Creates connectomics networks from fibers and parcellation. More...

#include <mitkConnectomicsNetworkCreator.h>

Inheritance diagram for mitk::ConnectomicsNetworkCreator:

Collaboration diagram for mitk::ConnectomicsNetworkCreator:

Public Types
enum	MappingStrategy { EndElementPosition, EndElementPositionAvoidingWhiteMatter, JustEndPointVerticesNoLabel, PrecomputeAndDistance }

typedef itk::Image< int, 3 >	ITKImageType

typedef itk::Point< float, 3 >	PointType

typedef itk::VectorContainer< unsigned int, PointType >	TractType

typedef itk::VectorContainer< unsigned int, TractType::Pointer >	TractContainerType

typedef mitk::ConnectomicsNetwork::VertexDescriptorType	VertexType

typedef mitk::ConnectomicsNetwork::EdgeDescriptorType	EdgeType

typedef mitk::ConnectomicsNetwork::NetworkNode	NetworkNode

typedef std::pair< VertexType, VertexType >	ConnectionType

typedef int	ImageLabelType

typedef std::pair< ImageLabelType, ImageLabelType >	ImageLabelPairType

Public Member Functions
	mitkClassMacroItkParent (ConnectomicsNetworkCreator, itk::Object)

Pointer	Clone () const

void	CreateNetworkFromFibersAndSegmentation ()

void	SetFiberBundle (mitk::FiberBundle::Pointer fiberBundle)

void	SetSegmentation (mitk::Image::Pointer segmentation)

mitk::ConnectomicsNetwork::Pointer	GetNetwork ()

virtual void	SetMappingStrategy (MappingStrategy _arg)

virtual void	SetEndPointSearchRadius (double _arg)

virtual void	SetZeroLabelInvalid (bool _arg)

void	CalculateCenterOfMass ()
	Calculate the locations of vertices. More...

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	ConnectomicsNetworkCreator ()

	ConnectomicsNetworkCreator (mitk::Image::Pointer segmentation, mitk::FiberBundle::Pointer fiberBundle)

	~ConnectomicsNetworkCreator ()

void	AddConnectionToNetwork (ConnectionType newConnection)

VertexType	ReturnAssociatedVertexForLabel (ImageLabelType label)

ConnectionType	ReturnAssociatedVertexPairForLabelPair (ImageLabelPairType labelpair)

ImageLabelPairType	ReturnLabelForFiberTract (TractType::Pointer singleTract, MappingStrategy strategy)

void	SupplyVertexWithInformation (ImageLabelType &label, VertexType &vertex)

std::string	LabelToString (ImageLabelType &label)

bool	IsNonWhiteMatterLabel (int labelInQuestion)

bool	IsBackgroundLabel (int labelInQuestion)

void	LinearExtensionUntilGreyMatter (std::vector< int > &indexVectorOfPointsToUse, TractType::Pointer singleTract, int &label, itk::Index< 3 > &mitkIndex)

void	RetractionUntilBrainMatter (bool retractFront, TractType::Pointer singleTract, int &label, itk::Index< 3 > &mitkIndex)

std::vector< double >	GetCenterOfMass (int label)
	Get the location of the center of mass for a specific label This can throw an exception if the label is not found. More...

itk::Point< float, 3 >	GetItkPoint (double point[3])

void	CreateNewNode (int label, itk::Index< 3 >, bool useIndex)
	Creates a new node. More...

