Regulatory interactions with the amygdala are thought to be critical for emotional processing in the extended limbic system. Structural equation modeling (path analysis) is a widely used method to quantify interactions among brain regions based on connectivity models, but is often limited by lack of precise anatomical and functional constraints. To address this issue, we developed an automated elaborative path analysis procedure guided by known anatomical connectivity in the macaque. We applied this technique to a large human fMRI data set acquired during perceptual processing of angry or fearful facial stimuli. The derived models were inferentially validated using a bootstrapping split-half approach in pairs of 500 independent groups. Significant paths across the groups were used to form a rigorously validated and consistent path model. We confirm and extend previous observations of amygdala regulation by an extended prefrontal network encompassing cingulate, orbitofrontal, insular, and dorsolateral prefrontal cortex, as well as strong interactions between amygdala and parahippocampal gyrus. This validated model can be used to study neurocognitive correlates as well as genotype or disease-related alterations of functional interactions in the limbic system.