itk::RegistrationBasedCTEFilter< TInputImage, TScalarType > Class Template Reference

Inheritance diagram for itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >:

Collaboration diagram for itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >:

Public Types
typedef TScalarType	VectorDataType
typedef RegistrationBasedCTEFilter	Self
typedef ImageToImageFilter < TInputImage, TInputImage >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef TInputImage	ImageType
typedef ImageType::PixelType	PixelType
typedef ImageType::Pointer	ImagePointer
typedef ImageType::SizeType	SizeType
typedef ImageType::IndexType	IndexType
typedef ImageType::RegionType	RegionType
typedef ImageType::SpacingType	SpacingType
typedef ImageType::PointType	OriginType
typedef ImageType::DirectionType	DirectionType
typedef Vector< VectorDataType, itkGetStaticConstMacro(Dimension) >	VectorPixelType
typedef Image< VectorPixelType, itkGetStaticConstMacro(Dimension) >	VectorImageType
typedef VectorImageType::Pointer	VectorImagePointer
typedef VectorImageType::SizeType	VectorImageSizeType
typedef VectorImageType::IndexType	VectorImageIndexType
typedef VectorImageType::RegionType	VectorImageRegionType
typedef VectorImageType::SpacingType	VectorImageSpacingType
typedef VectorImageType::PointType	VectorImagePointType
typedef VectorImageType::PointType	VectorImageOriginType
typedef VectorImageType::DirectionType	VectorImageDirectionType
typedef ImageFileReader < VectorImageType >	VectorImageReaderType
typedef ImageFileWriter < VectorImageType >	VectorImageWriterType
typedef ImageFileWriter < ImageType >	ScalarImageWriterType
typedef LinearInterpolateImageFunction < TInputImage, TScalarType >	LinearInterpolatorType
typedef GaussianSmoothVectorFieldFilter < TScalarType, itkGetStaticConstMacro(Dimension), itkGetStaticConstMacro(Dimension) >	ConvolveFilterType
typedef DisplacementFieldJacobianDeterminantFilter < VectorImageType, TScalarType, TInputImage >	JacobianFilterType
typedef MinimumMaximumImageCalculator < TInputImage >	MinMaxJacobianType
typedef SetOutputVectorToCurrentPositionFilter < TScalarType, itkGetStaticConstMacro(Dimension)>	InitializePhiFilterType
typedef SubtractImageFilter < VectorImageType, VectorImageType >	SubtractImageFilterType
typedef VectorMagnitudeImageFilter < VectorImageType, TInputImage >	VectorMagnitudeFilterType
typedef VectorVPlusLambdaUImageFilter < TScalarType, itkGetStaticConstMacro(Dimension)>	VectorVPlusLambdaUFilterType
typedef VectorPhiPlusDeltaTTimesVFilter < TScalarType, itkGetStaticConstMacro(Dimension)>	VectorPhiPlusDeltaTTimesVFilterType
typedef DasGradientFilter < TScalarType, itkGetStaticConstMacro(Dimension)>	DasGradientFilterType
typedef DasTransformImageFilter < TScalarType, itkGetStaticConstMacro(Dimension)>	DasTransformImageFilterType
typedef DiscreteGaussianImageFilter < ImageType, ImageType >	GaussianSmoothImageFilterType

Public Member Functions
virtual const char *	GetClassName () const
	itkStaticConstMacro (Dimension, unsigned int, TInputImage::ImageDimension)
void	SetWhiteMatterPVMap (ImagePointer image)
void	SetWhitePlusGreyMatterPVMap (ImagePointer image)
void	SetThicknessPriorMap (ImagePointer image)
void	SetGWI (ImagePointer image)
virtual void	SetMaxIterations (unsigned int _arg)
virtual unsigned int	GetMaxIterations ()
virtual void	SetM (unsigned int _arg)
virtual unsigned int	GetM ()
virtual void	SetN (unsigned int _arg)
virtual unsigned int	GetN ()
virtual void	SetLambda (double _arg)
virtual double	GetLambda ()
virtual void	SetSigma (double _arg)
virtual double	GetSigma ()
virtual void	SetEpsilon (double _arg)
virtual double	GetEpsilon ()
virtual void	SetAlpha (double _arg)
virtual double	GetAlpha ()
void	WriteDisplacementField (std::string filename)
virtual void	SetOutputAbsoluteLocation (bool _arg)
virtual bool	GetOutputAbsoluteLocation ()
virtual void	SetTrackJacobian (bool _arg)
virtual bool	GetTrackJacobian ()
virtual void	SetWriteMagnitudeOfDisplacementImage (bool _arg)
virtual bool	GetWriteMagnitudeOfDisplacementImage ()
virtual void	SetWriteTSurfImage (bool _arg)
virtual bool	GetWriteTSurfImage ()
virtual void	SetWriteGradientImage (bool _arg)
virtual bool	GetWriteGradientImage ()
virtual void	SetWriteVelocityImage (bool _arg)
virtual bool	GetWriteVelocityImage ()
virtual void	SetWriteTransformedMovingImage (bool _arg)
virtual bool	GetWriteTransformedMovingImage ()
virtual void	SetSmoothPVMaps (bool _arg)
virtual bool	GetSmoothPVMaps ()
virtual void	SetSmoothPVMapSigma (double _arg)
virtual double	GetSmoothPVMapSigma ()
virtual void	SetUseGradientMovingImage (bool _arg)
virtual bool	GetUseGradientMovingImage ()

