Individual skill
bids
Organizes, queries, validates, and converts neuroscience and biomedical datasets using the Brain Imaging Data Structure (BIDS) standard, covering MRI, PET, EEG, MEG, iEEG, EMG, NIRS, microscopy, motion capture, and behavioral data. Covers PyBIDS (BIDSLayout), the bids-validator, HeuDiConv, dcm2bids, BIDScoin, JSON sidecars, dataset_description.json, events.tsv, participants.tsv, .bidsignore, and derivatives. Use when arranging raw data into BIDS directories and filenames. Use when converting DICOM scans to BIDS. Use when validating a dataset before OpenNeuro or DANDI submission. Use when querying files or sidecar metadata with PyBIDS. Use when writing BIDS derivatives. For extracellular Neuropixels analysis, use neuropixels-analysis instead.
plugins/KalarisLabs/research-agent-skills/skills/bids/SKILL.md
Source commit d780783eba4ecc7c8b9429f95c9362df95f07c61
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 4, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 1,532
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-coding Repository topic
- awesome Repository topic
- awesome-list Repository topic
- codex Repository topic
- codex-plugins Repository topic
- openai Repository topic
- codex-skill Repository topic
- codex-skills Repository topic
- marketplace Repository topic
- codex-marketplace Repository topic
- neuroimaging,-bids,-mri,-eeg,-data-standards,-neuroscience Declared skill tag
- writing Derived category
- data Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
SKILL.mdcore · 15,650 bytesSKILL.mdcore · 15,650 bytesSKILL.mdcore · 15,650 bytesSKILL.mdcore · 15,650 bytesSKILL.mdcore · 15,650 bytesreferences/beps.ymlasset · 23,980 bytesreferences/bids_schema.jsonasset · 813,726 bytesreferences/bids_specification.mddoc · 8,408 bytesreferences/conversion_tools.mddoc · 18,617 bytesreferences/core_workflows.mddoc · 18,341 bytesreferences/metadata_fields.mddoc · 14,588 bytesscripts/update_schema.pyruns · 2,631 bytes
Read excerpt
# 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).
