Rapid Computation of Sodium Bioscales Using GPU-Accelerated Image Reconstruction

Ian C. Atkinson, Geng Liu, Nady Obeid, Keith R. Thulborn, Wen-mei Hwu
Center for Magnetic Resonance Research, University of Illinois at Chicago, Chicago, IL
International Journal of Imaging Systems and Technology, Volume 23, Issue 1, pages 29-35, 2013


   title={Rapid computation of sodium bioscales using gpu-accelerated image reconstruction},

   author={Atkinson, Ian C and Liu, Geng and Obeid, Nady and Thulborn, Keith R and Hwu, Wen-mei},

   journal={International Journal of Imaging Systems and Technology},





   publisher={Wiley Online Library}


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Quantitative sodium magnetic resonance imaging permits noninvasive measurement of the tissue sodium concentration (TSC) bioscale in the brain. Computing the TSC bioscale requires reconstructing and combining multiple datasets acquired with a non-Cartesian acquisition that highly oversamples the center of k-space. Even with an optimized implementation of the algorithm to compute TSC, the overall processing time exceeds the time required to collect data from the human subject. Such a mismatch presents a challenge for sustained sodium imaging to avoid a growing data backlog and provide timely results. The most computationally intensive portions of the TSC calculation have been identified and accelerated using a consumer graphics processing unit (GPU) in addition to a conventional central processing unit (CPU). A recently developed data organization technique called Compact Binning was used along with several existing algorithmic techniques to maximize the scalability and performance of these computationally intensive operations. The resulting GPU+CPU TSC bioscale calculation is more than 15 times faster than a CPU-only implementation when processing 256x256x256 data and 2.4 times faster when processing 128x128x128 data. This eliminates the possibility of a data backlog for quantitative sodium imaging. The accelerated quantification technique is suitable for general three-dimensional non-Cartesian acquisitions and may enable more sophisticated imaging techniques that acquire even more data to be used for quantitative sodium imaging. (c) 2013 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 23, 29-35, 2013.
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