“…To simplify and streamline operations, we based image processing mainly on ANTs (Avants et al, 2009), a flexible and powerful open source toolkit freely available to the scientific community. Importantly, our approach has been recently applied by our research group to map fine-grain brain anatomy alterations in different mutant mouse lines (Dodero et al, 2013;Lassi et al, 2015;Minervini et al, 2014;Sannino et al, 2014; and to describe large-scale networks of anatomical covariance between gray matter regions in wild-type mice (Pagani et al, 2016), with excellent agreement between MRI and manual morphometric measurements (Sannino et al, 2014), exhibiting corresponding morphoanatomical features in mice and reference clinical populations (Cutuli et al, 2016;Tucci et al, 2014). Below, we provide a detailed description of our procedural workflow and show its capabilities by describing its application to quantify morphological alterations in sociallyimpaired BTBR T+Itpr3tf/J mice with respect to normo social C57BL/6J controls (Dodero et al, 2013;Squillace et al, 2014), a comparison that has been recently described by our research group (Dodero et al, 2015) and others (Ellegood et al, 2013), thus permitting an empirical crosslaboratory assessment of the validity of our findings.…”