FreeSurfer Annotation to Individual Labels¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Extracts individual region labels from a surface annotation file into separate label files.
Modality: FreeSurfer annotation file (e.g., lh.aparc.annot).
Typical Use: Extracting individual ROIs from parcellation for targeted analysis.
Key Parameters¶
--subject (subject), --hemi (hemisphere), --annotation (annotation name), --outdir (output directory)
Key Points¶
Creates one .label file per region. Label files contain vertex indices and coordinates.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
subject |
string |
Yes | Subject name | --subject |
hemi |
enum |
Yes | Hemisphere (lh or rh) | --hemi |
annotation |
string |
No | Annotation name (default aparc) | --annotation |
surface |
string |
No | Surface name (default white) | --surface |
outdir |
string |
Yes | Output directory for label files | --outdir |
labelbase |
string |
No | Base name for output labels | --labelbase |
border |
string |
No | Output border file | --border |
borderdilate |
int |
No | Dilate border by N | --borderdilate |
ctab |
File |
No | Color table file | --ctab |
seg |
boolean |
No | Output segmentation instead of labels | --seg |
Accepted Input Extensions¶
- ctab:
.txt,.ctab
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
labels |
Directory |
$(inputs.outdir) |
border_file |
File |
$(inputs.border) |
log |
File |
mri_annotation2label.log |
Output Extensions¶
- border_file:
.border
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Structural MRI > FreeSurfer > Parcellation