Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively:
tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29
tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64
Please advise! regards, Vish
PS: i'm using tksurfer-fc5 as given in the online instructions.
Vish,
I think there might be two problems here. The first, the GLX error, is likely due to the video driver not supporting GLX (aka OpenGL X-Windows extensions). Does this error appear when running directly from the machine, or is this a remote connection?
The 'wrong ELF class: ELFCLASS64' error would occur is the wrong machine architecture is used. Are you certain your machine is 64bits? To check, you should type this:
uname -m
and see:
x86_64
On the distribution site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
the 32bit FC5 tksurfer stuff is:
tksurfer_fc5.gz
and the 64bit FC5 stuff is:
tksurfer_fc5_x86_64.gz
Nick
On Fri, 2006-08-11 at 15:11 -0400, Vishwadeep Ahluwalia wrote:
Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively:
tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29
tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64
Please advise! regards, Vish
PS: i'm using tksurfer-fc5 as given in the online instructions. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick, Thanks for the solution. For the first problem it took me quite a while to update the Nvidia driver. It finally installed after i updated my kernel to 2.6.17-1.2174_FC5. It may have installed just by updating xorg as well. For the second issue, i do have a x86_64 bit system and downloading tksurferx86_64 from the ftp site that u sent me worked.
however there is a third issue :) i ve FSL 3.3 installed. Ive configured FSL and freesurfer in .cshrc. i moved fsl 3.2 from within the freesurfer directory and created a link pointing to FSL3.3 directory. But now FSL 3.3 doesnt run. it gives the following error: --------------------------------------------------------------------- [vish@pathis185 ~]$ fsl Error in startup script: couldn't load file "/home/vish/apps/freesurfer/lib/tclt ktixblt/lib/libtix8.1.8.4.so": /home/vish/apps/freesurfer/lib/tcltktixblt/lib/li btix8.1.8.4.so: wrong ELF class: ELFCLASS64 while executing "load /home/vish/apps/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) == "wish" } { package require Tk package require Tix tix configure -scheme TixGr..." (file "/home/vish/apps/fsl3.3/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/home/vish/apps/fsl3.3/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/home/vish/apps/fsl3.3/bin/fsl" line 21) --------------------------------------------------------------------- My .cshrc file reads:
setenv FSLDIR /home/vish/apps/fsl3.3 source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} set path = ($path /home/vish/bin ) setenv FREESURFER_HOME /home/vish/apps/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh ------------------------------------------------------------------- Ofcourse , removing the freesurfer config from .cshrc,i can run fsl again. also i can configure freesurfer in another shell to run both FS/FSL. but how can i run both in the same shell? also another concern is since the freesurfer using FSL3.2 and my Feat directories are a result of FSL3.3 ...would i still be able to overlay functional data on the FS produced surface and subcortical segmented images? Thanks!
Cheers, Vish
Graduate Student Medical Physics VCU, Richmond
On Fri, 2006-08-11 at 17:43 -0400, Nick Schmansky wrote:
Vish,
I think there might be two problems here. The first, the GLX error, is likely due to the video driver not supporting GLX (aka OpenGL X-Windows extensions). Does this error appear when running directly from the machine, or is this a remote connection?
The 'wrong ELF class: ELFCLASS64' error would occur is the wrong machine architecture is used. Are you certain your machine is 64bits? To check, you should type this:
uname -m
and see:
x86_64
On the distribution site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
the 32bit FC5 tksurfer stuff is:
tksurfer_fc5.gz
and the 64bit FC5 stuff is:
tksurfer_fc5_x86_64.gz
Nick
On Fri, 2006-08-11 at 15:11 -0400, Vishwadeep Ahluwalia wrote:
Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively:
tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29
tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64
Please advise! regards, Vish
PS: i'm using tksurfer-fc5 as given in the online instructions. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Vish,
Try executing this after sourcing the Freesurfer setup script:
unsetenv TCLLIBPATH
Then try running fsl.
