FreeSurfer Subcortical Stats to Group Table¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Collects subcortical segmentation statistics across multiple subjects into a single table.
Modality: Multiple FreeSurfer subject directories with completed recon-all.
Typical Use: Group analysis of subcortical volumes.
Key Parameters¶
--subjects (subject list), --meas (measure: volume, mean), --tablefile (output table), --stats (stats file name)
Key Points¶
Creates one row per subject with subcortical volumes. Default uses aseg.stats.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
subjects |
string[] |
Yes | List of subject names | --subjects |
tablefile |
string |
Yes | Output table filename | --tablefile |
meas |
enum |
No | Measurement to extract (default volume) | --meas |
statsfile |
string |
No | Stats file name (default aseg.stats) | --statsfile |
delimiter |
enum |
No | Delimiter for output table | --delimiter |
subjectsfile |
File |
No | File containing subject list | --subjectsfile |
segno |
int[] |
No | Only output specific segmentation numbers | --segno |
segids |
File |
No | File with segmentation IDs to extract | --segids |
skip |
boolean |
No | Skip subjects with missing data | --skip |
all_segs |
boolean |
No | Include all segmentations | --all-segs |
common_segs |
boolean |
No | Only output segs common to all subjects | --common-segs |
transpose |
boolean |
No | Transpose output table | --transpose |
etiv |
boolean |
No | Include estimated total intracranial volume | --etiv |
etiv_only |
boolean |
No | Only output eTIV | --etiv-only |
eulerNo |
boolean |
No | Include Euler number | --euler |
Accepted Input Extensions¶
- subjectsfile:
.txt - segids:
.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
table |
File |
$(inputs.tablefile) |
log |
File |
asegstats2table.log |
Output Extensions¶
- table:
.txt,.csv,.dat
Enum Options¶
meas: volume, mean
delimiter: tab, comma, space, semicolon
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