ImageLabelPairType	EndElementPositionLabel (TractType::Pointer singleTract)

ImageLabelPairType	PrecomputeVertexLocationsBySegmentation (TractType::Pointer singleTract)

ImageLabelPairType	JustEndPointVerticesNoLabelTest (TractType::Pointer singleTract)

ImageLabelPairType	EndElementPositionLabelAvoidingWhiteMatter (TractType::Pointer singleTract)

void	FiberToSegmentationCoords (mitk::Point3D &fiberCoord, mitk::Point3D &segCoord)

void	SegmentationToFiberCoords (mitk::Point3D &segCoord, mitk::Point3D &fiberCoord)

Protected Attributes
mitk::FiberBundle::Pointer	m_FiberBundle

mitk::Image::Pointer	m_Segmentation

ITKImageType::Pointer	m_SegmentationItk

mitk::ConnectomicsNetwork::Pointer	m_ConNetwork

int	idCounter

std::map< ImageLabelType, VertexType >	m_LabelToVertexMap

std::map< ImageLabelType, NetworkNode >	m_LabelToNodePropertyMap

bool	allowLoops

bool	m_UseCoMCoordinates

std::map< int, std::vector< double > >	m_LabelsToCoordinatesMap

MappingStrategy	m_MappingStrategy

double	m_EndPointSearchRadius

bool	m_ZeroLabelInvalid

bool	m_AbortConnection

Static Protected Attributes
static const int	freesurfer_Left_Cerebral_White_Matter

static const int	freesurfer_Left_Cerebellum_White_Matter

static const int	freesurfer_Left_Cerebellum_Cortex

static const int	freesurfer_Brain_Stem

static const int	freesurfer_Right_Cerebral_White_Matter

static const int	freesurfer_Right_Cerebellum_White_Matter

static const int	freesurfer_Right_Cerebellum_Cortex

Detailed Description

Creates connectomics networks from fibers and parcellation.

This class needs a parcellation image and a fiber image to be set. Then you can create a connectomics network from the two, using different strategies.

Definition at line 42 of file mitkConnectomicsNetworkCreator.h.

Member Typedef Documentation

typedef std::pair< VertexType, VertexType > mitk::ConnectomicsNetworkCreator::ConnectionType

Definition at line 77 of file mitkConnectomicsNetworkCreator.h.

typedef mitk::ConnectomicsNetwork::EdgeDescriptorType mitk::ConnectomicsNetworkCreator::EdgeType

Definition at line 75 of file mitkConnectomicsNetworkCreator.h.

typedef std::pair< ImageLabelType, ImageLabelType > mitk::ConnectomicsNetworkCreator::ImageLabelPairType

Definition at line 81 of file mitkConnectomicsNetworkCreator.h.

typedef int mitk::ConnectomicsNetworkCreator::ImageLabelType

Types for labels

Definition at line 80 of file mitkConnectomicsNetworkCreator.h.

typedef itk::Image<int, 3 > mitk::ConnectomicsNetworkCreator::ITKImageType

Type for Images

Definition at line 65 of file mitkConnectomicsNetworkCreator.h.

typedef mitk::ConnectomicsNetwork::NetworkNode mitk::ConnectomicsNetworkCreator::NetworkNode

Definition at line 76 of file mitkConnectomicsNetworkCreator.h.

typedef itk::Point<float,3> mitk::ConnectomicsNetworkCreator::PointType

Types for the standardized Tract

Definition at line 68 of file mitkConnectomicsNetworkCreator.h.

typedef itk::VectorContainer< unsigned int, TractType::Pointer > mitk::ConnectomicsNetworkCreator::TractContainerType

Definition at line 70 of file mitkConnectomicsNetworkCreator.h.

typedef itk::VectorContainer<unsigned int, PointType> mitk::ConnectomicsNetworkCreator::TractType

Definition at line 69 of file mitkConnectomicsNetworkCreator.h.

typedef mitk::ConnectomicsNetwork::VertexDescriptorType mitk::ConnectomicsNetworkCreator::VertexType

Types for Network

Definition at line 74 of file mitkConnectomicsNetworkCreator.h.

Member Enumeration Documentation

enum mitk::ConnectomicsNetworkCreator::MappingStrategy

Enum for different ways to create the mapping from fibers to network

Enumerator
EndElementPosition
EndElementPositionAvoidingWhiteMatter
JustEndPointVerticesNoLabel
PrecomputeAndDistance

Definition at line 48 of file mitkConnectomicsNetworkCreator.h.

