The Annals of Applied Statistics

Meta-analysis of functional neuroimaging data using Bayesian nonparametric binary regression

Yu Ryan Yue, Martin A. Lindquist, and Ji Meng Loh
Source: Ann. Appl. Stat. Volume 6, Number 2 (2012), 697-718.

Abstract

In this work we perform a meta-analysis of neuroimaging data, consisting of locations of peak activations identified in 162 separate studies on emotion. Neuroimaging meta-analyses are typically performed using kernel-based methods. However, these methods require the width of the kernel to be set a priori and to be constant across the brain. To address these issues, we propose a fully Bayesian nonparametric binary regression method to perform neuroimaging meta-analyses. In our method, each location (or voxel) has a probability of being a peak activation, and the corresponding probability function is based on a spatially adaptive Gaussian Markov random field (GMRF). We also include parameters in the model to robustify the procedure against miscoding of the voxel response. Posterior inference is implemented using efficient MCMC algorithms extended from those introduced in Holmes and Held [Bayesian Anal. 1 (2006) 145–168]. Our method allows the probability function to be locally adaptive with respect to the covariates, that is, to be smooth in one region of the covariate space and wiggly or even discontinuous in another. Posterior miscoding probabilities for each of the identified voxels can also be obtained, identifying voxels that may have been falsely classified as being activated. Simulation studies and application to the emotion neuroimaging data indicate that our method is superior to standard kernel-based methods.

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Links and Identifiers

Permanent link to this document: http://projecteuclid.org/euclid.aoas/1339419613
Digital Object Identifier: doi:10.1214/11-AOAS523
Zentralblatt MATH identifier: 06062736
Mathematical Reviews number (MathSciNet): MR2976488

