├── .gitignore ├── LICENSE ├── README.md ├── pyproject.toml ├── scripts ├── README.md ├── active_learning │ ├── README.md │ └── spineps_refine.py ├── download_datasets.sh ├── prepare_datasets.sh ├── slurm │ └── train_job.sh └── train.sh └── totalspineseg ├── __init__.py ├── inference.py ├── init_inference.py ├── models ├── __init__.py └── transforms_gpu.json ├── resources ├── __init__.py ├── data │ └── training_data.json ├── datasets │ ├── README.md │ ├── dataset_full.json │ ├── dataset_step1.json │ └── dataset_step2.json └── labels_maps │ ├── README.md │ ├── levels_maps.json │ ├── nnunet_full.json │ ├── nnunet_step1.json │ ├── nnunet_step2.json │ ├── nnunet_step2_o2e.json │ └── tss_map.json └── utils ├── augment.py ├── average4d.py ├── cpdir.py ├── crop_image2seg.py ├── extract_alternate.py ├── extract_levels.py ├── extract_soft.py ├── fill_canal.py ├── image.py ├── install_weights.py ├── iterative_label.py ├── largest_component.py ├── map_labels.py ├── predict_nnunet.py ├── 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