Constructor & Destructor Documentation

mitk::ConnectomicsNetworkCreator::ConnectomicsNetworkCreator ( )

protected

Definition at line 34 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetworkCreator::ConnectomicsNetworkCreator	(	mitk::Image::Pointer	segmentation,
		mitk::FiberBundle::Pointer	fiberBundle
	)

protected

Definition at line 51 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::CastToItkImage(), and m_SegmentationItk.

mitk::ConnectomicsNetworkCreator::~ConnectomicsNetworkCreator ( )

protected

Definition at line 68 of file mitkConnectomicsNetworkCreator.cpp.

Member Function Documentation

void mitk::ConnectomicsNetworkCreator::AddConnectionToNetwork ( ConnectionType newConnection )

protected

Add a connection to the network

Definition at line 142 of file mitkConnectomicsNetworkCreator.cpp.

References MITK_DEBUG.

void mitk::ConnectomicsNetworkCreator::CalculateCenterOfMass ( )

Calculate the locations of vertices.

Calculate the center of mass for each label and store the information. This will need a set parcellation image. Unless this function is called the first location where a label is encountered will be used. After calling this function the center of mass will be used instead.

Definition at line 759 of file mitkConnectomicsNetworkCreator.cpp.

References max(), and min().

Pointer mitk::ConnectomicsNetworkCreator::Clone ( ) const

void mitk::ConnectomicsNetworkCreator::CreateNetworkFromFibersAndSegmentation ( )

Given a fiber bundle and a parcellation are set, this will create a network from both

Definition at line 92 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_INFO_NETWORK_CREATED, MBI_INFO, mitk::New(), and mitk::ConnectomicsNetwork::New().

void mitk::ConnectomicsNetworkCreator::CreateNewNode	(	int	label,
		itk::Index< 3 >	index,
		bool	useIndex
	)

protected

Creates a new node.

A new node will be created, using the label and either the supplied coordinates or the center of mass coordinates, depending on the supplied bool.

Definition at line 835 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsNetwork::NetworkNode::coordinates, and mitk::ConnectomicsNetwork::NetworkNode::label.

mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabel ( TractType::Pointer singleTract )

protected

Use the position of the end and starting element only to map to labels

Map a fiber to a vertex by taking the value of the parcellation image at the same world coordinates as the last and first element of the tract.

Definition at line 226 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3, and MBI_ERROR.

mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabelAvoidingWhiteMatter ( TractType::Pointer singleTract )

protected

Use the position of the end and starting element unless it is in white matter, then search for nearby parcellation to map to labels

Map a fiber to a vertex by taking the value of the parcellation image at the same world coordinates as the last and first element of the tract. If this happens to be white matter, then try to extend the fiber in a line and take the first non-white matter parcel, that is intersected.

Definition at line 276 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3, and MBI_ERROR.

void mitk::ConnectomicsNetworkCreator::FiberToSegmentationCoords	(	mitk::Point3D &	fiberCoord,
		mitk::Point3D &	segCoord
	)

protected

Convert fiber index to segmentation index coordinates

Definition at line 463 of file mitkConnectomicsNetworkCreator.cpp.

std::vector< double > mitk::ConnectomicsNetworkCreator::GetCenterOfMass ( int label )

protected

Get the location of the center of mass for a specific label This can throw an exception if the label is not found.

Definition at line 820 of file mitkConnectomicsNetworkCreator.cpp.

