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Hi Joy, From what I understand, the number of columns in your design.fts file must > match the number of rows in your design.con file and placing a 1 in a row > of your fts file is equivalent to clicking the f-test boxes in the contrast > GUI for that particular f-test. Is my set up correct? Yes, that's correct. > Also, is this f-test equivalent to doing an ANCOVA to get the main effect > of your groups on the dependent variable? > There are multiple different F-tests that you could construct, and if you'd like to compare the 3 disease groups with no regard for the controls, then I think the following would be more appropriate (using your current design.con file): design.fts 0 0 0 1 1 0 0 0 0 0 0 0 0 If you want to include the controls, then I think you'd want something as this: design.fts 1 1 1 0 0 0 0 0 0 0 0 0 0 That said, you need to modify your design: remove the intercept, because it's a linear combination of the 4 groups, then redefine the t-contrasts and then define the f-tests. Also, although for your current contrasts it won't make a difference, you may want to mean center sex, just as you did for age and education. If later you decide to create a contrast to look at the mean of individual groups, you'll already have the design properly set up. And yes, look at different groups/levels with an F-test in the presence of continuous nuisance variables is equivalent to an ANCOVA. Hope this helps! All the best, Anderson