Xander,
Tksurfer and Tkmedit will generate debug files called .xdebug_tksurfer and .xdebug_tkmedit in the directory in which the program is started. Can you send me the contents of those files?
Thanks,
Nick
On Sat, 2005-09-03 at 02:43 +0700, xmeadow@uchicago.edu wrote:
Hi,
I tried what you said, and after setting up the path and checking that $FREESURFER_HOME/lib/tcltktixblt/bin is at the front of the path I tried running tkmedit <subject> orig. When I did that a window popped up that had 'Medit:' in the title bar. The window had nothing but a gray background. The window stays open for about 7 seconds, and then the title switches from 'Medit:' to the name of the subject, but then the window closes. There are no error messages produced, the window just closes.
Xander
---- Original message ----
Date: Fri, 02 Sep 2005 15:09:33 -0400 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lib prob? To: Xander Meadow xmeadow@uchicago.edu Cc: "Fornito, Alexander" Alexander.Fornito@wh.org.au,
Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Xander,
Can you try executing these two statements after issuing the
source
SetUpFreeSurfer.csh command?
set path = ( $FREESURFER_HOME/lib/tcltktixblt/bin $path ) rehash
This will add to the binary search path the location of the
tcl-tk-tix-
blt tools. I noticed it is missing from the
FreeSurferEnv.csh setup
script. It is possible that the problem you are seeing is
because some
of the old tools are being used (from prior installed search
paths).
Can you then try running tkmedit, such as like this:
tkmedit <subjectname> orig
(replacing <subjectname> with your subject id).
Thanks,
Nick
On Fri, 2005-09-02 at 11:39 -0500, Xander Meadow wrote:
Hi,
Everything was just as you predicted, but I still get the
tcl and tk
errors.
source freesurfer/dev/SetUpFreeSurfer.csh
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/people/xmeadow/freesurfer/dev FSFAST_HOME /home/people/xmeadow/freesurfer/dev/fsfast SUBJECTS_DIR /home/people/xmeadow/freesurfer/dev/subjects FUNCTIONALS_DIR /home/people/xmeadow/freesurfer/dev/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5
echo $LD_LIBRARY_PATH
/usr/pubsw/packages/mni/current/lib:/home/people/xmeadow/freesurfer/
dev/lib/tclt ktixblt/lib:/home/people/xmeadow/freesurfer/dev/lib/
which tkmedit
/home/people/xmeadow/freesurfer/dev/bin//tkmedit
ldd `which tkmedit`
libtix8.1.8.3.so =>/home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/ lib/libtix8.1.8.3.so (0x005a2000) libtk8.4.so => /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/l ibtk8.4.so (0x004c1000) libtcl8.4.so => /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/ libtcl8.4.so (0x003b8000) libglut.so.3 => /usr/lib/libglut.so.3 (0x007ec000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00af8000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00b02000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00123000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x00101000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00139000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x001b0000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x009f9000) libgsl.so.0 => /usr/lib/libgsl.so.0 (0x0021e000) libgslcblas.so.0 => /usr/lib/libgslcblas.so.0
(0x00382000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00dad000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x04a99000) libz.so.1 => /usr/lib/libz.so.1 (0x00ad2000) libm.so.6 => /lib/tls/libm.so.6 (0x00451000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x03e64000) libc.so.6 => /lib/tls/libc.so.6 (0x008a3000) libdl.so.2 => /lib/libdl.so.2 (0x009f3000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6(0x00ac2000)
libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1(0x003b2000)
libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x005dc000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00ce0000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00cd6000) libpthread.so.0 => /lib/tls/libpthread.so.0(0x00ae4000)
/lib/ld-linux.so.2 (0x0088a000)Also, I am using the rh9 installation, because it is the
latest redhat
installation available, but the machine is currently
running Enterprise
version 4.
Thanks very much.
Xander
On Sep 2, 2005, at 10:43 AM, Nick Schmansky wrote:
Xander,
The new download includes the tcl/tk/tix and blt
libraries in the
$FREESURFER_HOME/lib/tcltktixblt directory, so this
freesurfer should
not be using any prior installation of tix (such at that in /usr/share).
You do not need to delete any prior installations of
tix/tcl/tk/blt.
The SetUpFreeSurfer.csh script (which calls
FreeSurferEnv.csh) will set
the LD_LIBRARY_PATH to contain
$FREESURFER_HOME/lib/tcltktixblt/lib.
