Implements section 2.3.1 Correction Of Segmentation in Bourgeat MICCAI 2008. More...

Inheritance diagram for itk::CorrectGMUsingPVMapFilter< TImageType >:

Collaboration diagram for itk::CorrectGMUsingPVMapFilter< TImageType >:

Public Types
typedef CorrectGMUsingPVMapFilter	Self

typedef BaseCTESegmentationFilter < TImageType >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::InputImageType	InputImageType

typedef Superclass::InputPixelType	InputPixelType

typedef Superclass::InputIndexType	InputIndexType

typedef Superclass::InputImagePointer	InputImagePointer

typedef Superclass::InputImageConstPointer	InputImageConstPointer

typedef Superclass::OutputPixelType	OutputPixelType

typedef Superclass::OutputImageType	OutputImageType

typedef Superclass::OutputImagePointer	OutputImagePointer

typedef Superclass::OutputImageConstPointer	OutputImageConstPointer

Public Types inherited from itk::BaseCTESegmentationFilter< TImageType >
typedef BaseCTESegmentationFilter	Self

typedef BaseCTEFilter< TImageType >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::InputImageType	InputImageType

typedef Superclass::InputPixelType	InputPixelType

typedef Superclass::InputIndexType	InputIndexType

typedef Superclass::InputSizeType	InputSizeType

typedef Superclass::InputImagePointer	InputImagePointer

typedef Superclass::InputImageConstPointer	InputImageConstPointer

typedef Superclass::OutputPixelType	OutputPixelType

typedef Superclass::OutputImageType	OutputImageType

typedef Superclass::OutputImagePointer	OutputImagePointer

typedef Superclass::OutputImageConstPointer	OutputImageConstPointer

typedef Superclass::OutputSizeType	OutputSizeType

Public Types inherited from itk::BaseCTEFilter< TImageType >
typedef BaseCTEFilter	Self

typedef ImageToImageFilter < TImageType, TImageType >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef TImageType	InputImageType

typedef InputImageType::PixelType	InputPixelType

typedef InputImageType::IndexType	InputIndexType

typedef InputImageType::SizeType	InputSizeType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputPixelType	OutputPixelType

typedef Image< OutputPixelType, TImageType::ImageDimension >	OutputImageType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::ConstPointer	OutputImageConstPointer

typedef OutputImageType::SizeType	OutputSizeType

Public Member Functions
virtual const char *	GetClassName () const

void	SetSegmentedImage (const InputImageType *image)

void	SetGMPVMap (const InputImageType *image)

const std::vector < InputIndexType > &	GetListOfGreyMatterPixelsBeforeCorrection () const

const std::vector < InputIndexType > &	GetListOfGreyMatterPixelsAfterCorrection () const

virtual void	SetGreyMatterThreshold (double _arg)

virtual double	GetGreyMatterThreshold ()

virtual void	SetDoGreyMatterCheck (bool _arg)

virtual bool	GetDoGreyMatterCheck ()

virtual void	SetDoCSFCheck (bool _arg)

virtual bool	GetDoCSFCheck ()

Public Member Functions inherited from itk::BaseCTESegmentationFilter< TImageType >
virtual void	SetTrustPVMaps (bool _arg)

virtual bool	GetTrustPVMaps ()

Public Member Functions inherited from itk::BaseCTEFilter< TImageType >
	itkStaticConstMacro (Dimension, unsigned int, TImageType::ImageDimension)

virtual InputPixelType	GetGreyMatterLabel ()

virtual InputPixelType	GetWhiteMatterLabel ()

virtual InputPixelType	GetExtraCerebralMatterLabel ()

void	SetLabelThresholds (InputPixelType greyMatterLabel, InputPixelType whiteMatterLabel, InputPixelType extraCerebralMatterLabel)

virtual bool	GetUserHasSetTheLabelThresholds ()

