Single-hemisphere FreeSurfer parcellation: vertex → region label plus embedded colortable. More...

#include <fs_annotation.h>

Public Types
typedef QSharedPointer< FsAnnotation >	SPtr
typedef QSharedPointer< const FsAnnotation >	ConstSPtr

Public Member Functions
	FsAnnotation ()
	FsAnnotation (const QString &p_sFileName)
	FsAnnotation (const QString &subject_id, qint32 hemi, const QString &surf, const QString &subjects_dir)
	FsAnnotation (const QString &path, qint32 hemi, const QString &surf)
	~FsAnnotation ()
void	clear ()
bool	isEmpty () const
qint32	hemi () const
Eigen::VectorXi &	getVertices ()
const Eigen::VectorXi	getVertices () const
Eigen::VectorXi &	getLabelIds ()
const Eigen::VectorXi	getLabelIds () const
FsColortable &	getColortable ()
const FsColortable	getColortable () const
bool	toLabels (const FsSurface &p_surf, QList< FsLabel > &p_qListLabels, QList< Eigen::RowVector4i > &p_qListLabelRGBAs, const QStringList &lLabelPicks=QStringList()) const
QString	filePath () const
QString	fileName () const

Static Public Member Functions
static bool	read (const QString &subject_id, qint32 hemi, const QString &atlas, const QString &subjects_dir, FsAnnotation &p_Annotation)
static bool	read (const QString &path, qint32 hemi, const QString &atlas, FsAnnotation &p_Annotation)
static bool	read (const QString &p_sFileName, FsAnnotation &p_Annotation)

Detailed Description

Single-hemisphere FreeSurfer parcellation: vertex → region label plus embedded colortable.

Holds the parsed contents of one .annot file: the dense per-vertex label assignment, the explicit vertex index list it was authored against, and the FsColortable describing the colour and name of every region. Indexing is aligned with the matching FsSurface for the same subject + hemisphere, so label[v] is the region of surface vertex v.

Definition at line 84 of file fs_annotation.h.

Member Typedef Documentation

◆ ConstSPtr

typedef QSharedPointer<const FsAnnotation> FSLIB::FsAnnotation::ConstSPtr

Const shared pointer type for FsAnnotation.

Definition at line 88 of file fs_annotation.h.

◆ SPtr

typedef QSharedPointer<FsAnnotation> FSLIB::FsAnnotation::SPtr

Shared pointer type for FsAnnotation.

Definition at line 87 of file fs_annotation.h.

Constructor & Destructor Documentation

◆ FsAnnotation() [1/4]

FsAnnotation::FsAnnotation ( )

Default constructor

Definition at line 46 of file fs_annotation.cpp.

◆ FsAnnotation() [2/4]

FsAnnotation::FsAnnotation ( const QString & p_sFileName )

explicit

Construts the annotation by reading it of the given file.

Parameters

[in] p_sFileName FsAnnotation file.

Definition at line 53 of file fs_annotation.cpp.

◆ FsAnnotation() [3/4]

FsAnnotation::FsAnnotation	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	surf,
		const QString &	subjects_dir )

explicit

Construts the annotation by reading it of the given file.

Parameters

[in]	subject_id	Name of subject.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[in]	subjects_dir	Subjects directory.

Definition at line 63 of file fs_annotation.cpp.

◆ FsAnnotation() [4/4]

FsAnnotation::FsAnnotation	(	const QString &	path,
		qint32	hemi,
		const QString &	surf )

explicit

Construts the annotation by reading it of the given file.

Parameters

[in]	path	path to surface directory.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	surf	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).

Definition at line 71 of file fs_annotation.cpp.

◆ ~FsAnnotation()

FsAnnotation::~FsAnnotation ( )

Destroys the annotation.

Definition at line 79 of file fs_annotation.cpp.

Member Function Documentation

◆ clear()

void FsAnnotation::clear ( )

Initializes the FsAnnotation.

Definition at line 85 of file fs_annotation.cpp.

◆ fileName()

QString FSLIB::FsAnnotation::fileName ( ) const

inline

annotation file name

Returns: the surf file name.

Definition at line 352 of file fs_annotation.h.

◆ filePath()

QString FSLIB::FsAnnotation::filePath ( ) const

inline

annotation file path

Returns: the surf file path.

Definition at line 345 of file fs_annotation.h.

◆ getColortable() [1/2]

FsColortable & FSLIB::FsAnnotation::getColortable ( )

inline

Returns the coloratable containing the label based nomenclature

Returns: colortable.

Definition at line 331 of file fs_annotation.h.

