├── .coveragerc ├── .dockerignore ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── labeler.yml └── workflows │ ├── changelog-build.yml │ ├── cherry-pick-release-commit.yml │ ├── close-inactive-issue-pr.yml │ ├── codeql.yml │ ├── config │ ├── changelog-config.json │ └── codeql.yml │ ├── coverage.yml │ ├── gh-docs.yml │ ├── labeler.yml │ └── tox.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── README.md ├── SECURITY.md ├── assets ├── atommic-logo.png └── atommic-schematic_overview.png ├── atommic ├── __init__.py ├── cli │ ├── __init__.py │ └── launch.py ├── collections │ ├── __init__.py │ ├── common │ │ ├── __init__.py │ │ ├── callbacks │ │ │ ├── __init__.py │ │ │ ├── callbacks.py │ │ │ └── ema.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── mri_loader.py │ │ │ └── subsample.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ ├── aggregator.py │ │ │ └── wasserstein.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ └── global_average_loss_metric.py │ │ ├── nn │ │ │ ├── __init__.py │ │ │ └── base.py │ │ └── parts │ │ │ ├── __init__.py │ │ │ ├── coil_sensitivity_maps.py │ │ │ ├── fft.py │ │ │ ├── patch_utils.py │ │ │ ├── transforms.py │ │ │ └── utils.py │ ├── motioncorrection │ │ ├── __init__.py │ │ └── parts │ │ │ ├── __init__.py │ │ │ └── motionsimulation.py │ ├── multitask │ │ ├── __init__.py │ │ └── rs │ │ │ ├── __init__.py │ │ │ ├── data │ │ │ ├── __init__.py │ │ │ └── mrirs_loader.py │ │ │ ├── nn │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── idslr.py │ │ │ ├── idslr_base │ │ │ │ ├── __init__.py │ │ │ │ └── idslr_block.py │ │ │ ├── idslr_unet.py │ │ │ ├── mtlrs.py │ │ │ ├── mtlrs_base │ │ │ │ ├── __init__.py │ │ │ │ └── mtlrs_block.py │ │ │ ├── recseg_unet.py │ │ │ ├── segnet.py │ │ │ ├── seranet.py │ │ │ └── seranet_base │ │ │ │ ├── __init__.py │ │ │ │ ├── convlstm.py │ │ │ │ ├── convlstm_unet.py │ │ │ │ └── seranet_block.py │ │ │ └── parts │ │ │ ├── __init__.py │ │ │ └── transforms.py │ ├── quantitative │ │ ├── __init__.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ └── qmri_loader.py │ │ ├── nn │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── qcirim.py │ │ │ ├── qrim_base │ │ │ │ ├── __init__.py │ │ │ │ ├── qrim_block.py │ │ │ │ └── utils.py │ │ │ ├── qvarnet.py │ │ │ ├── qvarnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── qvarnet_block.py │ │ │ └── qzf.py │ │ └── parts │ │ │ ├── __init__.py │ │ │ └── transforms.py │ ├── reconstruction │ │ ├── __init__.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ └── mri_reconstruction_loader.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ ├── na.py │ │ │ └── ssim.