Musculoskeletal MRI Pulse

Sequences: A Review for Residents

and Fellows
Stephanie Jo, MD, PhD, Steffen Sammet, MD, PhD,
Stephen Thomas, MD, G. Scott Stacy, MD
 Author affiliations:
From the Department of Radiology, University of Pennsylvania, Philadelphia, Pa (S.J.);
and Department of Radiology, University of Chicago, Chicago, Ill (S.S., S.T., G.S.S.). 

Address correspondence to S.J: 

Penn University City, 3737 Market St Mailbox 4,
Philadelphia, PA 19104S (email: [email protected]).

This material was partly presented as an electronic exhibit

at the 2018 RSNA  Annual Meeting (ID 18004613).

All authors have disclosed no relevant relationships.

 Abbreviations
2D = two dimensional, 3D = three dimensional, ABER = abduction –
external rotation, ADC = apparent diffusion coefficient, CHESS =
chemical shift selective fat suppression, DWI = diffusion weighted
imaging, EPI = echo planar imaging, ETL = echo train length, FABS =
flexion, abduction and supination, FSE = Fast Spin Echo, Gd =
Gadolinium, GRE = gradient echo, i.v. = intravenous, MAA = magic
angle artifact, MR = magnetic resonance, MRI = magnetic resonance
imaging, MSK = musculoskeletal, PD = proton density, RF =
radiofrequency, SE = spin echo, SNR = signal to noise ratio, STIR =
short-T1 inversion recovery, TE = echo time, TI = inversion time, TR =
repetition time, TSE = Turbo Spin Echo
 Learning Objectives
At the end of this presentation, the viewer should be able to:
1. Understand the basic MR physics principles used for creation of
common musculoskeletal MRI pulse sequences
2. Describe the fundamental differences between spin-echo and
gradient-echo pulse sequences
3. Describe the application and appropriate selection of various pulse
sequences used for musculoskeletal MR imaging
4. Describe various methods of fat suppression
5. Understand the basics of motion, susceptibility, and magic angle
artifacts
 Introduction
• A comprehensive musculoskeletal
(MSK) MRI protocol generally
requires different types of pulse
sequences to optimally manipulate
contrast of tissues and thereby
assess different tissue types,
including bone and bone marrow,
cartilage, synovium, muscle,
ligaments and tendons
• Following a brief review of
fundamental MR physics, we will
provide an overview of the pulse
sequences commonly used in
MSK MR imaging Multiple coronal images from wrist MR arthrogram. Fat-suppressed T 1-weighted
image (top left), fat-suppressed proton-density-weighted image (top right), non-fat-
suppressed T1-weighted image (bottom left), 3D T1-FFE (spoiled gradient echo) with
water excitation (bottom right).
 Basic MRI Physics – Simplified
• MRI involves absorption and emission

+
~
of energy by nuclei at a specific
resonance (Larmor) frequency
• Signals used to generate images arise
H
from hydrogen nuclei (protons) mainly
in water and fat molecules The hydrogen proton (top), “spins” around its axis, resulting
in a magnetic moment. Proton spins behave similar to “bar

• Each proton spins about an axis, magnets” with a north and a south pole.

resulting in a magnetic moment Outside the magnetic field of an MRI unit, the protons in the
human body spin with their axes randomly aligned (bottom).

• The magnetic moments behave like

bar magnets, which spin in the body
with their axes randomly aligned when
no external magnetic field is present
 Basic MRI Physics – Simplified
• When a patient is placed in the MR
magnet, the protons align with the
external magnetic field (Bo), and
generate “longitudinal magnetization” Patient
• Each nucleus precesses around its axis placed in When the human body is placed in
the MRI scanner, the protons align
external with the magnetic field B0, creating a
• The frequency of precession is magnetic longitudinal magnetization oriented
along the axis of the scanner. The
defined by the Larmor equation: field (MRI protons precess around their axes,
and are “primed” to absorb energy.
magnet)
ωo = Bo ・ γ

where ωo is the precessional frequency,

Bo the external magnetic field, and γ the
gyromagnetic ratio, a constant for any given Longitudinal
nucleus magnetization
Vector Mo
 Basic MRI Physics – Simplified z-axis

longitudinal
• A radiofrequency (RF) pulsed is magnetization

applied, which excites the protons

and flips their magnetization vector
x-axis
a certain angle away from the
longitudinal axis y-ax
is

• Fundamentally, there are two basic RF pulse

types of pulse sequences which
are in part characterized by how
the magnetization vector is flipped: A radiofrequency pulse deflects
• Spin echo (SE) pulse the magnetization vector by a
pre-determined flip angle away
sequences, and from the longitudinal axis. In this
example, the vector is flipped

• Gradient echo (GRE) pulse 90o into the xy-plane (i.e.

transverse plane).

sequences x-axis transverse

axis magnetization
y-
 Spin Echo (SE) Pulse Sequences
• Spin echo pulse sequences begin with a 90o RF pulse on
excitation pulse that flips the net magnetization
vector into the transverse plane resulting in
transverse
“transverse magnetization,” which is necessary x-axis
xis magnetization
a
for signal detection by a radiofrequency coil y-

• When the RF pulse is turned off, two relaxation

processes occur which are associated with RF pulse off
reduction of transverse magnetization:
x-axis
• Transverse relaxation T2 xis
y- a
• Longitudinal relaxation T1
• How quickly transverse and longitudinal
relaxation occur depend on intrinsic tissue
properties and magnetic field characteristics x-axis

axis
y-
 Spin Echo (SE) Pulse Sequences
y
• Transverse relaxation or T2 relaxation
refers to the tendency of proton spins
to dephase (i.e., become incoherent, x Time
pointing in different directions in the
transverse plane) After the 90o excitation pulse is turned off,
the proton spins in the transverse (xy) plane
• T2 relaxation decreases the Signal begin to dephase, which reduces the
induced signal in the RF-coil. The rates of
transverse magnetization vector and dephasing are different for different tissues,
which can be depicted on the T 2 relaxation
consequently the MR signal used for curves (below). In this example, the T 2 of
tissue A (e.g., fat) is shorter than the T 2 of
image production tissue B (e.g., fluid).
37%
• T2 is defined as the time by which tissue B

transverse magnetization is T2 T2
tissue A

decreased to 37% of its original value Time

tissue A tissue B
 Spin Echo (SE) Pulse Sequences
90o RF pulse turned off  A 180o pulse causes the proton Protons start to dephase
proton spins start to dephase spins to rephase and to produce a again
so-called spin echo
y

