Configuration

neuro-mcp is configured entirely through environment variables (see neuro_mcp/config.py), so the same binary works for a zero-setup local run and a shared clinical deployment without code changes.

Variable	Default	Purpose
DATABASE_URL	sqlite:///~/.neuro-mcp/neuro_mcp.db	The data/EHR store. Production: postgresql+psycopg://user:pass@host/db (requires the postgres extra).
BIDS_ROOT	~/.neuro-mcp/bids	Root of the BIDS-on-disk recording tree that import_recording writes into.
NEUROII_API_URL	(unset)	Base URL of a neuroii instance. Unset → the neuroii_* tools return the documented not_configured contract instead of calling out.
NEUROII_API_TOKEN	(unset)	Optional bearer token for NEUROII_API_URL.
NEURO_MCP_HOME	~/.neuro-mcp	Base directory used to derive the default SQLite path and BIDS root when DATABASE_URL/BIDS_ROOT aren't set.

The default (SQLite + a scratch BIDS dir under ~/.neuro-mcp) runs with zero setup — good for local development and the testing/ scripts (which override DATABASE_URL/BIDS_ROOT with temp directories so they never touch your real data home). Point DATABASE_URL at Postgres for a multi-user or clinical deployment.

Registering with an MCP host

python -m neuro_mcp     # stdio transport

{
  "mcpServers": {
    "neuro-analysis": {
      "command": "/path/to/envs/neuro-mcp/bin/python",
      "args": ["-m", "neuro_mcp"],
      "env": {
        "DATABASE_URL": "sqlite:////data/neuro_mcp.db",
        "BIDS_ROOT": "/data/bids"
      }
    }
  }
}

Point command at the interpreter inside the environment where you ran pip install -e . (or a released neuro-mcp install).

neuroii integration status

neuroii integration is greenfield: the tools in neuroii Integration define and return the expected REST contract (see neuro_mcp/neuroii/client.py). Until NEUROII_API_URL is set, they respond {"status": "not_configured", "contract": {...}} so the neuroii app has a fixed target to implement against:

• POST /api/v1/recordings
• POST /api/v1/viz-sessions
• GET /api/v1/recordings/{id}/annotations