GPU‐accelerated Bloch simulations and MR‐STAT reconstructions using the Julia programming language

MR-STAT is a relatively new multiparametric quantitative MRI technique in which quantitative paramater maps are obtained by solving a large-scale nonlinear optimization problem. Managing reconstruction times is one of the main challenges of MR-STAT. In this work we leverage GPU hardware to reduce MR...

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Bibliographic Details
Published in:Magnetic resonance in medicine Vol. 92; no. 2; pp. 618 - 630
Main Authors: van der Heide, Oscar, van den Berg, Cornelis A. T., Sbrizzi, Alessandro
Format: Journal Article
Language:English
Published: United States Wiley Subscription Services, Inc 01.08.2024
Subjects:
Algorithms
DNA fingerprinting
Fingerprinting
Graphics processing units
Hardware
Image reconstruction
Magnetic resonance imaging
Programming languages
Run time (computers)
Simulation
CUDA
Julia
quantitative MRI
Bloch simulations
MR-STAT
ISSN:0740-3194, 1522-2594, 1522-2594
Online Access:Get full text
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Summary:MR-STAT is a relatively new multiparametric quantitative MRI technique in which quantitative paramater maps are obtained by solving a large-scale nonlinear optimization problem. Managing reconstruction times is one of the main challenges of MR-STAT. In this work we leverage GPU hardware to reduce MR-STAT reconstruction times. A highly optimized, GPU-compatible Bloch simulation toolbox is developed as part of this work that can be utilized for other quantitative MRI techniques as well. The Julia programming language was used to develop a flexible yet highly performant and GPU-compatible Bloch simulation toolbox called BlochSimulators.jl. The runtime performance of the toolbox is benchmarked against other Bloch simulation toolboxes. Furthermore, a (partially matrix-free) modification of a previously presented (matrix-free) MR-STAT reconstruction algorithm is proposed and implemented using the Julia language on GPU hardware. The proposed algorithm is combined with BlochSimulators.jl and the resulting MR-STAT reconstruction times on GPU hardware are compared to previously presented MR-STAT reconstruction times. The BlochSimulators.jl package demonstrates superior runtime performance on both CPU and GPU hardware when compared to other existing Bloch simulation toolboxes. The GPU-accelerated partially matrix-free MR-STAT reconstruction algorithm, which relies on BlochSimulators.jl, allows for reconstructions of 68 seconds per two-dimensional (2D slice). By combining the proposed Bloch simulation toolbox and the partially matrix-free reconstruction algorithm, 2D MR-STAT reconstructions can be performed in the order of one minute on a modern GPU card. The Bloch simulation toolbox can be utilized for other quantitative MRI techniques as well, for example for online dictionary generation for MR Fingerprinting.
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ISSN:0740-3194
1522-2594
1522-2594
DOI:10.1002/mrm.30074