├── LICENSE ├── README.md ├── analysis ├── bootstrap_ranking.py ├── check_training_progress.ipynb ├── paper_analysis.py └── utils.py ├── assets ├── fd_figure1.svg ├── paper_table.png └── table_big_comparison_multimetric.html ├── dataset_splits ├── Dataset500_simple_fets_corruptions │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset503_BraTS19 │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset511_MnM_VendorB_train │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset514_MVSeg23 │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset515_KiTS23 │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset520_CovidLungCT │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset521_ProstateGonzalez │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset531_DoFEOpticDiscCup_512 │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset540_RETOUCH_ood=Cirrus │ ├── domain_mapping_00.json │ └── splits_final.json ├── Dataset560_OCTA500_pathology_split │ ├── domain_mapping_00.json │ └── splits_final.json └── readme.md ├── pyproject.toml ├── src └── segmentation_failures │ ├── callbacks │ ├── batch_logging.py │ ├── confidence_map_writer.py │ ├── network_graph_tb.py │ ├── prediction_writer.py │ ├── quality_estimator_monitor.py │ └── results_writer.py │ ├── conf │ ├── analysis │ │ ├── fail_thresholds │ │ │ └── fail_thresholds_general.yaml │ │ ├── failure_detection.yaml │ │ └── failure_detection_with_thresholds.yaml │ ├── backbone │ │ ├── dynamic_resencunet.yaml │ │ ├── dynamic_resencunet_deepsup.yaml │ │ ├── dynamic_resencunet_dropout.yaml │ │ ├── dynamic_unet.yaml │ │ ├── dynamic_unet_deepsup.yaml │ │ ├── dynamic_unet_dropout.yaml │ │ ├── dynamic_wideunet.yaml │ │ ├── dynamic_wideunet_dropout.yaml │ │ ├── monai_unet.yaml │ │ └── monai_unet_dropout.yaml │ ├── callbacks │ │ ├── default.yaml │ │ ├── none.yaml │ │ ├── test │ │ │ ├── confidence_saver.yaml │ │ │ ├── dummy.yaml │ │ │ ├── ensemble_prediction_saver.yaml │ │ │ ├── prediction_saver.yaml │ │ │ └── results_saver.yaml │ │ ├── train │ │ │ ├── batch_logging.yaml │ │ │ ├── model_checkpoint.yaml │ │ │ ├── prediction_saver.yaml │ │ │ ├── quality_training_monitor.yaml │ │ │ └── save_val_predictions.yaml │ │ ├── train_seg │ │ │ ├── batch_logging.yaml │ │ │ ├── model_checkpoint.yaml │ │ │ ├── prediction_saver.yaml │ │ │ ├── quality_training_monitor.yaml │ │ │ └── save_val_predictions.yaml │ │ └── validate │ │ │ ├── batch_logging.yaml │ │ │ ├── confidence_saver.yaml │ │ │ └── prediction_saver.yaml │ ├── config.yaml │ ├── csf_aggregation │ │ ├── all_simple.yaml │ │ ├── heuristic.yaml │ │ ├── radiomics.yaml │ │ └── simple_aggs │ │ │ ├── distance_weighting.yaml │ │ │ ├── foreground.yaml │ │ │ ├── mean.yaml │ │ │ ├── only_non_boundary.yaml │ │ │ ├── pairwise_gen_dice.yaml │ │ │ ├── pairwise_mean_dice.yaml │ │ │ └── patch_based.yaml │ ├── csf_image │ │ ├── mahalanobis.yaml │ │ ├── mahalanobis_gonzalez.yaml │ │ ├── quality_regression.yaml │ │ ├── vae_image_and_mask.yaml │ │ ├── vae_image_only.yaml │ │ ├── vae_iterative_surrogate.yaml │ │ └── vae_mask_only.yaml │ ├── csf_pixel │ │ ├── baseline.yaml │ │ ├── deep_ensemble.yaml │ │ └── mcdropout.yaml │ ├── datamodule │ │ ├── acdc_nnunet.yaml │ │ ├── brats19_lhgg_nnunet.yaml │ │ ├── covid_nnunet.yaml │ │ ├── dummy.yaml │ │ ├── heuristic_radiomics.yaml │ │ ├── kits23_nnunet.yaml │ │ ├── mnms_nnunet.yaml │ │ ├── mvseg23_nnunet.yaml │ │ ├── nnunet.yaml │ │ ├── octa500_nnunet.yaml │ │ ├── prostate_nnunet.yaml │ │ ├── quality_regression.yaml │ │ ├── retina_nnunet.yaml │ │ ├── retouch_cirrus_nnunet.yaml │ │ ├── retouch_spectralis_nnunet.yaml │ │ ├── retouch_topcon_nnunet.yaml │ │ ├── simple_agg.yaml │ │ ├── simple_fets22_corrupted.yaml │ │ └── vae.yaml │ ├── dataset │ │ ├── abstract.yaml │ │ ├── acdc.yaml │ │ ├── brats19_lhgg.yaml │ │ ├── covid_gonzalez.yaml │ │ ├── kits23.yaml │ │ ├── mnms.yaml │ │ ├── mvseg23.yaml │ │ ├── octa500.yaml │ │ ├── prostate_gonzalez.yaml │ │ ├── retina.yaml │ │ ├── retouch_cirrus.yaml │ │ ├── retouch_spectralis.yaml │ │ ├── retouch_topcon.yaml │ │ └── simple_fets22_corrupted.yaml │ ├── debug │ │ ├── default.yaml │ │ ├── limit_batches.yaml │ │ ├── lrfind.yaml │ │ ├── overfit.yaml │ │ └── step.yaml │ ├── hydra │ │ ├── cluster.yaml │ │ ├── debug.yaml │ │ └── local.yaml │ ├── logger │ │ ├── csv.yaml │ │ ├── default.yaml │ │ └── tensorboard.yaml │ ├── paths │ │ └── default.yaml │ ├── segmentation │ │ ├── baseline.yaml │ │ └── dynunet.yaml │ └── trainer │ │ ├── cpu.yaml │ │ └── single_gpu.yaml │ ├── data │ ├── __init__.py │ ├── corruptions │ │ ├── corrupt_data_torchio.py │ │ └── image_corruptions_tio.py │ ├── datamodules │ │ ├── __init__.py │ │ ├── additional_readers.py │ │ ├── dummy_modules.py │ │ ├── monai_modules.py │ │ ├── nnunet_module.py │ │ ├── nnunet_utils.py │ │ ├── quality_regression.py │ │ ├── simple_agg.py │ │ └── vae.py │ └── dataset_conversion │ │ ├── nnunet_acdc.py │ │ ├── nnunet_brats19.py │ │ ├── nnunet_covid.py │ │ ├── nnunet_fets22.py │ │ ├── nnunet_kits23.py │ │ ├── nnunet_mnm.py │ │ ├── nnunet_mnm2.py │ │ ├── nnunet_mvseg23.py │ │ ├── nnunet_octa500.py │ │ ├── nnunet_prostate.py │ │ ├── nnunet_retina.py │ │ ├── nnunet_retouch.py │ │ └── nnunet_simple_fets_corruptions.py │ ├── evaluation │ ├── __init__.py │ ├── experiment_data.py │ ├── failure_detection │ │ ├── __init__.py │ │ ├── fd_analysis.py │ │ └── metrics.py │ ├── ood_detection │ │ ├── __init__.py │ │ ├── metrics.py │ │ └── ood_analysis.py │ └── segmentation │ │ ├── __init__.py │ │ ├── compute_seg_metrics.py │ │ ├── custom_metrics │ │ ├── hausdorff.py │ │ └── surface_distance.py │ │ ├── distance_thresholds.py │ │ └── segmentation_metrics.py │ ├── experiments │ ├── __init__.py │ ├── cluster.py │ ├── experiment.py │ ├── experiments_paper.sh │ ├── experiments_revision_arch.sh │ ├── experiments_revision_ds_size.sh │ ├── experiments_revision_newdata.sh │ ├── launcher.py │ ├── nnunet_cluster.py │ └── prepare_auxdata.py │ ├── models │ ├── __init__.py │ ├── confidence_aggregation │ │ ├── __init__.py │ │ ├── base.py │ │ ├── heuristic.py │ │ ├── radiomics.py │ │ └── simple_agg.py │ ├── image_confidence │ │ ├── __init__.py │ │ ├── mahalanobis.py │ │ ├── regression_network.py │ │ └── vae_estimator.py │ ├── pixel_confidence │ │ ├── __init__.py │ │ ├── ensemble.py │ │ ├── posthoc.py │ │ └── scores.py │ └── segmentation │ │ ├── __init__.py │ │ ├── dynunet_module.py │ │ └── monai_segmenter.py │ ├── networks │ ├── __init__.py │ ├── dynunet.py │ ├── nnunet │ │ └── __init__.py │ └── vae │ │ ├── __init__.py │ │ ├── encoder_decoder.py │ │ ├── utils.py │ │ └── vae.py │ ├── scripts │ ├── check_dataset_splits.py │ ├── evaluate_experiment.py │ ├── prepare_data_quality_regression.py │ ├── test_fd.py │ ├── test_pixel_csf.py │ ├── train_image_csf.py │ ├── train_seg.py │ └── validate_pixel_csf.py │ └── utils │ ├── __init__.py │ ├── checkpointing.py │ ├── config_handling.py │ ├── data.py │ ├── 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