├── LICENSE ├── README.md ├── TriALS_2025_Interactive_Task_2 ├── baseline_interactive_task │ ├── README.md │ ├── requirements.txt │ └── sw_fastedit_src │ │ ├── __init__.py │ │ ├── simplified_inference.py │ │ ├── sw_fastedit │ │ ├── __init__.py │ │ ├── api.py │ │ ├── click_definitions.py │ │ ├── data.py │ │ ├── helper_transforms.py │ │ ├── interaction.py │ │ ├── transforms.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── argparser.py │ │ │ ├── calc_metric.py │ │ │ ├── compute_auc_final.py │ │ │ ├── distance_transform.py │ │ │ ├── helper.py │ │ │ ├── logger.py │ │ │ ├── simulate_clicks_TriALS.py │ │ │ ├── surface.py │ │ │ └── tensorboard_logger.py │ │ └── train.py ├── docker │ ├── ReadME.md │ ├── media │ │ ├── docker-image-select-evaluation-queue.png │ │ ├── docker-image-submit-to-challenge.png │ │ ├── project-docker-registry-view.png │ │ └── show-page-outline.png │ └── template_interactive │ │ ├── Dockerfile │ │ ├── sample-test-data │ │ ├── clicks │ │ │ ├── venous_0_clicks.json │ │ │ └── venous_11_clicks.json │ │ ├── ground_truth │ │ │ ├── venous_0.nii.gz │ │ │ └── venous_11.nii.gz │ │ └── test.csv │ │ └── src │ │ ├── Model.py │ │ ├── main.py │ │ ├── requirements.txt │ │ ├── run.sh │ │ ├── setup_.py │ │ └── sw_fastedit_src │ │ ├── __init__.py │ │ ├── simplified_inference.py │ │ ├── sw_fastedit │ │ ├── __init__.py │ │ ├── api.py │ │ ├── click_definitions.py │ │ ├── data.py │ │ ├── helper_transforms.py │ │ ├── interaction.py │ │ ├── transforms.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── argparser.py │ │ │ ├── calc_metric.py │ │ │ ├── compute_auc_final.py │ │ │ ├── distance_transform.py │ │ │ ├── helper.py │ │ │ ├── logger.py │ │ │ ├── simulate_clicks_TriALS.py │ │ │ ├── surface.py │ │ │ └── tensorboard_logger.py │ │ └── train.py └── eval_scripts_interactive_task │ ├── README.md │ ├── evaluate.py │ └── requirements.txt ├── checkpoints └── .gitignore ├── data ├── nnUNet_preprocessed │ ├── .gitignore │ └── Dataset003_Liver │ │ ├── nnUNetPlans.json │ │ └── splits_final.json ├── nnUNet_raw_data_base │ └── .gitignore └── nnUNet_results │ └── .gitignore ├── docker ├── ReadME.md ├── media │ ├── docker-image-select-evaluation-queue.png │ ├── docker-image-submit-to-challenge.png │ ├── project-docker-registry-view.png │ └── show-page-outline.png └── template │ ├── Dockerfile │ ├── sample-test-data │ ├── ground_truth │ │ ├── venous_0.nii.gz │ │ └── venous_11.nii.gz │ ├── team-check │ │ └── predictions │ │ │ ├── venous_0.nii.gz │ │ │ └── venous_11.nii.gz │ └── test.csv │ └── src │ ├── Model.py │ ├── main.py │ ├── nnUNet_results │ └── Dataset102_TriALS │ │ └── .gitignore │ ├── nnunetv2 │ ├── __init__.py │ ├── batch_running │ │ ├── __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 │ │ └── release_trainings │ │ │ ├── __init__.py │ │ │ └── nnunetv2_v1 │ │ │ ├── __init__.py │ │ │ ├── collect_results.py │ │ │ └── generate_lsf_commands.py │ ├── configuration.py │ ├── dataset_conversion │ │ ├── Dataset027_ACDC.py │ │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ │ ├── Dataset114_MNMs.py │ │ ├── Dataset115_EMIDEC.py │ │ ├── Dataset120_RoadSegmentation.py │ │ ├── Dataset137_BraTS21.py │ │ ├── Dataset218_Amos2022_task1.py │ │ ├── Dataset219_Amos2022_task2.py │ │ ├── Dataset220_KiTS2023.py │ │ ├── Dataset221_AutoPETII_2023.py │ │ ├── Dataset988_dummyDataset4.py │ │ ├── __init__.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 │ ├── experiment_planning │ │ ├── __init__.py │ │ ├── dataset_fingerprint │ │ │ ├── __init__.py │ │ │ └── fingerprint_extractor.py │ │ ├── experiment_planners │ │ │ ├── __init__.py │ │ │ ├── default_experiment_planner.py │ │ │ ├── network_topology.py │ │ │ ├── readme.md │ │ │ └── resencUNet_planner.py │ │ ├── plan_and_preprocess_api.py │ │ ├── plan_and_preprocess_entrypoints.py │ │ ├── plans_for_pretraining │ │ │ ├── __init__.py │ │ │ └── move_plans_between_datasets.