#include <itkMRIBiasFieldCorrectionFilter.h>

Inheritance diagram for itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >:

Collaboration diagram for itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >:

Detailed Description

template<class TInputImage, class TOutputImage, class TMaskImage>
class itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >

corrects 3D MRI bias field

This class is templated over the type of the input image (TInputImage) and the type of the output image (TOutputImage).

In MRI images, intensity inhomogenieties which are caused by magnetic settings, patients' position, and other factors are not unusual. The main purpose of this filter is to reduce such bias field. To estimate the bias field, we use Legendre polynomials. The 1+1 evolutionary optimizer searches for the best parameters of a Legendre polynomial (bias field estimate) which minimizes the total energy value of each image after bias field is eliminated. The default Legendre polynomial degree is 3.

The correction performs by default a multiplicative bias field correction by first log-transforming the input image. This log transform only works on images with grayscale values bigger than 0. The log-transform can be disabled and the filter computes an additive bias field.

There are three major processes in the whole bias correction scheme: slab identification, inter-slice intensity correction, and actual bias correction process. Users can turn on and off each process within the whole bias correction scheme using SetUsingSlabIdentification(bool, false by default), SetUsingInterSliceIntensityCorrection(bool, true by default), and SetUsingBiasFieldCorrection(bool, true by default) member function.

Only the last process (the actual bias field correction) is implemented in a multiresolution framework (without smoothing). Default is a standard level 2 multiresolution schedule (2 2 2 1 1 1)

The bias field correction method was initially developed and implemented by Martin Styner, Univ. of North Carolina at Chapel Hill, and his colleagues.

The multiresolution pyramid implementation is based on itkMultiTesolutionPyramidImageFilter (without Gaussian smoothing)

For more details. refer to the following articles. "Parametric estimate of intensity inhomogeneities applied to MRI" Martin Styner, Guido Gerig, Christian Brechbuehler, Gabor Szekely, IEEE TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000, (http://www.cs.unc.edu/~styner/docs/tmi00.pdf)

"Evaluation of 2D/3D bias correction with 1+1ES-optimization" Martin Styner, Prof. Dr. G. Gerig (IKT, BIWI, ETH Zuerich), TR-197 (http://www.cs.unc.edu/~styner/docs/StynerTR97.pdf)

Definition at line 225 of file itkMRIBiasFieldCorrectionFilter.h.

Public Types
typedef MultivariateLegendrePolynomial	BiasFieldType

typedef SmartPointer< const Self >	ConstPointer

typedef EnergyFunctionType::Pointer	EnergyFunctionPointer

typedef MRIBiasEnergyFunction < InternalImageType, ImageMaskType, BiasFieldType >	EnergyFunctionType

typedef ImageMaskType::Pointer	ImageMaskPointer

typedef ImageMaskType::RegionType	ImageMaskRegionType

typedef TMaskImage	ImageMaskType

typedef TInputImage::IndexType	InputImageIndexType

typedef TInputImage::PixelType	InputImagePixelType

typedef TInputImage::Pointer	InputImagePointer

typedef TInputImage::RegionType	InputImageRegionType

typedef TInputImage::SizeType	InputImageSizeType

typedef TInputImage	InputImageType

typedef MRASlabIdentifier < InputImageType >	MRASlabIdentifierType

typedef Statistics::NormalVariateGenerator	NormalVariateGeneratorType

typedef OnePlusOneEvolutionaryOptimizer	OptimizerType

typedef TOutputImage::IndexType	OutputImageIndexType

typedef TOutputImage::PixelType	OutputImagePixelType

typedef TOutputImage::Pointer	OutputImagePointer

typedef TOutputImage::RegionType	OutputImageRegionType

typedef TOutputImage::SizeType	OutputImageSizeType

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef Array2D< unsigned int >	ScheduleType

typedef MRIBiasFieldCorrectionFilter	Self

typedef SlabRegionVectorType::iterator	SlabRegionVectorIteratorType

typedef MRASlabIdentifierType::SlabRegionVectorType	SlabRegionVectorType

typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass


typedef Image< float, itkGetStaticConstMacro(ImageDimension) >	InternalImageType

typedef InternalImageType::PixelType	InternalImagePixelType

typedef InternalImageType::Pointer	InternalImagePointer

typedef InternalImageType::RegionType	InternalImageRegionType

Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef TInputImage	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource< TOutputImage >	Superclass

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

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	Self

typedef ProcessObject	Superclass

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
void	CorrectImage (BiasFieldType &bias, InputImageRegionType region)

void	CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)

virtual ::itk::LightObject::Pointer	CreateAnother (void) const

BiasFieldType	EstimateBiasField (InputImageRegionType region, unsigned int degree, int maximumIteration)

BiasFieldType::CoefficientArrayType	GetEstimatedBiasFieldCoefficients ()

virtual ImageMaskType *	GetInputMask ()

virtual const char *	GetNameOfClass () const

virtual unsigned int	GetNumberOfLevels () const

virtual double	GetOptimizerShrinkFactor () const

virtual ImageMaskType *	GetOutputMask ()

virtual const ScheduleType &	GetSchedule ()

virtual const InputImagePixelType &	GetSlabBackgroundMinimumThreshold ()

virtual const unsigned int &	GetSlabNumberOfSamples ()

virtual const double &	GetSlabTolerance ()

const unsigned int *	GetStartingShrinkFactors () const

void	Initialize () throw ( ExceptionObject )

void	IsBiasFieldMultiplicative (bool flag)

bool	IsBiasFieldMultiplicative ()

void	SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)

void	SetInputMask (ImageMaskType *inputMask)

