[Neurodebian-users] Configuring FSL

[Chuck Theobald]

Hello Assal,

If you have installed from the NeuroDebian repository, FSLDIR is set by 
/etc/fsl/fsl.sh. Here is what I put into each user's .bash_profile:

# Check for NeuroDebian-style installation of FSL.
if [ -e /etc/fsl/fsl.sh ]; then
   . /etc/fsl/fsl.sh
   export FSLPARALLEL=1
   echo "==> FSL is installed ..."
# Else check for manual installation.
elif [ -d /usr/local/fsl ]; then
   case `hostname | cut -f1 -d'.'` in
     bleu) export FSLVERSION=3.2 ;;
     *) export FSLVERSION=4.1.8 ;;
   esac
   export FSLDIR=/usr/local/fsl-${FSLVERSION}
   export PATH=${FSLDIR}/bin:${PATH}
   . ${FSLDIR}/etc/fslconf/fsl.sh
   echo "==> Welcome to FSL ${FSLVERSION} ..."
else
   echo "FSL is not installed"
fi

The above supports both NeuroDebian and my older method of manual 
installation to /usr/local. The elif clause is going away when my last 
Gentoo machines die from lack of use.

Hope this helps,
Chuck


On 2/10/12 11:34 AM, Assal Habibi wrote:
> Hi,
>
> I have downloaded (using synaptic package manager) and installed FSL but having trouble with configuration.
> As instructed on FSL website, I copied and pasted the following lines of commands  in the shell setup files. I tried .bashrc, .profile, .cshrc but none of them worked.  The error line is: fsl: command not found. Does anyone know hot to fix it?
>
>
> FSLDIR=/usr/local/fsl
> . ${FSLDIR}/etc/fslconf/fsl.sh
> PATH=${FSLDIR}/bin:${PATH}
> export FSLDIR PATH
>
> Thank you,
> Assal
>
>
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>    


-- 
Chuck Theobald
System Administrator
The Robert and Beverly Lewis Center for Neuroimaging
University of Oregon
P: 541-346-0343
F: 541-346-0345