I did end up committing to Penn for several reasons. It is technically a master's program, so full funding (tuition plus $18,000 stipend) was limited to three students. I was fortunate enough to get the funding, but it's contingent on me choosing radiation oncology as a specialization (versus nuclear medicine or radiology) and working with the other two students on a proton accelerator project. I was essentially rejected at Duke (applied as Ph.D., offered *possible* position as master's student), and the funding was virtually nonexistent. Penn only gave me until the end of February to decide, so I didn't have time to see the Wisconsin open house or get a financial offer from them. Basically, by the time I had to decide on Penn, Penn seemed like the best place financially. I visited their program before I made the decision. It is essentially run through the physics department. Graduate quantum mechanics and electricity and magnetism are required courses, which is kind of unique for a medical physics program. I liked this strong physics orientation. Also, anyone accepted into the medical physics program can do a Ph.D. in physics with a medical physics option. I liked how they are offering clinical residencies to select graduate students once they finish the program. They are building a proton therapy center on campus that will be finished by the end of the summer, too. The director of the program got her Ph.D. from Georgia Tech, which is where I go, and she is board certified, so I felt like she knew what she was doing.
So I guess that means I am out of the running for Chicago. Good luck to anyone who still has a shot!