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ └── reconstruction_metrics.py │ │ ├── nn │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── ccnn.py │ │ │ ├── ccnn_base │ │ │ │ ├── __init__.py │ │ │ │ └── ccnn_block.py │ │ │ ├── cirim.py │ │ │ ├── crnn.py │ │ │ ├── crnn_base │ │ │ │ ├── __init__.py │ │ │ │ └── crnn_block.py │ │ │ ├── crossdomain_base │ │ │ │ ├── __init__.py │ │ │ │ └── crossdomain_block.py │ │ │ ├── didn_base │ │ │ │ ├── __init__.py │ │ │ │ └── didn_block.py │ │ │ ├── dunet.py │ │ │ ├── jointicnet.py │ │ │ ├── kikinet.py │ │ │ ├── lpd.py │ │ │ ├── modl.py │ │ │ ├── modl_base │ │ │ │ ├── __init__.py │ │ │ │ └── modl_block.py │ │ │ ├── multidomainnet.py │ │ │ ├── multidomainnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── multidomainnet_block.py │ │ │ ├── mwcnn_base │ │ │ │ ├── __init__.py │ │ │ │ └── mwcnn_block.py │ │ │ ├── primaldualnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── primaldualnet_block.py │ │ │ ├── proximal_gradient.py │ │ │ ├── recurrentvarnet.py │ │ │ ├── recurrentvarnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── recurrentvarnet_block.py │ │ │ ├── rim_base │ │ │ │ ├── __init__.py │ │ │ │ ├── conv_layers.py │ │ │ │ ├── rim_block.py │ │ │ │ ├── rim_utils.py │ │ │ │ └── rnn_cells.py │ │ │ ├── sigmanet_base │ │ │ │ ├── __init__.py │ │ │ │ ├── dc_layers.py │ │ │ │ └── sensitivity_net.py │ │ │ ├── unet.py │ │ │ ├── unet_base │ │ │ │ ├── __init__.py │ │ │ │ └── unet_block.py │ │ │ ├── varnet.py │ │ │ ├── varnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── varnet_block.py │ │ │ ├── vsnet.py │ │ │ ├── vsnet_base │ │ │ │ ├── __init__.py │ │ │ │ └── vsnet_block.py │ │ │ ├── xpdnet.py │ │ │ └── zf.py │ │ └── parts │ │ │ ├── __init__.py │ │ │ └── transforms.py │ └── segmentation │ │ ├── __init__.py │ │ ├── data │ │ ├── __init__.py │ │ └── mri_segmentation_loader.py │ │ ├── losses │ │ ├── __init__.py │ │ ├── cross_entropy.py │ │ ├── dice.py │ │ └── utils.py │ │ ├── metrics │ │ ├── __init__.py │ │ └── segmentation_metrics.py │ │ ├── nn │ │ ├── __init__.py │ │ ├── attentionunet.py │ │ ├── attentionunet_base │ │ │ ├── __init__.py │ │ │ └── attentionunet_block.py │ │ ├── base.py │ │ ├── dynunet.py │ │ ├── dynunet_base │ │ │ ├── __init__.py │ │ │ └── dynunet_block.py │ │ ├── lambdaunet.py │ │ ├── lambdaunet_base │ │ │ ├── __init__.py │ │ │ └── lambdaunet_block.py │ │ ├── segmentationnet.py │ │ ├── unet.py │ │ ├── unet3d.py │ │ ├── unet3d_base │ │ │ ├── __init__.py │ │ │ └── unet3d_block.py │ │ ├── unetr.py │ │ ├── unetr_base │ │ │ ├── __init__.py │ │ │ └── unetr_block.py │ │ ├── vit_base │ │ │ ├── __init__.py │ │ │ ├── patchembedding.py │ │ │ ├── transformer_block.py │ │ │ ├── utils.py │ │ │ └── vit_block.py │ │ ├── vnet.py │ │ └── vnet_base │ │ │ ├── __init__.py │ │ │ └── vnet_block.py │ │ └── parts │ │ ├── __init__.py │ │ └── transforms.py ├── constants.py ├── core │ ├── __init__.py │ ├── classes │ │ ├── __init__.py │ │ ├── common.py │ │ ├── dataset.py │ │ ├── export.py │ │ ├── loss.py │ │ └── modelPT.py │ ├── conf │ │ ├── __init__.py │ │ ├── hydra_runner.py │ │ ├── modelPT.py │ │ ├── optimizers.py │ │ ├── schedulers.py │ │ └── trainer.py │ ├── connectors │ │ ├── __init__.py │ │ └── save_restore_connector.py │ ├── neural_types │ │ ├── __init__.py │ │ ├── axes.py │ │ ├── comparison.py │ │ ├── elements.py │ │ └── neural_type.py │ ├── optim │ │ ├── __init__.py │ │ ├── adafactor.py │ │ ├── lion.py │ │ ├── lr_scheduler.py │ │ ├── novograd.py │ │ ├── optimizer_with_main_params.py │ │ ├── optimizers.py │ │ └── radam.py │ └── utils │ │ ├── __init__.py │ │ ├── neural_type_utils.py │ │ ├── numba_utils.py │ │ └── process_launcher │ │ ├── __init__.py │ │ └── launcher.py ├── package_info.py └── utils │ ├── __init__.py │ ├── app_state.py │ ├── atommic_logging.py │ ├── callbacks │ ├── __init__.py │ ├── atommic_model_checkpoint.py │ └── preemption.py │ ├── cast_utils.py │ ├── decorators │ ├── __init__.py │ ├── deprecated.py │ ├── experimental.py │ └── port_docs.py │ ├── env_var_parsing.py │ ├── exceptions.py │ ├── exp_manager.py │ ├── export_utils.py │ ├── formaters │ ├── __init__.py │ ├── base.py │ ├── colors.py │ └── utils.py │ ├── get_rank.py │ ├── lightning_logger_patch.py │ ├── metaclasses.py │ ├── model_utils.py │ └── timers.py ├── codecov.yml ├── docs ├── Makefile ├── assets │ ├── crop.png │ ├── gdcc.png │ ├── gdccpw.png │ ├── logo-simple.png │ ├── masks.png │ ├── mosim.png │ ├── n2r.png │ ├── pw.png │ ├── sense.png │ ├── ssdu.png │ └── zfpad.png ├── make.bat ├── source │ ├── api │ │ ├── common │ │ │ ├── callbacks.rst │ │ │ ├── coil_sensitivity_maps.rst │ │ │ ├── data.rst │ │ │ ├── fft.rst │ │ │ ├── intro.rst │ │ │ ├── losses.rst │ │ │ ├── metrics.rst │ │ │ ├── nn.rst │ │ │ ├── parts.rst │ │ │ ├── transforms.rst │ │ │ └── utils.rst │ │ ├── core.rst │ │ ├── motioncorrection │ │ │ ├── intro.rst │ │ │ └── motionsimulation.rst │ │ ├── multitask │ │ │ ├── data.rst │ │ │ ├── intro.rst │ │ │ ├── nn.rst │ │ │ ├── parts.rst │ │ │ └── rs.rst │ │ ├── quantitative │ │ │ ├── data.rst │ │ │ ├── intro.rst │ │ │ ├── nn.rst │ │ │ └── parts.rst │ │ ├── reconstruction │ │ │ ├── data.rst │ │ │ ├── intro.rst │ │ │ ├── losses.rst │ │ │ ├── metrics.rst │ │ │ ├── nn.rst │ │ │ └── parts.rst │ │ └── segmentation │ │ │ ├── data.rst │ │ │ ├── intro.rst │ │ │ ├── losses.rst │ │ │ ├── metrics.rst │ │ │ ├── nn.rst │ │ │ └── parts.rst │ ├── conf.py │ ├── core │ │ ├── core.rst │ │ ├── exp_manager.rst │ │ └── export.rst │ ├── index.rst │ ├── mri │ │ ├── collections.rst │ │ ├── losses.rst │ │ ├── metrics.rst │ │ ├── transforms.rst │ │ └── undersampling.rst │ └── starthere │ │ ├── intro.rst │ │ ├── projects.rst │ │ ├── projects │ │ ├── multitask │ │ │ └── intro.rst │ │ ├── quantitative │ │ │ ├── ahead.rst │ │ │ └── intro.rst │ │ ├── reconstruction │ │ │ ├── cc359.rst │ │ │ ├── fastmribrainsmulticoil.rst │ │ │ ├── fastmrikneesmulticoil.rst │ │ │ ├── fastmrikneessinglecoil.rst │ │ │ ├── intro.rst │ │ │ ├── skmtea.rst │ │ │ └── stanfordknees2019.rst │ │ └── segmentation │ │ │ ├── brats2023adultglioma.rst │ │ │ ├── intro.rst │ │ │ └── isles2022subacutestroke.rst │ │ └── tutorials.rst └── update_docs_docker.sh ├── projects ├── ATOMMIC_paper │ ├── MTL │ │ └── SKMTEA │ │ │ ├── conf │ │ │ ├── targets │ │ │ │ └── Test_SENSE.yaml │ │ │ ├── test │ │ │ │ └── 4x │ │ │ │ │ ├── idslr.yaml │ │ │ │ │ ├── idslrunet.yaml │ │ │ │ │ ├── mtlrs.yaml │ │ │ │ │ └── segnet.yaml │ │ │ └── train │ │ │ │ ├── idslr.yaml │ │ │ │ ├── idslrunet.yaml │ │ │ │ ├── mtlrs.yaml │ │ │ │ └── segnet.yaml │ │ │ └── evaluate.sh │ ├── README.md │ ├── REC │ │ ├── CC359 │ │ │ ├── conf │ │ │ │ ├── targets │ │ │ │ │ └── 12_channel_Val_RSS.yaml │ │ │ │ ├── test │ │ │ │ │ ├── 10x │ │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ │ ├── modl.yaml │ │ │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ │ │ ├── rim.yaml │ │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ │ ├── unet.yaml │ │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ │ └── zerofilled.yaml │ │ │ │ │ └── 5x │ │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ │ ├── modl.yaml │ │ │ │ │ │ ├── rim.yaml │ │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ │ ├── unet.yaml │ │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ │ └── zerofilled.yaml │ │ │ │ └── train │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ └── xpdnet.yaml │ │ │ └── evaluate.sh │ │ ├── StanfordKnees2019 │ │ │ ├── conf │ │ │ │ ├── targets │ │ │ │ │ └── Test_SENSE.yaml │ │ │ │ ├── test │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ │ └── train │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ └── xpdnet.yaml │ │ │ └── evaluate.sh │ │ └── fastMRIBrainsMulticoil │ │ │ ├── conf │ │ │ ├── targets │ │ │ │ └── Val_RSS.yaml │ │ │ ├── test │ │ │ │ ├── 4x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ │ └── 8x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ │ └── evaluate.sh │ ├── SEG │ │ ├── BraTS2023AdultGlioma │ │ │ ├── conf │ │ │ │ ├── test │ │ │ │ │ ├── attentionunet.yaml │ │ │ │ │ ├── dynunet.yaml │ │ │ │ │ ├── unet2d.yaml │ │ │ │ │ ├── unet3d.yaml │ │ │ │ │ └── vnet.yaml │ │ │ │ └── train │ │ │ │ │ ├── attentionunet.yaml │ │ │ │ │ ├── dynunet.yaml │ │ │ │ │ ├── unet2d.yaml │ │ │ │ │ ├── unet3d.yaml │ │ │ │ │ └── vnet.yaml │ │ │ └── evaluate.sh │ │ ├── ISLES2022SubAcuteStroke │ │ │ ├── conf │ │ │ │ ├── test │ │ │ │ │ ├── attentionunet.yaml │ │ │ │ │ ├── dynunet.yaml │ │ │ │ │ ├── unet2d.yaml │ │ │ │ │ ├── unet3d.yaml │ │ │ │ │ └── vnet.yaml │ │ │ │ └── train │ │ │ │ │ ├── attentionunet.yaml │ │ │ │ │ ├── dynunet.yaml │ │ │ │ │ ├── unet2d.yaml │ │ │ │ │ ├── unet3d.yaml │ │ │ │ │ └── vnet.yaml │ │ │ └── evaluate.sh │ │ └── SKMTEA │ │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ └── vnet.yaml │ │ │ └── train │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ └── vnet.yaml │ │ │ └── evaluate.sh │ ├── data │ │ └── DL_MRI_Repositories_Overview.csv │ ├── evaluate.sh │ ├── generate_results.py │ ├── qMRI │ │ └── AHEAD │ │ │ ├── conf │ │ │ ├── quantitative_test │ │ │ │ ├── qcirim.yaml │ │ │ │ └── qvarnet.yaml │ │ │ ├── quantitative_train │ │ │ │ ├── qcirim.yaml │ │ │ │ └── qvarnet.yaml │ │ │ ├── reconstruction_test │ │ │ │ ├── cirim_test_set.yaml │ │ │ │ ├── cirim_train_set.yaml │ │ │ │ ├── cirim_val_set.yaml │ │ │ │ ├── varnet_test_set.yaml │ │ │ │ ├── varnet_train_set.yaml │ │ │ │ └── varnet_val_set.yaml │ │ │ ├── reconstruction_train │ │ │ │ ├── cirim.yaml │ │ │ │ └── varnet.yaml │ │ │ └── targets │ │ │ │ └── Test_SENSE.yaml │ │ │ └── evaluate.sh │ ├── run_models.sh │ └── set_paths.sh ├── MTL │ ├── __init__.py │ └── rs │ │ └── SKMTEA │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ ├── targets │ │ │ ├── Test_RSS.yaml │ │ │ └── Test_SENSE.yaml │ │ ├── test │ │ │ └── 4x │ │ │ │ ├── idslr.yaml │ │ │ │ ├── idslrunet.yaml │ │ │ │ ├── mtlrs.yaml │ │ │ │ └── segnet.yaml │ │ └── train │ │ │ ├── idslr.yaml │ │ │ ├── idslrunet.yaml │ │ │ ├── jrs.yaml │ │ │ ├── mtlrs.yaml │ │ │ ├── recsegnet.yaml │ │ │ ├── segnet.yaml │ │ │ └── seranet.yaml │ │ ├── evaluation │ │ ├── __init__.py │ │ ├── mtlrs_reconstruction.py │ │ └── mtlrs_segmentation.py │ │ ├── generate_sets.sh │ │ ├── scripts │ │ ├── __init__.py │ │ └── split_sets_json.py │ │ └── visualize.ipynb ├── README.md ├── REC │ ├── CC359 │ │ ├── README.md │ │ ├── __init__.py │ │ ├── compute_masks.sh │ │ ├── conf │ │ │ ├── targets │ │ │ │ └── 12_channel_Val_RSS.yaml │ │ │ ├── test │ │ │ │ ├── 10x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── proximalgradient.yaml │ │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ │ └── 5x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── proximalgradient.yaml │ │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ └── compute_masks.py │ │ └── visualize.ipynb │ ├── SKMTEA │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ ├── generate_sets.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ ├── StanfordKnees2019 │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── targets │ │ │ │ └── Test_SENSE.yaml │ │ │ ├── test │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── proximalgradient.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ ├── xpdnet.yaml │ │ │ │ └── zerofilled.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ ├── preprocess_dataset.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ ├── preprocess_dataset.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ ├── __init__.py │ ├── fastMRIBrainsMulticoil │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── targets │ │ │ │ └── Val_RSS.yaml │ │ │ ├── test │ │ │ │ ├── 4x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ │ └── 8x │ │ │ │ │ ├── ccnn.yaml │ │ │ │ │ ├── cirim.yaml │ │ │ │ │ ├── crnn.yaml │ │ │ │ │ ├── jointicnet.yaml │ │ │ │ │ ├── kikinet.yaml │ │ │ │ │ ├── lpdnet.yaml │ │ │ │ │ ├── modl.yaml │ │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ │ ├── rim.yaml │ │ │ │ │ ├── rvn.yaml │ │ │ │ │ ├── unet.yaml │ │ │ │ │ ├── varnet.yaml │ │ │ │ │ ├── vsnet.yaml │ │ │ │ │ ├── xpdnet.yaml │ │ │ │ │ └── zerofilled.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── recurrentvarnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ ├── fastMRIKneesMulticoil │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ │ └── train │ │ │ │ ├── ccnn.yaml │ │ │ │ ├── cirim.yaml │ │ │ │ ├── crnn.yaml │ │ │ │ ├── dunet.yaml │ │ │ │ ├── jointicnet.yaml │ │ │ │ ├── kikinet.yaml │ │ │ │ ├── lpdnet.yaml │ │ │ │ ├── modl.yaml │ │ │ │ ├── multidomainnet.yaml │ │ │ │ ├── rim.yaml │ │ │ │ ├── rvn.yaml │ │ │ │ ├── unet.yaml │ │ │ │ ├── varnet.yaml │ │ │ │ ├── vsnet.yaml │ │ │ │ └── xpdnet.yaml │ │ ├── evaluate.