Jaakko,
The message about the missing talairach.xfm file can be ignored (unless
things stop completely and issue an error message). The code performs a
relative path search to find the file if it doesnt find it in the hard-
coded path (a historical remnant).
About the Tcl problem, which Linux OS variant is being used? Freesurfer
does include Tcl/Tk/Tix/BLT (in $FREESURFER_HOME/lib/tcltktixblt) and
'tksurfer' is actually a wrapper script which performs the setup to use
those libs, then calls tksurfer.bin. This is intended to prevent
conflicts with other Tcl/Tk installations.
Maybe you have an existing Tcl/Tk installation that is conflicting and
not handled by our wrapper script. Before sourcing the freesurfer setup
file (SetupFreeSurferEnv.csh), can you type the following:
env | grep TCL
env | grep LD_LIBRARY_PATH
which tclsh
which tclsh8.4
This will tell you if you have an existing installation.
Also, are you trying to run tksurfer locally, or over a network
connection, like VNC?
Nick
On Fri, 2007-01-05 at 12:46 -0800, Jaakko Karras wrote:
> 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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