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After running them through ppmcenter/PCFE, drop it into Registax, use the 128 alignment box (the red spot is clear enough so use that to align on). Btw how many frames do you have? Have you read Mikes "How to" for Registax?
Anyway, when you get to the waveletting stage, wavelet gently (I usually use only 4, 5, and 6 sliders with 6 being the heaviest and then reducing by half for the next slider). Select RGBshift and click estimate. If there is still a strong colour cast to the limbs use the Lt, Rt, Up, Dn buttons to shift the colour around. Doing it manually sometimes is the only way to get it to work as it should.
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