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You should really only need a single T1 image (if any).  Personally, I would
simply realign the data as multiple sessions, coregistering all the data to
the same T1 image.  You could use both T1s though - averaging them in order
to improve your signal-to-noise.

Best regards,
-John

>    In the current project I am running, I have four runs of a task.
> Normally, I coregister all four sets of EPI data to my t1 taken at the
> beginning.  However, in one case, the subject had to be removed from the
> scanner after 2 runs and put back in.  Upon putting the subject back in
> the scanner, I ran another T1, and the remaining two runs of the task.
> In order to deal with analyzing all four runs of the data, I thought I
> would do the following:
> 1) Realign all four runs
> 2) Coregister my second T1 to my first T1 (in other words, make the
> first T1 the "target" and the second one the "source" and selecting no
> images when it asks for "others")
> 3) Coregister runs 1 and 2 to my first T1
> 4) Coregister runs 3 and 4 to my second T1
>
> Is this correct?  And if so, what T1 should I choose for my
> normalization step?  Also, when I coregister my T1's to eachother,
> should I select coregister only? or coregister and reslice?
>
> Is there anything else to be done in this situation?