Command-line reference
dlsurfer <command> [options]
Commands
| Command |
Purpose |
doctor |
Dependency / READY check |
smoke |
Doctor + dry-run core-lesion |
gates |
List production gates |
run |
Build/execute a profile plan |
engines |
Engine registry (--alternatives) |
atlases |
Atlas notes |
compare |
FS vs FastSurfer matrix |
gaps-remaining |
Gaps without DL alts |
cite |
Citation boilerplate for a profile |
handoff |
Print-only consumer notes |
bids-app |
BIDS App–style stub (bids_dir output_dir level) — status |
run — important flags
| Flag |
Meaning |
--profile |
Profile id (required) |
--t1 |
T1 NIfTI (required) |
--sd / --sid |
SUBJECTS_DIR / subject |
--fs-license |
FreeSurfer license |
--lesion-mask |
For lesion profiles |
--device |
auto / cpu / cuda |
--threads |
Thread count |
--batch-size |
FastSurfer --batch |
--viewagg-device |
FastSurfer view aggregation device |
--atlas |
Labeling scheme (default DKT) |
--no-cc / --no-cereb / --no-hypothal |
Module offs |
--vox-size |
FastSurfer voxel size |
--hpc |
srun / brun |
--execute |
Actually run |
--allow-experimental |
Override open gates |