A medical grade MRI scanner costs around $1 million, and maintenance costs are circa $100,000/year. With good utilisation, say 3000 hrs/year, the machine costs might be around $70/hr.
The $550/hr you are paying may be because you are using a particularly fancy scanner, or because utilisation rate is low, or because the amount is loaded with overheads, or w/e.
That’s in the ballpark for a 1.5T, but those are fairly old. About $1M per Tesla used to be a decent rule of thumb, but it’s come down a little at the low end. Still, I would be amazed to see a 3T for anything below $2M.
As for the $550/hr, it’s probably true that research scanners have lower utilization and higher costs to support all the weird stuff researchers want to do. An outpatient clinic specializing in knees can run much leaner. That said, that rate seems to be pretty standard across universities and I maintain that it's a very reasonable estimate of the cost. For example:
Most of these do not include F&A. It’s already coming out of the grants and external users pay a "Dean's Tax" on top of that to cover the missing overhead (which can often double the price).
The $550/hr you are paying may be because you are using a particularly fancy scanner, or because utilisation rate is low, or because the amount is loaded with overheads, or w/e.