Hi FreeSurfer Team, 

We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease in cortical volume over time except a few of them, who show a huge increase in volume at their 6th-month visit (or at their 12th-month in a couple of cases). 

When we tried to look at the reconstructed surfaces of the long brains in Freeview, the gray matter and white matter boundaries of the 6th-month were bigger overall than the boundaries of the baseline and 12th-month. 

Could you share with us your thoughts on what factors (with MPRAGE/Scanner/FreeSurfer) might have caused this problem? 

Thank you,

Jaiashre.