Hi Kristen,

If you are hitting a filesize limit, then you are tring to
create a file that is more than 2 GB on a 32-bit operating
system (or at least not a true 64-bit OS, such as some of
the "64-bit" macs, I believe).

Your 3dAllineate command will resample the EPI data grid
to match that of the anatomy, so it will be high resolution,
with many sub-bricks, and therefore large.

Consider adding either a -master option, to choose a grid
for the aligned EPI data (perhaps even using the EPI dataset,
itself). Or you can consider the -mast_dxyz option, to
specify a voxel size of your choosing.

-------------------

To take a step back, consider instead warping your anatomy
to match the EPI. That will remove the extra interpolation
steps on the EPI, plus removing any worries about running
out of memory or file sizes.

It's nice to do as little as necessary to the EPI data.

- rick