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Hi Ricky, Yes, it is possible. I think this thread (and the file linked therein) is exactly what you need: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;c9a13f1e.1506 Also, this other one might be useful, as it includes other contrasts of potential interest: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;dbf8f005.1503 If all 4 observations per subject have the same pairwise covariances, then they are exchangeable, and you can use randomise with the option "-e design.grp" to supply the exchangeability blocks (EB). In PALM the same is done with "-eb design.grp". If the above assumption about the covariance within-subject isn't met, but the errors are symmetric around zero (typically they are for FMRI data), then you can use whole-block sign-flipping: in randomise use the options "-e design.grp --permuteBlocks -1", or in PALM the options "-eb design.grp -whole -ise". More details about this are in the randomise paper <http://www.sciencedirect.com/science/article/pii/S1053811914000913>. Hope this helps. All the best, Anderson On 5 March 2016 at 03:58, Ricky Savjani <[log in to unmask]> wrote: > Hi FSLers, > > We were wondering if there is a way to run a 2x2 ANOVA with repeated > measures for each subject for each factor and level in randomize or in PALM? > > That is, we have 4 PEs for every subject organized like this: > > *Factor A* > Level 1 > Level 2 > > *Factor B* > Level 1 > Level 2 > > Each subject has measures for all conditions, giving 4 PEs for each of our > 67 subjects. We would like to ask is there a main effect of Factor A, for > Factor B, and if there is an interaction effect. However, we know we need > to account for the fact that that there are repeated measures. > > In AFNI, we can do such a command with 3dANOVA3 as follows: > > 3dANOVA3 -type 4 -alevels 2 -blevels 2 -clevels 67 > > where -alevels 2 states there are two levels for factor A, -blevels 2 > states that there are 2 levels for factor B, -c levels states that there 67 > subjects for the subject factor, which is treated as a random effect: > > the -type 4 states is used to denote: > > A,B factors are fixed; C random; AxBxC > > We would like to run this non-parametrically with FSL in PALM (or > Randomize). Is it possible to construct such a design and/or run a variant > of this type of ANOVA? > > Many thanks in advance! > > -Ricky >