On 2 March 2017 at 17:11, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Click the button that says to show the annotation in outline (since you
could not load it in outline mode

On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
> Hi Bruce,
>
> Sorry for the misunderstanding.
>
> After showing the message "Did not find any volume geometry
> information in the surface", the FreeView shows this image. It is not
> the same as the tutorial website.
>
>
>
> Is there anything I can do to view the data?
>
> Thank you.
>
> Xiuyi
>
> On 2 March 2017 at 16:31, Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto: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>>
> > > <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:
> > >

> > > 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>>>
> > > >
> > >
> >
> <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>
> > > > <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>>>
> > > <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
> <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>>>
> > > >>
> > >
> >
> <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>>
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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>>
> > >

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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> <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>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <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
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> > _______________________________________________
> > 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>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <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:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
>
>
> _______________________________________________
> 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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer