If I do a 3dAllineate on the volume before feeding it into @animal_warper, I still get the same error.
3dAllineate -source SingleSubject.nii.gz -base NMT_v2.0_sym.nii.gz -prefix SingleSubject_al.nii.gz -cmass -warp shift_rotate -overwrite -float -newgrid 0.5
The resulting file looks good and indeed pretty well aligned with the NMT. Within @animal_warper intermediate results, the pshft file also looks good, but the shft volume moves *away* from the already pretty well aligned input and NMT volumes, so I guess this is where things start to move off the rails...
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