auto_segmentation_starter

Cleaned up version of some 3D auto-segmentation code

Preliminary instructions

1. Clone this repo
2. create a new python virtual environment: python -m venv autosegmentation_env
3. activate the virtual environment: source autosegmentation_env/bin/activate
4. install requirements: pip install -r requirements.txt

Next up

0. Convert Dicom to Nifti
1. Combine structures into a single mask
2. use preprocess.py to preprocess the data
3. train using train.py
4. evaluate the results (using Hausdorff distance, mean distance-to-agreement, DSC...)