#include <itkSyNImageRegistrationMethod.h>

Inheritance diagram for itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform >:

Collaboration diagram for itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform >:

Detailed Description

template<typename TFixedImage, typename TMovingImage, typename TOutputTransform = DisplacementFieldTransform<double, TFixedImage::ImageDimension>>
class itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform >

Interface method for the performing greedy SyN image registration.

For greedy SyN we use m_Transform to map the time-parameterized middle image to the fixed image (and vice versa using m_Transform->GetInverseDisplacementField() ). We employ another ivar, m_InverseTransform, to map the time-parameterized middle image to the moving image.

Output: The output is the updated transform which has been added to the composite transform.

This implementation is based on the source code in Advanced Normalization Tools (ANTs)

Avants, B. B.; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A. & Gee, J. C. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, Penn Image Computing and Science Laboratory, University of Pennsylvania, 2011, 54, 2033-2044

The original paper discussing the method is here:

Avants, B. B.; Epstein, C. L.; Grossman, M. & Gee, J. C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal, Department of Radiology, University of Pennsylvania, 2008, 12, 26-41

The method evolved since that time with crucial contributions from Gang Song and Nick Tustison. Though similar in spirit, this implementation is not identical.

Todo:: Need to allow the fixed image to have a composite transform.

Author: Nick Tustison; Brian Avants

Definition at line 74 of file itkSyNImageRegistrationMethod.h.

Public Types
typedef Superclass::CompositeTransformType	CompositeTransformType

typedef SmartPointer< const Self >	ConstPointer

typedef DecoratedOutputTransformType::Pointer	DecoratedOutputTransformPointer

typedef Superclass::DecoratedOutputTransformType	DecoratedOutputTransformType

typedef OutputTransformType::DerivativeType	DerivativeType

typedef DerivativeType::ValueType	DerivativeValueType

typedef DisplacementFieldType::Pointer	DisplacementFieldPointer

typedef OutputTransformType::DisplacementFieldType	DisplacementFieldType

typedef DisplacementFieldType::PixelType	DisplacementVectorType

typedef ImageMetricType::FixedImageMaskType	FixedImageMaskType

typedef FixedImageType::Pointer	FixedImagePointer

typedef Superclass::FixedImagesContainerType	FixedImagesContainerType

typedef TFixedImage	FixedImageType

typedef ImageMetricType::Pointer	ImageMetricPointer

typedef Superclass::ImageMetricType	ImageMetricType

typedef ImageMetricType::MeasureType	MeasureType

typedef ImageMetricType::MovingImageMaskType	MovingImageMaskType

typedef MovingImageType::Pointer	MovingImagePointer

typedef Superclass::MovingImagesContainerType	MovingImagesContainerType

typedef TMovingImage	MovingImageType

typedef Superclass::MultiMetricType	MultiMetricType

typedef Array< SizeValueType >	NumberOfIterationsArrayType

typedef OutputTransformType::Pointer	OutputTransformPointer

typedef TOutputTransform	OutputTransformType

typedef SmartPointer< Self >	Pointer

typedef OutputTransformType::ScalarType	RealType

typedef SyNImageRegistrationMethod	Self

typedef ImageRegistrationMethodv4 < TFixedImage, TMovingImage, TOutputTransform >	Superclass

typedef CompositeTransformType::TransformType	TransformBaseType

typedef ImageMetricType::VirtualImageType	VirtualImageType

Public Types inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
typedef CompositeTransformType::Pointer	CompositeTransformPointer

typedef CompositeTransform < RealType, ImageDimension >	CompositeTransformType

typedef SmartPointer< const Self >	ConstPointer

typedef ProcessObject::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef DecoratedOutputTransformType::Pointer	DecoratedOutputTransformPointer

