{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/deep-learning-using-a-biophysical-model-for","title":"Deep learning using a biophysical model for Robust and Accelerated Reconstruction (RoAR) of quantitative and artifact-free R2* images","arxiv_id":"1912.07087","date":"2019-12-15","proceeding":null,"authors":["Max Torop","Satya VVN Kothapalli","Yu Sun","Jiaming Liu","Sayan Kahali","Dmitriy A. Yablonskiy","Ulugbek S. Kamilov"],"abstract":"Purpose: To introduce a novel deep learning method for Robust and Accelerated Reconstruction (RoAR) of quantitative and B0-inhomogeneity-corrected R2* maps from multi-gradient recalled echo (mGRE) MRI data. Methods: RoAR trains a convolutional neural network (CNN) to generate quantitative R2* maps free from field inhomogeneity artifacts by adopting a self-supervised learning strategy given (a) mGRE magnitude images, (b) the biophysical model describing mGRE signal decay, and (c) preliminary-evaluated F-function accounting for contribution of macroscopic B0 field inhomogeneities. Importantly, no ground-truth R2* images are required and F-function is only needed during RoAR training but not application. Results: We show that RoAR preserves all features of R2* maps while offering significant improvements over existing methods in computation speed (seconds vs. hours) and reduced sensitivity to noise. Even for data with SNR=5 RoAR produced R2* maps with accuracy of 22% while voxel-wise analysis accuracy was 47%. For SNR=10 the RoAR accuracy increased to 17% vs. 24% for direct voxel-wise analysis. Conclusion: RoAR is trained to recognize the macroscopic magnetic field inhomogeneities directly from the input magnitude-only mGRE data and eliminate their effect on R2* measurements. RoAR training is based on the biophysical model and does not require ground-truth R2* maps. Since RoAR utilizes signal information not just from individual voxels but also accounts for spatial patterns of the signals in the images, it reduces the sensitivity of R2* maps to the noise in the data. These features plus high computational speed provide significant benefits for the potential usage of RoAR in clinical settings.","url_abs":"http://arxiv.org/abs/1912.07087v3","url_pdf":"http://arxiv.org/pdf/1912.07087v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"deep-learning-using-a-biophysical-model-for","repo_url":"https://github.com/wustl-cig/RoAR","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"tf","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}