As a possibly related update - when I try and do volume registration with 3dAllineate using lpa+ZZ I get good registration but really weird clipping of the brain where, as I move to more sagittal slices, the front of the brain completely disappears (looks like a big black shape is moving from forward to back over the brain until you can't see it anymore).


So, alignment and volreg have issues when I try to use +ZZ...


Could this be because I have partial coverage? (though, this is noted in aea)


Thank you for your help


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Volreg code (alignment code in previous comment)

afni_proc.py -subj_id $subj \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-blocks volreg \
-volreg_align_to MIN_OUTLIER \
-volreg_method 3dAllineate \
-volreg_allin_cost lpa+zz \
-volreg_warp_dxyz 0.8 \
-volreg_motsim