├── .gitignore ├── README.md ├── code ├── __init__.py ├── models │ ├── __init__.py │ └── create_unet_model.py ├── sampling │ ├── __init__.py │ ├── dataloader.py │ ├── datasets.py │ └── transforms.py ├── training_2D │ ├── __init__.py │ ├── train_AE_augment.py │ ├── train_AE_sampler_noaug.py │ └── train_segmentation_augment.py └── training_3D │ ├── train_regression_3D.py │ └── train_segmentation_3D.py ├── data_2D ├── example_batch │ ├── 0_x.jpg │ ├── 0_y.jpg │ ├── 1_x.jpg │ ├── 1_y.jpg │ ├── 2_x.jpg │ ├── 2_y.jpg │ ├── 3_x.jpg │ ├── 3_y.jpg │ ├── 4_x.jpg │ ├── 4_y.jpg │ ├── 5_x.jpg │ ├── 5_y.jpg │ ├── 6_x.jpg │ ├── 6_y.jpg │ ├── 7_x.jpg │ ├── 7_y.jpg │ ├── 8_x.jpg │ ├── 8_y.jpg │ ├── 9_x.jpg │ ├── 9_y.jpg │ ├── 10_x.jpg │ ├── 10_y.jpg │ ├── 11_x.jpg │ ├── 11_y.jpg │ ├── 12_x.jpg │ ├── 12_y.jpg │ ├── 13_x.jpg │ ├── 13_y.jpg │ ├── 14_x.jpg │ ├── 14_y.jpg │ ├── 15_x.jpg │ ├── 15_y.jpg │ ├── 16_x.jpg │ ├── 16_y.jpg │ ├── 17_x.jpg │ ├── 17_y.jpg │ ├── 18_x.jpg │ ├── 18_y.jpg │ ├── 19_x.jpg │ ├── 19_y.jpg │ ├── 20_x.jpg │ ├── 20_y.jpg │ ├── 21_x.jpg │ ├── 21_y.jpg │ ├── 22_x.jpg │ ├── 22_y.jpg │ ├── 23_x.jpg │ ├── 23_y.jpg │ ├── 24_x.jpg │ ├── 24_y.jpg │ ├── 25_x.jpg │ ├── 25_y.jpg │ ├── 26_x.jpg │ ├── 26_y.jpg │ ├── 27_x.jpg │ ├── 27_y.jpg │ ├── 28_x.jpg │ ├── 28_y.jpg │ ├── 29_x.jpg │ ├── 29_y.jpg │ ├── 30_x.jpg │ ├── 30_y.jpg │ ├── 31_x.jpg │ └── 31_y.jpg ├── image_filemap.csv └── images │ ├── 0000H1_2D.nii.gz │ ├── 0000Mask_2D.nii.gz │ ├── 0001H1_2D.nii.gz │ ├── 0001Mask_2D.nii.gz │ ├── 0002H1_2D.nii.gz │ ├── 0002Mask_2D.nii.gz │ ├── 0003H1_2D.nii.gz │ ├── 0003Mask_2D.nii.gz │ ├── 0004H1_2D.nii.gz │ ├── 0004Mask_2D.nii.gz │ ├── 0005H1_2D.nii.gz │ ├── 0005Mask_2D.nii.gz │ ├── 0006H1_2D.nii.gz │ ├── 0006Mask_2D.nii.gz │ ├── 0007H1_2D.nii.gz │ ├── 0007Mask_2D.nii.gz │ ├── 0008H1_2D.nii.gz │ ├── 0008Mask_2D.nii.gz │ ├── 0009H1_2D.nii.gz │ ├── 0009Mask_2D.nii.gz │ ├── 0010H1_2D.nii.gz │ ├── 0010Mask_2D.nii.gz │ ├── 0011H1_2D.nii.gz │ ├── 0011Mask_2D.nii.gz │ ├── 0012H1_2D.nii.gz │ ├── 0012Mask_2D.nii.gz │ ├── 0013H1_2D.nii.gz │ ├── 0013Mask_2D.nii.gz │ ├── 0014H1_2D.nii.gz │ ├── 0014Mask_2D.nii.gz │ ├── 0015H1_2D.nii.gz │ ├── 0015Mask_2D.nii.gz │ ├── 0016H1_2D.nii.gz │ ├── 0016Mask_2D.nii.gz │ ├── 0017H1_2D.nii.gz │ ├── 0017Mask_2D.nii.gz │ ├── 0018H1_2D.nii.gz │ ├── 0018Mask_2D.nii.gz │ ├── 0019H1_2D.nii.gz │ ├── 0019Mask_2D.nii.gz │ ├── 0020H1_2D.nii.gz │ ├── 0020Mask_2D.nii.gz │ ├── 0021H1_2D.nii.gz │ ├── 0021Mask_2D.nii.gz │ ├── 0022H1_2D.nii.gz │ ├── 0022Mask_2D.nii.gz │ ├── 0023H1_2D.nii.gz │ ├── 0023Mask_2D.nii.gz │ ├── 0024H1_2D.nii.gz │ ├── 0024Mask_2D.nii.gz │ ├── 0025H1_2D.nii.gz │ ├── 0025Mask_2D.nii.gz │ ├── 0026H1_2D.nii.gz │ ├── 0026Mask_2D.nii.gz │ ├── 0027H1_2D.nii.gz │ ├── 0027Mask_2D.nii.gz │ ├── 0028H1_2D.nii.gz │ ├── 0028Mask_2D.nii.gz │ ├── 0029H1_2D.nii.gz │ ├── 0029Mask_2D.nii.gz │ ├── 0030H1_2D.nii.gz │ ├── 0030Mask_2D.nii.gz │ ├── 0031H1_2D.nii.gz │ ├── 0031Mask_2D.nii.gz │ ├── 0032H1_2D.nii.gz │ ├── 0032Mask_2D.nii.gz │ ├── 0033H1_2D.nii.gz │ ├── 0033Mask_2D.nii.gz │ ├── 0034H1_2D.nii.gz │ ├── 0034Mask_2D.nii.gz │ ├── 0035H1_2D.nii.gz │ ├── 0035Mask_2D.nii.gz │ ├── 0036H1_2D.nii.gz │ ├── 0036Mask_2D.nii.gz │ ├── 0037H1_2D.nii.gz │ ├── 0037Mask_2D.nii.gz │ ├── 0038H1_2D.nii.gz │ ├── 0038Mask_2D.nii.gz │ ├── 0039H1_2D.nii.gz │ ├── 0039Mask_2D.nii.gz │ ├── 0040H1_2D.nii.gz │ ├── 0040Mask_2D.nii.gz │ ├── 0041H1_2D.nii.gz │ ├── 0041Mask_2D.nii.gz │ ├── 0042H1_2D.nii.gz │ ├── 0042Mask_2D.nii.gz │ ├── 0043H1_2D.nii.gz │ ├── 0043Mask_2D.nii.gz │ ├── 0044H1_2D.nii.gz │ ├── 0044Mask_2D.nii.gz │ ├── 0045H1_2D.nii.gz │ ├── 0045Mask_2D.nii.gz │ ├── 0046H1_2D.nii.gz │ ├── 0046Mask_2D.nii.gz │ ├── 0047H1_2D.nii.gz │ ├── 0047Mask_2D.nii.gz │ ├── 0048H1_2D.nii.gz │ ├── 0048Mask_2D.nii.gz │ ├── 0049H1_2D.nii.gz │ ├── 0049Mask_2D.nii.gz │ ├── 0050H1_2D.nii.gz │ ├── 0050Mask_2D.nii.gz │ ├── 0051H1_2D.nii.gz │ ├── 0051Mask_2D.nii.gz │ ├── 0052H1_2D.nii.gz │ ├── 0052Mask_2D.nii.gz │ ├── 0053H1_2D.nii.gz │ ├── 0053Mask_2D.nii.gz │ ├── 0054H1_2D.nii.gz │ ├── 0054Mask_2D.nii.gz │ ├── 0055H1_2D.nii.gz │ ├── 0055Mask_2D.nii.gz │ ├── 0056H1_2D.nii.gz │ ├── 0056Mask_2D.nii.gz │ ├── 0057H1_2D.nii.gz │ ├── 0057Mask_2D.nii.gz │ ├── 0058H1_2D.nii.gz │ ├── 0058Mask_2D.nii.gz │ ├── 0059H1_2D.nii.gz │ ├── 0059Mask_2D.nii.gz │ ├── 0060H1_2D.nii.gz │ ├── 0060Mask_2D.nii.gz │ ├── 0061H1_2D.nii.gz │ ├── 0061Mask_2D.nii.gz │ ├── 0062H1_2D.nii.gz │ └── 0062Mask_2D.nii.gz ├── data_3D ├── image_filemap.csv └── images │ ├── seg │ ├── 28326_session1_T1_BrainSegmentation.nii.gz │ ├── 28327_session1_T1_BrainSegmentation.nii.gz │ ├── 28328_session1_T1_BrainSegmentation.nii.gz │ ├── 28332_session1_T1_BrainSegmentation.nii.gz │ ├── 28335_session1_T1_BrainSegmentation.nii.gz │ ├── 28336_session1_T1_BrainSegmentation.nii.gz │ ├── 28337_session1_T1_BrainSegmentation.nii.gz │ ├── 28341_session1_T1_BrainSegmentation.nii.gz │ ├── 28344_session1_T1_BrainSegmentation.nii.gz │ ├── 28345_session1_T1_BrainSegmentation.nii.gz │ ├── 28346_session1_T1_BrainSegmentation.nii.gz │ ├── 28347_session1_T1_BrainSegmentation.nii.gz │ ├── 28351_session1_T1_BrainSegmentation.nii.gz │ ├── 28354_session1_T1_BrainSegmentation.nii.gz │ └── 28355_session1_T1_BrainSegmentation.nii.gz │ └── t1 │ ├── 0028326 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028327 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028328 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028332 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028335 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028336 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028337 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028341 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028344 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028345 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028346 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028347 │ └── session_1 │ │ └── anat_1 │ │ └── anat.nii.gz │ ├── 0028351 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ ├── 0028354 │ └── session_1 │ │ ├── anat_1 │ │ └── anat.nii.gz │ │ └── pet_1 │ │ └── pet.nii.gz │ └── 0028355 │ └── session_1 │ ├── anat_1 │ └── anat.nii.gz │ └── pet_1 │ └── pet.nii.gz ├── example-original.png ├── example-rotate.png └── results_2D ├── dice_fig.png ├── loss_fig.png └── predictions ├── 00_pred.png ├── 00_truth.png ├── 01_pred.png ├── 01_truth.png ├── 02_pred.png ├── 02_truth.png ├── 03_pred.png ├── 03_truth.png ├── 04_pred.png ├── 04_truth.png ├── 05_pred.png ├── 05_truth.png ├── 06_pred.png ├── 06_truth.png ├── 07_pred.png ├── 07_truth.png ├── 08_pred.png ├── 08_truth.png ├── 09_pred.png ├── 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