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Recently, there has been increased interest in fusing multimodal imaging to better understand brain organization by integrating information on both brain structure and function. In particular, incorporating anatomical knowledge leads to desirable outcomes such as increased accuracy in brain network estimates and greater reproducibility of topological features across scanning sessions. Despite the clear advantages, major challenges persist in integrative analyses including an incomplete understanding of the structure-function relationship and inaccuracies in mapping anatomical structures due to inherent deficiencies in existing imaging technology. This calls for the development of advanced network modeling tools that appropriately incorporate anatomical structure in constructing brain functional networks. We propose a hierarchical Bayesian Gaussian graphical modeling approach which models the brain functional networks via sparse precision matrices whose degree of edge specific shrinkage is a random variable that is modeled using both anatomical structure and an independent baseline component. The proposed approach adaptively shrinks functional connections and flexibly identifies functional connections supported by structural connectivity knowledge. This enables robust brain network estimation even in the presence of misspecified anatomical knowledge, while accommodating heterogeneity in the structure-function relationship. We implement the approach via an efficient optimization algorithm which yields maximum a posteriori estimates. Extensive numerical studies involving multiple functional network structures reveal the clear advantages of the proposed approach over competing methods in accurately estimating brain functional connectivity, even when the anatomical knowledge is misspecified up to a certain degree. An application of the approach to data from the Philadelphia Neurodevelopmental Cohort (PNC) study reveals gender based connectivity differences across multiple age groups, and higher reproducibility in the estimation of network metrics compared to alternative methods.Incorporating anatomical connectivity improves estimation of functional connectivity.Resting state functional connectivity is reliably estimated across scanning sessions.Male and female connectivity differences exist in the executive control network.