FreeSurfer Surface Data Preprocessing for Group Analysis¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Concatenates surface data across subjects onto a common template surface for group-level analysis.
Modality: Per-subject surface overlays (thickness, area, etc.) from FreeSurfer processing.
Typical Use: Preparing surface data for group statistical analysis.
Key Parameters¶
--s (subject list), --meas (measure: thickness, area, volume), --target (target subject/template), --hemi (hemisphere), --o (output)
Key Points¶
Resamples all subjects to common surface (fsaverage). Can smooth on surface with --fwhm.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
output |
string |
Yes | Output concatenated surface file | --out |
target |
string |
Yes | Target subject (e.g., fsaverage) | --target |
hemi |
enum |
Yes | Hemisphere (lh or rh) | --hemi |
subjects |
string[] |
No | List of subject names | |
fsgd |
File |
No | FreeSurfer Group Descriptor file | --fsgd |
f |
File |
No | Text file with list of subjects | --f |
meas |
string |
No | Surface measure name (e.g., thickness, area) | --meas |
area |
string |
No | Extract vertex area from surface | --area |
iv |
string[] |
No | Volume and registration pairs | --iv |
projfrac |
double |
No | Projection fraction for vol2surf (default 0.5) | --projfrac |
fwhm |
double |
No | Smooth on target surface by FWHM in mm | --fwhm |
fwhm_src |
double |
No | Smooth on source surface by FWHM in mm | --fwhm-src |
niters |
int |
No | Smooth by N nearest neighbor iterations | --niters |
niters_src |
int |
No | Smooth source by N iterations | --niters-src |
cache_in |
string |
No | Use qcache data (e.g., thickness.fwhm10.fsaverage) | --cache-in |
paired_diff |
boolean |
No | Compute paired differences | --paired-diff |
paired_diff_norm1 |
boolean |
No | Paired diff normalized by average | --paired-diff-norm1 |
paired_diff_norm2 |
boolean |
No | Paired diff normalized by first timepoint | --paired-diff-norm2 |
mask |
File |
No | Mask label file | --mask |
cortex |
boolean |
No | Use cortex label as mask | --cortex |
Accepted Input Extensions¶
- fsgd:
.fsgd - f:
.txt - mask:
.label
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
out_file |
File |
$(inputs.output)* |
log |
File |
mris_preproc.log |
Output Extensions¶
- out_file:
.mgh,.mgz,.nii,.nii.gz
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¶
- Functional MRI > FreeSurfer > Functional Analysis