├── Downstream ├── README.md ├── monai │ ├── 3D-IRCADb │ │ ├── 3D-IRCADb.json │ │ ├── README.md │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-39.pyc │ │ │ │ ├── STUNet.cpython-39.pyc │ │ │ │ ├── dodnet.cpython-39.pyc │ │ │ │ ├── models.cpython-39.pyc │ │ │ │ └── unet.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── ACDC │ │ ├── ACDC.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-39.pyc │ │ │ │ ├── STUNet.cpython-39.pyc │ │ │ │ ├── dodnet.cpython-39.pyc │ │ │ │ ├── models.cpython-39.pyc │ │ │ │ └── unet.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── AIIB23 │ │ ├── AIIB23.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── PlainConvUNet_load.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── AMOS-MRI │ │ ├── AMOS_MRI.json │ │ ├── README.md │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── ASOCA │ │ ├── ASOCA.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── ATLAS-MRI │ │ ├── ATLAS-MRI.json │ │ ├── README.md │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-39.pyc │ │ │ │ ├── STUNet.cpython-39.pyc │ │ │ │ ├── dodnet.cpython-39.pyc │ │ │ │ ├── models.cpython-39.pyc │ │ │ │ └── unet.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Abdomen1k │ │ ├── dataset_abdomen1k.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── AbdomenAtlas │ │ ├── Atlas_test.py │ │ ├── Atlas_test.sh │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── dataloader_test.cpython-39.pyc │ │ │ ├── dataloader_bdmap.py │ │ │ ├── dataloader_test.py │ │ │ └── dataset_list │ │ │ │ ├── AbdomenAtlas1.0.txt │ │ │ │ ├── AbdomenAtlas1.0_train.txt │ │ │ │ └── AbdomenAtlas1.0_val.txt │ │ ├── main.py │ │ └── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── models_3dvit.py │ │ │ ├── neural_network.py │ │ │ ├── patch_embed.py │ │ │ ├── unet.py │ │ │ └── unetr.py │ ├── Amos │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ └── dataset.json │ │ ├── dataset_CT.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── test.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── data_test.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_test.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Aorta │ │ ├── README.md │ │ ├── aorta.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── BHSD │ │ ├── BHSD.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── BRATS │ │ ├── brats.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── BRATS21 │ │ ├── brats21_folds.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── BTCV │ │ ├── README.md │ │ ├── __pycache__ │ │ │ └── trainer.cpython-39.pyc │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ ├── dataset_0.json │ │ │ └── dataset_1.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── data_test.cpython-39.pyc │ │ │ ├── data_utils.cpython-38.pyc │ │ │ ├── utils.cpython-38.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_test.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── CC-CCII │ │ ├── csv │ │ │ ├── CC_CCII_fold0_train.csv │ │ │ ├── CC_CCII_fold0_valid.csv │ │ │ ├── CC_CCII_fold1_train.csv │ │ │ ├── CC_CCII_fold1_valid.csv │ │ │ ├── CC_CCII_fold2_train.csv │ │ │ ├── CC_CCII_fold2_valid.csv │ │ │ └── CC_CCII_metadata.csv │ │ ├── dataset │ │ │ └── __init__.py │ │ ├── eval.py │ │ ├── main.py │ │ ├── model.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-38.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── data_utils.cpython-38.pyc │ │ │ └── utils.cpython-38.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── CHAOS │ │ ├── chaos.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── COVID │ │ ├── Covid19_20_folds.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-39.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── dodnet.cpython-39.pyc │ │ │ │ ├── models.cpython-39.pyc │ │ │ │ └── unet.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_test.