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	RegistrationBasedCTEFilter ()
	~RegistrationBasedCTEFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	GenerateData ()

Member Typedef Documentation

template<class TInputImage , typename TScalarType >

typedef SmartPointer<const Self> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::ConstPointer

template<class TInputImage , typename TScalarType >

typedef GaussianSmoothVectorFieldFilter<TScalarType, itkGetStaticConstMacro(Dimension), itkGetStaticConstMacro(Dimension) > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::ConvolveFilterType

template<class TInputImage , typename TScalarType >

typedef DasGradientFilter<TScalarType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::DasGradientFilterType

template<class TInputImage , typename TScalarType >

typedef DasTransformImageFilter<TScalarType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::DasTransformImageFilterType

template<class TInputImage , typename TScalarType >

typedef ImageType::DirectionType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::DirectionType

template<class TInputImage , typename TScalarType >

typedef DiscreteGaussianImageFilter<ImageType,ImageType> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GaussianSmoothImageFilterType

template<class TInputImage , typename TScalarType >

typedef ImageType::Pointer itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::ImagePointer

template<class TInputImage , typename TScalarType >

typedef TInputImage itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::ImageType

Any further typedefs.

template<class TInputImage , typename TScalarType >

typedef ImageType::IndexType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::IndexType

template<class TInputImage , typename TScalarType >

typedef SetOutputVectorToCurrentPositionFilter<TScalarType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::InitializePhiFilterType

template<class TInputImage , typename TScalarType >

typedef DisplacementFieldJacobianDeterminantFilter<VectorImageType, TScalarType, TInputImage> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::JacobianFilterType

template<class TInputImage , typename TScalarType >

typedef LinearInterpolateImageFunction< TInputImage, TScalarType > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::LinearInterpolatorType

template<class TInputImage , typename TScalarType >

typedef MinimumMaximumImageCalculator<TInputImage> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::MinMaxJacobianType

template<class TInputImage , typename TScalarType >

typedef ImageType::PointType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::OriginType

template<class TInputImage , typename TScalarType >

typedef ImageType::PixelType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::PixelType

template<class TInputImage , typename TScalarType >

typedef SmartPointer<Self> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::Pointer

template<class TInputImage , typename TScalarType >

typedef ImageType::RegionType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::RegionType

template<class TInputImage , typename TScalarType >

typedef ImageFileWriter< ImageType > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::ScalarImageWriterType

template<class TInputImage , typename TScalarType >

typedef RegistrationBasedCTEFilter itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::Self

template<class TInputImage , typename TScalarType >

typedef ImageType::SizeType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SizeType

template<class TInputImage , typename TScalarType >

typedef ImageType::SpacingType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SpacingType

template<class TInputImage , typename TScalarType >

typedef SubtractImageFilter<VectorImageType, VectorImageType> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SubtractImageFilterType

template<class TInputImage , typename TScalarType >

typedef ImageToImageFilter<TInputImage, TInputImage> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::Superclass

template<class TInputImage , typename TScalarType >

typedef TScalarType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorDataType

Standard ITK typedefs.

template<class TInputImage , typename TScalarType >

typedef VectorImageType::DirectionType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageDirectionType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::IndexType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageIndexType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::PointType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageOriginType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::Pointer itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImagePointer

template<class TInputImage , typename TScalarType >

typedef VectorImageType::PointType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImagePointType

template<class TInputImage , typename TScalarType >

typedef ImageFileReader< VectorImageType > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageReaderType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::RegionType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageRegionType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::SizeType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageSizeType

template<class TInputImage , typename TScalarType >

typedef VectorImageType::SpacingType itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageSpacingType

template<class TInputImage , typename TScalarType >

typedef Image< VectorPixelType, itkGetStaticConstMacro(Dimension) > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageType

template<class TInputImage , typename TScalarType >

typedef ImageFileWriter< VectorImageType > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorImageWriterType

template<class TInputImage , typename TScalarType >

typedef VectorMagnitudeImageFilter<VectorImageType, TInputImage> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorMagnitudeFilterType

template<class TInputImage , typename TScalarType >

typedef VectorPhiPlusDeltaTTimesVFilter<TScalarType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorPhiPlusDeltaTTimesVFilterType

template<class TInputImage , typename TScalarType >

typedef Vector< VectorDataType, itkGetStaticConstMacro(Dimension) > itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorPixelType

template<class TInputImage , typename TScalarType >

typedef VectorVPlusLambdaUImageFilter<TScalarType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::VectorVPlusLambdaUFilterType

Constructor & Destructor Documentation

template<class TInputImage , typename TScalarType >

itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::RegistrationBasedCTEFilter ( )

protected

template<class TInputImage , typename TScalarType >

itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::~RegistrationBasedCTEFilter ( )

inlineprotected

Member Function Documentation

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GenerateData ( )

protectedvirtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetAlpha ( )

virtual

template<class TInputImage , typename TScalarType >

virtual const char* itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetClassName ( ) const

virtual

Run-time type information (and related methods).

