Dear freesurfer users,

I am having a problem visualizing results using tksurfer using the following command: tksurfer fsaverage lh inflated -annot lh.MIR137_area.glmdir/MIR137_test/mc-z.abs.sig.ocn.annot -fthresh 2 -curv -gray &

Please also see the terminal output stating that the vertices do not have an annotation. I do not have much experience with freesurfer - is there a way to resolve this?

Thank you for your help!

Sinead

[kellys37@tcin-n01 Freesurfer_data]$ setting fthresh to 2.0000
subject is fsaverage
hemi    is lh
surface is inflated
surfer: current subjects dir: /projects/pi-donoghug/HPC_11_00168/Freesurfer_data/
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /projects/pi-donoghug/HPC_11_00168/Freesurfer_data
checking for nofix files in 'inflated'
Reading image info (/projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage)
Reading /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz
surfer: Reading header info from /projects/pi-donoghug/HPC_11_00168/Freesurfer_data//fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
surfer: curvature read: min=-0.673989 max=0.540227
reading colortable from annotation file...
colortable with 12 entries read (originally none)
Found embedded color table in annotation.
149719 vertices did not have an annotation!
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
surfer: using interface /home/support/tcin/apps/freesurfer/5.2.0/tktools/tksurfer.tcl
Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_common.tcl
Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkm_wrappers.tcl
Reading /home/support/tcin/apps/freesurfer/5.2.0/lib/tcl/fsgdfPlot.tcl
Reading /home/support/tcin/apps/freesurfer/5.2.0/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
%

--
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8