Deep learning using a biophysical model for robust and accelerated reconstruction of quantitative, artifact-free and denoised R2* images

Max Torop, Satya V.V.N. Kothapalli, Yu Sun, Jiaming Liu, Sayan Kahali, Dmitriy A. Yablonskiy, Ulugbek S. Kamilov

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Purpose: To introduce a novel deep learning method for Robust and Accelerated Reconstruction (RoAR) of quantitative and B0-inhomogeneity-corrected (Formula presented.) maps from multi-gradient recalled echo (mGRE) MRI data. Methods: RoAR trains a convolutional neural network (CNN) to generate quantitative (Formula presented.) 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 (Formula presented.) images are required and F-function is only needed during RoAR training but not application. Results: We show that RoAR preserves all features of (Formula presented.) 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 (Formula presented.) 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. Conclusions: RoAR is trained to recognize the macroscopic magnetic field inhomogeneities directly from the input magnitude-only mGRE data and eliminate their effect on (Formula presented.) measurements. RoAR training is based on the biophysical model and does not require ground-truth (Formula presented.) 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 (Formula presented.) 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.

Original languageEnglish
Pages (from-to)2932-2942
Number of pages11
JournalMagnetic resonance in medicine
Issue number6
StatePublished - Dec 1 2020


  • MRI
  • R2* mapping
  • gradient recalled echo
  • self-supervised deep learning


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