UCTNet: Uncertainty-Guided CNN-Transformer Hybrid Networks for Medical Image Segmentation

This repo is the official implementation for UCTNet.

Prerequisites

Install packages

cd nnUNet
pip install -e .

cd UCTNet
pip install -e .

Datasets processing

Download datasets BCV(Synapse), ACDC and ISIC2018. The dataset partitioning of BCV(Synapse) and ACDC follows TransUNet and the ISIC 2018 is divided according to dataset_ISIC2018.json.

UCTNet_BCV -dataset_path DATASET_PATH
UCTNet_ACDC -dataset_path DATASET_PATH
UCTNet_ISIC2018 -dataset_path DATASET_PATH

Training

BCV

UCTNet_train -task 17 --fold 0 --custom_network UCTNet_3D -ei UCTNet --deterministic -pretrained_weights "/UCTNet/pretrained_weight/BCV/model_final_checkpoint.model"

ACDC

UCTNet_train -network 2d -task 27 --fold 0 --custom_network UCTNet_2D -ei UCTNet --deterministic -pretrained_weights "/UCTNet/pretrained_weight/ACDC/model_final_checkpoint.model"

ISIC2018

UCTNet_train -network 2d -task 100 --fold 0 --custom_network UCTNet_2D -ei UCTNet --deterministic

Testing

BCV

UCTNet_predict --task_name 17 --f 0 -ei UCTNet -chk model_final_checkpoint

ACDC

UCTNet_predict --task_name 27 -m 2d --f 0 -ei UCTNet -chk model_final_checkpoint

ISIC_2018

UCTNet_predict --task_name 100 -m 2d --f 0 -ei UCTNet -chk model_final_checkpoint

Acknowledgements