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Hi, There are probably multiple ways to do this, but here's what I recommend for your first design (I believe yours is rank deficient) EV1: 1 for G1 Cond1, -1 for G1 Cond2, 0 for all G2 EV2: 1 for G2 Cond1, -1 for G2 Cond2, 0 for all G1 next 20 EV's are the subject-specific means (your S1-S20) Then the contrast [1 -1 0....0] tests the group differences in the paired differences (i.e. your interaction effect). For the second design, I'm extrapolating from what was proposed in this FSL list email<https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=74308>, which apparently was summarizing from an earlier email you would have: EV1: 1 for G1 Cond1, -1 for G1 Cond2, 0 for all G2 EV2: 1 for G2 Cond1, -1 for G2 Cond2, 0 for all G1 EV3: avg estrogen for this subject in G1 Cond1, -1*avg estrogen for this subject G1 Cond2, 0 for G2 EV4: avg estrogen for this subject in G2 Cond1, -1*avg estrogen for this subject G2 Cond2, 0 for G2 EV's 5&6, similar to 3&4, but for progesterone next 20 EV's are the subject-specific means (your S1-S20) This will control for whether the within-subject difference is a function of estrogen or progesterone levels. Hope that helps! Jeanette On Tue, Jul 24, 2012 at 2:22 PM, Klara Mareckova <[log in to unmask]>wrote: > Hi, > > I have a question about repeated measures anova and covariates design. > I was reading the FSL manual and forum but since none of the examples > seem to fit my situation, I was wondering whether some of you > experienced FSLers could confirm whether I got it right/ what do I > need to change. > > Design # 1: Repeated measures anova - 2 groups (medication, control), > each participants scanned twice = two different conditions (cond1, > cond2). I want to have a look at the main effect of group, condition, > and the group by condition interaction. I have 40 subjects all > together; 10 in group1 cond1, 10 in group1 cond2, 10 in group2 cond1, > 10 in group2 cond2. I'm combining the F test with the repeated measure > design - can you please check list 1 of the attached spreadsheet and > see whether the design # 1 is correct? > > Design # 2: Repeated measures anova with 2 continuous variables. The > same dataset as above, but this time I want to look at the effect of > two hormone levels - estrogen and progesterone and just correct for > the fact that each participant was scanned twice (I believe that the > group and condition are described by the two hormone levels). I'm > combining the covariate analysis with the repeated measure design - > can you please check list 2 of the attached spreadsheet and see > whether design # 2 is correct? > > > Thanks a lot for your feedback and advice, > > Klara >