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── CT_CLIP │ │ ├── CTCLIPTrainer.py │ │ ├── README.md │ │ ├── baseline │ │ │ ├── __pycache__ │ │ │ │ ├── PCRL3d.cpython-38.pyc │ │ │ │ ├── configuration_m3d_clip.cpython-38.pyc │ │ │ │ ├── genesis_unet3d.cpython-38.pyc │ │ │ │ ├── genesis_unet3d_768.cpython-38.pyc │ │ │ │ ├── modeling_m3d_clip.cpython-38.pyc │ │ │ │ ├── models_3dvit.cpython-38.pyc │ │ │ │ ├── pcrlv2_model_3d.cpython-38.pyc │ │ │ │ ├── position_encoding.cpython-38.pyc │ │ │ │ ├── ptunifier_module.cpython-38.pyc │ │ │ │ ├── selfattention.cpython-38.pyc │ │ │ │ ├── transformerblock.cpython-38.pyc │ │ │ │ └── vit_3d_pure.cpython-38.pyc │ │ │ ├── swin.py │ │ │ └── swin_backup.py │ │ ├── bootstrap_values.py │ │ ├── clip_base.slurm │ │ ├── clip_huge.slurm │ │ ├── clip_large.slurm │ │ ├── ct_clip │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── ct_clip.cpython-38.pyc │ │ │ │ ├── ct_clip.cpython-39.pyc │ │ │ │ ├── mlm.cpython-38.pyc │ │ │ │ ├── mlm.cpython-39.pyc │ │ │ │ ├── visual_ssl.cpython-38.pyc │ │ │ │ └── visual_ssl.cpython-39.pyc │ │ │ ├── ct_clip.py │ │ │ ├── data │ │ │ │ └── bpe_simple_vocab_16e6.txt │ │ │ ├── distributed.py │ │ │ ├── mlm.py │ │ │ ├── tokenizer.py │ │ │ └── visual_ssl.py │ │ ├── ct_lipro_inference.py │ │ ├── ct_lipro_train.py │ │ ├── ct_rate_preprocess_val.json │ │ ├── ct_vocabfine_train.py │ │ ├── data.py │ │ ├── data_inference.py │ │ ├── eval.py │ │ ├── lipro_inference.sh │ │ ├── lipro_train.sh │ │ ├── patient_folders_train.json │ │ ├── patient_folders_valid.json │ │ ├── report_to_volume.py │ │ ├── run_train.py │ │ ├── run_zero_shot.py │ │ ├── src │ │ │ ├── __pycache__ │ │ │ │ ├── args.cpython-38.pyc │ │ │ │ └── args.cpython-39.pyc │ │ │ ├── args.py │ │ │ └── models │ │ │ │ ├── __pycache__ │ │ │ │ ├── utils.cpython-38.pyc │ │ │ │ └── utils.cpython-39.pyc │ │ │ │ ├── modeling.py │ │ │ │ └── utils.py │ │ ├── transformer_maskgit │ │ │ ├── MaskGITTransformer.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MaskGITTransformer.cpython-38.pyc │ │ │ │ ├── MaskGITTransformer.cpython-39.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── attention.cpython-38.pyc │ │ │ │ ├── attention.cpython-39.pyc │ │ │ │ ├── ctvit.cpython-38.pyc │ │ │ │ ├── ctvit.cpython-39.pyc │ │ │ │ ├── ctvit_trainer.cpython-38.pyc │ │ │ │ ├── ctvit_trainer.cpython-39.pyc │ │ │ │ ├── data.cpython-38.pyc │ │ │ │ ├── data.cpython-39.pyc │ │ │ │ ├── optimizer.cpython-38.pyc │ │ │ │ ├── optimizer.cpython-39.pyc │ │ │ │ ├── t5.cpython-38.pyc │ │ │ │ ├── t5.cpython-39.pyc │ │ │ │ ├── videotextdataset.cpython-38.pyc │ │ │ │ └── videotextdataset.cpython-39.pyc │ │ │ ├── attention.py │ │ │ ├── ctvit.py │ │ │ ├── ctvit_inference.py │ │ │ ├── ctvit_trainer.py │ │ │ ├── data.py │ │ │ ├── optimizer.py │ │ │ ├── setup.py │ │ │ ├── t5.py │ │ │ ├── train_transformer.py │ │ │ ├── transformer_maskgit.egg-info │ │ │ │ ├── PKG-INFO │ │ │ │ ├── SOURCES.txt │ │ │ │ ├── dependency_links.txt │ │ │ │ ├── requires.txt │ │ │ │ └── top_level.txt │ │ │ ├── videotextdataset.py │ │ │ ├── videotextdatasetsuperres.py │ │ │ ├── videotextdatasettransformersuperres.py │ │ │ └── videotextdatasetvalidation.py │ │ ├── tsne_latents.py │ │ ├── vocabfine_train_base.sh │ │ ├── vocabfine_train_huge.sh │ │ ├── vocabfine_train_large.sh │ │ ├── volume_to_volume.py │ │ └── zero_shot.py │ ├── Colon │ │ ├── README.md │ │ ├── colon.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── FUMPE │ │ ├── FUMPE.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── PlainConvUNet_load.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Flare22 │ │ ├── __init__.py │ │ ├── dataset.json │ │ ├── dataset │ │ │ ├── __init__.py │ │ │ ├── dataset.json │ │ │ ├── dataset_test50.json │ │ │ ├── gen_json_flare.py │ │ │ └── get_shape_affine.py │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── data_test.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_test.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Heart │ │ ├── heart.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Hip │ │ ├── Hip.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── KiTs │ │ ├── dataset_kits.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Kipa │ │ ├── kipa.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_test.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── LNDb │ │ ├── LNDb.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── PlainConvUNet_load.