├── .DS_Store ├── LICENSE ├── README.md ├── benchmark_backbones ├── README.md ├── dataset │ ├── dataloader_bdmap.py │ ├── dataset_list │ │ ├── .DS_Store │ │ ├── AbdomenAtlas1.0.txt │ │ └── AbdomenAtlas1.1.txt │ └── utils.py ├── hg.sh ├── logs │ └── README.md ├── model │ ├── SwinUNETR.py │ ├── __pycache__ │ │ ├── SwinUNETR.cpython-38.pyc │ │ └── unet3d.cpython-38.pyc │ └── unet3d.py ├── optimizers │ ├── __pycache__ │ │ ├── lr_scheduler.cpython-38.pyc │ │ └── lr_scheduler.cpython-39.pyc │ └── lr_scheduler.py ├── out │ ├── .DS_Store │ └── README.md ├── requirements.txt ├── train.py └── utils │ ├── loss.py │ └── utils.py ├── direct_inference ├── README.md ├── dataset │ ├── dataloader_test.py │ └── utils.py ├── hg.sh ├── inference.py ├── logs │ └── README.md ├── model │ ├── DiNTS.py │ ├── SwinUNETR.py │ ├── SwinUNETR_target.py │ ├── Unet.py │ └── Universal_model.py ├── pretrained_checkpoints │ └── README.md ├── utils │ └── utils.py └── vertebrae.md ├── document ├── BodyMapsLogo.png ├── LetsSegmentVertebrae.png ├── awesome_medical_backbone.md ├── awesome_medical_pretraining.md ├── awesome_medical_segment_anything.md ├── dom_wse_poster.pdf ├── fig_benchmark.png ├── fig_suprem_logo.png ├── frequently_asked_questions.md ├── promotion_slides.pdf ├── rsna2023_slides.pdf ├── rsna2024_slides.pdf ├── rsna_abstract.pdf ├── social_preview.jpeg └── social_preview.pptx ├── requirements.txt ├── supervised_pretraining ├── README.md ├── backbone │ ├── DiNTS.py │ ├── Universal_model.py │ ├── swinunetr.py │ └── unet.py ├── dataset │ ├── dataloader_bdmap.py │ ├── dataset_list │ │ ├── AbdomenAtlas1.0.txt │ │ └── AbdomenAtlas1.1.txt │ └── utils.py ├── logs │ └── README.md ├── optimizers │ └── lr_scheduler.py ├── pretrained_weights │ ├── txt_encoding_abdomenatlas1.0.pth │ └── txt_encoding_abdomenatlas1.1.pth ├── requirements.txt ├── run.sh ├── shell_scripts │ ├── train_abdomenatlas1.0_multigpu.sh │ ├── train_abdomenatlas1.0_singlegpu.sh │ ├── train_abdomenatlas1.1_multigpu.sh │ └── train_abdomenatlas1.1_singlegpu.sh ├── train.py └── utils │ ├── loss.py │ └── utils.py ├── target_applications ├── .DS_Store ├── imagecas │ ├── README.md │ ├── dataset │ │ ├── ImageCAS_ID.txt │ │ ├── dataloader.py │ │ ├── dataset_list │ │ │ ├── .DS_Store │ │ │ ├── test_1.txt │ │ │ ├── test_2.txt │ │ │ ├── test_3.txt │ │ │ ├── test_4.txt │ │ │ ├── test_5.txt │ │ │ ├── train_1.txt │ │ │ ├── train_2.txt │ │ │ ├── train_3.txt │ │ │ ├── train_4.txt │ │ │ ├── train_5.txt │ │ │ └── val.txt │ │ └── utils.py │ ├── hg.sh │ ├── logs │ │ └── README.md │ ├── model │ │ ├── DIYnnu │ │ │ ├── diynnu │ │ │ │ ├── __init__.py │ │ │ │ ├── configuration.py │ │ │ │ ├── inference │ │ │ │ │ ├── Inference_final.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── checkpoints │ │ │ │ │ │ ├── all │ │ │ │ │ │ │ ├── model_best.model.pkl │ │ │ │ │ │ │ └── progress.png │ │ │ │ │ │ └── plans.pkl │ │ │ │ │ ├── predict.py │ │ │ │ │ └── predict_simple.py │ │ │ │ ├── network_architecture │ │ │ │ │ ├── MiT_eccv.py │ │ │ │ │ ├── MiT_encoder_eccv.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── neural_network.py │ │ │ │ │ └── utils.py │ │ │ │ ├── run │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_configuration.py │ │ │ │ │ └── run_training.py │ │ │ │ └── training │ │ │ │ │ ├── .DS_Store │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── model_restore.py │ │ │ │ │ └── network_training │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── network_trainer.py │ │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ │ ├── nnUNetTrainerCascadeFullRes.py │ │ │ │ │ ├── nnUNetTrainerV2_CascadeFullRes.py │ │ │ │ │ └── nnUNetTrainerV2_ResTrans.py │ │ │ └── setup.py │ │ ├── SwinUNETR.py │ │ ├── configs.py │ │ ├── networkarch.py │ │ ├── nnUNet │ │ │ ├── .DS_Store │ │ │ ├── .gitignore │ │ │ ├── LICENSE │ │ │ ├── documentation │ │ │ │ ├── common_problems_and_solutions.md │ │ │ │ ├── common_questions.md │ │ │ │ ├── data_format_inference.md │ │ │ │ ├── dataset_conversion.md │ │ │ │ ├── expected_epoch_times.md │ │ │ │ ├── extending_nnunet.md │ │ │ │ ├── inference_example_Prostate.md │ │ │ │ ├── setting_up_paths.md │ │ │ │ ├── training_example_Hippocampus.md │ │ │ │ └── using_nnUNet_as_baseline.md │ │ │ ├── nnunet │ │ │ │ ├── .DS_Store │ │ │ │ ├── __init__.py │ │ │ │ ├── configuration.py │ │ │ │ ├── dataset_conversion │ │ │ │ │ ├── Task017_BeyondCranialVaultAbdominalOrganSegmentation.py │ │ │ │ │ ├── Task024_Promise2012.py │ │ │ │ │ ├── Task027_AutomaticCardiacDetectionChallenge.py │ │ │ │ │ ├── Task029_LiverTumorSegmentationChallenge.py │ │ │ │ │ ├── Task032_BraTS_2018.py │ │ │ │ │ ├── Task035_ISBI_MSLesionSegmentationChallenge.py │ │ │ │ │ ├── Task037_038_Chaos_Challenge.py │ │ │ │ │ ├── Task040_KiTS.py │ │ │ │ │ ├── Task043_BraTS_2019.py │ │ │ │ │ ├── Task055_SegTHOR.py │ │ │ │ │ ├── Task056_VerSe2019.py │ │ │ │ │ ├── Task056_Verse_normalize_orientation.py │ │ │ │ │ ├── Task058_ISBI_EM_SEG.py │ │ │ │ │ ├── Task059_EPFL_EM_MITO_SEG.py │ │ │ │ │ ├── Task061_CREMI.py │ │ │ │ │ ├── Task062_NIHPancreas.py │ │ │ │ │ ├── Task064_KiTS_labelsFixed.py │ │ │ │ │ ├── Task065_KiTS_NicksLabels.py │ │ │ │ │ ├── Task069_CovidSeg.py │ │ │ │ │ ├── Task075_Fluo_C3DH_A549_ManAndSim.py │ │ │ │ │ ├── Task076_Fluo_N3DH_SIM.py │ │ │ │ │ ├── Task082_BraTS_2020.py │ │ │ │ │ ├── Task089_Fluo-N2DH-SIM.py │ │ │ │ │ ├── Task114_heart_MNMs.py │ │ │ │ │ └── __init__.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 │ │ │ │ ├── experiment_planning │ │ │ │ │ ├── DatasetAnalyzer.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── alternative_experiment_planning │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── experiment_planner_baseline_3DUNet_v21_11GB.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 │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── experiment_planner_3DUNet_CT2.py │ │ │ │ │ │ │ └── experiment_planner_3DUNet_nonCT.py │ │ │ │ │ │ ├── patch_size │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── experiment_planner_3DUNet_isotropic_in_mm.py │ │ │ │ │ │ │ └── experiment_planner_3DUNet_isotropic_in_voxels.py │ │ │ │ │ │ ├── pooling_and_convs │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── experiment_planner_baseline_3DUNet_allConv3x3.py │ │ │ │ │ │ │ └── experiment_planner_baseline_3DUNet_poolBasedOnSpacing.py │ │ │ │ │ │ ├── readme.md │ │ │ │ │ │ └── target_spacing │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ └── experiment_planner_baseline_3DUNet_targetSpacingForAnisoAxis.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 │ │ │ │ │ ├── nnUNet_convert_decathlon_task.py │ │ │ │ │ ├── nnUNet_plan_and_preprocess.py │ │ │ │ │ ├── old │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── old_plan_and_preprocess_task.py │ │ │ │ │ ├── summarize_plans.py │ │ │ │ │ └── utils.py │ │ │ │ ├── inference │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── change_trainer.py │ │ │ │ │ ├── ensemble_predictions.py │ │ │ │ │ ├── predict.py │ │ │ │ │ ├── predict_simple.py │ │ │ │ │ ├── pretrained_models │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── collect_pretrained_models.py │ │ │ │ │ │ └── download_pretrained_model.py │ │ │ │ │ └── segmentation_export.py │ │ │ │ ├── network_architecture │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── custom_modules │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── conv_blocks.py │ │ │ │ │ │ ├── feature_response_normalization.py │ │ │ │ │ │ ├── helperModules.py │ │ │ │ │ │ └── mish.py │ │ │ │ │ ├── generic_UNet.py │ │ │ │ │ ├── generic_UNet_DP.py │ │ │ │ │ ├── generic_modular_UNet.py │ │ │ │ │ ├── generic_modular_residual_UNet.py │ │ │ │ │ ├── initialization.py │ │ │ │ │ └── neural_network.py │ │ │ │ ├── paths.py │ │ │ │ ├── postprocessing │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── connected_components.py │ │ │ │ │ ├── consolidate_all_for_paper.py │ │ │ │ │ ├── consolidate_postprocessing.py │ │ │ │ │ └── consolidate_postprocessing_simple.py │ │ │ │ ├── preprocessing │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── cropping.py │ │ │ │ │ ├── preprocessing.py │ │ │ │ │ └── sanity_checks.py │ │ │ │ ├── run │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── default_configuration.py │ │ │ │ │ ├── run_training.py │ │ │ │ │ ├── run_training_DDP.py │ │ │ │ │ └── run_training_DP.py │ │ │ │ ├── training │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── cascade_stuff │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── predict_next_stage.py │ │ │ │ │ ├── data_augmentation │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── custom_transforms.py │ │ │ │ │ │ ├── default_data_augmentation.py │ │ │ │ │ │ ├── downsampling.py │ │ │ │ │ │ └── pyramid_augmentations.py │ │ │ │ │ ├── dataloading │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── dataset_loading.py │ │ │ │ │ ├── learning_rate │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── poly_lr.py │ │ │ │ │ ├── loss_functions │ │ │ │ │ │ ├── TopK_loss.py │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── crossentropy.py │ │ │ │ │ │ ├── deep_supervision.py │ │ │ │ │ │ └── dice_loss.py │ │ │ │ │ ├── model_restore.py │ │ │ │ │ ├── network_training │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── competitions_with_custom_Trainers │ │ │ │ │ │ │ ├── BraTS2020 │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ ├── nnUNetTrainerV2BraTSRegions.py │ │ │ │ │ │ │ │ └── nnUNetTrainerV2BraTSRegions_moreDA.py │ │ │ │ │ │ │ ├── MMS │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ └── nnUNetTrainerV2_MMS.py │ │ │ │ │ │ │ └── __init__.py │ │ │ │ │ │ ├── network_trainer.py │ │ │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ │ │ ├── nnUNetTrainerCascadeFullRes.py │ │ │ │ │ │ ├── nnUNetTrainerV2.py │ │ │ │ │ │ ├── nnUNetTrainerV2_CascadeFullRes.py │ │ │ │ │ │ ├── nnUNetTrainerV2_DDP.py │ │ │ │ │ │ ├── nnUNetTrainerV2_DP.py │ │ │ │ │ │ ├── nnUNetTrainerV2_fp32.py │ │ │ │ │ │ └── nnUNet_variants │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── architectural_variants │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_3ConvPerStage.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_3ConvPerStage_samefilters.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_BN.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_FRN.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_GN.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_GeLU.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_LReLU_slope_2en1.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Mish.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_NoNormalization.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_NoNormalization_lr1en3.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ReLU.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ReLU_biasInSegOutput.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ReLU_convReLUIN.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ResencUNet.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_allConv3x3.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_lReLU_biasInSegOutput.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_lReLU_convlReLUIN.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_noDeepSupervision.