Hi Nic,

Having different orientations is not a big problem. As you mentioned,
3dresample can easily fix that (without any actual interpolation, since
the voxel coordinates don't change). To do that, I would use -orient
instead of -master (though they ought to imply the same thing in such a
case).

However, since with -master one of the images moves out of view, that
suggests the datasets do not have correct grids in the first place.
The orientation is not the real problem, the location in space is. If
you look at the 2 datasets in AFNI (overlay one EPI on top of the other),
are they in the same location? I guess not. And in such a case, you
really need to correct it, first.

How were these datasets created? Why are they different?

- rick