#include <itkMRASlabIdentifier.h>

Detailed Description

template<typename TInputImage>
class itk::MRASlabIdentifier< TInputImage >

Identifies slabs in MR images comparing minimum intensity averages.

This class is templated over the type of image. In many cases, a 3D MR image is constructed by merging smaller 3D blocks (slabs) which were acquired with different settings such as magnetic settings and patient positions. Therefore, stripe like patterns with slabs can be present in the resulting image. Such artifacts are called "slab boundary" artifacts or "venetian blind" artifacts.

Due to the slab boundary artifacts in an image, even same tissue class' intensity values might vary significantly along the borders of slabs. Such rough value changes are not appropriate for some image processing methods. For example, MRIBiasFieldCorrectionFilter assumes a smooth bias field. However, with the slab boundary artifacts, the bias field estimation scheme that MRIBiasFieldCorrectionFilter uses might not adapt well. The MRIBiasFieldCorrectionFilter creates regions for slabs using the MRASlabIdentifier and then applies its bias correction scheme to each slab.

For this identifier, a slice means 2D image data which is extracted from the input image along one of three axes \((x, y, z)\). Users can specify the slicing axis using the SetSlicingDirection(int dimension) member, where the dimension variable follows the convention \({X, Y, Z} : {0, 1, 2}\).

The identification scheme used works according to the following steps:

Users should specify how many pixels per slice the identifier will sample.
For each slice, the identifier searches the specified number of pixels of which intensity values are greater than 0 and less than those of the other pixels in the slice.
The identifier calculates the average for each slice and the overall average using the search results.
For each slice, it subtracts the overall average from the slice average. If the sign of the subtraction result changes, then it assumes that a slab ends and another slab begins.

Definition at line 67 of file itkMRASlabIdentifier.h.

Inheritance diagram for itk::MRASlabIdentifier< TInputImage >:

Collaboration diagram for itk::MRASlabIdentifier< TInputImage >:

Public Types
using	ConstPointer = SmartPointer< const Self >

using	ImageConstPointer = typename TInputImage::ConstPointer

using	ImageIndexType = typename TInputImage::IndexType

using	ImagePixelType = typename TInputImage::PixelType

using	ImagePointer = typename TInputImage::Pointer

using	ImageRegionType = typename TInputImage::RegionType

using	ImageSizeType = typename TInputImage::SizeType

using	ImageType = TInputImage

using	Pointer = SmartPointer< Self >

using	Self = MRASlabIdentifier

using	SlabRegionVectorType = std::vector< ImageRegionType >

using	Superclass = Object

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

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

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

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
void	GenerateSlabRegions ()

const char *	GetNameOfClass () const override

SlabRegionVectorType	GetSlabRegionVector ()


virtual void	SetImage (const ImageType *_arg)

virtual const ImageType *	GetImage () const


virtual void	SetNumberOfSamples (unsigned int _arg)

virtual const unsigned int &	GetNumberOfSamples () const


virtual void	SetBackgroundMinimumThreshold (ImagePixelType _arg)

virtual const ImagePixelType &	GetBackgroundMinimumThreshold () const


virtual void	SetTolerance (double _arg)

virtual const double &	GetTolerance () const


virtual void	SetSlicingDirection (int _arg)

virtual const int &	GetSlicingDirection () const

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

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

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 val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Protected Member Functions
	MRASlabIdentifier ()

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

	~MRASlabIdentifier () override=default

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

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~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 Attributes
ImagePixelType	m_BackgroundMinimumThreshold {}

ImageConstPointer	m_Image {}

unsigned int	m_NumberOfSamples {}

SlabRegionVectorType	m_Slabs {}

int	m_SlicingDirection {}

double	m_Tolerance {}

Additional Inherited Members
Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}