BIDS (Claude Skill)

Claude skill for the Brain Imaging Data Structure standard — dataset creation, validation, DICOM conversion, PyBIDS queries, and BIDS-Apps preparation across all 11 BIDS modalities.

   
Type Claude Skill
Supplier K-Dense Inc. (community OSS)
Availability GA — distributed with the K-Dense marketplace at v2.27.0
Pricing Free / OSS
Capabilities Read/Write — converts and reorganizes local neuroimaging data into BIDS layout

How to install

  • Also packaged in the NeuroClaw skill library (CUHK-AIM-Group (community OSS, MIT)): clone CUHK-AIM-Group/NeuroClaw and copy skills/bids-organizer into ~/.claude/skills/.
  • Claude Code / Claude.ai — Skills CLI (recommended): 
    npx skills add K-Dense-AI/scientific-agent-skills

    Installs the K-Dense collection; enable the bids skill when prompted (also works in Cursor/Codex via the Agent Skills spec; requires Node ≥ 18).

  • Claude Code / Claude Desktop — manual clone: 
    git clone https://github.com/K-Dense-AI/scientific-agent-skills
cp -r scientific-agent-skills/skills/bids ~/.claude/skills/

What it does

  • DICOM-to-BIDS conversion via HeuDiConv (ReproIn turnkey, map-into-reproin, custom heuristics), dcm2bids (config-file-based), and BIDScoin (GUI-based)
  • PyBIDS BIDSLayout queries against organized datasets
  • Sidecar / participants.tsv / scans.tsv / events.tsv authoring with metadata inheritance
  • BIDS validation before repository submission (OpenNeuro, DANDI)
  • BIDS-Apps invocation patterns (fMRIPrep, MRIQC, QSIPrep)
  • Reference for the full 35-entity BIDS schema and the beps.yml extension proposals (including Neuropixels)

Primary use cases: Organize raw neuroscience data for sharing, validate BIDS compliance before submission, prepare datasets for BIDS-Apps preprocessing pipelines, query large BIDS cohorts programmatically.

Notes

Covers the 11 current BIDS modalities — MRI (structural / functional / diffusion / perfusion), PET, microscopy, EEG, MEG, iEEG, EMG, NIRS, motion capture, behavioral, and MR spectroscopy. Pairs naturally with the Neuropixels-Analysis skill once the microelectrode-electrophysiology BEP lands.

Sources

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