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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@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> FileDrop: 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 . 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.
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
> 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
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 cschwiedrz@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 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 statefunctional > 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
> 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@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:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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@nmr.mgh.harvard.edu
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Caspar M. Schwiedrzik -
Douglas N Greve