On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

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
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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>
> <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>>>
> > > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>>>
> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422

> <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422>
> > <tel: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>
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> > > 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:
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> > >
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
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> > >
> > >
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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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> <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>
> <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>
> > <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>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
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> >
> >
> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> > 617-373-4789
> >
> >
> > _______________________________________________
> > 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
> Fax: 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:
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>
> _______________________________________________
> Freesurfer mailing list
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>
>
>
>
> --
> Jiahe Zhang
> Ph.D. Student
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
> _______________________________________________
> 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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
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Jiahe Zhang

Ph.D. Student

Department of Psychology

Northeastern University

617-373-4789