References

Albert, J. H. and Chib, S. (1993). Bayesian analysis of binary and polychotomous response data. J. Amer. Statist. Assoc. 88 669–679.
Mathematical Reviews (MathSciNet): MR1224394
Zentralblatt MATH: 0774.62031
Digital Object Identifier: doi:10.1080/01621459.1993.10476321
Andrews, D. F. and Mallows, C. L. (1974). Scale mixtures of normal distributions. J. Roy. Statist. Soc. Ser. B 36 99–102.
Mathematical Reviews (MathSciNet): MR359122
Brezger, A., Fahrmeir, L. and Hennerfeind, A. (2007). Adaptive Gaussian Markov random fields with applications in human brain mapping. J. Roy. Statist. Soc. Ser. C 56 327–345.
Mathematical Reviews (MathSciNet): MR2370993
Digital Object Identifier: doi:10.1111/j.1467-9876.2007.00580.x
Carter, C. K. and Kohn, R. (1996). Markov chain Monte Carlo in conditionally Gaussian state space models. Biometrika 83 589–601.
Mathematical Reviews (MathSciNet): MR1423876
Zentralblatt MATH: 0866.62018
Digital Object Identifier: doi:10.1093/biomet/83.3.589
Carvalho, C. M., Polson, N. G. and Scott, J. G. (2010). The horseshoe estimator for sparse signals. Biometrika 97 465–480.
Mathematical Reviews (MathSciNet): MR2650751
Zentralblatt MATH: 05773446
Digital Object Identifier: doi:10.1093/biomet/asq017
Choudhuri, N., Ghosal, S. and Roy, A. (2007). Nonparametric binary regression using a Gaussian process prior. Stat. Methodol. 4 227–243.
Mathematical Reviews (MathSciNet): MR2368147
Zentralblatt MATH: 1248.62053
Digital Object Identifier: doi:10.1016/j.stamet.2006.07.003
Crainiceanu, C. M., Ruppert, D., Carroll, R. J., Adarsh, J. and Goodner, B. (2007). Spatially adaptive penalized splines with heteroscedastic errors. J. Comput. Graph. Statist. 16 265–288.
Mathematical Reviews (MathSciNet): MR2370943
Digital Object Identifier: doi:10.1198/106186007X208768
Dale, A. M., Fischl, B. and Sereno, M. I. (1999). Cortical surface-based analysis. I. Segmentation and surface reconstruction. Neuroimage 9 179–194.
Devroye, L. (1986). Non-Uniform Random Variate Generation. Springer, New York.
Mathematical Reviews (MathSciNet): MR836973
Dey, D. K., Ghosh, S. K. and Mallick, B. K., eds. (2000). Generalized Linear Models: A Bayesian Perspective. Biostatistics 5. Dekker, New York.
Mathematical Reviews (MathSciNet): MR1893779
Fischl, B., Sereno, M. I. and Dale, A. M. (1999). Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9 195–207.
Gelman, A. (2006). Prior distributions for variance parameters in hierarchical models (comment on article by Browne and Draper). Bayesian Anal. 1 515–533 (electronic).
Mathematical Reviews (MathSciNet): MR2221284
Digital Object Identifier: doi:10.1214/06-BA117A
Gelman, A., van Dyk, D. A., Huang, Z. and Boscardin, W. J. (2008). Using redundant parameterizations to fit hierarchical models. J. Comput. Graph. Statist. 17 95–122.
Mathematical Reviews (MathSciNet): MR2424797
Digital Object Identifier: doi:10.1198/106186008X287337
Gu, C. (1990). Adaptive spline smoothing in non-Gaussian regression models. J. Amer. Statist. Assoc. 85 801–807.
Mathematical Reviews (MathSciNet): MR1138360
Hastie, T. J. and Tibshirani, R. J. (1990). Generalized Additive Models. Monographs on Statistics and Applied Probability 43. Chapman & Hall, London.
Mathematical Reviews (MathSciNet): MR1082147
Holmes, C. C. and Held, L. (2006). Bayesian auxiliary variable models for binary and multinomial regression. Bayesian Anal. 1 145–168 (electronic).
Mathematical Reviews (MathSciNet): MR2227368
Digital Object Identifier: doi:10.1214/06-BA105
Holmes, C. C. and Mallick, B. K. (2003). Generalized nonlinear modeling with multivariate free-knot regression splines. J. Amer. Statist. Assoc. 98 352–368.
Mathematical Reviews (MathSciNet): MR1995711
Zentralblatt MATH: 1041.62059
Digital Object Identifier: doi:10.1198/016214503000143
Kang, J., Johnson, T. D., Nichols, T. E. and Wager, T. D. (2011). Meta analysis of functional neuroimaging data via Bayesian spatial point processes. J. Amer. Statist. Assoc. 106 124–134.
Mathematical Reviews (MathSciNet): MR2816707
Digital Object Identifier: doi:10.1198/jasa.2011.ap09735
Kober, H., Barrett, L. F., Joseph, J., Bliss-Moreau, E., Lindquist, K. and Wager, T. D. (2008). Functional grouping and cortical-subcortical interactions in emotion: A meta-analysis of neuroimaging studies. Neuroimage 42 998–1031.
Krivobokova, T., Crainiceanu, C. M. and Kauermann, G. (2008). Fast adaptive penalized splines. J. Comput. Graph. Statist. 17 1–20.
Mathematical Reviews (MathSciNet): MR2424792
Digital Object Identifier: doi:10.1198/106186008X287328
Lindquist, M. A. (2008). The statistical analysis of fMRI data. Statist. Sci. 23 439–464.
Mathematical Reviews (MathSciNet): MR2530545
Digital Object Identifier: doi:10.1214/09-STS282
Project Euclid: euclid.ss/1242049389
Loader, C. (1999). Local Regression and Likelihood. Springer, New York.
Mathematical Reviews (MathSciNet): MR1704236
Zentralblatt MATH: 0929.62046
