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Hi, flirt -in inputimage -ref referenceimage -dof 12 -cost mutualinfo -out outputimage Does that help? All the best, Mark On 29 Aug 2011, at 20:28, Elisabeth Ploran wrote: > Dear Mark and Annouchka, > > I think I'm having a similar problem but I can't figure out how to structure the command line to change the cost function to mutual information. Could one of you post a sample of the FLIRT command? > > Thanks! > Elisabeth > > Postdoctoral Fellow > Human Factors and Applied Cognition > George Mason University >