# Bids

Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets.

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Writing
- License: MIT
- Last updated: 2026-10-26
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill bids -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill bids -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill bids -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill bids -g -a gemini-cli -y`

## Description

Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports 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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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 (reviewed against v1.11.2, released 2026-09-29) 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) proposes support for extracellular recordings including Neuropixels probes, bringing BIDS to a prevalent methodology in animal neuroscience research (see also the neuropixels-analysis skill).

Repository submission requirements vary by modality and archive; check the target archive before preparing a deposit.

The Python ecosystem for BIDS centers on **PyBIDS** (`pybids`) for querying and indexing BIDS datasets, and the **bids-validator** (Deno-based, available as PyPI package `bids-validator-deno` or via Deno directly) for compliance checking. Conversion from DICOM is typically done with **HeuDiConv**, **dcm2bids**, or **BIDScoin**.

## When to Use This Skill

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/bids/SKILL.md