I am fairly certain that fsl is built for 32bit systems, which will run on 64bit platforms, but I suspect that there is some conflict between the 64bit TCL stuff that comes with Freesurfer, and what fsl wants. Unsetting the TCLLIBPATH var should undo usage of the Freesurfer tcl stuff. Unfortunately, I am unable to replicate your problem here (we have fsl v3.3.2 also, and I am able to start the fsl gui on a 64bit system having setup fsl and freesurfer as you have done).
There should not be a problem with using fsl 3.3 results with Freesurfer.
Nick
On Mon, 2006-08-14 at 15:50 -0400, Vishwadeep Ahluwalia wrote:
Hi Nick, Thanks for the solution. For the first problem it took me quite a while to update the Nvidia driver. It finally installed after i updated my kernel to 2.6.17-1.2174_FC5. It may have installed just by updating xorg as well. For the second issue, i do have a x86_64 bit system and downloading tksurferx86_64 from the ftp site that u sent me worked.
however there is a third issue :) i ve FSL 3.3 installed. Ive configured FSL and freesurfer in .cshrc. i moved fsl 3.2 from within the freesurfer directory and created a link pointing to FSL3.3 directory. But now FSL 3.3 doesnt run. it gives the following error:
[vish@pathis185 ~]$ fsl Error in startup script: couldn't load file "/home/vish/apps/freesurfer/lib/tclt ktixblt/lib/libtix8.1.8.4.so": /home/vish/apps/freesurfer/lib/tcltktixblt/lib/li btix8.1.8.4.so: wrong ELF class: ELFCLASS64 while executing "load /home/vish/apps/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) == "wish" } { package require Tk package require Tix tix configure -scheme TixGr..." (file "/home/vish/apps/fsl3.3/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/home/vish/apps/fsl3.3/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/home/vish/apps/fsl3.3/bin/fsl" line 21)
My .cshrc file reads:
setenv FSLDIR /home/vish/apps/fsl3.3 source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} set path = ($path /home/vish/bin ) setenv FREESURFER_HOME /home/vish/apps/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh
Ofcourse , removing the freesurfer config from .cshrc,i can run fsl again. also i can configure freesurfer in another shell to run both FS/FSL. but how can i run both in the same shell? also another concern is since the freesurfer using FSL3.2 and my Feat directories are a result of FSL3.3 ...would i still be able to overlay functional data on the FS produced surface and subcortical segmented images? Thanks!
Cheers, Vish
Graduate Student Medical Physics VCU, Richmond
On Fri, 2006-08-11 at 17:43 -0400, Nick Schmansky wrote:
Vish,
I think there might be two problems here. The first, the GLX error, is likely due to the video driver not supporting GLX (aka OpenGL X-Windows extensions). Does this error appear when running directly from the machine, or is this a remote connection?
The 'wrong ELF class: ELFCLASS64' error would occur is the wrong machine architecture is used. Are you certain your machine is 64bits? To check, you should type this:
uname -m
and see:
x86_64
On the distribution site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
the 32bit FC5 tksurfer stuff is:
tksurfer_fc5.gz
and the 64bit FC5 stuff is:
tksurfer_fc5_x86_64.gz
Nick
On Fri, 2006-08-11 at 15:11 -0400, Vishwadeep Ahluwalia wrote:
Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively:
tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29
tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64
Please advise! regards, Vish
PS: i'm using tksurfer-fc5 as given in the online instructions. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick, After unsetting TCLLIBPATH ..fsl works. i have the FC4x86_64 binary version of FSL 3.3.7 which is running on FC5. I wonder if running FC4version on FC5 is the problem and that i've to download the source and build it on FC5.Like you said,there's a conflict between FS and FSL's TCL stuff..did u mean that the former is a 64bit lib. and the latter ,32bit.Plzz bear with me ... I'm kind of clueless about this stuff. So how do u recommend i set this up? after unsetting FS's tcl library ,does it use FSL's tcl library? coz even FS works after running that command. -Vish
On Mon, 2006-08-14 at 19:33 -0400, Nick Schmansky wrote:
Vish,
Try executing this after sourcing the Freesurfer setup script:
unsetenv TCLLIBPATH
Then try running fsl.
