[Update November 2022] This source code has been updated to work with current version of fastMONAI

Fully automatic whole-volume tumor segmentation in cervical cancer

Project Organization

├── figs            <- Generated figures
│      
├── notebooks       <- Tutorial-like Jupyter notebook 
│
├── src             <- Source code for use in this project
│
├── .ignore         <- Local files and folder to be ignored  
│
├── README.md       <- The top-level README for developers using this project 
│
└── environment.yml <- Config for conda, mamba and pip

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Setup

Run the following command to create a new conda environment from yml file:

conda env create --file environment.yml
conda activate cc-seg

[Optional] Run the following command with your conda environment activated:

conda env update --file environment.yml

[Note] If conda environment is not showing as a kernel in Jupyter Notebook run the following line:

python -m ipykernel install --user --name <ENVIRONMENT> --display-name "Python (cc-seg)"