cd mkdir .fslconf cd .fslconfand in this directory create a file called fsl.sh or fsl.csh, depending on the shell that you use, setting any or all of the variables that appear in the central ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh files.
DO NOT copy the central files into ~/.fslconf/ as it will cause a loop that will stop your login from working.
It is recommended that the files ~/.fslconf/fsl.sh or ~/.fslconf/fsl.csh only include a few variable definitions and nothing more. Note that whoever installs FSL can also edit the central files in $FSLDIR/etc/fslconf to change the preferences for all users.