afni.nimh.nih.gov

> if a subject doesn't have cond1, cond5, and cond7, than we cannot do this weighted contrast?

You can't take this subject for the specific contrast testing.

> What about pair-wise comparisons? For example, 1*cond1 -1*cond2 (cond1 and cond2 are never in the same subject).

Unfortunately the answer is still no.

Gang