BIDS Runtime¶

Workflows built with BIDS Dataset nodes support automatic input resolution from BIDS-formatted datasets at runtime. The resolver script reads your existing job file (which contains pre-configured scalar parameters like thresholds and flags) and merges in the resolved BIDS file paths, so no parameters are lost.

Prerequisites¶

A BIDS-valid dataset (validated with the BIDS Validator)
Python 3.6+ (standard library only — no additional packages required)

Usage¶

Important

The --bids-dir / --bids argument must be an absolute path to your BIDS dataset root directory (e.g. /home/user/data/my_bids_dataset, not a relative path).

Docker-based execution¶

./run.sh --bids /absolute/path/to/your/bids/dataset

Direct cwltool execution¶

python3 resolve_bids.py \
  --bids-dir /absolute/path/to/your/bids/dataset \
  --query bids_query.json \
  --job workflows/<name>_job.yml \
  --output job.yml \
  --relative-to .

cwltool workflows/<name>.cwl job.yml

The --job flag tells the resolver to read the existing job file first, preserving all scalar parameters. The --output flag specifies where to write the merged result.

Manual Override¶

You can edit the job file directly to specify custom file paths without using the BIDS resolver.