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Using SPM5 I am having trouble entering my own global normalisation factors. I 'm using "flexible factorial" to compare one FDG PET patient with a group of controls. Under "Global Calculation" I have chosen "User" and entered my own vector (in this case mean occipital lobe values). When I run this the "Global Calculation" changes - this is set in SPM.xGX.iGXcalc = 3. It should be 2. I've checked the results: the mean occipital lobe value should be what I set the proportional scaling to be (I checked this to be the case in SPM2), but its not - its normalised to global mean values. I think iGXcalc is reset in spm_config_factorial_design.m, line 1411, where it is set to = 3 when a relative threshold is set, and user entered values are then ignored. I would still like to set a relative threshold to mask out low intensities as I believe I did in SPM2. Can I do this? Am I doing something wrong? Please help. Regards Joel Dunn