Installation

neuro-mcp requires Python ≥ 3.10. The core install pulls in MNE-Python, SciPy/NumPy/scikit-learn, matplotlib, and Plotly; several capabilities are gated behind optional extras so you only pay for what you use.

Core install

conda create -n neuro-mcp python=3.11 -y   # or any Python >=3.10 env
conda activate neuro-mcp
pip install -e .

This gives you processing (tools_core.py), source imaging (tools_source.py), the data/EHR store on SQLite, and the neuroii visualization/annotation tools (tools_viz_neuroii.py, tools_neuroii.py) — everything except a production database driver and 3D brain rendering.

Optional extras

Extra	Installs	Unlocks
postgres	psycopg[binary]>=3.1	DATABASE_URL=postgresql+psycopg://... for a shared/production data store
viz3d	pyvista, pyvistaqt, PySide6	plot_source_brain renders a real 3D cortical surface instead of a "backend not available" note
dev	pytest, build, twine	Building/publishing the package, plus the testing/ scripts (which don't require pytest to run, but the extra keeps the tooling handy)
docs	mkdocs, mkdocs-material	Building this documentation site locally

pip install -e ".[postgres]"
pip install -e ".[viz3d]"
pip install -e ".[dev]"
pip install -e ".[docs]"
# combine as needed, e.g.:
pip install -e ".[postgres,dev]"

Verify the install

python -c "import neuro_mcp; print(neuro_mcp.__version__)"
python -c "from neuro_mcp.server import main; print(main)"

Don't run python -m neuro_mcp or the neuro-mcp console script directly in a shell you plan to keep using — it starts a blocking stdio MCP server with no --help flag. Register it with an MCP host instead (see Configuration), or drive it programmatically the way testing/verify.py does, via FastMCP's in-memory Client.

Run the test suite

python testing/verify.py        # fast smoke test
python testing/full_verify.py   # comprehensive, all 54 tools, writes testing/REPORT.md

See Testing & Verification for the full picture.