MNE-CPP  0.1.9
A Framework for Electrophysiology
Public Types | Public Member Functions | Static Public Member Functions | List of all members
FSLIB::Annotation Class Reference

Free surfer annotation. More...

#include <annotation.h>

Public Types

typedef QSharedPointer< AnnotationSPtr
 
typedef QSharedPointer< const AnnotationConstSPtr
 

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
 
ColortablegetColortable ()
 
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_sFileNameAnnotation file.

Definition at line 76 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_idName of subject.
[in]hemiWhich hemisphere to load {0 -> lh, 1 -> rh}.
[in]atlasName of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[in]subjects_dirSubjects directory.

Definition at line 86 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]pathpath to surface directory.
[in]hemiWhich hemisphere to load {0 -> lh, 1 -> rh}.
[in]atlasName of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
Returns
true if read sucessful, false otherwise.

Definition at line 96 of file annotation.cpp.

◆ ~Annotation()

Annotation::~Annotation ( )

Destroys the annotation.

Definition at line 106 of file annotation.cpp.

Member Function Documentation

◆ clear()

void Annotation::clear ( )

Initializes the Annotation.

Definition at line 112 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]

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.

Definition at line 336 of file annotation.h.

◆ getLabelIds() [1/2]

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.

Definition at line 322 of file annotation.h.

◆ getVertices() [1/2]

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.

Definition at line 308 of file annotation.h.

◆ 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 &  subject_id,
qint32  hemi,
const QString &  atlas,
const QString &  subjects_dir,
Annotation p_Annotation 
)
static

Reads a FreeSurfer annotation file

Parameters
[in]subject_idName of subject.
[in]hemiWhich hemisphere to load {0 -> lh, 1 -> rh}.
[in]atlasName of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[in]subjects_dirSubjects directory.
[out]p_AnnotationThe read annotation.
Returns
true if read sucessful, false otherwise.

Definition at line 122 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]pathpath to label directory.
[in]hemiWhich hemisphere to load {0 -> lh, 1 -> rh}.
[in]atlasName of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).
[out]p_AnnotationThe read annotation.
Returns
true if read sucessful, false otherwise.

Definition at line 134 of file annotation.cpp.

◆ read() [3/3]

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

Reads an annotation of a file

Parameters
[in]p_sFileNameAnnotation file.
[out]p_Annotationthe read annotation.
Returns
true if successful, false otherwise.

Definition at line 146 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_surfthe surface to read the vertex positions from.
[out]p_qListLabelsthe converted labels are appended to a given list. Stored data are not affected.
[out]p_qListLabelRGBAsthe converted label RGBAs are appended to a given list. Stored data are not affected.
[out]lLabelPicksthe label names which should be picked.
Returns
true if successful, false otherwise.

Definition at line 294 of file annotation.cpp.


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