Hello Corinna,
just remove the line ". /etc/fsl/5.0/fsl.sh" from your bashrc file
and paste the following to your bashrc
# for FSLDIR
FSLDIR=/usr/local/fsl/5.0
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

hope this will work


On Wed, Apr 17, 2013 at 7:36 PM, Corinna Bauer <[log in to unmask]> wrote:

I did that and added the source . /etc/fsl/5.0/fsl.sh to my .bashsc file. Which fixes the fsl5.0- issue.

However, I still have problems using FSL in conjunction with Freesurfer. I am getting still an error when using freesurfer's mkbrainmask-sess

/usr/share/fsl/5.0/bin/bet2: error while loading shared libraries: libmeshclass.so: cannot open shared object file: No such file or directory



On Wed, Apr 17, 2013 at 12:26 AM, Michael Hanke <[log in to unmask]> wrote:
Hi,


On Tue, Apr 16, 2013 at 10:26 PM, Corinna Bauer <[log in to unmask]> wrote:
Hello all,
In order to get fsl5.0 to work on my Ubuntu 12.04 OS, I need to type fsl5.0- prior to any command (e.g. fsl5.0-fsl, fsl5.0-bet2, etc). Otherwise I get errors.

Please run

    man fsl

in a terminal. The manpage has instruction on how to set up FSL properly. Basically just like setting up FSL on other systems by sourcing the config file.

Michael




--
Himanshu Joshi
M.Tech. Cognitive & Neuroscience.
Senior Research Fellow
Department of Psychiatry
NIMHANS, Bangalore

http://mbial.weebly.com/himanshu-joshi.html