On 2 March 2017 at 16:31, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

when you say it stops, you mean it crashes and returns control to the
command line? Or that the GUI stays up but is unresponsive?

On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> The program stops after displaying this message.
>
> So I guess your solution is to use FreeSurfer 6 and I am not able to
> view the data using FreeSurfer 5.3.
>
> Thanks.
>
> Xiuyi
>
> On 2 March 2017 at 16:26, Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto: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>>
> > >
> >
> <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>
> > > <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>>
> > <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:
> > >
> > > 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>>
> > >>
> >
> <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
> > 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> <tel:617-726-7422
> <tel:617-726-7422>>
> >
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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>
>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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