Inspired by problems in generate_initial_data/gen_STRUCTMOTION/script_STRUCTMOTION_subject.sh, where multiple active versions of FSL lead to an old version of smoothest creating problems, I've gone through and looked for all instances where FSL commands were called and added $FSLDIR/bin/ to make the paths absolute.
The notable exception to this is (1) fsl_sub... it's own evil beast, I didn't want to touch that, and (2) places in Matlab code that I saw call FSL tools with absolute paths... just not sure enough to fix thoses.