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 │ │ ├── __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 │ ├── nets │ │ ├── LightMUNet.py │ │ ├── UMambaBot.py │ │ ├── UMambaEnc.py │ │ ├── __init__.py │ │ ├── mednextv1 │ │ │ ├── MedNextV1.py │ │ │ ├── __init__.py │ │ │ ├── blocks.py │ │ │ └── create_mednext_v1.py │ │ ├── sam_lora_image_encoder.py │ │ └── segment_anything │ │ │ ├── __init__.py │ │ │ ├── automatic_mask_generator.py │ │ │ ├── build_sam.py │ │ │ ├── modeling │ │ │ ├── __init__.py │ │ │ ├── common.py │ │ │ ├── image_encoder.py │ │ │ ├── mask_decoder.py │ │ │ ├── prompt_encoder.py │ │ │ ├── sam.py │ │ │ └── transformer.py │ │ │ ├── predictor.py │ │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── amg.py │ │ │ ├── onnx.py │ │ │ └── transforms.py │ ├── paths.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 │ │ └── resampling │ │ │ ├── __init__.py │ │ │ ├── default_resampling.py │ │ │ └── utils.py │ ├── run │ │ ├── __init__.py │ │ ├── load_pretrained_weights.py │ │ └── run_training.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 │ │ │ │ ├── cascade_transforms.py │ │ │ │ ├── deep_supervision_donwsampling.py │ │ │ │ ├── limited_length_multithreaded_augmenter.py │ │ │ │ ├── manipulating_data_dict.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 │ │ │ ├── __init__.py │ │ │ ├── compound_losses.py │ │ │ ├── deep_supervision.py │ │ │ ├── dice.py │ │ │ └── robust_ce_loss.py │ │ ├── lr_scheduler │ │ │ ├── __init__.py │ │ │ ├── polylr.py │ │ │ └── samedlr.py │ │ └── nnUNetTrainer │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainer.py │ │ │ ├── nnUNetTrainerLightMUNet.py │ │ │ ├── nnUNetTrainerMedNext.py │ │ │ ├── nnUNetTrainerSAMed.py │ │ │ ├── nnUNetTrainerSegResNet.py │ │ │ ├── nnUNetTrainerSwinUNETR.py │ │ │ ├── nnUNetTrainerUMambaBot.py │ │ │ ├── nnUNetTrainerUMambaEnc.py │ │ │ ├── nnUNetTrainerUNETR.py │ │ │ └── variants │ │ │ ├── __init__.py │ │ │ ├── benchmarking │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ │ ├── data_augmentation │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerDA5.py │ │ │ ├── nnUNetTrainerDAOrd0.py │ │ │ ├── nnUNetTrainerNoDA.py │ │ │ └── nnUNetTrainerNoMirroring.py │ │ │ ├── loss │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerCELoss.py │ │ │ ├── nnUNetTrainerDiceLoss.py │ │ │ └── nnUNetTrainerTopkLoss.py │ │ │ ├── lr_schedule │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainerCosAnneal.py │ │ │ ├── network_architecture │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerBN.py │ │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ │ ├── optimizer │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainerAdam.py │ │ │ └── nnUNetTrainerAdan.py │ │ │ ├── sampling │ │ │ ├── __init__.py │ │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ │ └── training_length │ │ │ ├── __init__.py │ │ │ ├── nnUNetTrainer_Xepochs.py │ │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py │ └── utilities │ │ ├── __init__.py │ │ ├── collate_outputs.py │ │ ├── dataset_name_id_conversion.py │ │ ├── ddp_allgather.py │ │ ├── default_n_proc_DA.py │ │ ├── file_path_utilities.py │ │ ├── find_class_by_name.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 │ ├── run.sh │ └── setup.py ├── eval_scripts ├── LiTS_metrics_summary.csv ├── LiTS_metrics_summary_1000epochs.csv ├── README.md ├── __init__.py ├── evaluate.py ├── helpers │ ├── __init__.py │ ├── calc_metric.py │ ├── surface.py │ └── utils.py ├── metrics │ └── team-check │ │ ├── metrics.csv │ │ └── per_case_metrics.csv └── requirements.txt ├── main.py ├── nnunetv2 ├── __init__.py ├── batch_running │ ├── __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 │ └── release_trainings │ │ ├── __init__.py │ │ └── nnunetv2_v1 │ │ ├── __init__.py │ │ ├── collect_results.py │ │ └── generate_lsf_commands.py ├── configuration.py ├── dataset_conversion │ ├── Dataset027_ACDC.py │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ ├── Dataset114_MNMs.py │ ├── Dataset115_EMIDEC.py │ ├── Dataset120_RoadSegmentation.py │ ├── Dataset137_BraTS21.py │ ├── Dataset218_Amos2022_task1.py │ ├── Dataset219_Amos2022_task2.py │ ├── Dataset220_KiTS2023.py │ ├── Dataset221_AutoPETII_2023.py │ ├── Dataset260_TriALS_task2.py │ ├── Dataset988_dummyDataset4.py │ ├── __init__.