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_softDeepSupervision.py │ │ │ │ │ │ │ ├── cascade │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2CascadeFullRes_DAVariants.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2CascadeFullRes_lowerLR.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2CascadeFullRes_shorter.py │ │ │ │ │ │ │ └── nnUNetTrainerV2CascadeFullRes_shorter_lowerLR.py │ │ │ │ │ │ │ ├── copies │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_copies.py │ │ │ │ │ │ │ ├── data_augmentation │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_DA2.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_DA3.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_independentScalePerAxis.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_insaneDA.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_noDA.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_noMirroring.py │ │ │ │ │ │ │ ├── loss_function │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ForceBD.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_ForceSD.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_CE.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_CEGDL.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_Dice.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_DiceTopK10.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_Dice_lr1en3.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_Dice_squared.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_MCC.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Loss_TopK10.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_focalLoss.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_graduallyTransitionFromCEToDice.py │ │ │ │ │ │ │ ├── miscellaneous │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_fullEvals.py │ │ │ │ │ │ │ ├── nnUNetTrainerCE.py │ │ │ │ │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ │ │ │ │ ├── optimizer_and_lr │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Adam.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Adam_ReduceOnPlateau.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Adam_lr_3en4.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Ranger_lr1en2.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Ranger_lr3en3.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_Ranger_lr3en4.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_SGD_ReduceOnPlateau.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_SGD_fixedSchedule.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_SGD_fixedSchedule2.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_SGD_lrs.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_cycleAtEnd.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_fp16.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_momentum09.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_momentum095.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_momentum098.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_momentum09in2D.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_reduceMomentumDuringTraining.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_warmup.py │ │ │ │ │ │ │ ├── profiling │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── nnUNetTrainerV2_2epochs.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_dummyLoad.py │ │ │ │ │ │ │ └── resampling │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_resample33.py │ │ │ │ │ └── optimizer │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ └── ranger.py │ │ │ │ └── utilities │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── distributed.py │ │ │ │ │ ├── file_conversions.py │ │ │ │ │ ├── file_endings.py │ │ │ │ │ ├── folder_names.py │ │ │ │ │ ├── nd_softmax.py │ │ │ │ │ ├── one_hot_encoding.