Performs standard head-motion correction by using affine registration of the gradient images. More...

#include <mitkDWIHeadMotionCorrectionFilter.h>

Inheritance diagram for mitk::DWIHeadMotionCorrectionFilter:

Collaboration diagram for mitk::DWIHeadMotionCorrectionFilter:

Public Types
typedef short	DiffusionPixelType

typedef Superclass::InputImageType	InputImageType

typedef Superclass::OutputImageType	OutputImageType

typedef itk::VectorImage< DiffusionPixelType, 3 >	ITKDiffusionImageType

Public Types inherited from mitk::ImageToImageFilter
typedef ImageToImageFilter	Self

typedef ImageSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef mitk::Image	InputImageType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef SlicedData::RegionType	InputImageRegionType

Public Types inherited from mitk::ImageSource
typedef ImageSource	Self

typedef BaseDataSource	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...

typedef OutputImageType	OutputType

typedef OutputImageType::Pointer	OutputImagePointer

typedef SlicedData::RegionType	OutputImageRegionType

Public Types inherited from mitk::BaseDataSource
typedef BaseDataSource	Self

typedef itk::ProcessObject	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

typedef BaseData	OutputType

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType

Public Member Functions
	mitkClassMacro (DWIHeadMotionCorrectionFilter, ImageToImageFilter) static Pointer New()

Pointer	Clone () const

virtual unsigned long	GetSteps ()

virtual unsigned long	GetCurrentStep ()

virtual bool	GetIsInValidState ()

virtual void	SetAbortRegistration (bool _arg)

virtual void	SetAverageUnweighted (bool _arg)

Public Member Functions inherited from mitk::ImageToImageFilter
virtual std::vector< std::string >	GetClassHierarchy () const override

virtual const char *	GetClassName () const

Pointer	Clone () const

virtual void	SetInput (const InputImageType *image)

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

InputImageType *	GetInput (void)

InputImageType *	GetInput (unsigned int idx)

const InputImageType *	GetInput (void) const

const InputImageType *	GetInput (unsigned int idx) const

Public Member Functions inherited from mitk::ImageSource
Pointer	Clone () const

OutputType *	GetOutput ()
	Get the output data of this image source object. More...

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Make a DataObject of the correct type to used as the specified output. More...

virtual itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual vtkImageData *	GetVtkImageData ()

virtual const vtkImageData *	GetVtkImageData () const

Public Member Functions inherited from mitk::BaseDataSource
OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...

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

virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...

bool	Updating () const
	Access itk::ProcessObject::m_Updating. More...

Protected Member Functions
	DWIHeadMotionCorrectionFilter ()

virtual	~DWIHeadMotionCorrectionFilter ()

virtual void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...

Protected Member Functions inherited from mitk::ImageToImageFilter
	ImageToImageFilter ()

virtual	~ImageToImageFilter ()

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

virtual void	GenerateInputRequestedRegion () override

Protected Member Functions inherited from mitk::ImageSource
	ImageSource ()

virtual	~ImageSource ()

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...

virtual void	PrepareOutputs () override
	This method is intentionally left blank. More...

virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...

virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). More...

virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). More...

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()

virtual	~BaseDataSource ()

Protected Attributes
unsigned long	m_CurrentStep

unsigned long	m_Steps

bool	m_IsInValidState
	Whether the filter is in a valid state, false if error occured. More...

bool	m_AbortRegistration
	set flag to abort More...

bool	m_AverageUnweighted

Additional Inherited Members
Static Public Member Functions inherited from mitk::ImageToImageFilter
static const char *	GetStaticNameOfClass ()

static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageSource
static const char *	GetStaticNameOfClass ()

static Pointer	New ()
	Method for creation through the object factory. More...

Static Public Member Functions inherited from mitk::BaseDataSource
static const char *	GetStaticNameOfClass ()

Static Protected Member Functions inherited from mitk::ImageSource
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...

Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

Detailed Description

Performs standard head-motion correction by using affine registration of the gradient images.

(Head) motion correction is a essential pre-processing step before performing any further analysis of a diffusion-weighted images since all model fits ( tensor, QBI ) rely on an aligned diffusion-weighted dataset. The correction is done in two steps. First the unweighted images ( if multiple present ) are separately registered on the first one by means of rigid registration and normalized correlation as error metric. Second, the weighted gradient images are registered to the unweighted reference ( computed as average from the aligned images from first step ) by an affine transformation using the MattesMutualInformation metric as optimizer guidance.

Definition at line 45 of file mitkDWIHeadMotionCorrectionFilter.h.

Member Typedef Documentation

typedef short mitk::DWIHeadMotionCorrectionFilter::DiffusionPixelType

Definition at line 64 of file mitkDWIHeadMotionCorrectionFilter.h.

typedef Superclass::InputImageType mitk::DWIHeadMotionCorrectionFilter::InputImageType

Definition at line 65 of file mitkDWIHeadMotionCorrectionFilter.h.

typedef itk::VectorImage<DiffusionPixelType, 3> mitk::DWIHeadMotionCorrectionFilter::ITKDiffusionImageType

Definition at line 67 of file mitkDWIHeadMotionCorrectionFilter.h.

typedef Superclass::OutputImageType mitk::DWIHeadMotionCorrectionFilter::OutputImageType

Definition at line 66 of file mitkDWIHeadMotionCorrectionFilter.h.

Constructor & Destructor Documentation

mitk::DWIHeadMotionCorrectionFilter::DWIHeadMotionCorrectionFilter ( )

protected

Definition at line 41 of file mitkDWIHeadMotionCorrectionFilter.cpp.

virtual mitk::DWIHeadMotionCorrectionFilter::~DWIHeadMotionCorrectionFilter ( )

inlineprotectedvirtual

Definition at line 71 of file mitkDWIHeadMotionCorrectionFilter.h.

Member Function Documentation

Pointer mitk::DWIHeadMotionCorrectionFilter::Clone ( ) const

void mitk::DWIHeadMotionCorrectionFilter::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.