Can you run other tk commands like tkmedit and tksurfer?
On 02/09/2016 12:23 PM, Philip Brandner wrote:
Dear Freesurfer team,
I encountered a visualization error with tkregister-sess after trying to look at the
overlays of my 1st level analysis in a standard fMRI block designed localizer.
tkregister loads without errors (menu plus window) but only very faint and small colored dots are visible, no inflated hemisphere as a surface no significant overlay of the contrast, nothing.
It might seem like a specific problem with my setup, because from another computer in the lab the surface is visible (but no overlay).
*Here is the terminal output during tkregiter-sess:*
-bash-3.2$ tksurfer-sess -s NC211pre/ -analysis face.object.sm5.lh -c face-vs-object
Surface fsaverage lh
Map Surface fsaverage lh
$Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $
Linux wiener 2.6.18-407.el5 #1 SMP Fri Oct 16 12:04:40 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
Tue Feb 9 11:51:24 EST 2016
/Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/bin/tksurfer
list face-vs-object
con/map face-vs-object /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii
maplist /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii
mri_concat /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii --o /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii
ninputs = 1
Checking inputs
nframestot = 1
Allocing output
Done allocing
nframes = 1
Writing to /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii
cd /Freiwald/cpressl/imaging/tle
setenv SUBJECTS_DIR /Freiwald/cpressl/imaging/tle/
tksurfer fsaverage lh inflated -overlay /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000
Contrasts
0 face-vs-object
setting colscalebarflag to 1
setting fthresh to 2.0000
setting fmid to 3.0000
setting fslope to 0.5000
subject is fsaverage
hemi is lh
surface is inflated
surfer: current subjects dir: /Freiwald/cpressl/imaging/tle/
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Freiwald/cpressl/imaging/tle
checking for nofix files in 'inflated'
Reading image info (/Freiwald/cpressl/imaging/tle//fsaverage)
Reading /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz
surfer: Reading header info from /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
tkmedit: Trying to open /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.dat
surfer: Interpreting overlay volume /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii as encoded scalar volume.
surfer: curvature read: min=-0.673989 max=0.540227
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.
13887 vertices did not have an annotation!
surfer: double buffered window
surfer: tkoInitWindow(fsaverage)
surfer: using interface /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tksurfer.tcl
Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_common.tcl
Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_wrappers.tcl
Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/lib/tcl/fsgdfPlot.tcl
Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
%
Please let me know if you have encountered this before and whether you might have a solution for this issue.
Best regards,
Philip Brandner
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer