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Dear Albert, how did you set up your batch? Using spm_jobman GUI or in any other way? If you used the GUI, I would be interested in your batch.xml file to see whats happening. If not, you may want to check that your job.des....scans variable may need to be transposed before entered in your batch. Volkmar On Wed, 23 May 2007, Albert Compte wrote: > Hi, > > I was having the same problem and I realized that for my case there was > something funny in SPM when reviewing the 2nd level design SPM.mat file. I > am running a single-factor, 6-level design with 16 subjects per cell. > However, when reviewing the design in the SPM gui (Design->Explore->Files > and Factors), I realized that the level (1 through 6) and subject number (1 > through 16) were assigned wrongly to the contrast file paths, as if they had > been shuffled around (as if bootstrapping). In my case, this was solved by > changing line 39 in file spm_set_factorial_design.m > > from > P=[P;job.des.fd.icell(cell_num).scans]; > > to > P=[P;job.des.fd.icell(cell_num).scans']; > > so the correspondence now is correct. Getting this right allows me now to > run the 2nd level estimation without any problem, yielding reasonable results. > > This might be a general bug in SPM5, in which case similar changes would > probably be needed in two and three-way designs. > > Cheers, > > Albert > -- 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/