Re: [Freesurfer] FsFast Functional Connectivity Analysis

two ways:

1. run tkregister-sess to visually check them 2. look at the first value in register.dof6.dat.mincost. It is hard to say what a threshold is for a good registration, but typical values are about .5 or so. If it is .8 or more, it is probably a problem (and probably the initialization is not good)

On 08/11/2014 04:35 PM, Jiahe Zhang wrote:

I'm not sure how to check the registration. I see a register.dof6.dat being produced for each run but I can't tell if it contains the correct parameters. How can I tell if the registration was accurate?

On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
<mailto: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>
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> --
> Jiahe Zhang
> Ph.D. Student
> Department of Psychology
> Northeastern University
> 617-373-4789 <tel: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>

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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-- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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