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── LUNA16 │ │ ├── README.md │ │ ├── datasets_3D │ │ │ ├── Classification │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── base_classification.cpython-38.pyc │ │ │ │ │ └── luna_classification.cpython-38.pyc │ │ │ │ ├── base_classification.py │ │ │ │ └── luna_classification.py │ │ │ ├── MG │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── base_mg_pretask.cpython-36.pyc │ │ │ │ │ ├── base_mg_pretask.cpython-38.pyc │ │ │ │ │ ├── luna_mg_pretask.cpython-36.pyc │ │ │ │ │ └── luna_mg_pretask.cpython-38.pyc │ │ │ │ ├── base_mg_pretask.py │ │ │ │ └── luna_mg_pretask.py │ │ │ ├── PCRL │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── base_pcrl_pretask.cpython-36.pyc │ │ │ │ │ ├── base_pcrl_pretask.cpython-38.pyc │ │ │ │ │ ├── luna_pcrl_pretask.cpython-36.pyc │ │ │ │ │ └── luna_pcrl_pretask.cpython-38.pyc │ │ │ │ ├── base_pcrl_pretask.py │ │ │ │ └── luna_pcrl_pretask.py │ │ │ ├── Rubik_cube │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── base_rkb_pretask.cpython-38.pyc │ │ │ │ │ ├── luna_jigsaw_pretask.cpython-38.pyc │ │ │ │ │ ├── luna_rkb_plus_pretask.cpython-38.pyc │ │ │ │ │ └── luna_rkb_pretask.cpython-38.pyc │ │ │ │ ├── base_rkb_pretask.py │ │ │ │ ├── luna_jigsaw_pretask.py │ │ │ │ ├── luna_rkb_plus_pretask.py │ │ │ │ ├── luna_rkb_pretask.py │ │ │ │ └── permutations │ │ │ │ │ ├── permutations_hamming_max_100.npy │ │ │ │ │ └── permutations_hamming_max_1000.npy │ │ │ ├── Seg │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── base_seg.cpython-36.pyc │ │ │ │ │ ├── base_seg.cpython-38.pyc │ │ │ │ │ ├── btcv_seg.cpython-38.pyc │ │ │ │ │ ├── lits_seg.cpython-38.pyc │ │ │ │ │ ├── luna_seg.cpython-36.pyc │ │ │ │ │ ├── luna_seg.cpython-38.pyc │ │ │ │ │ └── msd_liver_seg.cpython-38.pyc │ │ │ │ ├── base_seg.py │ │ │ │ ├── btcv_seg.py │ │ │ │ ├── lits_seg.py │ │ │ │ ├── luna_seg.py │ │ │ │ └── msd_liver_seg.py │ │ │ ├── __init__.py │ │ │ └── paths.py │ │ ├── luna_ncc_3d_config.py │ │ ├── luna_ncc_3d_eval_config.py │ │ ├── models │ │ │ ├── BYOL.py │ │ │ ├── PCRL.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── BYOL.cpython-38.pyc │ │ │ │ ├── BYOL_v2.cpython-36.pyc │ │ │ │ ├── PCRL.cpython-38.pyc │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ └── pixel_BYOL.cpython-36.pyc │ │ │ └── pixel_BYOL.py │ │ ├── networks │ │ │ ├── MyPCLR3d.py │ │ │ ├── MyPCRL2d.py │ │ │ ├── PCRL.py │ │ │ ├── PCRL3d.py │ │ │ ├── __init__.py │ │ │ ├── swinunetr.py │ │ │ ├── unet.py │ │ │ └── unet3d.py │ │ ├── trainers │ │ │ ├── __init__.py │ │ │ ├── base_trainer.py │ │ │ ├── byol_trainer.py │ │ │ ├── classification2d_trainer.py │ │ │ ├── classification_trainer.py │ │ │ ├── jigsaw_trainer.py │ │ │ ├── mg_trainer.py │ │ │ ├── mypcrl3d_trainer.py │ │ │ ├── pcrl3d_trainer.py │ │ │ ├── pcrl_trainer.py │ │ │ ├── rkb_plus_trainer.py │ │ │ ├── rkb_trainer.py │ │ │ ├── seg2d_trainer.py │ │ │ ├── seg3d_ROI_trainer.py │ │ │ ├── seg3d_mclasses_trainer.py │ │ │ ├── seg3d_trainer.py │ │ │ ├── simclr_trainer.py │ │ │ ├── ssm_rot_trainer.py │ │ │ └── ssm_rpl_trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── dice_loss.py │ │ │ ├── losses.py │ │ │ ├── metrics.py │ │ │ ├── recorder.py │ │ │ └── tools.py │ ├── LiTs │ │ ├── dataset_lits.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Lung │ │ ├── README.md │ │ ├── dataset_MSD_Lung.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── PlainConvUNet_load.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── M2KT │ │ ├── README.md │ │ ├── chest_ctrg_r2gen_nitfy_ori_split.json │ │ ├── compute_ce.py │ │ ├── config │ │ │ ├── config.py │ │ │ ├── ctrg.yml │ │ │ ├── ctrg_resnet.yml │ │ │ ├── ctrg_swin3d.yml │ │ │ ├── iu.yml │ │ │ ├── iu_densenet.yml │ │ │ ├── iu_efficientnet.yml │ │ │ ├── iu_r2gen.yml │ │ │ ├── iu_resnet.yml │ │ │ ├── iu_resnet_cosine.yml │ │ │ ├── mimic.yml │ │ │ ├── mimic_resnet.yml │ │ │ └── opts.py │ │ ├── data_csv │ │ │ └── CTRG_finding_labels.csv │ │ ├── labeler.py │ │ ├── main.py │ │ ├── main_basic.py │ │ ├── main_label_feature.py │ │ ├── mainbaseline.py │ │ ├── metrics.py │ │ ├── misc │ │ │ ├── __pycache__ │ │ │ │ ├── utils.cpython-38.pyc │ │ │ │ └── utils.cpython-39.pyc │ │ │ └── utils.py │ │ ├── models │ │ │ ├── LabelFeature.