1800 refocusing
900
RF pulse
excitation Time
RF pulse Spin Echo:
signal/emitted energy can be
detected by receiver coil

• In a spin echo sequence, a 180o refocusing pulse is applied at a timepoint

TE/2 to rephase the protons spins. At a timepoint TE (echo time), the
protons realign, and a so called spin echo can be recorded for image
production. TE is the time between the application of the 90o excitation
pulse and the peak of the spin echo.
 Spin Echo (SE) Pulse Sequences
• Longitudinal relaxation or T1 relaxation
z
refers to the tendency of proton spins to magnetization
longitudinal
re-align along the longitudinal axis after vector
magnetization

termination of the RF excitation pulse xy

• T1 is defined as the time by which When the 90o RF pulse is discontinued, the protons
begin to realign along the longitudinal axis at different

longitudinal magnetization reaches 63% of rates depending on the tissue, which can be depicted
on a T1 curve (below). In this example, the T 1 of tissue

its original value Signal

A (e.g., fat) is shorter than the T 1 of tissue B (e.g., fluid).

• The next 90o RF excitation pulse is tissue A

applied at a time point TR (repetition time) 63%

tissue B

after the initial 90o RF excitation pulse,

and the spin echo sequence is repeated
• TR is responsible in large part for the
T1 T1
duration of a pulse sequence Time
tissue A tissue B
 Spin Echo (SE) Pulse Sequences
T1-weighted coronal MR image of
• Choosing a relatively short TR pelvis (left) shows diffusely
abnormal low signal intensity of
(<800 ms) and short TE will result bone marrow in this 30-year-old
patient with sickle cell disease.
in a T1-weighted image, on which Bone marrow on T2-weighted STIR
image (right) shows no appreciable
fluid is dark and fat is bright abnormality within fat-suppressed
marrow.

• T1-weighted images are useful in T1-weighted transverse MR image of thighs in patient

MSK imaging for delineating * with dermatomyositis shows fatty atrophy of

* musculature, particularly vastus lateralis bilaterally
(*), as well as foci of low-signal intensity calcification
anatomic detail, confirming (arrows).

replacement of normal fatty bone

marrow (e.g., by infection or
neoplasm), determining the T1-weighted transverse MR image of
thigh shows fatty mass (arrow, left) in
degree of fatty atrophy of muscles, vastus lateralis muscle. Note strand-like
non-adipocytic elements within mass,
and detecting and characterizing which was diagnosed as atypical
lipomatous tumor / well-differentiated
lipomatous lesions liposarcoma on histologic examination.
Mass is less conspicuous on fat-
suppressed T2-weighted image (right).
 Spin Echo (SE) Pulse Sequences
• Choosing a relatively long TE
(>70 ms) and long TR will T2-weighted coronal MR image of
result in a T2-weighted image, manubrium (top) shows
fracture/separation of right
on which fluid is bright costomanubrial junction (arrow) depicted
by high signal intensity between cartilage
and bone (arrow). Injury is not as
• T2-weighted images are apparent on T1-weighted image (bottom).

useful for detection of fluid,

including edema, and
therefore pathologic
processes
T2-weighted transverse MR image
of thoracic spine (left) in young
patient with back pain shows small
osteoid osteoma (arrow) in
transverse process, made more
conspicuous by adjacent edema. CT
image (right) confirms diagnosis.
 Spin Echo (SE) Pulse Sequences
• Although fat has less signal on T2-
weighted images than on T1-
weighted images, it appears
relatively bright; therefore fat-
suppression is often necessary
with T2-weighted images to better
emphasize pathology

T1-weighted transverse MR image of ankle (left) appears very similar to T 2-weighted image
(center) without fat suppression. Small amounts of fluid can be seen on both images, dark
on T1-weighted image and bright on T2-weighted image (arrows). With fat suppression
(right) small amounts of fluid become more conspicuous on T 2-weighted image.
 Spin Echo (SE) Pulse Sequences
• Proton density (PD) weighted images PD-weighted sagittal
MR image of knee
(top) shows tear of
minimize T1 and T2 characteristics of tissues posterior horn of
medial meniscus
by maximizing longitudinal recovery (long TR) contacting tibial
articular surface
and minimizing transverse decay (short TE) (arrow). This tear is
more conspicuous

• Tissues with more protons have higher signal compared with fat-
saturated T2-weighted

intensity; those with fewer protons have lower image (bottom).

Although PD-weighted
signal sequences are
preferred for meniscal
evaluation in most
• PD-weighted images have lower tissue practices, T2-weighted
sequences play an
contrast but a higher signal-to-noise ratio important role when
evaluating
compared to T1- or T2-weighted images; this postoperative menisci
by differentiating
allows identification of signal in signal-poor healing from recurrent
tear.
structures, and is often the sequence of
choice for imaging fibrocartilage
 Spin Echo (SE) Pulse Sequences
• Although the TR for PD-weighted * * PD-weighted sagittal MR
image of knee (left) shows

images is relatively long (>1000 joint fluid (*) similar in signal

intensity to fat. Same fluid is

ms), the TE is short (10-30 ms), appreciably brighter than fat

on T2-weighted image (right).
and fluid on PD weighted images
without fat-suppression is not as
bright as fluid on T2-weighted
images
• Fat-suppression is often used with
PD-weighted images to increase
the conspicuity of fluid

Fat-saturated PD-weighted sagittal MR image of knee (left) with high-signal-intensity fluid nicely
depicts tear of posterior horn of medial meniscus (arrow). On corresponding T 1-weighted image
(right), low-signal-intensity fluid in joint is difficult to distinguish from meniscus, giving appearance
of intact inner half of posterior horn.
 Spin Echo (SE) Pulse Sequences
• “Intermediate-weighted” pulse
sequences have TE values in the
range of 30-60 ms (between true * *

