Hi,
I tried both of those. Here is what I did in order:
source freesurfer/dev/SetUpFreeSurfer.csh
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
setenv TCLLIBPATH $FREESURFER_HOME/lib/tcltktixblt/tk8.4 csurf
But I still got the same problems. Then I opened up a new terminal and did the same thing except used
setenv TCL_LIBRARY $FREESURFER_HOME/lib/tcltktixblt/tk8.4
instead of TCLLIBPATH.
Is there a way I can send a log of the entire errors printed in the logs to you? Because it looks as though there are many errors that are being written but are scrolling off the screen before I can read them. Thanks very much.
Xander
---- Original message ----
Date: Fri, 02 Sep 2005 17:04:46 -0400 From: Nick Schmansky nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Lib prob? To: Xander Meadow xmeadow@uchicago.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu
Xander,
Can you try setting the TCLLIBPATH var, like this:
setenv TCLLIBPATH $FREESURFER_HOME/lib/tcltktixblt/tk8.4
and failing that:
setenv TCL_LIBRARY $FREESURFER_HOME/lib/tcltktixblt/tk8.4
Nick
On Fri, 2005-09-02 at 15:50 -0500, Xander Meadow wrote:
The files were in
$FREESURFER_HOME/subjects/<subject>/scripts. I've
removed the . that preceeds the files so my mail client
wouldn't have
problems.
Xander
On Sep 2, 2005, at 3:36 PM, Nick Schmansky wrote:
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) >>>> >>>> >>> >> >> >