├── .gitignore ├── README.md ├── configs ├── 2.5D │ ├── all_maps_config_unet_pct_multi_att_dsv.json │ ├── small_dataset_config_unet_pct_multi_att_dsv.json │ └── tmax_config_unet_pct_multi_att_dsv.json ├── 3D │ ├── all_maps_config_unet_pct_multi_att_dsv.json │ ├── small_dataset_config_unet_pct_multi_att_dsv.json │ ├── tmax_config_unet_pct_multi_att_dsv.json │ └── with_priors │ │ └── with_NCCT_with_penumbra_with_core_config_unet_pct_multi_att_dsv.json └── bayesian_skip │ ├── genevaStrokeDataset │ ├── additive_bayesian_skip.json │ ├── baseline_without_bayesianSkip │ │ ├── baseline.json │ │ ├── baseline_2fconv.json │ │ └── baseline_without_prior.json │ ├── cascading_additive_bayesian_skip.json │ ├── cascading_convolutional_bayesian_skip.json │ ├── convolutional_bayesian_skip.json │ └── noisy_prior_convolutional_bayesian_skip.json │ └── isles2018 │ ├── additive_bayesian_skip.json │ ├── additive_bayesian_skip_with_one_hot_encoded_core.json │ ├── baseline_without_bayesianSkip │ ├── baseline.json │ └── baseline_without_prior.json │ ├── convolutional_bayesian_skip.json │ └── noisy_prior_convolutional_bayesian_skip.json ├── dataio ├── __init__.py ├── loaders │ ├── __init__.py │ ├── geneva_stroke_dataset_25D_pCT.py │ ├── geneva_stroke_dataset_pCT.py │ ├── isles2018_training_dataset.py │ └── utils.py └── transformation │ ├── __init__.py │ ├── imageTransformations.py │ └── transforms.py ├── evaluate_saved_model.py ├── exploration_notebooks ├── csf_mask.ipynb ├── normalisation_exploration.ipynb ├── prior_knowledge.ipynb └── transformations_exploration.ipynb ├── figure_notebooks ├── example_segmentations.ipynb ├── ischemic_core_segmentation_figure.ipynb ├── loss_evolution.ipynb ├── prior_evaluation.ipynb ├── prior_integration_evaluation.ipynb └── prior_performance_correlation.ipynb ├── journal.md ├── models ├── __init__.py ├── base_model.py ├── feedforward_seg_model.py ├── layers │ ├── __init__.py │ ├── grid_attention_layer.py │ ├── loss.py │ └── nonlocal_layer.py ├── networks │ ├── __init__.py │ ├── half_unet_pCT_to_outcome.py │ ├── torch_patch.py │ ├── unet_2D.py │ ├── unet_3D.py │ ├── unet_grid_attention_3D.py │ ├── unet_nonlocal_2D.py │ ├── unet_nonlocal_3D.py │ ├── unet_pCT_bayesian_multi_att_dsv_3D.py │ ├── unet_pCT_cascading_bayesian_multi_att_dsv_3D.py │ ├── unet_pCT_multi_att_dsv_25D_convZ.py │ ├── unet_pCT_multi_att_dsv_25D_poolZ.py │ ├── unet_pCT_multi_att_dsv_3D.py │ ├── unet_pCT_multi_att_dsv_with_2fconv_3D.py │ └── utils.py ├── networks_other.py └── utils.py ├── requirements.txt ├── static ├── figures │ ├── bayesian_skip_net │ │ ├── bayesian_skip_net.eps │ │ └── bayesian_skip_net.svg │ ├── core_segmentation │ │ ├── cbf_map.eps │ │ ├── core_segmentation_figure.eps │ │ ├── core_segmentation_figure.svg │ │ ├── core_segmentation_figure_v2.eps │ │ ├── core_segmentation_figure_v2.svg │ │ ├── corrected_core_mask.eps │ │ ├── csf_mask.eps │ │ ├── presentation │ │ │ ├── CBF.eps │ │ │ ├── corrected_core_mask.eps │ │ │ ├── csf_mask.eps │ │ │ ├── mask.eps │ │ │ ├── masked_CBF.eps │ │ │ ├── masked_relative_CBF_0_1.eps │ │ │ ├── raw_core.eps │ │ │ ├── raw_core_v2.png │ │ │ ├── raw_mask.eps │ │ │ ├── relative_CBF.eps │ │ │ ├── relative_CBF_0_1.eps │ │ │ ├── skull_mask.eps │ │ │ ├── smooth_CBF.eps │ │ │ └── vessel_mask.eps │ │ ├── raw_core.eps │ │ ├── skull_mask.eps │ │ └── vessel_mask.eps │ ├── loss_evolution │ │ ├── all_datasets_validation_loss.eps │ │ ├── gsd_train_loss.eps │ │ ├── gsd_validation_loss.eps │ │ ├── isles_train_and_validation_loss.eps │ │ ├── isles_train_and_validation_loss.svg │ │ ├── isles_train_loss.eps │ │ ├── isles_validation_loss.eps │ │ ├── train_loss.eps │ │ └── validation_loss.eps │ ├── prior_model_perf_corr │ │ ├── Prior_to_model_perf_corr.eps │ │ ├── Prior_to_model_perf_corr.svg │ │ ├── gsd_prior_model_performance_corr.svg │ │ └── isles_prior_model_performance_corr.svg │ └── sample_predictions │ │ ├── gsd_test19_baseline_fig.eps │ │ ├── gsd_test19_conv_bayes_fig.eps │ │ ├── gsd_valid12_lbl_fig.eps │ │ ├── gsd_valid13_baseline_fig.eps │ │ ├── gsd_valid13_conv_bayes_fig.eps │ │ ├── gsd_valid15_lbl_fig.eps │ │ ├── sample_slices.svg │ │ ├── sample_slices2.eps │ │ ├── sample_slices_bright_colors.eps │ │ ├── sample_slices_labeled.eps │ │ └── sample_slices_labeled.svg └── journal │ ├── 2.5D │ ├── 2.5D_convZ_dice_loss_overallDice.png │ ├── 2.5D_convZ_overall_Dice.png │ ├── 2.5D_poolZ_dice_loss_overallDice.png │ ├── 2.5D_poolZ_overall_Dice.png │ ├── 3D_Unet_DiceLoss_baseline.png │ └── 3D_baseline_overall_dice.png │ ├── adam_lr_plateau_dice.png │ ├── adam_lr_step_dice.png │ ├── bayesianSkipNet │ ├── 3D_Unet_DiceLoss_baseline.png │ └── bayesianSkipNet_overall_dice.png │ ├── combined_loss_evaluation │ ├── dice_combined_loss.png │ ├── dice_dice_loss.png │ ├── dice_l1.png │ ├── dice_multi_class_ftl.png │ ├── dice_multi_class_volume_and_dice.png │ ├── dice_single_class_dice.png │ ├── dice_single_class_ftl.png │ ├── dice_volume_and_dice.png │ ├── dice_wbce.png │ ├── loss_combined_loss.png │ ├── loss_dice_loss.png │ ├── loss_l1.png │ ├── loss_multi_class_ftl.png │ ├── loss_multi_class_volume_and_dice.png │ ├── loss_single_class_dice.png │ ├── loss_single_class_ftl.png │ ├── loss_volume_and_dice.png │ └── loss_wbce.png │ ├── dual_output_channel_loss.png │ ├── focal_tversky_dice_over_time.svg │ ├── focal_tversky_loss_over_time.svg │ ├── formulas │ ├── R0_weight.png │ ├── R1_weight.png │ ├── focal_tversky_loss.png │ ├── l1_loss.png │ ├── tversky_loss.png │ ├── volume_loss.png │ └── wbce_loss.png │ ├── hd_evaluation │ └── dice_loss_160x160x96_pmaps_ftversky_unet.png │ ├── l2_evaluation │ ├── l2_e-1.png │ ├── l2_e-2.png │ └── l2_e-4.png │ ├── sgd_lr_plateau_dice.png │ ├── sgd_lr_step_dice.png │ ├── single_output_channel_loss.png │ ├── with_standardisation_dice_over_time.png │ └── without_standardisation_dice_over_time.png ├── train_25d_segmentation.py ├── train_segmentation.py └── utils ├── __init__.py ├── error_logger.py ├── html.py ├── metrics.py ├── plot_logs.py ├── utils.py └── 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