For example, the cost of a CT scanner can be as low as $65,000 for a refurbished one that produces only small images quickly. A larger and brand new CT scanner can run as high as $2.5 million.Prices are slightly higher for MRI machines, running up to about $3 million for a new machine.or example, the cost of a CT scanner can be as low as $65,000 for a refurbished one that produces only small images quickly. A larger and brand new CT scanner can run as high as $2.5 million.