Dear Freesurfer experts, I am trying to prepare some NHP functional data for a whole brain group analysis, and I was wondering which sequence of steps you would recommend, given that the data cannot be processed with recon-all. I have surfaces from 4 subjects, but one subject for which I do not have an anatomy of sufficient quality and won't be able to obtain one. I would also like to align the data to the 112RM atlas by Mclaren et al. I was thinking that I could probably align the functional data per subject to the atlas, and then use this registration with func2sph-sess to align all subjects for the group analysis (again to the atlas). Does that make sense, given that I have only four out of five individual surfaces?
A second question is when to smooth the data. I assume that it makes most sense to smooth it after it has been transformed into surface space. Would that be sphsmooth-sess?
Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe- sess, correct?
I am using Freesurfer v5.1. Thank you very much for your advice, Caspar