Hi, Tamara-

The two templates *do* have different per voxel values, even though they appear to overlay pretty much exactly.

The "3dinfo -history" of each file tells a bit of their respective stories. For MNI152_T1_2009c, its history is one primarily of scaling:

3dcalc -a mni_icbm152_t1_tal_nlin_asym_09c.nii -b mni_icbm152_t1_tal_nlin_asym_09c_mask.nii -expr 'a*step(b)*255/97.66312' -datum byte -nscale -prefix MNI152_T1_2009c

MNI152_2009_template_SSW.nii.gz is copied from an intermediate file called "MNI_temp+tlrc", and I don't know *its* origins; it does appear to have more tissue contrast in it.

On a minor methodological note, the SSW template actually includes several subvolumes, for use in skullstripping as well, and you can read more about the "SSW" templates here:
[afni.nimh.nih.gov]

To the main point: I do think that it would be best to use the @SSwarper method for all brains in your study, and not mix-and-match. That way, everyone should have fairly consistent skullstripping+warping.

--pt