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MRI: The basics

Back in 1632, the famous painter Rembrandt made an oil painting called The Anatomy Lesson of Dr. Nicolaes Tulp. Seven doctors gathered around a cadaver studying anatomy. Luckily, today we have radiological anatomy as a whole new discipline that enables doctors to visualize inner body structures by using technology to produce images of the specific body regions and organs.

Radiology today uses three modes of image production:

  • Transmission of energy
  • Reflection of energy
  • Emission of energy

The subject of interest in this specific article is the method that uses the emission of energy as a modality of image production, and that is Magnetic Resonance Imaging (MRI).

What is MRI and how it works?

Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body in both health and disease. MRI creates images by distinguishing between the nuclear magnetic properties of various tissues, a property that makes MRI capable for very precise tissue differentiation. MRI utilizes no ionizing radiation that could damage the tissue, but instead it produces images by using a magnetic field and radio waves.

Key Facts
Basis Creation of 2D and 3D images by distinguishing between the nuclear magnetic properties of various tissues
Energy Magnetic fields, radio waves
T1 Weighted Images High signal for fat, high signal for contrast substances (Gadolinium), low signal for water
T2 Weighted Images Low signal for fat, low signal for contrast substances, high signal for water
Fluid Attenuated Inversion Recovery Similar to T1 weighted images
Proton Density High signal for fat but lower than in T1, intermediate signal for water but lower than T2
Scanner Types Open, closed
Contraindications Metal implants, pregnancy, allergies to contrast substances, kidney disease
Advantages Safe (no ionizing radiation), excellent ability for soft tissue differentiation, multiplanar imaging, image quality not degraded by bone or air 

Since it is clear that an MRI image is made after interaction between a specific tissue and an MRI machine that uses some kind of physical mechanisms, let's define and explain both aspects of that interaction:

  • What tissue properties are relevant?
  • What is the MRI technical background?

When it comes to the tissue properties, it is all about protons. It is known that protons behave like magnet bars, which means they have one positive and one negative pole, and that makes them responsive to external magnetic fields. And since the human body consists mostly of water and fat molecules, that gives it a huge amount of hydrogen (H+) as a source of protons that is needed for interaction with specific radio-waves of the MRI scanner. So, in this manner of speaking, our body composition actually makes the MRI capable of mapping the location of water and fat in the body.

To fully understand the MRI technical background, let's clear up few more things that are important about protons. Each proton spins around its axis, like a ballerina doing a pirouette. While it spins, it constantly changes the ''phase''.

Behaviour of a 'relaxed' proton not exposed to a magnetic field

Proton spinning around its axis

When hydrogen protons are exposed to a strong magnetic field, such as the one of the MRI scanner, most of them will align with that field.

Behaviour of an excited proton in a MRI scanner

Proton aligns with strong magnetic fields


Afterward, the MRI hits protons with a radio wave pulse that gives them the energy to start rotating in the clockwise direction until full 180 degree rotation, when they realign with the magnetic field but in the opposite direction. 

Proton inside a MRI scanner that is turned on

Proton rotates and realigns with a magnetic field in the opposite direction

Since this radio wave is transmitting energy to protons (excites them), once it is turned off, protons relax and realign with the external magnetic field once again, releasing electromagnetic energy along the way. 

Proton inside an MRI scanner that is turned off

When a MRI scanner is turned off, protons release electromagnetic energy

The density of protons is one of the factors that defines the contrast and illumination of the final image. The more protons one specific tissue has, the final image will be lighter, and tissues with less protons will give darker image. That is the key of forming contrast resolution of a final image so each tissue can be differentiated based on the number of protons it has.

Besides the density of the protons, a couple of more factors contribute to forming of the final MRI image and they are related to the aforementioned relaxation of protons. Relaxation consists of two processes, called T1 relaxation time and T2 relaxation time. 

  • T1 relaxation time is the time that is needed for 63% of the protons to realign with the magnetic field once the radio wave pulse is turned off. This time is specific for every tissue.
  • T2 relaxation time is the time that is needed for 37% of the protons to stop spinning synchronously after turning off the radio wave. It is also tissue-specific.  

So, MRI is capable to detect the relaxation energy and differentiates the tissues based on how quickly they release that energy after the radio wave pulse is turned off. Combination of getting the image in T1 and T2 time gives a complete overview about the density of different tissues. 

