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MRI sequences (basic)

An MRI sequence is a number of radiofrequency pulses and gradients that result in a set of images with particular appearance. This article presents a simplified approach to recognizing and thinking about common MRI sequences, but does not concern itself with the particulars of each sequences.

For a more complete and accurate discussion please refer to MRI pulse sequences.


The simplest way to think about the multitude of sequences available on modern scanners is to divide them according to the dominant influence on the appearance of tissues. This leads to a division of all sequences into proton density (PD) weighted, T1 weighted, T2 weighted, diffusion weighted, flow sensitive and 'miscellaneous'. A number of 'optional add-ons' can also be considered, such as fat or fluid attenuation, or contrast enhanced. This leads to a broad categorisation as follows:

  • T1
    • gadolinium enhanced
    • fat suppressed
  • T2
    • fat suppressed
    • fluid attenuated
    • susceptibility sensitive
  • proton density
    • fat suppressed
  • diffusion weighted
  • flow sensitive
    • MR angiography
    • MR venography
    • CSF flow studies
  • miscellaneous
    • MR cholangiopancreatography (MRCP)
      • a special T2-weighted sequence
    • MR spectroscopy
    • MR perfusion
    • functional MRI
    • tractography



When describing most MRI sequences we refer to the shade of grey of tissues or fluid with the word intensity, leading to the following absolute terms:

  • high signal intensity = white
  • intermediate signal intensity = grey
  • low signal intensity = black

Often we refer to the appearance by relative terms:

  • hyperintense = brighter than the thing we are comparing it to
  • isointense = same brightness as the thing we are comparing it to
  • hypointense = darker than the thing we are comparing it to

Annoyingly these relative terms are used without reference to the tissue being used as the comparison. In some instances this does not lead to any problems; for example, a hyperintense lesion in the middle of the liver is clearly hyperintense compared to the surrounding liver parenchyma. In many other situations however use of relative terms leads to potential confusion. Imagine a lesion within the ventricles of the brain described as "hypointense". Does this denote a lesion darker than CSF or than the adjacent brain?

As such it is preferable to either use absolute terminology or, if using relative terms, to acknowledge the comparison tissue e.g. "the lesion is hyperintense to the adjacent spleen".

NB: the word density is for CT, and there are few better ways to show yourself as an MRI noob than by making this mistake.


When describing diffusion weighted sequences, we also use the term intensity but additionally we use the words restricted diffusion and facilitated diffusion to denote whether water can move around less easily (restricted) or more easily (facilitated) than expected for that tissue. Again many use these words as if they are absolute terms and this leads to confusion (more on this issue here).

T1 weighted sequences

T1 weighted sequences are part of almost all MRI protocols and are best thought of as the most 'anatomical' of images, resulting in images that most closely approximate the appearances of tissues macroscopically, although even this is a gross simplification.

The dominant signal intensities of different tissues are:

  • fluid (e.g. urine, CSF): low signal intensity (black)
  • muscle: intermediate signal intensity (grey)
  • fat: high signal intensity (white)
  • brain
    • grey matter: intermediate signal intensity (grey)
    • white matter: hyperintense compared to grey matter (white-ish)

Read more about T1 weighted sequences.

Contrast enhanced

The most commonly used contrast agents in MRI are gadolinium based. At the concentrations used, these agents have the effect or causing T1 signal to be increased (this is sometimes confusingly referred to as T1 shortening). The contrast is injected intravenously (typically 5-15 mL) and scans are obtained a few minutes after administration. Pathological tissues (tumors, areas of inflammation / infection) will demonstrate accumulation of contrast (mostly due to leaky blood vessels) and therefore appear as brighter than surrounding tissue. Often post contrast T1 sequences are also fat suppressed (see below) to make this easier to appreciate.

Fat suppression

Fat suppression (or attenuation or saturated) is a tweak performed on many T1 weighted sequences, to suppress the bright signal from fat. This is performed most commonly in two scenarios:

Firstly, and most commonly, after the administration of gadolinium contrast. This has the advantage of making enhancing tissue easier to appreciate.

Secondly, if you think that some particular tissue is fatty and want to prove it, showing that it becomes dark on fat suppressed sequences is handy.

Read more about fat suppressed sequences.

T2 weighted sequences

T2 weighted sequences are part of almost all MRI protocols. Without modification the dominant signal intensities of different tissues are:

  • fluid (e.g. urine, CSF): high signal intensity (white)
  • muscle: intermediate signal intensity (grey)
  • fat: high signal intensity (white)
  • brain
    • grey matter: intermediate signal intensity (grey)
    • white matter: hypointense compared to grey matter (dark-ish)

Read more about T2 weighted sequences.

Fat suppressed

In many instances one wants to detect edema in soft tissues which often have significant components of fat. As such suppressing the signal from fat allows fluid, which is of high signal, to stand out. This can be achieved in a number of ways (e.g. chemical fat saturation or STIR) but the end result is the same.

Read more about fat suppressed sequences.

