ITK  4.1.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Private Member Functions | Private Attributes
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 >:

List of all members.

Public Types

typedef
BSplineFilterType::ArrayType 
ArrayType
typedef
BSplineFilterType::PointDataImageType 
BiasFieldControlPointLatticeType
typedef
BSplineScatteredDataPointSetToImageFilter
< PointSetType,
ScalarImageType
BSplineFilterType
typedef SmartPointer< const SelfConstPointer
typedef TInputImage InputImageType
typedef TMaskImage MaskImageType
typedef MaskImageType::PixelType MaskPixelType
typedef TOutputImage OutputImageType
typedef SmartPointer< SelfPointer
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 Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
virtual RealType GetBiasFieldFullWidthAtHalfMaximum () const
const RealImageTypeGetConfidenceImage () const
virtual RealType GetConvergenceThreshold () const
virtual RealType GetCurrentConvergenceMeasurement () const
virtual unsigned int GetCurrentLevel () const
virtual unsigned int GetElapsedIterations () const
virtual
BiasFieldControlPointLatticeType::Pointer 
GetLogBiasFieldControlPointLattice () const
const MaskImageTypeGetMaskImage () const
virtual MaskPixelType GetMaskLabel () 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 SetMaskLabel (MaskPixelType _arg)
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)
void SetConfidenceImage (const RealImageType *image)
void SetInput3 (const RealImageType *image)

Static Public Member Functions

static Pointer New ()

Static Public Attributes

static const unsigned int ImageDimension = TInputImage::ImageDimension

Protected Member Functions

void GenerateData ()
 N4BiasFieldCorrectionImageFilter ()
void PrintSelf (std::ostream &os, Indent indent) const
 ~N4BiasFieldCorrectionImageFilter ()

Private Member Functions

RealType CalculateConvergenceMeasurement (const RealImageType *, const RealImageType *) const
 N4BiasFieldCorrectionImageFilter (const Self &)
void operator= (const Self &)
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
RealType m_WienerFilterNoise

Detailed Description

template<class TInputImage, class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 with a value equal to m_MaskLabel, are used to estimate the bias field. 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: http://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 93 of file itkN4BiasFieldCorrectionImageFilter.h.


Member Typedef Documentation

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineFilterType::ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ArrayType

Definition at line 136 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineFilterType::PointDataImageType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BiasFieldControlPointLatticeType

Definition at line 135 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineScatteredDataPointSetToImageFilter< PointSetType, ScalarImageType> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BSplineFilterType

B-sline filter typedefs

Definition at line 134 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef SmartPointer<const Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ConstPointer
template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef TInputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::InputImageType

Some convenient typedefs.

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

Definition at line 114 of file itkN4BiasFieldCorrectionImageFilter.h.

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

Definition at line 116 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef MaskImageType::PixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskPixelType

Definition at line 117 of file itkN4BiasFieldCorrectionImageFilter.h.

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

Some convenient typedefs.

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 115 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef SmartPointer<Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Pointer
template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef PointSetType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetPointer

B-spline smoothing filter argument typedefs

Definition at line 128 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 126 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef PointSetType::PointType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointType

B-spline smoothing filter argument typedefs

Definition at line 129 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef RealImageType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImagePointer

Definition at line 121 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef Image<RealType, ImageDimension> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImageType

Definition at line 120 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef float itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealType

Definition at line 119 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 127 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef Vector<RealType, 1> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarType

B-spline smoothing filter argument typedefs

Definition at line 125 of file itkN4BiasFieldCorrectionImageFilter.h.

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

Standard class typedefs.

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

Definition at line 98 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef ImageToImageFilter<TInputImage, TOutputImage> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Superclass
template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
typedef Array<unsigned int> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::VariableSizeArrayType

Definition at line 122 of file itkN4BiasFieldCorrectionImageFilter.h.


Constructor & Destructor Documentation

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( ) [protected]
template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::~N4BiasFieldCorrectionImageFilter ( ) [inline, protected]

Definition at line 373 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( const Self ) [private]

Member Function Documentation

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual::itk::LightObject::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CreateAnother ( void  ) 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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GenerateData ( ) [protected, virtual]

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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 193 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual BiasFieldControlPointLatticeType::Pointer 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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 161 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskLabel ( ) const [virtual]

Get mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfControlPoints ( ) const [virtual]

Get the control point grid size definining 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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
static Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::New ( ) [static]

Standard New method.

Reimplemented from itk::Object.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::operator= ( const Self ) [private]

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

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

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const [protected, virtual]

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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 176 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 141 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 153 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 180 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 149 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskLabel ( MaskPixelType  _arg) [virtual]

Set mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfControlPoints ( ArrayType  _arg) [virtual]

Set the control point grid size definining 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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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 295 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::FixedArray< TValueType, VLength >::Fill().

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<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.


Member Data Documentation

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
const unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ImageDimension = TInputImage::ImageDimension [static]

ImageDimension constants

Definition at line 111 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_BiasFieldFullWidthAtHalfMaximum [private]

Definition at line 419 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ConvergenceThreshold [private]

Definition at line 425 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentConvergenceMeasurement [private]

Definition at line 426 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentLevel [private]

Definition at line 427 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ElapsedIterations [private]

Definition at line 424 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_LogBiasFieldControlPointLattice [private]

Definition at line 432 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaskLabel [private]

Definition at line 413 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaximumNumberOfIterations [private]

Definition at line 423 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfControlPoints [private]

Definition at line 435 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfFittingLevels [private]

Definition at line 436 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfHistogramBins [private]

Definition at line 417 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_SplineOrder [private]

Definition at line 434 of file itkN4BiasFieldCorrectionImageFilter.h.

template<class TInputImage , class TMaskImage = Image<unsigned char, ::itk::GetImageDimension<TInputImage>::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_WienerFilterNoise [private]

Definition at line 418 of file itkN4BiasFieldCorrectionImageFilter.h.


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