Hi Caspar, with 5.1 you would not use any of those programs (ie, func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST, then see the tutorial for getting started. You'll need to set up the directory structure properly, then run preproc-sess, mkanalysis-sess, and selxavg3-sess. For the group analysis you'll run isxconcat-sess followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals for all subjects and you just want to use the average subject, then put the average subject into the subjectname file when you set up the directory structure.
doug On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote: > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
