Hi, Jef-

OK, we can look into this. It may be the initial overlap is not very good, and/or that the tissue contrast or level of detail is mismatched.

A couple background questions:
A) Your input dataset already been warped once? I'm guessing this by the filename. I'm a little curious why there might be multiple warps/alignments? That might be fine, but each regridding can blur the data a bit and then one might use other considerations to concatenate data.
B) Is your input a T1w anatomical? It is a little hard to tell from the image; there isn't a lot of structure that is discernible, and I can't tell whether that is due to the warp or to original dset properties.
C) What is the purpose of this alignment? Is it part of EPI/FMRI processing? That might affect the use choices, and maybe recommendation of a better tool to perform this step.
D) Is there any reason not to use full nonlinear alignment to template space? That is usually much preferred to auto_tlrc, which is only affine alignment---the level of detail matching will necessarily and generally be lower. We might recommend using @SSwarper, for example, to perform both nonlinear alignment to the template with skullstripping of the anatomical simultaneously.

--pt