From the picture I understand that you have done a sort of segmentation for the centerline and placed a fiducial. I would think you need a better way to define your fiducials along the centerline. You can try the suggestions given by @lassoan in this post (Virtual Bronchoscopy - #7 by lassoan) for extraction of the centerline as a curve and giving this as an input to the Endoscopy module.
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