Hi, I'm a new participant.
I'm using Elastix Software (S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, "elastix: a toolbox for intensity based medical image registration", IEEE Trans. Med. Imaging, vol. 29, no. 1, pp.196 – 205, Jan. 2010) in a very simple way. In my imageJ plugin, a just created a batch file which can call elastix and transformix as a command line (see elastix manual), then using exec(...) function I run the batch file.
Just try it, and if you are satisfied, I have a tip to call elastix invisibly.