Hi, Tamara-

It would be useful to have the exact, copy+pasted error message you are receiving, actually.

@SSwarper outputs *.nii files (and aff12.1D files), and I have used its results fine in afni_proc.py previously, so I don't think that naming should be a problem.

Some notes on that afni_proc.py command:

First, a sidenote: Probably it would be preferable to use MIN_OUTLIERS as the "-volreg_align_to ..." value:

-volreg_align_to MIN_OUTLIERS

since that should hopefully be a non-corrupted volume in general.

After running @SSwarper, your "-copy_anat ..." should be the thing output by @SSwarper; probably based on your other SSwarper output file names, I'm guessing:

anatSS.MNI152_2009_template_SSW.nii

Does that exist?

And then you would want to include this:

-anat_has_skull no                                       \

because you have run the skullstripping program already on the input.

Is it possible that it can't find the MNI152_2009_template_SSW.nii.gz template file-- is that in a different directory, and not somewhere automatic that AFNI can find it? What is the output of:

@FindAfniDsetPath MNI152_2009_template_SSW.nii.gz

--pt