Required
| Input |
Flag |
Notes |
| T1w NIfTI |
--t1 |
3D T1; FastSurfer will conform |
| SUBJECTS_DIR |
--sd |
Dedicated tree owned by DLSurfer |
| Subject ID |
--sid |
FreeSurfer-style, e.g. sub-01 |
| FS license |
--fs-license or FS_LICENSE |
Required for FS/FastSurfer tools |
Optional
| Input |
Flag |
When |
| Lesion mask |
--lesion-mask |
core-lesion / native lesion profiles |
| Device |
--device auto\|cpu\|cuda |
Default auto |
| Threads |
--threads |
FastSurfer / recon-surf |
| Atlas |
--atlas dkt\|dk\|… |
Default DKT labeling |
BIDS (stub only)
Preferred production API remains explicit paths (--t1, --sd, --sid).
A BIDS App–style stub exists but is short of the standard — see BIDS App status:
dlsurfer bids-app BIDS_DIR OUT_DIR participant --participant_label 01 --profile core