Hi everyone,
I have pre and post scans of 72 subjects divided into three groups, so 24 in each group and 144 scans altogether. I would like to do VBM to look for an effect of the "between" factor (group), as well as of the "within" factor (pre/post), on grey matter volume, while co-varying out gender and age. I am at the stage of the VBM pipeline where I need to create my design.mat and design.con, and I'm a bit confused as to how these should be created.
From a general GLM perspective, I guess both questions, i.e. both the effect of group and the effect of scan time (pre/post), could be answered by a single design; however I know that the order in which subjects are entered into design.mat has to be the same as the order in template_list, and I've named my structurals according to the template groupName_subjNr_preOrPost.nii.gz, which makes it difficult to see how the two factors should be coded into the same design matrix.
Also, I know factor demeaning is sometimes a contentious issue - which factors (if any) should be demeaned, exactly? And should categorical factors such as gender be demeaned as well?
Regarding contrasts: assuming that only one design.mat is enough to test both factors, is it correct that the design.con for the within factor should have -1 for pre and 1 for post (or vice-versa), with all other columns in the matrix receiving a 0? And that the contrast for the between factor should have a 2 for one group and -1 for each of the other two groups (with all three possible permutations of where the "2" goes)?
Also, what value should the covariate columns (age, gender) receive in the contrast?
Thanks very much in advance for any help, I really appreciate it!
Tudor
