IEEGLIB::IeegImplantation Class Reference

Contacts of an sEEG / ECoG implantation and the leads they belong to. More...

#include <ieeg_implantation.h>

Public Member Functions
	IeegImplantation ()=default
	IeegImplantation (const QVector< IeegContact > &contacts, const QString &coordinateSystem=QString())
const QVector< IeegContact > &	contacts () const
const QVector< IeegLead > &	leads () const
QString	coordinateSystem () const
bool	isEmpty () const
bool	setLeadType (const QString &lead, IeegLeadType type, int rows=0, int cols=0)
int	indexOf (const QString &name) const
Eigen::MatrixX3f	positions () const
bool	isScannerRas () const
IeegImplantation	transformed (const Eigen::Matrix4f &trans, const QString &frame) const

Static Public Member Functions
static IeegImplantation	readBids (const QString &electrodesTsv, QString *error=nullptr)

Static Public Attributes
static constexpr float	kMaxDepthSpacing = 0.006f

Detailed Description

Contacts of an sEEG / ECoG implantation and the leads they belong to.

Definition at line 92 of file ieeg_implantation.h.

Constructor & Destructor Documentation

IeegImplantation() [1/2]

IEEGLIB::IeegImplantation::IeegImplantation ( )

default

IeegImplantation() [2/2]

IeegImplantation::IeegImplantation ( const QVector< IeegContact > & contacts, const QString & coordinateSystem = QString() )

explicit

Group contacts into leads.

A contact without a lead name belongs to the lead named like the contact without its trailing number (LA1, LA10 -> LA; A'1 stays apart from A1, the prime marking the other hemisphere). Within a lead, contacts are ordered by that number. A lead whose closest neighbouring contacts are less than kMaxDepthSpacing apart is a depth lead, others are strips.

Parameters

[in]	contacts	Contacts, positions in metres.
[in]	coordinateSystem	Name of the frame of the positions, e.g. "ACPC".

Definition at line 66 of file ieeg_implantation.cpp.

Member Function Documentation

contacts()

const QVector< IeegContact > & IEEGLIB::IeegImplantation::contacts ( ) const

inline

Returns

All contacts.

Definition at line 132 of file ieeg_implantation.h.

coordinateSystem()

QString IEEGLIB::IeegImplantation::coordinateSystem ( ) const

inline

Returns

Name of the frame of the positions, e.g. "ACPC"; empty when unknown.

Definition at line 144 of file ieeg_implantation.h.

indexOf()

int IeegImplantation::indexOf

(

const QString &

name

)

const

Parameters

[in]

name

Contact name.

Returns

Index of the contact, or -1.

Definition at line 204 of file ieeg_implantation.cpp.

isEmpty()

bool IEEGLIB::IeegImplantation::isEmpty ( ) const

inline

Returns

True without contacts.

Definition at line 150 of file ieeg_implantation.h.

isScannerRas()

bool IeegImplantation::isScannerRas

(

)

const

Returns

True when the positions are scanner RAS of the subject's T1, which MNE-BIDS reads the BIDS iEEG systems "ACPC" and "ScanRAS" as. Such positions must be moved into the surface (tkr) RAS of the FreeSurfer surfaces before they are drawn on them.

Definition at line 215 of file ieeg_implantation.cpp.

leads()

const QVector< IeegLead > & IEEGLIB::IeegImplantation::leads ( ) const

inline

Returns

All leads, in order of their first contact.

Definition at line 138 of file ieeg_implantation.h.

positions()

Eigen::MatrixX3f IeegImplantation::positions

(

)

const

Returns

Contact positions, one row per contact, in metres.

Definition at line 233 of file ieeg_implantation.cpp.

readBids()

IeegImplantation IeegImplantation::readBids ( const QString & electrodesTsv, QString * error = nullptr )

static

Read a BIDS iEEG *_electrodes.tsv.

Units and the coordinate system come from the *_coordsystem.json in the same folder that shares the longest name prefix; without one the file is refused, since the units are then unknown. Contacts without coordinates are skipped. The group column assigns leads and the dimension column ("[4x8]") the grid shape; a type naming depth, strip or grid sets the lead type. Otherwise names and spacing decide, as in the constructor.

Parameters

[in]	electrodesTsv	Path to the *_electrodes.tsv file.
[out]	error	Optional: why the file was refused.

Returns

The implantation; empty when the file was refused or has no placed contacts.

Definition at line 102 of file ieeg_implantation.cpp.

setLeadType()

bool IeegImplantation::setLeadType	(	const QString &	lead,
		IeegLeadType	type,
		int	rows = 0,
		int	cols = 0 )

Set a lead's type when it is declared rather than inferred.

Parameters

[in]	lead	Lead name.
[in]	type	Lead type.
[in]	rows	Grid rows, or 0 when unknown.
[in]	cols	Grid columns, or 0 when unknown.

Returns

False when there is no such lead. A shape that does not match the contact count is dropped.

Definition at line 188 of file ieeg_implantation.cpp.

transformed()

IeegImplantation IeegImplantation::transformed	(	const Eigen::Matrix4f &	trans,
		const QString &	frame ) const

Parameters

[in]	trans	Affine, in metres, from the current frame to the new one.
[in]	frame	Name of the new frame.

Returns

A copy with every position transformed; leads are unchanged.

Definition at line 222 of file ieeg_implantation.cpp.

Member Data Documentation

kMaxDepthSpacing

float IEEGLIB::IeegImplantation::kMaxDepthSpacing = 0.006f

staticconstexpr

Leads whose closest neighbouring contacts are nearer than this are depth leads.

Definition at line 96 of file ieeg_implantation.h.

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

• src/libraries/ieeg/ieeg_implantation.h
• src/libraries/ieeg/ieeg_implantation.cpp