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	CorrectGMUsingPVMapFilter ()

virtual	~CorrectGMUsingPVMapFilter ()

virtual void	PrintSelf (std::ostream &, Indent) const

virtual void	GenerateData ()

Protected Member Functions inherited from itk::BaseCTESegmentationFilter< TImageType >
	BaseCTESegmentationFilter ()

virtual	~BaseCTESegmentationFilter ()

virtual void	CheckOrAssignLabels ()

virtual void	CheckPVMap (std::string name, const InputImageType *image)

Protected Member Functions inherited from itk::BaseCTEFilter< TImageType >
	BaseCTEFilter ()

virtual	~BaseCTEFilter ()

virtual void	GenerateInputRequestedRegion ()

virtual void	EnlargeOutputRequestedRegion (DataObject *itkNotUsed)

virtual void	CheckInputsAndOutputsSameSize ()

virtual bool	IsOnBoundary (const InputImageType *image, const InputIndexType &index, const InputPixelType boundaryValue, bool useFullyConnected)

virtual bool	IsOnCSFBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

virtual bool	IsOnWMBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

virtual bool	IsOnGMBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

Additional Inherited Members
Protected Attributes inherited from itk::BaseCTEFilter< TImageType >
InputPixelType	m_GreyMatterLabel

InputPixelType	m_WhiteMatterLabel

InputPixelType	m_ExtraCerebralMatterLabel

bool	m_UserHasSetTheLabelThresholds

Detailed Description

template<class TImageType>
class itk::CorrectGMUsingPVMapFilter< TImageType >

Implements section 2.3.1 Correction Of Segmentation in Bourgeat MICCAI 2008.

This class provides the segmentation correction as described in Bourgeat MICCAI 2008.

Usage:

filter->SetSegmentedImage(segmentedImage);

filter->SetGMPVMap(greyMatterPVMap);

filter->SetLabelThresholds(grey, white, csf);

filter->Update();

The filter implements two points. Briefly, if a GM voxel is on the GM/CSF boundary it is re-classified as CSF if GMPVC < 1. Also, if a CSF (WM resp) is on CSF/WM boundary its reclassified as GM regardless of the GMPVC fractional content. You should set the GM, WM and CSF boundaries yourself before calling Update, as its quicker.

This exposes 2 lists of indexes, one for all GM pixels before the update, and one for all GM pixels after the update.

See also: niftkCTEBourgeat2008

Member Typedef Documentation

template<class TImageType >

typedef SmartPointer<const Self> itk::CorrectGMUsingPVMapFilter< TImageType >::ConstPointer

template<class TImageType >

typedef Superclass::InputImageConstPointer itk::CorrectGMUsingPVMapFilter< TImageType >::InputImageConstPointer

template<class TImageType >

typedef Superclass::InputImagePointer itk::CorrectGMUsingPVMapFilter< TImageType >::InputImagePointer

template<class TImageType >

typedef Superclass::InputImageType itk::CorrectGMUsingPVMapFilter< TImageType >::InputImageType

Image typedef support.

template<class TImageType >

typedef Superclass::InputIndexType itk::CorrectGMUsingPVMapFilter< TImageType >::InputIndexType

template<class TImageType >

typedef Superclass::InputPixelType itk::CorrectGMUsingPVMapFilter< TImageType >::InputPixelType

template<class TImageType >

typedef Superclass::OutputImageConstPointer itk::CorrectGMUsingPVMapFilter< TImageType >::OutputImageConstPointer

template<class TImageType >

typedef Superclass::OutputImagePointer itk::CorrectGMUsingPVMapFilter< TImageType >::OutputImagePointer

template<class TImageType >

typedef Superclass::OutputImageType itk::CorrectGMUsingPVMapFilter< TImageType >::OutputImageType

template<class TImageType >

typedef Superclass::OutputPixelType itk::CorrectGMUsingPVMapFilter< TImageType >::OutputPixelType

template<class TImageType >

typedef SmartPointer<Self> itk::CorrectGMUsingPVMapFilter< TImageType >::Pointer

template<class TImageType >

typedef CorrectGMUsingPVMapFilter itk::CorrectGMUsingPVMapFilter< TImageType >::Self

Standard "Self" & Superclass typedef.

template<class TImageType >

typedef BaseCTESegmentationFilter<TImageType> itk::CorrectGMUsingPVMapFilter< TImageType >::Superclass

Constructor & Destructor Documentation

template<class TImageType >

itk::CorrectGMUsingPVMapFilter< TImageType >::CorrectGMUsingPVMapFilter ( )

protected

template<class TImageType >

virtual itk::CorrectGMUsingPVMapFilter< TImageType >::~CorrectGMUsingPVMapFilter ( )

inlineprotectedvirtual

Member Function Documentation

template<class TImageType >

virtual void itk::CorrectGMUsingPVMapFilter< TImageType >::GenerateData ( )

protectedvirtual

template<class TImageType >

virtual const char* itk::CorrectGMUsingPVMapFilter< TImageType >::GetClassName ( ) const

virtual

Run-time type information (and related methods)

Reimplemented from itk::BaseCTESegmentationFilter< TImageType >.

template<class TImageType >

virtual bool itk::CorrectGMUsingPVMapFilter< TImageType >::GetDoCSFCheck ( )

virtual

template<class TImageType >

virtual bool itk::CorrectGMUsingPVMapFilter< TImageType >::GetDoGreyMatterCheck ( )

virtual

template<class TImageType >

virtual double itk::CorrectGMUsingPVMapFilter< TImageType >::GetGreyMatterThreshold ( )

virtual

template<class TImageType >

const std::vector<InputIndexType>& itk::CorrectGMUsingPVMapFilter< TImageType >::GetListOfGreyMatterPixelsAfterCorrection ( ) const

Once the filter has run, a list of GM voxles in corrected segmented volume.

template<class TImageType >

const std::vector<InputIndexType>& itk::CorrectGMUsingPVMapFilter< TImageType >::GetListOfGreyMatterPixelsBeforeCorrection ( ) const

Once the filter has run, a list of GM voxels in original segmented volume

template<class TImageType >

static Pointer itk::CorrectGMUsingPVMapFilter< TImageType >::New ( )

static

Method for creation through the object factory.

template<class TImageType >

virtual void itk::CorrectGMUsingPVMapFilter< TImageType >::PrintSelf	(	std::ostream &	,
		Indent
	)		const

protectedvirtual

Standard Print Self.

Reimplemented from itk::BaseCTESegmentationFilter< TImageType >.

template<class TImageType >

virtual void itk::CorrectGMUsingPVMapFilter< TImageType >::SetDoCSFCheck ( bool _arg )

virtual

If true, we do the CSF check, if false we don't. Default true.

template<class TImageType >

virtual void itk::CorrectGMUsingPVMapFilter< TImageType >::SetDoGreyMatterCheck ( bool _arg )

virtual

If true, we do the grey matter check, if false we don't. Default true.

template<class TImageType >

void itk::CorrectGMUsingPVMapFilter< TImageType >::SetGMPVMap ( const InputImageType * image )

inline

Sets the pv map, at input 1.

template<class TImageType >

virtual void itk::CorrectGMUsingPVMapFilter< TImageType >::SetGreyMatterThreshold ( double _arg )

virtual

Set the grey matter threshold. Defaults to 1.

template<class TImageType >

void itk::CorrectGMUsingPVMapFilter< TImageType >::SetSegmentedImage ( const InputImageType * image )

inline

Sets the segmented image, at input 0.

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

itkCorrectGMUsingPVMapFilter.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

template<class TImageType> class itk::CorrectGMUsingPVMapFilter< TImageType >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

template<class TImageType>
class itk::CorrectGMUsingPVMapFilter< TImageType >