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* add feature varnet * Included copyright header and fixed linter tests * Re-adding fastmri/models/feature_varnet.py to ensure CI passes * Re-adding fastmri/models/feature_varnet.py to ensure CI passes - reinstalled black 22.3.0 * Re-adding fastmri/models/feature_varnet.py to ensure compatibility with mypy 1.1.1 * Change fastMRI version * Fix black * Move feature_varnet to fastmri_examples * Reformat feature_varnet * Move module imports * Reorganize imports --------- Co-authored-by: Matthew Muckley <[email protected]>
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# Accelerated MRI reconstructions via variational network and feature domain learning | ||
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This directory contains a PyTorch implementation for reproducing the following paper, to be published at MIDL 2022. | ||
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[Accelerated MRI reconstructions via variational network and feature domain learning (I. Giannakopoulos, et al., 2024).][feature_varnet] | ||
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## Installation | ||
We **strongly** recommend creating a separate conda environment for this example, as the | ||
PyTorch Lightning versions required differs from that of the base `fastmri` installation. | ||
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Before installing dependencies, first install PyTorch according to the directions at the | ||
PyTorch Website for your operating system and CUDA setup | ||
(we used `torch` version 1.7.0 for our experiments). Then run | ||
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```bash | ||
pip install -r fastmri_examples/feature_varnet/requirements.txt | ||
``` | ||
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## Example training commands: | ||
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This code provides a few ablations of the end-to-end variational network, namely, feature varnet with weight sharing, feature varnet without weight sharing, attention feature varnet with weight sharing, feature-image varnet, and image-feature varnet. Train and test each model with the same commands as the end-to-end variational network and include an additional input argument to your input file: | ||
For the end-to-end varnet | ||
> --varnet_type e2e_varnet | ||
For the feature varnet with weight sharing | ||
> --varnet_type feature_varnet_sh_w | ||
For the feature varnet without weight sharing | ||
> --varnet_type feature_varnet_n_sh_w | ||
For the attention feature varnet with weight sharing | ||
> --varnet_type attention_feature_varnet_sh_w | ||
For the feature-image varnet | ||
> --varnet_type fi_varnet | ||
For the image-feature varnet | ||
> --varnet_type if_varnet | ||
See `train_feature_varnet.py` for additional arguments. | ||
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## Example evaluation commands: | ||
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Evaluate the model as the end-to-end varnet | ||
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## Paths: | ||
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Data and log paths are defined the fastmri_dirs.yaml | ||
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## Citing | ||
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If you use this this code in your research, please cite the corresponding | ||
paper: | ||
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```BibTeX | ||
@article{giannakopoulos2024accelerated, | ||
title={Accelerated MRI reconstructions via variational network and feature domain learning}, | ||
author={Giannakopoulos, Ilias I and Muckley, Matthew J and Kim, Jesi and Breen, Matthew and Johnson, Patricia M and Lui, Yvonne W and Lattanzi, Riccardo}, | ||
journal={Scientific Reports}, | ||
volume={14}, | ||
number={1}, | ||
pages={10991}, | ||
year={2024}, | ||
publisher={Nature Publishing Group UK London} | ||
} | ||
``` | ||
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[feature_varnet]: https://www.nature.com/articles/s41598-024-59705-0 |
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