2 Mar
2017
2 Mar
'17
11:31 a.m.
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 > >> > >> > >> > >> > >> _______________________________________________ > >> 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>> > >> <mailto: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>> > >> <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>> > > <mailto: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>> > > <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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--
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
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