├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── chatops.yml │ ├── integration.yml │ └── packaging-algo.yml ├── .gitignore ├── .pre-commit-config.yaml ├── DAE ├── BTCV_Finetune │ ├── README.md │ ├── main.py │ ├── main_for_ngc.py │ ├── max_vol.py │ ├── mlp_new.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── patchembedding.py │ ├── requirements.txt │ ├── swin_unetr.py │ ├── swin_unetr_og.py │ ├── trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ └── utils.py ├── Feta_Finetune │ ├── README.md │ ├── main_for_ngc.py │ ├── mlp_new.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── patchembedding.py │ ├── requirements.txt │ ├── swin_unetr.py │ ├── swin_unetr_og.py │ ├── trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ └── utils.py └── Pretrain_full_contrast │ ├── config.py │ ├── data │ ├── __init__.py │ ├── data_finetune.py │ └── data_pretrain.py │ ├── figs │ ├── dae_overview.png │ └── dae_recon.png │ ├── logger.py │ ├── lr_scheduler.py │ ├── main_runner.py │ ├── models │ ├── __init__.py │ ├── build.py │ ├── simmim.py │ ├── simmim_advanced.py │ ├── swin_transformer.py │ ├── swin_transformer_3d.py │ └── vision_transformer.py │ ├── optimizer.py │ ├── readme.md │ ├── requirements.txt │ ├── run_me_local.sh │ ├── scripts │ ├── ablation_m20.sh │ ├── ablation_m30.sh │ ├── ablation_m40.sh │ ├── ablation_m50.sh │ ├── ablation_m70.sh │ ├── ablation_m80.sh │ └── ablation_m90.sh │ └── utils.py ├── DiNTS ├── README.md ├── arch_code_cvpr.pth ├── configs │ ├── config_Task01_BrainTumour.yaml │ ├── config_Task02_Heart.yaml │ ├── config_Task03_Liver.yaml │ ├── config_Task04_Hippocampus.yaml │ ├── config_Task05_Prostate.yaml │ ├── config_Task06_Lung.yaml │ ├── config_Task07_Pancreas.yaml │ ├── config_Task08_HepaticVessel.yaml │ ├── config_Task09_Spleen.yaml │ └── config_Task10_Colon.yaml ├── download_msd_datasets.py ├── ensemble.py ├── infer_multi-gpu.py ├── run_ensemble.sh ├── run_infer_multi-gpu.sh ├── run_install_monai.sh ├── run_train_4gpu.sh ├── run_train_multi-gpu.sh ├── train_multi-gpu.py ├── transforms.py └── utils.py ├── LICENSE ├── README.md ├── SkullRec ├── README.md ├── cranialDefects.py ├── facialDefects.py ├── figs │ ├── cranial_rec.png │ ├── dataset.png │ ├── facial_rec.png │ └── monai_results.png ├── monaiSkull.py ├── output_monai │ └── README.md ├── pre_trained_weights │ └── readme.md └── skullfix_pretrained_weight │ └── README.md ├── SwinMM ├── INSTALL.md ├── Pretrain │ ├── jsons │ │ ├── Download Pretrain Jsons Here │ │ └── __init__.py │ ├── losses │ │ └── loss.py │ ├── main.py │ ├── models │ │ └── ssl_head.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── run.sh │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ ├── dataset_in_memory.py │ │ ├── ops.py │ │ ├── view_ops.py │ │ └── view_transforms.py ├── README.md ├── TRAINING.md ├── WORD │ ├── README.md │ ├── dataset │ │ ├── Download Finetune Jsons Here │ │ └── __init__.py │ ├── inferers.py │ ├── main.py │ ├── models │ │ ├── __init__.py │ │ ├── cross_attention.py │ │ └── swin_unetr.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── outputs │ │ └── __init__.py │ ├── pretrained_models │ │ └── __init__.py │ ├── requirements.txt │ ├── run.sh │ ├── runs │ │ └── __init__.py │ ├── test.py │ ├── test_parallel.py │ ├── trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ ├── dataset_in_memory.py │ │ ├── misc.py │ │ ├── test_view_transforms.py │ │ ├── view_ops.py │ │ └── view_transforms.py ├── figures │ ├── ACDC.png │ ├── Result.png │ ├── SwinMMArch.png │ ├── finetune.png │ └── pretrain.png ├── requirements.txt └── scripts │ ├── setup_env.sh │ └── start_redis.sh ├── SwinUNETR ├── BRATS21 │ ├── README.md │ ├── assets │ │ ├── fig_brats21.png │ │ ├── swin_unetr.png │ │ └── swin_unetr_attention_.png │ ├── jsons │ │ └── __init__.py │ ├── main.