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
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?