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Publications of W.D. Penny

Books and proceedings

  1. K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press, 2007. Keyword(s): introduction. [bibtex-entry]


  2. R.S.J. Frackowiak, K.J. Friston, C. Frith, R. Dolan, C.J. Price, S. Zeki, J. Ashburner, and W.D. Penny. Human Brain Function. Academic Press, 2nd edition, 2003. Keyword(s): introduction. [bibtex-entry]


Articles in journal or book chapters

  1. G. Ridgway, V. Litvak, G. Flandin, K.J. Friston, and W.D. Penny. The problem of low variance voxels in statistical parametric mapping; a new hat avoids a 'haircut'. NeuroImage, 59(3):2131-2141, 2012. Keyword(s): EEG, MEG. [bibtex-entry]


  2. M.J. Rosa, K.J. Friston, and W.D. Penny. Post-hoc selection of dynamic causal models. NeuroImage, 2012. Note: In Press. [bibtex-entry]


  3. V. Litvak, J. Mattout, S.J. Kiebel, C. Phillips, R.N.A. Henson, J. Kilner, G. Barnes, R. Oostenveld, J. Daunizeau, G. Flandin, W.D. Penny, and K.J. Friston. EEG and MEG data analysis in SPM8. Comput. Intell. Neurosci., 2011(852961), 2011. Keyword(s): introduction, EEG, MEG. [bibtex-entry]


  4. M.J. Rosa, J. Kilner, and W.D. Penny. Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI. PLOS Computational Biology, 7(6):e1002070, 2011. Keyword(s): BMC. [bibtex-entry]


  5. V. Litvak, A. Eusebio, A. Jha, R. Oostenveld, G. Barnes, W.D. Penny, L. Zrinzo, M.I. Hariz, P. Limousin, K.J. Friston, and P. Brown. Optimised beamforming for simultaneous MEG and intracranial local field potential recordings in deep brain stimulation patients. NeuroImage, in press, 2010. [bibtex-entry]


  6. W.D. Penny, K.E. Stephan, J. Daunizeau, M.J. Rosa, K.J. Friston, T.M.Schofield, and A.P. Leff. Comparing Families of Dynamic Causal Models. PLoS Comput Biol, 6(3):e1000709, 2010. [bibtex-entry]


  7. K.E. Stephan, W.D. Penny, R. Moran, H.E. Den Ouden, J. Daunizeau, and K.J. Friston. Ten simple rules for dynamic causal modelling. NeuroImage, 49(4):3099-3109, 2010. Keyword(s): DCM. [bibtex-entry]


  8. W.D. Penny, V. Litvak, L. Fuentemilla, E. Duzel, and K.J. Friston. Dynamic Causal Models for phase coupling. Journal of Neuroscience Methods, 183(1):19-30, 2009. [bibtex-entry]


  9. M.J. Rosa, S. Bestmann, L. Harrison, and W.D. Penny. Bayesian Model Selection Maps for Group Studies. NeuroImage, 49(1):217-224, 2009. [bibtex-entry]


  10. M.J. Rosa, J. Kilner, F. Blankenburg, O. Josephs, and W.D. Penny. Estimating the transfer function from neuronal activity to BOLD using simultaneous EEG-fMRI. NeuroImage, 2009. [bibtex-entry]


  11. K.E. Stephan, W.D. Penny, J. Daunizeau, R. Moran, and K.J. Friston. Bayesian model selection for group studies. NeuroImage, 46(3):1004-10174, 2009. Keyword(s): DCM, BMC, Bayesian, group. [bibtex-entry]


  12. K.J. Friston, C. Chu, Janaina Mourão-Miranda, Oliver Hulme, G. Rees, W.D. Penny, and J. Ashburner. Bayesian decoding of brain images. NeuroImage, 39(1):181-205, 2008. Keyword(s): Bayesian, multivariate. [bibtex-entry]


  13. L. Harrison, W.D. Penny, J. Daunizeau, and K.J. Friston. Diffusion-based spatial priors for functional magnetic resonance images. NeuroImage, 41(2):408-423, 2008. Keyword(s): fMRI, spatial, bayesian. [bibtex-entry]


  14. L. Harrison, W.D. Penny, G. Flandin, C. Ruff, N. Weiskopf, and K.J. Friston. Sparse diffusion-based spatial models for functional magnetic resonance images. NeuroImage, 2008. Keyword(s): fMRI, spatial. [bibtex-entry]


  15. G. Flandin and W.D. Penny. Bayesian fMRI data analysis with sparse spatial basis function priors. NeuroImage, 34(3):1108-1125, 2007. Keyword(s): PPM, Bayesian, fMRI, GLM, spatial, hierarchical. [bibtex-entry]


  16. K.J. Friston, J. Mattout, N. Trujillo-Bareto, J. Ashburner, and W.D. Penny. Variational free energy and the Laplace approximation. NeuroImage, 34(1):220-234, 2007. [bibtex-entry]


  17. L. Harrison, W.D. Penny, J. Ashburner, N. Trujillo-Bareto, and K.J. Friston. Diffusion-based spatial priors for imaging. NeuroImage, 38:677-695, 2007. Keyword(s): fMRI, GLM, spatial. [bibtex-entry]


