His whole person will have to go in the tube - the bit that does the measuring is only the middle part of the cylinder. It's really important that he understands that the machine has special "eyes" that can see through people to their insides. I remember as a kid thinking that the only way they were going to get pictures of my bones was to put holes in me to see them, and that wasn't a reassuring option.
Can you find a youtube video of an MRI machine or at least show him some pictures such as this one: http://www.mbi.monash.edu.au/facilities/cmri.html and explain what happens - it will be noisy, you will not be able to see very much because you will be in the tube, and you have to stay really still so the machine can see. The bed moves you through the tube - you don't have to move you.
Can you ask if he gets to choose his music and if he does help him do that.