MRI sequences (overview) An 

MRI sequence is a number of radiofrequency pulses

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

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

Overview 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 enhancement. This leads to a broad
categorization as follows:

 T1 weighted (T1W)
o gadolinium enhanced
o fat suppressed
 T2 weighted (T2W)
o fat suppressed
o fluid attenuated
o susceptibility sensitive
 proton density (PD)
o fat suppressed
 diffusion weighted
 flow sensitive
o MR angiography (MRA)
o MR venography (MRV)
o CSF flow studies
 miscellaneous
o MR cholangiopancreatography (MRCP)
 a special T2-weighted sequence
o SPACE sequence
o MR spectroscopy (MRS)
o MR perfusion
o functional MRI
o tractography

Terminology
Intensity 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.

Diffusion When describing diffusion weighted sequences, we also use the term intensity but
additionally we use the terms "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 (T1W) sequences are part of almost all MRI
protocols and are best thought of as the most 'anatomical' of images (historically the T1W sequence
was known as the anatomical sequence), 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
o grey matter: intermediate signal intensity (grey)
o white matter: hyperintense compared to grey matter (white-ish)

Contrast enhanced The most commonly used contrast agents in MRI are gadolinium based.
At the concentrations used, these agents have the effect of 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 saturation) 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.

T2 weighted sequences T2 weighted (T2W) 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
o grey matter: intermediate signal intensity (grey)
o white matter: hypointense compared to grey matter (dark-ish)

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.

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.

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.

Proton density 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, which 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 gives insight 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.

DWI When we say "DWI" we usually are referring to what is in 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 an abnormal restricted diffusion. This phenomenon is known as T2 shine through.

ADC 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 images with the following appearances:

 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.

B=0 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.
Flow sensitive sequences One of the great advantages of MRI is its ability to image
physiological flow of fluids (e.g. blood flow) often without the need for intravenous contrast. This
allows for the imaging of arteries, veins and CSF flow..

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.

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, assessing histological grade of certain tumors, or distinguishing
radionecrosis from tumor progression.

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

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