Greetings Freesurfer Community, 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
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