├── .gitignore ├── 3D Unet ├── models │ ├── __init__.py │ ├── appearance_model.py │ ├── architectures.py │ ├── auto_encoder_flow.py │ ├── discriminator.py │ ├── encoder.py │ ├── flow_model.py │ ├── gan_model.py │ ├── generator.py │ ├── generator_style.py │ ├── unet.py │ └── unet3D.py ├── oasis_data.py ├── one_vol_test.py ├── optim │ ├── UNET3D_trainer.py │ ├── UNET_trainer.py │ ├── __init__.py │ ├── base_trainer.py │ ├── main.py │ └── utils.py ├── train.py ├── unet2d_test.py ├── utilities │ ├── __init__.py │ ├── iter_counter.py │ ├── util.py │ └── visualizer.py └── visualization │ ├── __init__.py │ └── visualization.py ├── OURS ├── README.md ├── dataset_loaders │ ├── __init__.py │ ├── flowsampler.py │ ├── mri.py │ └── transformations.py ├── evaluations │ ├── __init__.py │ ├── analysis.py │ ├── constants.py │ ├── evaluate_segmentation.py │ ├── figures.py │ ├── helpers.py │ ├── style_flow_analysis.py │ └── tnse_viz.py ├── generate_data.py ├── generate_fake_data.py ├── generate_flow.py ├── loss │ ├── __init__.py │ ├── cross_correlation.py │ ├── ganloss.py │ ├── gradient_loss.py │ ├── kld.py │ └── style_loss.py ├── models │ ├── __init__.py │ ├── adverserial_flow.py │ ├── appearance_model.py │ ├── architectures.py │ ├── discriminator.py │ ├── encoder.py │ ├── spatial_transformer.py │ ├── unet.py │ └── unet_flow_model.py ├── pipeline_v2-1.png ├── registration_tools │ ├── __init__.py │ └── methods.py ├── run_evaluations.py ├── timing.py ├── train.py ├── trainers │ ├── __init__.py │ ├── ae_trainer.py │ ├── style_trainer.py │ ├── train_adversarial_flow.py │ ├── train_appearance.py │ └── train_end_to_end.py └── utilities │ ├── __init__.py │ ├── iter_counter.py │ ├── util.py │ └── visualizer.py └── README.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/.gitignore -------------------------------------------------------------------------------- /3D Unet/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/__init__.py -------------------------------------------------------------------------------- /3D Unet/models/appearance_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/appearance_model.py -------------------------------------------------------------------------------- /3D Unet/models/architectures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/architectures.py -------------------------------------------------------------------------------- /3D Unet/models/auto_encoder_flow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/auto_encoder_flow.py -------------------------------------------------------------------------------- /3D Unet/models/discriminator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/discriminator.py -------------------------------------------------------------------------------- /3D Unet/models/encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/encoder.py -------------------------------------------------------------------------------- /3D Unet/models/flow_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/flow_model.py -------------------------------------------------------------------------------- /3D Unet/models/gan_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/gan_model.py -------------------------------------------------------------------------------- /3D Unet/models/generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/generator.py -------------------------------------------------------------------------------- /3D Unet/models/generator_style.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/generator_style.py -------------------------------------------------------------------------------- /3D Unet/models/unet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/unet.py -------------------------------------------------------------------------------- /3D Unet/models/unet3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/models/unet3D.py -------------------------------------------------------------------------------- /3D Unet/oasis_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/oasis_data.py -------------------------------------------------------------------------------- /3D Unet/one_vol_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/one_vol_test.py -------------------------------------------------------------------------------- /3D Unet/optim/UNET3D_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/UNET3D_trainer.py -------------------------------------------------------------------------------- /3D Unet/optim/UNET_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/UNET_trainer.py -------------------------------------------------------------------------------- /3D Unet/optim/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/__init__.py -------------------------------------------------------------------------------- /3D Unet/optim/base_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/base_trainer.py -------------------------------------------------------------------------------- /3D Unet/optim/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/main.py -------------------------------------------------------------------------------- /3D Unet/optim/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/optim/utils.py -------------------------------------------------------------------------------- /3D Unet/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/train.py -------------------------------------------------------------------------------- /3D Unet/unet2d_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/unet2d_test.py -------------------------------------------------------------------------------- /3D Unet/utilities/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/utilities/__init__.py -------------------------------------------------------------------------------- /3D Unet/utilities/iter_counter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/utilities/iter_counter.py -------------------------------------------------------------------------------- /3D Unet/utilities/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/utilities/util.py -------------------------------------------------------------------------------- /3D Unet/utilities/visualizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/utilities/visualizer.py -------------------------------------------------------------------------------- /3D Unet/visualization/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/visualization/__init__.py -------------------------------------------------------------------------------- /3D Unet/visualization/visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/3D Unet/visualization/visualization.py -------------------------------------------------------------------------------- /OURS/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/README.md -------------------------------------------------------------------------------- /OURS/dataset_loaders/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/dataset_loaders/__init__.py -------------------------------------------------------------------------------- /OURS/dataset_loaders/flowsampler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/dataset_loaders/flowsampler.py -------------------------------------------------------------------------------- /OURS/dataset_loaders/mri.