Public Member Functions
	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

	arguments ()

Public Attributes
std::string	inputImage

std::string	outputImage

std::string	inputImage1

std::string	inputImage2

bool	flgUserSetBorderValue

std::vector< double >	width

double	intensity

std::string	fileInputImage

std::string	fileOutputImage

std::string	fixedImage

std::string	movingImage

std::string	outputMatrixTransformFile

std::string	outputNiftyRegMatrixFile

std::string	outputUCLTransformFile

std::string	inputTransformFile

std::string	fixedMask

std::string	movingMask

int	finalInterpolator

int	registrationInterpolator

int	similarityMeasure

int	transformation

int	registrationStrategy

int	optimizer

int	bins

int	iterations

int	dilations

int	levels

int	startLevel

int	stopLevel

double	lowerIntensity

double	higherIntensity

double	dummyDefault

double	paramTol

double	funcTol

double	maxStep

double	minStep

double	gradTol

double	relaxFactor

double	learningRate

double	maskMinimumThreshold

double	maskMaximumThreshold

double	intensityFixedLowerBound

double	intensityFixedUpperBound

double	intensityMovingLowerBound

double	intensityMovingUpperBound

double	movingImagePadValue

int	symmetricMetric

bool	isRescaleIntensity

bool	userSetPadValue

bool	useWeighting

double	weightingThreshold

double	parameterChangeTolerance

bool	useCogInitialisation

bool	rotateAboutCog

double	translationWeighting

double	rotationWeighting

double	scaleWeighting

double	skewWeighting

std::string	dcmDirectoryIn

std::string	dcmDirectoryOut

std::string	strAdd2Suffix

bool	flgOverwrite

bool	flgVerbose

bool	flgDontAnonPatientsName

std::string	strPatientsName

bool	flgDontAnonPatientsBirthDate

std::string	strPatientsBirthDate

bool	flgDontAnonOtherPatientNames

std::string	strOtherPatientNames

bool	flgDontAnonPatientsBirthName

std::string	strPatientsBirthName

bool	flgDontAnonPatientsAddress

std::string	strPatientsAddress

bool	flgDontAnonPatientsMothersBirthName

std::string	strPatientsMothersBirthName

bool	flgDontAnonPatientsTelephoneNumbers

std::string	strPatientsTelephoneNumbers

std::string	iterFilename

bool	flgAnonymiseDICOMHeader

bool	flgAnonymiseImageLabel

bool	flgRescaleIntensitiesToMaxRange

bool	flgInvert

bool	flgFlipHorizontally

bool	flgFlipVertically

float	labelWidth

float	labelHeight

std::string	labelPosition

std::string	labelSide

bool	flgCombineMaskAndBoundingBoxViaUnion

bool	flgIndicesInMM

float	sx

float	sy

float	sz

float	st

float	ex

float	ey

float	ez

float	et

std::string	fileMaskImage

std::string	atlasImage

std::string	regionNumbers

int	firstArgumentAfterOptions

int	atlasBackgroundValue

double	dataBackgroundValue

bool	outputImageName

bool	outputHeader

bool	outputCount

bool	outputMin

bool	outputMax

bool	outputMean

bool	outputSD

bool	outputMedian

bool	outputIQM

bool	debugging

int	argc

char **	argv

std::vector< std::string >	inputImages

bool	flgDebug

bool	flgIsotropic

int	interpolator

std::string	outputITKTransformFile

std::string	outputPlainTransformFile

std::string	inputITKTransformFile

std::string	inputPlainTransformFile

int	pointMetric

int	strategy

int	maxIterationRoundMainLoop

int	powellMaxIters

int	powellMaxLineIters

int	superSamplingFactor

int	varianceInitialPercentage

int	variancePercentageLowerLimit

int	distanceInitialPercentage

int	distancePercentageLowerLimit

int	pyramidSubSampling [3]

