The General Linear Model (GLM) (SPSS Inc., 2009) was first used to determine whether subcortical volumes were correlated with the cranium size index. Since all subcortical volumes were significantly positively correlated with the cranium size, we used linear regression to adjust each structure volume for the cranium size index. For each subcortical structure, we then added the left and right volumes, resulting in 7 cranium size adjusted volumes per subject. We compared NSAC to STAA DOA (dependent on alcohol only), STAA DASD (dependent on alcohol with a co-occurring stimulant disorder), and to both LTAA DAO and LTAA DASD. We also compared STAA DAO with STAA DASD and LTAA DAO with LTAA DASD. For each of these analyses, we first performed a multivariate analysis across the seven subcortical volumes. Control for multiple comparisons was accomplished using a variant of Fisher's protected t-test, where comparisons of individual structures were only examined if the multivariate test across structures was significant. Partial eta squared was used as the measure of effect size. Partial eta squared measures the percent of variance of the dependent variable that is independently accounted for by the independent variable.
