I am running a longitudinal study using Freesurfer v.5.3 to compare rate of cortical thinning between 2 groups of subjects. I hope I can seek some expert advice on the following situation:

All data (both the baseline and follow-up) has been processed independently using recon-all. This has been done on Freesurfer 5.0.

Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed effect capability.

For the construction of base and longs, I understand that it is important to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. When must this be done?  

I am still new to Freesurer, and I'd greatly appreciate any advice regarding workflow.

Many Thanks,

Elijah

Elijah Mak, B.A.

Doctoral Candidate | Psychiatry

University of Cambridge | Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