MRI scanners using liquid helium (most in use today) are not sealed. As a result, some helium can escape. Heat leaks into the scanner and warms the helium which boils.

Some effort is made to reduce the boil off, typically a "cold finger" (more properly called a Gifford-McMahon cryocooler) is fitted at the top of the scanner. This is basically was a metal finger poking into the space above the liquid level, cooled to -271 C. The helium vapour condenses on the finger and drips back down into the liquid.

Early versions, especially in places like the US, where helium was plentiful and dirt cheap, had relatively weak coolers, so helium would gradually boil off, and periodic top ups would be needed. However, for about 20 years now, most MRI scanners have been zero boil-off because of upgraded coolers - so once started, shouldn't require topping up until obsolete. Older scanners may not have had facilities for recovery of the helium when obsolete - although newer ones are designed with recycling in mind, so that the magnet can go back to the factory still filled with helium, and the helium can then be recovered and reused.

However, helium can still be lost due to malfunction or maintenance. If the cooler stops for any reason, then the boiling helium won't condense and will leak out. Leave a faulty cooler long enough (a few weeks) and a top-up may be required to replace the lost helium. Some maintenance operations (such as controlled stop or start of the magnet) will also cause helium to escape enough to require a top up.

The most dramatic loss is due to a malfunction called "quench" when the magnet suddenly loses it's magnetism. A quench will typically result in the sudden eruption of all the helium from the machine - see https://www.youtube.com/watch?v=0O_FneLbPHo for an example. Quench is a rare malfunction but does happen from time to time. Quench can also be triggered manually - usually in an emergency if someone gets pinned to the scanner by a wheelchair or something. (In this case, it appears to be a manual quench triggered as part of decommissioning of an obsolete machine, where recycling of the helium wasn't practical).

The latest machines which are now available to buy, work differently - they work more like a refrigerator. Instead of submerging the magnet internals inside a vat of liquid helium, the cooling plate of a special refrigerator is attached directly to the magnet internals. The refrigerator circuit is sealed, just like in a regular domestic fridge. No liquid helium is needed - just a few grams of helium gas inside the refrigerator circuit. There should be no loss of helium at any point in the scanner's life time.

It stays in the machine.