Hi Jesse
the thickness files are scalar fields over the surface, not surfaces
themselves. Load it as an overlay, not as a surface
cheers
Bruce
On Fri, 22 May 2015, Jesse Bledsoe wrote:
Hi everyone,
I searched the wiki and old posts but couldn't find a solution to this
issue.
I had no problems with the full recon-all script though got hung up trying
to load surfaces in tksurfer. The surface files are there but the buttons in
tksurfer aren't bright so I tried to load them manually which causes a
crash. Build stamp is below.
#@#%# recon-all-run-time-hours 7.729
recon-all -s Epi001 finished without error at Thu May 21 21:15:58 PDT 2015
done
(Looks like recon-all finished without error, though quickly, only 7 hours)
Then I wanted to look at the surface overlays:
bledsoe1 @ivan:~/Desktop/Epilepsy$ tksurfer Epi001 rh inflated
Xlib: extension "NV-GLX" missing on display ":2002.0".
subject is Epi001
hemi is rh
surface is inflated
surfer: current subjects dir: /var/local/scratch/bledsoe1/Desktop/Epilepsy/
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /var/local/scratch/bledsoe1/Desktop/Epilepsy
checking for nofix files in 'inflated'
Reading image info (/var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001)
Reading /var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz
surfer: Reading header info from
/var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz
surfer: vertices=134040, faces=268076
surfer: single buffered window
surfer: tkoInitWindow(Epi001)
Xlib: extension "NV-GLX" missing on display ":2002.0".
surfer: using interface /usr/local/freesurfer/stable5_3/tktools/tksurfer.tcl
Reading /usr/local/freesurfer/stable5_3/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/stable5_3/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/stable5_3/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/stable5_3/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% surfer: loaded pial into set 3
nquads=12582916, nvertices=528
ERROR: MRISread: file
'/var/local/scratch/bledsoe1/Desktop/Epilepsy/Epi001/surf/lh.thickness' has
many more faces than vertices!
Probably trying to use a scalar data file as a surface!
I've done a lot of reconstructions on different data (this is a new data
set) and never seen this problem.
Build stamp:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable5_3
FSFAST_HOME /usr/local/freesurfer/stable5_3/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /var/local/scratch/bledsoe1/Desktop/Epilepsy/
MNI_DIR /usr/local/freesurfer/stable5_3/mni
FSL_DIR /usr/share/fsl/5.0
Thank you,
Jesse Bledsoe
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