afni.nimh.nih.gov

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.