | const |
Set method to add a gradient direction and its corresponding image.
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 > >.
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().
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.
static Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::New | ( | ) | [static] |
Method for creation through the object factory.
Reimplemented from itk::Object.
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 > >.
virtual void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetBValue | ( | TTensorPixelType | _arg | ) | [virtual] |
The BValue 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.
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.
void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetMaskImage | ( | MaskImageType * | maskImage | ) |
set an image mask
void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::SetMaskSpatialObject | ( | MaskSpatialObjectType * | maskSpatialObject | ) |
set a spatial object mask
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 itk::ProcessObject::SetNthInput().
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.
void itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::ThreadedGenerateData | ( | const OutputImageRegionType & | outputRegionForThread, |
ThreadIdType | |||
) | [protected] |
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::EqualityComparable< ReferencePixelType > | ) |
Begin concept checking This class requires ReferenceEqualityComparableCheck in the form of ( Concept::EqualityComparable< ReferencePixelType > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::EqualityComparable< TensorPixelType > | ) |
This class requires TensorEqualityComparableCheck in the form of ( Concept::EqualityComparable< TensorPixelType > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::Convertible< GradientPixelType, double > | ) |
This class requires GradientConvertibleToDoubleCheck in the form of ( Concept::Convertible< GradientPixelType, double > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::Convertible< double, TensorPixelType > | ) |
This class requires DoubleConvertibleToTensorCheck in the form of ( Concept::Convertible< double, TensorPixelType > )
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 > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::AdditiveAndAssignOperators< GradientPixelType, ReferencePixelType > | ) |
This class requires GradientReferenceAdditiveAndAssignOperatorsCheck in the form of ( Concept::AdditiveAndAssignOperators< GradientPixelType, ReferencePixelType > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::OStreamWritable< ReferencePixelType > | ) |
This class requires ReferenceOStreamWritableCheck in the form of ( Concept::OStreamWritable< ReferencePixelType > )
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::typedef | ( | Concept::OStreamWritable< TensorPixelType > | ) |
This class requires TensorOStreamWritableCheck in the form of ( Concept::OStreamWritable< TensorPixelType > )
CoefficientMatrixType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_BMatrix [private] |
Definition at line 310 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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.
GradientDirectionContainerType::Pointer itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_GradientDirectionContainer [private] |
container to hold gradient directions
Definition at line 313 of file itkDiffusionTensor3DReconstructionImageFilter.h.
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.
bool itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_MaskImagePresent [private] |
Mask Image Present
Definition at line 331 of file itkDiffusionTensor3DReconstructionImageFilter.h.
unsigned int itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_NumberOfBaselineImages [private] |
Number of baseline images
Definition at line 319 of file itkDiffusionTensor3DReconstructionImageFilter.h.
unsigned int itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_NumberOfGradientDirections [private] |
Number of gradient measurements
Definition at line 316 of file itkDiffusionTensor3DReconstructionImageFilter.h.
TensorBasisMatrixType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_TensorBasis [private] |
Definition at line 308 of file itkDiffusionTensor3DReconstructionImageFilter.h.
ReferencePixelType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::m_Threshold [private] |
Threshold on the reference image data
Definition at line 322 of file itkDiffusionTensor3DReconstructionImageFilter.h.