Thank you very much Brett to provide me a comprehensive information. Appreciate your help and looking forward to see more great jobs from you. If I face any issue, i will back to ask you.
Image Registration App is just a front end for the functionality of IMREGISTER.
IMREGISTER is actually a collection of algorithms (optimization + similarity metrics). Because of this, the correct citation would depend on what flavor of optimization and metric you're using.
Here are some applicable references:
Mutual Information based registration:
"Nonrigid multimodality image registration" D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank Medical Imaging 2001: Image Processing, 2001, pp. 1609-1620.  "PET-CT Image Registration in the Chest Using Free-form Deformations" D. Mattes, D. R. Haynor, H. Vesselle, T. Lewellen and W. Eubank IEEE Transactions in Medical Imaging. Vol.22, No.1, January 2003. pp.120-128.  "Optimization of Mutual Information for MultiResolution Image Registration" P. Thevenaz and M. Unser IEEE Transactions in Image Processing, 9(12) December 2000.
One Plus One Evolutionary Optimizer:
"Parametric estimate of intensity inhomogeneities applied to MRI" Martin Styner, G. Gerig, Christian Brechbuehler, Gabor Szekely, IEEE TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000, (http://www.cs.unc.edu/~styner/docs/tmi00.pdf)
"Evaluation of 2D/3D bias correction with 1+1ES-optimization" Martin Styner, Prof. Dr. G. Gerig (IKT, BIWI, ETH Zuerich), TR-197 (http://www.cs.unc.edu/~styner/docs/StynerTR97.pdf)
Most of the literature seems to take the basic similarity metric/ optimization framework for granted without citing references. The references are usually for specific parts of the framework (numeric optimization, image similarity metrics, ways of pyramiding, etc.).
Hope that helps,
Hello Mr. Brett Shoelson,
Thank you very much for provide this implementation. i want to use this method as comparison in my journal paper. i need to cite the basic journal paper of this implementation. please provide me the citation if any.
Thank you very much.