Head and Neck CT Image Segmentation
Installation
Execute the following command from the root of the repository to install the project:
pip install -e .
Note that this step is required to run the project.
Data
MICCAI 2015 Head and Neck Auto Segmentation Challenge
Executing the following code will download, extract, and split the dataset.
cd capstone/data
python download.py miccai
Note that if you're on the NYU cluster (Prince), then the data will be stored at the user's $BEEGFS
directory on the cluster.
Refer to the file paths.py
in the capstone
directory for more info
Requirements
We highly recommend using the specified versions of the listed packages, with which our code is tested with.
Base Requirements
- Python (3.7)
- pynrrd (0.4) - For loading MICCAI data in
.nrrd
format - Tqdm - For displaying progress bars
- PyTorch (1.7)
- Torchvision (0.8)
- Albumentations (0.5) - For data augmentation and transforms
- MONAI (0.3) - For domain specific models, losses, metrics, etc
- PyTorch-Lightning (1.0)
Additional Requirements
We use Weights and Biases for keeping a track of all our experiments and results.