Re: [Freesurfer] FsFast Functional Connectivity Analysis

How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did not do this, try it

tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t fmcpr.up.sm6.fsaverage.lh.nii.gz

This will bring up an overlay as well as a time course

On 08/11/2014 05:05 PM, Jiahe Zhang wrote:

Both looked fine. First value in .mincost is .45

On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
<mailto: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>>
>     <mailto: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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>     >     >
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>     >
>     >     --
>     >     Douglas N. Greve, Ph.D.
>     >     MGH-NMR Center
>     > greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
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>     >
>     >     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>     >
>     > --
>     > Jiahe Zhang
>     > Ph.D. Student
>     > Department of Psychology
>     > Northeastern University
>     > 617-373-4789 <tel:617-373-4789> <tel: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>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     Phone Number: 617-724-2358 <tel:617-724-2358>
<tel: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>
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>
> --
> 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
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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-- Jiahe Zhang Ph.D. Student Department of Psychology Northeastern University 617-373-4789

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