Fluid attenuated

Similarly in the brain, we often want to detect parenchymal edema without the glaring high signal from CSF. To do this we suppress CSF. This sequence is called FLAIR. Importantly, at first glance FLAIR images appear similar to T1 (CSF is dark). The best way to tell the two apart is to look at the grey-white matter. T1 sequences will have grey matter being darker than white matter. T2 weighted sequences, whether fluid attenuated or not, will have white matter being darker than grey matter.

Read more about FLAIR sequence.

Susceptibility sensitive sequences

Being able to detect blood products or calcium is important in many pathological processes. MRI offers a number of techniques that are sensitive to these sort of compounds. Generally these sequences exploit what is referred to as T2* (T2 star) which is highly sensitive to small perturbations in the local magnetic field. The most sensitive of these sequences is known as susceptibility weighted imaging (SWI) and is also able to distinguish calcium from blood.

Read more about susceptibility weighted imaging (SWI).

PD weighted sequences

Given that nuclear magnetic resonance of protons (hydrogen ions) forms the major basis of MRI, it is not surprising that signal can be weighted to reflect the actual density of protons; an intermediate sequence sharing some features of both T1 and T2.

Proton density images were extensively used for brain imaging, however they have largely been replaced by FLAIR. PD however continues to offer excellent signal distinction between fluid, hyaline cartilage and fibrocartilage makes this sequence ideal in the assessment of joints.  

The dominant signal intensities of different tissues are:

  • fluid (e.g. joint fluid, CSF): high signal intensity (white)
  • muscle: intermediate signal intensity (grey)
  • fat: high signal intensity (white)
  • hyaline cartilage: intermediate signal intensity (grey)
  • fibrocartilage: low signal intensity (black)

Diffusion weighted sequences

Diffusion weighted imaging assess the ease with which water molecules move around within a tissue (mostly representing fluid within the extracellular space) and give insights into cellularity (e.g. tumors), cell swelling (e.g. ischemia) and edema.

The dominant signal intensities of different tissues are:

  • fluid (e.g. urine, CSF): no restriction to diffusion
  • soft tissues (muscle, solid organs, brain): intermediate diffusion
  • fat: little signal due to paucity of water

Typically you will find three sets of images when diffusion weighted imaging is performed: DWI, ADC and B=0 images.


When we say "DWI" we usually are referring to what is better terms an isotropic T2 weighted map as it represents the combination of actual diffusion values and T2 signal.

It is a relatively low resolution image with the following appearance:

  • grey matter: intermediate signal intensity (grey)
  • white matter: slightly hypointense compared to grey matter
  • CSF: low signal (black)
  • fat: little signal due to paucity of water
  • other soft tissues: intermediate signal intensity (grey)

Acute pathology (ischemic stroke, cellular tumor, pus) usually appears as increased signal denoting restricted diffusion. However (and importantly) because there is a component of the image derived from T2 signal some tissues that are bright on T2 will appear bright on DWI images without there being and abnormal restricted diffusion. This phenomenon is known as T2 shine through.


Apparent diffusion coefficient maps (ADC) are images representing the actual diffusion values of the tissue without T2 effects. They are therefore much more useful, and objective measures of diffusion values can be obtained, however they are much less pretty to look at. They appear basically as grayscale inverted DWI images.

They are relatively low resolution image the following appearance:

  • grey matter: intermediate signal intensity (grey)
  • white matter: slightly hyperintense compared to grey matter
  • CSF: high signal (white)
  • fat: little signal due to paucity of water
  • other soft tissues: intermediate signal intensity (grey)

Acute pathology (ischemic stroke, cellular tumor, pus) usually appears as decreased signal denoting restricted diffusion.


If you see these, do not worry. They are only used to calculate ADC values. They are essentially T2 weighted images with a bit of susceptibility effects.

Read more about diffusion weighted imaging.

Flow sensitive sequences

One of the great advantages of MRI is its ability to image physiological flow (e.g. blood flow) often without the need for intravenous contrast. This allows for the imaging of arteries, veins and CSF flow.

Read more about MR angiography.

Read more about MR venography.

Read more about CSF flow studies.

Miscellaneous sequences

In addition to the aforementioned sequences, novel applications have been developed over the years, largely beyond the scope of this introductory article.

MR spectroscopy

Different compounds interact with the magnetic field of MRI scanners slightly differently and the amounts of these compounds can be detected in a quantifiable way in a prescribed region of tissue. These can be used to help characterize the tissue to aid in diagnosis or grading of tumors.

Read more about MR spectroscopy.

MR perfusion

The amount of blood flowing into tissue can also be detected and relatively quantified, generating values such as cerebral blood volume, cerebral blood flow and mean transit time. These values are useful in a number of clinical scenarios, including defining the ischemic penumbra in ischemic stroke, or assessing histological grade of certain tumors, or distinguishing radionecrosis from tumor progression.

Read more about MR perfusion.

Functional MRI

The brain controls its blood flow very tightly and locally. Active tissue demonstrates elevated blood flow and this can in turn be detected.

Read more about functional MRI.


The structure of tissue (e.g. axons tightly packed together) influences how easily diffusion of water occurs various directions. This can be detected and the direction of white matter tracts can be implied.

Read more about tractography.

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