nnUNet_NonLocal_WS

A modification code based on nnUNet (https://github.com/MIC-DKFZ/nnUNet)

How to use our code

• Preproccesing 0_NNUNET_Preprocess.ipynb base = "nnUNet_base/" preprocessing_output_dir = "nnUNet_preprocessed/" network_training_output_dir_base = "RESULTS_FOLDER/"

• Training 1_NNUNET_Training.ipynb Construct the training and validation datasets with 5 folds, we trained each with 5 segmentation models to run the voting ensemble.

• Prediction 2_NNUNET_Prediction.ipynb We applied the testset to 5 trained models and saved the results in a separate folder for each.

• Evaluation 3_NNUNET_Ensemble.ipynb We performed a pixel-wise 2/5 voting ensemble on the segmentation results of 5 models.

Code modified from original nnUNet

generic_Unet.py Non_Local

2022.08.01.