#include <mitkFiberfoxParameters.h>

Collaboration diagram for mitk::SignalGenerationParameters:

Public Types
enum	CoilSensitivityProfile : int { COIL_CONSTANT, COIL_LINEAR, COIL_EXPONENTIAL }

enum	AcquisitionType : int { SingleShotEpi, SpinEcho }

typedef itk::Image< double, 3 >	ItkDoubleImgType

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

typedef itk::Vector< double, 3 >	GradientType

typedef std::vector< GradientType >	GradientListType

Public Member Functions
	SignalGenerationParameters ()

void	GenerateGradientHalfShell ()
	Generates half shell of gradient directions (with m_NumGradients non-zero directions) More...

std::vector< int >	GetBaselineIndices ()
	Returns list of nun-diffusion-weighted image volume indices. More...

unsigned int	GetFirstBaselineIndex ()
	Returns index of first non-diffusion-weighted image volume. More...

bool	IsBaselineIndex (unsigned int idx)
	Checks if image volume with given index is non-diffusion-weighted volume or not. More...

unsigned int	GetNumWeightedVolumes ()
	Get number of diffusion-weighted image volumes. More...

unsigned int	GetNumBaselineVolumes ()
	Get number of non-diffusion-weighted image volumes. More...

unsigned int	GetNumVolumes ()
	Get number of baseline and diffusion-weighted image volumes. More...

GradientListType	GetGradientDirections ()
	Return gradient direction container. More...

GradientType	GetGradientDirection (unsigned int i)

void	SetNumWeightedVolumes (int numGradients)
	Automaticall calls GenerateGradientHalfShell() afterwards. More...

void	SetGradienDirections (GradientListType gradientList)

void	SetGradienDirections (mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList)

Public Attributes
itk::ImageRegion< 3 >	m_CroppedRegion
	Image size with reduced FOV. More...

itk::ImageRegion< 3 >	m_ImageRegion
	Image size. More...

itk::Vector< double, 3 >	m_ImageSpacing
	Image voxel size. More...

itk::Point< double, 3 >	m_ImageOrigin
	Image origin. More...

itk::Matrix< double, 3, 3 >	m_ImageDirection
	Image rotation matrix. More...

AcquisitionType	m_AcquisitionType
	determines k-space trajectory and maximum echo position(s) More...

double	m_SignalScale
	Scaling factor for output signal (before noise is added). More...

double	m_tEcho
	Echo time TE. More...

double	m_tRep
	Echo time TR. More...

double	m_tLine
	k-space line readout time (dwell time). More...

double	m_tInhom
	T2'. More...

bool	m_ReversePhase
	If true, the phase readout direction will be inverted (-y instead of y) More...

double	m_PartialFourier
	Partial fourier factor (0.5-1) More...

double	m_NoiseVariance
	Variance of complex gaussian noise. More...

int	m_NumberOfCoils
	Number of coils in multi-coil acquisition. More...

CoilSensitivityProfile	m_CoilSensitivityProfile
	Choose between constant, linear or exponential sensitivity profile of the used coils. More...

double	m_Bvalue
	Acquisition b-value. More...

bool	m_SimulateKspaceAcquisition
	Flag to enable/disable k-space acquisition simulation. More...

double	m_AxonRadius
	Determines compartment volume fractions (0 == automatic axon radius estimation) More...

bool	m_DoDisablePartialVolume
	Disable partial volume effects. Each voxel is either all fiber or all non-fiber. More...

unsigned int	m_Spikes
	Number of spikes randomly appearing in the image. More...

double	m_SpikeAmplitude
	amplitude of spikes relative to the largest signal intensity (magnitude of complex) More...

double	m_KspaceLineOffset
	Causes N/2 ghosts. Larger offset means stronger ghost. More...

double	m_EddyStrength
	Strength of eddy current induced gradients in mT/m. More...

double	m_Tau
	Eddy current decay constant (in ms) More...

