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BIDS Neuroimaging Data Standard Helper

A skill for organizing, querying, validating and converting neuroscience data to the BIDS standard.

Data & AnalyticsIntermediate★ 47,132⑂ 4,254AI score 9/10Last updated: Sep 29, 2026

What it does

  • Guides you in laying out data for 11 BIDS modalities (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion, behavioral, MRS, EMG) using correct directory structure and filename entities.
  • Covers PyBIDS querying (BIDSLayout, entity filters, metadata inheritance, index caching), compliance checking with bids-validator, and DICOM→BIDS conversion via HeuDiConv, dcm2bids or BIDScoin.
  • Explains dataset_description.json, JSON sidecars, events.tsv, participants.tsv, scans.tsv, derivatives layout, plus eight common validation failures with fixes.

Who it's for

  • Researchers preparing datasets for OpenNeuro, DANDI, or journal data-sharing requirements.
  • Imaging analysts who must convert scanner DICOMs reproducibly.
  • Students and staff who need a clean dataset before running BIDS-Apps like fMRIPrep, MRIQC or QSIPrep.

Example uses

  1. "Convert this DICOM directory to BIDS with HeuDiConv and validate it" → follows reconnaissance → heuristic → convert → validator.
  2. "Find sub-03's task-rest bold files and their sidecar metadata" → PyBIDS code with entity filters and inherited metadata.
  3. "The validator says 'Not a BIDS dataset'" → diagnoses the missing root dataset_description.json and writes a minimal one.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/bids/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/bids folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/bids/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/bids ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and create the skills folder: mkdir -p ~/.claude/skills
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy just this skill: cp -r scientific-agent-skills/skills/bids ~/.claude/skills/
  4. Install the tooling: uv pip install pybids bids-validator-deno nibabel pydicom (add heudiconv or dcm2bids for DICOM conversion).
  5. Restart Claude Code and ask something like "validate my BIDS dataset" — the skill should trigger automatically.
View source on GitHub ↗License: MIT