Hi Dan,
Thank you! Yes I found the documentation of -skullstrip_opts on the web version of the help (in the "full list of options" section). I was looking in the terminal after typing aling_epi_anat but didn't see that section. Next time I'll look at the webpage as well.
So you seem to already know my problem and you're also right. My main problem is actually bad alignment between EPI and anat. I thought it has to do with bad skull stripping. Well I can fix that now, but it didn't seem to help alignment. Do you have any pointers? Some more info: it's standard EPI and MPRAGE, and it works for six other subjects (all normal college sample). This particular subject has a bit more CSF outside parietal lobe, hence too much clipping in skull-stripping. Other than that, I can't tell what's so different about this subject. Yet the align_epi_anat script produces a result that is shifted by a lot in the I-S direction, plus also some rotation, which wasn't there to start with, as everything is within a session and subject didn't move much.
Your help is much appreciated. I'd be happy to send/upload the data if you want to look.
Thank you,

--Taosheng