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 pixi, which provides fast dependency resolution and environment management.
To install the app, first install pixi. On macOS and Linux, run:
curl -fsSL https://pixi.sh/install.sh | shOn Windows, run:
powershell -ExecutionPolicy Bypass -c "irm -useb https://pixi.sh/install.ps1 | iex"
Once pixi is installed, setup the environment:
pixi install
To verify that the installation was successful, run:
pixi run contactseg -h
You should see a help message listing all available command-line options.
If this runs successfully, you’re ready to use contactseg!
To use the BIDS App, run:
pixi run contactseg /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:
pixi install -e dev
You can then run quality checks and formatting with:
pixi run -e dev quality_check
pixi run -e dev quality_fix