Hi-
If I could make a few comments---
+ I notice you explicitly ask for the "basic" form of QC HTML:
-html_review_style basic \
The "pythonic" one is more complete and nicer-looking, and only adds the requirement of having Python's Matplotlib module (ver >=2.2.3) installed. That might provide a nicer QC experience?
+ You have nonlinear alignment to a template, which is great. It is certainly fine to implement that as you have here, but often we recommend running @SSwarper on the T1w volume prior to afni_proc.py to do this, and then to provide the calculated results to afni_proc.py. One benefit of this is that if you decide to rerun afni_proc.py later, changing and option or something, then you don't have to go through the nonlinear alignment process again---it is computationally expensive and so can take a while. Additionally, @SSwarper will perform skullstripping (that's the "SS" in the name), and often do a better job than 3dSkullStrip alone (which is the default in the current afni_proc.py command). You then don't have to skullstrip in afni_proc.py, either.
+ Your current "align" block options are good, particularly using lpc+ZZ for EPI-anatomical alignment, but we have recently developed another option to further help, esp. when the EPI has brightness inhomogeneity. This would be used by simply adding the following option+value to your existing command (while still also using your existing align options):
-align_unifize_epi local \
Even if your EPI is not inhomogeneous, then this doesn't seem to hurt, so it seems generally useful to include (in human MRI analysis).
+ For some further QC output, we often include this option:
-radial_correlate_blocks tcat volreg \
Happy to discuss any questions about these additional considerations, if any sound of interest.
--pt