PD- and T2-weighted sequences)

and TR values between 3000 ms
and 4000 ms
• These fluid-sensitive sequences
have become popular for
assessment of articular cartilage Intermediate-weighted sagittal MR image of knee (left) shows relatively increased signal intensity of
joint fluid (*) compared with fluid on proton-density-weighted image (right). Signal intensity changes
related to cartilage degeneration (arrow) are more evident on intermediate-weighted image.
 Spin Echo (SE) Pulse Sequences
• Intermediate-weighted pulse
sequences provide higher signal
intensity of cartilage than T2-
weighted sequences (allowing
better differentiation between
cartilage and bone), and provide
higher intrinsic contrast of articular
cartilage.
• They are also less prone to magic
angle artifacts than true PD-
weighted sequences; however,
PD-weighted sequences are still Intermediate-weighted sagittal MR image of knee (top) shows early delamination

preferred by many radiologists for (arrow) of cartilage along lateral femoral condyle. Inset (top right) shows layers depicted
as blue (cartilage), red (area of delamination) and yellow (subchondral bone plate).

meniscal evaluation Intermediate-weighted image obtained two weeks later (bottom) shows complete
detachment of cartilage (arrow).
 Spin Echo (SE) Pulse Sequences
T1 T2 PD
TR Short Long Long
• Conventional (“single-echo”) SE
TE Short Long Short
pulse sequences, which use a
single 180o refocusing pulse, are TR
lengthy and therefore seldomly RF pulse
used in today’s MSK MRI 90o 180o
½ TE for PD
180o

protocols ½ TE for T2

• Conventional “dual-echo” SE Echo

Generates PD image
sequences are occasionally used TE for PD

with modern MSK MRI protocols, TE for T2 Generates T2 image

PD-weighted (left) and T2-weighted (right)
applying two 180o refocusing coronal oblique MR images of the ankle

pulses following a single excitation were acquired during same acquisition

(TR = 5400 ms) using dual-echo technique

pulse to produce PD- (short TE) (TEs of 12 ms and 110 ms, respectively).

and T2- (long TE) weighted images

in one acquisition (with a long TR)
 Spin Echo (SE) Pulse Sequences
Conventional spin echo
• Most modern MSK MRI protocols TR
make use of echo-train SE (Fast
Spin Echo [FSE] or Turbo Spin RF pulse
90o 180o 90o
Echo [TSE]) sequences, with
TE
multiple 180o refocusing pulses per
single TR (as well as different Echo
phase-encoding gradients applied
Echo-train (fast, turbo) spin echo
with each pulse) resulting in TR
acquisition of more data per TR
and decreased scan time RF pulse
• The number of echoes is 90o 180o 180o 180o 90o

referred to as the “echo train TE

length” (ETL) Echo
 Spin Echo (SE) Pulse Sequences
• In addition to reduced acquisition
time, fast/turbo spin echo pulse
sequences result in reduced
* *
magnetic susceptibility artifacts
• The disadvantages of fast/turbo
spin echo include: Fast spin echo T2-weighted sagittal MR image (left) shows fluid along semimembranosus tendon (*) of
similar signal intensity to adjacent fat. Corresponding conventional spin echo T 2-weighted image
• Lower tissue contrast (right) shows greater signal intensity of fluid (*) relative to adjacent fat.

• Fat signal ~ fluid

• Edge blurring Fast recovery echo-train SE sequences are a modification
of fast/turbo SE sequences, using a -90o “flip-back” pulse
• Motion sensitivity (although
at the end of the echo train to quickly refocus
patients may be less likely to magnetization back into the longitudinal axis, thus
move during the relatively short further reducing acquisition time. Examples include
acquisition) FRFSE (GE), DRIVE (Philips) and RESTORE (Siemens).
 Spin Echo (SE) Pulse Sequences
• MSK MRI is dominated by 2D multislice acquisitions;
while these sequences provide excellent signal and
contrast between tissues, the anisotropic voxels
require that multiple planes of data be acquired
separately to minimize partial volume artifacts
• 3D techniques obtain a volume of data in one
acquisition, generating isotropic voxels
• Although 3D techniques require longer acquisition
times than 2D techniques, overall exam time can be
decreased, as thin images can be reformatted in
any plane from the single 3D acquisition
• 3D sequences, however, can suffer from limited Reformatted coronal oblique image from 3D

contrast characteristics, blurring, motion and other intermediate-weighted FSE dataset shows
fabellofibular ligament (short orange arrows) and

artifacts meniscofemoral ligament of Wrisberg (long orange

arrows).
 Spin Echo (SE) Pulse Sequences
• 3D FSE techniques with parallel imaging to
reduce scan time and flip angle modulation to
reduce blurring have made isotropic imaging
with spin echo contrast possible
• Variants of such sequences include CUBE (GE),
VISTA (Philips) and SPACE (Siemens); these
PD/intermediate-weighted images may or may
not be fat-suppressed
• While image quality currently does not quite
match that of 2D FSE sequences, 3D FSE
sequences can be used to aid diagnosis of
cartilage, meniscal and ligament defects, and Reformatted transverse (top) and coronal (bottom) images from 3D
intermediate-weighted FSE dataset demonstrate cartilage

have been touted as superior to 3D gradient- degeneration, from tiny surface defects (thin orange arrow, top) to full-
thickness cartilage loss (thick orange arrow, bottom). While 3D FSE

echo sequences (described later) techniques have not yet replaced standard 2D FSE sequences, they
show great promise for whole-organ evaluation of different joints, and
can depict subchondral bone marrow abnormalities better than
gradient-echo sequences.
 Gradient Echo (GRE) Pulse Sequences
Conventional spin echo sequence
TR
• Gradient Echo (GRE) pulse sequences
differ from SE sequences: RF pulse 90o 180o 90o
• GRE pulse sequences begin with a T2 relaxation curve

excitatory pulse that usually flips the Signal

magnetization vector less than 90o TE
• Gradients, instead of 180o RF pulses,
are used to dephase and rephase
transverse magnetization Gradient echo sequence
TR
• Transverse relaxation is affected by
RF pulse
magnetic field inhomogeneities,
αo (flip angle <90o) αo
yielding to T2*-relaxation (as opposed Gradient rephasing
dephasing T2* relaxation curve (combination of
to T2-relaxation with SE sequences) T2 relaxation and magnetic field
Signal inhomogeneities)

