Mouse Brain Volume Analysis Protocol

All statistical analyses were performed using the R statistical package (https://www.r-project.org/). Brain volumes were segmented according to the publicly available Dorr–Steadman–Ullman–Richards–Qiu–Egan 40-μm atlas, which defines 180 structures (356 bilaterally) within a three-dimensional atlas of adult C57Bl/6J mice66 (link),67 (link),68 (link),69 (link). Segmentation and labeling were performed using the RMINC package (https://github.com/Mouse-Imaging-Centre/RMINC). All regional volumes were normalized to total brain volume for each mouse before model fitting. A linear regression model with interaction-with-genotype and interaction-with-sex terms was fit to brain volume data to compare pairs of structures. Sex and interaction with sex were included as covariates in the structural covariance model used to measure the interaction-with-genotype effect. In this model, ‘genotype’ is a two-level factor, with ‘wild type’ and ‘mutant’ as the two levels. The interaction-with-genotype coefficients were tested for significance using a two-sided t-test. P values were corrected for multiple comparisons using the Benjamini–Hochberg procedure; these FDR-corrected P values are herein referred to as q values. The coefficient of determination (R²) for each model was also evaluated.