├── .gitignore ├── LICENSE ├── README.md ├── figs └── TumorCP.png └── nnunet ├── __init__.py ├── configuration.py ├── cp_configs.py ├── dataset_conversion ├── Task000_KiTSbaseline.py ├── Task001_KiTSrigid.py ├── Task002_KiTSelastic.py ├── Task003_KiTSgamma.py ├── Task004_KiTSblur.py ├── Task005_KiTScopy.py ├── 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 ├── Task100_LiTSbaseline.py ├── Task101_LiTSrigid.py ├── Task102_LiTSelastic.py ├── Task103_LiTSgamma.py ├── Task104_LiTSblur.py ├── Task105_LiTScopy.py ├── Task114_heart_MNMs.py ├── Task120_Massachusetts_RoadSegm.py ├── __init__.py └── utils.py ├── eval.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_2DUNet_v21_RGB_scaleto_0_1.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 │ │ └── experiment_planner_baseline_3DUNet_v21_customTargetSpacing_2x2x2.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 ├── extract_tumors.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 ├── metrics.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 ├── custom_preprocessors │ ├── __init__.py │ └── preprocessor_scale_RGB_to_0_1.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 │ ├── 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 │ ├── __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_ImgDAObjCPAllInter.py │ ├── nnUNetTrainerV2_ObjCPAllInter.py │ ├── nnUNetTrainerV2_fp32.py │ ├── nnUNetTrainerV2_noDA.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_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 ├── 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