double	minimumBlockSize

double	epsilon

double	powellStepLength

double	powellStepTolerance

double	powellValueTolerance

double	variancePercentageMultiplier

double	distancePercentageMultiplier

bool	dumpTransformed

bool	scaleByMillimetres

bool	gradientVariance

bool	writePointSet

bool	noZero

bool	userSpecifiedPyramid

bool	alignCentres

bool	alignAxes

int	bigN

int	bigO

int	bigDelta1

int	bigDelta2

double	resolutionReductionFactor

int	orientation

std::string	seriesName

std::string	fileNameFilter

std::string	fileInputTagKeys

std::string	fileOutputStem

std::string	fileOutputSuffix

std::string	dirDICOMInput

bool	flg2D

std::string	inputFilename1

std::string	inputFilename2

std::string	outputFilename

float	threshold

bool	doOrthogonal

bool	flg4DScalarImageTo3DVectorImage

float	rx

float	ry

float	rz

float	rt

std::string	strOutputType

std::string	fileInputDICOM

std::string	inputFile

std::string	outputFile

bool	flgRender

bool	flgFatSubtract

float	backgroundValue

float	forgroundValue

int	subsamplingFactorX

int	subsamplingFactorY

int	subsamplingFactorZ

float	radius

float	backgroundData

float	foregroundData

int	backgroundAtlas

bool	useForegroundValue

std::string	gmpvmapImage

std::string	laplacianImage

std::string	midlineImage

double	grey

double	white

double	csf

double	low

double	high

double	laplaceRatio

double	pdeRatio

int	laplaceIters

int	pdeIters

double	segThreshold

double	rayThreshold

double	maxDist

bool	doCSFCheck

bool	doGreyCheck

double	sigma

bool	userSetMaxDistance

bool	fullyConnected

int	method

double	maxLength

std::string	labelImage

std::string	wmpvmapImage

std::string	tauImage

std::string	outputThicknessImage

std::string	outputTransformedMovingImage

std::string	outputDisplacementImage

double	sigmaUpdate

double	sigmaDeformation

double	sigmaThickness

double	lambda

double	tau

double	alpha

int	maxIterations

int	m

bool	resampleToIsotropic

bool	rescalePVMaps

bool	useThicknessPriorImage

bool	useOld

int	kernelWidth

bool	blurOutput

int	grey

int	white

int	csf

bool	doAcostaCorrection

bool	doBourgeatCorrection

bool	useLagrangianInitialisation

int	voxelMultiplicationFactor

short int	grey

short int	white

short int	csf

unsigned long int	maxIterations

bool	useSmoothing

double	step

bool	dontUseGaussSeidel

bool	useLabel

std::string	maskImage

int	backgroundMask

bool	justMask

bool	doMean

std::string	greyPVImage

std::string	whitePVImage

std::string	csfPVImage

std::string	maskImageName

std::string	deepGreyPVImage

std::string	internalCSFPVImage

std::string	outputLabelImage

std::string	brainMaskImageName

std::string	whiteMaskImageName

std::string	greyMaskImageName

std::string	csfMaskImageName

std::string	clampGMPVImageName

int	whiteLabel

int	greyLabel

int	csfLabel

int	bgLabel

double	minPG

double	minPW

double	minPC

bool	connected

bool	bourgeatCorrection

bool	acostaCorrection

bool	doMaskFromThresholds

bool	orderedTraversal

bool	initBoundary

bool	sigma

int	nIterations

std::string	inputPolyDataFile

std::string	outputPolyDataFile

double	targetReductionFactor

double	maximumError

double	featureAngle

bool	preserveTopology

bool	maximumErrorSpecified

bool	featureAngleSpecified

bool	targetReductionFactorSpecified

char *	fileOutputStem

char *	fileOutputSuffix

float	dilateValue

int	radius

bool	internal

bool	invert

bool	absolute

int	minNumberOfSlices

std::string	fileMask

std::string	fileOutputMax

std::string	fileOutputAUC

std::string	fileOutputMaxRate

std::string	fileOutputTime2Max

std::string	fileOutputWashOut

std::vector< std::string >	filenames

std::string	fileInputSourceImage

std::string	fileInputTargetImage

std::string	fileSourceLandmarks

std::string	fileTargetLandmarks

std::string	fileInputElasticBodySplineMatrix

std::string	fileOutputElasticBodySplineMatrix

std::string	fileOutputDeformationField

float	poisson

float	stiffness

float	erodeValue

std::string	fileOutputCSV

std::vector< int >	regionSize

std::vector< int >	startingIndex

std::string	gaussianImage

std::string	meanImage

std::string	minImage

std::string	maxImage

int	sx

int	sy

int	sz

int	ix

int	iy

int	iz

std::string	inputMask

