afni.nimh.nih.gov

If I understand correctly, the view is "+orig" instead of the expected "+tlrc". Is that correct? Try replacing the "-master" option with a dataset like that of the template.

3dNwarpApply -nwarp 'anat_fs_brain_alQ_WARP+tlrc anat_fs_brain_al_al.aff12.1D' -master TT_N27+tlrc -source anat_fs_al+orig -prefix anat_fs_al_al

You may also change the view extension with:

3drefit -view tlrc anat_fs_al_al+orig