You need to setup the configuration by hand.

User shell setup is stored in a file called .bash_profile (BASH) or .profile (SH, KSH and sometimes BASH) in your home folder (eg ~/.bash_profile), you need to edit (or create) this file to add the following lines:

FSLDIR=/usr/local/fsl

. ${FSLDIR}/etc/fslconf/fsl.sh

PATH=${FSLDIR}/bin:${PATH}

export FSLDIR PATH

changing /usr/local/fsl to the directory path you installed FSL to.

You need to setup the configuration by hand.

User shell setup is stored in a file called .bash_profile (BASH) or .profile (SH, KSH and sometimes BASH) in your home folder (eg ~/.bash_profile), you need to edit (or create) this file to add the following lines:

FSLDIR=/usr/local/fsl

. ${FSLDIR}/etc/fslconf/fsl.sh

PATH=${FSLDIR}/bin:${PATH}

export FSLDIR PATH

changing /usr/local/fsl to the directory path you installed FSL to.

If Irene's answer doesn't fix your problem I suggest going to the FSL message boards. First do a search if anyone else has had your problem. After that post to the message boards. It is a better research for FSL questions than research gate.

Irene Bollettini is correct, you need to update your PATH:

Just run this script every time you open a console (I added this line to my ~/.bashrc file). It is necessary to update your PATH variable.

The script automatically adds all necessary fsl paths to PATH.

. /usr/share/fsl/5.0/etc/fslconf/fsl.sh

Tested and running on Ubuntu 12.04 x64

If you installed FSL 5.0 using NeuroDebian repository, prefix "fsl5.0-" to the command you are trying to execute.

For instance, fsl5.0-fsl or fsl5.0-Feat instead of fsl or Feat respectively.

System: FSL 5.0.6 on Ubuntu 12.04 x64

Thanks Ravnoor Singh it worked by prefixing fsl5.0

Thanks everyone for giving precious suggestions

Check both .bashrc and .bash_profile

Martin s script is working very well, thanks!