Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. More...

#include <itkTractsToDWIImageFilter.h>

Inheritance diagram for itk::TractsToDWIImageFilter< PixelType >:

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Collaboration diagram for itk::TractsToDWIImageFilter< PixelType >:

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Public Types
typedef TractsToDWIImageFilter	Self

typedef ImageSource< itk::VectorImage< PixelType, 3 > >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::OutputImageType	OutputImageType

typedef itk::Image< double, 4 >	ItkDoubleImgType4D

typedef itk::Image< double, 3 >	ItkDoubleImgType

typedef itk::Image< float, 3 >	ItkFloatImgType

typedef itk::Image< unsigned char, 3 >	ItkUcharImgType

typedef mitk::FiberBundle::Pointer	FiberBundleType

typedef itk::VectorImage< double, 3 >	DoubleDwiType

typedef itk::Matrix< double, 3, 3 >	MatrixType

typedef itk::Image< double, 2 >	SliceType

typedef itk::VnlForwardFFTImageFilter< SliceType >::OutputImageType	ComplexSliceType

typedef itk::VectorImage< vcl_complex< double >, 3 >	ComplexDwiType

typedef itk::Vector< double, 3 >	DoubleVectorType

Public Member Functions
Pointer	Clone () const

virtual const char *	GetClassName () const

virtual void	SetFiberBundle (FiberBundleType _arg)
	Input fiber bundle. More...

virtual void	SetInputImage (typename OutputImageType::Pointer _arg)
	Input diffusion-weighted image. If no fiber bundle is set, then the acquisition is simulated for this image without a new diffusion simulation. More...

virtual void	SetUseConstantRandSeed (bool _arg)
	Seed for random generator. More...

void	SetParameters (FiberfoxParameters< double > param)

FiberfoxParameters< double >	GetParameters ()

std::vector< ItkDoubleImgType::Pointer >	GetVolumeFractions ()

mitk::LevelWindow	GetLevelWindow ()

virtual std::string	GetStatusText ()

virtual DoubleDwiType::Pointer	GetPhaseImage ()

virtual DoubleDwiType::Pointer	GetKspaceImage ()

virtual mitk::PointSet::Pointer	GetCoilPointset ()

void	GenerateData ()

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	TractsToDWIImageFilter ()

virtual	~TractsToDWIImageFilter ()

itk::Point< float, 3 >	GetItkPoint (double point[3])

itk::Vector< double, 3 >	GetItkVector (double point[3])

vnl_vector_fixed< double, 3 >	GetVnlVector (double point[3])

vnl_vector_fixed< double, 3 >	GetVnlVector (Vector< float, 3 > &vector)

double	RoundToNearest (double num)

std::string	GetTime ()

bool	PrepareLogFile ()

void	PrintToLog (string m, bool addTime=true, bool linebreak=true, bool stdOut=true)

DoubleDwiType::Pointer	SimulateKspaceAcquisition (std::vector< DoubleDwiType::Pointer > &images)

void	SimulateExtraAxonalSignal (ItkUcharImgType::IndexType index, double intraAxonalVolume, int g=-1)

void	SimulateMotion (int g=-1)

void	CheckVolumeFractionImages ()

ItkDoubleImgType::Pointer	NormalizeInsideMask (ItkDoubleImgType::Pointer image)

void	InitializeData ()

void	InitializeFiberData ()

double	InterpolateValue (itk::Point< float, 3 > itkP, ItkDoubleImgType::Pointer img)

Protected Attributes
mitk::FiberfoxParameters< double >	m_Parameters

FiberBundleType	m_FiberBundle

OutputImageType::Pointer	m_InputImage

OutputImageType::Pointer	m_OutputImage

DoubleDwiType::Pointer	m_PhaseImage

DoubleDwiType::Pointer	m_KspaceImage

mitk::LevelWindow	m_LevelWindow

std::vector< ItkDoubleImgType::Pointer >	m_VolumeFractions

std::string	m_StatusText

itk::TimeProbe	m_TimeProbe

bool	m_UseConstantRandSeed

bool	m_MaskImageSet

ofstream	m_Logfile

std::string	m_MotionLog

std::string	m_SpikeLog

FiberBundleType	m_FiberBundleWorkingCopy
	we work on an upsampled version of the input bundle More...

FiberBundleType	m_FiberBundleTransformed
	transformed bundle simulating headmotion More...

itk::Vector< double, 3 >	m_WorkingSpacing

itk::Point< double, 3 >	m_WorkingOrigin

ImageRegion< 3 >	m_WorkingImageRegion

double	m_VoxelVolume

std::vector< DoubleDwiType::Pointer >	m_CompartmentImages

ItkUcharImgType::Pointer	m_TransformedMaskImage
	copy of mask image (changes for each motion step) More...

ItkUcharImgType::Pointer	m_UpsampledMaskImage
	helper image for motion simulation More...

