Hi Taylor,
I did this
3dZeropad \
-I -80 \
-S -40 \
-prefix T1w_recent_crop.nii.gz \
T1w_recent.nii.gz
I repeated the alignment we did before, no problem
I downloaded the NMTv2 and I did
@animal_warper -input T1w_recent_crop.nii.gz \
-base ~/Documents/Software/NMT-master/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm.nii.gz \
-atlas ~/Documents/Software/NMT-master/NMT_v2.0_sym/NMT_v2.0_sym_05mm/D99_atlas_in_NMT_v2.0_sym_05mm.nii.gz \
-outdir AW_out_sub-002/ -ok_to_exist
and the alignment works perfectly as you can see in the image
Thanks for the help.