What does a CT Scan show that an MRI can't?

I am on an HSA plan so I have to pay $3000 out of my pocket before my insurance pays anything. With this said, my dr at Kaiser ordered a CT Scan to see what the mes in my liver were. They ended up being common hemangiomas, but he says I may have gallstones blocking my duct and need to do an MRI to know for sure. Couldn't an MRI have found out the same thing as the CT scan with regards to the liver mes? Couldn't I have just paid for the MRI and not had the CT scan done?