ITK  4.2.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Private Attributes
itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType > Class Template Reference

#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 SelfConstPointer
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< SelfPointer
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 Types inherited from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
typedef
InputImageType::ConstPointer 
InputImageConstPointer
typedef InputImageType::PixelType InputImagePixelType
typedef InputImageType::Pointer InputImagePointer
typedef InputImageType::RegionType InputImageRegionType
typedef Image
< TReferenceImagePixelType, 3 > 
InputImageType
typedef
Superclass::OutputImagePixelType 
OutputImagePixelType
- Public Types inherited from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
typedef
Superclass::DataObjectIdentifierType 
DataObjectIdentifierType
typedef DataObject::Pointer DataObjectPointer
typedef
Superclass::DataObjectPointerArraySizeType 
DataObjectPointerArraySizeType
typedef OutputImageType::Pointer OutputImagePointer
- Public Types inherited from itk::ProcessObject
typedef std::vector
< DataObjectPointer
DataObjectPointerArray
typedef std::vector
< DataObjectIdentifierType
NameArray
- Public Types inherited from itk::Object
- Public Types inherited from itk::LightObject

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
virtual const char * GetNameOfClass () const
virtual ReferenceImageTypeGetReferenceImage ()
void SetGradientImage (GradientDirectionContainerType *, const GradientImagesType *image)
void SetMaskImage (MaskImageType *maskImage)
void SetMaskSpatialObject (MaskSpatialObjectType *maskSpatialObject)
void SetReferenceImage (ReferenceImageType *referenceImage)
 typedef (Concept::OStreamWritable< ReferencePixelType >) ReferenceOStreamWritableCheck
 typedef (Concept::OStreamWritable< TensorPixelType >) TensorOStreamWritableCheck
void AddGradientImage (const GradientDirectionType &, const GradientImageType *image)
const GradientImageTypeGetGradientImage (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
- Public Member Functions inherited from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
const InputImageTypeGetInput (void) const
const InputImageTypeGetInput (unsigned int idx) const
virtual void PopBackInput ()
virtual void PopFrontInput ()
virtual void PushBackInput (const InputImageType *image)
virtual void PushFrontInput (const InputImageType *image)
virtual void SetInput (const InputImageType *image)
virtual void SetInput (unsigned int, const Image< TReferenceImagePixelType, 3 > *image)
- Public Member Functions inherited from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
OutputImageTypeGetOutput (unsigned int idx)
virtual void GraftNthOutput (unsigned int idx, DataObject *output)
virtual void GraftOutput (DataObject *output)
virtual void GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
OutputImageTypeGetOutput (void)
const OutputImageTypeGetOutput (void) const
virtual
ProcessObject::DataObjectPointer 
MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx)
- Public Member Functions inherited from itk::ProcessObject
virtual void AbortGenerateDataOff ()
virtual void AbortGenerateDataOn ()
virtual void EnlargeOutputRequestedRegion (DataObject *)
virtual const bool & GetAbortGenerateData ()
NameArray GetInputNames () const
MultiThreader * GetMultiThreader () const
DataObjectPointerArraySizeType GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType GetNumberOfInputs () const
DataObjectPointerArraySizeType GetNumberOfOutputs () const
virtual
DataObjectPointerArraySizeType 
GetNumberOfValidRequiredInputs () const
NameArray GetOutputNames () const
virtual const float & GetProgress ()
NameArray GetRequiredInputNames () const
bool HasInput (const DataObjectIdentifierType &key) const
bool HasOutput (const DataObjectIdentifierType &key) const
virtual DataObjectPointer MakeOutput (const DataObjectIdentifierType &)
virtual void PrepareOutputs ()
virtual void PropagateRequestedRegion (DataObject *output)
virtual void ResetPipeline ()
virtual void SetAbortGenerateData (bool _arg)
virtual void SetProgress (float _arg)
virtual void Update ()
virtual void UpdateLargestPossibleRegion ()
virtual void UpdateOutputData (DataObject *output)
virtual void UpdateOutputInformation ()
void UpdateProgress (float amount)
DataObjectPointerArray GetInputs ()
DataObjectPointerArray GetOutputs ()
DataObjectPointerArray GetIndexedInputs ()
DataObjectPointerArray GetIndexedOutputs ()
DataObjectPointerArraySizeType GetNumberOfIndexedOutputs () const
virtual void SetReleaseDataFlag (bool flag)
virtual bool GetReleaseDataFlag () const
void ReleaseDataFlagOn ()
void ReleaseDataFlagOff ()
virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool & GetReleaseDataBeforeUpdateFlag ()
virtual void ReleaseDataBeforeUpdateFlagOn ()
virtual void ReleaseDataBeforeUpdateFlagOff ()
virtual void SetNumberOfThreads (ThreadIdType _arg)
virtual const ThreadIdTypeGetNumberOfThreads ()
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
unsigned long AddObserver (const EventObject &event, Command *) const
virtual void DebugOff () const
virtual void DebugOn () const
CommandGetCommand (unsigned long tag)
bool GetDebug () const
MetaDataDictionaryGetMetaDataDictionary (void)
const MetaDataDictionaryGetMetaDataDictionary (void) const
virtual unsigned long GetMTime () const
virtual const TimeStampGetTimeStamp () const
bool HasObserver (const EventObject &event) const
void InvokeEvent (const EventObject &)
void InvokeEvent (const EventObject &) const
virtual void Modified () const
virtual void Register () const
void RemoveAllObservers ()
void RemoveObserver (unsigned long tag)
void SetDebug (bool debugFlag) const
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void SetReferenceCount (int)
virtual void UnRegister () const
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
virtual int GetReferenceCount () const
 itkCloneMacro (Self)
void Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions

static Pointer New ()

