├── LICENSE ├── README.md ├── evaluation_scripts ├── run_evaluation_acdc.sh ├── run_evaluation_lung.sh ├── run_evaluation_synapse.sh └── run_evaluation_tumor.sh ├── media ├── UNETR++_Block_Diagram.jpg ├── UNETR++_results_fig_synapse.jpg ├── acdc_results.png ├── acdc_vs_unetr_suppl.jpg ├── intro_fig.png └── synapse_results.png ├── requirements.txt ├── training_scripts ├── run_training_acdc.sh ├── run_training_lung.sh ├── run_training_synapse.sh └── run_training_tumor.sh └── unetr_pp ├── __init__.py ├── configuration.py ├── 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 ├── unetr_pp_acdc_checkpoint │ └── unetr_pp │ │ └── 3d_fullres │ │ └── Task001_ACDC │ │ └── unetr_pp_trainer_acdc__unetr_pp_Plansv2.1 │ │ └── fold_0 │ │ └── .gitignore ├── unetr_pp_lung_checkpoint │ └── unetr_pp │ │ └── 3d_fullres │ │ └── Task006_Lung │ │ └── unetr_pp_trainer_lung__unetr_pp_Plansv2.1 │ │ └── fold_0 │ │ └── .gitignore ├── unetr_pp_synapse_checkpoint │ └── unetr_pp │ │ └── 3d_fullres │ │ └── Task002_Synapse │ │ └── unetr_pp_trainer_synapse__unetr_pp_Plansv2.1 │ │ └── fold_0 │ │ └── .gitignore └── unetr_pp_tumor_checkpoint │ └── unetr_pp │ └── 3d_fullres │ └── Task003_tumor │ └── unetr_pp_trainer_tumor__unetr_pp_Plansv2.1 │ └── fold_0 │ └── .gitignore ├── experiment_planning ├── DatasetAnalyzer.py ├── __init__.py ├── alternative_experiment_planning │ ├── experiment_planner_baseline_3DUNet_v21_11GB.py │ ├── experiment_planner_baseline_3DUNet_v21_16GB.py │ ├── experiment_planner_baseline_3DUNet_v21_32GB.py │ ├── experiment_planner_baseline_3DUNet_v21_3convperstage.py │ ├── experiment_planner_baseline_3DUNet_v22.py │ ├── experiment_planner_baseline_3DUNet_v23.py │ ├── experiment_planner_residual_3DUNet_v21.py │ ├── normalization │ │ ├── experiment_planner_2DUNet_v21_RGB_scaleto_0_1.py │ │ ├── experiment_planner_3DUNet_CT2.py │ │ └── experiment_planner_3DUNet_nonCT.py │ ├── patch_size │ │ ├── experiment_planner_3DUNet_isotropic_in_mm.py │ │ └── experiment_planner_3DUNet_isotropic_in_voxels.py │ ├── pooling_and_convs │ │ ├── experiment_planner_baseline_3DUNet_allConv3x3.py │ │ └── experiment_planner_baseline_3DUNet_poolBasedOnSpacing.py │ └── target_spacing │ │ ├── experiment_planner_baseline_3DUNet_targetSpacingForAnisoAxis.py │ │ ├── experiment_planner_baseline_3DUNet_v21_customTargetSpacing_2x2x2.py │ │ └── experiment_planner_baseline_3DUNet_v21_noResampling.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 ├── nnFormer_convert_decathlon_task.py ├── nnFormer_plan_and_preprocess.py ├── summarize_plans.py └── utils.py ├── inference ├── __init__.py ├── inferTs │ └── swin_nomask_2 │ │ └── plans.pkl ├── predict.py ├── predict_simple.py └── segmentation_export.py ├── inference_acdc.py ├── inference_synapse.py ├── inference_tumor.py ├── network_architecture ├── README.md ├── __init__.py ├── acdc │ ├── __init__.py │ ├── model_components.py │ ├── transformerblock.py │ └── unetr_pp_acdc.py ├── dynunet_block.py ├── generic_UNet.py ├── initialization.py ├── layers.py ├── lung │ ├── __init__.py │ ├── model_components.py │ ├── transformerblock.py │ └── unetr_pp_lung.py ├── neural_network.py ├── synapse │ ├── __init__.py │ ├── model_components.py │ ├── transformerblock.py │ └── unetr_pp_synapse.py └── tumor │ ├── __init__.py │ ├── model_components.py │ ├── transformerblock.py │ └── unetr_pp_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 ├── run ├── __init__.py ├── default_configuration.py └── run_training.py ├── training ├── __init__.py ├── cascade_stuff │ ├── __init__.py │ └── predict_next_stage.py ├── data_augmentation │ ├── __init__.py │ ├── custom_transforms.py │ ├── data_augmentation_insaneDA.py │ ├── data_augmentation_insaneDA2.py │ ├── data_augmentation_moreDA.py │ ├── data_augmentation_noDA.py │ ├── default_data_augmentation.py │ ├── downsampling.py │ └── pyramid_augmentations.py ├── dataloading │ ├── __init__.py │ └── dataset_loading.py ├── learning_rate │ └── poly_lr.py ├── loss_functions │ ├── TopK_loss.py │ ├── __init__.py │ ├── crossentropy.py │ ├── deep_supervision.py │ └── dice_loss.py ├── model_restore.py ├── network_training │ ├── Trainer_acdc.py │ ├── Trainer_lung.py │ ├── Trainer_synapse.py │ ├── Trainer_tumor.py │ ├── network_trainer_acdc.py │ ├── network_trainer_lung.py │ ├── network_trainer_synapse.py │ ├── network_trainer_tumor.py │ ├── unetr_pp_trainer_acdc.py │ ├── unetr_pp_trainer_lung.py │ ├── unetr_pp_trainer_synapse.py │ └── unetr_pp_trainer_tumor.py └── optimizer │ └── ranger.py └── utilities ├── __init__.py ├── distributed.py ├── file_conversions.py ├── file_endings.py ├── folder_names.py ├── nd_softmax.py ├── one_hot_encoding.py ├── overlay_plots.py ├── random_stuff.py ├── recursive_delete_npz.py ├── recursive_rename_taskXX_to_taskXXX.py ├── sitk_stuff.py ├── task_name_id_conversion.py ├── tensor_utilities.py └── to_torch.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Amshaker/unetr_plus_plus/HEAD/LICENSE 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