Hi Kristen,

That 2dImReg error seems to comes from having zeros in the input
dataset. Are your input datasets masked?

Of course, it shouldn't crash in any case...

---

In any case, I think you should work to align the anatomy to
the EPI. You probably just need one extra -master or -mast_dxyz
option for that.

The second best option may be to use 3dvolreg to align the EPI,
and then compute and apply a warp from EPI to anat via those
-1Dmatrix_* options in 3dAllineate. In that case, 3dAllineate
would not be used for volume registration, but only for the
alignment of the base EPI volume (or average of a few) with the
anatomy.

The last option might be to use 3dAllineate to warp each EPI
volume to align with the anatomy. I suggest you avoid this
(which it seems you are).

- rick