double	m_CroppingFactor
	FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts. More...

bool	m_DoAddGibbsRinging
	Add Gibbs ringing artifact. More...

bool	m_DoSimulateRelaxation
	Add T2 relaxation effects. More...

bool	m_DoAddMotion
	Enable motion artifacts. More...

bool	m_DoRandomizeMotion
	Toggles between random and linear motion. More...

std::vector< bool >	m_MotionVolumes
	with positive numbers, inverted logic with negative numbers. More...

itk::Vector< double, 3 >	m_Translation
	Maximum translational motion. More...

itk::Vector< double, 3 >	m_Rotation
	Maximum rotational motion. More...

ItkDoubleImgType::Pointer	m_FrequencyMap
	If != NULL, distortions are added to the image using this frequency map. More...

ItkUcharImgType::Pointer	m_MaskImage
	Signal is only genrated inside of the mask image. More...

Protected Attributes
unsigned int	m_NumGradients
	Number of diffusion-weighted image volumes. More...

unsigned int	m_NumBaseline
	Number of non-diffusion-weighted image volumes. More...

GradientListType	m_GradientDirections
	Total number of image volumes. More...

Detailed Description

Signal generation

Definition at line 46 of file mitkFiberfoxParameters.h.

Member Typedef Documentation

typedef std::vector<GradientType> mitk::SignalGenerationParameters::GradientListType

Definition at line 52 of file mitkFiberfoxParameters.h.

typedef itk::Vector<double,3> mitk::SignalGenerationParameters::GradientType

Definition at line 51 of file mitkFiberfoxParameters.h.

typedef itk::Image<double, 3> mitk::SignalGenerationParameters::ItkDoubleImgType

Definition at line 49 of file mitkFiberfoxParameters.h.

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

Definition at line 50 of file mitkFiberfoxParameters.h.

Member Enumeration Documentation

enum mitk::SignalGenerationParameters::AcquisitionType : int

Enumerator
SingleShotEpi
SpinEcho

Definition at line 60 of file mitkFiberfoxParameters.h.

enum mitk::SignalGenerationParameters::CoilSensitivityProfile : int

Enumerator
COIL_CONSTANT
COIL_LINEAR
COIL_EXPONENTIAL

Definition at line 54 of file mitkFiberfoxParameters.h.

Constructor & Destructor Documentation

mitk::SignalGenerationParameters::SignalGenerationParameters ( )

inline

Definition at line 66 of file mitkFiberfoxParameters.h.

Member Function Documentation

void mitk::SignalGenerationParameters::GenerateGradientHalfShell ( )

inline

Generates half shell of gradient directions (with m_NumGradients non-zero directions)

Definition at line 39 of file mitkFiberfoxParameters.cpp.

References M_PI.

std::vector< int > mitk::SignalGenerationParameters::GetBaselineIndices ( )

inline

Returns list of nun-diffusion-weighted image volume indices.

Definition at line 82 of file mitkFiberfoxParameters.cpp.

unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex ( )

inline

Returns index of first non-diffusion-weighted image volume.

Definition at line 91 of file mitkFiberfoxParameters.cpp.

mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection ( unsigned int i )

inline

Definition at line 126 of file mitkFiberfoxParameters.cpp.

mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections ( )

inline

Return gradient direction container.

Definition at line 121 of file mitkFiberfoxParameters.cpp.

Referenced by main().

unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes ( )

inline

Get number of non-diffusion-weighted image volumes.

Definition at line 111 of file mitkFiberfoxParameters.cpp.

unsigned int mitk::SignalGenerationParameters::GetNumVolumes ( )

inline

Get number of baseline and diffusion-weighted image volumes.

Definition at line 116 of file mitkFiberfoxParameters.cpp.

unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes ( )

inline

Get number of diffusion-weighted image volumes.

