In neuroscience, birds are becoming interesting animal models to study learning and memory but also response to stress. Nevertheless, bird’s brain organization and physiology suffers from a lack of neuroimaging tools to perform non-invasive and longitudinal investigations. In this study, we proposed a novel brain template of the Japanese quail (Coturnix Japonica), built from twenty animals dedicated to voxel-based morphometry approach. Using these tools we investigate differences in grey matter concentration (GMC) between two divergent lines of quails selected from their response to fear. Our results report structural differences between the both quail lineages within cognitives, motivational and motor systems.