mne_annot2labels
Overview
mne_annot2labels converts FreeSurfer annotation files (.annot) into individual label files. Each parcellation region in the annotation is written as a separate label file, suitable for use with MNE source space analysis and ROI-based workflows.
This is a C++ port of the original MNE-C tool by Matti Hämäläinen.
Usage
mne_annot2labels [options]
Options
| Option | Description |
|---|---|
--subject <name> | Subject name |
--subjects_dir <dir> | Subjects directory (default: $SUBJECTS_DIR) |
--annot <name> | Annotation name (e.g., aparc, aparc.a2009s) |
--hemi <hemi> | Hemisphere: lh or rh (default: both) |
--outdir <dir> | Output directory for label files (default: subject's label/) |
--surf <name> | Surface to use for coordinates (default: white) |
--help | Print help |
--version | Print version |
Description
FreeSurfer stores cortical parcellation information in binary annotation files. This tool reads those files and produces one label file per parcellation region. The label files contain vertex indices and their coordinates, which can be used for source-space ROI analysis.
Workflow Context
This tool is typically used after FreeSurfer's recon-all has completed, when you need individual label files for source localization analysis. The resulting labels can be used with mne_compute_mne or mne_compute_raw_inverse to extract time courses from specific cortical regions.
Example
# Convert the aparc parcellation to label files for both hemispheres
mne_annot2labels --subject sam --annot aparc
# Convert only the left hemisphere of aparc.a2009s
mne_annot2labels --subject sam --annot aparc.a2009s --hemi lh --outdir ./labels