Your simple sounding question has only complicated answers.
- How did you align the subjects? We recommend 3dQwarp (or its use in the @SSwarper or auto_warp.py scripts). Unless activation regions are large and strong, affine alignment does not do a good job.
- 3dMean is *not* a statistical analysis program for groups. It is just a convenience program for averaging datasets together. In particular, if you are using 3dMean to average statistical maps from 3dDeconvolve or 3dREMLfit, you are mis-using the program.
- Program 3dttest++ does simple group analyses, averaging beta maps across sets of subjects and carrying out voxel-wise t-tests. With the '-Clustsim' option, it can also produce cluster-level significance maps from the voxel-wise t-maps.
The above list is merely an outline of the procedures to carry out. We teach a class for a whole week on how to do this stuff. We have videos from the last time we taught this class, and are working on putting captions on them for distribution (required by Federal law). When they are available, we'll post some links on this message board.
