> So, does this mean I will have to change my matrix file for the
> first linear contrast from
>
> 0 0 0 0 0 0 -1 0 1 0 0 0 0 etc.....
>
> to
>
> 0 0 0 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 0 0.... etc?
Yes, that is right. However, you can use another more amenable option -gltsym to simplify the specification.
> It seems this matrix is specifying separate comparisons at each
> time point of the lags, when all I need is a single auc comparison for
> the LC, and a dumpout of the HRF response to each -stim_file class.
I assume the big matrix is for comparing two conditions. There are two approaches to set up such a contrast: (1) Comparing the condition at each time point; (2) Comparing their UAC. The two mean differently and you would come up with two different results, and it is your choice.
Gang