I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running
Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the
installation with the command "tkmedit bert orig.mgz":
$ tkmedit bert orig.mgz
Talairach transform
/autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm
The setup script ran flawlessly, producing the following output:
$ source SetUpFreeSurfer.csh
-------- freesurfer-Linux-centos4-stable-pub-v3.0.4 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer
FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast
SUBJECTS_DIR /home/fmri/fmrihome/dti/software/freesurfer/subjects
MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni
GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl
FSL_DIR /home/fmri/fmrihome/fsl
I was able to locate the "missing" talairach.xfm file in the appropriate
directory.
On another note, I run into the following tcl/tk error when running tksurfer:
Tk_Init failed: Can't find a usable tk.tcl in the following directories:
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /home/
fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 ./li
b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't access "::tk::Priv.::ffff:171.65.48.253:0": parent namespace doesn't exist
can't access "::tk::Priv.::ffff:171.65.48.253:0": parent namespace doesn't exist
while executing
"upvar #0 ::tk::Priv.::ffff:171.65.48.253:0 ::tk::Priv"
("uplevel" body line 1)
invoked from within
"uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv"
(procedure "tk::ScreenChanged" line 9)
invoked from within
"tk::ScreenChanged [winfo screen .]"
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 277)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca
n't import command "mc": already exists
can't import command "mc": already exists
while executing
"namespace import ::msgcat::mc"
(in namespace eval "::tk::msgcat" script line 21)
invoked from within
"namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [catch {package require msgcat}]} {
# The msgcat..."
(in namespace eval "::tk" script line 3)
invoked from within
"namespace eval ::tk {
# Set up the msgcat commands
namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [..."
(file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4
/tk.tcl" line 20)
invoked from within
"source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk
.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
This probably means that tk wasn't installed properly.
I run into the same error when opening the FSL 3.3 GUI, so I assume the error
from FreeSurfer is related. I understood that the latest FreeSurfer is packaged
with the required tcl/tk libraries, so this shouldn't be an issue. Any thoughts?
Note: I also installed the standard CentOS 4 (non 64 bit) distribution, but
encountered the same problems.
Thanks,
Jaakko
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