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/dataset_loaders/mri.py -------------------------------------------------------------------------------- /OURS/dataset_loaders/transformations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/dataset_loaders/transformations.py -------------------------------------------------------------------------------- /OURS/evaluations/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/__init__.py -------------------------------------------------------------------------------- /OURS/evaluations/analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/analysis.py -------------------------------------------------------------------------------- /OURS/evaluations/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/constants.py -------------------------------------------------------------------------------- /OURS/evaluations/evaluate_segmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/evaluate_segmentation.py -------------------------------------------------------------------------------- /OURS/evaluations/figures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/figures.py -------------------------------------------------------------------------------- /OURS/evaluations/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/helpers.py -------------------------------------------------------------------------------- /OURS/evaluations/style_flow_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/style_flow_analysis.py -------------------------------------------------------------------------------- /OURS/evaluations/tnse_viz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/evaluations/tnse_viz.py -------------------------------------------------------------------------------- /OURS/generate_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/generate_data.py -------------------------------------------------------------------------------- /OURS/generate_fake_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/generate_fake_data.py -------------------------------------------------------------------------------- /OURS/generate_flow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/generate_flow.py -------------------------------------------------------------------------------- /OURS/loss/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/__init__.py -------------------------------------------------------------------------------- /OURS/loss/cross_correlation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/cross_correlation.py -------------------------------------------------------------------------------- /OURS/loss/ganloss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/ganloss.py -------------------------------------------------------------------------------- /OURS/loss/gradient_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/gradient_loss.py -------------------------------------------------------------------------------- /OURS/loss/kld.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/kld.py -------------------------------------------------------------------------------- /OURS/loss/style_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/loss/style_loss.py -------------------------------------------------------------------------------- /OURS/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/__init__.py -------------------------------------------------------------------------------- /OURS/models/adverserial_flow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/adverserial_flow.py -------------------------------------------------------------------------------- /OURS/models/appearance_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/appearance_model.py -------------------------------------------------------------------------------- /OURS/models/architectures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/architectures.py -------------------------------------------------------------------------------- /OURS/models/discriminator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/discriminator.py -------------------------------------------------------------------------------- /OURS/models/encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/encoder.py -------------------------------------------------------------------------------- /OURS/models/spatial_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/spatial_transformer.py -------------------------------------------------------------------------------- /OURS/models/unet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/unet.py -------------------------------------------------------------------------------- /OURS/models/unet_flow_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/models/unet_flow_model.py -------------------------------------------------------------------------------- /OURS/pipeline_v2-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/pipeline_v2-1.png -------------------------------------------------------------------------------- /OURS/registration_tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /OURS/registration_tools/methods.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/registration_tools/methods.py -------------------------------------------------------------------------------- /OURS/run_evaluations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/run_evaluations.py -------------------------------------------------------------------------------- /OURS/timing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/timing.py -------------------------------------------------------------------------------- /OURS/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/train.py -------------------------------------------------------------------------------- /OURS/trainers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/__init__.py -------------------------------------------------------------------------------- /OURS/trainers/ae_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/ae_trainer.py -------------------------------------------------------------------------------- /OURS/trainers/style_trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/style_trainer.py -------------------------------------------------------------------------------- /OURS/trainers/train_adversarial_flow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/train_adversarial_flow.py -------------------------------------------------------------------------------- /OURS/trainers/train_appearance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/train_appearance.py -------------------------------------------------------------------------------- /OURS/trainers/train_end_to_end.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/trainers/train_end_to_end.py -------------------------------------------------------------------------------- /OURS/utilities/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/utilities/__init__.py -------------------------------------------------------------------------------- /OURS/utilities/iter_counter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/utilities/iter_counter.py -------------------------------------------------------------------------------- /OURS/utilities/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/utilities/util.py -------------------------------------------------------------------------------- /OURS/utilities/visualizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/OURS/utilities/visualizer.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/devavratTomar/SST/HEAD/README.md --------------------------------------------------------------------------------