Definition at line 106 of file mitkFiberfoxParameters.cpp.

bool mitk::SignalGenerationParameters::IsBaselineIndex ( unsigned int idx )

inline

Checks if image volume with given index is non-diffusion-weighted volume or not.

Definition at line 99 of file mitkFiberfoxParameters.cpp.

void mitk::SignalGenerationParameters::SetGradienDirections ( GradientListType gradientList )

inline

Definition at line 137 of file mitkFiberfoxParameters.cpp.

Referenced by main().

void mitk::SignalGenerationParameters::SetGradienDirections ( mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList )

inline

Definition at line 151 of file mitkFiberfoxParameters.cpp.

void mitk::SignalGenerationParameters::SetNumWeightedVolumes ( int numGradients )

inline

Automaticall calls GenerateGradientHalfShell() afterwards.

Definition at line 131 of file mitkFiberfoxParameters.cpp.

Member Data Documentation

AcquisitionType mitk::SignalGenerationParameters::m_AcquisitionType

determines k-space trajectory and maximum echo position(s)

Other acquisitions parameters

Definition at line 114 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_AxonRadius

Determines compartment volume fractions (0 == automatic axon radius estimation)

Definition at line 127 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_Bvalue

Acquisition b-value.

Definition at line 125 of file mitkFiberfoxParameters.h.

Referenced by main().

CoilSensitivityProfile mitk::SignalGenerationParameters::m_CoilSensitivityProfile

Choose between constant, linear or exponential sensitivity profile of the used coils.

Definition at line 124 of file mitkFiberfoxParameters.h.

itk::ImageRegion<3> mitk::SignalGenerationParameters::m_CroppedRegion

Image size with reduced FOV.

input/output image specifications

Definition at line 107 of file mitkFiberfoxParameters.h.

Referenced by mitk::SingleShotEpi::AdjustEchoTime(), mitk::CartesianReadout::CartesianReadout(), and mitk::SingleShotEpi::SingleShotEpi().

double mitk::SignalGenerationParameters::m_CroppingFactor

FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts.

Definition at line 136 of file mitkFiberfoxParameters.h.

bool mitk::SignalGenerationParameters::m_DoAddGibbsRinging

Add Gibbs ringing artifact.

Definition at line 137 of file mitkFiberfoxParameters.h.

bool mitk::SignalGenerationParameters::m_DoAddMotion

Enable motion artifacts.

Definition at line 139 of file mitkFiberfoxParameters.h.

bool mitk::SignalGenerationParameters::m_DoDisablePartialVolume

Disable partial volume effects. Each voxel is either all fiber or all non-fiber.

Definition at line 128 of file mitkFiberfoxParameters.h.

bool mitk::SignalGenerationParameters::m_DoRandomizeMotion

Toggles between random and linear motion.

Definition at line 140 of file mitkFiberfoxParameters.h.

bool mitk::SignalGenerationParameters::m_DoSimulateRelaxation

Add T2 relaxation effects.

Definition at line 138 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_EddyStrength

Strength of eddy current induced gradients in mT/m.

Definition at line 134 of file mitkFiberfoxParameters.h.

ItkDoubleImgType::Pointer mitk::SignalGenerationParameters::m_FrequencyMap

If != NULL, distortions are added to the image using this frequency map.

Definition at line 145 of file mitkFiberfoxParameters.h.

GradientListType mitk::SignalGenerationParameters::m_GradientDirections

protected

Total number of image volumes.

Definition at line 166 of file mitkFiberfoxParameters.h.

itk::Matrix<double, 3, 3> mitk::SignalGenerationParameters::m_ImageDirection

Image rotation matrix.

Definition at line 111 of file mitkFiberfoxParameters.h.

Referenced by main().

itk::Point<double,3> mitk::SignalGenerationParameters::m_ImageOrigin

Image origin.

Definition at line 110 of file mitkFiberfoxParameters.h.

Referenced by main().

itk::ImageRegion<3> mitk::SignalGenerationParameters::m_ImageRegion

Image size.

Definition at line 108 of file mitkFiberfoxParameters.h.

Referenced by main().

itk::Vector<double,3> mitk::SignalGenerationParameters::m_ImageSpacing

Image voxel size.

Definition at line 109 of file mitkFiberfoxParameters.h.

Referenced by main().

double mitk::SignalGenerationParameters::m_KspaceLineOffset

Causes N/2 ghosts. Larger offset means stronger ghost.

Definition at line 133 of file mitkFiberfoxParameters.h.

ItkUcharImgType::Pointer mitk::SignalGenerationParameters::m_MaskImage

Signal is only genrated inside of the mask image.

Definition at line 146 of file mitkFiberfoxParameters.h.

std::vector< bool > mitk::SignalGenerationParameters::m_MotionVolumes

with positive numbers, inverted logic with negative numbers.

Indicates the image volumes that are affected by motion

Definition at line 141 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_NoiseVariance

Variance of complex gaussian noise.

Definition at line 122 of file mitkFiberfoxParameters.h.

unsigned int mitk::SignalGenerationParameters::m_NumBaseline

protected

Number of non-diffusion-weighted image volumes.

Definition at line 165 of file mitkFiberfoxParameters.h.

int mitk::SignalGenerationParameters::m_NumberOfCoils

Number of coils in multi-coil acquisition.

Definition at line 123 of file mitkFiberfoxParameters.h.

unsigned int mitk::SignalGenerationParameters::m_NumGradients

protected

Number of diffusion-weighted image volumes.

Definition at line 164 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_PartialFourier

Partial fourier factor (0.5-1)

Definition at line 121 of file mitkFiberfoxParameters.h.

Referenced by mitk::SingleShotEpi::AdjustEchoTime().

bool mitk::SignalGenerationParameters::m_ReversePhase

If true, the phase readout direction will be inverted (-y instead of y)

Definition at line 120 of file mitkFiberfoxParameters.h.

Referenced by mitk::CartesianReadout::GetActualKspaceIndex(), and mitk::SingleShotEpi::GetActualKspaceIndex().

itk::Vector<double,3> mitk::SignalGenerationParameters::m_Rotation

Maximum rotational motion.

Definition at line 144 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_SignalScale

Scaling factor for output signal (before noise is added).

Definition at line 115 of file mitkFiberfoxParameters.h.

Referenced by main().

bool mitk::SignalGenerationParameters::m_SimulateKspaceAcquisition

Flag to enable/disable k-space acquisition simulation.

Definition at line 126 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_SpikeAmplitude

amplitude of spikes relative to the largest signal intensity (magnitude of complex)

Definition at line 132 of file mitkFiberfoxParameters.h.

unsigned int mitk::SignalGenerationParameters::m_Spikes

Number of spikes randomly appearing in the image.

Artifacts and other effects

Definition at line 131 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_Tau

Eddy current decay constant (in ms)

Definition at line 135 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_tEcho

Echo time TE.

Definition at line 116 of file mitkFiberfoxParameters.h.

Referenced by mitk::CartesianReadout::AdjustEchoTime(), and mitk::SingleShotEpi::AdjustEchoTime().

double mitk::SignalGenerationParameters::m_tInhom

T2'.

Definition at line 119 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_tLine

k-space line readout time (dwell time).

Definition at line 118 of file mitkFiberfoxParameters.h.

Referenced by mitk::CartesianReadout::AdjustEchoTime(), mitk::SingleShotEpi::AdjustEchoTime(), mitk::CartesianReadout::CartesianReadout(), and mitk::SingleShotEpi::SingleShotEpi().

itk::Vector<double,3> mitk::SignalGenerationParameters::m_Translation

Maximum translational motion.

Definition at line 143 of file mitkFiberfoxParameters.h.

double mitk::SignalGenerationParameters::m_tRep

Echo time TR.

Definition at line 117 of file mitkFiberfoxParameters.h.

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

Public Types

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation