The logic of 3dAutomask with a clip level of 0.33 is used to form the base image automask, after the base image is smoothed a little (4.5 voxels FWHM). Then the voxels surviving inside the automask are scaled to make the weight. This is the only function of the automask. The alignment proceeds with the weight volume which is separate from the base image volume. That volume is usually blurred a little but not otherwise processed for the matching algorithm. However, the parts of it that were outside the automask will not count at all in the matching algorithm, and will "flap in wind" of the nonlinear deformations from the other voxels. You can see what the automatically computed weight volume is by using the "-wtprefix" option to 3dQwarp.

If you supply your own weight volume, the whole blur+automask procedure is skipped in favor of your own weight volume. Note that the "-wball" option does not apply to a user-supplied weight volume. "-emask" does apply in either case (automatic or user-supplied weight).

There is no option to set the clip level (or other parameters) of the automatic weight volume computation. There are several such parameters, and it seems overly complicated to let these be adjusted -- you are the first person ever to ask about anything like that.

I hope this helps explain the process. If you are aligning T2-weighted images, then perhaps a little more care is needed, since the program has been tested mostly on T1-weighted images. What are you aligning TO - a template?