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 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.htmlhttp://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.htmlhttp://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 > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
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