Hi Daniel and Paul,
Below are the commands (including the afni.proc.py commands) that I used on my deobliqued anatomical data and original oblique EPI data for pre-processing. Thank you both again so much for helping me with this!
@Align_Centers -cm \
-base ../MNI152_T1_2009c+tlrc \
-dset T1.deoblique+orig \
-child Encoding1+orig Encoding2+orig
echo $name "Running SSwarper"
@SSwarper \
-input T1.deoblique_shft+orig \
-base ../MNI152_2009_template_SSW.nii.gz \
-subid ${name} \
-giant_move
echo $name "Running afni_proc.py"
afni_proc.py \
-subj_id $name \
-copy_anat anatSS.${name}.nii \
-anat_has_skull yes \
-anat_follower anat_w_skull anat T1.deoblique_shft+orig \
-dsets Encoding1_shft+orig Encoding2_shft+orig \
-blocks tshift align tlrc volreg blur mask scale regress \
-align_opts_aea -cost lpc+ZZ -check_flip \
-align_unifize_epi yes \
-tlrc_base ../MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
anatQQ.${name}.nii \
anatQQ.${name}.aff12.1D \
anatQQ.${name}_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 6.0 \
-blur_in_automask \
(omit -regress commands ...)
-execute
