cudaBayesreg: Parallel implementation of a Bayesian multilevel model for fMRI data analysis

Journal of Statistical Software

Volumn 44, Issue 4, 2011, Pages 1-24

  Ferreira da Silva, Adelino R ^a  

^a UNIVERSIDADE NOVA DE LISBOA   (Portugal)

Author keywords

Bayesian multilevel methods; CUDA; fMRI; GPU; R

Indexed keywords

EID: 84856244538     PISSN: None     EISSN: 15487660     Source Type: Journal    
DOI: None     Document Type: Article

References (32)

1. Ashburner J, Chen C, Flandin G, Henson R, Kiebel S, Kilner J, Litvak V, Moran R, Penny W, Stephan K, Hutton C, Glauche V, Mattout J, Phillips C (2008). The SPM8 Manual, Functional Imaging Laboratory, Wellcome Trust Centre for Neuroimaging, Institute of Neurology, UCL, London. URL http://www.fil.ion.ucl.ac.uk/spm/.
2. Box GEP, Tiao GC (1973). Bayesian Inference in Statistical Analysis, John Wiley & Sons.
3. Brent RP (2006). "Some Long-Period Random Number Generators Using Shifts and Xors. " 13th Biennial Computational Techniques and Applications Conference (CTAC06), Townsville. URL http://gan.anu.edu.au/~brent/pd/rpb224.pdf.
4. Fatahalian K, Houston M (2008). "A Closer Look at GPUs. " Communications of the ACM, 51(10), 50-57.
5. Ferreira da Silva AR (2010). "cudaBayesreg: Bayesian Computation in CUDA. " The R Journal, 2(2), 48-55. URL http://journal.R-project.org/archive/2010-2/RJournalff 2010-2ffFerreira~da~Silva.pdf.
6. Ferreira da Silva AR (2011a). "A Bayesian Multilevel Model for fMRI Data Analysis. " Computer Methods and Programs in Biomedicine, 102, 238-252.
7. Ferreira da Silva AR (2011b). cudaBayesreg: CUDA Parallel Implementation of a Bayesian Multilevel Model for fMRI Data Analysis, R package version 0.3-10, URL http://CRAN. R-project.org/package=cudaBayesreg.
8. Ferreira da Silva AR (2011c). cudaBayesregData: Data Sets for the Examples Used in the Package cudaBayesreg. R package version 0.3-10, URL http://CRAN.R-project.org/ package=cudaBayesregData.
9. Gelman A (2006). "Multilevel (Hierarchical) Modeling: What It Can and Cannot Do. " Technometrics, 48(3), 432-435.
10. Geweke J (2005). Contemporary Bayesian Econometrics and Statistics, John Wiley & Sons.
11. Judge GG, Hill RC, Griffths WE, Lütkephol H, Lee TC (1988). Introduction to the Theory and Practice of Econometrics, 2nd edition. John Wiley & Sons.
12. Lazar N (2008). The Statistical Analysis of Functional MRI Data, Springer-Verlag.
13. Lindley DV, Smith AFM (1972). "Bayes Estimates for the Linear Model. " Journal of the Royal Statistical Society B, 34(1), 1-41.
14. Mardia KV, Kent JT, Bibby JM (1979). Multivariate Analysis, Academic Press.
15. Marsaglia G (2003). "Random Number Generators. " Journal of Modern Applied Statistical Methods, 2(1), 2-13.
16. Matsumoto M, Nishimura T (1998). "Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudorandom Number Generator. " ACM Transactions on Modeling and Computer Simulation, 8, 3-30.
17. Nickolls J, Buck I, Garland M, Skadron K (2008). "Scalable Parallel Programming. " ACM Queue, 6(2), 40-53.
18. Nvidia Corporation (2010a). CUDA C Best Practices Guide Version 3.2, URL http://www. nvidia.com/CUDA.
19. Nvidia Corporation (2010b). Nvidia CUDA Programming Guide, Version 3.2, URL http: //www.nvidia.com/CUDA.
20. Owens JD, Houston M, Luebke D, Green S, Stone JE, Phillips JC (2008). "GPU Computing. " Proceedings of the IEEE, 96(5), 879-899.
21. Owens JD, Luebke D, Govindaraju N, Harris M, Krueger J, Lefohn AE, Purcell TJ (2007). "A Survey of General-Purpose Computation on Graphics Hardware. " Computer Graphics Forum, 26(1), 80-113.
22. Press J (2003). Subjective and Objective Bayesian Statistics, 2nd edition. John Wiley & Sons.
23. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007). Numerical Recipes, The Art of Scientiffc Computing, 3rd edition. Cambridge University Press.
24. R Development Core Team (2011). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http: //www.R-project.org.
25. Rossi P (2011). bayesm: Bayesian Inference for Marketing/Micro-Econometrics, R package version 2.2-4, URL http://CRAN.R-project.org/package=bayesm.
26. Rossi PE, Allenby GM, McCulloch R (2005). Bayesian Statistics and Marketing, John Wiley & Sons.
27. Smith BJ (2007). "boa: An R Package for MCMC Output Convergence Assessment and Posterior Inference. " Journal of Statistical Software, 21(11), 1-37. URL http://www. jstatsoft.org/v21/i11/.
28. Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, Johansen-Berg H, Bannister PR, Luca MD, Drobnjak I, Flitney DE, Niazy RK, Saunders J, Vickers J, Zhang Y, Stefano ND, Brad JM, Matthews PM (2004). "Advances in Functional and Structural MR Image Analysis and Implementation as FSL. " Technical Report TR04SS2, FMRIB (Oxford Centre for Functional Magnetic Resonance Imaging of the Brain). URL http: //www.fmrib.ox.ac.uk/fsl.
29. Tabelow K, Polzehl J (2011). "Statistical Parametric Maps for Functional MRI Experiments in R: The Package fmri. " Journal of Statistical Software, 44(11), 1-21. URL http://www. jstatsoft.org/v44/i11/.
30. Whitcher B, Schmid V, Thornton A (2011a). Oro. nifti: Rigorous-NIfTI+ANALYZE+AFNI Input / Output, R Package Version 0.2.6, URL http://CRAN.R-project.org/package= oro.nifti.
31. Whitcher B, Schmid VJ, Thornton A (2011b). "Working with the DICOM and NIfTI Data Standards in R. " Journal of Statistical Software, 44(6), 1-28. URL http://www. jstatsoft.org/v44/i06/.
32. Zellner A (1962). "An Effcient Method of Estimating Seemingly Unrelated Regressions and Tests for Aggregation Bias. " Journal of the American Statistical Association, 57, 348-368.