├── .gitignore ├── LICENSE ├── documentation ├── data_format_inference.md ├── dataset_conversion.md ├── extending_nnunet.md ├── inference_example_Prostate.md ├── setting_up_paths.md └── training_example_Hippocampus.md ├── nnUNet_architecture2.png ├── nnunet ├── __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 │ └── __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 │ ├── 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 │ │ ├── ND_Crossentropy.py │ │ ├── TopK_loss.py │ │ ├── __init__.py │ │ ├── deep_supervision.py │ │ └── dice_loss.py │ ├── model_restore.py │ ├── network_training │ │ ├── __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_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_O2.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 │ │ │ └── resampling │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerV2_resample33.py │ └── optimizer │ │ ├── __init__.py │ │ └── ranger.py └── utilities │ ├── __init__.py │ ├── distributed.py │ ├── file_endings.py │ ├── folder_names.py │ ├── nd_softmax.py │ ├── one_hot_encoding.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 ├── nnunet_complete_workflow.png ├── nnunetmec2020.ipynb ├── previous_results.png ├── readme.md ├── result.png ├── setup.cfg ├── setup.py └── tests └── test_steps_for_sliding_window_prediction.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/prateekgupta891/nnUNet/HEAD/.gitignore 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