Hi-

That looks like correct output with 2 ROIs. When you have N target ROIs, then every matrix will be of size 'N by N'-- in your case, 2x2.

These are like correlation matrices. Each element's coordinates tell you which targets' connections are being described.
So, for the mean FA matrix for example, you have
FA_{11} FA_{12}
FA_{21} FA_{22}
where 'FA_{12}' is the mean FA value in tracked regions that connect targets 1 and 2; the diagonal elements only have a single element, because they are like the 'OR-logic' connections through any target. And these matrices are symmetric, so that FA_{21}=FA{12}.

I'm not sure what is meant by: " However, it has two means and two standard deviations. " ?

To me, the FA values don't seem abnormally high, assuming you are looking at adult subjects. The FA threshold is usually 0.2 in adults, so having a mean FA of ~0.4 isn't so large, I don't believe. What average value were you expecting?

As a side note, for viewing results, you can use SUMA or the command line fat_mat_sel.py, as described in points #2 here:
[afni.nimh.nih.gov]

--pt