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Dear Mirko, SPM5 uses a generic approach to create this kind of designs. There are two ways to go - full or flexible factorial designs. Anyway, you should think of your design in terms of factors and levels. From what you said, I guess you have the following factor candidates: - group (2 levels) - subject (nsub1 levels in group 1, nsub2 levels in group 2) - condition (2 levels) or replication (2 levels), depending on the meaning of your 2 scans per subject You have to choose what kind of error covariance structure you expect - almost noone will be able to help you with this decision, but from an estimation point of view you should only assume unequal variance or dependent variance if there is a strong reason for it. Usually, you want to treat "subject" as random factor. If you do this, you can use "Full factorial design" with your remaining factors and you will end up with 2x2 cells of group/condition level combinations. Probably, you would assume unequal variance for your group factor levels(, and perhaps dependent variance between your condition levels). When using "Flexible factorial design", there is another decision to be made in design specification: which effects you want to test, i.e. which colums you want to appear in your design matrix. At least, you would want a group-by-condition interaction (which is just the same as a full factorial design), but perhaps also a group main effect (per-group mean) or even a group-by-subject interaction (per-subject mean). Hope this helps, Volkmar On Wed, 14 Feb 2007, mirko wrote: > Dear All, > > In SPM2 I used "multi-groups: conditions-covariates" but I can not find an > equivalent set up in the SPM5. I have two groups and in each group subjects > had two scans (paired scans). Could someone suggest to me how to set up this > calculation/comparison in SPM5? > > Many thanks, > > Mirko. > -- Volkmar Glauche - Department of Neurology [log in to unmask] Universitaetsklinikum Freiburg Phone 49(0)761-270-5331 Breisacher Str. 64 Fax 49(0)761-270-5416 79106 Freiburg http://fbi.uniklinik-freiburg.de/