Protected Types

enum  GradientImageTypeEnumeration {
  GradientIsInASingleImage = 1,
  GradientIsInManyImages,
  Else
}
- Protected Types inherited from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(OutputImageDimension),
itkGetStaticConstMacro(InputImageDimension) > 
InputToOutputRegionCopierType
typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(InputImageDimension),
itkGetStaticConstMacro(OutputImageDimension) > 
OutputToInputRegionCopierType

Protected Member Functions

void BeforeThreadedGenerateData ()
void ComputeTensorBasis ()
void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType)
 DiffusionTensor3DReconstructionImageFilter ()
 ~DiffusionTensor3DReconstructionImageFilter ()
void PrintSelf (std::ostream &os, Indent indent) const
- Protected Member Functions inherited from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
virtual void CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
virtual void CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
virtual void GenerateInputRequestedRegion ()
 ImageToImageFilter ()
virtual void VerifyInputInformation ()
 ~ImageToImageFilter ()
void PushBackInput (const DataObject *input)
void PushFrontInput (const DataObject *input)
- Protected Member Functions inherited from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
virtual void AfterThreadedGenerateData ()
virtual void AllocateOutputs ()
virtual void GenerateData ()
 ImageSource ()
virtual unsigned int SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
virtual void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
virtual ~ImageSource ()
- Protected Member Functions inherited from itk::ProcessObject
virtual void AddInput (DataObject *input)
virtual void AddOutput (DataObject *output)
bool AddRequiredInputName (const DataObjectIdentifierType &)
virtual void CacheInputReleaseDataFlags ()
virtual void GenerateOutputInformation ()
virtual void GenerateOutputRequestedRegion (DataObject *output)
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredInputs ()
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredOutputs ()
bool IsIndexedName (const DataObjectIdentifierType &) const
bool IsRequiredInputName (const DataObjectIdentifierType &) const
 itkLegacyMacro (virtual void RemoveInput(DataObject *input))
 itkLegacyMacro (virtual void RemoveOutput(DataObject *output))
 itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))
 itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))
DataObjectPointerArraySizeType MakeIndexFromName (const DataObjectIdentifierType &) const
DataObjectIdentifierType MakeNameFromIndex (DataObjectPointerArraySizeType) const
 ProcessObject ()
virtual void PropagateResetPipeline ()
virtual void ReleaseInputs ()
virtual void RemoveInput (const DataObjectIdentifierType &key)
virtual void RemoveInput (DataObjectPointerArraySizeType)
virtual void RemoveOutput (const DataObjectIdentifierType &key)
virtual void RemoveOutput (DataObjectPointerArraySizeType idx)
bool RemoveRequiredInputName (const DataObjectIdentifierType &)
virtual void RestoreInputReleaseDataFlags ()
virtual void SetInput (const DataObjectIdentifierType &key, DataObject *input)
virtual void SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
virtual void SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
void SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
void SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
virtual void SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual void SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual void SetOutput (const DataObjectIdentifierType &key, DataObject *output)
virtual void SetPrimaryInput (DataObject *input)
virtual void SetPrimaryOutput (DataObject *output)
void SetRequiredInputNames (const NameArray &)
virtual void VerifyPreconditions ()
 ~ProcessObject ()
DataObjectGetInput (const DataObjectIdentifierType &key)
const DataObjectGetInput (const DataObjectIdentifierType &key) const
DataObjectGetInput (DataObjectPointerArraySizeType)
const DataObjectGetInput (DataObjectPointerArraySizeType idx) const
DataObjectGetPrimaryInput ()
const DataObjectGetPrimaryInput () const
DataObjectGetOutput (const DataObjectIdentifierType &key)
const DataObjectGetOutput (const DataObjectIdentifierType &key) const
DataObjectGetOutput (DataObjectPointerArraySizeType idx)
const DataObjectGetOutput (DataObjectPointerArraySizeType idx) const
DataObjectGetPrimaryOutput ()
const DataObjectGetPrimaryOutput () const
- Protected Member Functions inherited from itk::Object
 Object ()
bool PrintObservers (std::ostream &os, Indent indent) const
virtual void SetTimeStamp (const TimeStamp &time)
virtual ~Object ()
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 LightObject ()
virtual void PrintHeader (std::ostream &os, Indent indent) const
virtual void PrintTrailer (std::ostream &os, Indent indent) const
virtual ~LightObject ()

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

Additional Inherited Members

- Static Public Attributes inherited from itk::ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
static const unsigned int InputImageDimension
static const unsigned int OutputImageDimension
- Static Public Attributes inherited from itk::ImageSource< Image< DiffusionTensor3D< TTensorPixelType >, 3 > >

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
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
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
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
template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>
typedef TensorImageType itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::OutputImageType
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
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 acquired 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
template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>
typedef DiffusionTensor3DReconstructionImageFilter itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::Self
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
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
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

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 ( )
inlineprotected

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  )
protectedvirtual

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
inlinevirtual

Return the gradient direction. idx is 0 based

Definition at line 224 of file itkDiffusionTensor3DReconstructionImageFilter.h.

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
template<class TReferenceImagePixelType , class TGradientImagePixelType = TReferenceImagePixelType, class TTensorPixelType = double, class TMaskImageType = Image<unsigned char, 3>>
virtual ReferenceImageType* itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType, TMaskImageType >::GetReferenceImage ( )
inlinevirtual

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
protectedvirtual
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 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::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< 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::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::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::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::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::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
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
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: