I am currently facing this problem, and have been tossing for several days because of it.
The problem is when i use Halcyon datasets, it works. **(**see in Halcyon.ipynb)
But when I use the same code and change the file name to Edge datasets, it gets stuck. (see in Edge.ipynb)
This generally means the phantom was not properly found in the dataset. The upcoming version of pylinac will give a more specific error. Based on your images it appears like you should move your catphan along the z-axis to get a better scan that includes all the modules. See CatPhan - pylinac 3.13.0 documentation