Analysis CLI Reference¶
Full reference for DCE_all.sh.
Usage¶
Flags¶
| Flag | Argument | Required | Description |
|---|---|---|---|
-d |
path |
Yes | Path to BIDS raw data directory. |
-C |
name |
No | Enable comparison mode. If a preprocessed run named <name> does not exist, copies essential files from the standard run. |
-f |
— | No | Enable FreeSurfer white matter parcellation for subregion Ktrans analysis. See FreeSurfer Parcellation. |
-s |
— | No | Skip cases where the Ktrans output file already exists. |
-S |
— | No | Enable iNESMA smoothing of the DCE input before Ktrans fitting. Requires a CUDA GPU. |
-T |
dir_path |
No | Target specific subject(s)/session(s). Default: sub-*/ses-*/. Accepts glob patterns or explicit paths. |