├── LICENSE ├── README.md ├── VTUNet ├── dataset.json ├── environment.yml ├── requirements.txt ├── setup.py └── vtunet │ ├── __init__.py │ ├── configs │ ├── vt_unet_base.yaml │ └── vt_unet_small.yaml │ ├── configuration.py │ ├── dataset_json │ └── tumor_dataset.json │ ├── 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 │ │ ├── rank_candidates.py │ │ ├── rank_candidates_StructSeg.py │ │ ├── rank_candidates_cascade.py │ │ ├── summarize_results_in_one_json.py │ │ └── summarize_results_with_plans.py │ ├── region_based_evaluation.py │ └── surface_dice.py │ ├── experiment_planning │ ├── DatasetAnalyzer.py │ ├── __init__.py │ ├── change_batch_size.py │ ├── common_utils.py │ ├── experiment_planner_baseline_2DUNet.py │ ├── experiment_planner_baseline_2DUNet_v21.py │ ├── experiment_planner_baseline_3DUNet.py │ ├── experiment_planner_baseline_3DUNet_v21.py │ ├── summarize_plans.py │ ├── utils.py │ ├── vtunet_convert_decathlon_task.py │ └── vtunet_plan_and_preprocess.py │ ├── inference │ ├── __init__.py │ ├── change_trainer.py │ ├── ensemble_predictions.py │ ├── inferTs │ │ └── swin_nomask_2 │ │ │ └── plans.pkl │ ├── predict.py │ ├── predict_simple.py │ ├── pretrained_models │ │ ├── __init__.py │ │ ├── change_trainer.py │ │ ├── collect_pretrained_models.py │ │ ├── download_pretrained_model.py │ │ ├── ensemble_predictions.py │ │ ├── predict.py │ │ ├── predict_simple.py │ │ └── segmentation_export.py │ └── segmentation_export.py │ ├── inference_tumor.py │ ├── network_architecture │ ├── README.md │ ├── __init__.py │ ├── generic_UNet.py │ ├── initialization.py │ ├── neural_network.py │ └── vtunet_tumor.py │ ├── paths.py │ ├── postprocessing │ ├── connected_components.py │ ├── consolidate_all_for_paper.py │ ├── consolidate_postprocessing.py │ └── consolidate_postprocessing_simple.py │ ├── preprocessing │ ├── cropping.py │ ├── custom_preprocessors │ │ └── preprocessor_scale_RGB_to_0_1.py │ ├── preprocessing.py │ └── sanity_checks.py │ ├── pretrained_ckpt │ └── init.py │ ├── run │ ├── __init__.py │ ├── default_configuration.py │ ├── load_pretrained_weights.py │ └── run_training.py │ ├── training │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ └── model_restore.cpython-36.pyc │ ├── cascade_stuff │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ └── predict_next_stage.cpython-36.pyc │ │ └── predict_next_stage.py │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── custom_transforms.cpython-36.pyc │ │ │ ├── data_augmentation_moreDA.cpython-36.pyc │ │ │ ├── data_augmentation_noDA.cpython-36.pyc │ │ │ ├── default_data_augmentation.cpython-36.pyc │ │ │ ├── downsampling.cpython-36.pyc │ │ │ └── pyramid_augmentations.cpython-36.pyc │ │ ├── custom_transforms.py │ │ ├── data_augmentation_moreDA.py │ │ ├── data_augmentation_noDA.py │ │ ├── default_data_augmentation.py │ │ ├── downsampling.py │ │ └── pyramid_augmentations.py │ ├── dataloading │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ └── dataset_loading.cpython-36.pyc │ │ └── dataset_loading.py │ ├── learning_rate │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── cos_lr.cpython-36.pyc │ │ │ └── poly_lr.cpython-36.pyc │ │ └── poly_lr.py │ ├── loss_functions │ │ ├── TopK_loss.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── TopK_loss.cpython-36.pyc │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── crossentropy.cpython-36.pyc │ │ │ ├── deep_supervision.cpython-36.pyc │ │ │ └── dice_loss.cpython-36.pyc │ │ ├── crossentropy.py │ │ ├── deep_supervision.py │ │ └── dice_loss.py │ ├── model_restore.py │ ├── network_training │ │ ├── README.md │ │ ├── __init__.py │ │ ├── network_trainer.py │ │ ├── vtunetTrainer.py │ │ ├── vtunetTrainerV2.py │ │ ├── vtunetTrainerV2_vtunet_tumor.py │ │ └── vtunetTrainerV2_vtunet_tumor_base.py │ └── optimizer │ │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ └── ranger.cpython-36.pyc │ │ └── ranger.py │ └── utilities │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-37.pyc │ ├── distributed.cpython-36.pyc │ ├── folder_names.cpython-36.pyc │ ├── nd_softmax.cpython-36.pyc │ ├── nd_softmax.cpython-37.pyc │ ├── one_hot_encoding.cpython-36.pyc │ ├── random_stuff.cpython-36.pyc │ ├── random_stuff.cpython-37.pyc │ ├── sitk_stuff.cpython-36.pyc │ ├── task_name_id_conversion.cpython-36.pyc │ ├── tensor_utilities.cpython-36.pyc │ ├── to_torch.cpython-36.pyc │ └── to_torch.cpython-37.pyc │ ├── distributed.py │ ├── file_conversions.py │ ├── file_endings.py │ ├── folder_names.py │ ├── nd_softmax.py │ ├── one_hot_encoding.py 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