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lamrg.cpython-38.pyc │ │ │ │ └── lamrg.cpython-39.pyc │ │ │ ├── baseline.py │ │ │ ├── lamrg.py │ │ │ └── r2gen.py │ │ ├── modules │ │ │ ├── AttModel.py │ │ │ ├── CaptionModel.py │ │ │ ├── Transformer.py │ │ │ ├── __pycache__ │ │ │ │ ├── AttModel.cpython-38.pyc │ │ │ │ ├── AttModel.cpython-39.pyc │ │ │ │ ├── CaptionModel.cpython-38.pyc │ │ │ │ ├── CaptionModel.cpython-39.pyc │ │ │ │ ├── PCRL3d.cpython-38.pyc │ │ │ │ ├── Transformer.cpython-38.pyc │ │ │ │ ├── Transformer.cpython-39.pyc │ │ │ │ ├── blocks.cpython-38.pyc │ │ │ │ ├── chexbert.cpython-39.pyc │ │ │ │ ├── configuration_m3d_clip.cpython-38.pyc │ │ │ │ ├── ctvit.cpython-38.pyc │ │ │ │ ├── dataloaders.cpython-38.pyc │ │ │ │ ├── dataloaders.cpython-39.pyc │ │ │ │ ├── datasets.cpython-38.pyc │ │ │ │ ├── datasets.cpython-39.pyc │ │ │ │ ├── fpn.cpython-38.pyc │ │ │ │ ├── genesis_unet3d.cpython-38.pyc │ │ │ │ ├── genesis_unet3d_768.cpython-38.pyc │ │ │ │ ├── loss.cpython-38.pyc │ │ │ │ ├── loss.cpython-39.pyc │ │ │ │ ├── metrics.cpython-38.pyc │ │ │ │ ├── metrics.cpython-39.pyc │ │ │ │ ├── metrics_clinical.cpython-39.pyc │ │ │ │ ├── modeling_m3d_clip.cpython-38.pyc │ │ │ │ ├── models_3dvit.cpython-38.pyc │ │ │ │ ├── optimizers.cpython-38.pyc │ │ │ │ ├── optimizers.cpython-39.pyc │ │ │ │ ├── pcrlv2_model_3d.cpython-38.pyc │ │ │ │ ├── position_encoding.cpython-38.pyc │ │ │ │ ├── selfattention.cpython-38.pyc │ │ │ │ ├── swin.cpython-38.pyc │ │ │ │ ├── text_encoder.cpython-38.pyc │ │ │ │ ├── text_encoder.cpython-39.pyc │ │ │ │ ├── tokenizers.cpython-38.pyc │ │ │ │ ├── tokenizers.cpython-39.pyc │ │ │ │ ├── trainer.cpython-38.pyc │ │ │ │ ├── trainer.cpython-39.pyc │ │ │ │ ├── transformerblock.cpython-38.pyc │ │ │ │ ├── utils.cpython-38.pyc │ │ │ │ ├── utils.cpython-39.pyc │ │ │ │ ├── visual_extractor.cpython-38.pyc │ │ │ │ ├── visual_extractor.cpython-39.pyc │ │ │ │ ├── vit_3d.cpython-38.pyc │ │ │ │ └── ynet3d.cpython-38.pyc │ │ │ ├── blocks.py │ │ │ ├── chexbert.py │ │ │ ├── dataloaders.py │ │ │ ├── datasets.py │ │ │ ├── efficientnet_pytorch │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-36.pyc │ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── model.cpython-36.pyc │ │ │ │ │ ├── model.cpython-38.pyc │ │ │ │ │ ├── model.cpython-39.pyc │ │ │ │ │ ├── utils.cpython-36.pyc │ │ │ │ │ ├── utils.cpython-38.pyc │ │ │ │ │ └── utils.cpython-39.pyc │ │ │ │ ├── model.py │ │ │ │ └── utils.py │ │ │ ├── fpn.py │ │ │ ├── loss.py │ │ │ ├── metrics.py │ │ │ ├── metrics_clinical.py │ │ │ ├── optimizers.py │ │ │ ├── position_encoding.py │ │ │ ├── selfattention.py │ │ │ ├── swin.py │ │ │ ├── text_encoder.py │ │ │ ├── tokenizers.py │ │ │ ├── trainer.py │ │ │ ├── transformerblock.py │ │ │ ├── utils.py │ │ │ └── visual_extractor.py │ │ ├── nlg_evaluation.py │ │ └── train.sh │ ├── MM-WHS-MRI │ │ ├── MM-WHS-MRI.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── MM-WHS │ │ ├── dataset.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-38.pyc │ │ │ └── lr_scheduler.py │ │ ├── pretrained_models │ │ │ └── __init__.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── data_utils.cpython-38.pyc │ │ │ └── utils.cpython-38.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── PANORAMA │ │ ├── PANORAMA.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── PENGWIN │ │ ├── PENGWIN.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Panc │ │ ├── dataset_panc.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Parse22 │ │ ├── Parse22.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── PlainConvUNet_load.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-310.pyc │ │ │ │ ├── models_3dvit.cpython-39.pyc │ │ │ │ ├── patch_embed.cpython-310.pyc │ │ │ │ ├── patch_embed.cpython-39.pyc │ │ │ │ ├── unetr.cpython-310.pyc │ │ │ │ └── unetr.cpython-39.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Prostate │ │ ├── Prostate.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-310.pyc │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── dodnet.cpython-310.pyc │ │ │ │ ├── models.cpython-310.pyc │ │ │ │ └── unet.cpython-310.