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.
npx skills add K-Dense-AI/scientific-agent-skills --skill bids --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 al
- Overview
- When to Use This Skill
- Installation
- Core Workflows
- Reference Materials
- Common Issues and Solutions
- 1. Validator reports "Not a BIDS dataset"
- 2. Inconsistent subjects warning
- 3. Missing SliceTiming
- 4. Phase encoding direction confusion
- 5. PyBIDS is slow on large datasets
- 6. Derivatives not found by PyBIDS
- 7. Events file timing is off
- 8. TSV files fail validation
Core BIDS querying library uv pip install pybids BIDS validator (Deno-based, installed via PyPI wrapper) uv pip install bids-validator-deno deno install -g -A npm:bids-validator DICOM-to-BIDS converters (install as needed) uv pip install heudiconv # HeuDiConv - heuristic-based DICOM conversion uv pip install dcm2bids # dcm2bids - config-file-based conversion Useful companions uv pip install nibabel # NIfTI/other neuroimaging file I/O
What does the bids skill do?
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.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill bids --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.