Nipoppy MCP Server

A Model Context Protocol (MCP) interface for the Nipoppy neuroimaging dataset framework. This server exposes a simple tool through MCP, allowing AI agents to list files in directories.

What is Nipoppy?

Nipoppy is a lightweight framework for standardized organization and processing of neuroimaging-clinical datasets. It follows the Brain Imaging Data Structure (BIDS) standard and provides tools for managing datasets and processing pipelines.

What is MCP?

The Model Context Protocol (MCP) is a standardized protocol that allows AI applications (LLMs) to access external tools and resources through a consistent interface. This server exposes a file listing tool as an MCP tool.

Features

This MCP server provides the following tool:

• list_files: List files in a given directory

Installation

Prerequisites

• Python 3.8 or higher

Install the package

# Clone the repository
git clone https://github.com/nipoppy/mcp.git
cd mcp

# Install dependencies
pip install -e .

Usage

Running the MCP Server

The server can be run in different modes depending on your use case:

1. STDIO Mode (for local desktop apps like Claude Desktop)

# Set the dataset root (optional, defaults to current directory)
export NIPOPPY_DATASET_ROOT=/path/to/your/nipoppy/dataset

# Run the server
python -m nipoppy_mcp.server
```bash
# Run the server
python -m nipoppy_mcp.server

2. Configure with Claude Desktop

Add to your Claude Desktop configuration file (~/Library/Application Support/Claude/claude_desktop_config.json on macOS):

{
  "mcpServers": {
    "nipoppy": {
      "command": "python",
      "args": ["-m", "nipoppy_mcp.server"]
    }
  }
}

Using the Tool

Once connected to an MCP-compatible client, you can use natural language to list files in directories:

Example queries:

• "List files in /path/to/directory"
• "What files are in my home directory?"

Development

Running Tests

# Install development dependencies
pip install -e ".[dev]"

# Run tests
pytest

Project Structure

mcp/
├── nipoppy_mcp/
│   ├── __init__.py
│   └── server.py          # Main MCP server implementation
├── tests/                 # Test files
├── pyproject.toml        # Project configuration
└── README.md

Contributing

Contributions are welcome! This is a Brainhack 2026 project. Please feel free to submit issues and pull requests.

License

MIT License - see LICENSE file for details.

Resources

• Nipoppy Documentation
• Nipoppy GitHub
• Model Context Protocol
• MCP Python SDK