When you crack your knuckles in an MRI machine, the bubbles that are seen are the result of the synovial fluid which contains dissolved gases, mostly carbon dioxide. This creates a pressure change which causes the bubbles to partially collapse, resulting in the sound we all know. It takes around 20 minutes for the remaining bubbles to dissolve before you can crack your knuckle again. This is different from the sound you hear when you stand up quickly, which is likely caused by the tendons snapping when they slide over bones.
Studies have shown that knuckle-cracking is probably not harmful, as was confirmed by Dr. Donald Unger who cracked the joints in just one of his hands for 60 years without developing arthritis. However, it may be harmful to those around you who can hear you!