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ └── fastMRIKneesSinglecoil │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ ├── test │ │ │ ├── ccnn.yaml │ │ │ ├── cirim.yaml │ │ │ ├── crnn.yaml │ │ │ ├── dunet.yaml │ │ │ ├── jointicnet.yaml │ │ │ ├── kikinet.yaml │ │ │ ├── lpdnet.yaml │ │ │ ├── modl.yaml │ │ │ ├── multidomainnet.yaml │ │ │ ├── rim.yaml │ │ │ ├── rvn.yaml │ │ │ ├── unet.yaml │ │ │ ├── varnet.yaml │ │ │ ├── vsnet.yaml │ │ │ └── xpdnet.yaml │ │ └── train │ │ │ ├── ccnn.yaml │ │ │ ├── cirim.yaml │ │ │ ├── crnn.yaml │ │ │ ├── dunet.yaml │ │ │ ├── jointicnet.yaml │ │ │ ├── kikinet.yaml │ │ │ ├── lpdnet.yaml │ │ │ ├── modl.yaml │ │ │ ├── multidomainnet.yaml │ │ │ ├── rim.yaml │ │ │ ├── rvn.yaml │ │ │ ├── unet.yaml │ │ │ ├── varnet.yaml │ │ │ ├── vsnet.yaml │ │ │ └── xpdnet.yaml │ │ └── visualize.ipynb ├── SEG │ ├── BraTS2023AdultGlioma │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ └── vnet.yaml │ │ │ └── train │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── lambdaunet2d.yaml │ │ │ │ ├── lambdaunet3d.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ ├── unetr.yaml │ │ │ │ └── vnet.yaml │ │ ├── preprocess_dataset.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ ├── compute_segmentation_classes_probabilities.py │ │ │ ├── preprocess_dataset.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ ├── ISLES2022SubAcuteStroke │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── lambdaunet3d.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ ├── unetr.yaml │ │ │ │ └── vnet.yaml │ │ │ └── train │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── lambdaunet2d.yaml │ │ │ │ ├── lambdaunet3d.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ ├── unetr.yaml │ │ │ │ └── vnet.yaml │ │ ├── preprocess_dataset.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ ├── compute_segmentation_classes_probabilities.py │ │ │ ├── evaluation.py │ │ │ ├── preprocess_dataset.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ ├── SKMTEA │ │ ├── README.md │ │ ├── __init__.py │ │ ├── conf │ │ │ ├── test │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ └── vnet.yaml │ │ │ └── train │ │ │ │ ├── attentionunet.yaml │ │ │ │ ├── dynunet.yaml │ │ │ │ ├── lambdaunet2d.yaml │ │ │ │ ├── lambdaunet3d.yaml │ │ │ │ ├── unet2d.yaml │ │ │ │ ├── unet3d.yaml │ │ │ │ ├── unetr.yaml │ │ │ │ └── vnet.yaml │ │ ├── generate_sets.sh │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ └── split_sets_json.py │ │ └── visualize.ipynb │ └── __init__.py ├── __init__.py └── qMRI │ ├── AHEAD │ ├── README.md │ ├── __init__.py │ ├── batch_preprocessing.sh │ ├── conf │ │ ├── e2erq_train │ │ │ ├── e2erq_qcirim.yaml │ │ │ └── e2erq_qvarnet.yaml │ │ ├── quantitative_test │ │ │ ├── qcirim.yaml │ │ │ └── qvarnet.yaml │ │ ├── quantitative_train │ │ │ ├── qcirim.yaml │ │ │ └── qvarnet.yaml │ │ ├── reconstruction_test │ │ │ ├── cirim_test_set.yaml │ │ │ ├── cirim_train_set.yaml │ │ │ ├── cirim_val_set.yaml │ │ │ ├── varnet_test_set.yaml │ │ │ ├── varnet_train_set.yaml │ │ │ └── varnet_val_set.yaml │ │ ├── reconstruction_train │ │ │ ├── cirim.yaml │ │ │ └── varnet.yaml │ │ └── targets │ │ │ └── Test_SENSE.yaml │ ├── getting-started.ipynb │ └── scripts │ │ ├── __init__.py │ │ ├── compute_segmentation_masks.py │ │ └── preprocessing.py │ └── __init__.py ├── pyproject.toml ├── reinstall.sh ├── requirements ├── requirements-ahead_stanfordknees.txt ├── requirements-isles22.txt ├── requirements.txt └── requirements_docs.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── collections │ ├── __init__.py │ ├── common │ │ ├── __init__.py │ │ ├── callbacks │ │ │ ├── __init__.py │ │ │ ├── test_callbacks.py │ │ │ └── test_ema.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── test_compute_coil_sensitivity_maps.py │ │ │ └── test_subsample.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ ├── test_aggregator.py │ │ │ └── test_wasserstein.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ └── test_global_average_loss_metric.py │ │ ├── nn │ │ │ ├── __init__.py │ │ │ └── test_base.py │ │ └── parts │ │ │ ├── __init__.py │ │ │ ├── test_fft.py │ │ │ ├── test_utils.py │ │ │ └── transforms │ │ │ ├── __init__.py │ │ │ ├── test_composer.py │ │ │ ├── test_cropper.py │ │ │ ├── test_gdcc.py │ │ │ ├── test_masker.py │ │ │ ├── test_n2r.py │ │ │ ├── test_noise_prewhitening.py │ │ │ ├── test_normalizer.py │ │ │ ├── test_snrestimator.py │ │ │ ├── test_ssdu.py │ │ │ └── test_zf.py │ ├── multitask │ │ ├── __init__.py │ │ └── rs │ │ │ ├── __init__.py │ │ │ └── models │ │ │ ├── __init__.py │ │ │ ├── test_idslr.py │ │ │ ├── test_idslrunet.py │ │ │ ├── test_mtlrs.py │ │ │ ├── test_recseg_unet.py │ │ │ ├── test_segnet.py │ │ │ └── test_seranet.py │ ├── quantitative │ │ ├── __init__.py │ │ └── models │ │ │ ├── __init__.py │ │ │ ├── test_qcirim.py │ │ │ ├── test_qrim.py │ │ │ └── test_qvn.py │ ├── reconstruction │ │ ├── __init__.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── test_ccnn.py │ │ │ ├── test_cirim.py │ │ │ ├── test_conv.py │ │ │ ├── test_conv2dgru.py │ │ │ ├── test_crnn.py │ │ │ ├── test_didn.py │ │ │ ├── test_dunet.py │ │ │ ├── test_jointicnet.py │ │ │ ├── test_kikinet.py │ │ │ ├── test_lpdnet.py │ │ │ ├── test_multidomainnet.py │ │ │ ├── test_mwcnn.py │ │ │ ├── test_recurrentvarnet.py │ │ │ ├── test_unet.py │ │ │ ├── test_varnet.py │ │ │ ├── test_vsnet.py │ │ │ └── test_xpdnet.py │ │ ├── mri_data │ │ │ ├── __init__.py │ │ │ ├── conftest.py │ │ │ ├── create_temp_data.py │ │ │ └── test_mri_data.py │ │ ├── test_subsample.py │ │ └── test_transforms.py │ └── segmentation │ │ ├── __init__.py │ │ └── models │ │ ├── __init__.py │ │ ├── test_3dunet.py │ │ ├── test_attention_unet.py │ │ ├── test_dynunet.py │ │ ├── test_lambda_unet.py │ │ ├── test_unet.py │ │ ├── test_unetr.py │ │ └── test_vnet.py ├── core │ ├── __init__.py │ ├── test_exp_manager.py │ ├── test_neural_types.py │ ├── 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