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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
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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Nick Schmansky