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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 > > -viewport 3d > > > > But I received another error message: > > > > Did not find any volume geometry information in the surface. > > > > So I still can not view the data. > > > > Thanks. > > > > Xiuyi > > > > On 2 March 2017 at 16:01, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > You can use that command, just remove annot_outline=1: > > > > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > > Hi, > > > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux > system. > > > > > > I followed the detailed instruction on the tutorial website. > > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>> > > > > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>>> > > > > > > These are the commands that I typed: > > > > > > freeview > > > > > > > -f$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 > > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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. If you believe this > e-mail was sent > > > to you in error and the e-mail contains patient > information, > > > please contact the Partners Compliance HelpLine at > > > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> . If the e-mail was > > > sent to you in error but does not contain patient > > information, > > > please contact the sender and properly dispose of the > > e-mail. > > > > > > _______________________________________________ > > > 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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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 gr...@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
