Add BIDS (Brain Imaging Data Structure) skill#125
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yarikoptic wants to merge 3 commits intoK-Dense-AI:mainfrom
Open
Add BIDS (Brain Imaging Data Structure) skill#125yarikoptic wants to merge 3 commits intoK-Dense-AI:mainfrom
yarikoptic wants to merge 3 commits intoK-Dense-AI:mainfrom
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Comprehensive skill covering the BIDS standard for organizing neuroimaging data: SKILL.md (746 lines): - BIDS directory structure, file naming, entity ordering - PyBIDS querying (BIDSLayout), dataset validation (bids-validator-deno) - DICOM-to-BIDS conversion with HeuDiConv (ReproIn turnkey, map-into-reproin, and custom heuristic modes), dcm2bids, and BIDScoin - JSON sidecar metadata and inheritance, events files, participants files - BIDS derivatives conventions, BIDS-Apps interface - All 25 current BEPs listed with status - bids-examples as canonical reference collection - 11 best practices, 8 common issues with solutions references/: - bids_schema.json: machine-readable schema (v1.2.1 / BIDS v1.11.1) from RTD - beps.yml: full BEP listing from bids-website - bids_specification.md: entity table in correct schema ordering (35 entities) - metadata_fields.md: required/recommended sidecar fields for all modalities - conversion_tools.md: detailed HeuDiConv/dcm2bids/BIDScoin workflows scripts/update_schema.py: stdlib-only script to refresh schema + BEPs from upstream Also listed in docs/scientific-skills.md under Neuroscience & Electrophysiology. Co-Authored-By: Claude Code 2.1.92 / Claude Opus 4.6 <noreply@anthropic.com>
BIDS now covers 11 modalities: imaging (MRI, PET, microscopy), electrophysiology (EEG, MEG, iEEG, EMG), and other data (NIRS, motion capture, behavioral, MR spectroscopy). Updated descriptions throughout to reflect this scope. Note BEP032 (microelectrode electrophysiology) connection to Neuropixels probes and the neuropixels-analysis skill. Co-Authored-By: Claude Code 2.1.92 / Claude Opus 4.6 <noreply@anthropic.com>
=== Do not change lines below ===
{
"chain": [],
"cmd": "python scientific-skills/bids/scripts/update_schema.py",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
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Add comprehensive BIDS (Brain Imaging Data Structure) skill covering the community standard for organizing and describing neuroscience and biomedical research datasets. While originating for MRI, BIDS now covers 11 modalities: imaging (MRI, PET, microscopy), electrophysiology (EEG, MEG, iEEG, EMG), and other data (NIRS, motion capture, behavioral, MR spectroscopy), with active BEPs extending to microelectrode electrophysiology (Neuropixels), stimuli, and more.
Changes
SKILL.md (746 lines)
BIDSLayout) with basic and advanced usagebids-validator-deno(PyPI) or Deno directlyspace-,desc-,GeneratedBy)references/
rules.entities), datatypes, file extensions, template spacesscripts/
--schema-urlfor PR previews or BEP-specific schemasdocs/scientific-skills.md
🤖 Generated with Claude Code and eyeballed and improved a little with my past BIDS steering committee member hat on, and heudiconv/reproin developer hat on, etc.