Hello,

I am looking to run a MANCOVA to examine cortical gray matter differences across three groups (accounting for several covariates), and I was hoping to get input on whether I am setting up my design matrix correctly.

Groups: 3
Covariates: Age (demeaned), disease duration (DD; demeaned), sex

Simplified Example:
Group   EV1(Grp1)    EV2(Grp2)     EV3(Grp3)     EV4(age)    EV5(DD)    EV6(sex)
1            1                     0                  0                0.25           0.75            -1
1            1                     0                  0                0.25           0.25            -1
1            0                     1                  0               -0.75          -0.25            1
1            0                     1                  0                0.5            -0.75            1
1            0                     0                  1               -0.5             0.5              1
1            0                     0                  1                0.25           0.25            -1

Questions:

1. Is this an appropriate way to do a three-group comparison with covariates? Or, is it better to just run three separate t-tests (including covariates)?

2. Regarding post-hoc testing, would I just do three separate t-tests? This issue here, I imagine, is that the individual t-test results may not reflect the original MANCOVA results (e.g., post-hoc testing reveals a new significant area that was not significant in the MANCOVA).

3. One other option is to run the initial MANCOVA within a statistical program (i.e., using global cortical gray matter volumes) and then follow up with postdoc testing within FSL (i.e., t-tests). Would this make sense?

Thanks in advance for your time and help,
Cristina