TE
 Gradient Echo (GRE) Pulse Sequences
• The smaller flip angles used in
GRE sequences lead to faster
recovery of longitudinal
magnetization, shorter TR, and
faster acquisition; “new” types of
tissue contrast can also be
obtained Fat-suppressed proton-density-weighted MR image of shoulder (left) shows infiltrative mass (arrow) in
glenohumeral joint containing regions of low signal intensity. Gradient-echo MR image (right) shows
• Since GRE pulse sequences are increased prominence of low-signal intensity regions (“blooming”) resulting from hemosiderin in this
patient with pigmented villonodular synovitis.
not efficient at reducing magnetic
inhomogeneity, susceptibility
artifacts can occur that can
degrade image quality or be used
to detect hemorrhage or
mineralization T1-weighted (left) and T2-STIR (center) coronal MR images of wrist show scaphoid waist
fracture (arrow). Gradient-echo image (right) fails to show fracture due to susceptibility
effects of trabeculae.
 Gradient Echo (GRE) Pulse Sequences
• In addition to “basic” GRE pulse sequences, a large
Gradient echo
number of GRE variants have been developed, many of pulse sequence
which are used in MSK MR imaging variants
• While a comprehensive analysis of these various (simplified)
sequences is beyond the scope of this presentation, on
a basic level, GRE sequences can be categorized
Coherent: Spoiled:
based on whether transverse magnetization is
transverse transverse
preserved (coherent GRE sequences) or disrupted magnetization magnetization
(spoiled GRE sequences) preserved disrupted
• Additional GRE sequences, such as ultra-short TE
imaging, are being investigated as novel methods of
evaluating tissues with short T2-relaxation times such as
tendons, ligaments, menisci and cortical bone
 Gradient Echo (GRE) Pulse Sequences
TR (extremely short)
• With coherent GRE sequences,
transverse magnetization is refocused RF pulse
to contribute to a steady state in which RF2
αo
RF3
αo
RF4
αo
longitudinal and transverse
magnetization is constant from one TR Signal
cycle to the next FID SE FID SE FID
of RF2 of RF1 of RF3 of RF2 of RF4
• Once equilibrium is reached, two types TE – FID
of signals are produced: (postexcitation)

• A postexcitation signal consisting of TEeffective – SE

(preexcitation)
free induction decay (FID) A steady-state of both longitudinal and transverse magnetization is achieved by keeping
• A preexcitation signal consisting of the TR shorter than the T2 relaxation times of the tissue. Since TR is shorter than T 2,
there is not enough time for transverse magnetization to decay completely before the
a spin echo (SE) next RF pulse excitation; therefore, there will be residual transverse magnetization left
over. With coherent steady-state sequences, two types of signals are produced: a
postexcitation signal and a preexcitation signal. The postexcitation signal, consisting of
free induction decay (FID) from the most recent RF pulse, has mixed T 1 and T2*
weighting. The preexcitation signal, resulting from refocusing of residual echo from the
previous RF excitation, is strongly T2-weighted.
 Gradient Echo (GRE) Pulse Sequences
Sequence GE Philips Siemens
• Depending on the signals sampled and used for
image formation, a variety of coherent, steady- Coherent steady-state
sequences with FID
sampling (partially-
GRASS FFE FISP

state sequences can be obtained with different refocused

“postexcitation”)
types of image weighting and applications, Coherent steady-state SSFP T2-FFE PSIF
including: sequences with SE
sampling (partially-

• FID refocusing (postexcitation) refocused

“preexcitation”)

• SE refocusing (preexcitation) Coherent steady-state

sequences with FID
FIESTA Balanced
FFE
True FISP

• FID & SE together (“fully-refocused” or and SE sampled

together (fully-
refocused “balanced”)
“balanced”)
Coherent steady-state MENSA DESS
• FID & SE acquired separately & then sequences with FID &
SE sampled separately,

combined (“double echo”) then combined

(“double echo”)
 Gradient Echo (GRE) Pulse Sequences
2D T2-weighted coherent steady-
state GRE coronal MR image of
infant with hip dysplasia shows
• In general, coherent, steady-state left femoral head directed into
dysplastic acetabulum. Note
sequences are used in MSK imaging in hyperintense fluid in bladder, as
well as contrast in left hip from
situations when bright fluid is desirable recent arthrogram.

• Postexcitation steady-state sequences Examples of 3D coherent steady-state GRE

sequences. 3D fully-refocused “balanced” steady-
have been largely replaced by fully- state sagittal MR image of knee (left) shows fluid-
filled cartilage defect (arrow) of medial femoral
refocused sequences which are less condyle. Double echo steady-state sequence
(bottom) shows fluid-filled cartilage defect (short

sensitive to motion; T2-weighted pre- arrow) of patella and displaced cartilage fragment
(long arrow). Such sequences have advantage of

excitation steady-state sequences have good fluid-to-tissue contrast and have been studied
for their ability to depict articular cartilage, as well

been used for MR myelography and as labral tears during MR arthrography, but are not
ideal for assessing adjacent subchondral bone.

diffusion imaging of the spine

• 3D fully-refocused and double-echo
steady-state sequences have shown
good results in detecting cartilage
lesions within reasonable scan times
 Gradient Echo (GRE) Pulse Sequences
• Spoiled GRE sequences are those in which transverse magnetization is
disrupted (“spoiled”)
• There are different methods of “spoiling,” and the terminology can be
confusing:
• The unqualified term “spoiled” usually refers to “RF-spoiling”; RF-spoiled
sequences are often used to create T1-weighted images, and include
SPGR (GE), T1-FFE (Philips) and FLASH (Siemens)
• “Long TR spoiling” occurs when TR>>T2*, allowing the transverse
magnetization to decay to zero “naturally”; sequences that take
advantage of this method include multiecho T2*-weighted GRE
• “Gradient spoiled” is a term occasionally used to refer to the previously
described steady-state sequences:
• Gradient-spoiled sequences (FID-refocusing): GRASS, FFE, FISP
• Reversed gradient-spoiled echo (echo-refocusing): SSFP, T2-FFE, PSIF
 Gradient Echo (GRE) Pulse Sequences
• RF-spoiled GRE sequences are weighted
based on TR, TE, and flip angle:
• As TR ↓, T1-weighting ↑
• As TE ↑, T2*-weighting ↑
Fat-suppressed T1-weighted spoiled gradient echo transverse MR images of
• As flip angle ↑, T1-weighting ↑ thigh obtained before (left) and after (right) intravenous administration of
gadolinium-chelate show enhancement of septae (arrow) within fatty mass in
• As flip angle ↓, T2*-weighting ↑ vastus lateralis (atypical lipomatous tumor).

