Instead of the script, use the process I wrote
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Here are my development modules:
http://pixinsight.com/forum/index.php?topic=2275.0The one you need is this one:
http://pteam.pixinsight.com/pcldev/carlos/x64/CMGeneral-pxm.dll(assuming you are using a 64bits windows)
You may use that process with an image container to batch process the images.
Please note that Fourier based registration is not very robust, specially with heavy noise. In the process you have a wavelets filtering option that may aid to better align the frames, and achieve higher accuracy. Also, note that this process only shifts the image. No distortions, rotation or scaling.
A better option may be to use the new TaylorRegister process that is currently under development. It may achieve very good subpixel accuracy with moderate translations, and small rotations (under 1º). At this point we are testing the algorithm with real data, so maybe yours is a good candidate for it. If you want to share a couple of images, it would be very nice to try the algorithm on them.