Medical Imaging Interaction Toolkit  2016.11.0
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itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections > Class Template Reference

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 orientation distribution function coefficients in a spherical harmonic basis. More...

#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>

Inheritance diagram for itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >:
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Collaboration diagram for itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >:
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Public Types

enum  Normalization {
  QBAR_STANDARD, QBAR_B_ZERO_B_VALUE, QBAR_B_ZERO, QBAR_NONE,
  QBAR_ADC_ONLY, QBAR_RAW_SIGNAL, QBAR_SOLID_ANGLE, QBAR_NONNEG_SOLID_ANGLE
}
 
typedef AnalyticalDiffusionQballReconstructionImageFilter Self
 
typedef SmartPointer< Self > Pointer
 
typedef SmartPointer< const Self > ConstPointer
 
typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > Superclass
 
typedef TReferenceImagePixelType ReferencePixelType
 
typedef TGradientImagePixelType GradientPixelType
 
typedef Vector< TOdfPixelType, NrOdfDirections > OdfPixelType
 
typedef TOdfPixelType BZeroPixelType
 
typedef Superclass::InputImageType ReferenceImageType
 
typedef Image< OdfPixelType, 3 > OdfImageType
 
typedef OdfImageType OutputImageType
 
typedef Image< Vector< TOdfPixelType,(NOrderL *NOrderL+NOrderL+2)/2+NOrderL >, 3 > CoefficientImageType
 
typedef Image< BZeroPixelType, 3 > BZeroImageType
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef Image< GradientPixelType, 3 > GradientImageType
 
typedef VectorImage< GradientPixelType, 3 > GradientImagesType
 
typedef vnl_matrix< TOdfPixelType > * OdfReconstructionMatrixType
 
typedef vnl_matrix< double > CoefficientMatrixType
 
typedef vnl_vector_fixed< double, 3 > GradientDirectionType
 
typedef VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType
 
typedef Image< float, 3 > FloatImageType
 

Public Member Functions

Pointer Clone () const
 
virtual const char * GetClassName () const
 
void SetGradientImage (const GradientDirectionContainerType *, const GradientImagesType *image)
 
virtual ReferenceImageType * GetReferenceImage ()
 
virtual GradientDirectionType GetGradientDirection (unsigned int idx) const
 
double Legendre0 (int l)
 
OdfPixelType Normalize (OdfPixelType odf, typename NumericTraits< ReferencePixelType >::AccumulateType b0)
 
vnl_vector< TOdfPixelType > PreNormalize (vnl_vector< TOdfPixelType > vec, typename NumericTraits< ReferencePixelType >::AccumulateType b0)
 
virtual void SetThreshold (ReferencePixelType _arg)
 
virtual ReferencePixelType GetThreshold ()
 
virtual void SetNormalizationMethod (Normalization _arg)
 
virtual Normalization GetNormalizationMethod ()
 
virtual BZeroImageType::Pointer GetBZeroImage ()
 
virtual FloatImageType::Pointer GetODFSumImage ()
 
virtual CoefficientImageType::Pointer GetCoefficientImage ()
 
virtual void SetBValue (TOdfPixelType _arg)
 
virtual const TOdfPixelType & GetBValue ()
 
virtual void SetLambda (double _arg)
 
virtual double GetLambda ()
 
virtual void SetUseMrtrixBasis (bool _arg)
 

Static Public Member Functions

static Pointer New ()
 
static void tofile2 (vnl_matrix< double > *A, std::string fname)
 
static void Cart2Sph (double x, double y, double z, double *cart)
 
static double Yj (int m, int k, double theta, double phi, bool useMRtrixBasis=false)
 

Protected Member Functions

 AnalyticalDiffusionQballReconstructionImageFilter ()
 
 ~AnalyticalDiffusionQballReconstructionImageFilter ()
 
void PrintSelf (std::ostream &os, Indent indent) const
 
void ComputeReconstructionMatrix ()
 
void BeforeThreadedGenerateData ()
 
void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType)
 

Detailed Description

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
class itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >

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 orientation distribution function coefficients in a spherical harmonic basis.