• RF-spoiled GRE sequences with large flip

angles are used to acquire fast pre- and
post-contrast T1-weighted images
• Spoiled 3D GRE variants include
FAME/LAVA (GE), THRIVE (Philips) and Spoiled 3D GRE T1-weighted axial image of wrist shows enhancement of
tissues surrounding distal ulna following resection of synovial sarcoma in this
VIBE (Siemens), which can be used for area. Using this rapidly-acquired 3D sequence, time-enhancement curves can
be generated by placing regions of interest on enhancing tissue and
dynamic multiphase imaging comparing curve to that of nearby artery. Curve morphology in this case was
more consistent with post-radiation changes than recurrent tumor, which
was confirmed on follow-up scans.
 Gradient Echo (GRE) Pulse Sequences
Fat-suppressed T1-weighted spoiled
gradient echo sagittal image of knee
shows normally bright articular
• 3D RF-spoiled GRE sequences (typically cartilage. Heterogeneous “blooming”
mass (arrow) in Hoffa’s fat pad
with fat suppression via fat saturation or represents localized intra-articular
tenosynovial giant cell tumor (PVNS).
selective water excitation) have been the
standard for quantitative morphologic
imaging of cartilage, although they suffer Spoiled 3D GRE T1-weighted sagittal

from long imaging times and suboptimal image of ankle shows hyperintense
articular cartilage (long arrow). Cysts

evaluation of surface/internal cartilage in subchondral bone along subtalar

joint are nearly isointense to skeletal

defects, menisci, ligaments and marrow muscle (short arrow).

• These sequences produce high cartilage

signal using low flip angles (12o-30o, with Spoiled 3D coronal MR image of wrist
obtained following intra-articular
TR = 20-30 ms, TE = 7-12 ms) injection of gadolinium-chelate into
radiocarpal joint shows extension of

• Adjacent joint fluid is of low signal, contrast into midcarpal joint through
torn scapholunate ligament (circle).

although cartilage can be nicely outlined Note signal abnormality in distal

radius representing edema from

with intra-articular injection of dilute Gd fracture not readily visualized on this

GRE sequence.
 Gradient Echo (GRE) Pulse Sequences
• Long TR-spoiled sequences in which
multiple gradient echoes are generated
after each RF pulse and combined to
form an image can be used to create T2*- Spoiled T2*-weighted GRE transverse MR image of cervical spine using

weighting; the early echoes provide

multiple combined free induction decays (left) shows better gray/white
matter contrast in cord than T2-weighted spin echo image (right).

increased SNR and the later echoes

Spoiled T2*-weighted GRE transverse
improve contrast MR image of shoulder using multiple
combined free induction decays shows
• Such sequences include MERGE (GE), bright fluid outlining full-thickness tear
of subscapularis tendon (arrow).
M-FFE (Philips) and MEDIC (Siemens)
• They are commonly used for c-spine 3D spoiled T2*-weighted GRE

imaging, showing excellent gray/white coronal MR image of elbow using

multiple combined free induction

matter contrast in the cord, but can have decays shows bright fluid (long
arrow) and articular cartilage

other uses in MSK imaging as well; they (short arrow).

are prone to susceptibility (metal) artifact

 Gradient Echo (GRE) Pulse Sequences
• Protons from fat and protons from • The Larmor frequency
water precess at slightly different difference between fat and
Larmor frequencies water is 220 Hz, equivalent to
• A GRE in-and-opposed-phase a TE difference of 4.4 ms at
sequence (usually spoiled) can 1.5 Tesla.
take advantage of this 0 1.1 2.2 3.3 4.4ms
phenomenon to image fat and
water protons when their 1H nuclei
are spinning in-phase as well as
out-of-phase Water

opposed in phase
Fat
phase
 Gradient Echo (GRE) Pulse Sequences
TE 0 1.1 2.2 3.3 4.4 5.5 6.6ms • With an echo time (TE) at
which the fat and water
signals are in phase, the
1.5T signals add constructively;
Water
when they are out of phase,
the signals cancel
opposed in phase “opposed
Fat
phase phase"

Opposed-phase image needs to be acquired

Signal - fat before the in-phase image because signal losses
due to T2*-effects can confound signal losses due
to fat-water cancellation. An approximate 20%
signal drop off is recommended to distinguish non-
Signal – non-fat neoplastic from neoplastic lesions.
 Gradient Echo (GRE) Pulse Sequences
• With in-and-out-of-phase
imaging, signal is suppressed on
out-of-phase images if both fat
and water protons are present in
the same voxel
• This can be used to detect
microscopic fat in bone and thus
T2-weighted transverse MRI image through
distinguish red marrow from proximal femora (top left) shows heterogeneous

infiltrated marrow bone marrow suggesting possibility of metastatic

disease in this patient with renal cell cancer.
Between in-phase (top right) and out-of-phase
(bottom right) images, there is decrease in bone
marrow signal on out-of-phase image compatible
with benign red marrow reconversion.
 Echo-Planar Imaging (EPI)
• Echo-planar imaging (EPI) is the
fastest MR technique in which an RF αo
entire two-dimensional image can
be acquired with a single excitation Frequency
(“single shot”) or a small number encoding
of excitations (“multi-shot”)
• EPI sequences are extremely fast, Phase
encoding
and therefore often used to
evaluate physiologic processes
(e.g., diffusion) Signal
• They are not frequently used with
routine MSK MR imaging outside Diagram of a Echo Planar Imaging (EPI) sequence. After an RF excitation pulse, an alternating
frequency-encoding gradient is switched simultaneously with a blipped low magnitude phase-

of diffusion-weighted imaging encoding gradient. The collected gradient echoes are sorted in a meander-shape into k-space
allowing acquisition of an entire MR image after a single excitation.
 Diffusion-Weighted Imaging
• Diffusion-weighted imaging (DWI)
evaluates the random motion of water
molecules and allows distinction of
unrestricted diffusion from restricted
diffusion of water protons
• Areas with higher cellularity (e.g., Tissues with lower
cellularity (top) allow for

malignant tumors) restrict the motion of greater mobility of water

molecules (blue arrows)

water, resulting in a decrease in the than tissues with higher

cellularity (bottom)

apparent diffusion coefficient (ADC)

