Markov chain Monte Carlo random effects modeling in magnetic resonance image processing using the BRugs interface to WinBUGS

Journal of Statistical Software

Volumn 44, Issue 2, 2011, Pages 1-23

  King, Martin D ^a   Clark, Chris A ^a   Calamante, Fernando ^b,c   Gadian, David G ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b FLOREY INSTITUTE OF NEUROSCIENCE AND MENTAL HEALTH   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

BRugs; GeoBUGS; Magnetic resonance imaging; Markov chain Monte Carlo; R; Random effects; WinBUGS

Indexed keywords

EID: 84856302452     PISSN: None     EISSN: 15487660     Source Type: Journal    
DOI: 10.18637/jss.v044.i02     Document Type: Article

References (50)

1. Bacon DW, Watts DG (1971). "Estimating the Transition Between Two Intersecting Straight Lines. " Biometrika, 58, 525-534.
2. Bates D, Maechler M, Bolker B (2011). lme4: Linear Mixed-Effects Models Using S4 Classes. R package version 0.999375-38, URL http://CRAN.R-project.org/package=lme4.
3. Besag J, York J, Molliffe A (1991). "Bayesian Image Restoration, with Two Applications in Spatial Statistics. " Annals of the Institute of Statistical Mathematics, 43, 1-59.
4. Calamante F (2005). "Artifacts and Pitfalls in Perfusion MR Imaging. " In JH Gillard, AD Waldman, PB Barker (eds.), Clinical MR Neuroimaging: Diffusion, Perfusion and Spectroscopy, pp. 141-160. Cambridge University Press, Cambridge.
5. Calamante F, Thomas DL, Pell GS, Wiersma J, Turner R (1999). "Measuring Cerebral Blood Flow Using Magnetic Resonance Imaging Techniques. " Journal of Cerebral Blood Flow and Metabolism, 19, 701-735.
6. Calamante F, Vonken EPA, van Osch MJP (2007). "Contrast Agent Concentration Measurements Affecting Quantiffcation of Bolus-Tracking Perfusion MRI. " Magnetic Resonance in Medicine, 58, 544-553.
7. Carlin BP, Gelfand AE, Smith AFM (1992). "Hierarchical Bayesian Analysis of Changepoint Problems. " Applied Statistics, 41, 389-405.
8. Carlin BP, Louis TA (2000). Bayes and Empirical Bayes Methods for Data Analysis, 2nd edition. Chapman & Hall/CRC, Boca Raton.
9. Cowles MK, Carlin BP (1996). "Markov Chain Monte Carlo Convergence Diagnostics: A Comparative Review. " Journal of the American Statistical Association, 91, 883-904.
10. Crawley MJ (2007). The R Book, John Wiley & Sons, Chichester.
11. Crowder M (1992). "Interlaboratory Comparisons: Round Robins with Random Effects. " Journal of the Royal Statistical Society C, 42, 409-425.
12. Crowder MJ, Hand DJ (1990). Analysis of Repeated Measures, Chapman & Hall, London.
13. Crowder MJ, Tredger JA (1981). "The Use of Exponentially Damped Polynomials for Biological Recovery Data. " Applied Statistics, 30, 147-152.
14. Gelman A (1996). "Inference and Monitoring Convergence. " In WR Gilks, S Richardson, DJ Spiegelhalter (eds.), Markov Chain Monte Carlo in Practice, pp. 131-143. Chapman & Hall, London.
15. Gelman A (2006). "Prior Distributions for Variance Parameters in Hierarchical Models (Comment on Article by Browne and Draper). " Bayesian Analysis, 1, 515-534.
16. Gelman A, Bois F, Jiang J (1996). "Physiological Pharmacokinetic Analysis using Population Modeling and Informative Prior Distributions. " Journal of the American Statistical Association, 91, 1400-1412.
17. Gelman A, Carlin JB, Stern HS, Rubin DB (2004). Bayesian Data Analysis, 2nd edition. Chapman & Hall/CRC, Boca Raton.
18. Gelman A, Rubin DB (1992). "A Single Series from the Gibbs Sampler Provides a False Sense of Security. " In JM Bernardo, JO Berger, AP Dawid, AFM Smith (eds.), Bayesian Statistics, volume 4, pp. 625-631. Oxford University Press, Oxford.
19. Gilks WR, Richardson S, Spiegelhalter DJ (eds.) (1996). Markov Chain Monte Carlo in Practice, Chapman & Hall, London.
20. Hand D, Crowder M (1996). Practical Longitudinal Data Analysis, Chapman & Hall, London.
21. Jones RH (1993). Longitudinal Data with Serial Correlation: A State-Space Approach, Chapman & Hall, London.
22. Kass RE, Carlin BP, Gelman A, Neal RM (1998). "Markov Chain Monte Carlo in Practice: A Roundtable Discussion. " The American Statistician, 52, 93-100.
23. King MD, Crowder MJ, Hand DJ, Harris NG, Williams SR, Obrenovitch TP, Gadian DG (2003). "Temporal Relation Between the ADC and DC Potential Responses to Transient Focal Ischemia in the Rat: A Markov Chain Monte Carlo Simulation Analysis. " Journal of Cerebral Blood Flow and Metabolism, 23, 677-688.
