Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong.
By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar
2013/10/3 Douglas N Greve greve@nmr.mgh.harvard.edu
On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote:
Hi Doug,
when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit.
I don't understand what you mean. Can you elaborate?
I am not sure why this is happening.
In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those?
Thanks, Caspar
2013/10/1 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: > 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? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. > *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. > *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)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug > I'd also be happy to look this up but I'd need to know where I can > find this information. > > Thanks, Caspar > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@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 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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