were registered MNI152 standard space template using FSL's FNIRT (FMRIB's Nonlinear Image Registration Tool). The warped (registered) MRIs were then processed through FIRST to extract the surface mesh of each of the subcortical structures. The surfaces were then transformed back to the original MRI space, filled and boundary corrected using the FSL tool “first_utils” (preventing voxel overlap between structures). Boundaries of each structure were visually inspected for gross errors. Visual inspection also showed that subcortical volume estimates were unaffected by subcortical hyperintensities, when present. Each extracted structure was measured in cubic millimeters. Cranium size estimation (an estimate of premorbid brain size) was also performed using FSL's SIENAX (Structural Image Evaluation, using Normalization, of Atrophy) tool. We have previously shown that the FSL cranium size index is an excellent surrogate for the intracranial vault volume (Fein et al., 2004b).