References MITK_ERROR.

itk::Point< float, 3 > mitk::ConnectomicsNetworkCreator::GetItkPoint ( double point[3] )

protected

Convert point to itk point

Definition at line 83 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkCreator::GetNetwork ( )

Definition at line 458 of file mitkConnectomicsNetworkCreator.cpp.

bool mitk::ConnectomicsNetworkCreator::IsBackgroundLabel ( int labelInQuestion )

protected

Check whether the label in question belongs to background according to the freesurfer table

Definition at line 498 of file mitkConnectomicsNetworkCreator.cpp.

bool mitk::ConnectomicsNetworkCreator::IsNonWhiteMatterLabel ( int labelInQuestion )

protected

Check whether the label in question belongs to white matter according to the freesurfer table

Definition at line 481 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::JustEndPointVerticesNoLabelTest ( TractType::Pointer singleTract )

protected

Use the position of the end and starting element only to map to labels

Just take first and last position, no labelling, nothing

Definition at line 395 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3, and MBI_ERROR.

std::string mitk::ConnectomicsNetworkCreator::LabelToString ( ImageLabelType & label )

protected

Create a string from the label

Definition at line 448 of file mitkConnectomicsNetworkCreator.cpp.

void mitk::ConnectomicsNetworkCreator::LinearExtensionUntilGreyMatter	(	std::vector< int > &	indexVectorOfPointsToUse,
		TractType::Pointer	singleTract,
		int &	label,
		itk::Index< 3 > &	mitkIndex
	)

protected

Extend a straight line through the given points and look for the first non white matter label

It will try extend in the direction of the points in the vector so a vector {B,C} will result in extending from C in the direction C-B

Definition at line 507 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_DID_NOT_FIND_WHITE, mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_END, mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_START, mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_LESS_THAN_2, mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_MORE_POINTS_THAN_PRESENT, and MBI_WARN.

mitk::ConnectomicsNetworkCreator::mitkClassMacroItkParent	(	ConnectomicsNetworkCreator	,
		itk::Object
	)

Standard class typedefs. Method for creation through the object factory.

static Pointer mitk::ConnectomicsNetworkCreator::New ( )

static

Referenced by main().

mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::PrecomputeVertexLocationsBySegmentation ( TractType::Pointer singleTract )

protected

Map by distance between elements and vertices depending on their volume

First go through the parcellation and compute the coordinates of the future vertices. Assign a radius according on their volume. Then map an edge to a label by considering the nearest vertices and comparing the distance to them to their radii.

Definition at line 269 of file mitkConnectomicsNetworkCreator.cpp.

void mitk::ConnectomicsNetworkCreator::RetractionUntilBrainMatter	(	bool	retractFront,
		TractType::Pointer	singleTract,
		int &	label,
		itk::Index< 3 > &	mitkIndex
	)

protected

Retract fiber until the first brain matter label is hit

The bool parameter controls whether the front or the end is retracted

Definition at line 632 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetworkCreator::VertexType mitk::ConnectomicsNetworkCreator::ReturnAssociatedVertexForLabel ( ImageLabelType label )

protected

Determine if a label is already identified with a vertex, otherwise create a new one

Definition at line 169 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetworkCreator::ConnectionType mitk::ConnectomicsNetworkCreator::ReturnAssociatedVertexPairForLabelPair ( ImageLabelPairType labelpair )

protected

Return the vertexes associated with a pair of labels

Definition at line 190 of file mitkConnectomicsNetworkCreator.cpp.

mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::ReturnLabelForFiberTract	(	TractType::Pointer	singleTract,
		MappingStrategy	strategy
	)

protected

Return the pair of labels which identify the areas connected by a single fiber

Definition at line 198 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_MAPPING, and MBI_ERROR.

void mitk::ConnectomicsNetworkCreator::SegmentationToFiberCoords	(	mitk::Point3D &	segCoord,
		mitk::Point3D &	fiberCoord
	)

protected

Convert segmentation index to fiber index coordinates

Definition at line 472 of file mitkConnectomicsNetworkCreator.cpp.

virtual void mitk::ConnectomicsNetworkCreator::SetEndPointSearchRadius ( double _arg )

virtual

void mitk::ConnectomicsNetworkCreator::SetFiberBundle ( mitk::FiberBundle::Pointer fiberBundle )

Definition at line 72 of file mitkConnectomicsNetworkCreator.cpp.

virtual void mitk::ConnectomicsNetworkCreator::SetMappingStrategy ( MappingStrategy _arg )

virtual

void mitk::ConnectomicsNetworkCreator::SetSegmentation ( mitk::Image::Pointer segmentation )

Definition at line 77 of file mitkConnectomicsNetworkCreator.cpp.