• MRI measures water diffusivity by
applying diffusion sensitizing gradients to
T2-weighted images (either fast GRE or
echo-planar imaging sequences)
 Diffusion-Weighted Imaging
• The DWI MR signal equals the T2 *
Diffusion-weighted MR images with
increasing b-values (top to bottom)
reflecting stronger diffusion weighting
signal intensity minus signal loss in this patient with necrotic malignant

determined by: peripheral nerve sheath tumor. As b-

(stronger diffusion weighting)

value increases, fluid within bladder
(*) as well as central necrotic area
• Free motion of water molecules within tumor (thin arrow) show
decreased signal relative to viable

Increasing b values
• Strength of the applied tumor (thick arrow). The viable
tumor remains hyperintense due to
diffusion weighting, indicated * restricted diffusion on DWI. DW
sequences are often applied in
by its “b-value” conjunction with apparent diffusion
coefficient (ADC) mapping techniques
(not shown); tissues with restricted
• MSK applications include diffusion appear dark on ADC maps,
and tissues with unrestricted
evaluation of bone malignancy and diffusion appear bright.

soft tissue tumors, tumor follow-up *

after therapy, vertebral fractures,
and infection
 Methods of Suppressing Fat Signal
• Fat-suppression is important for improving T2-weighted coronal oblique
MR image of shoulder (top)

visibility of lesions on PD-, T2-, and contrast- of patient with long-

standing inflammatory
arthritis shows joint effusion
enhanced T1-weighted images, for evaluating fat and diffuse loss of articular
cartilage. Addition of fat-
in soft-tissue lesions, and for differentiating high- suppression (bottom)
reveals bone marrow edema
signal-intensity structures seen on both T1- and in humeral head not readily
seen on non-fat-suppressed
T2-weighted images (e.g., methemoglobin) image.

• The main techniques of fat suppression are

• Inversion-based, e.g., Short-T1 Inversion
Recovery (STIR)
• Chemical-shift based, e.g., Chemical Shift
Selective Fat Suppression (CHESS), Dixon
techniques, and water excitation
 Methods of Suppressing Fat Signal
Fat
Water

• Short-T1 Inversion Recovery (STIR) is a 1800 900

variation of spin-echo that takes advantage “preparatory” “excitatory”
pulse pulse
of the different longitudinal relaxation
properties of fat and water (T1fat < T1water) TI
80-150 ms
• An initial 180o pulse inverts the longitudinal Time

magnetization of fat and water protons Cannot generate

transverse
• As the magnetization recovers, a 90o RF Short T1
magnetization

pulse is applied at a time TI (inversion time) Long T1

Can generate
transverse
when the net vector of fat is close to zero magnetization
(i.e., with little/no longitudinal magnetization Longitudinal
of fat) magnetization

• Therefore, the 90o pulse generates no Time interval –

signal from fat, but some signal from water set to T1 of fat
 Methods of Suppressing Fat Signal
• STIR is not as susceptible to magnetic T2-weighted STIR coronal MR
image of knee (left) shows
field heterogeneities as CHESS, and homogeneous fat
suppression despite
can therefore be used with off-center presence of screws in
proximal tibia. Same knee
imaging and in patients with metal scanned with chemical shift
selective technique shows
implants; it can also be used on MRI poor suppression of
subcutaneous and marrow
systems with lower field strength fat.

• However, signal from ANY short T1 Images from patient who

tissue/fluid, including gadolinium, underwent right hip MR
arthrogram with dilute
melanin, proteinaceous material, and gadolinium injected into
joint. On STIR image (left),
blood, can also be suppressed signal from short T1
tissues/fluid is suppressed,

• This technique also tends to be lengthy including fat and intra-

articular gadolinium (arrow).

and results in a relatively low signal-to- On T1-weighted CHESS image

(right), fat is suppressed by
noise ratio frequency specific RF pulse,
and intra-articular
gadolinium remains bright
(arrow).
 Methods of Suppressing Fat Signal
• CHESS (often called “fat saturation”)
z y
takes advantage of the fact that
protons from fat precess at a slightly

Water
lower Larmor frequency than protons x x
in water (“chemical shift”) Fat

Excitation
y
• Using an RF pulse specific for the fat RF pulse
specific for fat “Spoiler” gradient  fat
resonance frequency and a transverse magnetization
subsequent dephasing gradient, the signal is lost

fat signal can be suppressed

• A standard imaging sequence is then z
Standard (e.g. FSE or GRE)
performed, producing images from sequence is performed, and
water protons with minimal net fat contributes minimal
signal because its protons
magnetization from fat protons have dephased Water

x
Fat
y
 Methods of Suppressing Fat Signal
Note: Vendors also offer hybrid fat-suppression
sequences which combine a chemical-shift
selective pulse with inversion delay; these
• The advantages of CHESS include include SPECIAL (GE), SPIR (Philips) and SPAIR
(Philips and Siemens)
its ability to be used with any T1-weighted transverse image through
imaging sequence, and with T1- axilla shows two hyperintense lesions
(thin and thick arrows). With chemical-
shortening contrast agents; it is shift selective fat suppression, anterior
lesion (thin arrow) looses signal,
relatively fast, and yields relatively indicating lipoma. Posterior lesion (thick
arrow) remains hyperintense, indicating
high SNR hematoma.

• However, it is sensitive to
magnetic field inhomogeneities Patient with subcutaneous

(resulting in “incomplete fat shoulder mass (arrow). At edge of

T2-weighted CHESS image (left)
saturation”), and is not as effective there is poor fat suppression due
to magnetic field inhomogeneities,
on low-field MRI scanners; it is not resulting in mass having
appearance of cyst. STIR image
optimal for off-center imaging or (right) is less affected by magnetic
field inhomogeneity; there is
patients with metallic implants uniform fat suppression, revealing
correct diagnosis of lipoma.
 Methods of Suppressing Fat Signal
• Water excitation is based on the
selective excitation of non-fat-
bound protons
• This method of fat suppression is
most commonly used with gradient
echo MSK MR imaging, 3D coronal T1-weighted spoiled gradient echo
particularly cartilage imaging MR image of ankle obtained with water
excitation method of fat suppression. Note
because of its fast imaging time, hyperintense articular cartilage of tibiotalar
joint.
and high signal- and contrast-to-
noise ratios
• Sequences include Spectral
Spatial RF (GE), ProSet (Philips)
and Water Excitation (Siemens)
 Methods of Suppressing Fat Signal
• The Dixon technique of fat suppression is
based on the previously-described in-
and-out-of-phase imaging technique
• The Dixon technique can generate 4
different images:
1. A: In-phase = water + fat signal
2. B: Out-of-phase = water – fat signal
3. A + B = water signal (fat-suppressed)
4. A - B = fat signal (water-suppressed)
• Fat suppression with the Dixon technique
is uniform, and can be combined with a
variety of image weighting; sequences Four sagittal MR images of ankle generated during one
include IDEAL and Flex (GE), mDixon acquisition, including fat-suppressed image using Dixon
technique. Top left: in- phase image. Top right: out-of-phase
(Philips) and Dixon (Siemens) image. Bottom left: fat-suppressed (water signal) image.
Bottom right: fat-signal (water-suppressed) image.
 Contrast-Enhanced MR Imaging
• Injection of gadolinium (Gd)
contrast agents causes T1-
shortening and therefore Fat-suppressed T1-weighted transverse MR image of hand following intravenous administration of Gd-contrast
agent (left) shows extensor tenosynovitis (arrows). Tenosynovitis is not readily apparent on fat-suppressed T2-
hyperintensity on T1-weighted weighted image (right).

