How to select which scans get processed

By default RABIES processes every functional scan it can find in the input BIDS directory. There are two independent ways to narrow that down: change which files count as functional or anatomical scans, or list the individual scans to keep or drop.

Change which files RABIES recognises

RABIES identifies functional scans by the bold or cbv suffix and structural scans by the T1w or T2w suffix. Files matching neither are ignored.

Override this with --bids_filter, which takes a JSON file with the functional filter under func and the structural filter under anat. This JSON reproduces the defaults:

Listing 1 bids_filter.json

{
    "func": {
        "suffix": ["bold", "cbv"]
    },
    "anat": {
        "suffix": ["T1w", "T2w"]
    }
}

Pass it at the preprocessing stage:

rabies preprocess input_BIDS/ preprocess_outputs/ --bids_filter bids_filter.json

Add any BIDS entity to either filter to be more specific. To use only the RARE anatomical acquisition and only the resting-state functional runs:

Listing 2 bids_filter.json

{
    "func": {
        "suffix": ["bold"],
        "task": ["rest"]
    },
    "anat": {
        "suffix": ["T2w"],
        "acquisition": ["RARE"]
    }
}

Tip

Reach for --bids_filter when your dataset contains scans that are not meant for this pipeline at all — a second anatomical modality, a task run alongside the resting-state runs. Reach for --inclusion_ids below when you want a subset of otherwise-eligible scans.

Include or exclude individual scans

--inclusion_ids and --exclusion_ids take the full paths of BOLD files. They are execution options, so they go before the processing stage name, and they can be given at any stage.

Process only two scans:

rabies --inclusion_ids input_BIDS/sub-001/ses-1/func/sub-001_ses-1_task-rest_bold.nii.gz \
                       input_BIDS/sub-002/ses-1/func/sub-002_ses-1_task-rest_bold.nii.gz \
  -p MultiProc preprocess input_BIDS/ preprocess_outputs/

Process everything except one scan:

rabies --exclusion_ids input_BIDS/sub-003/ses-1/func/sub-003_ses-1_task-rest_bold.nii.gz \
  -p MultiProc preprocess input_BIDS/ preprocess_outputs/

For longer lists, put one file path per row in a text file and pass the file:

rabies --inclusion_ids scans_to_process.txt -p MultiProc preprocess input_BIDS/ preprocess_outputs/

Warning

Do not put --inclusion_ids or --exclusion_ids immediately before the processing stage name. The stage name gets swallowed into the list and argument parsing fails. Put another option, such as -p or --verbose, between them — as in every example above.

--inclusion_ids and --exclusion_ids cannot be used together.