Marc,
Or you can set the path to your own, newer fsl with something like setenv FSL_DIR /usr/local/fsl
if you'd rather not use the fsl distro that comes with freesurfer.
Don
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, June 29, 2006 11:05 AM To: Marc D. Yelle Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] FreeSurfer Newbie can't get working with FSL onMac OS 10.4
Marc,
After sourcing the $FREESURFER_HOME/SetUpFreeSurfer.csh file, add this line:
unsetenv TCLLIBPATH
This is what is causing the conflict with FSL's TCL libs.
Nick
On Thu, 2006-06-29 at 12:26 -0400, Marc D. Yelle wrote:
Hello, I am in need of some help. I have spent the last two days trying to get fsl and freesurfer to play well together. I have the newest version of FSL installed and it works perfectly. I then installed freesurfer per the instructions listed in the wiki. After these steps, freesurfer works, but fsl won't open. I get
this error
message:
MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/../System/Library/Perl/5.8.6:/sw/l ib/perl5:/sw/lib/perl5/darwin GSL_DIR /usr/local/freesurfer/lib/gsl TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib MISC_LIB /usr/local/freesurfer/lib/misc/lib FSL_DIR /usr/local/freesurfer/fsl
Marc-Yelles-Computer 1% echo $FSLDIR /usr/local/fsl
Marc-Yelles-Computer 2% fsl Error in startup script: no suitable image found. Did find: /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a 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 "/usr/local/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/usr/local/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/usr/local/fsl/bin/fsl" line 21
I tinkered with the setupfreesurfer.csh and the freesurferenv.csh files and got it to list FSL_DIR as usr/local/fsl but the program still wouldn't work.
If I comment out the two freesurfer lines in my .cshrc
file, fsl works
perfectly once again. My only guess is that there is a
problem with
both fsl and freesurfer having tktcl libraries. But my
understanding
of UNIX, etc is somewhat limited. Below I have also attached my .cshrc :
#!/bin/tcsh set path = (/usr/X11R6/bin $path /sw/sbin /sw/bin /Users/marcyelle/bin) set prompt="`hostname -s` !% " source /sw/bin/init.csh source /usr/local/rsi/idl_5.6/bin/idl_setup setenv IDL_PATH "<IDL_DEFAULT>:+/usr/local/rsi/idl_5.6/local_lib" setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} unsetenv LANG
Thank you in advance for your assistance, I need it! Sorry for the long email, I simply wanted to give you as much info as I
could. Take
care.
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