  18. W.D. Penny and K.J. Friston. Functional Imaging. Scholarpedia, 2(5):1478, 2007. Keyword(s): fMRI, EEG, MEG, introduction. [bibtex-entry]


  19. W.D. Penny, J. Kilner, and F. Blankenburg. Robust Bayesian General Linear Models. NeuroImage, 36(3):661-671, 2007. Keyword(s): GLM. [bibtex-entry]


  20. K.E. Stephan, L. Harrison, S.J. Kiebel, O. David, W.D. Penny, and K.J. Friston. Dynamic causal models of neural system dynamics: current state and future extensions. Journal of Biosciences, pp 129-144, 2007. Keyword(s): DCM, fMRI. [bibtex-entry]


  21. K.E. Stephan, J.C. Marshall, W.D. Penny, K.J. Friston, and G.R. Fink. Interhemispheric integration of visual processing during task-driven lateralization. Journal of Neuroscience, 27:3512-3522, 2007. Keyword(s): DCM, fMRI. [bibtex-entry]


  22. J. Mattout, C. Phillips, W.D. Penny, M. Rugg, and K.J. Friston. MEG source localization under multiple constraints: an extended Bayesian framework. NeuroImage, 30(3):753-767, 2006. Keyword(s): EEG, MEG. [bibtex-entry]


  23. U. Noppeney and W.D. Penny. Two approaches to repetition suppression. Human Brain Mapping, 27:411-416, 2006. Keyword(s): fMRI. [bibtex-entry]


  24. K.J. Friston, W.D. Penny, and O. David. Modelling brain responses. In M.F. Glabus, editor, International Review of Neurobiology, Neuroimaging, Part A. Elsevier, 2005. Keyword(s): Introduction. [bibtex-entry]


  25. K.J. Friston, W.D. Penny, and D.E. Glaser. Conjunction revisited. NeuroImage, 25(3):661-667, 2005. Keyword(s): conjunction. [bibtex-entry]


  26. W.D. Penny, G. Flandin, and N. Trujillo-Bareto. Bayesian Comparison of Spatially Regularised General Linear Models. Human Brain Mapping, 28:275-293, 2005. Keyword(s): Bayesian, fMRI, PPM, GLM. [bibtex-entry]


  27. W.D. Penny, Z. Ghahramani, and K.J. Friston. Bilinear Dynamical Systems. Phil Trans R Soc B, 360(1457):983-993, 2005. Keyword(s): Dynamic, Markov, fMRI. [bibtex-entry]


  28. W.D. Penny, N. Trujillo-Bareto, and K.J. Friston. Bayesian fMRI time series analysis with spatial priors. NeuroImage, 24(2):350-362, 2005. Keyword(s): Spatial, fMRI. [bibtex-entry]


  29. K.E. Stephan, W.D. Penny, J.C. Marshall, G.R. Fink, and K.J. Friston. Investigating the functional role of Callosal connections with Dynamic Causal Models. Ann. N.Y. Acad. Sci., 1064:16-36, 2005. Keyword(s): DCM. [bibtex-entry]


  30. W.D. Penny and K.J. Friston. Classical and Bayesian Iinference in fMRI. In L. Landini, editor, Advanced Image Processing in Magnetic Resonance Imaging. Marcel Dekker, 2004. Keyword(s): introduction. [bibtex-entry]


  31. W.D. Penny, K.E. Stephan, A. Mechelli, and K.J. Friston. Comparing Dynamic Causal Models. NeuroImage, 22(3):1157-1172, 2004. Keyword(s): Bayesian, connectivity, fMRI, DCM, BMC. [bibtex-entry]


  32. W.D. Penny, K.E. Stephan, A. Mechelli, and K.J. Friston. Modelling Functional Integration: A Comparison of Structural Equation and Dynamic Causal and Models. NeuroImage, 23:264-274, 2004. Note: Supplement 1. Keyword(s): introduction, connectivity, DCM. [bibtex-entry]


  33. N. Ramnani, T.E.J. Behrens, W.D. Penny, and P.M. Matthews. New approaches for exploring anatomic and functional connectivity in the human brain. Biological Psychiatry, 2004. Note: In Press. Keyword(s): introduction, DCM. [bibtex-entry]


  34. K.E. Stephan, L. Harrison, W.D. Penny, and K.J. Friston. Biophysical models of fMRI responses. Current Opinion in Neurobiology, 14(5):629-635, 2004. [bibtex-entry]


  35. M. Brett, W.D. Penny, and S.J. Kiebel. Introduction to Random field theory. In R.S.J. Frackowiak, K.J. Friston, C. Frith, R. Dolan, K.J. Friston, C.J. Price, S. Zeki, J. Ashburner, and W.D. Penny, editors, Human Brain Function. Academic Press, 2nd edition, 2003. Keyword(s): introduction, RFT. [bibtex-entry]


