itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage > Class Template Reference

#include <itkN4BiasFieldCorrectionImageFilter.h>

Inheritance diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:

Collaboration diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:

Detailed Description

template<typename TInputImage, typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
class itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >

Implementation of the N4 bias field correction algorithm.

The nonparametric nonuniform intensity normalization (N3) algorithm, as introduced by Sled et al. in 1998 is a method for correcting nonuniformity associated with MR images. The algorithm assumes a simple parametric model (Gaussian) for the bias field and does not require tissue class segmentation. In addition, there are only a couple of parameters to tune with the default values performing quite well. N3 has been publicly available as a set of perl scripts (http://www.bic.mni.mcgill.ca/ServicesSoftwareAdvancedImageProcessingTools/HomePage)

The N4 algorithm, encapsulated with this class, is a variation of the original N3 algorithm with the additional benefits of an improved B-spline fitting routine which allows for multiple resolutions to be used during the correction process. We also modify the iterative update component of algorithm such that the residual bias field is continually updated

Notes for the user:

1. Since much of the image manipulation is done in the log space of the intensities, input images with negative and small values (< 1) can produce poor results.
2. The original authors recommend performing the bias field correction on a downsampled version of the original image.
3. A binary mask or a weighted image can be supplied. If a binary mask is specified, those voxels in the input image which correspond to the voxels in the mask image are used to estimate the bias field. If a UseMaskLabel value is set to true, only voxels in the MaskImage that match the MaskLabel will be used; otherwise, all non-zero voxels in the MaskImage will be masked. If a confidence image is specified, the input voxels are weighted in the b-spline fitting routine according to the confidence voxel values.
4. The filter returns the corrected image. If the bias field is wanted, one can reconstruct it using the class itkBSplineControlPointImageFilter. See the IJ article and the test file for an example.
5. The 'Z' parameter in Sled's 1998 paper is the square root of the class variable 'm_WienerFilterNoise'.

The basic algorithm iterates between sharpening the intensity histogram of the corrected input image and spatially smoothing those results with a B-spline scalar field estimate of the bias field.

Author

Nicholas J. Tustison

Contributed by Nicholas J. Tustison, James C. Gee in the Insight Journal paper: https://hdl.handle.net/10380/3053

REFERENCE

J.G. Sled, A.P. Zijdenbos and A.C. Evans. "A Nonparametric Method for Automatic Correction of Intensity Nonuniformity in Data" IEEE Transactions on Medical Imaging, Vol 17, No 1. Feb 1998.

N.J. Tustison, B.B. Avants, P.A. Cook, Y. Zheng, A. Egan, P.A. Yushkevich, and J.C. Gee. "N4ITK: Improved N3 Bias Correction" IEEE Transactions on Medical Imaging, 29(6):1310-1320, June 2010.

Definition at line 95 of file itkN4BiasFieldCorrectionImageFilter.h.

