I am using Freesurfer version 7.1.1 to perform longitudinal Samseg processing (using run_samseg_long) on my T1 longitudinal data.

1) First, I run the mri_robust_template to generate the mean.mgz using T1.mgz from the cross sectional recon-all pipeline. Would it be better to use T1.mgz from the longitudinally processed data?

2) There are few subjects who do not have followup data. How do I process these subjects to avoid the bias introduced by the longitudinal Samseg pipeline?

3) For the same subject, I see that the subcortical volumes from longitudinal recon-all pipeline from aseg.stats (e.g Left-Hippocampus volume is 3321.5mm3) are different to the subcortical volumes from longitudinal samseg pipeline from samseg.stats (e.g Left-Hippocampus volume is 3899.628686mm3). Which of these measures would be recommended?

Thank you very much for your support!

Best wishes

Jay