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FSL Version

This is the code that goes in the user section of the script to specify the FSL version:

# Specify FSL 4.1                 

FSLDIR=/usr/local/fsl-4.1.0-centos4_64
export FSLDIR
source $FSLDIR/etc/fslconf/fsl.sh 

You can also make changes to your profile. Do nedit ~/.bash_profile to find the following:

.bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
    . ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/bin
export PATH

Then we need to make sure to specify the path when we call the function like

"$FSLDIR/bin/feat" rather than just "feat".