Hi,
I was trying to use the FreeSurfer tutorials for the first time, and had a problem whenever I tried to use the command tksurfer. After I defined FREESURFER_HOME, TUTORIAL_DATA and SUBJECTS_DIR I tried to visualise a surface. The result was that a window opened where the surface should have appeared but nothing appeared in it (however, the menu underneath did open properly).
Here is the terminal output:
assafs $ tksurfer 004 lh inflated -annot aparc.annot subject is 004 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial
surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdataarch2/Leon_Lab/Experiments/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial
Reading image info (/usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004)
Reading /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz
surfer: Reading header info from /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz
surfer: vertices=152763, faces=305522 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Found embedded color table in annotation. 9938 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(004) Window type not found! surfer: failed, trying double buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... %
I am using Linux version Fedora, Release 12 (Constantine). The FreeSurfer version I am using is stable v.5.0.0.
Thanks, Tali Shrem