typedef DataObjectDecorator < OutputTransformType >	DecoratedOutputTransformType

typedef OutputTransformType::DerivativeType	DerivativeType

typedef DerivativeType::ValueType	DerivativeValueType

typedef FixedImageType::Pointer	FixedImagePointer

typedef std::vector < FixedImagePointer >	FixedImagesContainerType

typedef TFixedImage	FixedImageType

typedef ImageToImageMetricv4 < FixedImageType, MovingImageType >	ImageMetricType

typedef InitialTransformType::Pointer	InitialTransformPointer

typedef Transform< RealType, ImageDimension, ImageDimension >	InitialTransformType

typedef MetricType::Pointer	MetricPointer

typedef ImageMetricType::FixedSampledPointSetType	MetricSamplePointSetType

typedef Array< RealType >	MetricSamplingPercentageArrayType

enum	MetricSamplingStrategyType { NONE, REGULAR, RANDOM }

typedef ObjectToObjectMetricBase	MetricType

typedef MovingImageType::Pointer	MovingImagePointer

typedef std::vector < MovingImagePointer >	MovingImagesContainerType

typedef TMovingImage	MovingImageType

typedef ObjectToObjectMultiMetricv4 < ImageDimension, ImageDimension >	MultiMetricType

typedef OptimizerType::Pointer	OptimizerPointer

typedef ObjectToObjectOptimizerBase	OptimizerType

typedef OutputTransformType::Pointer	OutputTransformPointer

typedef TOutputTransform	OutputTransformType

typedef SmartPointer< Self >	Pointer

typedef OutputTransformType::ScalarType	RealType

typedef ImageRegistrationMethodv4	Self

typedef Array< SizeValueType >	ShrinkFactorsArrayType

typedef ShrinkFilterType::ShrinkFactorsType	ShrinkFactorsPerDimensionContainerType

typedef ShrinkImageFilter < FixedImageType, VirtualImageType >	ShrinkFilterType

typedef Array< RealType >	SmoothingSigmasArrayType

typedef ProcessObject	Superclass

typedef TransformParametersAdaptorType::Pointer	TransformParametersAdaptorPointer

typedef std::vector < TransformParametersAdaptorPointer >	TransformParametersAdaptorsContainerType

typedef TransformParametersAdaptor < OutputTransformType >	TransformParametersAdaptorType

typedef ImageMetricType::VirtualImageType	VirtualImageType

Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef std::vector < DataObjectPointer >	DataObjectPointerArray

typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

typedef Object	Superclass

Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef Object	Self

typedef LightObject	Superclass

Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer

typedef SmartPointer< Self >	Pointer

typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const

virtual const char *	GetNameOfClass () const


virtual void	SetLearningRate (RealType _arg)

virtual RealType	GetLearningRate () const


virtual void	SetNumberOfIterationsPerLevel (NumberOfIterationsArrayType _arg)

virtual NumberOfIterationsArrayType	GetNumberOfIterationsPerLevel () const


virtual void	SetConvergenceThreshold (RealType _arg)

virtual RealType	GetConvergenceThreshold () const


virtual void	SetConvergenceWindowSize (unsigned int _arg)

virtual unsigned int	GetConvergenceWindowSize () const


virtual void	SetDownsampleImagesForMetricDerivatives (bool _arg)

virtual bool	GetDownsampleImagesForMetricDerivatives () const


virtual void	SetAverageMidPointGradients (bool _arg)

virtual bool	GetAverageMidPointGradients () const


virtual void	SetGaussianSmoothingVarianceForTheUpdateField (RealType _arg)

virtual const RealType &	GetGaussianSmoothingVarianceForTheUpdateField ()


virtual void	SetGaussianSmoothingVarianceForTheTotalField (RealType _arg)

virtual const RealType &	GetGaussianSmoothingVarianceForTheTotalField ()


virtual const OutputTransformType *	GetFixedToMiddleTransform () const

virtual const OutputTransformType *	GetMovingToMiddleTransform () const

Public Member Functions inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
virtual const RealType &	GetCurrentConvergenceValue ()

virtual const SizeValueType &	GetCurrentIteration ()

virtual SizeValueType	GetCurrentLevel () const

virtual const RealType &	GetCurrentMetricValue ()

