Preprocessing CLI Reference¶

Full reference for preprocess_all.sh.

Usage¶

./preprocess_all.sh -d <rawdata_path> [options]

Flag	Argument	Required	Description
`-d`	`rawdata_path`	Yes	Path to BIDS raw data folder.
`-a`	`suffix`	No	AIF mask file suffix (default: `desc-AIF_mask`). `.nii.gz` is appended automatically.
`-A`	`mode`	No	Enable AutoAIF. Mode: `A` = fully automatic, `M` = manual if available else auto, `T` = manual + training data generation. Requires the AutoAIF repo.
`-b`	—	No	Enable first round of bias field correction on VFA and DCE images.
`-B`	—	No	Enable second round of bias field correction (applied after z-normalization). Only relevant when `-Z` is also set.
`-c`	—	No	Clean the case's derivatives folder before processing. Ensures a fresh run; disables skip behavior.
`-C`	`name`	No	Enable comparison mode. Writes outputs to `derivatives/sub-##/ses-##/<name>/`.
`-m`	—	No	Enable head motion correction using FSL `mcflirt`.
`-s`	—	No	Skip preprocessing if the final DCE output file already exists.
`-t`	—	No	Run only up to T1 map generation (skip DCE processing). Useful for T1-only protocols.
`-T`	`dir_path`	No	Target specific subject(s)/session(s). Default: `sub-/ses-/`. Accepts glob patterns or explicit paths.
`-w`	`path`	No	Path to the AutoAIF neural network weights file.
`-Z`	—	No	Enable z-axis slice normalization on VFA and DCE images.

./preprocess_all.sh -d /data/rawdata -b

./preprocess_all.sh -d /data/rawdata -b -B -Z -m -c

./preprocess_all.sh -d /data/rawdata -b -Z -A A -w /opt/AutoAIF/weights.h5

./preprocess_all.sh -d /data/rawdata -b -Z -T sub-01/ses-01 -C withZ

./preprocess_all.sh -d /data/rawdata -b -t