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Dear Joy, Yes, that's right. No need for site, sex or education if you have subject-specific regressors as nuisance. Alternatively, and perhaps easier to see, you can just subtract one timepoint from another, in which case you'll have 1 image per subject, and things should look more familiar then. All the best, Anderson On 2 December 2013 02:10, Joy Matsui <[log in to unmask]> wrote: > Hi FSL Experts. > > I've been reading all the emails about creating design matrices and > contrasts for doing a longitudinal analysis on TBSS outputs. For my > purposes, I'm trying to evaluate DTI scalars along tract skeletons in 4 > groups (1 control, 3 disease) where each subject has 2 time points. There > are a few variables I want to control for: age, gender (1=male, 0=female), > education, and site of collection. Based on one of the emails from the list > ( > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1302&L=fsl&D=0&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=461525), > I was thinking of making my design matrix as follows. I simplified my > example to two groups, age (which is time), gender, education, and two > different sites. > > (Data) (Grp) (Time,controls) (Time,patients) (Gender,controls) > (Gender,patients) (Educ,controls) (Educ,patients) (Site1,controls) > (Site1patients) (Site2,controls) (Site2,patients) > ((Intercept,subj1) (Intercept,subj2) (Intercept,subj3) > (Intercept,subj4) > (Subj1,Visit1) 1 a11 0 1 0 9 0 1 > 0 0 0 1 0 0 0 > (Subj1,Visit2) 1 a12 0 1 0 9 0 1 > 0 0 0 1 0 0 0 > (Subj2,Visit1) 2 a21 0 0 0 7 0 0 > 1 0 0 0 1 0 0 > (Subj2,Visit2) 2 a22 0 0 0 7 0 0 > 1 0 0 0 1 0 0 > (Subj3,Visit1) 3 0 a31 0 1 0 12 0 > 0 1 0 0 0 1 0 > (Subj3,Visit2) 3 0 a32 0 1 0 12 0 > 0 1 0 0 0 1 0 > (Subj4,Visit1) 4 0 a41 0 0 0 6 0 > 0 0 1 0 0 0 1 > (Subj4,Visit2) 4 0 a42 0 0 0 6 0 > 0 0 1 0 0 0 1 > > But then I came across this other email ( > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1111&L=fsl&P=R28722&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4) > that suggested that I don't need the gender, education, and site columns > because the intercept subject columns account for gender, education, and > site. Each subject's gender, education, and site also do not change between > time point 1 and 2 (not time varying), which sort of helps me understand > why columns for those variables aren't needed in a longitudinal analysis. > However, site has always had to be accounted for in our past > cross-sectional analyses so I'm a little nervous to drop site. > > If anyone has suggestions, I'd be happy to hear them. > > > Thank you, > > Joy >