├── LICENSE ├── README.md ├── configs ├── Brats │ ├── decoder_only.yaml │ ├── encoder_only.yaml │ └── encoder_plus_decoder.yaml ├── Synapse │ ├── decoder_only.yaml │ ├── encoder_only.yaml │ └── encoder_plus_decoder.yaml └── Vessel │ ├── decoder_only.yaml │ ├── encoder_only.yaml │ └── encoder_plus_decoder.yaml ├── doc ├── data.md └── usage.md ├── inference.py ├── measure_dice.py ├── nn_transunet ├── __init__.py ├── configuration.py ├── data │ ├── __init__.py │ ├── custom_transforms.py │ ├── data_augmentation.py │ ├── data_augmentation_moreDA.py │ ├── dataset_loading.py │ ├── default_data_augmentation.py │ ├── downsampling.py │ ├── preprocessing.py │ └── pyramid_augmentations.py ├── default_configuration.py ├── eval │ ├── __init__.py │ └── evaluator.py ├── networks │ ├── __init__.py │ ├── d2util.py │ ├── mask2former_modeling │ │ ├── __init__.py │ │ └── transformer_decoder │ │ │ ├── __init__.py │ │ │ ├── mask2former_transformer_decoder3d.py │ │ │ ├── position_encoding.py │ │ │ ├── transformer.py │ │ │ └── transformer3d.py │ ├── neural_network.py │ ├── nnunet_model.py │ ├── transunet3d_model.py │ ├── vit_configs.py │ └── vit_modeling.py ├── optimizers │ ├── __init__.py │ ├── lr_scheduler.py │ └── optim_factory.py ├── plans │ ├── data_convert.py │ └── pickle_load.py ├── trainer │ ├── __init__.py │ ├── loss_functions.py │ ├── network_trainer.py │ ├── nnUNetTrainer.py │ ├── nnUNetTrainerV2.py │ └── nnUNetTrainerV2_DDP.py └── utils │ ├── __init__.py │ ├── dist_utils.py │ └── segmentation_export.py ├── scripts ├── inference.sh ├── install.sh └── train.sh └── train.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/README.md -------------------------------------------------------------------------------- /configs/Brats/decoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Brats/decoder_only.yaml -------------------------------------------------------------------------------- /configs/Brats/encoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Brats/encoder_only.yaml -------------------------------------------------------------------------------- /configs/Brats/encoder_plus_decoder.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Brats/encoder_plus_decoder.yaml -------------------------------------------------------------------------------- /configs/Synapse/decoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Synapse/decoder_only.yaml -------------------------------------------------------------------------------- /configs/Synapse/encoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Synapse/encoder_only.yaml -------------------------------------------------------------------------------- /configs/Synapse/encoder_plus_decoder.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Synapse/encoder_plus_decoder.yaml -------------------------------------------------------------------------------- /configs/Vessel/decoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Vessel/decoder_only.yaml -------------------------------------------------------------------------------- /configs/Vessel/encoder_only.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Vessel/encoder_only.yaml -------------------------------------------------------------------------------- /configs/Vessel/encoder_plus_decoder.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/configs/Vessel/encoder_plus_decoder.yaml -------------------------------------------------------------------------------- /doc/data.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /doc/usage.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/inference.py -------------------------------------------------------------------------------- /measure_dice.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/measure_dice.py -------------------------------------------------------------------------------- /nn_transunet/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/configuration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/configuration.py -------------------------------------------------------------------------------- /nn_transunet/data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/data/custom_transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/custom_transforms.py -------------------------------------------------------------------------------- /nn_transunet/data/data_augmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/data_augmentation.py -------------------------------------------------------------------------------- /nn_transunet/data/data_augmentation_moreDA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/data_augmentation_moreDA.py -------------------------------------------------------------------------------- /nn_transunet/data/dataset_loading.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/dataset_loading.py -------------------------------------------------------------------------------- /nn_transunet/data/default_data_augmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/default_data_augmentation.py -------------------------------------------------------------------------------- /nn_transunet/data/downsampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/downsampling.py -------------------------------------------------------------------------------- /nn_transunet/data/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/preprocessing.py -------------------------------------------------------------------------------- /nn_transunet/data/pyramid_augmentations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/data/pyramid_augmentations.py -------------------------------------------------------------------------------- /nn_transunet/default_configuration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/default_configuration.py -------------------------------------------------------------------------------- /nn_transunet/eval/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/eval/evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/eval/evaluator.py -------------------------------------------------------------------------------- /nn_transunet/networks/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/networks/d2util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/d2util.py -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/mask2former_modeling/__init__.py -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/transformer_decoder/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/transformer_decoder/mask2former_transformer_decoder3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/mask2former_modeling/transformer_decoder/mask2former_transformer_decoder3d.py -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/transformer_decoder/position_encoding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/mask2former_modeling/transformer_decoder/position_encoding.py -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/transformer_decoder/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/mask2former_modeling/transformer_decoder/transformer.py -------------------------------------------------------------------------------- /nn_transunet/networks/mask2former_modeling/transformer_decoder/transformer3d.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/mask2former_modeling/transformer_decoder/transformer3d.py -------------------------------------------------------------------------------- /nn_transunet/networks/neural_network.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/neural_network.py -------------------------------------------------------------------------------- /nn_transunet/networks/nnunet_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/nnunet_model.py -------------------------------------------------------------------------------- /nn_transunet/networks/transunet3d_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/transunet3d_model.py -------------------------------------------------------------------------------- /nn_transunet/networks/vit_configs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/vit_configs.py -------------------------------------------------------------------------------- /nn_transunet/networks/vit_modeling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/networks/vit_modeling.py -------------------------------------------------------------------------------- /nn_transunet/optimizers/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/optimizers/lr_scheduler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/optimizers/lr_scheduler.py -------------------------------------------------------------------------------- /nn_transunet/optimizers/optim_factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/optimizers/optim_factory.py -------------------------------------------------------------------------------- /nn_transunet/plans/data_convert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/plans/data_convert.py -------------------------------------------------------------------------------- /nn_transunet/plans/pickle_load.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/plans/pickle_load.py -------------------------------------------------------------------------------- /nn_transunet/trainer/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/trainer/loss_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/trainer/loss_functions.py -------------------------------------------------------------------------------- /nn_transunet/trainer/network_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/trainer/network_trainer.py -------------------------------------------------------------------------------- /nn_transunet/trainer/nnUNetTrainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/trainer/nnUNetTrainer.py -------------------------------------------------------------------------------- /nn_transunet/trainer/nnUNetTrainerV2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/trainer/nnUNetTrainerV2.py -------------------------------------------------------------------------------- /nn_transunet/trainer/nnUNetTrainerV2_DDP.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/trainer/nnUNetTrainerV2_DDP.py -------------------------------------------------------------------------------- /nn_transunet/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /nn_transunet/utils/dist_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/utils/dist_utils.py -------------------------------------------------------------------------------- /nn_transunet/utils/segmentation_export.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/nn_transunet/utils/segmentation_export.py -------------------------------------------------------------------------------- /scripts/inference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/scripts/inference.sh -------------------------------------------------------------------------------- /scripts/install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/scripts/install.sh -------------------------------------------------------------------------------- /scripts/train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/scripts/train.sh -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Beckschen/3D-TransUNet/HEAD/train.py --------------------------------------------------------------------------------