title: Accelerating fibre orientation estimation from diffusion weighted magnetic resonance imaging using GPUs.
abstract: With the performance of central processing units (CPUs) having effectively reached a limit, parallel processing offers an alternative for applications with high computational demands. Modern graphics processing units (GPUs) are massively parallel processors that can execute simultaneously thousands of light-weight processes. In this study, we propose and implement a parallel GPU-based design of a popular method that is used for the analysis of brain magnetic resonance imaging (MRI). More specifically, we are concerned with a model-based approach for extracting tissue structural information from diffusion-weighted (DW) MRI data. DW-MRI offers, through tractography approaches, the only way to study brain structural connectivity, non-invasively and in-vivo. We parallelise the Bayesian inference framework for the ball & stick model, as it is implemented in the tractography toolbox of the popular FSL software package (University of Oxford). For our implementation, we utilise the Compute Unified Device Architecture (CUDA) programming model. We show that the parameter estimation, performed through Markov Chain Monte Carlo (MCMC), is accelerated by at least two orders of magnitude, when comparing a single GPU with the respective sequential single-core CPU version. We also illustrate similar speed-up factors (up to 120x) when comparing a multi-GPU with a multi-CPU implementation.
authors: Department of Computer Science, University of Murcia, Murcia, Spain. moises.hernandez@um.es
authors: Moisés
authors: M
authors: Hernández
authors: Ginés D
authors: GD
authors: Guerrero
authors: José M
authors: JM
authors: Cecilia
authors: José M
authors: JM
authors: García
authors: Alberto
authors: A
authors: Inuggi
authors: Saad
authors: S
authors: Jbabdi
authors: Timothy E J
authors: TE
authors: Behrens
authors: Stamatios N
authors: SN
authors: Sotiropoulos
mesh_terms: D000465:Algorithms; D001921:Brain / Q000502:physiology / Q000648:ultrastructure*; D003196:Computer Graphics / Q000706:statistics & numerical data; D038524:Diffusion Magnetic Resonance Imaging / Q000706:statistics & numerical data*; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D008297:Male; D008390:Markov Chains; D009010:Monte Carlo Method; D012984:Software
references: Radiology. 1986 Nov;161(2):401-7
references: 3763909
references: Magn Reson Med. 2010 May;63(5):1144-53
references: 20432285
references: IEEE Trans Vis Comput Graph. 2007 Nov-Dec;13(6):1480-7
references: 17968100
references: IEEE Trans Vis Comput Graph. 2007 Nov-Dec;13(6):1488-95
references: 17968101
references: Magn Reson Med. 2003 Nov;50(5):1077-88
references: 14587019
references: Neuroimage. 2004;23 Suppl 1:S208-19
references: 15501092
references: Neuroimage. 2012 Oct 1;62(4):2222-31
references: 22366334
references: IEEE Trans Biomed Eng. 2011 Jun;58(6):1789-96
references: 21335302
references: J Magn Reson Imaging. 2003 Aug;18(2):242-54
references: 12884338
references: J Digit Imaging. 2011 Apr;24(2):339-51
references: 20155382
references: Neuroimage. 2003 Nov;20(3):1601-8
references: 14642471
references: Magn Reson Med. 2012 Dec;68(6):1846-55
references: 22334356
references: Neuroimage. 2007 Jan 1;34(1):144-55
references: 17070705
references: J Magn Reson B. 1994 Mar;103(3):247-54
references: 8019776
references: IEEE Trans Med Imaging. 2012 Jun;31(6):1250-62
references: 22345529
references: IEEE Trans Med Imaging. 2008 Apr;27(4):538-47
references: 18390350
references: Magn Reson Med. 2000 Oct;44(4):625-32
references: 11025519
references: J Parallel Distrib Comput. 2008 Oct;68(10):1307-1318
references: 21796230
references: Neuroimage. 2009 Mar;45(1 Suppl):S173-86
references: 19059349
references: Radiology. 1996 Dec;201(3):637-48
references: 8939209
references: IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):1433-40
references: 19834218
references: Neuroimage. 2012 Apr 2;60(2):1412-25
references: 22270351
references: NMR Biomed. 2002 Nov-Dec;15(7-8):435-55
references: 12489094