The -3T flag was not used because differences in Freesurfer processing of other datasets were not observed in our lab. The parameters have been specified as follows:

“A neuroradiologist reviewed all images to screen for major artifacts and pathology. The standard Freesurfer \cite{freesurferPaper} version 5.3.0 cross-sectional pipeline (recon-all) was run on each site’s native T1-weighted protocol, using the RedHat 7 operating system. Both 1.5T and 3T scans were run with the same parameters (without using the -3T flag), meaning that the non-uniformity correction parameters were kept at the default values.”