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── outputs │ │ └── __init__.py │ ├── pretrained_models │ │ └── __init__.py │ ├── requirements.txt │ ├── test.py │ ├── trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ └── utils.py ├── BTCV │ ├── README.md │ ├── assets │ │ └── swin_unetr.png │ ├── dataset │ │ └── __init__.py │ ├── main.py │ ├── optimizers │ │ ├── __init__.py │ │ └── lr_scheduler.py │ ├── outputs │ │ └── __init__.py │ ├── pretrained_models │ │ └── __init__.py │ ├── requirements.txt │ ├── runs │ │ └── __init__.py │ ├── test.py │ ├── trainer.py │ └── utils │ │ ├── __init__.py │ │ ├── data_utils.py │ │ └── utils.py └── Pretrain │ ├── README.md │ ├── assets │ ├── inpaint.gif │ ├── ssl_swin.png │ └── swin_unetr.png │ ├── jsons │ └── __init__.py │ ├── losses │ └── loss.py │ ├── main.py │ ├── models │ └── ssl_head.py │ ├── optimizers │ ├── __init__.py │ └── lr_scheduler.py │ ├── requirements.txt │ ├── runs │ └── __init__.py │ └── utils │ ├── __init__.py │ ├── data_utils.py │ └── ops.py ├── UNETR └── BTCV │ ├── .gitkeep │ ├── README.md │ ├── dataset │ └── __init__.py │ ├── main.py │ ├── networks │ ├── __init__.py │ └── unetr.py │ ├── optimizers │ ├── __init__.py │ └── lr_scheduler.py │ ├── pretrained_models │ └── __init__.py │ ├── requirements.txt │ ├── runs │ └── __init__.py │ ├── test.py │ ├── trainer.py │ └── utils │ ├── __init__.py │ ├── data_utils.py │ └── utils.py ├── auto3dseg ├── README.md ├── algorithm_templates │ ├── dints │ │ ├── __init__.py │ │ ├── configs │ │ │ ├── hyper_parameters.yaml │ │ │ ├── hyper_parameters_search.yaml │ │ │ ├── network.yaml │ │ │ ├── network_search.yaml │ │ │ ├── transforms_infer.yaml │ │ │ ├── transforms_train.yaml │ │ │ └── transforms_validate.yaml │ │ ├── docs │ │ │ └── README.md │ │ └── scripts │ │ │ ├── __init__.py │ │ │ ├── algo.py │ │ │ ├── arch_code.pth │ │ │ ├── dummy_runner.py │ │ │ ├── infer.py │ │ │ ├── search.py │ │ │ ├── train.py │ │ │ ├── utils.py │ │ │ └── validate.py │ ├── segresnet │ │ ├── __init__.py │ │ ├── configs │ │ │ └── hyper_parameters.yaml │ │ ├── docs │ │ │ └── README.md │ │ └── scripts │ │ │ ├── __init__.py │ │ │ ├── algo.py │ │ │ ├── infer.py │ │ │ ├── segmenter.py │ │ │ ├── train.py │ │ │ ├── utils.py │ │ │ └── validate.py │ ├── segresnet2d │ │ ├── __init__.py │ │ ├── configs │ │ │ └── hyper_parameters.yaml │ │ ├── docs │ │ │ └── README.md │ │ └── scripts │ │ │ ├── __init__.py │ │ │ ├── algo.py │ │ │ ├── infer.py │ │ │ ├── segmenter.py │ │ │ ├── segmenter_2d.py │ │ │ ├── train.py │ │ │ ├── utils.py │ │ │ └── validate.py │ └── swinunetr │ │ ├── __init__.py │ │ ├── configs │ │ ├── hyper_parameters.yaml │ │ ├── network.yaml │ │ ├── transforms_infer.yaml │ │ ├── transforms_train.yaml │ │ └── transforms_validate.yaml │ │ ├── docs │ │ └── README.md │ │ └── scripts │ │ ├── __init__.py │ │ ├── algo.py │ │ ├── dummy_runner.py │ │ ├── infer.py │ │ ├── train.py │ │ └── validate.py ├── configs │ └── metadata.json └── tests │ ├── test_algo_templates.py │ └── test_gpu_customization.py ├── coplenet-pneumonia-lesion-segmentation ├── README.md ├── __init__.py ├── coplenet.py ├── fig │ ├── img.png │ └── seg.png ├── run_inference.py └── test_coplenet.py ├── lamp-automated-model-parallelism ├── README.md ├── __init__.py ├── data_utils.py ├── fig │ └── acc_speed_han_0_5hor.png ├── test_unet_pipe.py ├── train.py └── unet_pipe.py ├── prostate-mri-lesion-seg ├── LICENSE ├── README.md ├── build_and_run.ipynb ├── imgs │ ├── lesion_mask.png │ ├── lesion_prob.png │ ├── organ_seg.png │ └── workflow-diagram.png ├── prostate_mri_lesion_seg_app │ ├── __main__.py │ ├── app.py │ ├── app.yaml │ ├── common.py │ ├── custom_lesion_classifier_operator.py │ ├── custom_lesion_seg_operator.py │ ├── organ_seg_operator.py │ ├── requirements.txt │ ├── resnet.py │ └── rrunet3D.py └── scripts │ ├── compare_output.sh │ ├── eval_dice.py │ ├── test_MAP.sh │ └── test_local.sh ├── pyproject.toml └── setup.cfg /.github/ISSUE_TEMPLATE/bug_report.md: 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