Hi, Tamara-

Thanks very much for posting those details-- I do see what the problem is right now. I think it is extremely subtle.

I think it has to do with the fact that the outputs of @SSwarper in this case have a funny name ending with multiple volumetric file extensions: instead of being just ".nii.gz" or ".nii", they are ".nii.gz.nii".

afni_proc.py can find the initial datasets and copy them-- at this stage, it is trying to change them to BRIK/HEAD format (because that is what afni_proc.py uses), but the "SS" anat here is staying NIFTI because it has *two layers* of NIFTI extensions!

OK, so to solve this in the present case, you should be able to rename the files that have 2 layers of extensions. I will suggest:

3dcopy anatSS.MNI152_2009_template_SSW.nii.gz.nii anatSS.fixedname.nii
3dcopy anatQQ.MNI152_2009_template_SSW.nii.gz.nii anatQQ.fixedname.nii

Note that that I don't think the other two files from SSwarper need to be renamed:
+ "anatQQ.MNI152_2009_template_SSW.nii.gz.aff12.1D" is just a text file of linear affine transformation values-- doesn't get renamed
+ "anatQQ.MNI152_2009_template_SSW.nii.gz_WARP.nii" still has a funny name with the NIFTI extensions buried inside, but at the end it only has one extension (because the "_WARP" string is sitting there).

Once you have renamed the two problematic files and replaced their name in the afni_proc.py script, you should be good to go.

Note also that in the future, using @SSwarper you can avoid this problem with the newer version of @SSwarper, which makes clearer what parts of the inputs are file names and what are paths/etc. In your present/old version, the syntax for inputs is:

@SSwarper T1dataset SubID [minp]

so you can see that the 2nd argument for the program is not the name of a target file, but instead the "subject ID".

--pt