  36. W.D. Penny and K.J. Friston. Classical and Bayesian inference. In R.S.J. Frackowiak, K.J. Friston, C. Frith, R. Dolan, K.J. Friston, C.J. Price, S. Zeki, J. Ashburner, and W.D. Penny, editors, Human Brain Function. Academic Press, 2nd edition, 2003. Keyword(s): Bayesian, fMRI, hierarchical, nonsphericity, PPM, REML. [bibtex-entry]


  37. W.D. Penny, A.P. Holmes, and K.J. Friston. Hierarchical Models. In R.S.J. Frackowiak, K.J. Friston, C. Frith, R. Dolan, K.J. Friston, C.J. Price, S. Zeki, J. Ashburner, and W.D. Penny, editors, Human Brain Function. Academic Press, 2nd edition, 2003. Keyword(s): Bayesian, GLM, group, introduction, RFX, hierarchical. [bibtex-entry]


  38. W.D. Penny, A.P. Holmes, and K.J. Friston. Random effects analysis. In R.S.J. Frackowiak, K.J. Friston, C. Frith, R. Dolan, K.J. Friston, C.J. Price, S. Zeki, J. Ashburner, and W.D. Penny, editors, Human Brain Function. Academic Press, 2nd edition, 2003. Keyword(s): RFX, group, introduction. [bibtex-entry]


  39. K.J. Friston, L. Harrison, and W.D. Penny. Dynamic Causal Modelling. NeuroImage, 19(4):1273-1302, 2003. Keyword(s): connectivity, fMRI, DCM. [bibtex-entry]


  40. K.J. Friston and W.D. Penny. Posterior probability maps and SPMs. NeuroImage, 19(3):1240-1249, 2003. Keyword(s): Bayesian, hierarchical, PPM, EM. [bibtex-entry]


  41. D.R. Gitelman, W.D. Penny, J. Ashburner, and K.J. Friston. Modeling regional and psychophysiologic interactions in fMRI: the importance of hemodynamic deconvolution. NeuroImage, 19:200-207, 2003. Keyword(s): connectivity, fMRI, PPI. [bibtex-entry]


  42. L. Harrison, W.D. Penny, and K.J. Friston. Multivariate Autoregressive Modelling of fMRI time series. NeuroImage, 19(4):1477-1491, 2003. [bibtex-entry]


  43. W.D. Penny and K.J. Friston. Mixtures of General Linear Models for Functional Neuroimaging. IEEE Transactions on Medical Imaging, 22(4):504-514, 2003. Keyword(s): Mixture, GLM, Bayesian, fMRI, spatial, EM. [bibtex-entry]


  44. W.D. Penny, S.J. Kiebel, and K.J. Friston. Variational Bayesian Inference for fMRI time series. NeuroImage, 19(3):727-741, 2003. Keyword(s): autocorrelation, Bayesian, fMRI, PPM. [bibtex-entry]


  45. K.J. Friston, W.D. Penny, C. Phillips, S.J. Kiebel, G. Hinton, and J. Ashburner. Classical and Bayesian Inference in Neuroimaging: Theory. NeuroImage, 16:465-483, 2002. Keyword(s): Bayesian, PPM, EM, REML. [bibtex-entry]


  46. A. Mechelli, W.D. Penny, C.J. Price, D.R. Gitelman, and K.J. Friston. Effective connectivity and intersubject variability: using a multisubject network to test differences and commonalities. NeuroImage, 17(3):1459-1469, 2002. Keyword(s): connectivity, group. [bibtex-entry]


Conference articles

  1. W.D. Penny and G. Flandin. Bayesian analysis of fMRI data with spatial priors. In Proceedings of the Joint Statistical Meeting (JSM), Section on Statistical Graphics [CDROM], 2005. Note: Alexandria, VA: American Statistical Association. Keyword(s): PPM, Bayesian, fMRI. [bibtex-entry]


  2. K.J. Friston and W.D. Penny. Bayesian Inference and Posterior Probability Maps. In Proceedings of the 9th International Conference on Neural Information Processing (ICONIP'02), pages 413-417, 2002. Keyword(s): PPM. [bibtex-entry]


Internal reports

  1. W.D. Penny and G. Flandin. Bayesian analysis of single-subject fMRI: SPM implementation. Technical report, Wellcome Department of Imaging Neuroscience, 2005. Keyword(s): PPM, Bayesian, fMRI. [bibtex-entry]


  2. K.E. Stephan, K.J. Friston, and W.D. Penny. Computing the objective function in DCM. Technical report, Wellcome Department of Imaging Neuroscience, ION, UCL, 2005. Keyword(s): DCM. [bibtex-entry]


  3. R.N.A. Henson and W.D. Penny. ANOVAs and SPM. Technical report, Wellcome Department of Imaging Neuroscience, 2003. Keyword(s): ANOVA. [bibtex-entry]


  4. W.D. Penny. Wavelet smoothing of fMRI activation images. Technical report, Wellcome Department of Imaging Neuroscience, ION, UCL, 2002. Keyword(s): fMRI, spatial. [bibtex-entry]


  5. W.D. Penny. Statistical Parametric Mapping: an annotated bibliography. Technical report, Wellcome Department of Imaging Neuroscience, ION, UCL, 2001. Keyword(s): introduction. [bibtex-entry]



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