Intera scanner

T1-weighted MRI anatomical brain scans were acquired using three different scanners: a 1.5T Philips Intera scanner (158 scans), a 3T Siemens Trio scanner (300 scans), and a 3T Siemens Prisma scanner (178 scans); see Figs. S2 and S3, Table S2. The proportion of scans acquired with each scanner did not differ between 22q11DS and controls (p = 0.07) or LA-PS and N-PS groups (p = 0.83).
Anatomical segmentation of T1-weighted images was performed using FreeSurfer (http://surfer.nmr.mgh.harvard.edu); CT and SA were computed at each vertex. Details of image acquisition and processing are reported in the Supplementary Method.

Due to the wide timespan of the study, MRI scans were acquired with three different scanners: 1.5 T Philips Intera scanner was used for the first 20 scans, 3 T Siemens Trio for the subsequent 94 scans, and 3 T Siemens Prisma for the remaining 93 scans. T1-weighted images were acquired at the Center for Biomedical Imaging in Geneva with a three-dimensional volumetric pulse. 1.5 T scanner parameters were TR = 35 ms, TE = 6 ms, flip angle = 45°, NEX = 1, matrix size = 256 × 192, field of view = 24 cm², slice thickness = 1.5 mm, and 124 slices. The parameters for both 3 T scanners were TR = 2500 ms, TE = 3 ms, flip angle = 8°, acquisition matrix = 256 × 256, field of view = 23.5 cm, slice thickness = 3.2 mm, and 192 slices. To minimize any potential confounder effects, the scanner model was used as a covariate in statistical analyses using neuroimaging measurements.