On Tuesday, September 27, 2011 13:01:30 you wrote:
> When I typed in your command in my termina, I got:
>
> [fsl@localhost ~]$ find / -name fsl.sh
> /home/fsl/fsl/etc/fslconf/fsl.sh
> /home/fsl/Desktop/fsldoc/fsl/etc/fslconf/fsl.sh
> [fsl@localhost ~]$ grep -i fsl ~/.bash_profile
> # FSL Configuration
> FSLDIR=/home/fsl//fsl
> PATH=${FSLDIR}/bin:${PATH}
> . ${FSLDIR}/etc/fslconf/fsl.sh
> export FSLDIR PATH
> [fsl@localhost ~]$ echo $FSLDIR
> /tmp/fsl
> [fsl@localhost ~]$ ls $FSLDIR
> ls: /tmp/fsl: No such file or directory
> [fsl@localhost ~]$ echo $PATH
> /tmp/fsl/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:
> /home/fsl/bin [fsl@localhost ~]$
I'm assuming you did this before you loaded your bash profile with ".
.bash_profile" as Dave instructed. It appears that, prior to setting the
variables in your bash profile, your shell thinks that FSL is installed in
/tmp/fsl and that the fsl binaries (i.e. commands) are in /home/fsl/bin. In
reality, it looks like fsl is installed in /home/fsl/fsl and the binaries are
in /home/fsl/fsl/bin.
Since fsl seems to work when you load your bash profile, I would suggest you
either keep doing just that or figure out why your shell isn't loading your
bash profile automatically. The "find: ... Permission denied" stuff is, as
Dominic correctly points out, a permission issue that you may safely ignore.
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