Hi, Korann-

Well, indeed, cat_matvec shouldn't be trying to combine 1D text file with a volumetric data set...

One thing is that you should pass skullstripped anat with "copy_anat", and then tell afni_proc.py that you have already skullstripped the brain:

-copy_anat anatSS.${subj}.nii
-anat_has_skull no

where ${subj} stands for where your subject ID would be. You can still pass your anatomical that has a skull as a follower, with:

-anat_follower     anat_w_skull anat 004_SurfVol.nii

This is also a pretty common line to put in, so that in case the anat and EPI dsets are far apart, they should have less troubles:

-align_opts_aea -giant_move -cost lpc+ZZ -check_flip

One other question: can you please copy+paste your @SSwarper command? I am concerned that since "-base" is in the place where your subject ID would be that something might have gone amiss with that...

-pt