Bids
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets...
Install
npx skills add synthetic-sciences/openscience --skill bids -g -a claude-code -y- Repository
- synthetic-sciences/openscience4.3k
- Category
- Writing
- Updated
- 5d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 3,000 tokens
- Runs scripts
- Yes, review before use
What it does
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
Brain Imaging Data Structure (BIDS)
Overview
The Brain Imaging Data Structure (BIDS) is a community standard for organizing and describing neuroscience and biomedical research datasets. It defines a consistent file naming convention, directory hierarchy, and metadata schema so that datasets are immediately understandable by humans and software tools alike. BIDS is governed by the BIDS Specification (currently v1.11.x) and is maintained by the community via the BIDS-Standard GitHub organization.
While BIDS originated for MRI, it has grown well beyond neuroimaging. The specification now covers 11 modalities spanning imaging, electrophysiology, and behavioral data:
- Imaging: MRI (structural, functional, diffusion, fieldmaps, perfusion/ASL), PET, microscopy
- Electrophysiology: EEG, MEG, iEEG (intracranial EEG), EMG
- Other: NIRS (near-infrared spectroscopy), motion capture, behavioral data (without imaging), MR spectroscopy
Active BEPs are extending BIDS further, notably BEP032 (microelectrode electrophysiology) will add support for extracellular recordings including Neuropixels probes, bringing BIDS to a prevalent methodology in animal neuroscience research (see also the neuropixels-analysis skill).
Adoption is required or strongly encouraged by major data repositories (OpenNeuro, DANDI), leading journals (NeuroImage, Human Brain Mapping, Scientific Data), and funding agencies (NIH, ERC).
The Python ecosystem for BIDS centers on PyBIDS (pybids) for querying and indexing BIDS datasets, and the bids-validator (Deno-based, available as PyPI package bids-validator-deno or via Deno directly) for compliance checking. Conversion from DICOM is typically done with HeuDiConv, dcm2bids, or BIDScoin.
