Skip to content
Get packs

BIDS Neuroimaging Data Organizer

Organize, query, validate and convert brain imaging datasets to the BIDS standard

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
7 files

What it does

BIDS (Brain Imaging Data Structure) is a shared standard for naming and organizing neuroscience research files, such as MRI, EEG, and MEG recordings, so that other people and software can read them. With this skill installed, the agent knows the BIDS rules and can help build compliant folder layouts, search existing datasets by subject, session or task, check them with the validator, convert scanner DICOM files into BIDS, write JSON metadata sidecars, and create derivative outputs. It also points to bundled reference notes and an updater script for refreshing the standard's schema.

Great for

  • Neuroscience labs preparing scanner or EEG data for sharing on repositories such as OpenNeuro or DANDI
  • Researchers writing scripts that query BIDS datasets with PyBIDS
  • Students learning how the BIDS standard is structured

Skip it if

  • Clinical or identifiable patient data without de-identification review, since the skill does not address privacy and sharing approval
  • Final compliance sign-off by itself: the skill itself warns that successful indexing is not a full check and the official validator must still be run

Try asking

  • “Convert my DICOM scanner folder into a BIDS dataset with dcm2bids and write the sidecar files”
  • “Validate this dataset against the BIDS specification and explain the warnings”
  • “Find all T1w and bold files for subject 03 in this BIDS folder using PyBIDS”
  • “Set up dataset_description.json and a .bidsignore file for my new EEG study”
Step-by-step guide: how to use BIDS Neuroimaging Data OrganizerInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 7 original files, the MIT licence and an attribution note.

    bids.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip bids.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip bids.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run the official BIDS validator after any conversion and record its version along with the schema version
  • Review the bundled schema snapshot before relying on newer or draft BEP features, since BEPs are not adopted requirements
  • Inspect the scripts and install tools in an isolated environment, because the workflows execute Python and external converter commands on your data

What's inside

  • references/beps.yml
  • references/bids_specification.md
  • references/conversion_tools.md
  • references/core_workflows.md
  • references/metadata_fields.md
  • scripts/update_schema.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.