FSLIB::FsAnnotation Class Reference

Free surfer annotation. 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

Free surfer annotation.

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

Definition at line 80 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 85 of file fs_annotation.h.

SPtr

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

Shared pointer type for FsAnnotation.

Definition at line 84 of file fs_annotation.h.

Constructor & Destructor Documentation

FsAnnotation() [1/4]

FsAnnotation::FsAnnotation

(

)

Default constructor

Definition at line 67 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 74 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]	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 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]	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 fs_annotation.cpp.

~FsAnnotation()

FsAnnotation::~FsAnnotation

(

)

Destroys the annotation.

Definition at line 100 of file fs_annotation.cpp.

Member Function Documentation

clear()

void FsAnnotation::clear

(

)

Initializes the FsAnnotation.

Definition at line 106 of file fs_annotation.cpp.

fileName()

QString FSLIB::FsAnnotation::fileName ( ) const

inline

annotation file name

Returns

the surf file name.

Definition at line 350 of file fs_annotation.h.

filePath()

QString FSLIB::FsAnnotation::filePath ( ) const

inline

annotation file path

Returns

the surf file path.

Definition at line 343 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 329 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 336 of file fs_annotation.h.

getLabelIds() [1/2]

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

inline

Returns the vertix labels

Returns

vertix labels.

Definition at line 315 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 322 of file fs_annotation.h.

getVertices() [1/2]

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

inline

Returns the vertix indeces

Returns

vertix indeces.

Definition at line 301 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 308 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 287 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 294 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 140 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 128 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 116 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

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 fs_annotation.cpp.

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

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