Magnetic resonance imaging

About MRI

Magnetic Resonance Imaging (MRI) is used throughout medicine for such things as detecting cancerous growths, diagnosing heart function and monitoring babies in the womb.

Scanners use very powerful magnets to image the soft tissue parts of the body. MRI has been used for 40 years but the basic science behind this technology is over 70 years old.

Most often medical MR images, like the neonatal head image, are produced by detecting the location of hydrogen atoms that are part of water molecules, H2O, within the body. However, Magnetic Resonance is a much more versatile tool for detecting different chemicals.

MRI scanner
MR image of a neonatal head

Guide to how magnetic resonance imaging works

Molecules, atoms and the nucleus

From mobile phones to the body, everything is made of molecules. These are a collection of atoms held together by chemical bonds to form a single unit.

For example, the diagram below shows a molecule called lactate. Lactate is made from three carbon (blue), three oxygen (red) and five hydrogen (grey) atoms. Lactate is produced throughout the body and is most commonly found in muscles during exercise.

Hydrogen is the simplest atom containing a single, positively charged, proton nucleus and one outer, negatively charged, electron.

Atoms are governed by the laws of quantum mechanics, which are very different to the physical laws of the large scale world.

The nucleus located at the centre of an atom has an internal structure with quantum mechanical properties that make it behave like a bar magnet.

Atoms and the nucleus in a magnetic field

When we place a molecule in a much larger magnet two things happen. Just like a compass the nucleus of each Hydrogen atom lines up with the external magnet.

Also, the presence of the external magnetic field cause the nuclear magnet to spin on its axis. We measure the rate of spin as a frequency.

The Earth has a weak magnetic field. Even so the water molecules of your body contain Hydrogen atoms and the nucleus spins with a frequency between 1300 to 2500 revolutions per second, or Hertz for short.

A compass aligns itself with the Earth’s magnetic field to point towards magnetic North.

Detecting the radio waves from the nucleus

To be able to detect the frequency of the nucleus within molecules, each atom needs to be stimulated. To do this, a radio signal is transmitted that is absorbed by the nucleus.

The nuclei absorb some of the energy from the radio signal and then emit it at different frequencies. A radio antenna then picks up the weak radio signals being emitted by each atom.

The way magnetic resonance experiments are performed is analogous to the way you can hear all the notes of a bell after it has been struck with a hammer. In the case of magnetic resonance, the hammer is a burst from the radio frequency transmitter. The energy released from the atoms can then be heard on a special detector.

Molecular detector

Magnetic Resonance is a powerful technique because different molecules emit slightly different frequencies depending on the type of chemical they are. All these different frequencies from each molecule can be detected and tell us which chemicals are present.

The MR image shown relies on locating water molecules to form an image. In this case, the frequency detected is specific to hydrogen nuclei in the water molecules.

The Lactate molecule has a more complicated structure than water containing three different carbon and oxygen atoms. In addition to carbon and oxygen there are five hydrogen atoms that can be grouped into distinct types called molecular groups.

These three hydrogen atoms bonded to a carbon is called a methyl group – CH3.
A single hydrogen atom bonded to a carbon- called a methyne group – CH.

Finally, this single hydrogen atom bonded to an oxygen- called a hydroxyl group – OH.

Each of these groups will emit a unique frequency that can be identified. The lactate molecule has three molecular groups and this will produce three different frequencies in the spectrum.

Hear and see how the frequency changes at each position in the spectrum.

In the spectrum shown below, there are three peaks that can be assigned to the three molecular groups. The methyl group on the far left has a frequency of 1.33 ppm, the middle is from the methyne group at 4.10 ppm, finally, the hydroxyl peaks is at 4.70 ppm on the left.

What is ppm?

PPM stands for parts per million. For our experiments, the frequencies are in the megaHertz range or a million revolutions per second. Reporting frequencies as ppm makes the units more manageable.

A closer look at the spectrum

There is more fine detail in the peaks from the methyl and methyne groups. This is due to the nucleus of one molecular group sensing a nearby nucleus in an adjacent molecular group. This is know as J-coupling.

For example, in lactate, the peak on the far right with a frequency of 1.33 ppm is split into two parts due to the single neighbouring peaks at 4.10 ppm.

Similarly, the middle peak with a frequency of 4.10 ppm is split into four parts due to sensing three near neighbours at 1.33 ppm. This fine detail helps in identifying different molecules in the spectrum.

J-coupled molecular groups

How many peaks – Pascal’s triangle

In Pascal’s triangle, the numbers in the current row are formed by adding the numbers in the row above together.

For the triangle in the diagram, the two numbers in the second row, 1 and 1, are formed from the number above, 1. The three numbers in the third row, 1, 2 and 1, are formed from adding the two numbers above, 1 and 1.

To find the peak pattern in our spectrum we select the row that corresponds to the number of nearby atoms.

