2 Mar
2017
2 Mar
'17
11:26 a.m.
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 >> >> >> >> >> _______________________________________________ >> 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> > <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>> > The information in this e-mail is intended only for the person > to whom it is addressed. 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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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