std::string	outputScalpImage

float	tskull

float	tscalp

float	foreGround

float	backGround

float	tolerance

int	mode

int	subsampling

float	foregroundValue

std::string	fileInputMask

std::string	fileOutputMask

bool	flgExtrudeInX

bool	flgExtrudeInY

bool	flgExtrudeInZ

std::string	dxImage

std::string	dyImage

std::string	dzImage

bool	normalize

float	alpha

float	beta

std::string	fileSourceImage

std::string	fileReferenceImage

std::string	fileFixedImage

std::string	fileMovingImage

std::string	fileFixedMask

std::string	fileMovingMask

std::string	fileOutputTransformFile

std::string	fileTransform

std::string	fileTarget

std::string	fileSource

std::string	fileOutput

int	numberOfSubdivisions

bool	flgPreserveImageRange

bool	flgUseMinimumIntensityFit

bool	flgRemovePectoralMuscle

float	lowerDensityBound

float	upperDensityBound

std::string	outputMask

std::string	outputFatEstimation

std::string	outputPlateRegion

std::string	outputPectoralMask

std::string	outputPectoralTemplate

std::string	outputDensityImage

std::string	outputDensityValue

std::string	outputIntensityVsEdgeDist

std::string	outputFit

bool	flgPectoralis

bool	flgIncludeBorderRegion

std::string	outputTemplate

bool	flgIgnoreView

bool	flgSSD

std::string	inputSurface

std::string	outputPolyData

int	steps

float	isoSurfaceValue

bool	isStructuredPoints

bool	withScalars

bool	withGradients

bool	withNormals

bool	flgInvertOutputMask

std::string	inputFilename

unsigned int	imagePadSizeX

unsigned int	imagePadSizeY

unsigned int	imagePadSizeZ

int	paddingValue

bool	flgResetOriginToZero

std::string	strInputOrientation

std::string	strOutputOrientation

short	min

short	max

bool	flgClipOutput

float	inLowerPercentile

float	inUpperPercentile

float	outLowerLimit

float	outUpperLimit

std::string	orientation

float	defaultPixelValue

float	origin [3]

float	spacing [3]

float	direction [9]

bool	directionSetByUser

bool	originSetByUser

bool	spacingSetByUser

bool	flgLargestObject

float	distanceThreshold

float	minSize

float	minLabelRank

float	maxLabelRank

float	border

bool	flgLabel

bool	flgApplyMaskToImage

int	nObjects

float	minSizeInMM

float	value

int	factor

int	numberIterations

float	convergenceThreshold

float	edgeAngle

float	featureAngle

float	relaxationFactor

bool	smoothFeatures

bool	smoothEdges

bool	generateErrorScalars

bool	generateErrorVectors

int	sliceDimension

std::string	fileInput

float	subx

float	suby

float	subz

float	a

float	b

double	tolerance

bool	doVoxelCheck

bool	doMinCheck

bool	doMaxCheck

double	min

double	max

int	size [3]

float	resolution [3]

double	stiffness

std::string	dimension

std::string	fileInputMITK

std::string	fileInputPointSet

bool	flgDoNotUseR2LogRThinPlateSpline

std::string	fileInputThinPlateSplineMatrix

std::string	fileOutputThinPlateSplineMatrix

float	upper

float	lower

float	inside

float	outside

std::string	globalTransformName

std::string	deformableTransformName

std::string	deformationFieldName

int	finalInterp

bool	verbose

bool	halfAffineTransformation

bool	invertAffineTransformation

bool	halfNonLinearTransformation

bool	invertNonLinearTransformation

bool	isIdentity

float	isoVoxelSize

bool	doIsotropicVoxels

int	defaultPixelValue

bool	affineJacobianIntensityCorrection

bool	isSymMidway

int	numberOfSymImages

std::string *	symImages

std::vector< std::string >	transformNames

std::string	inDirectory

std::string	outDirectory

std::string	outPixelType

std::string	outImageFileFormat

std::string	imOperation

std::string	rescaleIntensities

std::string	inputImageName

std::string	outputImageName

std::string	brainImageName

unsigned int	scales

unsigned int	mod

float	max

float	min

float	alphaone

float	alphatwo

bool	isBin

bool	isCT

bool	isTOF

bool	doIntensity

unsigned int	radius

unsigned int	majority

unsigned int	numberOfIterations

std::string	targetPolyDataFile

std::string	sourcePolyDataFile

int	maxPoints

bool	visualise

bool	randomTransform

bool	perturbTarget

bool	writeout

std::string	outPolyDataFile

Constructor & Destructor Documentation

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

arguments::arguments ( )

inline

Member Data Documentation

float arguments::a

bool arguments::absolute

bool arguments::acostaCorrection

bool arguments::affineJacobianIntensityCorrection

bool arguments::alignAxes

bool arguments::alignCentres

float arguments::alpha

double arguments::alpha

float arguments::alphaone

float arguments::alphatwo

int arguments::argc

char** arguments::argv

int arguments::atlasBackgroundValue

std::string arguments::atlasImage

float arguments::b

float arguments::backGround

int arguments::backgroundAtlas

float arguments::backgroundData

int arguments::backgroundMask

float arguments::backgroundValue

float arguments::beta

int arguments::bgLabel

int arguments::bigDelta1

int arguments::bigDelta2

int arguments::bigN

int arguments::bigO

int arguments::bins

bool arguments::blurOutput

float arguments::border

bool arguments::bourgeatCorrection

std::string arguments::brainImageName

std::string arguments::brainMaskImageName

std::string arguments::clampGMPVImageName

bool arguments::connected

float arguments::convergenceThreshold

int arguments::csf

short int arguments::csf

double arguments::csf

int arguments::csfLabel

std::string arguments::csfMaskImageName

std::string arguments::csfPVImage

double arguments::dataBackgroundValue

std::string arguments::dcmDirectoryIn

std::string arguments::dcmDirectoryOut

bool arguments::debugging

std::string arguments::deepGreyPVImage

float arguments::defaultPixelValue

int arguments::defaultPixelValue

std::string arguments::deformableTransformName

std::string arguments::deformationFieldName

float arguments::dilateValue

int arguments::dilations

std::string arguments::dimension

std::string arguments::dirDICOMInput

float arguments::direction[9]

