Yes the copy function would be good but it does not work as intended as it creates the mat files in the raw data dir instead of the workflow dir. What i implemented is the solution to this issue, as you described in this post: https://groups.google.com/d/msg/nipy-user/fEeNhBl5eAY/3LeQ7Sljo-EJ

Do you have any idea on how to copy the input file locally without creating the output the mat files in the raw data dir? Note that spm_coreg does not touch the file (no header modification) in this function, so maybe the local copy is not necessary.