That was just a informational message and it can be ignored. Try check “Show Outline only” on the GUI, since it should be invoked from the command-line in V6.

On Mar 2, 2017, at 11:50 AM, Xiuyi Wang <xw1365@york.ac.uk> 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.

<group_analysis.png>
​
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> 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>>
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>     <tel:617-726-7422>>
>     >
>     >     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>     >     Outgoing:
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>     <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
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>     MGH-NMR Center
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>     <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
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Fax: 617-726-7422

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