afni.nimh.nih.gov

The align_epi_anat.py script removes the skull for both the anat and epi datasets. If you have done this separately outside the script, then use these two additional options to skip those steps :

-anat_has_skull no -epi_strip None

3dSkullStrip is used as the default program for doing the skull stripping for both anat and epi datasets. If 3dSkullStrip can not remove the skull (or outside brain), then try "-epi_strip 3dAutomask" instead.