Without seeing the data, it is hard to say.
Personally, I would first look at the two .1D files -- are the numbers "reasonable"?
Then, I would plot them, as in
1dplot -noline -x r$run.dy1.PCC.1D r$run.dy1.LmPFC.1D
and
1dplot -one -nopush r$run.dy1.PCC.1D r$run.dy1.LmPFC.1D
and see how these plots look. Depending on what I saw, then I'd proceed further.
Also, when you say something like "the output is zero", it is MUCH MUCH better if you give the actual output. Was it EXACTLY zero, or just close to zero? I can't tell from your posting what really happened. It's good that you gave the exact commands you used. You should give the exact output as well.
