(1) For only 4 slices, 3dvolreg may not be a good choice since it is hard to deal with the out of slice motion with only 20 mm of coverage in the z direction -- voxels in the outer 2 slices will be mixed with zeros from the non-existent neighboring slices, which will make their data confused.

(2) Perhaps 2dImReg if in-plane motion needs to be corrected. But for small motion, then correction isn't really needed, since the correction estimates of motion are not exact, and neither is the interpolation process at the end.

(3) Do you have a reference for the spectral method you are using? I'm curious.

(4) Thanks a lot for helping Ziad out!