├── .gitignore ├── DataSet ├── Readme.md └── testData │ ├── 001 │ ├── 001_LI.nii.gz │ ├── 001_LI_mask.nii.gz │ ├── 001_RI.nii.gz │ ├── 001_RI_mask.nii.gz │ ├── 001_SA.nii.gz │ └── 001_SA_mask.nii.gz │ ├── 002 │ ├── 002_LI.nii.gz │ ├── 002_LI_mask.nii.gz │ ├── 002_RI.nii.gz │ ├── 002_RI_mask.nii.gz │ ├── 002_SA.nii.gz │ └── 002_SA_mask.nii.gz │ ├── 003 │ ├── 003_LI.nii.gz │ ├── 003_LI_mask.nii.gz │ ├── 003_RI.nii.gz │ ├── 003_RI_mask.nii.gz │ ├── 003_SA.nii.gz │ └── 003_SA_mask.nii.gz │ ├── 004 │ ├── 004_LI.nii.gz │ ├── 004_LI_mask.nii.gz │ ├── 004_RI.nii.gz │ ├── 004_RI_mask.nii.gz │ ├── 004_SA.nii.gz │ └── 004_SA_mask.nii.gz │ └── 005 │ ├── 005_LI.nii.gz │ ├── 005_LI_mask.nii.gz │ ├── 005_RI.nii.gz │ ├── 005_RI_mask.nii.gz │ ├── 005_SA.nii.gz │ └── 005_SA_mask.nii.gz ├── LICENSE ├── README.md ├── code ├── Readme.md ├── Training │ ├── batchgenerators │ │ └── Readme.md │ └── fracSegNet │ │ ├── __init__.py │ │ ├── basicFunc.py │ │ ├── dataset_conversion │ │ └── utils.py │ │ ├── experiment_planning │ │ ├── configuration.py │ │ └── nnUNet_plan_and_preprocess.py │ │ ├── inference │ │ ├── nii2stl.py │ │ ├── predict_single.py │ │ └── segmentation_export.py │ │ ├── network_architecture │ │ └── neural_network.py │ │ ├── preprocessing │ │ ├── calculate_disMap.py │ │ ├── cropping.py │ │ └── preprocessing.py │ │ ├── run │ │ └── run_training.py │ │ └── training │ │ ├── __init__.py │ │ ├── data_augmentation │ │ ├── data_augmentation_moreDA.py │ │ └── default_data_augmentation.py │ │ ├── dataloading │ │ └── dataset_loading.py │ │ ├── loss_functions │ │ ├── crossentropy.py │ │ ├── deep_supervision.py │ │ └── dice_loss.py │ │ ├── model_restore.py │ │ └── network_training │ │ ├── network_trainer.py │ │ ├── nnUNetTrainer.py │ │ └── nnUNetTrainerV2.py └── inference │ ├── AnatomicalSegModel │ ├── cascadeFullres_model │ │ ├── Ana_cascadeFullres.model.pkl │ │ ├── Readme.md │ │ └── replace-with-Ana_cascadeFullres.model │ └── lowres_model │ │ ├── Ana_lowres.model.pkl │ │ ├── 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