CLI overview

The brkraw CLI is organized around a few core tasks:

• Initialize a reproducible config root (init, config)
• Keep defaults across commands in a shell session (session)
• Inspect datasets (info, params)
• Convert scans and write outputs (convert, convert-batch)
• Manage mapping logic and extensions (prune, addon, hook)

This section documents what each command is for and how they fit together.

Recommended starting sequence:

1. Initialize:

   brkraw init
   

2. Inspect a dataset:

   brkraw info /path/to/study
   

3. Convert a scan:

   brkraw convert /path/to/study --scan-id 3
   

4. When running many conversions, use session defaults:

   eval "$(brkraw session set --path /path/to/study --scan-id 3 --reco-id 1)"
   brkraw convert
   

Notes:

• Output naming is controlled by configuration (config.yaml) and optionally by a context_map YAML at runtime.
• Extensions are installed as addons (rules/specs/transforms files) and plugins (hook packages and CLI plugins as Python packages).

Roadmap:

• Practical BIDS organization requiring scan_id mapping, modality-aware naming, and project-specific rules is planned as brkraw-bids.