>3. I'm not sure why you wouldn't align all of your EPI data
>together, and separately register the anats. Note that
>3dvolreg should work for both of those steps, of course.

>You could start by registering the anats, and then treat
>everything like 4 runs plus an anat.

To register the anats, some do not like the idea of aligning
anat2 to anat1 and then averaging, since anat2 will be a bit
more blurred (since interpolated). To even this out, one
might extract the alignment matrix and apply the square root
to anat2 and the inverse square root to anat1, so they are
both transformed, meeting in the center say. Then average.

I am sorry Rick for the delay in following up with you. I don't know how to do this (register both anatomicals using extracting the alignment matrix? could you help me with that and tell me what are commands for that? keep in mind my background is medical not neuroscience or biophysics (translation: I am dumb in math!)I read somewhere I can use 3dUniformize?