◆ getColortable() [2/2]

const FsColortable FSLIB::FsAnnotation::getColortable ( ) const

inline

Returns the coloratable containing the label based nomenclature

Returns: colortable.

Definition at line 338 of file fs_annotation.h.

◆ getLabelIds() [1/2]

Eigen::VectorXi & FSLIB::FsAnnotation::getLabelIds ( )

inline

Returns the vertix labels

Returns: vertix labels.

Definition at line 317 of file fs_annotation.h.

◆ getLabelIds() [2/2]

const Eigen::VectorXi FSLIB::FsAnnotation::getLabelIds ( ) const

inline

Returns the vertix labels

Returns: vertix labels.

Definition at line 324 of file fs_annotation.h.

◆ getVertices() [1/2]

Eigen::VectorXi & FSLIB::FsAnnotation::getVertices ( )

inline

Returns the vertix indeces

Returns: vertix indeces.

Definition at line 303 of file fs_annotation.h.

◆ getVertices() [2/2]

const Eigen::VectorXi FSLIB::FsAnnotation::getVertices ( ) const

inline

Returns the vertix indeces

Returns: vertix indeces.

Definition at line 310 of file fs_annotation.h.

◆ hemi()

qint32 FSLIB::FsAnnotation::hemi ( ) const

inline

Returns the hemisphere id (0 = lh; 1 = rh)

Returns: hemisphere id.

Definition at line 289 of file fs_annotation.h.

◆ isEmpty()

bool FSLIB::FsAnnotation::isEmpty ( ) const

inline

Returns whether FsAnnotation is empty.

Returns: true if is empty, false otherwise.

Definition at line 296 of file fs_annotation.h.

◆ read() [1/3]

bool FsAnnotation::read	(	const QString &	p_sFileName,
		FsAnnotation &	p_Annotation )

static

Reads an annotation of a file

Parameters

[in]	p_sFileName	FsAnnotation file.
[out]	p_Annotation	the read annotation.

Returns: true if successful, false otherwise.

Definition at line 119 of file fs_annotation.cpp.

◆ read() [2/3]

bool FsAnnotation::read	(	const QString &	path,
		qint32	hemi,
		const QString &	atlas,
		FsAnnotation &	p_Annotation )

static

Reads a FreeSurfer annotation file

Parameters

[in]	path	path to label directory.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	atlas	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[out]	p_Annotation	The read annotation.

Returns: true if read sucessful, false otherwise.

Definition at line 107 of file fs_annotation.cpp.

◆ read() [3/3]

bool FsAnnotation::read	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	atlas,
		const QString &	subjects_dir,
		FsAnnotation &	p_Annotation )

static

Reads a FreeSurfer annotation file

Parameters

[in]	subject_id	Name of subject.
[in]	hemi	Which hemisphere to load {0 -> lh, 1 -> rh}.
[in]	atlas	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[in]	subjects_dir	Subjects directory.
[out]	p_Annotation	The read annotation.

Returns: true if read sucessful, false otherwise.

Definition at line 95 of file fs_annotation.cpp.

◆ toLabels()

bool FsAnnotation::toLabels	(	const FsSurface &	p_surf,
		QList< FsLabel > &	p_qListLabels,
		QList< Eigen::RowVector4i > &	p_qListLabelRGBAs,
		const QStringList &	lLabelPicks = QStringList() ) const

python labels_from_parc

Converts annotation to a label list and colortable, like mne.read_labels_from_annot: one label per region with vertices, named "<region>-lh|rh", values 1, sorted by name.

Parameters

[in]	p_surf	the surface to read the vertex positions from.
[out]	p_qListLabels	the converted labels are appended to a given list. Stored data are not affected.
[out]	p_qListLabelRGBAs	the converted label RGBAs are appended to a given list. Stored data are not affected.
[out]	lLabelPicks	the label names which should be picked.

Returns: true if successful, false otherwise.

Definition at line 263 of file fs_annotation.cpp.

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

src/libraries/fs/fs_annotation.h
src/libraries/fs/fs_annotation.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ FsAnnotation() [1/4]

◆ FsAnnotation() [2/4]

◆ FsAnnotation() [3/4]

◆ FsAnnotation() [4/4]

◆ ~FsAnnotation()

Member Function Documentation

◆ clear()

◆ fileName()

◆ filePath()

◆ getColortable() [1/2]

◆ getColortable() [2/2]

◆ getLabelIds() [1/2]

◆ getLabelIds() [2/2]

◆ getVertices() [1/2]

◆ getVertices() [2/2]

◆ hemi()

◆ isEmpty()

◆ read() [1/3]

◆ read() [2/3]

◆ read() [3/3]

◆ toLabels()