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