Hi, Tamara-

Could you please paste the full output of the errors that afni_proc.py is giving you?

Please also paste what is returned by:

afni -ver

Without these outputs, it will be impossible to know what afni_proc.py is having troubles with.

If @SSwarper has run, then its outputs should be usable by afni_proc.py fine.

Another sidenote for future reference:
@SSwarper's syntax has changed. It used to be that the user only input the anatomical and possibly a prefix, and one specific MNI template was used. Now, to increase flexibility, it uses command line options to input a reference "base" data set (each of those includes "SSW" in the name, to flag their significance for this purpose), specify the input data set, etc. These option flags are:

-base   -input  -minp   -odir   -subid

So, if you ran @SSwarper successfully *without* those, that is fine-- the output data sets are the same as before, it's just that now you can send outputs to a different directory, etc. The switch to @SSwarper was advertised in the "AFNI_DIGEST" list email (which every AFNI user should subscribe to, in my opinion) a month before the change, and then the new version with options was added to AFNI on July 1, 2018.

Part of the reason I mention the old-vs-new @SSwarper is because it looks like you are trying to combine "new" @SSwarper usage (specifying the reference base data set) wtih the old program; in the present case, "MNI152_2009_template_SSW.nii.gz" is being treated as a subject-ID by @SSwarper, not a target. That is why the output files have that in it, and the extensions look a bit funny: ".nii.gz.nii"

--pt