Hi, Pawel-
Indeed, I typically process my data in a "level-by-level" manner, checking each step before proceeding. So, I would run @animal_warper on each N subjects, check and be happy with the results, and then run afni_proc.py and check all results, etc. This is easier for me conceptually and QC-wise---differences among subjects are more apparent this way, for example. Even more specifically, I try to set up processing for 1 subj in a cohort (or 1-3, just some small number), and set everything to run pretty well for that subject, and then expand that to the full cohort---that seems an easier way to troubleshoot.
And yes, processing on biowulf/HPC makes sense. It can be tough to check things there sometimes, but hopefully the automatic QC images made by these programs helps that process: you can scp them to another computer and go through them quickly. And I am sure Daniel's input is useful, too!
In terms of hopping between systems: most things in AW are all local, and most things in AP are all local; the template is the hardest part. I would put the template+atlases into a global sessions directory on each computer, set the global sessions environment variable in ~/.afnirc on each computer, and then refer to the template name as much as possible. Both AW and AP make use of "@FindAfniDsetPath" under the hood, so you should be able to specify the dset name as much as possible. For AW, this even applies to: the brainmask follower, atlas_followers, template_followers and seg_followers. That should be more flexible across more systems.
I am not sure what this means:
<<But now I have this question whether the issue of the template location may affect the analysis itself. Because I have been puzzled for quite a while by inconsistencies between HPC and local results.>>
If you had different NMTv2 versions on your system, this could cause confusion potentially. But you can avoid that by... not having that be the case.
Daniel mentioned the alignment behaving differently thing---this is something I would like to look more at perhaps separately and individually. If talking about anat-to-template alignment, perhaps there are slightly different templates on each system? If talking about EPI-to-anat alignment, it is hard to see how the template could affect it. One would want to rule out having slightly different dsets in different cases (e.g., deobliquing a dset on one system, but not on the other), but barring that, this is something I would like to hunt down if it comes from the alignment (alignment is stochastic, because of random seeding, so that is one source of potential variability across systems).
--pt
