Hi Doug,
thanks for the clarification.
If I understand your instructions and the walktrough correctly, I would be running something like this after isxconcat-sess:

mri_glmfit \
--surf averagesubject hemisphere \
--y pcc.nii \
--no-cortex \
--osgm \
--glmdir analysisname

*Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? I assume it is a t-test of the Fisher-transformed r-values against 0?
*Is the average r-value or z-value saved somewhere?
*Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)?

Thanks, Caspar





2013/9/23 Douglas N Greve <greve@nmr.mgh.harvard.edu>

Use ppc.nii as input to mri_glmfit and proceed as usual with the group analysis.
doug



On 09/23/2013 12:31 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
thanks for the info.
If I run isxconcat-sess with -m pcc, I get only a pcc file as output. Should I put this into mri_glmfit as --y pcc.nii, or should I re-run isxconcat-sess without -m pcc?
Thanks again, Caspar



2013/9/23 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>


    Hi Caspar, just use -m pcc in isxconcat-sess and continue as
    normal with
    the group analysis
    doug

    On 09/23/2013 09:50 AM, Caspar M. Schwiedrzik wrote:
    > Hi Freesurfer Experts,
    > I am trying to calculate group pcc maps for resting state functional
    > connectivity analyses. Unfortunately, the walkthrough does not cover
    > this.
    >
    > I found several posts regarding this on the mailing list, but I
    am not
    > sure which one is the right way to go:
    >
    > There is -m pcc in isxconcat-sess
    >
    (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30456.html)
    > and there is also fast_glm_pcc (e.g.,
    >
    http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html),
    > however, the various posts on the later functional all seem to
    differ
    > in how to properly use it.
    >
    > This is in version 5.1.
    > Please advise.
    > Thanks, Caspar
    >
    >
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    MGH-NMR Center
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