Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run
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? Is it 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)? I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar 2013/9/24 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu> > 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 <gr...@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 <gr...@nmr.mgh.harvard.edu <mailto: >>> gr...@nmr.mgh.harvard.**edu <gr...@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/**freesur...@nmr.mgh.harvard.** >>> edu/msg30456.html<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/**freesur...@nmr.mgh.harvard.** >>> edu/msg22648.html<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 >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >>> > >>> >>> > >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> >>> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.** >>> harvard.edu <Freesurfer@nmr.mgh.harvard.edu>> >>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> 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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >
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