In fsl.py --> check_first it uses SGE_ROOT to check for the sge queuing system; however, not all sge queuing systems use SGE_ROOT (e.g., Gridengine on Debian/Ubuntu). If both SGE_ROOT or FSLPARALLEL were checked for, this would work on more folks' systems. I am not a python coder, but on my system simply replacing SGE_ROOT with FSLPARALLEL resolved the issue. I don't know if SGE_ROOT is still used by others, however.