Time series analysis of fMRI data: Spatial modelling and Bayesian computation

Abstract

Time series analysis of fMRI data is an important area of medical statistics for neuroimaging data. Spatial models and Bayesian approaches for inference in such models have advantages over more traditional mass univariate approaches; however, a major challenge for such analyses is the required computation. As a result, the neuroimaging community has embraced approximate Bayesian inference based on mean-field variational Bayes (VB) approximations. These approximations are implemented in standard software packages such as the popular statistical parametric mapping software. While computationally efficient, the quality of VB approximations remains unclear even though they are commonly used in the analysis of neuroimaging data. For reliable statistical inference, it is important that these approximations be accurate and that users understand the scenarios under which they may not be accurate. We consider this issue for a particular model that includes spatially varying coefficients. To examine the accuracy of the VB approximation, we derive Hamiltonian Monte Carlo (HMC) for this model and conduct simulation studies to compare its performance with VB in terms of estimation accuracy, posterior variability, the spatial smoothness of estimated images, and computation time. As expected, we find that the computation time required for VB is considerably less than that for HMC. In settings involving a high or moderate signal-to-noise ratio (SNR), we find that the 2 approaches produce very similar results suggesting that the VB approximation is useful in this setting. On the other hand, when one considers a low SNR, substantial differences are found, suggesting that the approximation may not be accurate in such cases and we demonstrate that VB produces Bayes estimators with larger mean squared error. A comparison of the 2 computational approaches in an application examining the hemodynamic response to face perception in addition to a comparison with the traditional mass univariate approach in this application is also considered. Overall, our work clarifies the usefulness of VB for the spatiotemporal analysis of fMRI data, while also pointing out the limitation of VB when the SNR is low and the utility of HMC in this case.

Keywords: Hamiltonian Monte Carlo; SPM; fMRI; spatial model; time series; variational Bayes.