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> 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 > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot: > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig. > mgh:overlay_threshold=4,5 > > -viewport 3d > > > > But I received another error message: > > > > Did not find any volume geometry information in the surface. > > > > So I still can not view the data. > > > > Thanks. > > > > Xiuyi > > > > On 2 March 2017 at 16:01, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > You can use that command, just remove annot_outline=1: > > > > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > > > Hi, > > > > > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > > > > > I followed the detailed instruction on the tutorial website. > > > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> > > > > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > >> > > > > > > These are the commands that I typed: > > > > > > freeview > > > > > -f$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 > > > <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 > >> > > >> > > >> > > >> 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. 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>> . 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> > > > 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:freesur...@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 >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
