Hello all,

Real basic question: How do I calculate the thickness of the cortex, preferably at each vertex/face?  I have tried read_curv.m, but get this error:

[thickness, f] = read_curv('lh.thickness')
??? Undefined function or method 'fread3' for input arguments of type 'double'.

Error in ==> read_curv at 21
vnum = fread3(fid) ;

This should be simple, but the discussion board starts one step after me I think :)  Any help would be appreciate!

Second, when I try to load it in freesurfer, I get an error:
[FSuser@cluster ~]$ tksurfer 050080_S01 lh thickness
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /export/home/FSuser
  Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from /share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz

I tried loading the inflated first, then loading the thickness, which works, but the surface just turns all red.  Are the minimum thicknesses maxing out my color map?  This seems unlikely.  Can anybody help me?

[FSuser@cluster ~]$ tksurfer 050080_S01 lh inflated
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /export/home/FSuser
  Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from /share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz
surfer: vertices=144686, faces=289368
  Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ...
Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/surf/../mri/transforms/talairach.xfm
surfer: single buffered window
libGL error: open DRM failed (Operation not permitted)
libGL error: reverting to (slow) indirect rendering
surfer: using interface /share/apps/freesurfer/lib/tcl/tksurfer.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_common.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /share/apps/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /share/apps/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl

(And then File -> Load Curvature -> lh.thickness)
% surfer: curvature read: min=0.226951 max=5.000000

Thanks you very much,
Jeff Sadino

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