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Conrad, No. Without SGE, and assuming there are no differences in the paramaters or loading of the machine, there should be no difference at all. ------Original Message------ From: Conrad Rockel Sender: FSL - FMRIB's Software Library To: [log in to unmask] ReplyTo: FSL - FMRIB's Software Library Subject: [FSL] speed of GUI vs command-line Sent: 26 Aug 2009 21:39 Hi there, We are currently racing a probtrackx launched from GUI vs the same track launched from command-line. Though I have not set up an SGE, it still seems as though the GUI works faster. Does this make sense? Conrad Sent using BlackBerry® from Orange