Inputs and Usage
When you have the 'n' gradient and one or more reference images in a single multi-component image (VectorImage), you can specify the images 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 the reconstruction.
Outputs
The output image is an image of vectors that must be understood as ODFs:
Image< Vector< TPixelType, OdfNrDirections >, 3 >
Parameters
  • Threshold - Threshold on the reference image data. The output ODF will be a null pdf 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. If the input gradient directions g_i are majorly sampled on one half of the sqhere, then each input image I_i will be duplicated and assign -g_i in order to guarantee stability of the algorithm.
  • OdfDirections - directions of resulting orientation distribution function
  • EquatorNrSamplingPoints - number of sampling points on equator when performing Funk Radeon Transform (FRT)
  • BasisFunctionCenters - the centers of the basis functions are used for the sRBF (spherical radial basis functions interpolation). If not set, they will be defaulted to equal m_EquatorNrSamplingPoints
Template parameters
The class is templated over
  • the pixel type of the reference and gradient images (expected to be scalar data types)
  • the internal representation of the ODF pixels (double, float etc).
  • the number of OdfDirections
  • the number of basis function centers for the sRBF
References:
  • [1] Tuch DS, "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72.

Definition at line 91 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

Member Typedef Documentation

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Image< BZeroPixelType, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::BZeroImageType

Definition at line 140 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef TOdfPixelType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::BZeroPixelType

Definition at line 128 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Image< Vector< TOdfPixelType, (NOrderL*NOrderL + NOrderL + 2)/2 + NOrderL >, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::CoefficientImageType

Definition at line 138 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef vnl_matrix< double > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::CoefficientMatrixType

Definition at line 158 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef SmartPointer<const Self> itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::ConstPointer

Definition at line 111 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Image<float, 3> itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::FloatImageType

Definition at line 205 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef VectorContainer< unsigned int, GradientDirectionType > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GradientDirectionContainerType

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

Definition at line 165 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef vnl_vector_fixed< double, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GradientDirectionType

Holds each magnetic field gradient used to acquire one DWImage

Definition at line 161 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef VectorImage< GradientPixelType, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::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 152 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Image< GradientPixelType, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GradientImageType

Typedef defining one (of the many) gradient images.

Definition at line 146 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef TGradientImagePixelType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GradientPixelType

Definition at line 124 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Image< OdfPixelType, 3 > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OdfImageType

Definition at line 134 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Vector< TOdfPixelType, NrOdfDirections > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OdfPixelType

Definition at line 126 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef vnl_matrix< TOdfPixelType >* itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OdfReconstructionMatrixType

Holds the ODF reconstruction matrix

Definition at line 156 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Superclass::OutputImageRegionType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OutputImageRegionType

Definition at line 143 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef OdfImageType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OutputImageType

Definition at line 136 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef SmartPointer<Self> itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::Pointer

Definition at line 110 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef Superclass::InputImageType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::ReferenceImageType

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

Definition at line 132 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef TReferenceImagePixelType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::ReferencePixelType

Definition at line 122 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef AnalyticalDiffusionQballReconstructionImageFilter itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::Self

Definition at line 109 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::Superclass

Definition at line 113 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

Member Enumeration Documentation

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
enum itk::AnalyticalDiffusionQballReconstructionImageFilter::Normalization
Enumerator
QBAR_STANDARD 
QBAR_B_ZERO_B_VALUE 
QBAR_B_ZERO 
QBAR_NONE 
QBAR_ADC_ONLY 
QBAR_RAW_SIGNAL 
QBAR_SOLID_ANGLE 
QBAR_NONNEG_SOLID_ANGLE 

Definition at line 98 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

Constructor & Destructor Documentation

template<class T , class TG , class TO , int L, int NODF>
itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::AnalyticalDiffusionQballReconstructionImageFilter ( )
protected

Definition at line 46 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::~AnalyticalDiffusionQballReconstructionImageFilter ( )
inlineprotected

Definition at line 242 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

Member Function Documentation

template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::BeforeThreadedGenerateData ( void  )
protected

