> There was a lot of significant activation outside of the brain
This is irrelevant.
> the results were completely different than we expected from previous comparison tests
> of the groups we are examining. Here is the script used in the 3dRegAna
A couple of potential problems:
1) Do the two genders have roughly the same average value for each of the three quantitative variables (AgeMD, STAI, and BMI)? If it's not the case, things could be complicated.
2) Are the three quantitative variables centered properly? It's not surprising that the result looks strange to you because STAI is not centered, which means that the gender difference is provided at STAI = 0 in the output.
3) You're assuming that the two genders have the same effect for all the three quantitative variables, which may or may not true.
Gang