Hi Laura
> Each subject had 2 runs during each session, and 6 conditions per run
> (please see the matrix).
>
> Now when I set up the design matrix for the first level, I choose 2 session.
> In the contrast manager after specification of the contrast I choose the
> "replicate over session" because the same contrast is used for the second
> run.
>
> However, I find it tricky, as if all my 6 condition (A, B, C, A1, B1, C1),
> let's say I am interested in only A - A1 if it is replicate over sessions
> the contrast is [ 1 0 0 -1 0 0 1 0 0 -1 0 0]. It seems to be wrong. Simple
> equation (A-B) - (A-B) = A - B - A B [ 1 - 1 -1 1]
If I understand you, you are interested in the average effect of A -
A1 across two sessions, in which case your contrast
[ 1 0 0 -1 0 0 1 0 0 -1 0 0]
is correct. In your notation this would correspond to
(A-B) + (A-B)
The way you express it, (A-B) - (A-B), would be an interaction, where
the difference between two conditions in session 1 is different than
session 2.
Hope this helps,
Jonathan
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