You can confirm this setting by typing:
env |grep LD_
and checking that the path is found in LD_LIBRARY_PATH.
Also, can you run the following commands for me?
which tkmedit ldd `which tkmedit`
The first will tell you which tkmedit you are using, to
confirm that it
is the one that you installed. The second command will
tell you
exactly which libraries tkmedit uses (note: the ` character is
not the '
character, rather ` is in the upper left-hand corner of
the keyboard,
usually).
You should see something like this for a rh9 system:
[kani:lib] (nmr-dev-env) which tkmedit /usr/local/freesurfer/dev/bin//tkmedit [kani:lib] (nmr-dev-env) ldd `which tkmedit` libtix8.1.8.3.so =>
/usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtix8.1.8.3.so
(0x40017000) libtk8.4.so => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtk8.4.so (0x40051000) libtcl8.4.so => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000) libglut.so.3 => /usr/lib/libglut.so.3 (0x401be000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401f3000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6
(0x401fc000)
libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6(0x40214000)
libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x4022a000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1(0x40232000)
libGL.so.1 => /usr/lib/tls/libGL.so.1 (0x402af000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6(0x40318000)
libgsl.so.0 => /usr/lib/libgsl.so.0 (0x403f7000) libgslcblas.so.0 => /usr/lib/libgslcblas.so.0(0x40570000)
libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x405a2000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x405c0000) libz.so.1 => /usr/lib/libz.so.1 (0x40602000) libm.so.6 => /lib/tls/libm.so.6 (0x40610000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x40632000) libc.so.6 => /lib/tls/libc.so.6 (0x42000000) libdl.so.2 => /lib/libdl.so.2 (0x40660000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x40664000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6(0x406b6000)
libstdc++.so.5 => /usr/lib/libstdc++.so.5(0x406c4000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40777000) libGLcore.so.1 => /usr/lib/tls/libGLcore.so.1(0x40780000)
/lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)[kani:lib] (nmr-dev-env)
Notice that the tix/tk/tcl libraries are found in the new freesurfer/dev installation path. It is necessary to have consistency
among these
libraries (BLT is loaded dynamically).
I'm curious to know the output of this for your machine.
It seems to
be difficult for us to predict exactly how a rh9 machine
will respond to
our install.
Thanks! And again, I appreciate your patience! We're
trying to make
this install easier to use.
Nick
On Fri, 2005-09-02 at 22:24 +0700, xmeadow@uchicago.edu
wrote:
Hi,
I installed the version you recommeneded and I had to make a few changes (for instance tix8.1 is installed in /usr/share instead of /usr/lib) on my machine. After creating some
soft
links to get around this I started up Freesurfer with the csurf command, and then inflated a brain. The brain came up like last time but I'm still getting errors in the logs, and the tools pallette still doesn't appear. However,
Freesurfer
no longer becomes unresponsive, it's just none of the tools are available. The errors I'm getting are:
surfer: Error sending tcl command SelectVertex -1: invalid command name "SelectVertex"
Whenever I move the mouse over the image of the brain. One thing to note, I don't have enough room on my /usr partition so I installed Freesurfer in my home space, but I did change the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any thoughts on why I'm still getting tcl errors? Thanks
very much.
Xander
---- Original message ----
Date: Thu, 01 Sep 2005 21:30:34 -0400 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lib prob? To: xmeadow@uchicago.edu Cc: "Fornito, Alexander" Alexander.Fornito@wh.org.au,
Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Xander and Alex,
The special rh9 dev release is available now to
download at:
http://surfer.nmr.mgh.harvard.edu/pub/dist/
Look for the file:
freesurfer-Linux-rh9-dev20050901.tar.gz
The installation readme is:
freesurfer-Linux-rh9-dev20050901.README.txt
You will also need the MINC tools if you don't already
have them:
mni-Linux2-2.3-i386.tar.gz
and its readme is:
mni-Linux2-README.txt
Nick
On Fri, 2005-09-02 at 03:33 +0700, xmeadow@uchicago.edu
wrote:
> Hi, > > I downloaded what hopefully is the correct version of
blt, and
> after that ran your script and said everything was fine in > terms of libraries. However, I did have to create two
soft
> links. The first one was a softlink from libtix8.1.8.3 to > libtix8.1.8.4 in /usr/lib. The second was a softlink from > tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After
making
> both of these changes I was able to run csurf, but when I > tried to view an inflated brain the brain image would
come up,
> but then freesurfer freezes and I can't do anything.
