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The MRI machine's magnetic field, which runs straight down the tube of the machine along the line of the patient's body, actually realigns the body's hydrogen atoms (or, in this case, the atoms in the head). Normally, the nuclei of the body's atoms spin on axes aligned in all different directions. But the MRI's powerful magnet realigns the protons of the body's hydrogen atoms so that they all spin along the same axis, along the "line" down the length of the person's body.
Now, the protons of the hydrogen atoms are facing either up or down (toward the top of the head or toward the feet). For the most part, the directions of these atoms almost entirely cancel each other out: The ones facing one direction cancel out those that are facing the other. But there are a few that are not canceled out.
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