Hello,
I was able to align the majority of my images by replacing the 3dAutomask image with 3dSkullStrip. This is the command script that I used:

#!/bin/tcsh
#
foreach subj ( 32A )
cd /Volumes/Yay_HD/VS_motion_kj/subjects/$subj

rm -vi *_align-py_stdout.txt
# Aligns anatomy volume to EPI volumes
align_epi_anat.py \
-anat ${subj}_Struct_brain+orig \
-epi ${subj}_Run1_nd+orig \
-epi_base 0 \
-suffix _a2e \
-child_epi ${subj}_Run2_nd+orig ${subj}_Run3_nd+orig ${subj}_Run4_nd+orig \
-anat_has_skull no \
-partial_axial \
-epi_strip 3dSkullStrip \
-tshift off \
-giant_move \
-save_vr \
-volreg_method 3dvolreg \
-volreg on \
-volreg_opts -twopass -Fourier -zpad 4 \
-maxdisp -verbose -AddEdge | & tee ${subj}_align-py_stdout.txt

end
echo 'done.'; date




However there was still one image (see attachments) that would not successfully align. I tried using all of the suggested commands, as well as 3dSkullStrip. Do you happen to have any more suggestions?

Thank you,
Kelly