In the
> logs I get the following errors: > > can't read "glMenuGroups(mg_FieldSignLoaded)": no such > varialble surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: > > can't read "glMenuGroups(mg_FieldMaskLoaded)": no such > variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 > > Unfortunately these error messages mean nothing to me,
so I
> was wondering if anyone else had seen them before. Thanks > very much. > >> Xander > > > > ---- Original message ---- >> Date: Thu, 01 Sep 2005 11:08:52 -0400 >> From: Nick Schmansky nicks@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Lib prob? >> To: xmeadow@uchicago.edu, "Fornito, Alexander" > Alexander.Fornito@wh.org.au >> Cc: Freesurfer Mailing List
freesurfer@nmr.mgh.harvard.edu
>> >> Alex and Xander, >> >>> From reading the error messages in your emails, it
appears that
>> freesurfer is not able to find the tcl/tk, and tix
libraries
> on your >> platform. >> >> We have been working on trying to provide a seamless
solution
> to the >> problem of freesurfer finding the external libraries upon > which it >> depends, on the varied platforms that it supports. >> >> To help, later today, a new 'dev' build for rh9 that
includes
> many of >> the necessary libraries will be posted for download.
This is
> not a >> 'stable' release (which is still undergoing testing),
but a
>> 'development' (dev) build, so it is still possible to
have
> installation >> problems, but hopefully it will install and work for
you. I
> will email >> you again when it is ready, and your patience is
appreciated.
>> >> In the meantime, I've attached a script, called > 'fs_lib_check', which >> will check your system for the libraries that freesurfer > requires. I'm >> curious to know the results of its output for your
systems.
> Just type >> 'fs_lib_check' to run it, and 'fs_lib_check --help'
for help
> text. >> >> Nick >> >> >> On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander
wrote:
>>> Hi, >>> We've recently installed the > freesurfer-Linux-rh9-dev20050729.tar.gz distribution
along
> with fs_supportlibs.tar.gz. >>> csurf works ok, but if i try to run tksurfer, I get the > error message below. We'd appreciate any help as we've
been
> stuck for a while. >>> Thanks! >>> >>> tksurfer 1000027 rh white >>> surfer: current subjects dir: > /data/flanders/work/alex/freesurfer/subjects >>> surfer: not in "scripts" dir ==> using cwd for
session root
>>> surfer: session root data dir ($session) set to: >>> surfer: /data/flanders/work/alex/freesurfer/subjects >>> surfer: Reading header info from >
/data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info
>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc
cannot be
> found. >>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc
cannot be
> found. >>> surfer: vertices=152190, faces=304376 >>> surfer: single buffered window >>> Xlib: extension "XFree86-DRI" missing on display
":0.0".
>>> Tix_Init failed: version conflict for package "Tcl":
have
> 8.3, need 8.4 >>> surfer: using interface > /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >>> Reading
/usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl
>>> Reading
/usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl
>>> Reading
/usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl
>>> couldn't load file "/usr/lib/libtix8.1.8.4.so": > /usr/lib/libtix8.1.8.4.so: cannot open shared object
file: No
> such file or directorysurfer: Error sending tcl command > UpdateUndoItemLabel "Nothing to Undo": >>> invalid command name "UpdateUndoItemLabel" >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >>> can't read "glMenuGroups(mg_OriginalVSetLoaded)":
no such
> variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >>> can't read "glMenuGroups(mg_InflatedVSetLoaded)":
no such
> variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >>> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such > variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >>> can't read "glMenuGroups(mg_PialVSetLoaded)": no such
variable
>>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >>> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such > variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >>> can't read "glMenuGroups(mg_OverlayLoaded)": no such
variable
>>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >>> can't read "glMenuGroups(mg_CurvatureLoaded)": no such > variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >>> can't read "glMenuGroups(mg_LabelLoaded)": no such
variable
>>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such > variable >>> surfer: Error sending tcl command > tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such > variable >>> % surfer: Error sending tcl command MoveToolWindow
663 670:
>>> invalid command name "MoveToolWindow" >>> surfer: Error sending tcl command MoveToolWindow 663
670:
>>> invalid command name "MoveToolWindow" >>> surfer: Error sending tcl command MoveToolWindow 663
670:
>>> invalid command name "MoveToolWindow" >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>> >> ________________ >> fs_lib_check (4k bytes) > >