Problem with fill holes (beginner help)

I was following along with the segmentation video for beginners but when it came time to compute the length of the termite digestive tract using skeletonization I had some trouble after changing it to RGB, doing color threshold, and creating the mask - specifically, when I did “fill holes” the entire tract became the same color as the background. Help? I didn’t save my mask, but it looked something like this (the tutorial example)

Dear @lfrankle,

could you please check if you have the Black Background option activated in Process > Binary > Options? Try to activate it and redo the Fill Holes operations. With that option disabled, ImageJ interprets the black region as foreground and tries to fill the hole (the mask of the worm), which results in a black image.