Hmm, okay, to use the Ha stack as your reference, you will need to do the star analysis on the Ha-stack, so registration becomes possible. Then selecht the Ha as reference and unselect the Ha stack before starting the registration proces. Let me know if this works ?
Usually I don’t work in the workflow. I make the stacks per channel. And then load all stacked channels and perform registration. But your method should work, let me know if you encounter this error again. I think APP fails here because the Ha stack wasn’t star analysed and I dont’catch this error properly..