Pouya, this is probably a setup or filenaming problem.  Ziad Saad was unable to reproduce the problem (he is the primary developer of afni_matlab).  I suspect because its failing while attempting to run a shell command that this could be something related to your setup.  The unix() command you've left uncommented is simply running 3dcopy , and should be running the same as what you ran manually.  Can you remove the semicolon from the end of line 422 (eg. so it will spit out the text for the shell command it will run)?  That will probably tell us whats going on.  Also, did you customize your Mac setup at all?  How do you have AFNI installed?
Erik