├── .github ├── schemas │ ├── meta.schema.json │ ├── mhubtoml.schema.json │ └── testmodel.schema.json ├── scripts │ ├── comment_check.py │ ├── mhub_check.py │ └── utils.py └── workflows │ ├── model_compliance.yml │ └── submission_review.yml ├── .gitignore ├── LICENSE ├── README.md ├── base ├── bin │ ├── mhub.run │ ├── mhub.test │ ├── mhub.update │ └── mhub.version ├── buildutils │ ├── download_weights.sh │ ├── import_mhub_model.sh │ └── import_mhubio_collection.sh ├── collections.json ├── configs │ └── dicomsort.yml └── dockerfiles │ └── Dockerfile └── models ├── bamf_nnunet_ct_kidney ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── BamfProcessorRunner.py │ └── __init__.py ├── bamf_nnunet_ct_liver ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── BamfProcessorRunner.py │ └── __init__.py ├── bamf_nnunet_mr_liver ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── BamfProcessorRunner.py │ └── __init__.py ├── bamf_nnunet_mr_prostate ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── BamfProcessorRunner.py │ └── __init__.py ├── bamf_pet_ct_breast_tumor ├── config │ ├── composite.yml │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── BreastPostProcessor.py │ ├── ExtractorPostProcessor.py │ ├── NNUnetPETCTRunner.py │ ├── Registration.py │ ├── SegmentResampler.py │ └── TotalSegmentatorMLRunner.py ├── bamf_pet_ct_lung_tumor ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── LungPostProcessor.py │ ├── LungSegmentatorRunner.py │ ├── NNUnetPETCTRunner.py │ └── Registration.py ├── casust ├── config │ ├── default.yml │ ├── dseg.json │ ├── heart.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── scripts │ ├── run.py │ └── slicer_run.py └── utils │ └── CasustRunner.py ├── fmcib_radiomics ├── config │ ├── default.yml │ ├── from_centroids.yml │ ├── from_json.yml │ ├── from_nifti_mask.yml │ ├── from_rtstruct.yml │ └── from_slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── CentroidExtractor.py │ ├── FMCIBRunner.py │ ├── __init__.py │ ├── coords.schema.json │ ├── roi.coords.schema.json │ └── slicermarkup.schema.json ├── gc_autopet_fpr ├── config │ ├── default.yml │ └── mha_pipeline.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── src │ └── cli.py └── utils │ ├── AutoPETRunner.py │ ├── FDGPETCTResampleProcessor.py │ └── __init__.py ├── gc_grt123_lung_cancer ├── __init__.py ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── LungCancerClassifierRunner.py │ └── __init__.py ├── gc_lunglobes ├── README.md ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── LobeSegmentationRunner.py │ ├── __init__.py │ └── run38.py ├── gc_nnunet_pancreas ├── __init__.py ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── GCNNUnetPancreasRunner.py │ ├── __init__.py │ └── cli.py ├── gc_node21_baseline ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── src │ └── cli.py └── utils │ ├── Node21BaselineRunner.py │ └── __init__.py ├── gc_picai_baseline ├── config │ ├── default.yml │ └── mha-pipeline.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── PicaiBaselineRunner.py │ ├── __init__.py │ └── cli.py ├── gc_spider_baseline ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── SpiderBaselineRunner.py │ └── __init__.py ├── gc_stoic_baseline ├── __init__.py ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── StoicBaselineRunner.py │ └── __init__.py ├── gc_tiger_lb2 ├── __init__.py ├── config │ ├── default.yml │ └── tiff_pipeline.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── TigerLB2Runner.py │ ├── __init__.py │ └── cli.py ├── gc_wsi_bgseg ├── config │ ├── default.yml │ └── tiff.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── WSIBackgroundSegmentationRunner.py │ └── __init__.py ├── lungmask ├── README.md ├── __init__.py ├── config │ ├── default.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ └── LungMaskRunner.py ├── monai_prostate158 ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── Prostate158Runner.py │ └── __init__.py ├── mrsegmentator ├── README.md ├── __init__.py ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── MRSegmentatorMLRunner.py │ └── __init__.py ├── msk_smit_lung_gtv ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── src │ ├── README.md │ ├── edit_inference_utils.py │ ├── get_weights.sh │ ├── requirements.txt │ ├── run_segmentation.py │ ├── smit_models │ │ ├── __init__.py │ │ ├── _features.py │ │ ├── _features_fx.py │ │ ├── configs_smit.py │ │ ├── cross_swin_networks │ │ │ ├── SwinTransModels.py │ │ │ ├── __init__.py │ │ │ └── unetr.py │ │ ├── format.py │ │ ├── smit.py │ │ ├── smit_cross_attention.py │ │ └── smit_plus.py │ └── utils │ │ ├── data_utils.py │ │ ├── gen_data_json.py │ │ └── utils.py └── utils │ └── SMITRunner.py ├── nnunet_liver ├── README.md ├── config │ ├── default.yml │ ├── meta.json │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── scripts │ ├── run.py │ └── slicer_run.py ├── nnunet_pancreas ├── README.md ├── config │ ├── default.yml │ ├── dseg.json │ ├── probmasks.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── scripts │ └── run.py ├── nnunet_prostate_task24 ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json └── mhub.toml ├── nnunet_prostate_zonal_task05 ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml └── utils │ ├── ProstateResampler.py │ └── ProstateRunner.py ├── nnunet_segthor ├── config │ └── default.yml ├── dockerfiles │ └── Dockerfile ├── meta.json └── mhub.toml ├── platipy ├── README.md ├── __init__.py ├── config │ ├── default.yml │ ├── default_config.json │ ├── dicomseg_metadata.json │ ├── dseg.yml │ └── slicer.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── scripts │ ├── run.py │ └── slicer_run.py └── utils │ ├── PlatipyRunner.py │ └── __init__.py ├── pyradiomics ├── config │ ├── default.yml │ └── from_rtstruct.yml ├── dockerfiles │ └── Dockerfile ├── meta.json ├── mhub.toml ├── res │ └── params.yml └── utils │ └── 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