Have you tried lower case?

i.e. $bet or $flirt

if it does not work,  then follow the instruction on the fsl webpage to complete the configuration (see below).

http://www.fmrib.ox.ac.uk/fsl/fsl/linux....

Configuring

Put the following somewhere in your shell setup file (.bashrc, .profile, .cshrc etc., depending on what shell you use), replacing "/usr/local/fsl" with a path appropriate for where you have installed FSL:

• bash / sh / ksh:
  

  FSLDIR=/usr/local/fsl
  
  . ${FSLDIR}/etc/fslconf/fsl.sh
  
  PATH=${FSLDIR}/bin:${PATH}
  
  export FSLDIR PATH

• tcsh / csh
  

  setenv FSLDIR /usr/local/fsl
  
  source ${FSLDIR}/etc/fslconf/fsl.csh
  
  setenv PATH ${FSLDIR}/bin:${PATH}

hope it helps,