References mitk::CastToItkImage().

virtual void mitk::ConnectomicsNetworkCreator::SetZeroLabelInvalid ( bool _arg )

virtual

void mitk::ConnectomicsNetworkCreator::SupplyVertexWithInformation	(	ImageLabelType &	label,
		VertexType &	vertex
	)

protected

Assign the additional information which should be part of the vertex

Definition at line 438 of file mitkConnectomicsNetworkCreator.cpp.

Member Data Documentation

bool mitk::ConnectomicsNetworkCreator::allowLoops

protected

Definition at line 211 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Brain_Stem

staticprotected

Definition at line 239 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Left_Cerebellum_Cortex

staticprotected

Definition at line 238 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Left_Cerebellum_White_Matter

staticprotected

Definition at line 237 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Left_Cerebral_White_Matter

staticprotected

Definition at line 236 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Right_Cerebellum_Cortex

staticprotected

Definition at line 242 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Right_Cerebellum_White_Matter

staticprotected

Definition at line 241 of file mitkConnectomicsNetworkCreator.h.

const int mitk::ConnectomicsNetworkCreator::freesurfer_Right_Cerebral_White_Matter

staticprotected

Definition at line 240 of file mitkConnectomicsNetworkCreator.h.

int mitk::ConnectomicsNetworkCreator::idCounter

protected

Definition at line 202 of file mitkConnectomicsNetworkCreator.h.

bool mitk::ConnectomicsNetworkCreator::m_AbortConnection

protected

Definition at line 230 of file mitkConnectomicsNetworkCreator.h.

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkCreator::m_ConNetwork

protected

Definition at line 199 of file mitkConnectomicsNetworkCreator.h.

double mitk::ConnectomicsNetworkCreator::m_EndPointSearchRadius

protected

Definition at line 223 of file mitkConnectomicsNetworkCreator.h.

mitk::FiberBundle::Pointer mitk::ConnectomicsNetworkCreator::m_FiberBundle

protected

Definition at line 194 of file mitkConnectomicsNetworkCreator.h.

std::map< int, std::vector< double> > mitk::ConnectomicsNetworkCreator::m_LabelsToCoordinatesMap

protected

Definition at line 217 of file mitkConnectomicsNetworkCreator.h.

std::map< ImageLabelType, NetworkNode > mitk::ConnectomicsNetworkCreator::m_LabelToNodePropertyMap

protected

Definition at line 208 of file mitkConnectomicsNetworkCreator.h.

std::map< ImageLabelType, VertexType > mitk::ConnectomicsNetworkCreator::m_LabelToVertexMap

protected

Definition at line 205 of file mitkConnectomicsNetworkCreator.h.

MappingStrategy mitk::ConnectomicsNetworkCreator::m_MappingStrategy

protected

Definition at line 220 of file mitkConnectomicsNetworkCreator.h.

mitk::Image::Pointer mitk::ConnectomicsNetworkCreator::m_Segmentation

protected

Definition at line 195 of file mitkConnectomicsNetworkCreator.h.

ITKImageType::Pointer mitk::ConnectomicsNetworkCreator::m_SegmentationItk

protected

Definition at line 196 of file mitkConnectomicsNetworkCreator.h.

Referenced by ConnectomicsNetworkCreator().

bool mitk::ConnectomicsNetworkCreator::m_UseCoMCoordinates

protected

Definition at line 214 of file mitkConnectomicsNetworkCreator.h.

bool mitk::ConnectomicsNetworkCreator::m_ZeroLabelInvalid

protected

Definition at line 226 of file mitkConnectomicsNetworkCreator.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation