#include <svkVarianCSFidMapper.h>

Inheritance diagram for svkVarianCSFidMapper:

Public Member Functions
	vtkTypeMacro (svkVarianCSFidMapper, svkVarianFidMapper)

virtual void	ReadFidFile (string fidFileName, svkImageData *data)

Public Member Functions inherited from svkVarianFidMapper
	vtkTypeMacro (svkVarianFidMapper, vtkObject)

virtual void	InitializeDcmHeader (map< string, vector< vector< string > > > procparMap, svkDcmHeader header, svkMRSIOD iod, int swapBytes)

Static Public Member Functions
static svkVarianCSFidMapper *	New ()

Protected Member Functions
	svkVarianCSFidMapper ()

	~svkVarianCSFidMapper ()

virtual void	InitMultiFrameFunctionalGroupsModule ()

virtual void	InitAcquisitionContextModule ()

virtual void	InitPlaneOrientationMacro ()

virtual void	InitSharedFunctionalGroupMacros ()

virtual void	InitPerFrameFunctionalGroupMacros ()

virtual void	InitPixelMeasuresMacro ()

virtual void	InitMRReceiveCoilMacro ()

virtual void	InitMRSpectroscopyPulseSequenceModule ()

virtual void	InitMRSpectroscopyModule ()

virtual void	InitMRSpectroscopyFOVGeometryMacro ()

virtual void	InitMRSpectroscopyDataModule ()

virtual void	SetCellSpectrum (vtkImageData *data, int x, int y, int z, int timePt, int coilNum)

Protected Member Functions inherited from svkVarianFidMapper
	svkVarianFidMapper ()

	~svkVarianFidMapper ()

void	InitPatientModule ()

void	InitGeneralStudyModule ()

void	InitGeneralSeriesModule ()

void	InitGeneralEquipmentModule ()

virtual void	InitMultiFrameDimensionModule ()

virtual void	InitMRModifierMacro ()

virtual void	InitMRTransmitCoilMacro ()

virtual void	InitMRAveragesMacro ()

virtual void	InitMREchoMacro ()

virtual void	InitMRTimingAndRelatedParametersMacro ()

string	GetDcmPatientPositionString ()

virtual void	ConvertCmToMm ()

int	GetHeaderValueAsInt (string keyString, int valueIndex=0, int procparRow=0)

float	GetHeaderValueAsFloat (string keyString, int valueIndex=0, int procparRow=0)

string	GetHeaderValueAsString (string keyString, int valueIndex=0, int procparRow=0)

Additional Inherited Members
Protected Attributes inherited from svkVarianFidMapper
map< string, vector< vector < string > > >	procparMap

svkDcmHeader *	dcmHeader

float *	specData

svkDcmHeader::DcmDataOrderingDirection	dataSliceOrder

int	numSlices

int	numFrames

svkMRSIOD *	iod

int	swapBytes

Detailed Description

This is a concrete instance of an svkVarianFIDMapper for Varian 3D compressed sensing data. This mapper is used by the svkVarianFidReader to convert Varian FID/Procpar data, from the UCSF compressed sensing pulse sequence, into an svkImageData object (includeing a DICOM MR Spectroscopy header). The Varian compressed sensing pulse sequence was implemented by Dr. Sukumar Subramaniam (UCSF NMR Lab) based on the work of Drs. Hu, Lustig et al.: Simon Hu, Michael Lustig, Asha Balakrishnan, Peder E. Z. Larson, Robert Bok, John Kurhanewicz, Sarah J. Nelson, Andrei Goga, John M. Pauly, Daniel B. Vigneron: "3D compressed sensing for highly accelerated hyperpolarized 13c mrsi with in vivo applications to transgenic mouse models of cancer", Magn. Reson. Med., 63(2), 312-321 (2009).

This mapper takes the sparsely sampled compressed sensing k-space data and reorganizes it into a rectalinear data array with kt, kx, ky and kz organized into a regular 4D grid with missing points from undersampling filled in with zeros. At the moment, the data sampling order is hardcoded into this class for this specific acquisition.

This missing k-space data from undersampling (encoded in the output data as zeros) needs to be filled in using the L1 algorithm described here: Lusting M, Donoho D.L., Pauly J.M: "Sparse MRI: the application of compressed sensing for rapid MR imaging", Magn. Reson. Med., 58, 1182-1195 (2007).

Additionally, phase correction for the flyback encoding needs to be accounted for by downstream algorithms.

Thanks to Dr. Simon Hu and Dr. Sukumar Subramaniam from the Vigneron and Kurhanewicz labs at the UCSF Department of Radiology and Biomedical Imaging for help implementing this class.

Constructor & Destructor Documentation

svkVarianCSFidMapper ( )

protected

~svkVarianCSFidMapper ( )

protected

References svkVarianFidMapper::specData.

Member Function Documentation

void InitAcquisitionContextModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

void InitMRReceiveCoilMacro ( )

protectedvirtual

Receive Coil:

Reimplemented from svkVarianFidMapper.

