Responding to my own message because someone fixed it for me. I never set the paths right during install. The issue was fixed by pasting the following into ".bashrc" in my home folder (just remember to set the FSLDIR to its actual directory):
LD_LIBRARY_PATH=/usr/share/fsl/5.0
FSLDIR=/usr/share/fsl/5.0
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
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