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Registration │ │ ├── IXI │ │ │ ├── Baseline_Transformers │ │ │ │ ├── data │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── data_utils.py │ │ │ │ │ ├── datasets.py │ │ │ │ │ ├── rand.py │ │ │ │ │ └── trans.py │ │ │ │ ├── infer_CoTr.py │ │ │ │ ├── infer_PVT.py │ │ │ │ ├── infer_ViTVNet.py │ │ │ │ ├── infer_nnFormer.py │ │ │ │ ├── label_info.txt │ │ │ │ ├── losses.py │ │ │ │ ├── models │ │ │ │ │ ├── CoTr │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── configuration.py │ │ │ │ │ │ ├── network_architecture │ │ │ │ │ │ │ ├── CNNBackbone.py │ │ │ │ │ │ │ ├── DeTrans │ │ │ │ │ │ │ │ ├── DeformableTrans.py │ │ │ │ │ │ │ │ ├── ops │ │ │ │ │ │ │ │ │ ├── functions │ │ │ │ │ │ │ │ │ │ └── ms_deform_attn_func.py │ │ │ │ │ │ │ │ │ └── modules │ │ │ │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ │ │ │ └── ms_deform_attn.py │ │ │ │ │ │ │ │ └── position_encoding.py │ │ │ │ │ │ │ ├── ResTranUnet.py │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ └── neural_network.py │ │ │ │ │ │ ├── run │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── default_configuration.py │ │ │ │ │ │ │ └── run_training.py │ │ │ │ │ │ └── training │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── model_restore.py │ │ │ │ │ │ │ └── network_training │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── network_trainer.py │ │ │ │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ │ │ │ └── nnUNetTrainerV2_ResTrans.py │ │ │ │ │ ├── PVT.py │ │ │ │ │ ├── SwinTransformer.py │ │ │ │ │ ├── ViTVNet.py │ │ │ │ │ ├── configs_PVT.py │ │ │ │ │ ├── configs_ViTVNet.py │ │ │ │ │ └── nnFormer │ │ │ │ │ │ ├── Swin_Unet_l_gelunorm.py │ │ │ │ │ │ ├── Swin_Unet_s_ACDC_2laterdown.py │ │ │ │ │ │ ├── generic_UNet.py │ │ │ │ │ │ ├── initialization.py │ │ │ │ │ │ └── neural_network.py │ │ │ │ ├── train_CoTr.py │ │ │ │ ├── train_PVT.py │ │ │ │ ├── train_ViTVNet.py │ │ │ │ ├── train_nnFormer.py │ │ │ │ ├── train_pre_swin.py │ │ │ │ └── utils.py │ │ │ └── TransMorph │ │ │ │ ├── data │ │ │ │ ├── __init__.py │ │ │ │ ├── data_utils.py │ │ │ │ ├── datasets.py │ │ │ │ ├── rand.py │ │ │ │ └── trans.py │ │ │ │ ├── infer_TransMorph.py │ │ │ │ ├── infer_TransMorph_Bayes.py │ │ │ │ ├── infer_TransMorph_bspl.py │ │ │ │ ├── infer_TransMorph_diff.py │ │ │ │ ├── label_info.txt │ │ │ │ ├── losses.py │ │ │ │ ├── models │ │ │ │ ├── TransMorph.py │ │ │ │ ├── TransMorph_Bayes.py │ │ │ │ ├── TransMorph_bspl.py │ │ │ │ ├── TransMorph_diff.py │ │ │ │ ├── __init__.py │ │ │ │ ├── configs_TransMorph.py │ │ │ │ ├── configs_TransMorph_Bayes.py │ │ │ │ ├── configs_TransMorph_bspl.py │ │ │ │ ├── configs_TransMorph_diff.py │ │ │ │ ├── finite_differences.py │ │ │ │ └── transformation.py │ │ │ │ ├── train_TransMorph.py │ │ │ │ ├── train_TransMorph_Bayes.py │ │ │ │ ├── train_TransMorph_bspl.py │ │ │ │ ├── train_TransMorph_diff.py │ │ │ │ └── utils.py │ │ ├── OASIS │ │ │ ├── TransMorph │ │ │ │ ├── data │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── data_utils.py │ │ │ │ │ ├── datasets.py │ │ │ │ │ ├── rand.py │ │ │ │ │ └── trans.py │ │ │ │ ├── losses.py │ │ │ │ ├── models │ │ │ │ │ ├── SwinTransformer.py │ │ │ │ │ ├── TransMorph.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── configs_TransMorph.py │ │ │ │ ├── submit_TransMorph.py │ │ │ │ ├── train_TransMorph.py │ │ │ │ ├── train_pre_swin.py │ │ │ │ └── utils.py │ │ │ ├── TransMorph_on_OASIS.md │ │ │ ├── evaluation.py │ │ │ └── surface_distance │ │ │ │ ├── __init__.py │ │ │ │ ├── lookup_tables.py │ │ │ │ └── metrics.py │ │ └── README.md │ ├── SegThor │ │ ├── README.md │ │ ├── dataset.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-310.pyc │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── dodnet.cpython-310.pyc │ │ │ │ ├── models.cpython-310.pyc │ │ │ │ └── unet.cpython-310.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Sliver07 │ │ ├── SLIVER07.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Spleen │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── MiT.cpython-310.pyc │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── dodnet.cpython-310.pyc │ │ │ │ ├── models.cpython-310.pyc │ │ │ │ └── unet.cpython-310.pyc │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── spleen.json │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── StructSeg19 │ │ ├── Structseg.