virtual const bool &	GetIsConverged ()

virtual const DecoratedOutputTransformType *	GetOutput () const

virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType)

void	SetMetricSamplingPercentage (const RealType)

virtual void	SetFixedImage (const FixedImageType *image)

virtual const FixedImageType *	GetFixedImage () const

virtual void	SetFixedImage (SizeValueType, const FixedImageType *)

virtual const FixedImageType *	GetFixedImage (SizeValueType) const

virtual void	SetMovingImage (const MovingImageType *image)

virtual const MovingImageType *	GetMovingImage () const

virtual void	SetMovingImage (SizeValueType, const MovingImageType *)

virtual const MovingImageType *	GetMovingImage (SizeValueType) const

virtual void	SetOptimizer (OptimizerType *_arg)

virtual OptimizerType *	GetModifiableOptimizer ()

virtual const OptimizerType *	GetOptimizer () const

virtual void	SetMetric (MetricType *_arg)

virtual MetricType *	GetModifiableMetric ()

virtual const MetricType *	GetMetric () const

virtual void	SetMetricSamplingStrategy (MetricSamplingStrategyType _arg)

virtual MetricSamplingStrategyType	GetMetricSamplingStrategy () const

virtual void	SetMetricSamplingPercentagePerLevel (MetricSamplingPercentageArrayType _arg)

virtual MetricSamplingPercentageArrayType	GetMetricSamplingPercentagePerLevel () const

virtual void	SetFixedInitialTransform (InitialTransformType *_arg)

virtual InitialTransformType *	GetModifiableFixedInitialTransform ()

virtual const InitialTransformType *	GetFixedInitialTransform () const

virtual void	SetMovingInitialTransform (InitialTransformType *_arg)

virtual InitialTransformType *	GetModifiableMovingInitialTransform ()

virtual const InitialTransformType *	GetMovingInitialTransform () const

void	SetTransformParametersAdaptorsPerLevel (TransformParametersAdaptorsContainerType &)

const TransformParametersAdaptorsContainerType &	GetTransformParametersAdaptorsPerLevel () const

void	SetNumberOfLevels (const SizeValueType)

virtual SizeValueType	GetNumberOfLevels () const

void	SetShrinkFactorsPerLevel (ShrinkFactorsArrayType factors)

ShrinkFactorsPerDimensionContainerType	GetShrinkFactorsPerDimension (const unsigned int level) const

void	SetShrinkFactorsPerDimension (unsigned int level, ShrinkFactorsPerDimensionContainerType factors)

virtual void	SetSmoothingSigmasPerLevel (SmoothingSigmasArrayType _arg)

virtual SmoothingSigmasArrayType	GetSmoothingSigmasPerLevel () const

virtual void	SetSmoothingSigmasAreSpecifiedInPhysicalUnits (bool _arg)

virtual bool	GetSmoothingSigmasAreSpecifiedInPhysicalUnits () const

virtual void	SmoothingSigmasAreSpecifiedInPhysicalUnitsOn ()

virtual void	SmoothingSigmasAreSpecifiedInPhysicalUnitsOff ()

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData ()

NameArray	GetInputNames () const

MultiThreader *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

virtual const float &	GetProgress ()

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	SetProgress (float _arg)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float amount)

DataObjectPointerArray	GetInputs ()

DataObjectPointerArray	GetOutputs ()

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

virtual void	SetReleaseDataFlag (bool flag)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag ()

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	ReleaseDataBeforeUpdateFlagOff ()

virtual void	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads ()

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

unsigned long	AddObserver (const EventObject &event, Command *) const

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary (void)

const MetaDataDictionary &	GetMetaDataDictionary (void) const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

virtual void	Register () const

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const

Public Member Functions inherited from itk::LightObject
virtual void	Delete ()

virtual int	GetReferenceCount () const

	itkCloneMacro (Self)

void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
static Pointer	New ()

Static Public Attributes
static const unsigned int	ImageDimension = TFixedImage::ImageDimension

