Customising FSL

FSL can be customised for different output datatypes and other features. There are several environment variables which FSL uses to determine certain user preferences, such as the output file format (NIFTI, Analyze, etc). The defaults for these are set when you source the setup file as shown above (i.e., ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh). If you wish to change these defaults then you need to:
cd
mkdir .fslconf
cd .fslconf
and 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.