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Hi Michael, Please, see below: On 25 June 2014 01:32, Michael Spilka <[log in to unmask]> wrote: > Dear FSLers, > > I know this is not a new topic but I wanted to seek input regarding a > higher-level repeated-measures ANOVA I am trying to set up in feat: > > I have 28 participants who completed 5 different runs (analyzed separately > at the first-level), and I want to test whether there is any difference > between these runs in order to determine whether or not I can combine them > for further analyses (I have multiple groups who completed the same runs > that I would like to compare eventually). > > I have followed the instructions for a a repeated-measures ANOVA on the > wiki ( > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#ANOVA:_1-factor_4-levels_.28Repeated_Measures.29) > but have several questions: > > 1) How does one determine what the reference run/scan is when adding EVs > and setting up contrasts? It is clear to me in the non-repeated-measures > example on the wiki ( > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT/UserGuide#ANOVA:_1-factor_4-levels), > where there is a clear grand mean, but this is not the case for > repeated-measures. How does the order of the input runs relate to the way > the contrasts are set up? > There's no grand mean, but one mean per subject. I have attached an example set-up with only 3 participants and 3 different > runs (named Anger, Fear, and Happy). Can someone confirm that this set-up > would indeed model individual participant means and test the omnibus F-test > for any treatment effect of emotion? I am specifically wondering about > whether I have correctly omitted the reference run based on the order of my > input data, and whether the contrasts are specified correctly. If so, would > the contrasts be the same had the ordering of my inputs been different? > Looks fine to me. 2) While I have followed the set-up illustrated in the wiki, it seems like > I should be able to set up the same model and contrasts using the cell > means approach, in which I would have an extra EV to model the "happy" run, > and my contrasts would then look like [1 0 -1], [0 1 -1], and [1 -1 0]. > When I tried to run the analysis in this way, I got a warning about my > design matrix being rank deficient and my F-test being invalid. Is this > warning common when trying to set up a repeated-measures ANOVA this way or > is it more likely something specific to my data? > It won't work in this case, because there would be 2 sets of EVs that, once added up, would be equal to vectors of all-ones. For a repeated measurements design as this, following the example is probably the simplest route. > > 3) Since I plan to include 28 participants in this analysis, is there a > less unwieldy approach that does not require an EV for each subject? > Nope I'm afraid. One EV is needed per subject. However, if the concern is creating this using the GUI, the design can be created in an external program pasted into a text editor and used to create the design.mat (use another design.mat as a template, it's quite straightforward). Hope this helps! All the best, Anderson