images Fat-suppressed PD-weighted transverse

image of knee (left) shows joint effusion

• When injected intravenously, Gd *

(*). Fat-suppressed T1-weighted image
following intravenous administration of

concentrates in vascular tissue

Gd-contrast (right) shows moderate
enhancement along joint (arrows)
indicating synovitis.
and therefore can help distinguish
between synovitis and effusion,
solid and cystic components of a Fat-suppressed T2-weighted coronal
tumor, and inflammation versus MR image of foot (left) shows
increased signal intensity of first
necrosis; contrast also helps proximal phalanx (*) due to
* osteomyelitis. Fat-suppressed T1-
detect abscesses and sinus tracts weighted image (right) better shows
outline of sinus tract (arrows)
extending from skin surface to bone.
 Contrast-Enhanced MR Imaging
• Sequences following i.v. Gd
administration are typically T1-
weighted, often with fat saturation
• A T1-weighted image obtained Fat-suppressed T2-weighted transverse MR image of elbow (left) shows homogeneous high signal intensity mass
(arrow) posterior to olecranon process, mimicking cyst. Fat-suppressed T1-weighted images obtained prior to

without fat suppression prior to i.v. (center image) and following (right) intravenous Gd administration shows vivid enhancement of mass, indicating
solid vascular tissue. Glomus tumor was diagnosed following resection.

Gd administration can be
subtracted from a similar image
obtained following Gd
administration to render
enhancement more conspicuous;
this can be beneficial if fat- * *
suppression is limited (e.g., due to
metal susceptibility artifact) T1-weighted transverse MR image of knee (left) shows heterogeneous soft tissue sarcoma with high- and low-
signal intensity components. Following intravenous administration of Gd-contrast agent (center image), portions
of mass enhance (*), indicating vascularity. Enhancing solid components can be rendered more conspicuous by
subtracting non-enhanced image from enhanced image (right).
 Contrast-Enhanced MR Imaging
• When diluted and injected into
joints, Gd can help to delineate *
tears of the glenoid and acetabular
labrum as well as tears of small
ligaments (MR-arthrography)
• Fat-suppressed T1-weighted T2-weighted coronal oblique MR image of shoulder shows cyst (*) in suprascapular notch. No
labral tear is identified. Fat-suppressed T 1-weighted image obtained following intra-articular
images are typically acquired injection of dilute gadolinium shows superior labral tear (arrow).

following intra-articular Gd
administration, but other
sequences including proton- PD-weighted axial-oblique MR image of hip
following intra-articular injection of dilute
density and intermediate-weighted gadolinium-chelate shows anterior labral tear
(arrow).
sequences with or without fat
suppression can be obtained
Quantitative Compositional Cartilage Imaging
• Cartilage consists predominantly of interstitial
water (60-80% by weight), as well as collagen
(15-20%) and proteoglycans with attached
glycosaminoglycans (10%)
• In addition to the various pulse sequences
previously described that can assess the
morphology of cartilage, special sequences can
be used to quantitatively assess the biochemical
composition of cartilage before morphologic
changes are appreciated
• T2-mapping (briefly described on the next slide)
is the most common of these sequences; other
methods include dGEMRIC, T1r-imaging,
sodium imaging and DWI T2-mapping of articular cartilage in the knee with a pulse sequence
that acquires images with different echo times TE (top right graph).
Quantitative Compositional Cartilage Imaging
• The T2 relaxation time of cartilage is a
function of its water content and collagen
• T2 values of cartilage can be obtained using a
pulse sequence with multiple echoes at
different TEs; software can then be used to
create color-coded maps for assessment
• Superficial cartilage layers have higher water
content and longer T2 relaxation times,
whereas deeper layers have lower water
content and shorter T2 relaxation times T2-mapping of patellofemoral articular cartilage. Pulse sequence
acquires images at multiple different TEs (top row). Pixel-by-pixel T 2

• Cartilage degeneration generally results in calculations are displayed on color-coded map. Note higher T 2-
values in superficial cartilage layer (green) compared to lower T 2-

increased water content and increased T2 values in deeper cartilage layer (orange).

relaxation times
 MRI Artifacts
• A variety of image artifacts can be
encountered on MSK MRI exams
which can degrade image quality
or even simulate lesions
• Some artifacts are dependent on
the pulse sequence used; a few Proton density-weighted sagittal MR image of knee (left) shows motion artifact simulating meniscal
such artifacts, including motion tear (arrow). Fat-suppressed proton density-weighted image from the same scan (right) shows no tear.

artifact, susceptibility artifact, and T2-weighted sagittal MR

magic angle artifact, will be briefly image of knee with chemical
shift selective fat saturation
described (left) shows high signal
intensity surrounding tibial
interference screw (arrow)
mimicking pathology. T2-
weighted image using Dixon
method of fat suppression
(right) shows no lesion.
 Motion Artifacts
• Motion artifacts are typically propagated in
phase encoding direction, and can be caused by
patient motion, cardiac motion, respiratory
motion, peristalsis, and pulsatile flow Motion artifact (arrow) on fat-suppressed transverse PD-
weighted image of shoulder (left) is reduced on PROPELLER
• When motion is periodic, discrete “ghosts” form sequence (right)

