Hi Doug

Thanks a lot for your reply.
what I mean by native space, is to register each subject's functional data on their own anatomical data. 
yes, I was using --surf self in my preprocessing and mkanalysis, but since I was not using any smoothing, fwhm=0 in both native and fsaverage analysis, I thought the results should not differ.

Thanks
Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, December 11, 2019 6:41 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] selxavg in native space vs fsaverage space
 
Hi Mona, not sure what you are trying to do. When you say "native"
space, do you mean native functional space or native anatmical space? 
If you want to analyze the data on the native surface, you can use
--surf self when you run preproc-sess and mkanalysis-sess (instead of
specifying fsaverage) and analyze the session separately (which is
better if you are trying to do a longitudinal analysis).

it is hard to answer your other question about why there is a diff
between fsaverage and native space analyses without seeing what the
differences are and without knowing what the actual native space is.
They are different analyses, so they will not give exactly the same
results.

doug

On 12/11/19 11:30 AM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I was trying to do selxavg in native space for individual subjects
> which I have analyzed them in "fsaverage" space before.
> I have two sessions of functional data for each subject. In order to
> register them on one T1, I put the functional data from both sessions
> in one bold folder and registered all of them to one T1.
> The maps that I acquired from these analysis are slightly different
> from "fsaverage" maps.  In "fsaverage" analysis, I analyzed each
> session separately (selxavg) and then concatenated (isxconcat) the two
> sessions at the end. I believe it is not possible to do this in
> "native" space, since I have to register all the functional data to
> one T1, right?
> I need to know what is causing the differences in "native" and
> "fsaverage" maps?
> I appreciate if you could reply.
>
> Thanks a lot
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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