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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