After MRI builds a map of the tissue types of the scanned area, a computer that is connected to the scanner integrates all of the information using specific mathematical formula, and finally produces 2D and 3D images of the tissue.  After comparing the properties of emitted signals from tissue that is filmed to the values of the normal tissue, it is easier to conclude if those tissues are undergoing some pathological process.

What are the types of MRI?

An MRI sequence is a particular setting of radiofrequency pulses and gradients, resulting in particular image appearance. The most common MRI sequences are T1-weighted, T2-weighted, Fluid Attenuated Inversion Recovery (FLAIR) and Proton Density weighted image (PD). 

To fully understand the sequences, let’s define a couple of terms used in radiology:

  • Repetition Time (TR) is the amount of time between successive pulse sequences applied to the same slice of tissue. 
  • Time to Echo (TE) is the time between the delivery of radio wave pulse to the tissue and the receipt of its echo signal. 

Combining different values of the Repetition Time and Time to Echo defines the upper mentioned MRI sequences. So, in this manner of speaking, we can state the following:

  • T1 weighted images are produced by using short TR and short TE, as well. Simply speaking, this modality measures how quickly the tissue becomes magnetized. Therefore, the contrast and the brightness of the image are determined by T1 properties of the tissue, which defines its main clinical distinctions:
    • High signal for fat
    • High signals for paramagnetic substances, such as MRI contrast agents. The contrast agent commonly used in T1-weighted images is Gadolinium. It is a non-toxic agent that appears very bright on T1-weighted images. For that reason, using T1-weighted imaging that is enhanced with Gadolinium is very useful in looking at vascular structures and breakdown in blood-brain barrier.
    • Lower signal for the content consisted mainly of water, such as edema, tumor, hemorrhage.

T1 MRI through the wrist at the level of the extensor carpi ulnaris tendon

T1 MRI through the wrist at the level of the extensor carpi ulnaris tendon

  • T2 weighted images are produced by using longer TR and TE, and contrast and brightness of the image depend on T2 properties of the tissue. So basically, this modality measures how quickly the tissue loses its magnetization, so when it’s compared to T1 weighted images, it has the opposite clinical distinctions:
    • High signal for more water content, which enables this sequence to visualize edema, tumor, infarction, infection, and inflammation.
    • Lower signal for fat
    • Lower signal for paramagnetic substances (MRI contrast agents).

T2 MRI through the lower pons

T2 MRI through the lower pons

In general, T1 and T2-weighted images can easily be differentiated by the look on the cerebrospinal fluid. On T1-weighted images, cerebrospinal fluid is dark, while on T2-weighted images is bright.

  • Fluid Attenuated Inversion Recovery (FLAIR) is the third commonly used modality. It is similar to T2-weighted sequence, except that TR and TE are even longer. It has significant ability to selectively suppress, or “null”, the signals from any given substance, in this case fluid, based on its T1-value. So basically, on FLAIR images cerebrospinal fluid appears dark, which makes this sequence very useful when it comes to neuroimaging. The clinicians use it to get images of the following lesions:
    • Lacunar infarctions
    • Multiple Sclerosis plaques
    • Subarachnoid hemorrhage
    • Meningitis
  • Proton density (PD) weighted image is the sequence often used for the visualization of the brain and the joints. In order to get quality PD weighted image, T1 and T2 sequences must be turned off. This modality visualizes the number of protons per volume, witch is actually the proton density as the name says for itself. Because of this, tissues with high proton density have high signal intensity, whereas the tissues with less protons have low signal intensity.
    • Fat has high signal intensity, but not higher than in T1 sequence
    • Fluid has intermediate intensity, lower than in T2 sequence

For this reasons, PD sequence is very useful within the following clinical procedures:

  • Injuries of the knee meniscus
  • Evaluation of the gray and white matter pathology
    • Gray matter has higher signal intensity than the white matter
    • The CSF has intermediate signal intensity that makes it easier to spot the contrast between the CSF and the tissue with the undergoing pathological process

PD MRI through the proximal shaft of the humerus

PD MRI through the proximal shaft of the humerus

Types of MRI scanners

When it is about physical properties of a scanner, we can talk about closed or open MRI. A regular MRI scanner, or closed MRI, is a large tube surrounded by a magnet. The patient is placed on the sliding table and then slid into the tube.

For claustrophobic or overweight individuals, more convenient type of scanner is an open MRI, but it produces images of a slightly less quality than the closed variant.

