afni.nimh.nih.gov

Hmm... That program (siemenstoafni) is really old and not part of the AFNI distribution. You can see this thread. I'd recommend using the AFNI program Dimon or dcm2nii. There's a handy blog post on this as well.

As for processing, we recommend that users take a look at the "new" afni_proc.py script included in the distribution. The class handouts from bootcamps are helpful and can be accessed here. And of course if you have further questions, post them to the message board.

-Pete