Automatic Contact Segmentation

Automatic Contact Segmentation is a BIDS App for localizing stereoelectroencephalography (SEEG) contacts from post-operative CT scans. It uses the nnUNetv2 framework to train a 3D U-Net model for automatic SEEG contact segmentation. The app integrates Snakemake and SnakeBIDS for workflow management and reproducibility. The project is managed using uv, which provides fast dependency resolution and environment management.

To install the app, first install uv. On macOS and Linux, run:

curl -LsSf https://astral.sh/uv/install.sh | sh

On Windows, run:

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Alternatively, you can install it from PyPI using:

pip install uv

or with pipx:

pipx install uv

Once uv is installed, create and activate a virtual environment:

uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

Then install the package in editable mode:

uv pip install -e .

To verify that the installation was successful, run:

nnunet_contact_seg -h

This should display the help message for the CLI. If it doesn’t, ensure that your virtual environment is activated and that the installation completed without errors.

To use the BIDS App, run:

nnunet_contact_seg /path/to/bids/dataset /path/to/output/derivatives participant --cores all

Replace /path/to/bids/dataset with the path to your BIDS-compliant input dataset and /path/to/output/derivatives with the desired output directory.

If you're developing the app and want to install development dependencies such as linters and formatters, run:

uv pip install -e .[dev]