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:
> > ---------------------------------------------------------------------
> > [EMAIL PROTECTED] ~]$ 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
> > > >
> > > >
> >
> >
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