MRI scanner

MRI scanner


MRI has a wide range of indications when it comes to medical diagnosis. Generally speaking, it is the method of choice when the staging of the majority of cancers (prostate, breast, lung etc) is required. 

To be more specific, let's list the usage of MRI by organ or system:

  • Neuroimaging
    • Posterior fossa
    • Demyelinating diseases
    • Dementia
    • Cerebrovascular disease
    • Infectious disease
    • Epilepsy

MRI of a brain tumour

MRI of a brain tumour

  • Cardiovascular 
    • Myocardial ischemia
    • Cardiomyopathies
    • Myocarditis
    • Iron overload
    • Vascular diseases
    • Congenital heart disease
  • Musculoskeletal 
    • Spinal imaging
    • Assessment of joint disease
    • Soft tissue tumors
  • Liver and gastrointestinal
  • Angiography 
    • Stenosis
    • Aneurysms


As much as being familiar with indications for MRI, knowing the contraindications can literally save someone's life. Here is the must-know list:

  • People with metal implants inside their body, which include clips for treating brain aneurysms, pacemakers and cardiac defibrillators, cochlear implants and stents. This is the one only absolute contraindication for the MRI usage. 

The rest of the contraindications are relative and they refer to the contrast agents and not the MRI itself, so the MRI can be used as the method of diagnostics but without using the contrast agents. These are:

  • Pregnant women must not use the contrast agents since the usage is associated with the increased risk of the rheumatological and inflammatory conditions, as well as stillbirth and neonatal death. However, MRI without contrast is perfectly safe for pregnant women.
  • Allergic people that are sensitive to contrast agents may develop allergic reactions that wide in range from simple rash to severe anaphylactic reaction.
  • Kidney diseases may cause the excretion of contrast to be slower, or the contrast itself can contribute to the existent kidney disease to get worse.

Advantages over other techniques?

Advantages over other imaging modalities are numerous. MRI is mostly compared to CT, ultrasound and PET scan.

First of all, unlike the ultrasound, it can produce images through the entire section of the body while the presence of the bone or air will not degrade the quality of the image. MRI spectroscopy provides important clinical benefits through the in vivo characterization of chemical composition and metabolic activity.

But since MRI is mostly compared to CT, let’s be more specific about that.

  • First of all, MRI uses no ionizing radiation that could potentially harm the human body, while CT uses certain doses of ionizing X-rays. 
  • MRI has the supreme ability of soft tissue differentiation, and therefore all of the pathological processes that involve soft tissues are indicated to be examined by MRI. On the other hand, CT is excellent for bone examination, but requests contrast agents if used for soft tissue imaging, a thing that is not mandatory while using MRI. 
  • Furthermore, in comparing to CT that only takes up to 10 minutes for complete examination, MRI can be very time consuming, because it can take from 15 minutes up to 2 hours depending on the part of the body that is being scanned. 
  • When it’s about comfort, anxiety caused by the narrow tube of the MRI was a strong disadvantage in comparing to CT, but since nowadays open MRI machines are being used, that kind of problem soon will be history. 
  • And last, but certainly not least, MRI is able to image in multiple planes, including sagittal, coronal, axial, and various obliquities, although reconstruction of axial data now allows CT to provide multiplanar imaging as well.


MRI is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body in both health and disease. Because it’s mostly non-invasive, it gives a full image of a patient’s inner state to the clinician without performing complex procedures, and because it utilizes no ionizing radiation, it guarantees safety to the patient.

The capability of understanding how MRI works is very important for future clinicians. Here’s why:

  • With creating images by distinguishing between the nuclear magnetic properties of various tissues, MRI has the supreme capability of very precise tissue differentiation.
  • High resolution images are a very powerful tool for observing the anatomy of the body, in the process of diagnostics in radiology, and in research as well.
  • MRI has numerous advantages over other imaging techniques.
  • The technique is indicated as a diagnostic method in a very wide spectrum of diseases.

MRI is the most commonly performed diagnostic test after the CT and X-rays, so mastering your knowledge in each field of that radiological triad is ‘a must’ that will benefit your studying process and make your life as a future clinician a lot easier.

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Article, Review, Layout:

  • Jana Vaskovic
  • Dimitrios Mytilinaios
  • Adrian Rad


© Unless stated otherwise, all content, including illustrations are exclusive property of Kenhub GmbH, and are protected by German and international copyright laws. All rights reserved.

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