void	SetNumberOfLevels (unsigned int num)

virtual void	SetOptimizerShrinkFactor (double _arg)

void	SetOutputMask (ImageMaskType *outputMask)

void	SetSchedule (const ScheduleType &schedule)

virtual void	SetSlabBackgroundMinimumThreshold (InputImagePixelType _arg)

virtual void	SetSlabNumberOfSamples (unsigned int _arg)

virtual void	SetSlabTolerance (double _arg)

virtual void	SetSlicingDirection (int _arg)

void	SetStartingShrinkFactors (unsigned int factor)

void	SetStartingShrinkFactors (unsigned int *factors)

void	SetTissueClassStatistics (const Array< double > &means, const Array< double > &sigmas) throw ( ExceptionObject )


virtual void	SetUsingInterSliceIntensityCorrection (bool _arg)

virtual const bool &	GetUsingInterSliceIntensityCorrection ()


virtual void	SetUsingSlabIdentification (bool _arg)

virtual const bool &	GetUsingSlabIdentification ()


virtual void	SetUsingBiasFieldCorrection (bool _arg)

virtual const bool &	GetUsingBiasFieldCorrection ()


virtual void	SetGeneratingOutput (bool _arg)

virtual const bool &	GetGeneratingOutput ()


virtual void	SetBiasFieldDegree (int _arg)

virtual int	GetBiasFieldDegree () const


virtual void	SetVolumeCorrectionMaximumIteration (int _arg)

virtual int	GetVolumeCorrectionMaximumIteration () const

virtual void	SetInterSliceCorrectionMaximumIteration (int _arg)

virtual int	GetInterSliceCorrectionMaximumIteration () const


void	SetOptimizerInitialRadius (double initRadius)

double	GetOptimizerInitialRadius ()


virtual void	SetOptimizerGrowthFactor (double _arg)

virtual double	GetOptimizerGrowthFactor () const

Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual double	GetCoordinateTolerance ()

const InputImageType *	GetInput (void) const

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

virtual void	PushBackInput (const InputImageType *image)

virtual void	PushFrontInput (const InputImageType *image)

virtual void	SetCoordinateTolerance (double _arg)

virtual void	SetInput (const InputImageType *image)

virtual void	SetInput (unsigned int, const TInputImage *image)

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance ()

Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, DataObject *output)

virtual void	GraftOutput (DataObject *output)

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

OutputImageType *	GetOutput (void)

const OutputImageType *	GetOutput (void) const

virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx)

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 bool	IsScheduleDownwardDivisible (const ScheduleType &schedule)

static Pointer	New ()

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

Static Public Attributes inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static const unsigned int	InputImageDimension = TInputImage::ImageDimension

static const unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Static Public Attributes inherited from itk::ImageSource< TOutputImage >
static const unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Protected Member Functions
void	AdjustSlabRegions (SlabRegionVectorType &slabs, OutputImageRegionType requestedRegion)

bool	CheckMaskImage (ImageMaskType *mask)

template<class TSource , class TTarget >
void	CopyAndConvertImage (const TSource source, TTarget target, typename TTarget::RegionType requestedRegion)

void	ExpImage (InternalImageType source, InternalImageType target)

void	GenerateData ()

void	GetBiasFieldSize (InputImageRegionType region, BiasFieldType::DomainSizeType &domainSize)

void	Log1PImage (InternalImageType source, InternalImageType target)

	MRIBiasFieldCorrectionFilter ()

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

virtual	~MRIBiasFieldCorrectionFilter ()

Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

virtual void	GenerateInputRequestedRegion ()

virtual void	VerifyInputInformation ()

void	PushBackInput (const DataObject *input)

void	PushFrontInput (const DataObject *input)

	ImageToImageFilter ()

	~ImageToImageFilter ()

Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)

virtual	~ImageSource ()

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

virtual void	AddOutput (DataObject *output)

bool	AddRequiredInputName (const DataObjectIdentifierType &)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (void SetNumberOfOutputs(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)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

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)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyPreconditions ()

	~ProcessObject ()

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

DataObject *	GetInput (DataObjectPointerArraySizeType)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()

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 ()

Private Member Functions
	MRIBiasFieldCorrectionFilter (const Self &)

void	operator= (const Self &)

Private Attributes
BiasFieldType::CoefficientArrayType	m_BiasFieldCoefficients

int	m_BiasFieldDegree

bool	m_BiasMultiplicative

EnergyFunctionPointer	m_EnergyFunction

BiasFieldType::CoefficientArrayType	m_EstimatedBiasFieldCoefficients

bool	m_GeneratingOutput

ImageMaskPointer	m_InputMask

InternalImagePointer	m_InternalInput

int	m_InterSliceCorrectionMaximumIteration

NormalVariateGeneratorType::Pointer	m_NormalVariateGenerator

unsigned int	m_NumberOfLevels

double	m_OptimizerGrowthFactor

double	m_OptimizerInitialRadius

double	m_OptimizerShrinkFactor

ImageMaskPointer	m_OutputMask

ScheduleType	m_Schedule

InputImagePixelType	m_SlabBackgroundMinimumThreshold

unsigned int	m_SlabNumberOfSamples

SlabRegionVectorType	m_Slabs

double	m_SlabTolerance

int	m_SlicingDirection

Array< double >	m_TissueClassMeans

Array< double >	m_TissueClassSigmas

bool	m_UsingBiasFieldCorrection

bool	m_UsingInterSliceIntensityCorrection

bool	m_UsingSlabIdentification

int	m_VolumeCorrectionMaximumIteration

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType

typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType

Static Protected Member Functions inherited from itk::ImageSource< TOutputImage >
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating