├── .gitignore ├── README.md ├── cfg.py ├── figs ├── overview.png └── result_combo.png ├── main.py ├── models ├── .ipynb_checkpoints │ ├── efficientnet-checkpoint.py │ ├── resnet-checkpoint.py │ └── sam_LoRa-checkpoint.py ├── discriminator.py ├── efficientnet.py ├── implicitefficientnet.py ├── implicitnet.py ├── resnet.py ├── sam │ ├── .ipynb_checkpoints │ │ ├── __init__-checkpoint.py │ │ ├── automatic_mask_generator-checkpoint.py │ │ ├── build_sam-checkpoint.py │ │ └── predictor-checkpoint.py │ ├── __init__.py │ ├── automatic_mask_generator.py │ ├── build_sam.py │ ├── modeling │ │ ├── .ipynb_checkpoints │ │ │ ├── __init__-checkpoint.py │ │ │ ├── common-checkpoint.py │ │ │ ├── image_encoder-checkpoint.py │ │ │ ├── mask_decoder-checkpoint.py │ │ │ ├── prompt_encoder-checkpoint.py │ │ │ ├── sam-checkpoint.py │ │ │ ├── tiny_vit_sam-checkpoint.py │ │ │ ├── transformer-checkpoint.py │ │ │ └── vit-checkpoint.py │ │ ├── __init__.py │ │ ├── common.py │ │ ├── image_encoder.py │ │ ├── mask_decoder.py │ │ ├── prompt_encoder.py │ │ ├── sam.py │ │ ├── tiny_vit_sam.py │ │ ├── transformer.py │ │ └── vit.py │ ├── predictor.py │ └── utils │ │ ├── .ipynb_checkpoints │ │ └── transforms-checkpoint.py │ │ ├── __init__.py │ │ ├── amg.py │ │ ├── onnx.py │ │ └── transforms.py ├── sam_LoRa.py ├── senet.py ├── squeezenet.py ├── tag │ ├── __init__.py │ ├── tag.py │ └── tag_layers.py ├── types_.py ├── unet │ ├── .ipynb_checkpoints │ │ ├── __init__-checkpoint.py │ │ └── unet_model-checkpoint.py │ ├── __init__.py │ ├── res_net.py │ ├── unet_model.py │ └── unet_parts.py ├── utils.py ├── vae.py └── vgg.py ├── requirements.txt └── utils ├── .ipynb_checkpoints ├── dataset-checkpoint.py ├── dsc-checkpoint.py └── funcs-checkpoint.py ├── dataset.py └── metrics.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/README.md -------------------------------------------------------------------------------- /cfg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/cfg.py -------------------------------------------------------------------------------- /figs/overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/figs/overview.png -------------------------------------------------------------------------------- /figs/result_combo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/figs/result_combo.png -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/main.py -------------------------------------------------------------------------------- /models/.ipynb_checkpoints/efficientnet-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/.ipynb_checkpoints/efficientnet-checkpoint.py -------------------------------------------------------------------------------- /models/.ipynb_checkpoints/resnet-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/.ipynb_checkpoints/resnet-checkpoint.py -------------------------------------------------------------------------------- /models/.ipynb_checkpoints/sam_LoRa-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/.ipynb_checkpoints/sam_LoRa-checkpoint.py -------------------------------------------------------------------------------- /models/discriminator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/discriminator.py -------------------------------------------------------------------------------- /models/efficientnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/efficientnet.py -------------------------------------------------------------------------------- /models/implicitefficientnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/implicitefficientnet.py -------------------------------------------------------------------------------- /models/implicitnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/implicitnet.py -------------------------------------------------------------------------------- /models/resnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/resnet.py -------------------------------------------------------------------------------- /models/sam/.ipynb_checkpoints/__init__-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/.ipynb_checkpoints/__init__-checkpoint.py -------------------------------------------------------------------------------- /models/sam/.ipynb_checkpoints/automatic_mask_generator-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/.ipynb_checkpoints/automatic_mask_generator-checkpoint.py -------------------------------------------------------------------------------- /models/sam/.ipynb_checkpoints/build_sam-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/.ipynb_checkpoints/build_sam-checkpoint.py -------------------------------------------------------------------------------- /models/sam/.ipynb_checkpoints/predictor-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/.ipynb_checkpoints/predictor-checkpoint.py -------------------------------------------------------------------------------- /models/sam/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/__init__.py -------------------------------------------------------------------------------- /models/sam/automatic_mask_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/automatic_mask_generator.py -------------------------------------------------------------------------------- /models/sam/build_sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/build_sam.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/__init__-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/__init__-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/common-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/common-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/image_encoder-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/image_encoder-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/mask_decoder-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/mask_decoder-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/prompt_encoder-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/prompt_encoder-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/sam-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/sam-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/tiny_vit_sam-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/tiny_vit_sam-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/transformer-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/transformer-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/.ipynb_checkpoints/vit-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/.ipynb_checkpoints/vit-checkpoint.py -------------------------------------------------------------------------------- /models/sam/modeling/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/__init__.py -------------------------------------------------------------------------------- /models/sam/modeling/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/common.py -------------------------------------------------------------------------------- /models/sam/modeling/image_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/image_encoder.py -------------------------------------------------------------------------------- /models/sam/modeling/mask_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/mask_decoder.py -------------------------------------------------------------------------------- /models/sam/modeling/prompt_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/prompt_encoder.py -------------------------------------------------------------------------------- /models/sam/modeling/sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/sam.py -------------------------------------------------------------------------------- /models/sam/modeling/tiny_vit_sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/tiny_vit_sam.py -------------------------------------------------------------------------------- /models/sam/modeling/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/transformer.py -------------------------------------------------------------------------------- /models/sam/modeling/vit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/modeling/vit.py -------------------------------------------------------------------------------- /models/sam/predictor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/predictor.py -------------------------------------------------------------------------------- /models/sam/utils/.ipynb_checkpoints/transforms-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/utils/.ipynb_checkpoints/transforms-checkpoint.py -------------------------------------------------------------------------------- /models/sam/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/utils/__init__.py -------------------------------------------------------------------------------- /models/sam/utils/amg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/utils/amg.py -------------------------------------------------------------------------------- /models/sam/utils/onnx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/utils/onnx.py -------------------------------------------------------------------------------- /models/sam/utils/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam/utils/transforms.py -------------------------------------------------------------------------------- /models/sam_LoRa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/sam_LoRa.py -------------------------------------------------------------------------------- /models/senet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/senet.py -------------------------------------------------------------------------------- /models/squeezenet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/squeezenet.py -------------------------------------------------------------------------------- /models/tag/__init__.py: -------------------------------------------------------------------------------- 1 | from .tag import * -------------------------------------------------------------------------------- /models/tag/tag.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/tag/tag.py -------------------------------------------------------------------------------- /models/tag/tag_layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/tag/tag_layers.py -------------------------------------------------------------------------------- /models/types_.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/types_.py -------------------------------------------------------------------------------- /models/unet/.ipynb_checkpoints/__init__-checkpoint.py: -------------------------------------------------------------------------------- 1 | from .unet_model import TransUNet 2 | -------------------------------------------------------------------------------- /models/unet/.ipynb_checkpoints/unet_model-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/unet/.ipynb_checkpoints/unet_model-checkpoint.py -------------------------------------------------------------------------------- /models/unet/__init__.py: -------------------------------------------------------------------------------- 1 | from .unet_model import TransUNet 2 | -------------------------------------------------------------------------------- /models/unet/res_net.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/unet/res_net.py -------------------------------------------------------------------------------- /models/unet/unet_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/unet/unet_model.py -------------------------------------------------------------------------------- /models/unet/unet_parts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/unet/unet_parts.py -------------------------------------------------------------------------------- /models/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/utils.py -------------------------------------------------------------------------------- /models/vae.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/vae.py -------------------------------------------------------------------------------- /models/vgg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/models/vgg.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | einops 2 | scikit-image 3 | monai==1.5 4 | -------------------------------------------------------------------------------- /utils/.ipynb_checkpoints/dataset-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/utils/.ipynb_checkpoints/dataset-checkpoint.py -------------------------------------------------------------------------------- /utils/.ipynb_checkpoints/dsc-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/utils/.ipynb_checkpoints/dsc-checkpoint.py -------------------------------------------------------------------------------- /utils/.ipynb_checkpoints/funcs-checkpoint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/utils/.ipynb_checkpoints/funcs-checkpoint.py -------------------------------------------------------------------------------- /utils/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/utils/dataset.py -------------------------------------------------------------------------------- /utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mazurowski-lab/mri_foundation/HEAD/utils/metrics.py --------------------------------------------------------------------------------