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 ├── experiment_planning │ ├── __init__.py │ ├── dataset_fingerprint │ │ ├── __init__.py │ │ └── fingerprint_extractor.py │ ├── experiment_planners │ │ ├── __init__.py │ │ ├── default_experiment_planner.py │ │ ├── network_topology.py │ │ ├── readme.md │ │ └── resencUNet_planner.py │ ├── plan_and_preprocess_api.py │ ├── plan_and_preprocess_entrypoints.py │ ├── plans_for_pretraining │ │ ├── __init__.py │ │ └── move_plans_between_datasets.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 │ ├── __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 ├── nets │ ├── LightMUNet.py │ ├── UMambaBot.py │ ├── UMambaEnc.py │ ├── mednextv1 │ │ ├── MedNextV1.py │ │ ├── __init__.py │ │ ├── blocks.py │ │ └── create_mednext_v1.py │ ├── sam_lora_image_encoder.py │ └── segment_anything │ │ ├── __init__.py │ │ ├── automatic_mask_generator.py │ │ ├── build_sam.py │ │ ├── modeling │ │ ├── __init__.py │ │ ├── common.py │ │ ├── image_encoder.py │ │ ├── mask_decoder.py │ │ ├── prompt_encoder.py │ │ ├── sam.py │ │ └── transformer.py │ │ ├── predictor.py │ │ └── utils │ │ ├── __init__.py │ │ ├── amg.py │ │ ├── onnx.py │ │ └── transforms.py ├── paths.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 │ └── resampling │ │ ├── __init__.py │ │ ├── default_resampling.py │ │ └── utils.py ├── run │ ├── __init__.py │ ├── load_pretrained_weights.py │ └── run_training.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 │ │ │ ├── cascade_transforms.py │ │ │ ├── deep_supervision_donwsampling.py │ │ │ ├── limited_length_multithreaded_augmenter.py │ │ │ ├── manipulating_data_dict.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 │ │ ├── __init__.py │ │ ├── compound_losses.py │ │ ├── deep_supervision.py │ │ ├── dice.py │ │ └── robust_ce_loss.py │ ├── lr_scheduler │ │ ├── __init__.py │ │ ├── polylr.py │ │ └── samedlr.py │ └── nnUNetTrainer │ │ ├── __init__.py │ │ ├── nnUNetTrainer.py │ │ ├── nnUNetTrainerLightMUNet.py │ │ ├── nnUNetTrainerMedNext.py │ │ ├── nnUNetTrainerSAMed.py │ │ ├── nnUNetTrainerSegResNet.py │ │ ├── nnUNetTrainerSwinUNETR.py │ │ ├── nnUNetTrainerUMambaBot.py │ │ ├── nnUNetTrainerUMambaEnc.py │ │ ├── nnUNetTrainerUNETR.py │ │ └── variants │ │ ├── __init__.py │ │ ├── benchmarking │ │ ├── __init__.py │ │ ├── nnUNetTrainerBenchmark_5epochs.py │ │ └── nnUNetTrainerBenchmark_5epochs_noDataLoading.py │ │ ├── data_augmentation │ │ ├── __init__.py │ │ ├── nnUNetTrainerDA5.py │ │ ├── nnUNetTrainerDAOrd0.py │ │ ├── nnUNetTrainerNoDA.py │ │ └── nnUNetTrainerNoMirroring.py │ │ ├── loss │ │ ├── __init__.py │ │ ├── nnUNetTrainerCELoss.py │ │ ├── nnUNetTrainerDiceLoss.py │ │ └── nnUNetTrainerTopkLoss.py │ │ ├── lr_schedule │ │ ├── __init__.py │ │ └── nnUNetTrainerCosAnneal.py │ │ ├── network_architecture │ │ ├── __init__.py │ │ ├── nnUNetTrainerBN.py │ │ └── nnUNetTrainerNoDeepSupervision.py │ │ ├── optimizer │ │ ├── __init__.py │ │ ├── nnUNetTrainerAdam.py │ │ └── nnUNetTrainerAdan.py │ │ ├── sampling │ │ ├── __init__.py │ │ └── nnUNetTrainer_probabilisticOversampling.py │ │ └── training_length │ │ ├── __init__.py │ │ ├── nnUNetTrainer_Xepochs.py │ │ └── nnUNetTrainer_Xepochs_NoMirroring.py └── utilities │ ├── __init__.py │ ├── collate_outputs.py │ ├── dataset_name_id_conversion.py │ ├── ddp_allgather.py │ ├── default_n_proc_DA.py │ ├── file_path_utilities.py │ ├── find_class_by_name.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 └── setup.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xmed-lab/TriALS/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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