├── .gitignore ├── LICENSE ├── README.md ├── create-json.py ├── docker ├── Dockerfile ├── Dockerfile.base ├── Dockerfile.structseg ├── README.md ├── Segmentation.py ├── images │ ├── nnU-Net-2D.png │ └── nnU-Net-3D.png ├── predict-commands-all.sh ├── predict-commands-structseg-2d.sh ├── predict-commands-structseg-3d.sh ├── predict-commands.sh ├── rename-images.py ├── rename-seg.py ├── rename_input.py ├── run-all.sh ├── run-structseg.sh └── run.sh ├── nnunet ├── __init__.py ├── dataset_conversion │ ├── AutomaticCardiacDetectionChallenge.py │ ├── BeyondCranialVaultAbdominalOrganSegmentation.py │ ├── BraTS_2019.py │ ├── ISBI_MSLesionSegmentationChallenge.py │ ├── LiverTumorSegmentationChallenge.py │ ├── Promise2012.py │ ├── __init__.py │ └── readme.md ├── evaluation │ ├── __init__.py │ ├── add_dummy_task_with_mean_over_all_tasks.py │ ├── add_mean_dice_to_json.py │ ├── collect_results_files.py │ ├── evaluator.py │ ├── metrics.py │ └── model_selection │ │ ├── __init__.py │ │ ├── collect_all_fold0_results_and_summarize_in_one_csv.py │ │ ├── ensemble.py │ │ ├── figure_out_what_to_submit.py │ │ ├── summarize_results_in_one_json.py │ │ └── summarize_results_with_plans.py ├── experiment_planning │ ├── DatasetAnalyzer.py │ ├── __init__.py │ ├── common_utils.py │ ├── configuration.py │ ├── experiment_planner_baseline_2DUNet.py │ ├── experiment_planner_baseline_3DUNet.py │ ├── find_classes_in_slice.py │ ├── plan_and_preprocess_task.py │ └── summarize_plans.py ├── inference │ ├── __init__.py │ ├── ensemble_predictions.py │ ├── predict.py │ ├── predict_simple.py │ └── segmentation_export.py ├── network_architecture │ ├── __init__.py │ ├── generic_UNet.py │ ├── initialization.py │ └── neural_network.py ├── paths.py ├── preprocessing │ ├── __init__.py │ ├── cropping.py │ └── preprocessing.py ├── run │ ├── __init__.py │ ├── default_configuration.py │ └── run_training.py ├── training │ ├── __init__.py │ ├── cascade_stuff │ │ └── predict_next_stage.py │ ├── data_augmentation 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