afni.nimh.nih.gov

3dDeconvolve cannot produce a beta for each condition, one must be the baseline against which other would be compared.
For such a case you should declare some condition 'C' to be the baseline, and consider the 3 contrasts as those A-B, A and B betas (which would mean A-B, A-C, B-C, viewing condition C as the baseline).

I think this is essentially what you must do, regardless of the software.

- rick