24. King MD, Crowder MJ, Hand DJ, Harris NG, Williams SR, Obrenovitch TP, Gadian DG (2005). "Is Anoxic Depolarisation Associated with an ADC Threshold? A Markov Chain Monte Carlo Analysis. " NMR in Biomedicine, 18, 587-594.
25. King MD, Gadian DG, Clark CA (2009). "A Random Effects Modelling Approach to the Crossing-Fibre Problem in Tractography. " NeuroImage, 44, 753-768.
26. Laird NM, Ware JH (1982). "Random-Effects Models for Longitudinal Data. " Biometrics, 38, 963-974.
27. Lawson AB, Browne WJ, Vidal Rodeiro CL (2003). Disease Mapping with WinBUGS and MLwiN, John Wiley & Sons, Chichester.
28. Lindley DV, Smith AFM (1972). "Bayes Estimates for the Linear Model. " Journal of the Royal Statistical Society B, 34, 1-41.
29. Lunn D, Spiegelhalter D, Thomas A, Best N (2009). "The BUGS Project: Evolution, Critique and Future Directions. " Statistics in Medicine, 28, 3049-3067.
30. Lunn DJ, Thomas A, Best N, Spiegelhalter D (2000). "WinBUGS-A Bayesian Modelling Framework: Concepts, Structure, and Extensibility. " Statistics and Computing, 10, 325-337.
31. McLean RA, Sanders WL, Stroup WW(1991). "A Uniffed Approach to Mixed Linear Models. " The American Statistician, 45, 54-64.
32. Sstergaard L, Weisskoff RM, Chesler DA, Gyldensted C, Rosen BR (1996). "High Resolution Measurement of Cerebral Blood Flow Using Intravascular Tracer Bolus Passages. Part 1: Mathematical Approach and Statistical Analysis. " Magnetic Resonance in Medicine, 36, 715-725.
33. Park JH (2011). "CRAN Task View: Bayesian Inference. " Version 2011-10-07, URL http: //CRAN.R-project.org/view=Bayesian.
34. Penny WD, Friston KJ (2004). "Hierarchical Models. " In RSJ Frackowiak, KJ Friston, CD Frith, RJ Dolan, CJ Price, S Zeki, JT Ashburner, WD Penny (eds.), Human Brain Function, pp. 851-863. Academic Press, San Diego.
35. Pinheiro J, Bates D, DebRoy S, Sarkar D, R Development Core Team (2011). nlme: Linear and Nonlinear Mixed Effects Models, R package version 3.1-98, URL http: //CRAN.R-project.org/package=nlme.
36. Pinheiro JC, Bates DM (2000). Mixed-Effects Models in S and S-PLUS. Springer Verlag, New York.
37. Plummer M (2011). rjags: Bayesian Graphical Models using MCMC, R package version 2.1.0-6, URL http://CRAN.R-project.org/package=rjags.
38. Plummer M, Best N, Cowles K, Vines K (2006). "coda: Convergence Diagnosis and Output Analysis for MCMC. " R News, 6(1), 7-11. URL http://CRAN.R-project.org/doc/ Rnews/.
39. Rawlings JO (1988). Applied Regression Analysis: A Research Tool, Wadsworth and Brooks, Belmont.
40. 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/.
41. Richardson S, Thomson A, Best N, Elliott P (2004). "Interpreting Posterior Relative Risk Estimates in Disease-Mapping Studies. " Environmental Health Perspectives, 112, 1016-1025.
42. Schmid VJ, Whitcher B, Padhani AR, Taylor NJ, Yang GZ (2006). "Bayesian Methods for Pharmacokinetic Models in Dynamic Contrast-Enhanced Magnetic Resonance Imaging. " IEEE Transactions on Medical Imaging, 25, 1627-1636.
43. Schmid VJ, Whitcher B, Padhani AR, Taylor NJ, Yang GZ (2009). "A Bayesian Hierarchi-cal Model for the Analysis of a Longitudinal Dynamic Contrast-Enhanced MRI Oncology Study. " Magnetic Resonance in Medicine, 61, 163-174.
44. Spiegelhalter D, Thomas A, Best N, Gilks W (1995). "BUGS 0.5. Bayesian Inference Using Gibbs Sampling Manual. " MRC Biostatistics Unit, Institute of Public Health, Cambridge, URL http://www.mrc-bsu.cam.ac.uk/bugs/documentation/bugs05/manual05.html.
45. Spiegelhalter D, Thomas A, Best N, Lunn D (2003). "WinBUGS User Manual. " MRC Biostatistics Unit, Institute of Public Health, Cambridge, URL http://www.mrc-bsu.cam. ac.uk/bugs/winbugs/manual14.pdf.
46. Sturtz S, Ligges U, Gelman A (2005). "R2WinBUGS: A Package for Running WinBUGS from R. " Journal of Statistical Software, 12(3), 1-16. URL http://www.jstatsoft.org/ v12/i03/.
47. Thomas A, O'Hara B, Ligges U, Sturtz S (2006). "Making BUGS Open. " R News, 6(1), 12-17. URL http://CRAN.R-project.org/doc/Rnews/.
48. Wakeffeld J (1996). "The Bayesian Analysis of Population Pharmacokinetic Models. " Journal of the American Statistical Association, 91, 62-75.
49. Wakeffeld JC, Best NG, Waller L (2000). "Bayesian Approaches to Disease Mapping. " In P Elliott, JC Wakeffeld, NG Best, DJ Briggs (eds.), Spatial Epidemiology: Methods and Applications, pp. 104-127. Oxford University Press, Oxford.
50. Walker-Samuel S, Orton M, Boult JKR, Robinson SP (2011). "Improving Apparent Diffusion Coeffcient Estimates and Elucidating Tumor Heterogeneity using Bayesian Adaptive Smoothing. " Magnetic Resonance in Medicine, 65, 438-447.