DoubleVectorType	m_Rotation

DoubleVectorType	m_Translation

std::vector< DoubleVectorType >	m_Rotations
	stores the individual rotation of each volume (needed for k-space simulation to obtain correct frequency map position) More...

std::vector< DoubleVectorType >	m_Translations
	stores the individual translation of each volume (needed for k-space simulation to obtain correct frequency map position) More...

double	m_mmRadius

double	m_SegmentVolume

bool	m_UseRelativeNonFiberVolumeFractions

mitk::PointSet::Pointer	m_CoilPointset

int	m_MotionCounter

int	m_NumMotionVolumes

itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer	m_RandGen

Detailed Description

template<class PixelType>
class itk::TractsToDWIImageFilter< PixelType >

Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.

Definition at line 38 of file itkTractsToDWIImageFilter.h.

Member Typedef Documentation

template<class PixelType>

typedef itk::VectorImage< vcl_complex< double >, 3 > itk::TractsToDWIImageFilter< PixelType >::ComplexDwiType

Definition at line 58 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::VnlForwardFFTImageFilter<SliceType>::OutputImageType itk::TractsToDWIImageFilter< PixelType >::ComplexSliceType

Definition at line 57 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef SmartPointer< const Self > itk::TractsToDWIImageFilter< PixelType >::ConstPointer

Definition at line 46 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::VectorImage< double, 3 > itk::TractsToDWIImageFilter< PixelType >::DoubleDwiType

Definition at line 54 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Vector< double,3> itk::TractsToDWIImageFilter< PixelType >::DoubleVectorType

Definition at line 59 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef mitk::FiberBundle::Pointer itk::TractsToDWIImageFilter< PixelType >::FiberBundleType

Definition at line 53 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Image<double, 3> itk::TractsToDWIImageFilter< PixelType >::ItkDoubleImgType

Definition at line 50 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Image<double, 4> itk::TractsToDWIImageFilter< PixelType >::ItkDoubleImgType4D

Definition at line 49 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Image<float, 3> itk::TractsToDWIImageFilter< PixelType >::ItkFloatImgType

Definition at line 51 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Image<unsigned char, 3> itk::TractsToDWIImageFilter< PixelType >::ItkUcharImgType

Definition at line 52 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Matrix<double, 3, 3> itk::TractsToDWIImageFilter< PixelType >::MatrixType

Definition at line 55 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef Superclass::OutputImageType itk::TractsToDWIImageFilter< PixelType >::OutputImageType

Definition at line 48 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef SmartPointer< Self > itk::TractsToDWIImageFilter< PixelType >::Pointer

Definition at line 45 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef TractsToDWIImageFilter itk::TractsToDWIImageFilter< PixelType >::Self

Definition at line 43 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef itk::Image< double, 2 > itk::TractsToDWIImageFilter< PixelType >::SliceType

Definition at line 56 of file itkTractsToDWIImageFilter.h.

template<class PixelType>

typedef ImageSource< itk::VectorImage< PixelType, 3 > > itk::TractsToDWIImageFilter< PixelType >::Superclass

Definition at line 44 of file itkTractsToDWIImageFilter.h.

Constructor & Destructor Documentation

template<class PixelType >

itk::TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter ( )

protected

Definition at line 61 of file itkTractsToDWIImageFilter.cpp.

References itk::TractsToDWIImageFilter< PixelType >::m_RandGen.

template<class PixelType >

itk::TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter ( )

protectedvirtual

Definition at line 71 of file itkTractsToDWIImageFilter.cpp.

Member Function Documentation

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::CheckVolumeFractionImages ( )

protected

Definition at line 375 of file itkTractsToDWIImageFilter.cpp.

References mitk::New().

template<class PixelType>

Pointer itk::TractsToDWIImageFilter< PixelType >::Clone ( ) const

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::GenerateData ( )

Definition at line 863 of file itkTractsToDWIImageFilter.cpp.

References max(), min(), and mitk::New().

template<class PixelType>

virtual const char* itk::TractsToDWIImageFilter< PixelType >::GetClassName ( ) const

virtual

template<class PixelType>

virtual mitk::PointSet::Pointer itk::TractsToDWIImageFilter< PixelType >::GetCoilPointset ( )

virtual

template<class PixelType >

itk::Point< float, 3 > itk::TractsToDWIImageFilter< PixelType >::GetItkPoint ( double point[3] )

protected

Definition at line 1615 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType >

itk::Vector< double, 3 > itk::TractsToDWIImageFilter< PixelType >::GetItkVector ( double point[3] )

protected

Definition at line 1625 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType>

virtual DoubleDwiType::Pointer itk::TractsToDWIImageFilter< PixelType >::GetKspaceImage ( )

virtual

template<class PixelType>

mitk::LevelWindow itk::TractsToDWIImageFilter< PixelType >::GetLevelWindow ( )

inline

Definition at line 76 of file itkTractsToDWIImageFilter.h.

