Free surfer annotation. More...

#include <annotation.h>

Public Types
typedef QSharedPointer< Annotation >	SPtr

typedef QSharedPointer< const Annotation >	ConstSPtr

Public Member Functions
	Annotation ()

	Annotation (const QString &p_sFileName)

	Annotation (const QString &subject_id, qint32 hemi, const QString &surf, const QString &subjects_dir)

	Annotation (const QString &path, qint32 hemi, const QString &surf)

	~Annotation ()

void	clear ()

bool	isEmpty () const

qint32	hemi () const

Eigen::VectorXi &	getVertices ()

const Eigen::VectorXi	getVertices () const

Eigen::VectorXi &	getLabelIds ()

const Eigen::VectorXi	getLabelIds () const

Colortable &	getColortable ()

const Colortable	getColortable () const

bool	toLabels (const Surface &p_surf, QList< Label > &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, Annotation &p_Annotation)

static bool	read (const QString &path, qint32 hemi, const QString &atlas, Annotation &p_Annotation)

static bool	read (const QString &p_sFileName, Annotation &p_Annotation)

Detailed Description

Free surfer annotation.

Free surfer annotation contains vertix label relations and a color/name lookup table

Definition at line 80 of file annotation.h.

Member Typedef Documentation

◆ ConstSPtr

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

Const shared pointer type for Annotation.

Definition at line 85 of file annotation.h.

◆ SPtr

typedef QSharedPointer<Annotation> FSLIB::Annotation::SPtr

Shared pointer type for Annotation.

Definition at line 84 of file annotation.h.

Constructor & Destructor Documentation

◆ Annotation() [1/4]

Annotation::Annotation ( )

Default constructor

Definition at line 67 of file annotation.cpp.

◆ Annotation() [2/4]

Annotation::Annotation ( const QString & p_sFileName )

explicit

Construts the annotation by reading it of the given file.

Parameters

[in] p_sFileName Annotation file.

Definition at line 74 of file annotation.cpp.

◆ Annotation() [3/4]

Annotation::Annotation	(	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]	atlas	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[in]	subjects_dir	Subjects directory.

Definition at line 84 of file annotation.cpp.

◆ Annotation() [4/4]

Annotation::Annotation	(	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]	atlas	Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).

Returns: true if read sucessful, false otherwise.

Definition at line 92 of file annotation.cpp.

◆ ~Annotation()

Annotation::~Annotation ( )

Destroys the annotation.

Definition at line 100 of file annotation.cpp.

Member Function Documentation

◆ clear()

void Annotation::clear ( )

Initializes the Annotation.

Definition at line 106 of file annotation.cpp.

◆ fileName()

QString FSLIB::Annotation::fileName ( ) const

inline

annotation file name

Returns: the surf file name.

Definition at line 350 of file annotation.h.

◆ filePath()

QString FSLIB::Annotation::filePath ( ) const

inline

annotation file path

Returns: the surf file path.

Definition at line 343 of file annotation.h.

◆ getColortable() [1/2]

const Colortable FSLIB::Annotation::getColortable ( )

inline

Returns the coloratable containing the label based nomenclature

Returns: colortable.

Definition at line 329 of file annotation.h.

◆ getColortable() [2/2]

const Colortable FSLIB::Annotation::getColortable ( ) const

inline

Returns the coloratable containing the label based nomenclature

Returns: colortable.

◆ getLabelIds() [1/2]

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

inline

Returns the vertix labels

Returns: vertix labels.

Definition at line 315 of file annotation.h.

◆ getLabelIds() [2/2]

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

inline

Returns the vertix labels

Returns: vertix labels.

◆ getVertices() [1/2]

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

inline

Returns the vertix indeces

Returns: vertix indeces.

Definition at line 301 of file annotation.h.

◆ getVertices() [2/2]

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

inline

Returns the vertix indeces

Returns: vertix indeces.

◆ hemi()

qint32 FSLIB::Annotation::hemi ( ) const

inline

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

Returns: hemisphere id.

Definition at line 287 of file annotation.h.

◆ isEmpty()

bool FSLIB::Annotation::isEmpty ( ) const

inline

Returns whether Annotation is empty.

Returns: true if is empty, false otherwise.

Definition at line 294 of file annotation.h.

◆ read() [1/3]

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

static

Reads an annotation of a file

Parameters

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

Returns: true if successful, false otherwise.

Definition at line 140 of file annotation.cpp.

◆ read() [2/3]

bool Annotation::read	(	const QString &	path,
		qint32	hemi,
		const QString &	atlas,
		Annotation &	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 128 of file annotation.cpp.

◆ read() [3/3]

bool Annotation::read	(	const QString &	subject_id,
		qint32	hemi,
		const QString &	atlas,
		const QString &	subjects_dir,
		Annotation &	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 116 of file annotation.cpp.

◆ toLabels()

bool Annotation::toLabels	(	const Surface &	p_surf,
		QList< Label > &	p_qListLabels,
		QList< Eigen::RowVector4i > &	p_qListLabelRGBAs,
		const QStringList &	lLabelPicks = `QStringList()`
	)		const

python labels_from_parc

Converts annotation to a label list and colortable

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 288 of file annotation.cpp.

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

src/libraries/fs/annotation.h
src/libraries/fs/annotation.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ Annotation() [1/4]

◆ Annotation() [2/4]

◆ Annotation() [3/4]

◆ Annotation() [4/4]

◆ ~Annotation()

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()