Nitrogen is 300x cheaper than helium, so someone must really have thought about why they would need to use the latter.
Compared to the rest of the costs of the systems which use it, the helium cost is not a big problem. It's less than the labor cost of keeping the machine ready for use. An MRI uses over 100 MWh a year, the machine costs millions to start with, the personnel cost is hundreds per hour... The machine uses roughly 100-200 liters of helium, which is now $30-50/liter. So $3000 to $10000 for a full fill. Boil-off rates range from 0 to 0.2%/day. A refill occurs every 6-24 months. So we're looking at a max of about $20000/year for the helium, or about 33 1/3 days of personnel costs.
(These numbers were pulled from various obviously AI-authored pieces on MRI refill costs, so they might be fairly bullshit-ish, but since multiple articles were around the same numbers I've used them here anyway.)