References itk::TractsToDWIImageFilter< PixelType >::m_LevelWindow.

template<class PixelType>

FiberfoxParameters<double> itk::TractsToDWIImageFilter< PixelType >::GetParameters ( )

inline

Output

Definition at line 73 of file itkTractsToDWIImageFilter.h.

References itk::TractsToDWIImageFilter< PixelType >::m_Parameters.

template<class PixelType>

virtual DoubleDwiType::Pointer itk::TractsToDWIImageFilter< PixelType >::GetPhaseImage ( )

virtual

template<class PixelType>

virtual std::string itk::TractsToDWIImageFilter< PixelType >::GetStatusText ( )

virtual

template<class PixelType >

std::string itk::TractsToDWIImageFilter< PixelType >::GetTime ( )

protected

Definition at line 1660 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType >

vnl_vector_fixed< double, 3 > itk::TractsToDWIImageFilter< PixelType >::GetVnlVector ( double point[3] )

protected

Definition at line 1635 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType >

vnl_vector_fixed< double, 3 > itk::TractsToDWIImageFilter< PixelType >::GetVnlVector ( Vector< float, 3 > & vector )

protected

Definition at line 1645 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType>

std::vector< ItkDoubleImgType::Pointer > itk::TractsToDWIImageFilter< PixelType >::GetVolumeFractions ( )

inline

Definition at line 74 of file itkTractsToDWIImageFilter.h.

References itk::TractsToDWIImageFilter< PixelType >::m_VolumeFractions.

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::InitializeData ( )

protected

Definition at line 485 of file itkTractsToDWIImageFilter.cpp.

References mitk::New(), and itk::ResampleDwiImageFilter< TScalarType >::New().

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::InitializeFiberData ( )

protected

Definition at line 741 of file itkTractsToDWIImageFilter.cpp.

References M_PI.

template<class PixelType >

double itk::TractsToDWIImageFilter< PixelType >::InterpolateValue	(	itk::Point< float, 3 >	itkP,
		ItkDoubleImgType::Pointer	img
	)

protected

Definition at line 1544 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType>

static Pointer itk::TractsToDWIImageFilter< PixelType >::New ( )

static

Referenced by main().

template<class PixelType >

TractsToDWIImageFilter< PixelType >::ItkDoubleImgType::Pointer itk::TractsToDWIImageFilter< PixelType >::NormalizeInsideMask ( ItkDoubleImgType::Pointer image )

protected

Definition at line 343 of file itkTractsToDWIImageFilter.cpp.

References max(), min(), and mitk::New().

template<class PixelType >

bool itk::TractsToDWIImageFilter< PixelType >::PrepareLogFile ( )

protected

Definition at line 774 of file itkTractsToDWIImageFilter.cpp.

References mitk::IOUtil::GetTempPath(), max(), and MITK_ERROR.

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::PrintToLog	(	string	m,
		bool	addTime = `true`,
		bool	linebreak = `true`,
		bool	stdOut = `true`
	)

protected

Prepares the log file and returns true if successful or false if failed.

Definition at line 1227 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType >

double itk::TractsToDWIImageFilter< PixelType >::RoundToNearest ( double num )

protected

Definition at line 1655 of file itkTractsToDWIImageFilter.cpp.

template<class PixelType>

virtual void itk::TractsToDWIImageFilter< PixelType >::SetFiberBundle ( FiberBundleType _arg )

virtual

Input fiber bundle.

Input

template<class PixelType>

virtual void itk::TractsToDWIImageFilter< PixelType >::SetInputImage ( typename OutputImageType::Pointer _arg )

virtual

Input diffusion-weighted image. If no fiber bundle is set, then the acquisition is simulated for this image without a new diffusion simulation.

template<class PixelType>

void itk::TractsToDWIImageFilter< PixelType >::SetParameters ( FiberfoxParameters< double > param )

inline

Parameters

param Simulation parameters.

Definition at line 69 of file itkTractsToDWIImageFilter.h.

References itk::TractsToDWIImageFilter< PixelType >::m_Parameters.

template<class PixelType>

virtual void itk::TractsToDWIImageFilter< PixelType >::SetUseConstantRandSeed ( bool _arg )

virtual

Seed for random generator.

template<class PixelType >

void itk::TractsToDWIImageFilter< PixelType >::SimulateExtraAxonalSignal	(	ItkUcharImgType::IndexType	index,
		double	intraAxonalVolume,
		int	g = `-1`
	)

protected

Generate signal of non-fiber compartments.

Definition at line 1377 of file itkTractsToDWIImageFilter.cpp.

References MITK_ERROR.

template<class PixelType >

TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer itk::TractsToDWIImageFilter< PixelType >::SimulateKspaceAcquisition ( std::vector< DoubleDwiType::Pointer > & images )