McCullagh, P. and Nelder, J. (1989). Generalized Linear Models, 2nd ed. Chapman & Hall/CRC, Boca Raton, FL.
Mathematical Reviews (MathSciNet): MR727836
O’Sullivan, F., Yandell, B. S. and Raynor, W. J. Jr. (1986). Automatic smoothing of regression functions in generalized linear models. J. Amer. Statist. Assoc. 81 96–103.
Mathematical Reviews (MathSciNet): MR830570
Digital Object Identifier: doi:10.1080/01621459.1986.10478243
Penny, W. D., Trujillo-Barreto, N. J. and Friston, K. J. (2005). Bayesian fMRI time series analysis with spatial priors. Neuroimage 24 350–362.
Psarakis, S. and Panaretos, J. (1990). The folded $t$ distribution. Comm. Statist. Theory Methods 19 2717–2734.
Mathematical Reviews (MathSciNet): MR1086030
Digital Object Identifier: doi:10.1080/03610929008830342
Rue, H. and Held, L. (2005). Gaussian Markov Random Fields: Theory and Applications. Monographs on Statistics and Applied Probability 104. Chapman & Hall/CRC, Boca Raton, FL.
Mathematical Reviews (MathSciNet): MR2130347
Rue, H., Martino, S. and Chopin, N. (2009). Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J. R. Stat. Soc. Ser. B Stat. Methodol. 71 319–392.
Mathematical Reviews (MathSciNet): MR2649602
Zentralblatt MATH: 1248.62156
Digital Object Identifier: doi:10.1111/j.1467-9868.2008.00700.x
Ruppert, D. and Carroll, R. J. (2000). Spatially-adaptive penalties for spline fitting. Aust. N. Z. J. Stat. 42 205–223.
Spiegelhalter, D. J., Best, N. G., Carlin, B. P. and van der Linde, A. (2002). Bayesian measures of model complexity and fit. J. R. Stat. Soc. Ser. B Stat. Methodol. 64 583–639.
Mathematical Reviews (MathSciNet): MR1979380
Zentralblatt MATH: 1067.62010
Digital Object Identifier: doi:10.1111/1467-9868.00353
Talairach, J. and Tournoux, P. (1988). Co-planar Stereotaxic Atlas of the Human Brain: 3-Dimensional Proportional System—an Approach to Cerebral Imaging. Thieme Medical Publishers, New York.
Tipping, M. E. (2001). Sparse Bayesian learning and the relevance vector machine. J. Mach. Learn. Res. 1 211–244.
Mathematical Reviews (MathSciNet): MR1875838
Zentralblatt MATH: 0997.68109
Trippa, L. and Muliere, P. (2009). Bayesian nonparametric binary regression via random tessellations. Statist. Probab. Lett. 79 2273–2280.
Mathematical Reviews (MathSciNet): MR2591984
Turkeltaub, P., Eden, G., Jones, K. and Zeffiro, T. A. T. (2002). Meta-analysis of the functional neuroanatomy of single-word reading: Method and validation. NeuroImage 16 765–780.
Wager, T. D., Jonides, J. and Reading, S. (2004). Neuroimaging studies of shifting attention: A meta-analysis. Neuroimage 22 1679–1693.
Wager, T. D., Lindquist, M. A. and Kaplan, L. (2007). Meta-analysis of functional neuroimaging data: Current and future directions. Social Cognitive and Affective Neuroscience 2 150–158.
Wager, T. D., Barrett, L. F., Bliss-Moreau, E., Lindquist, K., Duncan, S., Kober, H., Joseph, J., Davidson, M. and Mize, J. (2008). The neuroimaging of emotion. In Handbook of Emotion (M. Lewis, ed.) 249–271. Guilford Press, New York.
Wager, T. D., Lindquist, M. A., Nichols, T. E., Kober, H. and Van Snellenberg, J. X. (2009). Evaluating the consistency and specificity of neuroimaging data using meta-analysis. Neuroimage 45 S210–S221.
Wahba, G., Wang, Y., Gu, C., Klein, R. and Klein, B. (1995). Smoothing spline ANOVA for exponential families, with application to the Wisconsin Epidemiological Study of Diabetic Retinopathy. Ann. Statist. 23 1865–1895.
Mathematical Reviews (MathSciNet): MR1389856
Zentralblatt MATH: 0854.62042
Digital Object Identifier: doi:10.1214/aos/1034713638
Project Euclid: euclid.aos/1034713638
Wiper, M. P., Girón, F. J. and Pewsey, A. (2008). Objective Bayesian inference for the half-normal and half-$t$ distributions. Comm. Statist. Theory Methods 37 3165–3185.
Mathematical Reviews (MathSciNet): MR2467759
Digital Object Identifier: doi:10.1080/03610920802105184
Wood, S. A. and Kohn, R. (1998). A Bayesian approach to robust binary nonparametric regression. J. Amer. Statist. Assoc. 93 203–213.
Wood, S. A., Kohn, R., Cottet, R., Jiang, W. and Tanner, M. (2008). Locally adaptive nonparametric binary regression. J. Comput. Graph. Statist. 17 352–372.
Mathematical Reviews (MathSciNet): MR2439964
Digital Object Identifier: doi:10.1198/106186008X318576
Yue, Y., Loh, J. M. and Lindquist, M. A. (2010). Adaptive spatial smoothing of fMRI images. Stat. Interface 3 3–13.
Mathematical Reviews (MathSciNet): MR2609707
Zentralblatt MATH: 1245.62118
Yue, Y. R. and Loh, J. M. (2011). Bayesian semiparametric intensity estimation for inhomogeneous spatial point processes. Biometrics 67 937–946.
Mathematical Reviews (MathSciNet): MR2829268
Digital Object Identifier: doi:10.1111/j.1541-0420.2010.01531.x
Yue, Y. and Speckman, P. L. (2010). Nonstationary spatial Gaussian Markov random fields. J. Comput. Graph. Statist. 19 96–116.
Mathematical Reviews (MathSciNet): MR2654402
Digital Object Identifier: doi:10.1198/jcgs.2009.08124

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