[Freesurfer] Across Scanner Comparisons

Hi All,

Our group recently scanned subjects with two different scanners in order to determine how reliable FreeSurfer comparisons between the two scanners are. After putting each session through the regular cross-sectional Freesurfer pipeline, we noticed that there is much greater variability between the two scanners when we compare structures in the right hemisphere than in the left. Is there any FreeSurfer related reason for this?

Also, we are currently running each subject through the longitudinal pipeline (i.e. Scanner 1 as TP1, Scanner 2 as TP2). Is there any reason to think that this will help reduce the variability seen between the two scanners?

Thanks in advance for any help.

- Tyler Blazey