I’m part of Kristina Simonyan’s group and I am currently working with afni_proc.py. Doing quality control with the index.html function, I’m finding some inconsistencies in the anatomy to template volume alignments. I’m wondering if there is a manual way to fix the alignment?
Not sure what you mean by manual way, but there are options you can add to various alignment programs. The -tlrc_opts option controls some of these options. The options depend on what kinds of issues there are in the data. For example, skullstripping may be a problem there that can depend on the anatomy of the subject and the scan. Consider using @SSwarper for both skullstripping and alignment of the anatomical dataset to some templates. Then feed the results of that as input to afni_proc.py.
To add to Daniel’s comment: would you be able to post your afni_proc.py command here? We might have some suggestions for that.
And also, as Daniel noted, for human data we lean on @SSwarper now pretty strongly for both skullstripping and nonlinear registration (in humans; for animal data, we would use @animal_warper—but I assume you are looking at human data at the moment). You would run that program before afni_proc.py, and then hand the results to afni_proc.py to use in processing. Is that what you are doing currently?