Skip to main content

FsAnnotation

Namespace: FSLIB  ·  Library: FreeSurfer Library

Python equivalent

mne.read_annot in MNE-Python.

#include <fs/fs_annotation.h>

class FSLIB::FsAnnotation

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](/docs/api/fs/fs-colortable) describing the colour and name of every region. Indexing is aligned with the matching [FsSurface](/docs/api/fs/fs-surface) for the same subject + hemisphere, so label[v] is the region of surface vertex v.

Public Methods​

FsAnnotation()​

Default constructor.

FsAnnotation(p_sFileName)​

Construts the annotation by reading it of the given file.

Parameters:

FsAnnotation(subject_id, hemi, surf, subjects_dir)​

Construts the annotation by reading it of the given file.

Parameters:

  • subject_id : const QString & Name of subject.

  • hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.

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

  • subjects_dir : const QString & Subjects directory.

FsAnnotation(path, hemi, surf)​

Construts the annotation by reading it of the given file.

Parameters:

  • path : const QString & path to surface directory.

  • hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.

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

Returns:

  • true if read sucessful, false otherwise.

~FsAnnotation()​

Destroys the annotation.

clear()​

Initializes the FsAnnotation.

isEmpty()​

Returns whether FsAnnotation is empty.

Returns:

  • bool — true if is empty, false otherwise.

hemi()​

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

Returns:

  • qint32 — hemisphere id.

getVertices()​

Returns the vertix indeces.

Returns:

  • Eigen::VectorXi & — vertix indeces.

getVertices()​

Returns the vertix indeces.

Returns:

  • const Eigen::VectorXi — vertix indeces.

getLabelIds()​

Returns the vertix labels.

Returns:

  • Eigen::VectorXi & — vertix labels.

getLabelIds()​

Returns the vertix labels.

Returns:

  • const Eigen::VectorXi — vertix labels.

getColortable()​

Returns the coloratable containing the label based nomenclature.

Returns:

getColortable()​

Returns the coloratable containing the label based nomenclature.

Returns:

toLabels(p_surf, p_qListLabels, p_qListLabelRGBAs, lLabelPicks)​

python labels_from_parc

Converts annotation to a label list and colortable

Parameters:

  • p_surf : const FsSurface & the surface to read the vertex positions from.

  • p_qListLabels : QList< FsLabel > & the converted labels are appended to a given list. Stored data are not affected.

  • p_qListLabelRGBAs : QList< Eigen::RowVector4i > & the converted label RGBAs are appended to a given list. Stored data are not affected.

  • lLabelPicks : const QStringList & the label names which should be picked.

Returns:

  • bool — true if successful, false otherwise.

filePath()​

annotation file path

Returns:

  • QString — the surf file path.

fileName()​

annotation file name

Returns:

  • QString — the surf file name.

Static Methods​

read(subject_id, hemi, atlas, subjects_dir, p_Annotation)​

Reads a FreeSurfer annotation file.

Parameters:

  • subject_id : const QString & Name of subject.

  • hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.

  • atlas : const QString & Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).

  • subjects_dir : const QString & Subjects directory.

  • p_Annotation : FsAnnotation & The read annotation.

Returns:

  • bool — true if read sucessful, false otherwise.

read(path, hemi, atlas, p_Annotation)​

Reads a FreeSurfer annotation file.

Parameters:

  • path : const QString & path to label directory.

  • hemi : qint32 Which hemisphere to load {0 -> lh, 1 -> rh}.

  • atlas : const QString & Name of the atlas to load (eg. aparc.a2009s, aparc, aparc.DKTatlas40, BA, BA.thresh, ...).

  • p_Annotation : FsAnnotation & The read annotation.

Returns:

  • bool — true if read sucessful, false otherwise.

read(p_sFileName, p_Annotation)​

Reads an annotation of a file.

Parameters:

Returns:

  • bool — true if successful, false otherwise.

Authors of this file​