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>
>
> 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/>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>> 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>
>>
>>
>>         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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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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