Detecting the multiple chemicals in a mixture

The lactate spectrum was for just one type of molecule. But the spectrum from cells are much more complicated with the many different molecules present each providing their own unique set of frequencies.

Watch the video to see and hear the spectrum sample.

A spectrum of mixtures like this is complicated but its possible to match the patterns using a spectrum from a known molecule, like lactate – shown superimposed in red on the spectrum of semen.

Other, more complicated experiments, allow the spectrum to be separated into two or more dimensions like map.

Hydrogen is not the only atom for Magnetic Resonance

Whilst a lot of magnetic resonance experiments detect the Hydrogen atoms, this is not the only detectable atom. Nearly every element in the periodic table has an isotope that is detectable by magnetic resonance.

The elements, carbon, nitrogen and phosphorous, are particularly relevant to biology. Unfortunately there is a problem, often the detectable form of these elements are rarely found in a molecule.


An element in the periodic table is defined by the number of positively charged protons contained within the nucleus. Hydrogen has one proton, helium has two, lithium has three and so on.

However, an atom can also contain another neutral particle called the neutron. These do not alter the type of atom but they increase its atomic weight. For example hydrogen has another isotope called deuterium, that has one proton and one neutron, and another radioactive isotope, tritium, that has one proton and two neutrons.

For example, the most abundant form of carbon, carbon-12, with 99 out of 100 atoms has nucleus with six protons and six neutrons and cannot be detected by Magnetic Resonance.

However, an isotope of carbon contains six protons and seven neutrons, carbon-13, and is detectable. Of all the carbon atoms about 1 in 100 is carbon-13, the rest being almost entirely carbon-12.

Whilst carbon-13 can be detected at 1% abundance if the amount of carbon-13 is increased it can help the sensitivity of our experiments. It is possible to build molecules with added carbon-13 at desired locations so that is 100% abundant.

Importantly this does not change the chemistry of the molecule. Adding carbon-13 atoms increases the signal of the magnetic resonance experiment and allows us to track chemical reactions as a result of metabolism.

Using Magnetic Resonance to monitor chemical reactions

A feature of Magnetic Resonance is that the strength of the signal is in direct proportion to the number of molecules being detected. This can be used to estimate the rate of a chemical reaction by measuring the size of a peak with time.

Using carbon-13 labelled tracer molecules, it is possible to track one molecule being converted by an enzyme into another molecule by observing how one signal disappears and another signal increases. This helps to identify a particular enzyme pathway within a cell. The ability to measure metabolism in live biological cells is one of the main aims of the spermNMR study.

An example of using Magnetic Resonance to study chemical reactions is with the pyruvate molecule. Pyruvate is made by cells as they release energy during metabolism within cells. Pyruvate can be further converted into lactate or bicarbonate + acetate as it is metabolised by different enzymes in a cell.

The effect of the above reaction can be seen in this carbon-13 magnetic resonance spectrum. Three peaks can be seen at frequencies for pyruvate, lactate and bicarbonate. Repeating the measurement over time we would see the pyruvate peak decrease with a corresponding increase in lactate and bicarbonate peaks.

Note that the carbon-13 atom does not move. It is the other atoms of pyruvate that are altered as it is converted into lactate or bicarbonate. Acetate is split off from pyruvate and does not contain carbon-13 and so it is not seen in the magnetic resonance spectrum.

Going faster - Hyperpolarisation

Magnetic Resonance is a very powerful technique, however, its sensitivity means that it requires considerable time to collect data. To reduce the need for this, scientists and engineers have, over the years, improved the technology by developing more powerful magnets and sensitive detectors. More recently a new method know as hyperpolarisation has been developed that could provide the ultimate increase in signal.

The diagram shows how the signal for carbon-13 and an electron changes as we go from room temperature down to absolute zero, the lowest possible temperature at -273 degrees Celsius.

As the temperature decreases, the signal from the electron increases much faster than that for carbon-13. We can then transfer the signal from the electrons to nearby carbon-13 atoms by applying microwaves at just the right frequency.

Magnetic Resonance Hyperpolariser

Hyperpolarised samples are prepared in a machine called a polariser that operates at very low temperature, -272 degrees Celsius.

The sample is microwave irradiated for about one hour to transfer the signal from the electrons to the carbon-13 atoms in a frozen solid. To return the sample to a useable state, we add super heated water to produce a hyperpolarised sample.

The hyperpolarised sample is then added to our biological sample and carbon-13 data is collected rapidly, about once a second, to follow the chemical reaction as our sample is metabolised.

Monitoring Rapid Metabolism

The diagram below shows an example for hyperpolarised pyruvate, the large signal on the right hand side, is pyruvate. This is being metabolised to lactate by cells – the signal on the left hand side.

Note the short length of time that the signal is collected for. From this we can estimate the metabolic state of the cells.