FreeSurfer Complete Cortical Reconstruction Pipeline¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Fully automated pipeline for cortical surface reconstruction and parcellation, including skull stripping, segmentation, surface tessellation, topology correction, inflation, registration, and parcellation.
Modality: T1-weighted 3D NIfTI or DICOM. Optional T2w or FLAIR for pial surface refinement.
Typical Use: Complete cortical reconstruction for surface-based morphometry, parcellation-based analysis, and as prerequisite for fMRI surface analysis.
Key Parameters¶
-s (subject ID), -i (input T1w), -T2 (T2w image for pial), -FLAIR (FLAIR for pial), -all (run full pipeline), -autorecon1/-autorecon2/-autorecon3 (run specific stages)
Key Points¶
Runtime 6-24 hours per subject. Creates cortical surfaces (white, pial), parcellations (Desikan-Killiany, Destrieux), subcortical segmentation (aseg), and morphometric measures. Use -T2pial or -FLAIRpial for improved pial surface placement.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer subjects directory | |
fs_license |
File |
Yes | FreeSurfer license file | |
subject_id |
string |
Yes | Subject identifier | -s |
input_t1 |
File |
Yes | Input T1-weighted image | -i |
run_all |
boolean |
No | Run full pipeline (autorecon1 + autorecon2 + autorecon3) | -all |
autorecon1 |
boolean |
No | Run autorecon1 (motion correction, skull stripping, Talairach) | -autorecon1 |
autorecon2 |
boolean |
No | Run autorecon2 (segmentation, surface generation, topology fix) | -autorecon2 |
autorecon3 |
boolean |
No | Run autorecon3 (parcellation, statistics, cortical thickness) | -autorecon3 |
t2_image |
File |
No | T2-weighted image for pial surface refinement | -T2 |
flair_image |
File |
No | FLAIR image for pial surface refinement | -FLAIR |
t2pial |
boolean |
No | Use T2 image for pial surface placement | -T2pial |
flair_pial |
boolean |
No | Use FLAIR image for pial surface placement | -FLAIRpial |
openmp |
int |
No | Number of OpenMP threads | -openmp |
parallel |
boolean |
No | Enable parallel processing where possible | -parallel |
Accepted Input Extensions¶
- input_t1:
.mgz,.mgh,.nii,.nii.gz - t2_image:
.mgz,.mgh,.nii,.nii.gz - flair_image:
.mgz,.mgh,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
subjects_output_dir |
Directory |
$(inputs.subject_id) |
log |
File |
recon-all.log |
err_log |
File |
recon-all.err.log |
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 > Surface Reconstruction
- Pipelines > FreeSurfer > Surface Reconstruction