Like X ray, MRI is based on a discovery in the physic lab: when the nuclei of hydrogen atoms--single protons, all spinning randomly--are caught suddenly in a strong magnetic field, they tend to line up like so many compass needles.  If the protons are then hit with a short, precisely tuned burst of radio waves, they will momentarily flip around.  Then, in the process of returning to their original orientation, they resound with a brief radio signal of their own.  The intensity of this emission reflects the number of protons in a particular "slice" of matter.

Illustrations and descriptions taken from "How Things Work"

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