On 2 March 2017 at 16:26, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

That is not an error, the program should have run normally after that.
This has been fixed in v6.

On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> Thank you for your reply.
>
> I have tried to delete “:annot_outline=1: before andthe command lines are:
>
> freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
> But I received another error message:
>
> Did not find any volume geometry information in the surface.
>
> So I still can not view the data.
>
> Thanks.
>
> Xiuyi
>
> On 2 March 2017 at 16:01, Douglas N Greve <greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> You can use that command, just remove annot_outline=1:
>
>
> On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > Hi,
> >
> > I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
> >
> > I followed the detailed instruction on the tutorial website.
> >
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
> >
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>
> >
> > These are the commands that I typed:
> >
> > freeview
> >
> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg
> <http://sig.mg>
> > <http://sig.mg/>h:overlay_thres
> > hold=4,5 -viewport 3d
> >
> > But I got an error message "Unrecognized sub-option flag
> > ‘annot_outline’ " when running this command to visualize uncorrected
> > significance map with freeview.
> >
> > Douglas Greve told me it's because the outline only works on 6.0.
> >
> > I am wondering what commands should I use to visualize the
> uncorrected
> > significance map with freeview 5.3.
> >
> > Thank you for your help.
> >
> >
> > On 10 February 2017 at 17:47, Douglas 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:
> >
> > The outline only works on 6.0
> >
> >
> > On 2/10/17 11:57 AM, Xiuyi Wang wrote:
> >>
> >> Hi,
> >>
> >>
> >> I am learning GroupAnalysis using FreeSurfer 5.3 on
> Linux system.
> >>
> >>
> >> I followed the detailed instruction on the tutorial
> website.
> >>
> >>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
> >>
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>
> >>
> >>
> >> But I got an error message when running this command to
> >> visualize uncorrected significance map with freeview.
> >>
> >>
> >> This is the command I typed:
> >>
> >> freeview -f
> >>
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> I received this error message:
> >>
> >> Unrecognized sub-option flag ‘annot_outline’
> >>
> >>
> >> I browsed the internet and found that “That option is only
> >> available in the development version of freeview. You
> can try
> >> removing :annot_ouline=1 from the command-line and turn
> it on
> >> manually from the GUI.”
> >>
> >>
> >> So I deleted “:annot_outline=1” and the command line is :
> >>
> >> freeview -f
> >>
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> But I received another error message:
> >>
> >> Did not find any volume geometry information in the
> surface.
> >>
> >>
> >> I found some researchers also have encountered this
> problem,
> >> but it has not been solved.
> >>
> >>
> >> Could you please tell me the solution of the problem?
> >>
> >> Thank you for your suggestion.
> >>
> >>
> >> Best.
> >>
> >> Xiuyi Wang
> >>
> >>
> >>
> >>
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> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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