References svkDcmHeader::AddSequenceItemElement(), and svkVarianFidMapper::dcmHeader.

Referenced by svkVarianCSFidMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyDataModule ( )

protectedvirtual

Current PixelData ordering:

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsInt(), and svkDcmHeader::SetValue().

void InitMRSpectroscopyFOVGeometryMacro ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkDcmHeader::AddSequenceItemElement(), svkVarianFidMapper::dcmHeader, svkDcmHeader::GetDataDcos(), svkVarianFidMapper::GetHeaderValueAsFloat(), and svkVarianFidMapper::GetHeaderValueAsInt().

Referenced by svkVarianCSFidMapper::InitSharedFunctionalGroupMacros().

void InitMRSpectroscopyModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), svkVarianFidMapper::GetHeaderValueAsString(), and svkDcmHeader::SetValue().

void InitMRSpectroscopyPulseSequenceModule ( )

protectedvirtual

Implements svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsInt(), svkVarianFidMapper::GetHeaderValueAsString(), and svkDcmHeader::SetValue().

void InitMultiFrameFunctionalGroupsModule ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsString(), svkVarianCSFidMapper::InitPerFrameFunctionalGroupMacros(), svkVarianCSFidMapper::InitSharedFunctionalGroupMacros(), and svkDcmHeader::SetValue().

void InitPerFrameFunctionalGroupMacros ( )

protectedvirtual

This is initialized to represent the target reconstructed params. FID toplc is the center of the first voxel.

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dataSliceOrder, svkVarianFidMapper::dcmHeader, svkDcmHeader::GetDataDcos(), svkDcmHeader::GetDimensionIndexVector(), svkVarianFidMapper::GetHeaderValueAsFloat(), svkVarianFidMapper::GetHeaderValueAsInt(), svkDcmHeader::GetPixelSize(), svkDcmHeader::InitPerFrameFunctionalGroupSequence(), svkVarianFidMapper::numSlices, svkDcmHeader::SetDimensionVectorValue(), svkDcmHeader::SetSliceOrder(), and svkDcmHeader::SLICE_INDEX.

Referenced by svkVarianCSFidMapper::InitMultiFrameFunctionalGroupsModule().

void InitPixelMeasuresMacro ( )

protectedvirtual

Pixel Spacing:

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), svkVarianFidMapper::GetHeaderValueAsInt(), and svkDcmHeader::InitPixelMeasuresMacro().

Referenced by svkVarianCSFidMapper::InitSharedFunctionalGroupMacros().

void InitPlaneOrientationMacro ( )

protectedvirtual

The DICOM PlaneOrientationSequence is set from orientational params defined in the Varian procpar file. According to the VNMR User Programming documentation available at http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/nmr/apps/pubs/sys_vn&cid=975JIOILOKPQNGMKIINKNGK&zsb=1060363007.usergroup (VNMR 6.1C, Pub No. 01-999165-00, Rev B0802, page 155), the Euler angles are defined in the "User Guide Imaging. The Varian User Guide: Imaging (Pub. No. 01-999163-00, Rev. A0201, page 272) provides the following definition of the procpar euler angles:

For this psd, the flyback encoding represents the outer data loop (essentially the slice). This complicates the interpretation of the Varian conventions which define coronal acquisitions as those with readout along the z direction and slice selection along the y direction in the magnet frame (not relevant to mrs and flyback). Therefore the euler angles definitions need to be redefined here for this application context.

Currently only support "coronal" defined by varian to be readout along z, which for us is the most slowly varying outer loop (slice loop) or rather an axial data set.

Reimplemented from svkVarianFidMapper.

References svkDcmHeader::AddSequenceItemElement(), svkVarianFidMapper::dataSliceOrder, svkVarianFidMapper::dcmHeader, svkVarianFidMapper::GetHeaderValueAsFloat(), svkVarianFidMapper::GetHeaderValueAsString(), svkDcmHeader::GetNormalVector(), svkDcmHeader::INCREMENT_ALONG_NEG_NORMAL, and svkDcmHeader::INCREMENT_ALONG_POS_NORMAL.

Referenced by svkVarianCSFidMapper::InitSharedFunctionalGroupMacros().

void InitSharedFunctionalGroupMacros ( )

protectedvirtual

Reimplemented from svkVarianFidMapper.

References svkVarianFidMapper::InitMRAveragesMacro(), svkVarianFidMapper::InitMREchoMacro(), svkVarianFidMapper::InitMRModifierMacro(), svkVarianCSFidMapper::InitMRReceiveCoilMacro(), svkVarianCSFidMapper::InitMRSpectroscopyFOVGeometryMacro(), svkVarianFidMapper::InitMRTimingAndRelatedParametersMacro(), svkVarianCSFidMapper::InitPixelMeasuresMacro(), and svkVarianCSFidMapper::InitPlaneOrientationMacro().

Referenced by svkVarianCSFidMapper::InitMultiFrameFunctionalGroupsModule().

static svkVarianCSFidMapper* New ( )

static