fMRI Processing (Claude Skill)

Perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox.

   
Type Claude Skill
Supplier CUHK-AIM-Group (community OSS, MIT)
Availability GA — part of the NeuroClaw neuroimaging skill library
Pricing Free / OSS (MIT)
Capabilities Read/Write — Claude runs the skill’s Python locally (Bash), not as an MCP tool

How to install

  • Claude Code — clone and copy the skill into your skills directory: 
    git clone https://github.com/CUHK-AIM-Group/NeuroClaw
cp -r NeuroClaw/skills/fmri-skill ~/.claude/skills/

    Project-scoped alternative: copy into .claude/skills/ instead. NeuroClaw skills assume the collection’s shared helpers (claw-shell, modality tool skills) and the upstream neuroimaging stack (FreeSurfer/FSL/fMRIPrep/etc.) — install those dependencies, or run the bundled installer for the full environment:

    cd NeuroClaw && python installer/setup.py

    which configures the Python env, CUDA/GPU, and the neuroimaging tools.

What it does

Use this skill whenever the user wants to perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox. Triggers include: ‘fmri’, ‘fMRI analysis’, ‘functional connectivity’, ‘effective connectivity’, ‘ROI extraction’, ‘seed-based correlation’, ‘PPI’, ‘DCM’, ‘atlas alignment’, ‘MNI152’, ‘HCP pipeline’, ‘CONN toolbox’, or any request involving BOLD data.

Primary use cases: ‘fmri’, ‘fMRI analysis’, ‘functional connectivity’, ‘effective connectivity’, ‘ROI extraction’, ‘seed-based correlation’, ‘PPI’, ‘DCM’, ‘atlas alignment’, ‘MNI152’, ‘HCP pipeline’, ‘CONN toolbox’, or any request involving BOLD data.

Notes

Distributed as a SKILL.md (plus code examples) in the NeuroClaw skill library — Claude executes it locally via Bash/Python rather than as an MCP server. Upstream license: MIT. The skill directory upstream is skills/fmri-skill.

Sources

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