Hi Dr. Zalesky,

First of all, thank you for providing researchers with this very useful tool.

I wanted to write a contrast that compares two groups A and B. A subset of the subjects were scanned twice. I have 200 data sets, and 25 were from the same subject . I was wondering how to account for the repeat scans in the design matrix and include this as a covariate in the contrast. My other covariates are age and gender.

I did:
1 0 1 24
1 0 2 18
1 0 1 35
1 0 1 42
0 1 2 16
0 1 2 18
0 1 1 29
0 1 1 32

Where
Column 1 = group A
Column 2 = group B
Column 3 = gender (1 = male)
Column 4 = age

In the example above, rows 3 and 4 are the same subject, scanned twice at age 35 and 42. Rows 7 and 8 are also the same individual, scanned at different times.

I plan to do a [-1 1 0 0] contrast to compare the two groups. May I ask what is the proper way to add repeat scans in the design matrix?
Thank you!

Best,
Jay