bool arguments::directionSetByUser

int arguments::distanceInitialPercentage

int arguments::distancePercentageLowerLimit

double arguments::distancePercentageMultiplier

float arguments::distanceThreshold

bool arguments::doAcostaCorrection

bool arguments::doBourgeatCorrection

bool arguments::doCSFCheck

bool arguments::doGreyCheck

bool arguments::doIntensity

bool arguments::doIsotropicVoxels

bool arguments::doMaskFromThresholds

bool arguments::doMaxCheck

bool arguments::doMean

bool arguments::doMinCheck

bool arguments::dontUseGaussSeidel

bool arguments::doOrthogonal

bool arguments::doVoxelCheck

double arguments::dummyDefault

bool arguments::dumpTransformed

std::string arguments::dxImage

std::string arguments::dyImage

std::string arguments::dzImage

float arguments::edgeAngle

double arguments::epsilon

float arguments::erodeValue

float arguments::et

float arguments::ex

float arguments::ey

float arguments::ez

int arguments::factor

double arguments::featureAngle

float arguments::featureAngle

bool arguments::featureAngleSpecified

std::string arguments::fileFixedImage

std::string arguments::fileFixedMask

std::string arguments::fileInput

std::string arguments::fileInputDICOM

std::string arguments::fileInputElasticBodySplineMatrix

std::string arguments::fileInputImage

std::string arguments::fileInputMask

std::string arguments::fileInputMITK

std::string arguments::fileInputPointSet

std::string arguments::fileInputSourceImage

std::string arguments::fileInputTagKeys

std::string arguments::fileInputTargetImage

std::string arguments::fileInputThinPlateSplineMatrix

std::string arguments::fileMask

std::string arguments::fileMaskImage

std::string arguments::fileMovingImage

std::string arguments::fileMovingMask

std::string arguments::fileNameFilter

std::vector<std::string> arguments::filenames

std::string arguments::fileOutput

std::string arguments::fileOutputAUC

std::string arguments::fileOutputCSV

std::string arguments::fileOutputDeformationField

std::string arguments::fileOutputElasticBodySplineMatrix

std::string arguments::fileOutputImage

std::string arguments::fileOutputMask

std::string arguments::fileOutputMax

std::string arguments::fileOutputMaxRate

char* arguments::fileOutputStem

std::string arguments::fileOutputStem

char* arguments::fileOutputSuffix

std::string arguments::fileOutputSuffix

std::string arguments::fileOutputThinPlateSplineMatrix

std::string arguments::fileOutputTime2Max

std::string arguments::fileOutputTransformFile

std::string arguments::fileOutputWashOut

std::string arguments::fileReferenceImage

std::string arguments::fileSource

std::string arguments::fileSourceImage

std::string arguments::fileSourceLandmarks

std::string arguments::fileTarget

std::string arguments::fileTargetLandmarks

std::string arguments::fileTransform

int arguments::finalInterp

int arguments::finalInterpolator

int arguments::firstArgumentAfterOptions

std::string arguments::fixedImage

std::string arguments::fixedMask

bool arguments::flg2D

bool arguments::flg4DScalarImageTo3DVectorImage

bool arguments::flgAnonymiseDICOMHeader

bool arguments::flgAnonymiseImageLabel

bool arguments::flgApplyMaskToImage

bool arguments::flgClipOutput

bool arguments::flgCombineMaskAndBoundingBoxViaUnion

bool arguments::flgDebug

bool arguments::flgDoNotUseR2LogRThinPlateSpline

bool arguments::flgDontAnonOtherPatientNames

bool arguments::flgDontAnonPatientsAddress

bool arguments::flgDontAnonPatientsBirthDate

bool arguments::flgDontAnonPatientsBirthName

bool arguments::flgDontAnonPatientsMothersBirthName

bool arguments::flgDontAnonPatientsName

bool arguments::flgDontAnonPatientsTelephoneNumbers

bool arguments::flgExtrudeInX

bool arguments::flgExtrudeInY

bool arguments::flgExtrudeInZ

bool arguments::flgFatSubtract

bool arguments::flgFlipHorizontally

bool arguments::flgFlipVertically

bool arguments::flgIgnoreView

bool arguments::flgIncludeBorderRegion

bool arguments::flgIndicesInMM

bool arguments::flgInvert

bool arguments::flgInvertOutputMask

bool arguments::flgIsotropic

bool arguments::flgLabel

bool arguments::flgLargestObject

bool arguments::flgOverwrite

bool arguments::flgPectoralis

bool arguments::flgPreserveImageRange

bool arguments::flgRemovePectoralMuscle

bool arguments::flgRender

bool arguments::flgRescaleIntensitiesToMaxRange

bool arguments::flgResetOriginToZero

bool arguments::flgSSD

bool arguments::flgUseMinimumIntensityFit

bool arguments::flgUserSetBorderValue

bool arguments::flgVerbose

float arguments::foreGround

float arguments::foregroundData

float arguments::foregroundValue

float arguments::forgroundValue

bool arguments::fullyConnected

double arguments::funcTol

std::string arguments::gaussianImage

bool arguments::generateErrorScalars

bool arguments::generateErrorVectors

std::string arguments::globalTransformName

std::string arguments::gmpvmapImage

bool arguments::gradientVariance

double arguments::gradTol

int arguments::grey

short int arguments::grey

double arguments::grey

int arguments::greyLabel

std::string arguments::greyMaskImageName

std::string arguments::greyPVImage

bool arguments::halfAffineTransformation

bool arguments::halfNonLinearTransformation

double arguments::high

double arguments::higherIntensity

unsigned int arguments::imagePadSizeX

unsigned int arguments::imagePadSizeY

unsigned int arguments::imagePadSizeZ

std::string arguments::imOperation

std::string arguments::inDirectory

bool arguments::initBoundary

float arguments::inLowerPercentile

std::string arguments::inputFile

std::string arguments::inputFilename

std::string arguments::inputFilename1

std::string arguments::inputFilename2

std::string arguments::inputImage

std::string arguments::inputImage1

std::string arguments::inputImage2

std::string arguments::inputImageName

std::vector< std::string > arguments::inputImages

std::string arguments::inputITKTransformFile

std::string arguments::inputMask

std::string arguments::inputPlainTransformFile

std::string arguments::inputPolyDataFile

std::string arguments::inputSurface

std::string arguments::inputTransformFile

float arguments::inside

double arguments::intensity

double arguments::intensityFixedLowerBound

double arguments::intensityFixedUpperBound

double arguments::intensityMovingLowerBound

double arguments::intensityMovingUpperBound

bool arguments::internal

std::string arguments::internalCSFPVImage

int arguments::interpolator

float arguments::inUpperPercentile

bool arguments::invert

bool arguments::invertAffineTransformation

bool arguments::invertNonLinearTransformation

bool arguments::isBin

bool arguments::isCT

bool arguments::isIdentity

float arguments::isoSurfaceValue

float arguments::isoVoxelSize

bool arguments::isRescaleIntensity

bool arguments::isStructuredPoints

bool arguments::isSymMidway

bool arguments::isTOF

int arguments::iterations

std::string arguments::iterFilename

int arguments::ix

int arguments::iy

int arguments::iz

bool arguments::justMask

int arguments::kernelWidth

float arguments::labelHeight

std::string arguments::labelImage

std::string arguments::labelPosition

std::string arguments::labelSide

float arguments::labelWidth

double arguments::lambda

int arguments::laplaceIters

double arguments::laplaceRatio

std::string arguments::laplacianImage

double arguments::learningRate

int arguments::levels

double arguments::low

float arguments::lower

float arguments::lowerDensityBound

double arguments::lowerIntensity

int arguments::m

unsigned int arguments::majority

std::string arguments::maskImage

std::string arguments::maskImageName

double arguments::maskMaximumThreshold

double arguments::maskMinimumThreshold

short arguments::max

double arguments::max

float arguments::max

double arguments::maxDist

std::string arguments::maxImage

double arguments::maximumError

bool arguments::maximumErrorSpecified

int arguments::maxIterationRoundMainLoop

unsigned long int arguments::maxIterations

int arguments::maxIterations

float arguments::maxLabelRank

double arguments::maxLength

int arguments::maxPoints

double arguments::maxStep

std::string arguments::meanImage

int arguments::method

std::string arguments::midlineImage

short arguments::min

double arguments::min

float arguments::min

std::string arguments::minImage

double arguments::minimumBlockSize

float arguments::minLabelRank

int arguments::minNumberOfSlices

double arguments::minPC

double arguments::minPG

double arguments::minPW

float arguments::minSize

float arguments::minSizeInMM

double arguments::minStep

unsigned int arguments::mod

int arguments::mode

std::string arguments::movingImage

double arguments::movingImagePadValue

std::string arguments::movingMask

int arguments::nIterations

int arguments::nObjects

bool arguments::normalize

bool arguments::noZero

int arguments::numberIterations

unsigned int arguments::numberOfIterations

int arguments::numberOfSubdivisions

int arguments::numberOfSymImages

int arguments::optimizer

bool arguments::orderedTraversal

std::string arguments::orientation

int arguments::orientation

float arguments::origin

bool arguments::originSetByUser

std::string arguments::outDirectory

std::string arguments::outImageFileFormat

float arguments::outLowerLimit

std::string arguments::outPixelType

std::string arguments::outPolyDataFile

bool arguments::outputCount

std::string arguments::outputDensityImage

std::string arguments::outputDensityValue

std::string arguments::outputDisplacementImage

std::string arguments::outputFatEstimation

std::string arguments::outputFile

std::string arguments::outputFilename

std::string arguments::outputFit

bool arguments::outputHeader

std::string arguments::outputImage

bool arguments::outputImageName

std::string arguments::outputImageName

std::string arguments::outputIntensityVsEdgeDist

bool arguments::outputIQM

std::string arguments::outputITKTransformFile

std::string arguments::outputLabelImage

std::string arguments::outputMask

std::string arguments::outputMatrixTransformFile

bool arguments::outputMax

bool arguments::outputMean

bool arguments::outputMedian

bool arguments::outputMin

std::string arguments::outputNiftyRegMatrixFile

std::string arguments::outputPectoralMask

std::string arguments::outputPectoralTemplate

std::string arguments::outputPlainTransformFile

std::string arguments::outputPlateRegion

std::string arguments::outputPolyData

std::string arguments::outputPolyDataFile

std::string arguments::outputScalpImage

bool arguments::outputSD

std::string arguments::outputTemplate

std::string arguments::outputThicknessImage

std::string arguments::outputTransformedMovingImage

std::string arguments::outputUCLTransformFile

float arguments::outside

float arguments::outUpperLimit

int arguments::paddingValue

double arguments::parameterChangeTolerance

double arguments::paramTol

int arguments::pdeIters

double arguments::pdeRatio

bool arguments::perturbTarget

int arguments::pointMetric

float arguments::poisson

int arguments::powellMaxIters

int arguments::powellMaxLineIters

double arguments::powellStepLength

double arguments::powellStepTolerance

double arguments::powellValueTolerance

bool arguments::preserveTopology

int arguments::pyramidSubSampling[3]

