RE: [Freesurfer] FreeSurfer Newbie can't get working with FSL onMac OS 10.4 - Freesurfer

29 Jun 2006


      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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