FreeSurfer Surface Anatomical Statistics¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Computes surface-based morphometric measures (thickness, area, volume, curvature) for each region in a parcellation.
Modality: FreeSurfer subject directory with completed recon-all.
Typical Use: Extracting regional cortical thickness, area, and volume measures.
Key Parameters¶
-a (annotation file), -f (output stats file), -b (output table format)
Key Points¶
Outputs per-region cortical thickness, surface area, gray matter volume, and curvature.
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 | |
hemi |
enum |
Yes | Hemisphere (lh or rh) | |
annotation |
File |
No | Annotation file for parcellation | -a |
tablefile |
string |
No | Output table filename | -f |
white |
string |
No | White surface name (default white) | |
pial |
string |
No | Pial surface name | -pial |
label |
File |
No | Limit stats to label region | -l |
cortex |
File |
No | Cortex label file | -cortex |
th3 |
boolean |
No | Use tetrahedra for volume (recommended) | -th3 |
thickness |
string |
No | Thickness file name | -t |
b |
boolean |
No | Report total brain volume | -b |
noglobal |
boolean |
No | Do not compute global stats | -noglobal |
log |
string |
No | Log file name | -log |
ctab |
File |
No | Color table file | -ctab |
mgz |
boolean |
No | Use mgz format | -mgz |
Accepted Input Extensions¶
- annotation:
.annot - label:
.label - cortex:
.label - ctab:
.txt,.ctab
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats_table |
File |
$(inputs.tablefile) |
stats |
File |
*.stats |
log_file |
File |
mris_anatomical_stats.log |
Output Extensions¶
- stats_table:
.txt,.csv,.dat - stats:
.stats
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 > Morphometry