Re: [Freesurfer] FsFast Functional Connectivity Analysis

did you check the registration?

On 08/11/2014 03:53 PM, Jiahe Zhang wrote:

There's nothing even when the threshold is set to 0.

I just checked the preprocessing outputs. I can see normal-looking volumes fmcpr.nii.gz fmcpr.up.nii.gz fmcpr.up.sm6.mni305.2mm.nii.gz

But there is nothing when I open fmcpr.up.sm6.fsaverage.lh.nii.gz or fmcpr.up.sm6.fsaverage.rh.nii.gz

On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

When you say that they are "empty" what do you mean? That there is
nothing above threshold or that there is nothing regardless of how low
the threshold is? See if you get something if you set the thresh close
to 0. Does this happen in the volume and the surface? Have you checked
the registration to assure that it is accurate?

On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> Hi Doug,
>
> I was trying to run functional connectivity analysis following
> instructions on the FreeSurferWiki
>
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> I was able to successfully run the following commands (nothing
errored
> as far as I can tell) but the resulting partial correlation and
> significance maps turned out to be empty. Could you take a look
at the
> commands and let me know if anything can be improved?
>
> 1. PREPROC
> preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh
> -mni305-2mm -fsd bold -per-run -stc up
>
> 2. SEED CONFIG
> fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold
> -mean -cfg mean.L_Posteriorcingulate.config
>
> 3. SEED TIMECOURSE
> fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
>
> (wm.dat and vcsf.dat were similarly created)
>
> 4. ANALYSIS CONFIG
> mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage
> lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg
> vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold
> -TR 5 -per-run -lpf .1
>
> 5. ANALYSIS
> selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001
>
> Thanks,
> Jiahe
>
>
> --
> Jiahe Zhang
> Ph.D. Student
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
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--
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>

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-- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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