What happens during an MRI?

MRI is complex, but the basic events in the scanner are quite straight-forward. Below is a short, simple guide to what happens during an MRI scan without too much physics to complicate matters. It explains the actual events in the scanner and a simplified overview of the parameters we can use to change the images we collect.


  1. First we align the protons in the object we want to scan with the magnetic field of the scanner (B0). This happens naturally when the object is placed into the scanner, as the slightly magnetic protons adjust themselves to match the magnetic field of the scanner.
  2. Second, we use a radio frequency (RF) pulse to ‘tip’ these aligned protons out of their alignment with the magnetic field. This pulse is sometimes called B1 and is applied at a 90° angle to B0. This causes the protons to rotate, and we can measure this rotation with RF measurement coils. RF coils are essentially loops of wire, and the changing magnetic flux of the protons induces an electric current through these loops. This is because changes in electrical currents generate magnetic fields, and changes in magnetic fields generate electrical currents. RF coils may often be designed to both deliver the RF pulse (through an applied electrical current) and receive the signal (through the resulting change in magnetic flux). During the rotation, two things happen.
    1. Protons begin to align themselves again with B0. The speed of this realignment is called the T1 relaxation time. For any given type of object (or tissue, if we are doing medical imaging), the composition of the object will cause its protons to realign at different rates. Faster realignment means brighter signal.
    2. Protons become out of phase with eachother. This reduces the signal we can measure with our coil (as the rotation of the photons are no longer ‘pulling in the same direction’). The speed at which this happens is called T2 relaxation time. Protons remaining in phase for longer means brighter signal.
  3. The RF pulse is applied again, to repeat the procedure. The average of all these repeats gives us a clear MR image.

The contrasts of the scan (T1, T2) are determined by two parameters: relaxation time (TR) and echo time (TE).

TR is the time between the RF pulses. If we have a long TR, all protons in the object have time to realign with B0. If we have a short TR, some protons may not have fully realigned by the time the next RF pulse arrives. In terms of medical imaging, some tissues will need longer to have all their protons realign than other tissues. If the ‘slow’ tissues have not realigned within the TR, the signal from these tissues will be less than the ‘fast’ tissues. This way, we can tell the difference between different tissues.

TE is the time we use to measure the signal induced by the rotating protons. Some types of tissue will have protons that fall out of phase (‘dephase’) faster than protons in other types of tissue. For example, protons that are in fluids have less obstacles, and will remain in phase for quite a long time. Protons that are constrained by structures may not remain in phase that long. Longer TEs means that the protons have more time to dephase, and this will reduce the signal from tissues that dephase quickly more than from tissues that dephase slowly.

Generally speaking, we have three types of contrast: T1-weighted, T2-weighted and proton-density (PD) weighted

A scan sequence with a short TR and short TE is usually called T1-weighted. By ‘a short TE’ we usually mean that the TE is shorter than the T2. In other words, there is not enough time for the protons dephasing properly, and the T2 effects are masked. The shorter TR, on the other hand, means we can easily differentiate between tissues with longer and shorter T1. The scan is therefore T1-weighted. Tissues that are bright in T1-weighted scans are fat and white brain matter. Muscle and grey brain matter are less bright (grey in colour), and fluids tend to be black.

A long TR and long TE scan sequence is usually called T2-weighted. Longer TE means that we get differentiation based on protons dephasing at different rates, and the T2 effects are visible. The longer TR, however, means all tissues have time to have all their protons realigned to B0, so we get no differentiation based on T1 times. The scan is therefore T2-weighted. Tissues that are bright in T2-weighted scans are fat and fluids. Muscle and grey brain matter are grey, and white brain matter is almost black.

A long TR and a short TE means we get both T1 differentiation and T2 differentiation, and we call this proton-density weighted. This gives us the actual density of protons in the tissues. A short TR and long TE means we get neither T1 nor T2 differentiation. We don’t use this type of scan, as it doesn’t yield any useful information.


In this post, I have summarised some of the basics about MR imaging. In my next post, I will move on to outline some of the basics about raw MR data processing, covering k-space and Fourier transforms.


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s