svkMetaboliteRatioZScores Class Reference

#include <svkMetaboliteRatioZScores.h>

Inheritance diagram for svkMetaboliteRatioZScores:

Public Member Functions
	vtkTypeMacro (svkMetaboliteRatioZScores, svkImageAlgorithm)
void	SetSeriesDescription (vtkstd::string newSeriesDescription)
void	SetVerbose (bool isVerbose)
void	LimitToSelectedVolume (float fraction=0.5001)
void	LimitToSelectedVolume (short *selectedVolumeMask)
void	SetInputNumerator (vtkDataObject *in)
void	SetInputDenominator (vtkDataObject *in)
void	SetInputMrsData (vtkDataObject *in)
void	SetZScoreThresholds (double lowerThreshold, double upperThreshold)
Public Member Functions inherited from svkImageAlgorithm
	vtkTypeMacro (svkImageAlgorithm, vtkImageAlgorithm)
svkImageData *	GetOutput ()
svkImageData *	GetOutput (int port)
svkImageData *	GetImageDataInput (int port)

Static Public Member Functions
static svkMetaboliteRatioZScores *	New ()

Protected Member Functions
	svkMetaboliteRatioZScores ()
	~svkMetaboliteRatioZScores ()
virtual int	RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
virtual int	FillInputPortInformation (int vtkNotUsed(port), vtkInformation *info)
virtual int	FillOutputPortInformation (int vtkNotUsed(port), vtkInformation *info)
Protected Member Functions inherited from svkImageAlgorithm
	svkImageAlgorithm ()
	~svkImageAlgorithm ()

Detailed Description

Class to generate z-scores (aka metabolite indices) from metabolite ratios. Z-scores are analyzed over the entire MRS volume (or sub-set of voxels, e.g. within the selected volume) and represent the number of standard deviations (perpendicular distance) a given metabolite ratio is from the linear regresion. This computation is repeated with z-score outliers thrown out in subsequent iterations until the regresion fit converges. This class takes metabolite map inputs for already quantified values. These may be integrated area maps, peak_ht maps, or maps derived from other quantification methods. This class only computes the z-score map for the given input. The z-scores are computed as defined in reference 1. The reported map is the ratio of the perpendicular distance of a point from the regression line, normalized by the standard deviation of these distance values.

References:

1. Tracy R. McKnight PhD, Susan M. Noworolski PhD, Daniel B. Vigneron PhD, Sarah J. Nelson PhD, "An Automated Technique for the Quantitative Assessment of 3D-MRSI Data from Patients with Glioma", Journal of Magnetic Resonance Imaging, 13:167-177 (2001).

Constructor & Destructor Documentation

svkMetaboliteRatioZScores ( )

protected

~svkMetaboliteRatioZScores ( )

protected

Member Function Documentation

int FillInputPortInformation ( int   vtkNotUsedport, vtkInformation *  info  )

protectedvirtual

input ports: 0 & 1 are required (numerator and denominator met maps) 2 is optional MRS data used for masking by selection box

Reimplemented from svkImageAlgorithm.

int FillOutputPortInformation ( int   vtkNotUsedport, vtkInformation *  info  )

protectedvirtual

Output from this algo is an svkMriImageData object.

Reimplemented from svkImageAlgorithm.

void LimitToSelectedVolume

(

float

fraction = 0.5001

)

Limits regression analysis to voxels within the selected volume. Fraction indicates if voxels partially (fraction %) within the selected volume are included in regression. The default is to include all voxels in the calculation (fraction = 0).

Referenced by svkMetaboliteRatioZScores::LimitToSelectedVolume().

void LimitToSelectedVolume

(

short *

selectedVolumeMask

)

Limits regression analysis to voxels within the given mask. Default is to use all voxels in calculation.

References svkMetaboliteRatioZScores::LimitToSelectedVolume().

static svkMetaboliteRatioZScores* New ( )

static

int RequestData ( vtkInformation *  request, vtkInformationVector **  inputVector, vtkInformationVector *  outputVector  )

protectedvirtual

Generate the z-score image. This method sets up the masks and image templates

References svkImageData::DeepCopy(), svkImageData::GetDcmHeader(), svkImageAlgorithm::GetImageDataInput(), svkImageAlgorithm::GetOutput(), svkDcmHeader::InsertUniqueUID(), and svkDcmHeader::SetValue().

void SetInputDenominator ( vtkDataObject *  in )

inline

void SetInputMrsData ( vtkDataObject *  in )

inline

void SetInputNumerator ( vtkDataObject *  in )

inline

void SetSeriesDescription

(

vtkstd::string

newSeriesDescription

)

Set the series description for the DICOM header of the output image.

void SetVerbose

(

bool

isVerbose

)

Write the integrals for each voxel to stdout. Default is false.

void SetZScoreThresholds	(	double	lowerThreshold,
		double	upperThreshold
	)

Set the ZScore threshold for voxels to be included in the regression analysis. Voxels with Zscores ouside this z-score threshold (+/-) will be removed from regression interations until all remaining voxels are within this range.

vtkTypeMacro	(	svkMetaboliteRatioZScores	,
		svkImageAlgorithm
	)

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

• svkMetaboliteRatioZScores.h
• svkMetaboliteRatioZScores.cc