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

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

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

Public Types
typedef TScalarType	VectorDataType
typedef RegistrationBasedCorticalThicknessFilter	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 TScalarType	MaskPixelType
typedef Image< MaskPixelType, itkGetStaticConstMacro(Dimension)>	MaskImageType
typedef MaskImageType::Pointer	MaskImagePointer
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 Image< VectorPixelType, itkGetStaticConstMacro(Dimension)+1 >	TimeVaryingVectorImageType
typedef TimeVaryingVectorImageType::Pointer	TimeVaryingVectorImagePointer
typedef TimeVaryingVectorImageType::PixelType	TimeVaryingVectorImagePixelType
typedef TimeVaryingVectorImageType::SizeType	TimeVaryingVectorImageSizeType
typedef TimeVaryingVectorImageType::IndexType	TimeVaryingVectorImageIndexType
typedef TimeVaryingVectorImageType::SpacingType	TimeVaryingVectorImageSpacingType
typedef TimeVaryingVectorImageType::PointType	TimeVaryingVectorImagePointType
typedef TimeVaryingVectorImageType::DirectionType	TimeVaryingVectorImageDirectionType
typedef TimeVaryingVectorImageType::RegionType	TimeVaryingVectorImageRegionType

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 (MaskImagePointer image)
void	SetGreyMask (MaskImagePointer image)
virtual void	SetMaxIterations (unsigned int _arg)
virtual unsigned int	GetMaxIterations ()
virtual void	SetM (unsigned int _arg)
virtual unsigned int	GetM ()
virtual void	SetLambda (double _arg)
virtual double	GetLambda ()
virtual void	SetUpdateSigma (double _arg)
virtual double	GetUpdateSigma ()
virtual void	SetDeformationSigma (double _arg)
virtual double	GetDeformationSigma ()
virtual void	SetEpsilon (double _arg)
virtual double	GetEpsilon ()
virtual void	SetAlpha (double _arg)
virtual double	GetAlpha ()
virtual double	GetFieldEnergy ()
virtual double	GetCostFunction ()
virtual double	GetMinJacobian ()
virtual double	GetMaxJacobian ()
virtual double	GetRMSChange ()
virtual double	GetSSD ()
virtual double	GetCost ()
VectorImageType *	GetInterfaceDisplacementImage () const

Static Public Member Functions
static Pointer	New ()

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

Member Typedef Documentation

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

Any further typedefs.

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

typedef MaskImageType::Pointer itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::MaskImagePointer

template<class TInputImage , typename TScalarType >

typedef Image< MaskPixelType, itkGetStaticConstMacro(Dimension)> itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::MaskImageType

template<class TInputImage , typename TScalarType >

typedef TScalarType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::MaskPixelType

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::DirectionType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageDirectionType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::IndexType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageIndexType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::PixelType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImagePixelType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::Pointer itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImagePointer

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::PointType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImagePointType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::RegionType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageRegionType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::SizeType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageSizeType

template<class TInputImage , typename TScalarType >

typedef TimeVaryingVectorImageType::SpacingType itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageSpacingType

template<class TInputImage , typename TScalarType >

typedef Image< VectorPixelType, itkGetStaticConstMacro(Dimension)+1> itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::TimeVaryingVectorImageType

template<class TInputImage , typename TScalarType >

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

Standard ITK typedefs.

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

template<class TInputImage , typename TScalarType >

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

Constructor & Destructor Documentation

template<class TInputImage , typename TScalarType >

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

protected

template<class TInputImage , typename TScalarType >

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

inlineprotected

Member Function Documentation

template<class TInputImage , typename TScalarType >

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

protectedvirtual

template<class TInputImage , typename TScalarType >

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

virtual

template<class TInputImage , typename TScalarType >

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

virtual

Run-time type information (and related methods).

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetCost ( )

virtual

Get the cost.

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetCostFunction ( )

virtual

Get the cost function = (1-alpha)(field energy) + alpha*(image similarity)

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetDeformationSigma ( )

virtual

template<class TInputImage , typename TScalarType >

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

virtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetFieldEnergy ( )

virtual

Get the field energy of the deformation. Thats the sum of the Euclidean norm of each velocity vector.

template<class TInputImage , typename TScalarType >

VectorImageType* itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetInterfaceDisplacementImage ( ) const

inline

Get the interface displacement image.

template<class TInputImage , typename TScalarType >

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

virtual

template<class TInputImage , typename TScalarType >

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

virtual

template<class TInputImage , typename TScalarType >

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

virtual

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetMaxJacobian ( )

virtual

Get the max jacobian.

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetMinJacobian ( )

virtual

Get the min jacobian.

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetRMSChange ( )

virtual

Get the RMS change.

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetSSD ( )

virtual

Get the SSD.

template<class TInputImage , typename TScalarType >

virtual double itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::GetUpdateSigma ( )

virtual

template<class TInputImage , typename TScalarType >

itk::RegistrationBasedCorticalThicknessFilter< 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::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::New ( )

static

Method for creation through the object factory.

template<class TInputImage , typename TScalarType >

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

protected

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCorticalThicknessFilter< 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::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::SetDeformationSigma ( double  _arg )

virtual

Set/Get the isotropic standard deviation of the gaussian kernel used for smoothing the deformation field Default 0.

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCorticalThicknessFilter< 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::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::SetGreyMask ( MaskImagePointer  image )

inline

Set the Grey Mask image.

template<class TInputImage , typename TScalarType >

void itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::SetGWI ( MaskImagePointer  image )

inline

Set the GWI image.

template<class TInputImage , typename TScalarType >

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

virtual

Set/Get the number of steps in integration of the ODE. Default 10. Also note that deltat t = 1/M.

template<class TInputImage , typename TScalarType >

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

virtual

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

template<class TInputImage , typename TScalarType >

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

inline

Set the thickness prior image

template<class TInputImage , typename TScalarType >

virtual void itk::RegistrationBasedCorticalThicknessFilter< TInputImage, TScalarType >::SetUpdateSigma ( double  _arg )

virtual

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

template<class TInputImage , typename TScalarType >

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

inline

Set the white matter PV image.

template<class TInputImage , typename TScalarType >

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

inline

Set the white+grey matter PV image.

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

• itkRegistrationBasedCorticalThicknessFilter.h