Public Types
typedef BSplineFilterType::ArrayType	ArrayType
typedef BSplineFilterType::PointDataImageType	BiasFieldControlPointLatticeType
typedef BSplineScatteredDataPointSetToImageFilter < PointSetType, ScalarImageType >	BSplineFilterType
typedef SmartPointer< const Self >	ConstPointer
typedef TInputImage	InputImageType
typedef TMaskImage	MaskImageType
typedef MaskImageType::PixelType	MaskPixelType
typedef TOutputImage	OutputImageType
typedef SmartPointer< Self >	Pointer
typedef RealImageType::Pointer	RealImagePointer
typedef Image< RealType, ImageDimension >	RealImageType
typedef float	RealType
typedef N4BiasFieldCorrectionImageFilter	Self
typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass
typedef Array< unsigned int >	VariableSizeArrayType
typedef Vector< RealType, 1 >	ScalarType
typedef PointSet< ScalarType, itkGetStaticConstMacro(ImageDimension)>	PointSetType
typedef Image< ScalarType, itkGetStaticConstMacro(ImageDimension)>	ScalarImageType
typedef PointSetType::Pointer	PointSetPointer
typedef PointSetType::PointType	PointType
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 MultiThreader	MultiThreaderType
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 () const
virtual RealType	GetBiasFieldFullWidthAtHalfMaximum () const
const RealImageType *	GetConfidenceImage () const
virtual RealType	GetConvergenceThreshold () const
virtual RealType	GetCurrentConvergenceMeasurement () const
virtual unsigned int	GetCurrentLevel () const
virtual unsigned int	GetElapsedIterations () const
virtual const BiasFieldControlPointLatticeType *	GetLogBiasFieldControlPointLattice () const
const MaskImageType *	GetMaskImage () const
virtual VariableSizeArrayType	GetMaximumNumberOfIterations () const
virtual const char *	GetNameOfClass () const
virtual ArrayType	GetNumberOfControlPoints () const
virtual ArrayType	GetNumberOfFittingLevels () const
virtual unsigned int	GetNumberOfHistogramBins () const
virtual unsigned int	GetSplineOrder () const
virtual RealType	GetWienerFilterNoise () const
virtual void	SetBiasFieldFullWidthAtHalfMaximum (RealType _arg)
virtual void	SetConvergenceThreshold (RealType _arg)
void	SetInput1 (const InputImageType *image)
virtual void	SetMaximumNumberOfIterations (VariableSizeArrayType _arg)
virtual void	SetNumberOfControlPoints (ArrayType _arg)
virtual void	SetNumberOfFittingLevels (ArrayType _arg)
void	SetNumberOfFittingLevels (unsigned int n)
virtual void	SetNumberOfHistogramBins (unsigned int _arg)
virtual void	SetSplineOrder (unsigned int _arg)
virtual void	SetWienerFilterNoise (RealType _arg)
void	SetMaskImage (const MaskImageType *mask)
void	SetInput2 (const MaskImageType *mask)
virtual void	SetMaskLabel (MaskPixelType _arg)
virtual MaskPixelType	GetMaskLabel () const
virtual void	SetUseMaskLabel (bool _arg)
virtual bool	GetUseMaskLabel () const
virtual void	UseMaskLabelOn ()
virtual void	UseMaskLabelOff ()
void	SetConfidenceImage (const RealImageType *image)
void	SetInput3 (const RealImageType *image)
Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
const InputImageType *	GetInput () const
const InputImageType *	GetInput (unsigned int idx) const
virtual void	PopBackInput () override
virtual void	PopFrontInput () override
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)
virtual void	SetInput (const InputImageType *image)
virtual void	SetInput (unsigned int, const TInputImage *image)
virtual void	SetCoordinateTolerance (double _arg)
virtual double	GetCoordinateTolerance () const
virtual void	SetDirectionTolerance (double _arg)
virtual double	GetDirectionTolerance () const
Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
OutputImageType *	GetOutput ()
const OutputImageType *	GetOutput () const
virtual void	GraftOutput (DataObject *output)
virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
virtual ProcessObject::DataObjectPointer	MakeOutput (const ProcessObject::DataObjectIdentifierType &) override
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData () const
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
NameArray	GetInputNames () const
DataObjectPointerArray	GetInputs ()
MultiThreaderType *	GetMultiThreader () const
DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
NameArray	GetOutputNames () const
DataObjectPointerArray	GetOutputs ()
virtual const float &	GetProgress () const
NameArray	GetRequiredInputNames () const
bool	HasInput (const DataObjectIdentifierType &key) const
bool	HasOutput (const DataObjectIdentifierType &key) const
virtual void	PrepareOutputs ()
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float progress)
void	SetProgress (float progress)
virtual void	SetReleaseDataFlag (bool flag)
virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool &	GetReleaseDataBeforeUpdateFlag () const
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	SetNumberOfThreads (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfThreads () const
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 ()
const MetaDataDictionary &	GetMetaDataDictionary () 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 override
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int) override
virtual void	UnRegister () const noexceptoverride
virtual void	SetObjectName (std::string _arg)
virtual const std::string &	GetObjectName () 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::Object
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool flag)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
static Pointer	New ()

Static Public Attributes
static const unsigned int	ImageDimension = TInputImage::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	GenerateData () override
	N4BiasFieldCorrectionImageFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const override
	~N4BiasFieldCorrectionImageFilter () override
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 () override
	ImageToImageFilter ()
virtual void	VerifyInputInformation () override
	~ImageToImageFilter () override
void	PushBackInput (const DataObject *input) override
void	PushFrontInput (const DataObject *input) override
Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()
virtual void	AllocateOutputs ()
virtual void	BeforeThreadedGenerateData ()
virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const
	ImageSource ()
virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
virtual	~ImageSource () override
Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)
void	AddOptionalInputName (const DataObjectIdentifierType &)
void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
virtual void	AddOutput (DataObject *output)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
virtual void	CacheInputReleaseDataFlags ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const
bool	IsIndexedInputName (const DataObjectIdentifierType &) const
bool	IsIndexedOutputName (const DataObjectIdentifierType &) const
bool	IsRequiredInputName (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)
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	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
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 () override
DataObject *	GetInput (DataObjectPointerArraySizeType idx)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryInputName (void) const
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 () override
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
RealType	CalculateConvergenceMeasurement (const RealImageType *, const RealImageType *) const
RealImagePointer	ReconstructBiasField (BiasFieldControlPointLatticeType *)
RealImagePointer	SharpenImage (const RealImageType *) const
RealImagePointer	UpdateBiasFieldEstimate (RealImageType *)