Static Public Attributes inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
static const unsigned int	ImageDimension = TFixedImage::ImageDimension

Protected Member Functions
virtual DisplacementFieldPointer	ComputeUpdateField (const FixedImagesContainerType, const TransformBaseType , const MovingImagesContainerType, const TransformBaseType , const FixedImageMaskType *, MeasureType &)

virtual DisplacementFieldPointer	GaussianSmoothDisplacementField (const DisplacementFieldType *, const RealType)

virtual void	GenerateData ()

virtual void	InitializeRegistrationAtEachLevel (const SizeValueType)

virtual DisplacementFieldPointer	InvertDisplacementField (const DisplacementFieldType , const DisplacementFieldType =NULL)

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

virtual void	StartOptimization ()

	SyNImageRegistrationMethod ()

virtual	~SyNImageRegistrationMethod ()

Protected Member Functions inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
	ImageRegistrationMethodv4 ()

virtual void	SetMetricSamplePoints ()

virtual	~ImageRegistrationMethodv4 ()

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

virtual void	AddOutput (DataObject *output)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateInputRequestedRegion ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	ReleaseInputs ()

virtual void	RemoveInput (const DataObjectIdentifierType &key)

virtual void	RemoveInput (DataObjectPointerArraySizeType)

virtual void	RemoveOutput (const DataObjectIdentifierType &key)

virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)

virtual void	RestoreInputReleaseDataFlags ()

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)

virtual void	SetPrimaryInput (DataObject *input)

virtual void	SetPrimaryOutput (DataObject *output)

virtual void	VerifyInputInformation ()

virtual void	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

virtual void	PushBackInput (const DataObject *input)

virtual void	PopBackInput ()

virtual void	PushFrontInput (const DataObject *input)

virtual void	PopFrontInput ()

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

void	SetRequiredInputNames (const NameArray &)

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object ()

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

virtual void	PrintHeader (std::ostream &os, Indent indent) const

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Protected Attributes
bool	m_AverageMidPointGradients

RealType	m_ConvergenceThreshold

unsigned int	m_ConvergenceWindowSize

bool	m_DownsampleImagesForMetricDerivatives

OutputTransformPointer	m_FixedToMiddleTransform

RealType	m_LearningRate

OutputTransformPointer	m_MovingToMiddleTransform

NumberOfIterationsArrayType	m_NumberOfIterationsPerLevel

Protected Attributes inherited from itk::ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform >
CompositeTransformPointer	m_CompositeTransform

RealType	m_CurrentConvergenceValue

SizeValueType	m_CurrentIteration

SizeValueType	m_CurrentLevel

RealType	m_CurrentMetricValue

InitialTransformPointer	m_FixedInitialTransform

FixedImagesContainerType	m_FixedSmoothImages

bool	m_IsConverged

MetricPointer	m_Metric

MetricSamplingPercentageArrayType	m_MetricSamplingPercentagePerLevel

MetricSamplingStrategyType	m_MetricSamplingStrategy

InitialTransformPointer	m_MovingInitialTransform

MovingImagesContainerType	m_MovingSmoothImages

SizeValueType	m_NumberOfFixedImages

SizeValueType	m_NumberOfLevels

SizeValueType	m_NumberOfMovingImages

OptimizerPointer	m_Optimizer

OutputTransformPointer	m_OutputTransform

std::vector < ShrinkFactorsPerDimensionContainerType >	m_ShrinkFactorsPerLevel

bool	m_SmoothingSigmasAreSpecifiedInPhysicalUnits

SmoothingSigmasArrayType	m_SmoothingSigmasPerLevel

TransformParametersAdaptorsContainerType	m_TransformParametersAdaptorsPerLevel

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Private Member Functions
void	operator= (const Self &)

	SyNImageRegistrationMethod (const Self &)

Private Attributes
RealType	m_GaussianSmoothingVarianceForTheTotalField

RealType	m_GaussianSmoothingVarianceForTheUpdateField

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType