Am I the only person who thinks this is insane?! You want to reorient your EPI before preprocessing it, and when you do that, all the slice-timing information is thrown away! And that this has happened is not made obvious to the user!

Is it guaranteed that this command

3drefit -atrcopy OLD+orig TAXIS_OFFSETS -atrcopy OLD+orig TAXIS_NUMS NEWi+orig

will restore the slice-timing information in a way that will be correctly interpreted by a subsequent call to 3dTshift -- no matter which orientation has been switched to which other?

In the general case, where Chris' constraints on the order in which processing can occur do not hold, is it better to run 3dTshift first and then 3dresample? I suppose after 3dTshift has been run, there is no need to keep slice-timing information.

Thanks!
Dan