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
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:a nnot_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: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.
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