Hyperparameter-Free Medical Image Synthesis for Sharing Data and Improving Site-Specific Segmentation

Setup

Create & activate a conda environment:

conda env create --file env_autoshare.yml
conda activate autoshare

Install the nnunetv2_mod:

cd nnunetv2_mod
pip install -e .

Set environmental variables

export OMP_NUM_THREADS=4
export OPENBLAS_NUM_THREADS=4
export VECLIB_MAXIMUM_THREADS=4
export NUMEXPR_NUM_THREADS=4
export MKL_NUM_THREADS=1
ulimit -n 500000

Running experiments

python run_nnunet.py --config-name=cervix_000 ++data.fold=0

Configs for all experiments are in the config dir. Note that configs need to be modified to refer to your paths and the names/IPs of your servers (for Ray).