A note that could save some one some time: Recent versions of FreeSurfer are still being distributed with a version of 3dvolreg from late 2006.
If you use freesurfer and its location is mentioned in the environment PATH before the AFNI tools directory, that will be the 3dvolreg you end up invoking. I ran into a problem when using the align_epi_anat.py, which seems to invoke 3dvolreg with the "-1Dmatrix_save" option. This option is not supported by the 3dvolreg distributed with FS.
Oori
