Magnetic resonance is a phenomenon whereby the nuclei of certain atoms, when placed in a magnetic field, absorb and emit energy at a specific or resonant frequency. 

Nuclei suitable for MR are those that have an odd number of protons and/or neutrons, having an overall nuclear charge distribution. They also exhibit the property of nuclear spin, which gives them angular momentum. The combination of charge and angular momentum causes these nuclei to behave as magnetic dipoles or microscopic bar magnets. Almost all clinical MR images are produced using the simplest of all nuclei, that of hydrogen (comprising a single proton), which is present in virtually all biological material and exhibits relatively high MR sensitivity. Other relevant naturally occurring MR active nuclei include phosphorus (31P), sodium (23Na), carbon (13C) and potassium (39K). Inert gases such as helium (3He) and xenon (129Xe) can also be made sufficiently sensitive using what are termed pre-polarisation techniques.

The proton can be regarded as a small, freely suspended bar magnet spinning rapidly about its magnetic axis. Place a group of protons or 'spins' in a uniform magnetic field (B0) and their magnetic moments experience a force tending to line them up with the applied field. This is termed nuclear polarisation. Due to thermal energy, not all spins line up and at body temperatures the difference in numbers between those that do and those that don't (the net magnetisation) is small; typically, there will only be an excess of 10 in every two million nuclei. The stronger the applied magnetic field, the larger this net magnetisation or polarisation and the higher the available MR signal. The direction of the applied magnetic field conventionally defines the z-axis, which is generally in the craniocaudal direction in the common cylindrical clinical system.

The slight excess of spins that line up with the field are in a lower energy state than those that line up against it. This difference in energy levels (ΔE) is dependent on the magnetic field strength (B0): the higher the B0, the greater the difference between energy states. Spins can move between these two energy states: to enter the higher energy state, the spins need to undergo excitation; to return back to the lower energy state the spins need to undergo relaxation. A combination of these two processes generates a signal from the spins within the patient.

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