├── .gitignore ├── .travis.yml ├── README.md ├── docs ├── Makefile ├── conf.py ├── datasets.rst ├── index.rst ├── patterns.rst ├── readers.rst └── samplers.rst ├── examples ├── 01_brain_segmentation_MRI │ ├── architecture.py │ ├── datasets │ │ ├── inference.py │ │ ├── mappings.py │ │ └── training.py │ ├── inference_canvas.py │ ├── readme.md │ ├── segment.py │ ├── train.py │ ├── train_segment.py │ └── utils.py ├── 02_brain_segmentation_NonAdjLoss_MRI │ ├── architecture.py │ ├── datasets │ │ ├── inference.py │ │ ├── mappings.py │ │ └── training.py │ ├── inference_canvas.py │ ├── loss.py │ ├── readme.md │ ├── segment.py │ ├── train.py │ ├── train_segment.py │ └── utils.py └── scripts │ ├── adjacency │ ├── extract_3d_adjacency.py │ └── extract_3d_adjacency_from_seg.py │ ├── preprocessing │ ├── ibsr_v2.py │ ├── mappings.py │ ├── miccai12.py │ └── oasis.py │ └── report │ ├── plot_boxplot_labels_by_metric.py │ ├── plot_boxplot_patients_by_metric.py │ ├── write_label_by_metric.py │ ├── write_model_by_metric.py │ ├── write_patient_by_metric.py │ └── write_top_label_by_metric.py ├── requirements.txt ├── setup.py ├── test ├── evaluation │ ├── __init__.py │ └── test_dice.py └── patterns │ ├── __init__.py │ └── test_patch2d.py └── torchmed ├── __init__.py ├── datasets ├── __init__.py ├── medcombiner.py ├── medfile.py └── medfolder.py ├── patterns ├── __init__.py └── patch.py ├── readers ├── __init__.py ├── cv.py ├── nib.py ├── pil.py ├── reader.py └── simpleitk.py ├── samplers ├── __init__.py ├── mask_sampler.py └── sampler.py └── utils ├── __init__.py ├── augmentation.py ├── file.py ├── logger_plotter.py ├── loss.py ├── metric.py ├── multiproc.py ├── preprocessing.py └── transforms.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/trypag/torchmed/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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