├── README.md ├── assets ├── CESAR_Network.png ├── costa.png └── logo.png ├── costa ├── __init__.py ├── dataset_conversion │ ├── COSTA_dataset_convert.py │ └── __init__.py ├── experiment_planning │ ├── COSTA_plan_and_preprocess.py │ ├── __init__.py │ ├── experiment_planner.py │ ├── experiment_planner_baseline_2DUNet_v21.py │ ├── experiment_planner_baseline_3DUNet.py │ └── utils.py ├── inference │ ├── __init__.py │ ├── plan_inference_input.py │ ├── predict.py │ └── predict_sample.py ├── network_architecture │ ├── __init__.py │ ├── costa.py │ └── swin_transformer.py ├── paths.py ├── preprocessing │ ├── __init__.py │ ├── bet2 │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-311.pyc │ │ │ └── skull_stripping.cpython-311.pyc │ │ └── skull_stripping.py │ ├── cropping.py │ ├── hist_standardization │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-311.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── intensity_hist_stand.cpython-311.pyc │ │ │ ├── intensity_hist_stand.cpython-39.pyc │ │ │ └── train_landmarks.cpython-311.pyc │ │ ├── intensity_hist_stand.py │ │ ├── landmarks.pth │ │ └── train_landmarks.py │ ├── preprocessing.py │ └── sanity_checks.py ├── run │ ├── __init__.py │ ├── default_configuration.py │ ├── run_evaluation.py │ └── run_training.py └── training │ ├── COSTA.py │ ├── __init__.py │ ├── data_augmentation │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── data_augmentation_moreDA.cpython-311.pyc │ │ └── data_augmentation_moreDA.cpython-39.pyc │ └── data_augmentation_moreDA.py │ ├── loss_functions │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-311.pyc │ │ ├── __init__.cpython-37.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── crossentropy.cpython-311.pyc │ │ ├── crossentropy.cpython-37.pyc │ │ ├── crossentropy.cpython-39.pyc │ │ ├── deep_supervision.cpython-311.pyc │ │ ├── deep_supervision.cpython-37.pyc │ │ ├── deep_supervision.cpython-39.pyc │ │ ├── dice_loss.cpython-311.pyc │ │ ├── dice_loss.cpython-37.pyc │ │ ├── dice_loss.cpython-38.pyc │ │ ├── dice_loss.cpython-39.pyc │ │ ├── style_loss.cpython-311.pyc │ │ └── style_loss.cpython-39.pyc │ ├── crossentropy.py │ ├── deep_supervision.py │ ├── dice_loss.py │ └── style_loss.py │ ├── model_restore.py │ ├── network_trainer.py │ ├── nnUNetBasicTrainer.py │ └── nnUNetTrainer.py └── setup.py /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/README.md -------------------------------------------------------------------------------- /assets/CESAR_Network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/assets/CESAR_Network.png -------------------------------------------------------------------------------- /assets/costa.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/assets/costa.png -------------------------------------------------------------------------------- /assets/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/assets/logo.png -------------------------------------------------------------------------------- /costa/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/__init__.py -------------------------------------------------------------------------------- /costa/dataset_conversion/COSTA_dataset_convert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/dataset_conversion/COSTA_dataset_convert.py -------------------------------------------------------------------------------- /costa/dataset_conversion/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/experiment_planning/COSTA_plan_and_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/experiment_planning/COSTA_plan_and_preprocess.py -------------------------------------------------------------------------------- /costa/experiment_planning/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/experiment_planning/experiment_planner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/experiment_planning/experiment_planner.py -------------------------------------------------------------------------------- /costa/experiment_planning/experiment_planner_baseline_2DUNet_v21.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/experiment_planning/experiment_planner_baseline_2DUNet_v21.py -------------------------------------------------------------------------------- /costa/experiment_planning/experiment_planner_baseline_3DUNet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/experiment_planning/experiment_planner_baseline_3DUNet.py -------------------------------------------------------------------------------- /costa/experiment_planning/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/experiment_planning/utils.py -------------------------------------------------------------------------------- /costa/inference/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/inference/plan_inference_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/inference/plan_inference_input.py -------------------------------------------------------------------------------- /costa/inference/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/inference/predict.py -------------------------------------------------------------------------------- /costa/inference/predict_sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/inference/predict_sample.py -------------------------------------------------------------------------------- /costa/network_architecture/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/network_architecture/costa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/network_architecture/costa.py -------------------------------------------------------------------------------- /costa/network_architecture/swin_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/network_architecture/swin_transformer.py -------------------------------------------------------------------------------- /costa/paths.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/paths.py -------------------------------------------------------------------------------- /costa/preprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/preprocessing/bet2/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/preprocessing/bet2/__pycache__/__init__.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/bet2/__pycache__/__init__.cpython-311.pyc -------------------------------------------------------------------------------- /costa/preprocessing/bet2/__pycache__/skull_stripping.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/bet2/__pycache__/skull_stripping.cpython-311.pyc -------------------------------------------------------------------------------- /costa/preprocessing/bet2/skull_stripping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/bet2/skull_stripping.py -------------------------------------------------------------------------------- /costa/preprocessing/cropping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/cropping.py -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__pycache__/__init__.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/__pycache__/__init__.cpython-311.pyc -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/__pycache__/__init__.cpython-39.pyc -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__pycache__/intensity_hist_stand.