Dear Freesurfer experts, I would be very greatful if you could help me with three (probably basic) questions regarding an mri_glmfit design. For the design and contrasts I used FSGDF. I have a 2x2 factorial design with one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2) and the covariate in one model, because I would like to test for the interaction between A and B (regressing out the effects of age). Age was demeaned using the mean of all subjects (i.e. of all 4 groups). My first question regards the contrasts: If, besides the interaction and main affects of A and B, I would like to assess the difference between individual groups, for example A1B1 - A1B2, is it okay to use the same model (1 -1 0 0 + further 0's for the age regressors); or should I make a new FSGDF containing only the subjects of group A1B1 and A1B2? My second question is associated with the first: If it is allowed to use the same model, how does freesurfer deal withdemeaning? Since I used the mean of all subjects to demean and not just of the subjects of for example A1B1 and A1B2. My third question regards the DODS/DOSS issue. I used DODS, because I do not believe the slopes of age by volume (or age by area/thickness) will be exactly parallel between groups. I tested this also be using contrasts of the age regressors, (for example using the contrast 0 0 0 0 1 -1 -1 1 for a AxBxage interaction) and indeed there are interactions with age in some brain areas. For thickness, they were FDR corrected still significant, for other measeurs the were not significant after correction, but that seems natural given the sample sizes. No I wondered whether it would suffice to use a DODS design (since slopes differ between groups) or whether I should stratify groups further for age (for example use two models, one for young subjects, on for old subjects). If the latter is the case, I would end up with very small samples, I am afraid. Thanking you in advance, Maaike
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