It's been awhile and I thought I'd update my progress and findings.

I've been looking at other scripts and programs and decided to use @SSwarper to perform nonlinear alignment and skullstrip T1 to standard MNI space.

@SSwarper \
	-input $subj_id \
	-base ~/abin/MNI152_2009_template_SSW.nii.gz \
	-subid SSW$subj_id \

I've selected 6 brains (2 control, 1 mild cognitive impairment, 3 Alzheimer's) that failed to align in my first run (similar misalignment/warping in my first post). In the first attached image, you can see that the skull-stripping is not working well on these sets of brains (sometimes it leaves the upper portion of the skull alone, sometimes it decides to consume most of the frontal lobe, sometimes both).

I've ran @SSwarper on another control brain (took 1.4 hours to finish) that succeeded in skull-stripping and alignment and ran afni_proc based on example 9b using -anat_has_skull no and -tlrc_NL_warped_dsets. The second image shows the resulting QC, which looks acceptable in my view (of course this is debatable, but I couldn't find a reference or criteria for an acceptable QC). Unless there are other suggestions on improving the skull-stripping other than -deoblique and -giant_move (I've tried those two already), I am going to assume that failed attempts are unsuitable for analysis.

I'd like to note that running @SSwarper on these 6 brains took 28 hours. It's a small sample size but I've noticed that it takes a lot longer on the brains with cortical atrophy (MCI and AD). It could be purely coincidental, since one of the AD brains was stripped successfully. Also, when I used @SSwarper on a subject that successfully aligned in my first run, it took less than an hour.