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"
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)
Xander,
Thanks for taking the extra step and installing BLT. That installation can be tricky.
Our experience has been that Tcl/Tk/Tix and BLT must all be built against each other to ensure the greatest chance of success in running the freesurfer tools that use them. For this reason (as well as the reason that it appears that BLT is not commonly installed in some Linux platforms), we will be distributing a Tcl/Tk/Tix/BLT library build within Freesurfer. This will be included in the 'dev' build for rh9 that I will be posting later today.
So, I would wait until that is posted, and to give that a try, as the error messages that you are experiencing seem pretty strange to me, and indicate some deep incompatibility in tcl/tk/tix and blt.
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"
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)
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"
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)
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
xmeadow＠uchicago.edu