If you can create an average subject and register your individual surfaces to that subject, then it can be done. By default, recon-all will register to the human atlas to create ?h.sphere.reg doug
On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote: > Hi Doug, > thank you very much. > One more question: From the documentation, I wasn't really sure > whether it would also be possible to do the analysis of the functional > data in a common volume space (not MNI, as it is NHP data). > Thanks again, Caspar > > > 2013/2/12 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > 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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > -- 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
