pyNIBS (Claude Skill)

Guides Claude through transcranial magnetic stimulation (TMS) and non-invasive brain stimulation analysis with pyNIBS — managing subject/session data, optimizing coil placement, and mapping motor-evoked potentials onto cortical electric fields.

   
Type Claude Skill
Supplier NeuroForge (community OSS, MIT)
Availability GA — part of the NeuroForge neuroscience skill set
Pricing Free / OSS (MIT)
Capabilities Read/Write — Claude writes and runs pyNIBS Python locally (Bash), not as an MCP tool
Verified works · 2026-07-20
Security caution · 2026-07-20 — no LICENSE on GitHub despite MIT claim, single-maintainer, stale

How to install

  • Claude Code — clone and copy the skill into your skills directory: 
    git clone https://github.com/HughYau/neuroforge-skills
cp -r neuroforge-skills/skills/pynibs ~/.claude/skills/

    Project-scoped alternative: copy into .claude/skills/ instead. The skill invokes pyNIBS in your Python environment — install it first:

    pip install pynibs

    (pyNIBS processes electric-field simulation outputs; a SimNIBS install is expected for generating the underlying field data.)

What it does

Covers the pyNIBS TMS/NIBS analysis workflow across six domains:

  • Subject & session I/O — in-memory containers and persistence for MRI/mesh/ROI metadata.
  • Mesh & ROI structures — geometric containers with structural metadata for cortical regions of interest.
  • HDF5 data layout — file I/O that splits geometry from field data.
  • Optimization — coil-placement and multichannel-current scoring.
  • Regression & localization — nonlinear, element-wise MEP-to-E-field mapping.
  • Experiment import & QC — CSV ingestion, trial filtering, and navigator-data cleanup.

Primary use cases: TMS coil-placement optimization, cortical localization from motor-evoked potentials, NIBS electric-field analysis.

Notes

Distributed as a SKILL.md plus references/*.md in the NeuroForge skill set — Claude executes pyNIBS locally via Bash/Python rather than as an MCP server. Upstream skill front-matter name is pynibs; the skill directory upstream is skills/pynibs. Upstream license: MIT. The README documents context-injection usage for other agents, but the copy-into-~/.claude/skills/ path above is the standard Claude Code Agent Skills install.

Sources

Installed this tool?

Share feedback — install path, OS, errors, workarounds. The form opens with this tool pre-selected and a link back to this page.