├── .github └── workflows │ └── test.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── OASIS_list.csv ├── README.md ├── apt.txt ├── examples ├── gt_image.npy ├── gt_kspace.npy ├── mri_reconstruction_intro.ipynb └── non_cartesian_reconstruction.ipynb ├── experiments ├── qualitative_validation_for_net.ipynb └── qualitative_validation_for_net_oasis.ipynb ├── fastmri_recon ├── __init__.py ├── config.py ├── data │ ├── __init__.py │ ├── datasets │ │ ├── __init__.py │ │ ├── fastmri_pyfunc.py │ │ ├── fastmri_pyfunc_denoising.py │ │ ├── fastmri_pyfunc_non_cartesian.py │ │ ├── multicoil │ │ │ ├── __init__.py │ │ │ ├── coil_selection.py │ │ │ ├── fastmri_postproc_h5.py │ │ │ ├── fastmri_postproc_tf_records.py │ │ │ ├── fastmri_pyfunc.py │ │ │ ├── fastmri_pyfunc_non_cartesian.py │ │ │ ├── non_cartesian_tf_records.py │ │ │ └── preprocessing.py │ │ ├── oasis_preprocessing.py │ │ ├── oasis_pyfunc_non_cartesian.py │ │ ├── oasis_tf_records.py │ │ ├── preprocessing.py │ │ └── slice_selection.py │ ├── scripts │ │ ├── multicoil_nc_tf_records_generation.py │ │ ├── oasis_tf_records_generation.py │ │ ├── oasis_train_test_split.py │ │ └── postproc_volumes_tf_records_generation.py │ ├── sequences │ │ ├── __init__.py │ │ ├── fastmri_sequences.py │ │ ├── oasis_sequences.py │ │ └── test_generators.py │ └── utils │ │ ├── __init__.py │ │ ├── crop.py │ │ ├── fourier.py │ │ ├── h5.py │ │ ├── masking │ │ ├── __init__.py │ │ ├── acceleration_factor.py │ │ ├── gen_mask.py │ │ └── gen_mask_tf.py │ │ ├── multicoil │ │ ├── __init__.py │ │ └── smap_extract.py │ │ ├── nii.py │ │ ├── non_cartesian.py │ │ ├── normalize.py │ │ └── tfrecords.py ├── evaluate │ ├── __init__.py │ ├── metrics │ │ ├── __init__.py │ │ ├── np_metrics.py │ │ └── tf_metrics.py │ ├── reconstruction │ │ ├── __init__.py │ │ ├── cross_domain_reconstruction.py │ │ ├── dip_reconstruction.py │ │ ├── iterative_reconstruction.py │ │ ├── non_cartesian_dcomp_reconstruction.py │ │ ├── unet_reconstruction.py │ │ ├── wavelet_reconstruction.py │ │ └── zero_filled_reconstruction.py │ ├── scripts │ │ ├── __init__.py │ │ ├── dealiasing_eval.py │ │ ├── debug_nc_dip_eval.py │ │ ├── denoising_eval.py │ │ ├── dip_qualitative_validation.py │ │ ├── download_checkpoints.py │ │ ├── nc_dip_eval.py │ │ ├── nc_eval.py │ │ ├── paper_eval.py │ │ ├── paper_eval_oasis.py │ │ ├── pdnet_sense_eval.py │ │ ├── postprocess_eval.py │ │ ├── postprocess_inference.py │ │ ├── qualitative_validation.py │ │ ├── updnet_sense_eval.py │ │ ├── updnet_sense_inference.py │ │ ├── xpdnet_eval.py │ │ └── xpdnet_inference.py │ └── utils │ │ ├── __init__.py │ │ ├── save_figure.py │ │ └── write_results.py ├── models │ ├── __init__.py │ ├── functional_models │ │ ├── __init__.py │ │ ├── cascading.py │ │ ├── discriminator.py │ │ ├── kiki.py │ │ ├── kiki_sep.py │ │ ├── old_unet.py │ │ ├── pdnet.py │ │ ├── unet.py │ │ └── zerofill_net.py │ ├── subclassed_models │ │ ├── __init__.py │ │ ├── cnn.py │ │ ├── cross_domain.py │ │ ├── denoisers │ │ │ ├── __init__.py │ │ │ ├── didn.py │ │ │ ├── dncnn.py │ │ │ ├── focnet.py │ │ │ ├── mwcnn.py │ │ │ └── proposed_params.py │ │ ├── dip.py │ │ ├── feature_level_multi_domain_learning │ │ │ ├── __init__.py │ │ │ ├── fourier.py │ │ │ ├── multi_domain_convolution.py │ │ │ ├── mwcnn.py │ │ │ ├── proposed_params.py │ │ │ └── unet.py │ │ ├── multiscale_complex.py │ │ ├── ncpdnet.py │ │ ├── parallel_multicoil.py │ │ ├── pdnet.py │ │ ├── post_processing_3d.py │ │ ├── unet.py │ │ ├── updnet.py │ │ ├── vnet.py │ │ └── xpdnet.py │ ├── training │ │ ├── __init__.py │ │ ├── adversarial │ │ │ ├── __init__.py │ │ │ ├── adversarial_training.py │ │ │ ├── loss.py │ │ │ └── metrics.py │ │ ├── compile.py │ │ ├── image_tboard_cback.py │ │ └── keras_utils.py │ └── utils │ │ ├── __init__.py │ │ ├── attention.py │ │ ├── complex.py │ │ ├── data_consistency.py │ │ ├── fastmri_format.py │ │ ├── fourier.py │ │ ├── gpu_placement.py │ │ ├── masking.py │ │ ├── non_linearities.py │ │ └── pad_for_pool.py ├── pysap_requirements.txt ├── tests │ ├── conftest.py │ ├── data │ │ ├── datasets │ │ │ ├── fastmri_pyfunc_denoising_test.py │ │ │ ├── fastmri_pyfunc_non_cartesian_test.py │ │ │ ├── fastmri_pyfunc_test.py │ │ │ ├── multicoil │ │ │ │ └── fastmri_pyfunc_multicoil_test.py │ │ │ └── preprocessing_test.py │ │ └── utils │ │ │ ├── crop_test.py │ │ │ ├── h5_test.py │ │ │ ├── masking │ │ │ └── gen_mask_tf_test.py │ │ │ └── multicoil │ │ │ └── smap_extract_test.py │ ├── evaluate │ │ ├── paper_eval_oasis_test.py │ │ └── paper_eval_test.py │ ├── models │ │ ├── functional_models │ │ │ ├── cascading_test.py │ │ │ ├── kiki_sep_test.py │ │ │ ├── kiki_test.py │ │ │ ├── pdnet_test.py │ │ │ ├── unet_test.py │ │ │ └── zerofill_net_test.py │ │ ├── subclassed_models │ │ │ ├── cnn_test.py │ │ │ ├── denoisers │ │ │ │ ├── didn_test.py │ │ │ │ ├── dncnn_test.py │ │ │ │ ├── focnet_test.py │ │ │ │ └── mwcnn_test.py │ │ │ ├── dip_test.py │ │ │ ├── feature_level_multi_domain_learning │ │ │ │ ├── mwcnn_flmd_test.py │ │ │ │ └── unet_flmd_test.py │ │ │ ├── ncpdnet_test.py │ │ │ ├── pdnet_subclassed_test.py │ │ │ ├── unet_complex_test.py │ │ │ ├── updnet_test.py │ │ │ ├── vnet_test.py │ │ │ └── xpdnet_test.py │ │ └── utils │ │ │ ├── attention_test.py │ │ │ ├── fourier_test.py │ │ │ ├── gpu_placement_test.py │ │ │ └── pad_for_pool_test.py │ └── training_scripts │ │ ├── dealiasing_train_test.py │ │ ├── denoising │ │ └── generic_train_test.py │ │ ├── multi_coil │ │ └── pdnet_approach_sense_test.py │ │ ├── ncpdnet_train_test.py │ │ ├── postprocess_train_test.py │ │ ├── unet_nc_train_test.py │ │ ├── updnet_train_test.py │ │ └── xpdnet_train_test.py ├── training_scripts │ ├── __init__.py │ ├── custom_objects.py │ ├── dealias_train.py │ ├── denoising │ │ ├── __init__.py │ │ └── generic_train.py │ ├── model_saving_workaround.py │ ├── multi_coil │ │ ├── __init__.py │ │ ├── pdnet_approach.py │ │ └── pdnet_approach_sense.py │ ├── nc_train.py │ ├── nc_train_block.py │ ├── postprocess_train.py │ ├── single_coil │ │ ├── cascadenet_approach_af4.py │ │ ├── cascadenet_approach_af4_oasis.py │ │ ├── kikinet_approach_af4.py │ │ ├── kikinet_sep_approach_af4.py │ │ ├── kikinet_sep_approach_af4_oasis.py │ │ ├── pdnet_approach.py │ │ ├── pdnet_approach_af4_oasis.py │ │ ├── pdnet_approach_fine_tuning.py │ │ ├── unet_approach_af4.py │ │ └── unet_approach_af4_oasis.py │ ├── updnet_train.py │ ├── xpdnet_train.py │ └── xpdnet_train_block.py └── wavelets.py ├── loraks_recon ├── T2_single_channel.mat ├── crop_center.m ├── ex7.m ├── ex8.m ├── gen_mask.m ├── preprocess_kspaces.m ├── reco.m ├── single_slice_reco.m └── val_metrics.m ├── postBuild ├── requirements.txt └── setup.py /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zaccharieramzi/fastmri-reproducible-benchmark/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: 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