Hi Javier, I'm very sorry -- your email got lost in my pile, and I forgot about it! Did anyone else get back to you about this? And/or did you manage to work it out yourself? If not, in rough terms, I think you want to specify flexible factorial and include a factor for subject, as well as your other factors. Then when you specify scans (or "specify all" and a factor matrix) you can denote the levels of the other factors for each subject. So e.g. for "specify all", the factor matrix might have a first column of all ones for replication, then a column with blocks of four numbers (1 1 1 1 2 2 2 2 ... 9 9 9 9) for each subject, and then columns for the levels of the other two factors (e.g. 1 1 2 2 1 1 2 2 ... and 1 2 1 2 1 2 1 2 ...). It's possibly simpler to treat the 2*2 factorial as a 1*4 if you don't need different non-sphericity options for the different factors. [Or maybe it is genuinely 1*4? -- I'm not sure I completely understood your original description...] In that case you would have just the subject factor and the other factor, with its column in the factor matrix being (1 2 3 4 1 2 3 4 ...). This should match the design matrix that I suggested before: [kron(ones(4,1), eye(9)) kron(eye(4), ones(9,1))] Does that help? Or, if not, there have been a few more recent posts on this, perhaps some of those have helped / will help? Sorry for the very slow reply, Ged. Javier Gonzalez-Castillo wrote: > Hello Ged, > > Thanks very much for your answer. And now sorry for what I imagine is a > very simple question: how do I define the within-subject ANOVA model in SPM5 > so I get a design matrix such as the one you propose (X = > [kron(ones(4,1), eye(9)) kron(eye(4), ones(9,1))] ) > > What second-level model type should I use: Full Factorial, Flexible > Factorial? Could you please give me some fast guidelines about how to define > the model the way you propose. I've tried different approaches, but I > definitelly don't know how to do it.Do I have to do something different at > the first level or I just use the same con files I was using in my previous > approach? > > Thanks again, > > Javier Gonzalez-Castillo > PhD Student - Biomedical Engineering - Purdue University > >