Freesurfer actually contains a copy of 3dvolreg (called 3dvolreg.afni). I've seen this issue resolved in the past by copying (or better yet linking) the AFNI version of the program to the appropriate freesurfer directory. Get the location of the Freesurfer version with:
which 3dvolreg.afni
and replacing that with the file from
which 3dvolreg
If the two commands above both give output, and you were feeling extra shell-happy you can do:
cp `which 3dvolreg` `which 3dvolreg.afni`
If that doesn't seem to fix it, post the output of:
afni_system_check.py -check_all
