Hi, Dane-
Would it be possible/desirable to convert your processing to an afni_proc.py command? Since you already have the 3dDeconvolve command worked out, I would think that the mapping of that to "-regress_* ..." options would not be too bad. The QC HTML would be a major benefit of doing this; hopefully, the other steps that get taken care of by afni_proc.py (like concatenation of warps, etc.) would just be icing on the cake.
I will have to leave it for someone else to comment on the use of 3dSynthesize to further isolate regressors of interest. I am afraid I don't have a good sense of how that would work. Have you previously taken your output regressors of interest, and they didn't provide adequate contrasts or something?
I would tend to start with a simple or "classical" analysis of regressors and see how the results look there, before moving into the 3dSynthesize realm. For example, it would be a good sign to see approximate effect estimates that you expect, even if they are a little weak or with too low of statistics. That would give you more confidence in the acquired data and modeling before trying any higher order analyses after.
--pt
