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Kelly, To follow up on Steve's reply, if you've got paired (aka repeated measures) data, then you *must *use a group file to tell randomise about what is exchangeable. If you have 3 subjects in group A and 2 subjects in group B, then your design matrix might look like 1 0 1 0 0 0 0 # Sick, Pre -1 0 1 0 0 0 0 # Sick, Post 1 0 0 1 0 0 0 # Sick, Pre -1 0 0 1 0 0 0 # Sick, Post 1 0 0 0 1 0 0 # Sick, Pre -1 0 0 0 1 0 0 # Sick, Post 0 1 0 0 0 1 0 # Not Sick, Pre 0 -1 0 0 0 1 0 # Not Sick, Post 0 1 0 0 0 0 1 # Not Sick, Pre 0 -1 0 0 0 0 1 # Not Sick, Post and your contrast of interest [-1 1 ]. Randomise doesn't have to worry about different group variance, but it *does* need to know that it only make sense (under Ho) to swap pre and post data within subject. Hence you need to use a group file consisting of 1 1 2 2 3 3 4 4 5 5 which defines 5 'groups' (technically known as exchangeability blocks). Can you try this and let me know if works? -Tom ____________________________________________ Thomas Nichols, PhD Director, Modelling & Genetics GlaxoSmithKline Clinical Imaging Centre Senior Research Fellow Oxford University FMRIB Centre On Jan 24, 2008 10:10 PM, SUBSCRIBE FSL Kelly Brown <[log in to unmask]> wrote: > Hi FSLers, > > I have a question, if I am using randomise to analyze an ANOVA type > design, > do I need to include a design.grp file for my two groups? I want to look > at > differences in pre and post and differences in sick and not sick... And if > so, how should it look because I keep getting an error when I try to run > randomise with the design.grp file and the design.fts file...I have > checked > the number of rows etc and they match my datapoints... > > group.datis not a valid vest file > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Aborted > > I get the same message when I try to make a F test file... > > design.grp > > %! VEST > /NumWaves 1 > /NumPoints 10 > /Skip > /PPheights 1 1 > > /Matrix > 1 > 1 > 1 > 2 > 2 > 1 > 1 > 1 > 2 > 2 > > > Thanks! > Kelly Brown > UCHSC Research Fellow > >