bids

Organize and validate neuroscience data according to the BIDS specification.

2|Updated Jun 4, 2026

Search Tags:#research #neuroscience #neuroimaging #eeg #data-standardization #bids #mri

Ready to run

npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill bids-lord1egypt

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bids
Source: https://github.com/Lord1Egypt/scientific-agent-toolkit/tree/main/scientific-skills/bids
Command: npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill bids-lord1egypt

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pybids, bids-validator-deno, heudiconv, dcm2bids, nibabel, pydicom, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This skill solves the complexity of organizing, validating, and querying diverse neuroscience and biomedical research data, ensuring compliance with the global BIDS standard.

Core Features & Use Cases

Dataset Organization: Automatically structure raw imaging (MRI, EEG, MEG) and behavioral data into BIDS-compliant hierarchies.
Compliance Validation: Run automated checks to ensure datasets meet the BIDS specification before submission to repositories like OpenNeuro or DANDI.
Advanced Querying: Use PyBIDS to index and filter large-scale datasets by subject, session, task, or modality for streamlined analysis.

Quick Start

Use the bids skill to validate the dataset located in the current directory and generate a summary report of any compliance issues.

Frequently Asked Questions about bids

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I convert raw DICOM files into BIDS format for neuroimaging datasets?▼

You can convert raw DICOM files into BIDS format using heudiconv or dcm2bids to automatically structure raw imaging data into BIDS-compliant hierarchies. This ensures your neuroimaging datasets are standardized for reproducibility and interoperability.

What is the best way to validate neuroimaging data against the BIDS specification?▼

Validating neuroimaging data against the BIDS specification involves running automated compliance checks using bids-validator-deno. This identifies compliance issues in MRI, EEG, or behavioral data before submission to repositories like OpenNeuro or DANDI.

Can I query multi-modal BIDS datasets by subject or task using PyBIDS?▼

Yes, you can use PyBIDS to query multi-modal BIDS datasets by subject, session, task, or modality. It indexes and filters large-scale datasets efficiently, streamlining subsequent analysis of your neuroimaging and electrophysiology data.

Does BIDS compliance validation support electrophysiology and behavioral data?▼

Yes, BIDS compliance validation supports electrophysiology and behavioral data alongside neuroimaging. The process checks EEG, MEG, and behavioral data to ensure the entire dataset meets the BIDS specification for interoperability and reproducibility.

How do I organize raw MRI and EEG data into a BIDS-compliant hierarchy?▼

You can organize raw MRI and EEG data into a BIDS-compliant hierarchy using automated dataset organization tools that structure multi-modal data according to the Brain Imaging Data Structure specification. This standardizes research data for querying and repository submission.