Ciao Cristina,
If the spikes are throwing the registration off, then you should certainly run 3ddespike first. Note that 3dAllineate may give you less than optimal results for registering EPI to EPI in this case. Consider using 3dWarpDrive or 3dvolreg for that purpose or at least download the latest version of 3dAllineate which is still being polished.
cheers,
z