• For motion-prone patients, using pulse

sequences with short acquisition times (e.g.,
GRE or EPI) or that use radial k-space filling
techniques (e.g., PROPELLER [GE)], MultiVane
[Philips], BLADE [Siemens]) can be effective
• Saturation pulses, cardiac/respiratory gating Pulsation artifact from popliteal artery mimics bone lesion
methods, and swapping frequency- and phase- (arrow, left) and cartilage lesion (arrow, right) in patella on
these fat-suppressed PD-weighted knee MR images.
encoding directions are other options Swapping phase and frequency encoding directions (not
shown) would result in more desirable propagation of artifact
horizontally on image (rather than vertically as shown).
 Susceptibility Artifacts
• Susceptibility artifacts arise due to
heterogeneity of the local
magnetic field at the interface of
structures with differing magnetic
susceptibilities
• While such artifacts may point to
specific disease processes (e.g.,
PVNS), more often they degrade Lateral knee radiograph (top left) shows
quality (e.g., foreign bodies) small metallic foreign body (needle) in
subcutaneous fat anterior to patellar
tendon. Foreign body results in signal
• Artifacts from surgical implants void and distortion on PD-weighted
sagittal MR image (top right) and
depend on the type of metal, with regional failure of fat suppression
(arrows) on PD-weighted transverse
stainless steel causing more image with chemical shift selective fat
suppression (bottom right).
severe artifact than titanium alloy
 Susceptibility Artifacts
• Strategies to reduce magnetic susceptibility
artifacts include: Metal artifact is more pronounced on transverse GRE MR

• Avoid GRE sequences (which are prone to image of shoulder (arrows, left) than on FSE image (right).

susceptibility artifacts); use FSE sequences

with short echo times instead
• Lengthen ETL, increase receiver
bandwidth, decrease TE and voxel size
STIR MR image (left) shows more homogeneous fat
• Use STIR and Dixon sequences; these will suppression than CHESS image (right) of patient with total
knee arthroplasty (arrow, prosthetic tibial stem).
reduce artifact relative to CHESS
sequences and provide more
homogeneous fat suppression
• Consider proprietary metal artifact
reduction sequences (SEMAC, MAVRIC)
Coronal STIR MR image of knee in patient with arthroplasty
shows signal distortion (left), which is markedly reduced
on MAVRIC metal artifact reduction sequence (right).
 Magic Angle Artifact (MAA)
• When collagen-containing tissues
with parallel molecular alignment
are oriented ~55o relative to the
main magnetic field, they may
exhibit increased signal intensity
on pulse sequences with TE < 30
ms
• Such tissues include tendons, Increased signal intensity in supraspinatus tendon on PD-weighted MR image with TE=14 ms
(arrow, left) disappears on T2-weighted image with TE=80 ms (arrow, right).

ligaments, entheses, peripheral

nerves, labra, menisci and
articular cartilage
 Magic Angle Artifact (MAA)
• MAA is most common with T1- and
PD-weighted sequences, but can
also be seen on T2-weighted
sequences; the artifact can be
eliminated with TE values >70 ms;
the artifact can also be seen on
GRE, STIR, and DWI sequences
Spoiled GRE sagittal MR image
• The angular range (beyond 55o) with TE=4 ms (top left) and PD
image with TE=14 ms (top right)
over which MAA occurs increases show increased signal intensity
due to magic angle artifact at
with decreasing TE proximal patellar enthesis and in
posterior cruciate ligament
(arrows). Signal disappears on
T2-weighted image with TE=90
ms (bottom).
 In Conclusion
• A basic knowledge of MR pulse sequences is essential for planning
diagnostic musculoskeletal magnetic resonance imaging examinations
• Understanding fundamental MR physics allows better appreciation of
the properties of various pulse sequences and methods of fat
suppression
• Fast/turbo spin echo pulse sequences remain the most common pulse
sequences used in typical MSK MR imaging protocols; however,
gradient echo pulse sequences have the advantage of rapid acquisition
and therefore are frequently used to create 3D datasets
• Chemical shift selective fat saturation is a commonly used method of fat
suppression, but is more sensitive to magnetic field heterogeneity than
inversion-based techniques
 In Conclusion
• Some artifacts, such as motion artifacts, susceptibility artifacts, and
magic angle artifacts, are dependent upon the pulse sequence used;
these artifacts often can be minimized with forethought
• We hope that this presentation has served as a useful introduction
and/or review for residents and fellows studying musculoskeletal MRI
 Summary table
Pulse Sequence Useful for…
T1-weighted Confirming replacement of fatty bone marrow, determining degree of fatty atrophy of muscles, detecting/
characterizing fatty and hemorrhagic lesions

T2-weighted (often with fat suppression) Detection of fluid and edema (and therefore abnormalities in a variety of tissues)
Proton-density-weighted Identifying abnormal signal in normally signal-poor structures (e.g., fibrocartilage); conspicuity of fluid is
increased with fat suppression; typically sequence of choice for meniscal imaging

“Intermediate-weighted” Assessment of articular (hyaline) cartilage

Gradient-echo Detection of susceptibility artifacts (e.g., hemosiderin in patient with PVNS)
Rapid scanning allows
- 3D volumetric acquisition  isotropic voxels  thin/multiplanar reconstructions (e.g., morphologic
imaging of cartilage), often at expense of contrast, blurring
- Dynamic multiphase imaging (e.g., for tumor vascularity)
Images can be T1-, T2- or T2*-weighted

In-and-opposed-phase Detection of microscopic fat (e.g., to distinguish red marrow from marrow infiltrated by tumor)
Diffusion-weighted Determining restriction of diffusion due to cellularity (e.g., bone and soft-tissue tumors, follow-up of
tumors post-therapy, vertebral fractures and infection)
Fat-suppression (e.g., CHESS, STIR, water excitation, Dixon Improving visibility of lesions on PD-, T 2- and contrast-enhanced T1-weighted images, evaluating fat in soft-
techniques) tissue lesions, methemoglobin; STIR and Dixon techniques best with hardware

Contrast-enhanced T1-weighted Intravascular Gd injection: detecting vascular tissue (e.g., inflammation, tumor)
Intra-articular Gd injection: delineating small intra-articular structures (e.g., labrum, ligaments) and
associated abnormalities

Quantitative compositional cartilage imaging (e.g., T 2-mapping, Quantitative assessment of biochemical composition of cartilage
dGEMRIC, T1r-imaging, sodium imaging)
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• We also suggest the web site www.mriquestions.com by Allen D. Elster (© 2018) as a comprehensive but easily digestible resource for material pertaining to general
MRI physics.