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Hi Mark, How are the .ppm files generated (i.e. rot.ppm, trans.ppm & disp.ppm)? I'm running the following command: mcflirt -in myfile -o myfile_mc -cost mutualinfo -refvol 0 -stats -plots -rmsrel -rmsabs -report but I'm not seeing any .ppm files. The feat report.log doesn't show any other commands that could possibly generate them. thanks, jack