afni.nimh.nih.gov

> What would you recommend? Processing both runs separately or separate the .errts file?

Either one is fine. I would not fret about it. The difference is whether you minimize the total sum of squares separately for each run or together in the least squares method of solving the regression model, and it would not make a big deal most of the time. If you're really concerned, try both and see the differences yourself.

Gang