Hi, Tamara-

Please note that actually there is a newer (and better) syntax for using @SSwarper since the start of July, as described in this post:
[afni.nimh.nih.gov]

From the **pre-July version** of @SSwarper's helpfile, the syntax is:

------------------------------------------------------------------------------------------
Usage: @SSwarper T1dataset SubID [minp]

T1dataset = a T1-weighted dataset, not skull-stripped,
            with resolution about 1 mm.
SubID     = name code for output datasets (e.g., 'sub007').
minp      = optional: minimum patch size on final 3dQwarp
                      (if not given, 11 is used)
------------------------------------------------------------------------------------------

and only the specific MNI template could be used as a reference; there is no place for a reference dset to be entered, so it should not be as in your "old" syntax. Whatever the third argument is is probably being interpreted as "minpath"; in your case, what you identify as a subj id is being identified as a minpatch size, and causing woe (I guess).

Note that the **modern, post-July version** of @SSwarper has nicer syntax, more flexibility of choosing reference datasets, and more "-prefix" functionality:

@SSwarper          \
        -input  AA        \
        -base   BB        \
        -subid  SS        \
       {-odir OD}         \
       {-minp MP}

The processing guts of the program are the same. I would strongly consider the modern @SSwarper because of the syntax/flexibility.

--pt