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── TCIA_Panc │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── tcia_panc.json │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Totalsegmentator │ │ ├── README.md │ │ ├── Totalsegmentator.json │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ ├── Vessel │ │ ├── main.py │ │ ├── models │ │ │ ├── MiT.py │ │ │ ├── MiT_encoder.py │ │ │ ├── MiT_utils.py │ │ │ ├── Patch_embeds.py │ │ │ ├── PlainConvUNet_load.py │ │ │ ├── STUNet.py │ │ │ ├── __init__.py │ │ │ ├── dodnet.py │ │ │ ├── models.py │ │ │ ├── neural_network.py │ │ │ └── unet.py │ │ ├── optimizers │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-310.pyc │ │ │ │ ├── __init__.cpython-311.pyc │ │ │ │ ├── __init__.cpython-38.pyc │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ │ └── lr_scheduler.cpython-39.pyc │ │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── utils.cpython-39.pyc │ │ │ ├── data_utils.py │ │ │ └── utils.py │ │ └── vessel.json │ └── Word │ │ ├── dataset │ │ ├── __init__.py │ │ └── dataset.json │ │ ├── main.py │ │ ├── models │ │ ├── MiT.py │ │ ├── MiT_encoder.py │ │ ├── MiT_utils.py │ │ ├── Patch_embeds.py │ │ ├── PlainConvUNet_load.py │ │ ├── STUNet.py │ │ ├── __init__.py │ │ ├── dodnet.py │ │ ├── models.py │ │ ├── neural_network.py │ │ └── unet.py │ │ ├── optimizers │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── lr_scheduler.cpython-310.pyc │ │ │ ├── lr_scheduler.cpython-311.pyc │ │ │ ├── lr_scheduler.cpython-38.pyc │ │ │ └── lr_scheduler.cpython-39.pyc │ │ └── lr_scheduler.py │ │ ├── train.sh │ │ ├── trainer.py │ │ └── utils │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── utils.cpython-310.pyc │ │ ├── utils.cpython-311.pyc │ │ ├── utils.cpython-38.pyc │ │ └── utils.cpython-39.pyc │ │ ├── data_utils.py │ │ └── utils.py ├── nnUNet │ ├── LICENSE │ ├── README.md │ ├── 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 │ │ │ ├── Dataset017_BTCV.py │ │ │ ├── Dataset027_ACDC.py │ │ │ ├── Dataset073_Fluo_C3DH_A549_SIM.py │ │ │ ├── Dataset083_Verse20.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 │ │ │ ├── Dataset224_AbdomenAtlas1.0.py │ │ │ ├── Dataset988_dummyDataset4.py │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── generate_dataset_json.cpython-39.pyc │ │ │ ├── convert_MSD_dataset.py │ │ │ ├── convert_raw_dataset_from_old_nnunet_format.py │ │ │ ├── convert_totalsegmentor.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 │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── evaluate_predictions.cpython-39.pyc │ │ │ ├── accumulate_cv_results.py │ │ │ ├── evaluate_predictions.py │ │ │ └── find_best_configuration.py │ │ ├── experiment_planning │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── plan_and_preprocess_api.cpython-39.pyc │ │ │ │ ├── plan_and_preprocess_entrypoints.cpython-39.pyc │ │ │ │ └── verify_dataset_integrity.cpython-39.pyc │ │ │ ├── dataset_fingerprint │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── fingerprint_extractor.cpython-39.pyc │ │ │ │ └── fingerprint_extractor.py │ │ │ ├── experiment_planners │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── default_experiment_planner.cpython-39.pyc │ │ │ │ │ └── network_topology.cpython-39.pyc │ │ │ │ ├── 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 │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── base_reader_writer.cpython-39.pyc │ │ │ │ ├── natural_image_reader_writer.cpython-39.pyc │ │ │ │ ├── nibabel_reader_writer.cpython-39.pyc │ │ │ │ ├── reader_writer_registry.cpython-39.pyc │ │ │ │ ├── simpleitk_reader_writer.cpython-39.pyc │ │ │ │ └── tif_reader_writer.cpython-39.pyc │ │ │ ├── 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 │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── data_iterators.cpython-39.pyc │ │ │ │ ├── export_prediction.cpython-39.pyc │ │ │ │ ├── predict_from_raw_data.cpython-39.pyc │ │ │ │ └── sliding_window_prediction.cpython-39.pyc │ │ │ ├── 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 │ │ ├── paths.py │ │ ├── postprocessing │ │ │ ├── __init__.py │ │ │ └── remove_connected_components.py │ │ ├── preprocessing │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ └── __init__.cpython-39.pyc │ │ │ ├── cropping │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── cropping.cpython-39.pyc │ │ │ │ └── cropping.py │ │ │ ├── normalization │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── default_normalization_schemes.cpython-39.pyc │ │ │ │ │ └── map_channel_name_to_normalization.cpython-39.pyc │ │ │ │ ├── default_normalization_schemes.py │ │ │ │ ├── map_channel_name_to_normalization.py │ │ │ │ └── readme.md │ │ │ ├── preprocessors │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── default_preprocessor.cpython-39.pyc │ │ │ │ └── default_preprocessor.py │ │ │ └── resampling │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ ├── default_resampling.cpython-39.pyc │ │ │ │ └── utils.cpython-39.pyc │ │ │ │ ├── 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 │ │ │ ├── __pycache__ │ │ │ │ └── __init__.cpython-39.pyc │ │ │ ├── data_augmentation │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── compute_initial_patch_size.cpython-39.pyc │ │ │ │ ├── compute_initial_patch_size.py │ │ │ │ └── custom_transforms │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── cascade_transforms.cpython-39.pyc │ │ │ │ │ ├── deep_supervision_donwsampling.cpython-39.pyc │ │ │ │ │ ├── limited_length_multithreaded_augmenter.cpython-39.pyc │ │ │ │ │ ├── masking.cpython-39.pyc │ │ │ │ │ ├── region_based_training.cpython-39.pyc │ │ │ │ │ └── transforms_for_dummy_2d.cpython-39.pyc │ │ │ │ │ ├── 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 │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── base_data_loader.cpython-39.pyc │ │ │ │ │ ├── data_loader_2d.cpython-39.pyc │ │ │ │ │ ├── data_loader_3d.cpython-39.pyc │ │ │ │ │ ├── nnunet_dataset.cpython-39.pyc │ │ │ │ │ └── utils.cpython-39.pyc │ │ │ │ ├── base_data_loader.py │ │ │ │ ├── data_loader_2d.py │ │ │ │ ├── data_loader_3d.py │ │ │ │ ├── nnunet_dataset.py │ │ │ │ └── utils.py │ │ │ ├── logging │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── nnunet_logger.cpython-39.pyc │ │ │ │ └── nnunet_logger.py │ │ │ ├── loss │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ ├── compound_losses.cpython-39.pyc │ │ │ │ │ ├── deep_supervision.cpython-39.pyc │ │ │ │ │ ├── dice.cpython-39.pyc │ │ │ │ │ └── robust_ce_loss.cpython-39.pyc │ │ │ │ ├── compound_losses.py │ │ │ │ ├── deep_supervision.py │ │ │ │ ├── dice.py │ │ │ │ └── robust_ce_loss.py │ │ │ ├── lr_scheduler │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ │ └── polylr.cpython-39.pyc │ │ │ │ └── polylr.py │ │ │ └── nnUNetTrainer │ │ │ │ ├── __init__.py │ │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── nnUNetTrainer.cpython-39.pyc │ │ │ │ ├── nnUNetTrainer.py │ │ │ │ ├── nnUNetTrainer_pretrain.py │ │ │ │ ├── nnUNetTrainer_swin.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 │ │ │ │ └── vit.py │ │ └── utilities │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── collate_outputs.cpython-39.pyc │ │ │ ├── dataset_name_id_conversion.cpython-39.pyc │ │ │ ├── ddp_allgather.cpython-39.pyc │ │ │ ├── default_n_proc_DA.cpython-39.pyc │ │ │ ├── file_path_utilities.cpython-39.pyc │ │ │ ├── find_class_by_name.cpython-39.pyc │ │ │ ├── get_network_from_plans.cpython-39.pyc │ │ │ ├── helpers.cpython-39.pyc │ │ │ ├── json_export.cpython-39.pyc │ │ │ ├── network_initialization.cpython-39.pyc │ │ │ └── utils.cpython-39.pyc │ │ │ ├── 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 │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── label_handling.cpython-39.pyc │ │ │ └── label_handling.py │ │ │ ├── network_initialization.py │ │ │ ├── overlay_plots.py │ │ │ ├── plans_handling │ │ │ ├── __init__.py │ │ │ ├── __pycache__ │ │ │ │ ├── __init__.cpython-39.pyc │ │ │ │ └── plans_handler.cpython-39.pyc │ │ │ └── plans_handler.py │ │ │ └── utils.py │ ├── pyproject.toml │ └── setup.py ├── test.py ├── train.sh └── val.py ├── LICENSE ├── Omni-supervised ├── README.md ├── assets │ └── decision.png ├── dist_B.sh ├── dist_H.sh ├── dist_L.sh ├── jsons │ ├── ColonographyTrials.json │ ├── DeepLesion.json │ ├── HNSCC.json │ ├── HeadNeckPet.json │ ├── LIDC.json │ ├── MELA.json │ ├── NLST_convert_v1.json │ ├── OPCRadiomics.json │ ├── PANORAMA.json │ ├── QIN_HeadNeck.json │ ├── StonyBrookChestCT.json │ ├── TCGA_HNSC.json │ ├── Totalsegmentator_dataset.json │ ├── VoComni.json │ ├── __init__.py │ ├── btcv.json │ ├── ct_rate.json │ ├── dataset_LUNA16_0.json │ ├── dataset_TCIAcolon_v2_0.json │ ├── dataset_TCIAcovid19_0.json │ ├── dataset_kits.json │ ├── dataset_kits19_test.json │ ├── dataset_list │ │ └── AbdomenAtlas1.0.txt │ ├── dataset_lits.json │ ├── dataset_panc.json │ ├── dataset_word.json │ ├── flare23.json │ ├── flare23_new.json │ ├── healthy_ct_kidney.json │ ├── healthy_ct_liver.json │ ├── healthy_ct_panc.json │ ├── stoic21.json │ └── txt │ │ ├── healthy_CT_kidney.txt │ │ ├── healthy_CT_liver.txt │ │ ├── healthy_CT_panc.txt │ │ ├── kidney_real_tumor_val_0.txt │ │ ├── liver_real_tumor_val_1.txt │ │ └── panc_real_tumor_val_3.txt ├── models │ ├── PlainConvUNet_load.