Individual skill

bids

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.

backend/cli/skills/biology/bids/SKILL.md

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Repository stars (not skill ratings): 4,351
Repository last updated: Nov 6, 2026
License: Apache-2.0

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SKILL.mdcore · 15,393 bytes
SKILL.mdcore · 15,393 bytes
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references/beps.ymlasset · 23,980 bytes
references/bids_schema.jsonasset · 813,726 bytes
references/bids_specification.mddoc · 8,408 bytes
references/conversion_tools.mddoc · 18,617 bytes
references/core_workflows.mddoc · 18,341 bytes
references/metadata_fields.mddoc · 14,588 bytes
scripts/update_schema.pyruns · 2,631 bytes

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# 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).