├── .gitignore ├── BraTS ├── DataSet.py ├── Patient.py ├── __init__.py ├── load_utils.py ├── modalities.py ├── structure.py ├── test.py └── test_load.py ├── README.md ├── __init__.py ├── augmentation ├── __init__.py └── augmentation.py ├── cloudml-gpu.yaml ├── download-brats.sh ├── evaluate.sh ├── gcs-seg.sh ├── local-seg.sh ├── preprocessing ├── BraTS_partition │ ├── __init__.py │ ├── test_ids │ ├── train_ids │ └── validation_ids ├── __init__.py ├── _legacy_code.py ├── createTFRecords.py ├── normalization.py ├── normalize.py ├── partition-data.py ├── partitioning.py ├── partitions.py ├── patches.py └── records.py ├── proposal.md ├── segmentation ├── UNet3D.py ├── __init__.py ├── cloudml-gpu.yaml ├── config.py ├── config_gcp.ini ├── config_local.ini ├── evaluate.py ├── keras_UNet3D.py ├── metrics.py ├── params.json ├── params.py ├── train.py ├── train_patches.py └── visualization.py ├── setup.py ├── submissions ├── final_report │ ├── Brats18_2013_12_1_108.png │ ├── Brats18_CBICA_AUN_1_111.png │ ├── Brats18_TCIA08_406_1_127.png │ ├── Brats18_TCIA10_420_1_97.png │ ├── Brats18_TCIA10_449_1_162.png │ ├── CS230.png │ ├── brain_example.png │ ├── main.pdf │ ├── main.synctex.gz │ ├── main.tex │ ├── model_arch.png │ ├── nips_2017.sty │ ├── references.bib │ └── stanford.png └── poster_final.pdf ├── tensorboard └── 2018-06-05.10:57_lr_0.0001 │ └── events.out.tfevents.1528221429.Cams-MacBook-Air.local ├── trained_models └── unet │ ├── cross_entropy_loss │ ├── checkpoint │ ├── unet-6765.data-00000-of-00001 │ ├── unet-6765.index │ ├── unet-6765.meta │ ├── unet-6970.data-00000-of-00001 │ ├── unet-6970.index │ ├── unet-6970.meta │ ├── unet-7175.data-00000-of-00001 │ ├── unet-7175.index │ ├── unet-7175.meta │ ├── unet-7380.data-00000-of-00001 │ ├── unet-7380.index │ ├── unet-7380.meta │ ├── unet-7585.data-00000-of-00001 │ ├── unet-7585.index │ └── unet-7585.meta │ ├── original_no_noise │ ├── checkpoint │ ├── model-43036.data-00000-of-00001 │ ├── model-43036.index │ ├── model-43036.meta │ ├── model-43848.data-00000-of-00001 │ ├── model-43848.index │ ├── model-43848.meta │ ├── model-44660.data-00000-of-00001 │ ├── model-44660.index │ ├── model-44660.meta │ ├── model-45472.data-00000-of-00001 │ ├── model-45472.index │ ├── model-45472.meta │ ├── model-46284.data-00000-of-00001 │ ├── model-46284.index │ └── model-46284.meta │ └── original_noisy │ ├── checkpoint │ ├── model-11368.data-00000-of-00001 │ ├── model-11368.index │ ├── model-11368.meta │ ├── model-12992.data-00000-of-00001 │ ├── model-12992.index │ ├── model-12992.meta │ ├── model-14616.data-00000-of-00001 │ ├── model-14616.index │ ├── model-14616.meta │ ├── model-16240.data-00000-of-00001 │ ├── model-16240.index │ ├── model-16240.meta │ ├── model-17864.data-00000-of-00001 │ ├── model-17864.index │ └── model-17864.meta └── trained_models_cam └── unet └── original_no_noise ├── checkpoint ├── model_outputs-1624.data-00000-of-00001 ├── model_outputs-1624.index ├── model_outputs-1624.meta ├── model_outputs-2436.data-00000-of-00001 ├── model_outputs-2436.index ├── model_outputs-2436.meta ├── model_outputs-3248.data-00000-of-00001 ├── model_outputs-3248.index ├── model_outputs-3248.meta ├── model_outputs-7790.data-00000-of-00001 ├── model_outputs-7790.index ├── model_outputs-7790.meta ├── model_outputs-7995.data-00000-of-00001 ├── model_outputs-7995.index ├── model_outputs-7995.meta ├── model_outputs-812.data-00000-of-00001 ├── model_outputs-812.index ├── model_outputs-812.meta ├── model_outputs-8200.data-00000-of-00001 ├── model_outputs-8200.index ├── model_outputs-8200.meta ├── model_outputs-8405.data-00000-of-00001 ├── model_outputs-8405.index ├── model_outputs-8405.meta ├── model_outputs-8610.data-00000-of-00001 ├── model_outputs-8610.index └── model_outputs-8610.meta /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jondeaton/BraTS18-Project/HEAD/.gitignore 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