Hi, Pawel-

Indeed, I would start with 3dAllineate---can always add nonlinear tweaks later, but also if this step fails badly, nonlinear wouldn't start well.

Note that 3dAllineate and 3dQwarp both have this opt:

-emask ee   = This option lets you specify a mask of voxels to EXCLUDE from
               the analysis. The voxels where the dataset 'ee' is nonzero
               will not be included (i.e., their weights will be set to zero).
             * Like all the weight options, it applies in the base image
               coordinate system.
            ** Like all the weight options, it means nothing if you are using
               one of the 'apply' options.

So can you make a mask of the implant artifact to provide as an "exclusion mask," so that doesn't drive/distract alignment?

I would have started with lpc (or lpc+ZZ) between the subject T2w and NMT T1w reference; maybe with the emask that will have better traction?

I agree that starting with non-skullstripped to non-skullstripped might be best way to start (and then use that alignment to help remove skull---that is what @animal_warper does; actually, I could probably add an "-emask .." opt to @animal_warper, too). *But* if the skull is relatively bright in both datasets, while the internal tissue contrasts are opposite, then it might be worth adopting a different strategy. Would you mind sharing an image of one of your T2w volumes, either sagittal or coronal?

--pt