README.md

Probabilistic Shape Completion with Multi-target Conditional Variational Autoencoders

This repository accompanies the article expected to be published in the 22nd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2019), which will be held from October 13th to 17th, 2019, in Shenzhen, China.

Please consider citing our MICCAI 2019 paper if you enjoyed the implementation. The draft can be accessed here.

@InProceedings{10.1007/978-3-030-32254-0_26,
    author="Abdi, Amir H.
    and Pesteie, Mehran
    and Prisman, Eitan
    and Abolmaesumi, Purang
    and Fels, Sidney",
    title="Variational Shape Completion for Virtual Planning of Jaw Reconstructive Surgery",
    booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2019",
    year="2019",
    publisher="Springer International Publishing",
    address="Cham",
    pages="227--235",
}

Download data

To download the data and set the environment variable $DATASETS to where the data is downloaded, run

source download-data.sh 

Train and Test Model

This is a Python3 implementation. To train the conditional VAE model for shape completion with the default data (mandible dataset), install the requirements by running

pip install -r requirements.txt

And run the training script

bash scripts/train-CVAE-vwDice-TWcvae

To test the model, set the --test=true and set the --load_model_path flag to where the trained model is stored.

Sample Results