Hello experts,

   I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups.

I usually  do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the volumes of same structure of a single subject calculated by freesurfer using two mprages are different.

I did longitudinal run using the two mprages from same subject, however then also the volumes show differences.

May you please advise me what to do.

Thanks,

Rashmi