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 │ │ │ ├── readme.md │ │ │ ├── setup.cfg │ │ │ ├── setup.py │ │ │ └── tests │ │ │ │ └── test_steps_for_sliding_window_prediction.py │ │ └── unet3d.py │ ├── optimizers │ │ └── lr_scheduler.py │ ├── pretrained_weights │ │ └── README.md │ ├── run.sh │ ├── test.py │ ├── train.py │ └── utils │ │ ├── .DS_Store │ │ ├── generate_model_medical_net.py │ │ ├── loss.py │ │ ├── resnet.py │ │ ├── utils.py │ │ ├── utils_CLIP.py │ │ └── utils_test.py ├── pancreas_tumor_detection │ ├── README.md │ ├── dataset │ │ ├── .DS_Store │ │ ├── dataloader.py │ │ └── dataset_list │ │ │ ├── .DS_Store │ │ │ ├── jhh_test.txt │ │ │ ├── jhh_train.txt │ │ │ ├── jhh_train_mini.txt │ │ │ └── split_test_into_multiple_files.py │ ├── document │ │ ├── .DS_Store │ │ ├── roc_curve.png │ │ └── roc_curve_zoomin.png │ ├── eval.py │ ├── inference.py │ ├── logs │ │ ├── .DS_Store │ │ └── README.md │ ├── model │ │ ├── .DS_Store │ │ ├── SwinUNETR.py │ │ └── unet3d.py │ ├── optimizers │ │ ├── .DS_Store │ │ └── lr_scheduler.py │ ├── pretrained_weights │ │ ├── .DS_Store │ │ └── README.md │ ├── run.sh │ ├── shell_scripts │ │ ├── .DS_Store │ │ ├── step1.train.multigpu.sh │ │ ├── step1.train.singlegpu.sh │ │ ├── step2.inference.multigpu.sh │ │ ├── step2.inference.singlegpu.sh │ │ └── step3.eval.sh │ ├── train.py │ └── utils │ │ ├── .DS_Store │ │ ├── plot_roc_curve │ │ ├── .DS_Store │ │ ├── patientID_pr_gt_pos_flag.csv │ │ └── plot_roc_curve.py │ │ └── utils_test.py ├── pancreas_tumor_detection_5foldCV │ ├── .DS_Store │ ├── README.md │ ├── cufile.log │ ├── dataset │ │ ├── .DS_Store │ │ ├── __pycache__ │ │ │ └── dataloader.cpython-38.pyc │ │ ├── dataloader.py │ │ └── dataset_list │ │ │ ├── .DS_Store │ │ │ ├── cv_datalist.py │ │ │ ├── jhh_test.txt │ │ │ ├── jhh_test_fold_0.txt │ │ │ ├── jhh_test_fold_1.txt │ │ │ ├── jhh_test_fold_2.txt │ │ │ ├── jhh_test_fold_3.txt │ │ │ ├── jhh_test_fold_4.txt │ │ │ ├── jhh_train.txt │ │ │ ├── jhh_train_fold_0.txt │ │ │ ├── jhh_train_fold_1.txt │ │ │ ├── jhh_train_fold_2.txt │ │ │ ├── jhh_train_fold_3.txt │ │ │ ├── jhh_train_fold_4.txt │ │ │ ├── jhh_train_mini.txt │ │ │ └── split_test_into_multiple_files.py │ ├── document │ │ ├── .DS_Store │ │ ├── roc_curve.png │ │ └── roc_curve_zoomin.png │ ├── eval.py │ ├── inference.py │ ├── logs │ │ ├── .DS_Store │ │ └── README.md │ ├── model │ │ ├── .DS_Store │ │ ├── SwinUNETR.py │ │ ├── __pycache__ │ │ │ ├── SwinUNETR.cpython-38.pyc │ │ │ └── unet3d.cpython-38.pyc │ │ └── unet3d.py │ ├── optimizers │ │ ├── .DS_Store │ │ ├── __pycache__ │ │ │ └── lr_scheduler.cpython-38.pyc │ │ └── lr_scheduler.py │ ├── pretrained_weights │ │ ├── .DS_Store │ │ └── README.md │ ├── run.sh │ ├── shell_scripts │ │ ├── step1.train.multigpu.sh │ │ ├── step2.inference.multigpu.sh │ │ └── step3.eval.sh │ ├── train.py │ └── utils │ │ ├── .DS_Store │ │ └── utils_test.py └── totalsegmentator │ ├── .DS_Store │ ├── README.md │ ├── dataset │ ├── .DS_Store │ ├── __pycache__ │ │ ├── dataloader.cpython-39.pyc │ │ └── dataloader_original.cpython-39.pyc │ ├── dataloader.py │ ├── dataloader_original.py │ ├── dataset_list │ │ ├── .DS_Store │ │ ├── .ipynb_checkpoints │ │ │ └── split_dataset-checkpoint.ipynb │ │ ├── test.txt │ │ ├── train.txt │ │ ├── train_1024.txt │ │ ├── train_1081.txt │ │ ├── train_128.txt │ │ ├── train_256.txt │ │ ├── train_512.txt │ │ ├── train_64.txt │ │ └── val.txt │ └── utils.py │ ├── hg.sh │ ├── logs │ └── README.md │ ├── model │ ├── .DS_Store │ ├── SwinUNETR.py │ ├── __pycache__ │ │ ├── SwinUNETR.cpython-39.pyc │ │ └── unet3d.cpython-39.pyc │ └── unet3d.py │ ├── optimizers │ ├── __pycache__ │ │ └── lr_scheduler.cpython-39.pyc │ └── lr_scheduler.py │ ├── pretrained_weights │ └── README.md │ ├── test.py │ ├── train.py │ └── 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