Hi Greg -

I think the help text is more restrictive than the code - try using an initial nonrigid transformation; it should work.

Note, however, that some warp options will no longer be working, e.g., you will not be able invert the initial alignment, or to configure the initial grid size, only refine further from whatever your initial transformation grid is. If you want to start with something coarser, you can first use fit_spline_xform to fit a coarser spline transformation to your existing warp (likewise, you should be able to fit a spline to the inverse of an existing transformation).

Another option, which will always work, is to use your initial transformation to reslice the moving image, then use that resliced image for registration. You will pay a price in image quality, but since further reslices can always simply concatenate multiple transformations, you can always go back to the original image for interpolation.

Hope this makes sense.

Torsten