Private Attributes
RealType	m_BiasFieldFullWidthAtHalfMaximum
RealType	m_ConvergenceThreshold
RealType	m_CurrentConvergenceMeasurement
unsigned int	m_CurrentLevel
unsigned int	m_ElapsedIterations
BiasFieldControlPointLatticeType::Pointer	m_LogBiasFieldControlPointLattice
MaskPixelType	m_MaskLabel
VariableSizeArrayType	m_MaximumNumberOfIterations
ArrayType	m_NumberOfControlPoints
ArrayType	m_NumberOfFittingLevels
unsigned int	m_NumberOfHistogramBins
unsigned int	m_SplineOrder
bool	m_UseMaskLabel
RealType	m_WienerFilterNoise

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 const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime
bool	m_Updating
Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineFilterType::ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ArrayType

Definition at line 138 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineFilterType::PointDataImageType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BiasFieldControlPointLatticeType

Definition at line 137 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineScatteredDataPointSetToImageFilter< PointSetType, ScalarImageType> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BSplineFilterType

B-sline filter typedefs

Definition at line 136 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef SmartPointer<const Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ConstPointer

Definition at line 103 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TInputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::InputImageType

Some convenient typedefs.

Definition at line 116 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TMaskImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskImageType

Definition at line 118 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef MaskImageType::PixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskPixelType

Definition at line 119 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TOutputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::OutputImageType

Definition at line 117 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef SmartPointer<Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Pointer

Definition at line 102 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSetType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetPointer

B-spline smoothing filter argument typedefs

Definition at line 130 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSet<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetType

B-spline smoothing filter argument typedefs

Definition at line 128 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSetType::PointType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointType

B-spline smoothing filter argument typedefs

Definition at line 131 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef RealImageType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImagePointer

Definition at line 123 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Image<RealType, ImageDimension> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImageType

Definition at line 122 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef float itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealType

Definition at line 121 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Image<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarImageType

B-spline smoothing filter argument typedefs

Definition at line 129 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Vector<RealType, 1> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarType

B-spline smoothing filter argument typedefs

Definition at line 127 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef N4BiasFieldCorrectionImageFilter itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Self

Standard class typedefs.

Definition at line 100 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef ImageToImageFilter<TInputImage, TOutputImage> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Superclass

Definition at line 101 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Array<unsigned int> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::VariableSizeArrayType

Definition at line 124 of file itkN4BiasFieldCorrectionImageFilter.h.

Constructor & Destructor Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( )

protected

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::~N4BiasFieldCorrectionImageFilter ( )

inlineoverrideprotected

Definition at line 383 of file itkN4BiasFieldCorrectionImageFilter.h.

Member Function Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CalculateConvergenceMeasurement ( const RealImageType *  , const RealImageType *    ) const

private

Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual::itk::LightObject::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CreateAnother ( ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GenerateData ( )

overrideprotectedvirtual

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See Also

ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetBiasFieldFullWidthAtHalfMaximum ( ) const

virtual

Get the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const RealImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConfidenceImage ( ) const

inline

Get confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 218 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConvergenceThreshold ( ) const

virtual

Get the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentConvergenceMeasurement ( ) const

virtual

Get the current convergence measurement. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentLevel ( ) const

virtual

Get the current fitting level. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetElapsedIterations ( ) const

virtual

Get the number of elapsed iterations. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual const BiasFieldControlPointLatticeType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetLogBiasFieldControlPointLattice ( ) const

virtual

Typically, a reduced size image is used as input to the N4 filter using something like itkShrinkImageFilter. Since the output is a corrected version of the input, the user will probably want to apply the bias field correction to the full resolution image. This can be done by using the LogBiasFieldControlPointLattice to reconstruct the bias field at the full image resolution (using the class BSplineControlPointImageFilter).