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetEpsilon ( )

virtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetLambda ( )

virtual

template<class TInputImage , typename TScalarType >

virtual unsigned int itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetM ( )

virtual

template<class TInputImage , typename TScalarType >

virtual unsigned int itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetMaxIterations ( )

virtual

template<class TInputImage , typename TScalarType >

virtual unsigned int itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetN ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetOutputAbsoluteLocation ( )

virtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetSigma ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetSmoothPVMaps ( )

virtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetSmoothPVMapSigma ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetTrackJacobian ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetUseGradientMovingImage ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetWriteGradientImage ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetWriteMagnitudeOfDisplacementImage ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetWriteTransformedMovingImage ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetWriteTSurfImage ( )

virtual

template<class TInputImage , typename TScalarType >

virtual bool itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::GetWriteVelocityImage ( )

virtual

template<class TInputImage , typename TScalarType >

itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::itkStaticConstMacro	(	Dimension	,
		unsigned	int,
		TInputImage::ImageDimension
	)

Get the number of dimensions we are working in.

template<class TInputImage , typename TScalarType >

static Pointer itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::New ( )

static

Method for creation through the object factory.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protected

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetAlpha ( double  _arg )

virtual

Set/Get the Alpha, the weighting in the cost function between image similarity and velocity field energy. Default 1.0. The cost function (equation 2 in paper) is weighted:

(1-alpha)*(velocity field energy) + alpha*(image similarity)

so an alpha of 0.9 gives 90% image similarity, and 10% velocity field energy.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetEpsilon ( double  _arg )

virtual

Set/Get the epsilon, the fractional tolerance between successive evaluations of equation 2 in paper. Default 0.0001.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetGWI ( ImagePointer  image )

inline

Set the GWI image.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetLambda ( double  _arg )

virtual

Set/Get the lambda, the gradient descent parameter. Default 1.0

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetM ( unsigned int  _arg )

virtual

Set/Get the number of steps in integration of the ODE. Default 10.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetMaxIterations ( unsigned int  _arg )

virtual

Set/Get the maximum number of iterations. Default 100.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetN ( unsigned int  _arg )

virtual

Set/Get the number of steps in the temporal discretization of the velocity field. Default 10.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetOutputAbsoluteLocation ( bool  _arg )

virtual

Set/Get a flag to determine if (when we write the displacement field), we output the absolute location, or a vector offset. Default is false, so the output will be a vector offset at each position, as this is more easily visualized.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetSigma ( double  _arg )

virtual

Set/Get the sigma, isotropic standard deviation of the gaussian kernel used for smoothing. Default 1.5

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetSmoothPVMaps ( bool  _arg )

virtual

Set/Get a flag to decide if we smooth the GM and GM+WM Pv maps. Default false.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetSmoothPVMapSigma ( double  _arg )

virtual

Set/Get the Gaussian standard deviation for when we are smoothing the GM and GM+WM PV maps. Default 2mm.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetThicknessPriorMap ( ImagePointer  image )

inline

Set the thickness prior image

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetTrackJacobian ( bool  _arg )

virtual

Set/Get a flag to decide if we bother tracking jacobian. Default true. When we say tracking, it just means that the min and max Jacobian are printed in the debug output.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetUseGradientMovingImage ( bool  _arg )

virtual

Set/Get flag to use the gradient of the moving image, as opposed to the gradient of the transformed moving image. Default false.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWhiteMatterPVMap ( ImagePointer  image )

inline

Set the white matter PV image.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWhitePlusGreyMatterPVMap ( ImagePointer  image )

inline

Set the white+grey matter PV image.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWriteGradientImage ( bool  _arg )

virtual

Set/Get a flag to decide if we write out the gradient image. Default false. For N discretisations of the velocity field, we write to file tmp.gradient..nii. So after each iteration you have N gradient images.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWriteMagnitudeOfDisplacementImage ( bool  _arg )

virtual

Set/Get a flag to write an image showing the magnitude of the displacement field. Default false. So for each iteration you get one magnitude image in file tmp.mag.nii. This gives a relatively simple way of checking that the registration is progressing.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWriteTransformedMovingImage ( bool  _arg )

virtual

Set/Get a flag to decide if we write out the transformed moving image. Default false.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWriteTSurfImage ( bool  _arg )

virtual

Set/Get a flag to decide if we write out TSurf. Default false. This is done after registration to file tmp.tsurf.nii, just before we propogate the thickness value through the grey matter.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::SetWriteVelocityImage ( bool  _arg )

virtual

Set/Get a flag to decide if we write out the velocity image. Default false. For N discretisations of the velocity field, we write to file tmp.velocity..nii. So after each iteration you have N velocity images.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCTEFilter< TInputImage, TScalarType >::WriteDisplacementField

(

std::string

filename

)

So we can write the displacement field after registration

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

• itkRegistrationBasedCTEFilter.h