Anybody who has undergone an MRI scan can tell you that other than the claustrophobia of being in an enclosed cylinder, the other bothersome part is the knocking sound that occurs. Here's a video (see below) that localizes where and why that knocking sound occurs.
The bottom line is that the sound is due to a helium pump that disperses liquid helium in order to cool the wires that control the magnets down to -269.1 degrees Celsius. MRI machines work by generating a very large magnetic field using a super conducting magnet and many coils of wires through which a current is passed. Maintaining a large magnetic field requires a lot of energy. By cooling the wires with liquid helium down to as close to -269 degrees Celsius as possible, the resistance in the wires is almost zero allowing for highly efficient maintenance of a high magnetic field. A typical MRI scanner uses almost two tons of liquid helium.
On a related note, check out this video of what happens inside a CT Scanner!
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