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:> <mailto:greve@nmr.mgh.harvard.edu
>
> 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:Freesurfer@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:greve@nmr.mgh.harvard.edu <mailto:greve@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>
> <tel:617-724-2358 <tel:617-724-2358>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> <tel:617-726-7422>>> <mailto:Freesurfer@nmr.mgh.harvard.edu
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > 617-373-4789 <tel:617-373-4789>
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> >
> >
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> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>
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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
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