int arguments::radius

unsigned int arguments::radius

float arguments::radius

bool arguments::randomTransform

double arguments::rayThreshold

std::string arguments::regionNumbers

std::vector<int> arguments::regionSize

int arguments::registrationInterpolator

int arguments::registrationStrategy

float arguments::relaxationFactor

double arguments::relaxFactor

bool arguments::resampleToIsotropic

std::string arguments::rescaleIntensities

bool arguments::rescalePVMaps

float arguments::resolution[3]

double arguments::resolutionReductionFactor

bool arguments::rotateAboutCog

double arguments::rotationWeighting

float arguments::rt

float arguments::rx

float arguments::ry

float arguments::rz

bool arguments::scaleByMillimetres

unsigned int arguments::scales

double arguments::scaleWeighting

double arguments::segThreshold

std::string arguments::seriesName

bool arguments::sigma

double arguments::sigma

double arguments::sigmaDeformation

double arguments::sigmaThickness

double arguments::sigmaUpdate

int arguments::similarityMeasure

int arguments::size[3]

double arguments::skewWeighting

int arguments::sliceDimension

bool arguments::smoothEdges

bool arguments::smoothFeatures

std::string arguments::sourcePolyDataFile

float arguments::spacing

bool arguments::spacingSetByUser

float arguments::st

std::vector<int> arguments::startingIndex

int arguments::startLevel

double arguments::step

int arguments::steps

double arguments::stiffness

float arguments::stiffness

int arguments::stopLevel

std::string arguments::strAdd2Suffix

int arguments::strategy

std::string arguments::strInputOrientation

std::string arguments::strOtherPatientNames

std::string arguments::strOutputOrientation

std::string arguments::strOutputType

std::string arguments::strPatientsAddress

std::string arguments::strPatientsBirthDate

std::string arguments::strPatientsBirthName

std::string arguments::strPatientsMothersBirthName

std::string arguments::strPatientsName

std::string arguments::strPatientsTelephoneNumbers

int arguments::subsampling

int arguments::subsamplingFactorX

int arguments::subsamplingFactorY

int arguments::subsamplingFactorZ

float arguments::subx

float arguments::suby

float arguments::subz

int arguments::superSamplingFactor

float arguments::sx

int arguments::sx

float arguments::sy

int arguments::sy

std::string* arguments::symImages

int arguments::symmetricMetric

float arguments::sz

int arguments::sz

std::string arguments::targetPolyDataFile

double arguments::targetReductionFactor

bool arguments::targetReductionFactorSpecified

double arguments::tau

std::string arguments::tauImage

float arguments::threshold

double arguments::tolerance

float arguments::tolerance

int arguments::transformation

std::vector<std::string> arguments::transformNames

double arguments::translationWeighting

float arguments::tscalp

float arguments::tskull

float arguments::upper

float arguments::upperDensityBound

bool arguments::useCogInitialisation

bool arguments::useForegroundValue

bool arguments::useLabel

bool arguments::useLagrangianInitialisation

bool arguments::useOld

bool arguments::userSetMaxDistance

bool arguments::userSetPadValue

bool arguments::userSpecifiedPyramid

bool arguments::useSmoothing

bool arguments::useThicknessPriorImage

bool arguments::useWeighting

float arguments::value

int arguments::varianceInitialPercentage

int arguments::variancePercentageLowerLimit

double arguments::variancePercentageMultiplier

bool arguments::verbose

bool arguments::visualise

int arguments::voxelMultiplicationFactor

double arguments::weightingThreshold

int arguments::white

short int arguments::white

double arguments::white

int arguments::whiteLabel

std::string arguments::whiteMaskImageName

std::string arguments::whitePVImage

std::vector<double> arguments::width

bool arguments::withGradients

bool arguments::withNormals

bool arguments::withScalars

std::string arguments::wmpvmapImage

bool arguments::writeout

bool arguments::writePointSet

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

Public Member Functions

Public Attributes

Constructor & Destructor Documentation

Member Data Documentation