Definition at line 243 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References mitk::New().

template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::Cart2Sph ( double  x,
double  y,
double  z,
double *  cart 
)
static

Definition at line 456 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References mitk::eps, and M_PI.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
Pointer itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::Clone ( ) const
template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::ComputeReconstructionMatrix ( )
protected

Definition at line 524 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References QBALL_ANAL_RECON_PI.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual const TOdfPixelType& itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetBValue ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual BZeroImageType::Pointer itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetBZeroImage ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual const char* itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetClassName ( ) const
virtual

Runtime information support.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual CoefficientImageType::Pointer itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetCoefficientImage ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual GradientDirectionType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetGradientDirection ( unsigned int  idx) const
inlinevirtual

Return the gradient direction. idx is 0 based

Definition at line 181 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual double itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetLambda ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual Normalization itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetNormalizationMethod ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual FloatImageType::Pointer itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetODFSumImage ( )
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual ReferenceImageType* itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetReferenceImage ( )
inlinevirtual

Get reference image

Definition at line 177 of file itkAnalyticalDiffusionQballReconstructionImageFilter.h.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual ReferencePixelType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::GetThreshold ( )
virtual
template<class T , class TG , class TO , int L, int NODF>
double itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::Legendre0 ( int  l)

Definition at line 506 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
static Pointer itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::New ( )
static

Method for creation through the object factory.

template<class TReferenceImagePixelType , class TGradientImagePixelType , class TOdfPixelType , int NOrderL, int NrOdfDirections>
itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::OdfPixelType itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::Normalize ( OdfPixelType  odf,
typename NumericTraits< ReferencePixelType >::AccumulateType  b0 
)

Definition at line 76 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References QBALL_ANAL_RECON_PI.

template<class TReferenceImagePixelType , class TGradientImagePixelType , class TOdfPixelType, int NOrderL, int NrOdfDirections>
vnl_vector< TOdfPixelType > itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::PreNormalize ( vnl_vector< TOdfPixelType >  vec,
typename NumericTraits< ReferencePixelType >::AccumulateType  b0 
)

Definition at line 156 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
protected

Definition at line 801 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual void itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::SetBValue ( TOdfPixelType  _arg)
virtual
template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::SetGradientImage ( const GradientDirectionContainerType *  gradientDirection,
const GradientImagesType *  image 
)

set method to add 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.

Definition at line 757 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References mitk::New().

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual void itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::SetLambda ( double  _arg)
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual void itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::SetNormalizationMethod ( Normalization  _arg)
virtual
template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual void itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::SetThreshold ( ReferencePixelType  _arg)
virtual

Threshold on the reference image data. The output ODF will be a null pdf for pixels in the reference image that have a value less than this threshold.

template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
virtual void itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NOrderL, NrOdfDirections >::SetUseMrtrixBasis ( bool  _arg)
virtual
template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::ThreadedGenerateData ( const OutputImageRegionType &  outputRegionForThread,
ThreadIdType   
)
protected

this would be the place to implement a non-negative solver for quadratic programming problem: min .5*|| Bc-s ||^2 subject to -CLPc <= 4*pi*ones (refer to MICCAI 2009 Goh et al. "Estimating ODFs with PDF constraints") .5*|| Bc-s ||^2 == .5*c'B'Bc - x'B's + .5*s's

Definition at line 302 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References Normalize(), and QBALL_ANAL_RECON_PI.

template<class T , class TG , class TO , int L, int NODF>
void itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::tofile2 ( vnl_matrix< double > *  A,
std::string  fname 
)
static

Definition at line 429 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

template<class T , class TG , class TO , int L, int NODF>
double itk::AnalyticalDiffusionQballReconstructionImageFilter< T, TG, TO, L, NODF >::Yj ( int  m,
int  k,
double  theta,
double  phi,
bool  useMRtrixBasis = false 
)
static

Definition at line 478 of file itkAnalyticalDiffusionQballReconstructionImageFilter.cpp.

References M_PI.

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