Creates a region of interest for tract-specific analysis of existing TBSS data. More...

#include <mitkTractAnalyzer.h>

Collaboration diagram for mitk::TractAnalyzer:

Public Types
typedef itk::Image< unsigned char, 3 >	CharImageType

typedef itk::Image< float, 3 >	FloatImageType

Public Member Functions
	TractAnalyzer ()

	~TractAnalyzer ()

void	MakeRoi ()
	Main method for region of interest calculation. More...

mitk::TbssRoiImage::Pointer	GetRoiImage ()
	Returns the TbssRoiImage. More...

void	SetInputImage (mitk::Image::Pointer inputImage)
	Sets the input image. More...

void	SetPointSet (mitk::PointSet::Pointer pointSet)
	Sets the user-defined point set. More...

void	SetThreshold (double threshold)
	Sets a lower bound for the threshold. More...

std::string	GetPathDescription ()
	Returns a string with the indices of points on the region of interest. More...

virtual double	GetCostSum ()

Protected Member Functions
std::vector< itk::Index< 3 > >	CreateSegment (itk::Index< 3 > startPoint, itk::Index< 3 > endPoint)
	Calculates a segment of the region of interest. More...

Protected Attributes
mitk::TbssRoiImage::Pointer	m_TbssRoi
	Output TbssRoiImage. More...

mitk::Image::Pointer	m_InputImage
	Inputimage. More...

double	m_Threshold
	Threshold for ROI search. More...

mitk::PointSet::Pointer	m_PointSetNode
	User defined point set. More...

std::string	m_PathDescription
	Path description in as string for display in GUI. More...

double	m_CostSum
	Total cost of the path. More...

Detailed Description

Creates a region of interest for tract-specific analysis of existing TBSS data.

This class needs a 3D image, which is the mean FA skeleton as produced by the standard TBSS pipeline of FSL. How this dataset can be obtained can be found in the TBSS user manual: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index Furthermore, this class requires a user-defined point set defining the points through which the region of interest should pass. The output is a TBSS roi image, which is a binary images defining the roi and metadata containing indices that can be used for plotting graphs using the QmitkTbssRoiAnalysisWidget

Definition at line 42 of file mitkTractAnalyzer.h.

Member Typedef Documentation

typedef itk::Image<unsigned char,3> mitk::TractAnalyzer::CharImageType

Image type definitions

Definition at line 53 of file mitkTractAnalyzer.h.

typedef itk::Image<float,3> mitk::TractAnalyzer::FloatImageType

Definition at line 54 of file mitkTractAnalyzer.h.

Constructor & Destructor Documentation

mitk::TractAnalyzer::TractAnalyzer ( )

Definition at line 38 of file mitkTractAnalyzer.cpp.

mitk::TractAnalyzer::~TractAnalyzer ( )

inline

Definition at line 49 of file mitkTractAnalyzer.h.

Member Function Documentation

std::vector< itk::Index< 3 > > mitk::TractAnalyzer::CreateSegment	(	itk::Index< 3 >	startPoint,
		itk::Index< 3 >	endPoint
	)

protected

Calculates a segment of the region of interest.

The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).

Definition at line 162 of file mitkTractAnalyzer.cpp.

References mitk::CastToItkImage(), and mitk::New().

virtual double mitk::TractAnalyzer::GetCostSum ( )

virtual

std::string mitk::TractAnalyzer::GetPathDescription ( )

inline

Returns a string with the indices of points on the region of interest.

The region of interest calculated by the TractAnalyzer contains a list of ITK indices. This method returns a string containing these indices for display in the GUI

Definition at line 111 of file mitkTractAnalyzer.h.

mitk::TbssRoiImage::Pointer mitk::TractAnalyzer::GetRoiImage ( )

inline

Returns the TbssRoiImage.

Definition at line 67 of file mitkTractAnalyzer.h.

void mitk::TractAnalyzer::MakeRoi ( )

Main method for region of interest calculation.

A region of interest is calculated adding the segments between the points on the ROI that was specified by the user.

Definition at line 41 of file mitkTractAnalyzer.cpp.

References mitk::CastToItkImage(), mitk::ProgressBar::GetInstance(), MITK_INFO, mitkThrow, mitk::New(), mitk::Image::New(), and mitk::ProgressBar::Progress().

void mitk::TractAnalyzer::SetInputImage ( mitk::Image::Pointer inputImage )

inline

Sets the input image.

The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).

Definition at line 78 of file mitkTractAnalyzer.h.

void mitk::TractAnalyzer::SetPointSet ( mitk::PointSet::Pointer pointSet )

inline

Sets the user-defined point set.

Set the user-defined point sets. The region of interest must pass through these points.

Definition at line 88 of file mitkTractAnalyzer.h.

void mitk::TractAnalyzer::SetThreshold ( double threshold )

inline

Sets a lower bound for the threshold.

Low fractional anisotropy values can indicate partial volume of non white matter tissue. This thresholds limits the search for a region of interest to voxels with a minimum value.

Definition at line 99 of file mitkTractAnalyzer.h.

Member Data Documentation

double mitk::TractAnalyzer::m_CostSum

protected

Total cost of the path.

Definition at line 146 of file mitkTractAnalyzer.h.

mitk::Image::Pointer mitk::TractAnalyzer::m_InputImage

protected

Inputimage.

Definition at line 134 of file mitkTractAnalyzer.h.

std::string mitk::TractAnalyzer::m_PathDescription

protected

Path description in as string for display in GUI.

Definition at line 143 of file mitkTractAnalyzer.h.

mitk::PointSet::Pointer mitk::TractAnalyzer::m_PointSetNode

protected

User defined point set.

Definition at line 140 of file mitkTractAnalyzer.h.

mitk::TbssRoiImage::Pointer mitk::TractAnalyzer::m_TbssRoi

protected

Output TbssRoiImage.

Definition at line 131 of file mitkTractAnalyzer.h.

double mitk::TractAnalyzer::m_Threshold

protected

Threshold for ROI search.

Definition at line 137 of file mitkTractAnalyzer.h.

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation