Changing the environment variable DISPLAY will cause nodes to begin to rerun unnecessarily. The 'environ' input claims to have differing values: Error from a multisubject connectivity pipeline study (for a cmtk.Parcellate node): " values differ in fields: environ: {'DISPLAY': ':1', 'SUBJECTS_DIR': '/media/Mobsol/subjects'} != {u'SUBJECTS_DIR': u'/media/Mobsol/subjects'}" Removing: display_variable = :1 from the nipype.cfg file fixed it. Maybe we can work around this problem with a list of relevant environment variables (e.g. FSLOUTPUTTYPE, FSL_DIR, etc..)?