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"
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
Hi,
I ran your script to check for libraries and got the following results:
------------ FreeSurfer library check
checking for rpm package gsl... [ ok ] checking for rpm package jpeg... [ ok ] checking for rpm package tiff... [ ok ] checking for rpm package tcl-8... [ ok ] checking for rpm package tk-8... [ ok ] checking for rpm package tix-8... [ ok ] checking for rpm package blt... [ failure ]
While checking for rpm package blt. The library/package does not seem to exist on your system. Exiting with code '2'. -------------
I'm guessing this means I'm missing the blt rpm, but when I look at the RedHat site and do a package search for blt I come up with nothing. When I do a google search I got a ton of responses, so I was wondering what the correct blt rpm for freesurfer is? Thanks very much.
Xander
On Sep 1, 2005, at 10:08 AM, Nick Schmansky wrote:
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>
freesurfer@nmr.mgh.harvard.edu
-
Fornito, Alexander -
Nick Schmansky -
Xander Meadow