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const MaskImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskImage ( ) const

inline

Get mask image function. If a binary mask image is specified, only those input image voxels inside the mask image values are used in estimating the bias field.

Definition at line 163 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskLabel ( ) const

virtual

Deprecated:

Set/Get mask label value. If a binary mask image is specified and if UseMaskValue is true, only those input image voxels corresponding with mask image values equal to MaskLabel are used in estimating the bias field. If a MaskImage is specified and UseMaskLabel is false, all input image voxels corresponding to non-zero voxels in the MaskImage are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaximumNumberOfIterations ( ) const

virtual

Get the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual const char* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNameOfClass ( ) const

virtual

Runtime information support.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfControlPoints ( ) const

virtual

Get the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfFittingLevels ( ) const

virtual

Get the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfHistogramBins ( ) const

virtual

Get number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetSplineOrder ( ) const

virtual

Get the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual bool itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetUseMaskLabel ( ) const

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to true.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetWienerFilterNoise ( ) const

virtual

Get the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

static Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::New ( )

static

Standard New method.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PrintSelf ( std::ostream &  os, Indent  indent  ) const

overrideprotectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ReconstructBiasField ( BiasFieldControlPointLatticeType *  )

private

Reconstruct bias field given the control point lattice.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetBiasFieldFullWidthAtHalfMaximum ( RealType  _arg )

virtual

Set the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage ( const RealImageType *  image )

inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 201 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConvergenceThreshold ( RealType  _arg )

virtual

Set the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput1 ( const InputImageType *  image )

inline

The image expected for input for bias correction.

Definition at line 143 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ImageToImageFilter< TInputImage, TOutputImage >::SetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2 ( const MaskImageType *  mask )

inline

Set mask image function. If a binary mask image is specified, only those input image voxels inside the mask image values are used in estimating the bias field.

Definition at line 155 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3 ( const RealImageType *  image )

inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 205 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage ( const MaskImageType *  mask )

inline

Set mask image function. If a binary mask image is specified, only those input image voxels inside the mask image values are used in estimating the bias field.

Definition at line 151 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskLabel ( MaskPixelType  _arg )

virtual

Deprecated:

Set/Get mask label value. If a binary mask image is specified and if UseMaskValue is true, only those input image voxels corresponding with mask image values equal to MaskLabel are used in estimating the bias field. If a MaskImage is specified and UseMaskLabel is false, all input image voxels corresponding to non-zero voxels in the MaskImage are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaximumNumberOfIterations ( VariableSizeArrayType  _arg )

virtual

Set the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfControlPoints ( ArrayType  _arg )

virtual

Set the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( ArrayType  _arg )

virtual

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( unsigned int  n )

inline

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Definition at line 306 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::FixedArray< TValue, VLength >::Fill(), and itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfHistogramBins ( unsigned int  _arg )

virtual

Set number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetSplineOrder ( unsigned int  _arg )

virtual

Set the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetUseMaskLabel ( bool  _arg )

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to true.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetWienerFilterNoise ( RealType  _arg )

virtual

Set the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SharpenImage ( const RealImageType *  ) const

private

Sharpen the intensity histogram of the current estimate of the corrected image and map those results to a new estimate of the unsmoothed corrected image.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::UpdateBiasFieldEstimate ( RealImageType *  )

private

Given the unsmoothed estimate of the bias field, this function smooths the estimate and adds the resulting control point values to the total bias field estimate.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::UseMaskLabelOff ( )

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to true.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::UseMaskLabelOn ( )

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to true.

Member Data Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ImageDimension = TInputImage::ImageDimension

static

ImageDimension constants

Definition at line 113 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_BiasFieldFullWidthAtHalfMaximum

private

Definition at line 433 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ConvergenceThreshold

private

Definition at line 439 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentConvergenceMeasurement

private

Definition at line 440 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentLevel

private

Definition at line 441 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ElapsedIterations

private

Definition at line 438 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_LogBiasFieldControlPointLattice

private

Definition at line 446 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaskLabel

private

Definition at line 425 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaximumNumberOfIterations

private

Definition at line 437 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfControlPoints

private

Definition at line 449 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfFittingLevels

private

Definition at line 450 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfHistogramBins

private

Definition at line 431 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_SplineOrder

private

Definition at line 448 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

bool itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_UseMaskLabel

private

Definition at line 426 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_WienerFilterNoise

private

Definition at line 432 of file itkN4BiasFieldCorrectionImageFilter.h.

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

• itkN4BiasFieldCorrectionImageFilter.h