Re: [Freesurfer] preparing NHP data for whole brain analysis

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 <greve@nmr.mgh.harvard.edu mailto:greve@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
>
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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