tksurfer: "can't find talairach file" - Freesurfer

8 Sep 2009


      Hello,
I installed version 4.50 of freesurfer on a Ubuntu 8.10 system, the tests
listed in the wiki all run well. Starting tksurfer with other data a
warning is shown in the terminal (the talairach.xfm can't be found), but
the program starts after that.  As far as we can judge after a quick
examination, everything is working fine, it's just the warning.
Another issue is the warning concerning the missing colortable.
Hope anyone can help.
Greetings
Philipp
ps: the terminal output:
...
...
...
/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1$ tksurfer
FS_spm_CanonicalBrain rh pial
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1
can't find talairach file
'/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info/../transforms/talairach.xfm'
surfer: Reading header info from
/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info
surfer: vertices=171090, faces=342176
can't find talairach file
'/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/surf/../mri/orig/COR-.info/../transforms/talairach.xfm'
WARNING: No colortable found!
surfer: single buffered window
surfer: tkoInitWindow(FS_spm_CanonicalBrain)
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...
% surfer: dmin=0.1820, vno=121693, x=60.0832, y=26.3634, z=-18.3935 %
surfer: curv=0.000000, fs=0.000000
% surfer: val=0.000000, val2=0.000000
% surfer: amp=0.000000, angle=0.000000 deg (0.000000)
% surfer: vertex 121693 marked (curv=0.000000, stat=0.000000)
x = (60.1, 26.4, -18.4), n = (0.7, -0.1, -0.8).
surfer: dmin=0.8543, vno=79701, x=72.6551, y=-6.2425, z=-27.2842
% surfer: curv=0.000000, fs=0.000000
<<<
It has to be added, that COR-.info isn't a folder at all, so the path
can't be correct.