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── resnet.cpython-38.pyc │ │ └── ssl_head.cpython-38.pyc │ └── voco_head.py ├── optimizers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── lr_scheduler.cpython-311.pyc │ │ └── lr_scheduler.cpython-38.pyc │ └── lr_scheduler.py ├── single_train.sh ├── utils │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── data_trans.cpython-39.pyc │ │ ├── data_utils_abdomen.cpython-39.pyc │ │ ├── data_utils_tumor.cpython-39.pyc │ │ ├── ops.cpython-311.pyc │ │ ├── ops.cpython-38.pyc │ │ ├── utils.cpython-311.pyc │ │ ├── utils.cpython-38.pyc │ │ └── voco_trans.cpython-39.pyc │ ├── data_trans.py │ ├── data_utils.py │ ├── data_utils_abdomen.py │ ├── data_utils_chest.py │ ├── data_utils_headneck.py │ ├── data_utils_omni.py │ ├── data_utils_tumor.py │ ├── dataloader_bdmap.py │ ├── ops.py │ ├── utils.py │ └── voco_trans.py └── voco_train.py ├── README.md ├── Self-supervised ├── README.md ├── assets │ ├── framework.png │ ├── positions.png │ ├── prior.png │ └── table1.png ├── dist_B.sh ├── dist_H.sh ├── dist_L.sh ├── jsons │ ├── ColonographyTrials.json │ ├── DeepLesion.json │ ├── HNSCC.json │ ├── HeadNeckPet.json │ ├── LIDC.json │ ├── MELA.json │ ├── NLST_convert_v1.json │ ├── OPCRadiomics.json │ ├── PANORAMA.json │ ├── QIN_HeadNeck.json │ ├── StonyBrookChestCT.json │ ├── TCGA_HNSC.json │ ├── Totalsegmentator_dataset.json │ ├── __init__.py │ ├── btcv.json │ ├── ct_rate.json │ ├── dataset_LUNA16_0.json │ ├── dataset_TCIAcolon_v2_0.json │ ├── dataset_TCIAcovid19_0.json │ ├── dataset_kits.json │ ├── dataset_kits19_test.json │ ├── dataset_list │ │ └── AbdomenAtlas1.0.txt │ ├── dataset_lits.json │ ├── dataset_panc.json │ ├── dataset_word.json │ ├── flare23.json │ ├── flare23_new.json │ ├── healthy_ct_kidney.json │ ├── healthy_ct_liver.json │ ├── healthy_ct_panc.json │ ├── stoic21.json │ └── txt │ │ ├── healthy_CT_kidney.txt │ │ ├── healthy_CT_liver.txt │ │ ├── healthy_CT_panc.txt │ │ ├── kidney_real_tumor_val_0.txt │ │ ├── liver_real_tumor_val_1.txt │ │ └── panc_real_tumor_val_3.txt ├── models │ ├── PlainConvUNet_load.py │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── resnet.cpython-38.pyc │ │ ├── ssl_head.cpython-38.pyc │ │ └── voco_head.cpython-39.pyc │ └── voco_head.py ├── optimizers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── lr_scheduler.cpython-311.pyc │ │ └── lr_scheduler.cpython-38.pyc │ └── lr_scheduler.py ├── single_train.sh ├── utils │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── data_trans.cpython-39.pyc │ │ ├── data_utils_abdomen.cpython-39.pyc │ │ ├── data_utils_tumor.cpython-39.pyc │ │ ├── ops.cpython-311.pyc │ │ ├── ops.cpython-38.pyc │ │ ├── utils.cpython-311.pyc │ │ ├── utils.cpython-38.pyc │ │ └── voco_trans.cpython-39.pyc │ ├── data_trans.py │ ├── data_utils.py │ ├── data_utils_abdomen.py │ ├── data_utils_chest.py │ ├── data_utils_headneck.py │ ├── data_utils_tumor.py │ ├── dataloader_bdmap.py │ ├── ops.py │ ├── utils.py │ ├── vis_voco.py │ └── voco_trans.py └── voco_train.py ├── Semi-supervised ├── README.md ├── VoComni.json ├── dist_B.sh ├── dist_H.sh ├── dist_L.sh ├── gen_json.py ├── optimizers │ ├── __init__.py │ └── lr_scheduler.py ├── single_train.sh ├── utils │ ├── __init__.py │ ├── data_utils.py │ ├── ops.py │ └── utils.py └── voco_train.py ├── VoComni ├── README.md ├── VoComni.json ├── assets │ └── vocomni.png ├── main.py ├── models │ ├── MiT.py │ ├── MiT_encoder.py │ ├── MiT_utils.py │ ├── Patch_embeds.py │ ├── PlainConvUNet_load.py │ ├── STUNet.py │ ├── __init__.py │ ├── dodnet.py │ ├── models.py │ ├── neural_network.py │ └── unet.py ├── nnUNet_preprocessed │ ├── dataset_fingerprint.json │ └── nnUNetPlans.json ├── omni_B.sh ├── omni_H.sh ├── omni_L.sh ├── optimizers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── lr_scheduler.cpython-310.pyc │ │ ├── lr_scheduler.cpython-311.pyc │ │ ├── lr_scheduler.cpython-38.pyc │ │ └── lr_scheduler.cpython-39.pyc │ └── lr_scheduler.py ├── trainer.py └── utils │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-39.pyc │ └── utils.cpython-39.pyc │ ├── data_utils.py │ └── utils.py ├── assets └── data.svg └── requirements.txt /Downstream/README.md: 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