You may set the options to how align_epi_anat.py sets the 3dSkullStrip options with "-skullstrip_opts" (possibly via afni_proc.py's "-align_opts_aea" option). Also consider skullstripping your data separately beforehand and skipping any skullstripping in afni_proc.py or align_epi_anat.py. Affine alignment is usually not very sensitive to precise skullstripping, so only extreme cases are critical here. For afni_proc.py, masking of the functional results to the skullstripped anatomical data is an option. See the MASKING note in afni_proc.py's help and the -mask_apply option.
Edited 1 time(s). Last edit at 03/06/2015 12:05PM by Daniel Glen.
