├── .github └── workflows │ └── codespell.yml ├── .gitignore ├── LICENSE ├── coors_new.csv ├── datasets.json ├── multitalent ├── __init__.py ├── architectures │ ├── MedNeXt │ │ ├── MedNeXt.py │ │ ├── __init__.py │ │ └── blocks.py │ └── __init__.py ├── batch_running │ ├── 2023_autoPET │ │ ├── __init__.py │ │ └── collect_results_autopet.py │ ├── __init__.py │ ├── benchmarking │ │ ├── __init__.py │ │ ├── generate_benchmarking_commands.py │ │ └── summarize_benchmark_results.py │ ├── collect_results_custom_Decathlon.py │ ├── collect_results_custom_Decathlon_2d.py │ ├── generate_lsf_runs_customDecathlon.py │ ├── learning_from_sparse_annotations │ │ ├── __init__.py │ │ ├── collect_results_sparse_annotations.py │ │ ├── estimate_annotation_percentages.py │ │ ├── evaluate_low_data_regime.py │ │ ├── generate_lsf_runs_sparseSegEval.py │ │ ├── plan_and_preprocess │ │ └── plot_results.py │ ├── optimize_trainers_for_sparse_annotation │ │ ├── __init__.py │ │ ├── collect_results.py │ │ └── generate_lsf_runs.py │ └── release_trainings │ │ ├── __init__.py │ │ └── nnunetv2_v1 │ │ ├── __init__.py │ │ ├── collect_results.py │ │ └── generate_lsf_commands.py ├── configuration.py ├── dataset_conversion │ ├── Dataset021_CTAAorta.py │ ├── Dataset022_LIDC.py │ ├── Dataset023_AbdomenAtlas1_1Mini.py │ ├── Dataset027_ACDC.py │ ├── Dataset042_BraTS18.py │ ├── Dataset043_BraTS19.py │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ ├── Dataset114_MNMs.py │ ├── Dataset115_EMIDEC.py │ ├── Dataset119_ToothFairy2_All.py │ ├── Dataset120_RoadSegmentation.py │ ├── Dataset137_BraTS21.py │ ├── Dataset201_MS_Flair.py │ ├── Dataset204_stanfordbrainmetshare.py │ ├── Dataset206_crossmoda22_sourceseq.py │ ├── Dataset214_brats23_met_t1ce.py │ ├── Dataset218_Amos2022_task1.py │ ├── Dataset219_Amos2022_task2.py │ ├── Dataset220_KiTS2023.py │ ├── Dataset221_AutoPETII_2023.py │ ├── Dataset222_AutoPETII_2023_15_1_1.py │ ├── Dataset223_AMOS2022postChallenge.py │ ├── Dataset224_AbdomenAtlas1.0.py │ ├── Dataset353_hecktor2022.py │ ├── Dataset401_MBAS.py │ ├── Dataset402_MBH_SEG.py │ ├── Dataset403_Aims_tbi.py │ ├── Dataset404_isles24.py │ ├── Dataset405_brats24_task1_AGPT.py │ ├── Dataset406_brats24_task2_Africa.py │ ├── Dataset407_brats24_task3_MenRT.py │ ├── Dataset408_brats24_task4_Met.py │ ├── Dataset409_brats24_task5_Ped.py │ ├── Dataset412_UCFS_brainmet_forbrats.py │ ├── Dataset413_UCFS_brainmet_nobratsstyle.py │ ├── Dataset414_epvs.py │ ├── Dataset415_brats24_task4_Met_org.py │ ├── Dataset417_isles24_all.py │ ├── Dataset420_epvs_artificial.py │ ├── Dataset422_MBH_SEG_pseudo.py │ ├── Dataset423_instance22.py │ ├── Dataset424_brainhem.py │ ├── Dataset654_word.py │ ├── Dataset655_AbdomenCT1K.py │ ├── Dataset656_Atlas.py │ ├── Dataset657_CTORG.py │ ├── Dataset701_HanSeg.py │ ├── Dataset703_hahnsegmri.py │ ├── Dataset850_fullCoW_ct_mutilabel.py │ ├── Dataset851_fullCoW_all_mutilabel.py │ ├── Dataset980ff_ALEGRA_findStartingBudget.py │ ├── Dataset988_dummyDataset4.py │ ├── Dataset990_Daniel.py │ ├── __init__.py │ ├── balints_registration.py │ ├── convert_MSD_dataset.py │ ├── convert_raw_dataset_from_old_nnunet_format.py │ ├── datasets_for_integration_tests │ │ ├── Dataset996_IntegrationTest_Hippocampus_regions_ignore.py │ │ ├── Dataset997_IntegrationTest_Hippocampus_regions.py │ │ ├── Dataset998_IntegrationTest_Hippocampus_ignore.py │ │ ├── Dataset999_IntegrationTest_Hippocampus.py │ │ └── __init__.py │ └── generate_dataset_json.py ├── ensembling │ ├── __init__.py │ └── ensemble.py ├── evaluation │ ├── __init__.py │ ├── accumulate_cv_results.py │ ├── evaluate_predictions.py │ ├── find_best_configuration.py │ └── surface_dice.py ├── experiment_planning │ ├── __init__.py │ ├── dataset_fingerprint │ │ ├── __init__.py │ │ └── fingerprint_extractor.py │ ├── experiment_planners │ │ ├── __init__.py │ │ ├── convnextUNet_planner.py │ │ ├── default_experiment_planner.py │ │ ├── force_zscore_planner.py │ │ ├── isotropic │ │ │ ├── __init__.py │ │ │ └── isotropic_nnunet.py │ │ ├── multitalent_planners.py │ │ ├── network_topology.py │ │ ├── resampling │ │ │ ├── __init__.py │ │ │ └── resample_with_torch.py │ │ ├── resencUNet_planner.py │ │ └── residual_unets │ │ │ ├── __init__.py │ │ │ └── residual_encoder_unet_planners.py │ ├── plan_and_preprocess_api.py │ ├── plan_and_preprocess_entrypoints.py │ ├── plans_for_pretraining │ │ ├── __init__.py │ │ ├── move_plans_between_datasets.py │ │ └── move_plans_between_datasets_onlyconfig.py │ └── verify_dataset_integrity.py ├── imageio │ ├── __init__.py │ ├── base_reader_writer.py │ ├── natural_image_reader_writer.py │ ├── nibabel_reader_writer.py │ ├── reader_writer_registry.py │ ├── readme.md │ ├── simpleitk_reader_writer.py │ └── tif_reader_writer.py ├── inference │ ├── JHU_inference.py │ ├── __init__.py │ ├── data_iterators.py │ ├── examples.py │ ├── export_prediction.py │ ├── predict_from_raw_data.py │ ├── readme.md │ └── sliding_window_prediction.py ├── model_sharing │ ├── __init__.py │ ├── entry_points.py │ ├── model_download.py │ ├── model_export.py │ └── model_import.py ├── network_architecture │ ├── __init__.py │ └── hrnet │ │ ├── __init__.py │ │ └── hrnet.py ├── paths.py ├── playground │ ├── ALEGRA │ │ ├── __init__.py │ │ ├── evaluate_sparse_slicewise_annotations │ │ │ ├── __init__.py │ │ │ ├── cleanup.sh │ │ │ ├── collect_results.py │ │ │ ├── compute_annotation_percentage.py │ │ │ ├── configuration.py │ │ │ ├── generate_configurations.py │ │ │ ├── generate_splits.py │ │ │ ├── generate_train_commands.py │ │ │ ├── results │ │ │ │ ├── ALEGRA_SLICEWISE_ANNO - plot_ALEGRA.csv │ │ │ │ ├── ALEGRA_SLICEWISE_ANNO - plot_AMOS.csv │ │ │ │ ├── ALEGRA_SLICEWISE_ANNO - plot_BraTS.csv │ │ │ │ └── plot_results.py │ │ │ ├── run_commands.sh │ │ │ └── run_preprocessing.sh │ │ └── find_starting_budget │ │ │ ├── __init__.py │ │ │ ├── compute_annotation_percent.py │ │ │ ├── eval.md │ │ │ ├── eval_commands.sh │ │ │ ├── inference_commands.sh │ │ │ ├── plot_results.py │ │ │ └── train_commands.sh │ ├── T3_Nako_swaps │ │ ├── __init__.py │ │ └── playground.py │ └── __init__.py ├── postprocessing │ ├── __init__.py │ └── remove_connected_components.py ├── preprocessing │ ├── __init__.py │ ├── cropping │ │ ├── __init__.py │ │ └── cropping.py │ ├── normalization │ │ ├── __init__.py │ │ ├── default_normalization_schemes.py │ │ ├── map_channel_name_to_normalization.py │ │ └── readme.md │ ├── preprocessors │ │ ├── __init__.py │ │ ├── default_preprocessor.py │ │ └── simulate_sparse_annotations │ │ │ ├── __init__.py │ │ │ ├── blobs.py │ │ │ ├── hybrid.py │ │ │ ├── hybrid2.py │ │ │ ├── pixels.py │ │ │ └── slices.py │ └── resampling │ │ ├── __init__.py │ │ ├── default_resampling.py │ │ ├── resample_torch.py │ │ ├── softmax_on_gpu.py │ │ └── utils.py ├── run │ ├── __init__.py │ ├── load_pretrained_weights.py │ ├── load_pretrained_weights_MT.py │ ├── run_training.py │ └── run_training_MT.py ├── tests │ ├── __init__.py │ └── integration_tests │ │ ├── __init__.py │ │ ├── add_lowres_and_cascade.py │ │ ├── cleanup_integration_test.py │ │ ├── lsf_commands.sh │ │ ├── prepare_integration_tests.sh │ │ ├── readme.md │ │ ├── run_integration_test.sh │ │ ├── run_integration_test_bestconfig_inference.py │ │ └── run_integration_test_trainingOnly_DDP.sh ├── training │ ├── __init__.py │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── compute_initial_patch_size.py │ │ └── custom_transforms │ │ │ ├── __init__.py │ │ │ ├── alegra.py │ │ │ ├── cascade_transforms.py │ │ │ ├── cleaner_spatial_transform.py │ │ │ ├── deep_supervision_donwsampling.py │ │ │ ├── masking.py │ │ │ ├── region_based_training.py │ │ │ └── transforms_for_dummy_2d.py │ ├── dataloading │ │ ├── __init__.py │ │ ├── base_data_loader.py │ │ ├── data_loader_2d.py │ │ ├── data_loader_3d.py │ │ ├── nnunet_dataset.py │ │ └── utils.py │ ├── logging │ │ ├── __init__.py │ │ └── nnunet_logger.py │ ├── loss │ │ ├── Recall.py │ │ ├── __init__.py │ │ ├── compound_losses.py │ │ ├── deep_supervision.py │ │ ├── dice.py │ │ ├── focal_loss.py │ │ ├── focal_loss_2.py │ │ ├── focal_loss_3.py │ │ ├── recall_loss.py │ │ ├── rmi_loss.py │ │ └── robust_ce_loss.py │ ├── lr_scheduler │ │ ├── __init__.py │ │ └── polylr.py │ └── nnUNetTrainer │ │ ├── STUNetTrainer.py │ │ ├── __init__.py │ │ ├── nnUNetTrainer.py │ │ ├── project_specific │ │ ├── MultiTalent_native │ │ │ ├── MultiTalent_meets_mednext.py │ │ │ ├── MultiTalent_meets_nndet.py │ │ │ ├── MultiTalent_multistem.py │ │ │ ├── MultiTalent_trainer.py │ │ │ └── __init__.py │ │ ├── __init__.py │ │ └── alegra │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainer_airwayAug_new.py │ │ └── variants │ │ ├── __init__.py │ │ ├── benchmarking │ │ ├── __init__.py │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ ├── competitions │ │ ├── __init__.py │ │ └── aortaseg24.py │ │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── nnUNetTrainerDA5.py │ │ ├── nnUNetTrainerDAOrd0.py │ │ ├── nnUNetTrainerNoDA.py │ │ ├── nnUNetTrainerNoMirroring.py │ │ └── nnUNetTrainer_newSpatialAug.py │ │ ├── loss │ │ ├── __init__.py │ │ ├── nnUNetTrainerCELoss.py │ │ ├── nnUNetTrainerDiceLoss.py │ │ ├── nnUNetTrainerFocalLoss.py │ │ ├── nnUNetTrainerRMILoss.py │ │ ├── nnUNetTrainerTopkLoss.py │ │ ├── nnUNetTrainer_memEffCEDice.py │ │ ├── nnUNetTrainer_switchToDice.py │ │ └── nnUNetTrainer_v1loss.py │ │ ├── lr_schedule │ │ ├── __init__.py │ │ └── nnUNetTrainerCosAnneal.py │ │ ├── mednext │ │ ├── __init__.py │ │ └── mednext_trainer.py │ │ ├── network_architecture │ │ ├── __init__.py │ │ ├── nnUNetTrainerBN.py │ │ ├── nnUNetTrainerNoDeepSupervision.py │ │ ├── nnUNetTrainer_HRNet.py │ │ └── nnUNetTrainer_convnextenc.py │ │ ├── optimizer │ │ ├── __init__.py │ │ ├── nnUNetTrainerAdam.py │ │ ├── nnUNetTrainerAdan.py │ │ └── nnUNetTrainer_lowerLR.py │ │ ├── pretraining │ │ ├── __init__.py │ │ ├── multiple_inputs_warmup.py │ │ └── pretrained_special_trainer.py │ │ ├── sampling │ │ ├── __init__.py │ │ ├── nnUNetTrainer_moreDiverseSampling.py │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ ├── sparse_labels │ │ ├── __init__.py │ │ ├── nnUNetTrainer_betterIgnoreSampling.py │ │ ├── nnUNetTrainer_fixCEAggr.py │ │ └── nnUNetTrainer_ignoreLabel_lossBalancing.py │ │ └── training_length │ │ ├── __init__.py │ │ ├── nnUNetTrainer_Xepochs.py │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py └── utilities │ ├── MultiTalent │ ├── MedNeXt_meets_MultiTalent.py │ ├── MultiTalent_architecture.py │ ├── MultiTalent_meets_nndet │ │ ├── __init__.py │ │ └── build_nndet_model.py │ ├── __init__.py │ ├── base_data_loader_MT.py │ ├── collate_MT.py │ ├── create_MT_trainingsjson.py │ ├── encoders_MT.py │ ├── get_MT_network_from_plans.py │ ├── label_splitting.py │ ├── logger.py │ └── predict_from_raw_data_multitalent.py │ ├── __init__.py │ ├── bpreg │ ├── all_res_c_10.json │ └── all_res_l_10.json │ ├── collate_outputs.py │ ├── copy_mamba_stunet_B │ ├── copy_mamba_stunet_L │ ├── copy_mamba_stunet_S │ ├── crossval_split.py │ ├── dataset_name_id_conversion.py │ ├── ddp_allgather.py │ ├── default_n_proc_DA.py │ ├── eval_all_mamba.py │ ├── file_path_utilities.py │ ├── find_class_by_name.py │ ├── get_all_resjsons.py │ ├── get_network_from_plans.py │ ├── helpers.py │ ├── json_export.py │ ├── label_handling │ ├── __init__.py │ └── label_handling.py │ ├── network_initialization.py │ ├── overlay_plots.py │ ├── plans_handling │ ├── __init__.py │ └── plans_handler.py │ └── utils.py ├── nnUNetResEncUNetLPlansIso1x1x1.json ├── pyproject.toml ├── readme.md └── setup.py /.github/workflows/codespell.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MIC-DKFZ/MultiTalent/HEAD/.github/workflows/codespell.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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