I am fairly certain that fsl is built for 32bit systems, which will run on 64bit platforms, but I suspect that there is some conflict between the 64bit TCL stuff that comes with Freesurfer, and what fsl wants. Unsetting the TCLLIBPATH var should undo usage of the Freesurfer tcl stuff. Unfortunately, I am unable to replicate your problem here (we have fsl v3.3.2 also, and I am able to start the fsl gui on a 64bit system having setup fsl and freesurfer as you have done).
There should not be a problem with using fsl 3.3 results with Freesurfer.
Nick
On Mon, 2006-08-14 at 15:50 -0400, Vishwadeep Ahluwalia wrote:
Hi Nick, Thanks for the solution. For the first problem it took me quite a while to update the Nvidia driver. It finally installed after i updated my kernel to 2.6.17-1.2174_FC5. It may have installed just by updating xorg as well. For the second issue, i do have a x86_64 bit system and downloading tksurferx86_64 from the ftp site that u sent me worked.
however there is a third issue :) i ve FSL 3.3 installed. Ive configured FSL and freesurfer in .cshrc. i moved fsl 3.2 from within the freesurfer directory and created a link pointing to FSL3.3 directory. But now FSL 3.3 doesnt run. it gives the following error:
[vish@pathis185 ~]$ fsl Error in startup script: couldn't load file "/home/vish/apps/freesurfer/lib/tclt ktixblt/lib/libtix8.1.8.4.so": /home/vish/apps/freesurfer/lib/tcltktixblt/lib/li btix8.1.8.4.so: wrong ELF class: ELFCLASS64 while executing "load /home/vish/apps/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ info exists env(TCLTKSHELL) ] && $env(TCLTKSHELL) == "wish" } { package require Tk package require Tix tix configure -scheme TixGr..." (file "/home/vish/apps/fsl3.3/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/home/vish/apps/fsl3.3/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/home/vish/apps/fsl3.3/bin/fsl" line 21)
My .cshrc file reads:
setenv FSLDIR /home/vish/apps/fsl3.3 source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} set path = ($path /home/vish/bin ) setenv FREESURFER_HOME /home/vish/apps/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh
Ofcourse , removing the freesurfer config from .cshrc,i can run fsl again. also i can configure freesurfer in another shell to run both FS/FSL. but how can i run both in the same shell? also another concern is since the freesurfer using FSL3.2 and my Feat directories are a result of FSL3.3 ...would i still be able to overlay functional data on the FS produced surface and subcortical segmented images? Thanks!
Cheers, Vish
Graduate Student Medical Physics VCU, Richmond
On Fri, 2006-08-11 at 17:43 -0400, Nick Schmansky wrote:
Vish,
I think there might be two problems here. The first, the GLX error, is likely due to the video driver not supporting GLX (aka OpenGL X-Windows extensions). Does this error appear when running directly from the machine, or is this a remote connection?
The 'wrong ELF class: ELFCLASS64' error would occur is the wrong machine architecture is used. Are you certain your machine is 64bits? To check, you should type this:
uname -m
and see:
x86_64
On the distribution site:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
the 32bit FC5 tksurfer stuff is:
tksurfer_fc5.gz
and the 64bit FC5 stuff is:
tksurfer_fc5_x86_64.gz
Nick
On Fri, 2006-08-11 at 15:11 -0400, Vishwadeep Ahluwalia wrote:
Hi Freesurfers, I just installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 on FC5 linux,x86_64 platform. I'm getting the following errors for tkmedit and tksurfer respectively:
tkmedit bert orig.mgz freeglut (tkmedit): Unable to create direct context rendering for window 'Medit: 'This may hurt performance. X Error of failed request: GLXBadContext Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 29 Current serial number in output stream: 29
tksurfer bert rh pial tksurfer: error while loading shared libraries: libtix8.1.8.4.so: wrong ELF class: ELFCLASS64
Please advise! regards, Vish
PS: i'm using tksurfer-fc5 as given in the online instructions. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Vishwadeep Ahluwalia