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/__pycache__/intensity_hist_stand.cpython-311.pyc -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__pycache__/intensity_hist_stand.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/__pycache__/intensity_hist_stand.cpython-39.pyc -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/__pycache__/train_landmarks.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/__pycache__/train_landmarks.cpython-311.pyc -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/intensity_hist_stand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/intensity_hist_stand.py -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/landmarks.pth: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/landmarks.pth -------------------------------------------------------------------------------- /costa/preprocessing/hist_standardization/train_landmarks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/hist_standardization/train_landmarks.py -------------------------------------------------------------------------------- /costa/preprocessing/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/preprocessing.py -------------------------------------------------------------------------------- /costa/preprocessing/sanity_checks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/preprocessing/sanity_checks.py -------------------------------------------------------------------------------- /costa/run/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/run/default_configuration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/run/default_configuration.py -------------------------------------------------------------------------------- /costa/run/run_evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/run/run_evaluation.py -------------------------------------------------------------------------------- /costa/run/run_training.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/run/run_training.py -------------------------------------------------------------------------------- /costa/training/COSTA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/COSTA.py -------------------------------------------------------------------------------- /costa/training/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/training/data_augmentation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /costa/training/data_augmentation/__pycache__/__init__.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/data_augmentation/__pycache__/__init__.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/data_augmentation/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/data_augmentation/__pycache__/__init__.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/data_augmentation/__pycache__/data_augmentation_moreDA.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/data_augmentation/__pycache__/data_augmentation_moreDA.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/data_augmentation/__pycache__/data_augmentation_moreDA.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/data_augmentation/__pycache__/data_augmentation_moreDA.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/data_augmentation/data_augmentation_moreDA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/data_augmentation/data_augmentation_moreDA.py -------------------------------------------------------------------------------- /costa/training/loss_functions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__init__.py -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/__init__.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/__init__.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/__init__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/__init__.cpython-37.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/__init__.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/__init__.cpython-38.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/__init__.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/crossentropy.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/crossentropy.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/crossentropy.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/crossentropy.cpython-37.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/crossentropy.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/crossentropy.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/deep_supervision.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/deep_supervision.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/deep_supervision.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/deep_supervision.cpython-37.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/deep_supervision.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/deep_supervision.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/dice_loss.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/dice_loss.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/dice_loss.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/dice_loss.cpython-37.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/dice_loss.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/dice_loss.cpython-38.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/dice_loss.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/dice_loss.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/style_loss.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/style_loss.cpython-311.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/__pycache__/style_loss.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/__pycache__/style_loss.cpython-39.pyc -------------------------------------------------------------------------------- /costa/training/loss_functions/crossentropy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/crossentropy.py -------------------------------------------------------------------------------- /costa/training/loss_functions/deep_supervision.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/deep_supervision.py -------------------------------------------------------------------------------- /costa/training/loss_functions/dice_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/dice_loss.py -------------------------------------------------------------------------------- /costa/training/loss_functions/style_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/loss_functions/style_loss.py -------------------------------------------------------------------------------- /costa/training/model_restore.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/model_restore.py -------------------------------------------------------------------------------- /costa/training/network_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/network_trainer.py -------------------------------------------------------------------------------- /costa/training/nnUNetBasicTrainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/nnUNetBasicTrainer.py -------------------------------------------------------------------------------- /costa/training/nnUNetTrainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/costa/training/nnUNetTrainer.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iMED-Lab/COSTA/HEAD/setup.py --------------------------------------------------------------------------------