Hi,

Just a clarification, you said that you were using each subject's mask after warping them to standard space. But your syntax shows that the input files are still in +orig. Even in your 3dinfo statement you have avg_group_mask+orig, which suggests that the masks are not in standard space.

If it's not a typo, then you will need to warp the masks to standard space using @auto_tlrc (usage 2) or adwarp or various other programs that can also apply a transformation matrix.

If you use afni_proc.py, you can add -volreg_tlrc_warp to your script to automatically warp all of your results to standard space during processing.

-PM