MRI Pulse

sequences

1. SPIN ECHO (SE )

2. FAST SPIN ECHO (FSE)
3. INVERSION RECOVERY ( STIR, FLAIR)
4. GRADIENT READING ECH0 ( GRE )

The spin echo sequence

The spin echo sequence is a very basic and simple

sequence
The two main parameters of a spin echo (SE) sequence
are the TR and the TE.
TR is the time between two 90 excitation pulses. In
regular SE sequences, TR is about 100 to 3000 ms.
TR is the time allowed for longitudinal magnetization to
recover (T1 relaxation). The longer the TR is, the more
complete the longitudinal magnetization recovery will be.
If the TR is short, not all tissues will have undergone
complete T1 relaxation and image contrast will become
more dependent on the T1 relaxation process.

With a regular SE sequence, only one line of k-space is filled

during a repetition (which lasts for time TR). The time of
acquisition (TA) of the full k-space is therefore proportional to
the TR (TA = TR * number of lines).

TE is the time between the 90 excitation pulse and the echo

signal acquisition. The echo concerns transverse
magnetization and is the result of spin rephasing due to the
180 RF pulse applied at time TE/2. The 180 RF pulse is
responsible for a cancelation of spin dephasing due to static
field inhomogeneities so that the transverse magnetization
decay is T2-dependent instead of T2*-dependent.



Spin Echo
SE sequences serve as reference for tissue contrast.
Pros:
Anatomic imaging
Reference for tissue signal and image contrast
Cons:
Very long acquisition time
Clinical use:
Almost all the organs explored in MRI

T1-weighted

If the TR is very long, the longitudinal magnetization of all the

tissues will have recovered completely (complete T1 relaxation).

On the contrary, if the TR is short, tissue signal and image contrast

will depend on the T1 characteristics of tissues as not all the tissues
will have completely recovered their longitudinal magnetization.
If the TE is also short, there is little time for T2 relaxation and image
contrast will not be very dependent on T2.

When both the TR and the TE are short, the image is said to be T1weighted.



Spin Echo
T1-weighted
Pros:
Anatomic imaging
Cons:
Very long acquisition time
Clinical use:
Almost all the organs explored in MRI

T2-weighted

To obtain a T2-weighted image in SE, the TR

must be long so that the longitudinal
magnetization of the tissues has time to recover
completely and the TE must be long to let T2
relaxation happen.

A long TR is about 2000 ms or more and a long

TE is about 80 to 140 ms.

With such parameters, the tissues with a long T2

time will have a stronger signal than the tissues
with a short T2 time.

T2-weighted

Pros:
Imaging of water/fluids (CSF, edema, biliary MRI)

Cons:
Very long acquisition time

PD-weighted

If we use a long TR (> 2000 ms) and a short TE

(10 - 20 ms), the tissue signal will not be very
dependent on T1 and T2 relaxation.
Therefore, image contrast is mainly due to proton
density.
Tissues with a rich Hydrogen content (like water)
will be bright whereas tissues with low Hydrogen
content will be dark.

PD-weighted

Cons:
Very long acquisition time
Clinical use:
Osteoarticular
Pediatric Neuroradiology

2.Fast Spin Echo ( Turbo Spin Echo)

A regular SE sequence requires as many repetitions as there are

lines in the k-space to complete a slice acquisition.

Instead of acquiring k-space lines of other slices at different

positions during the wasted time, it is possible to acquire several kspace lines for the same slice.

Such fast spin echo sequences use one 90 excitation pulse and
two or more 180 pulses in the same repetition time and with
different phase-encoding gradient steps, to acquire multiple echoes
that will fill the k-space.

The number of echoes acquired after a single 90

excitation is called the Turbo Factor or Echo Train
Length.

As each echo undergoes more and more T2 decay, the

image contrast is modified.
The effective echo time, determined by when the central
lines of k-space are acquired, indicates approximately
what the image contrast obtained is like (rather T1weighted or T2-weighted).



Pros:
Reduction of scan time
Low sensitivity to magnetic susceptibility artifacts
Cons:
Modification of tissue contrast
Clinical use:
Almost all the organs explored in MRI

Single Shot Spin Echo

Single Shot Spin Echo, Rare

If there are as many echoes as the number of kspace lines to fill, the entire k-space can be
acquired after a unique 90 excitation pulse. This
is called a single-shot sequence.
The resulting images are strongly T2-weighted as
most of the k-space lines are acquired with a long
TE.

Rare

Pros:

Excellent contrast between tissues and still fluids

Very fast : useful for moving organs

Cons:
Decreased signal to noise ratio
Low spatial resolution
Clinical use:
Biliary and urinary tract exploration ,myelography

HASTE, SSFSE, SSTSE

Single Shot Spin Echo with Partial Filling of K-Space

Commercial name: HASTE (Siemens), SSFSE (GE), SSTSE (Philips).

Pros:
Excellent contrast between tissues (gray or dark) and still fluids (bright)
Very fast : less sensitive to motion, breath-hold sequences

Cons:
Decrease of signal to noise ratio (low signal amplitude of late echoes, long
effective TE, partial filling of k-space)
Low spatial resolution
Clinical use:
Hepato-biliary and urinary tract exploration
Cardiac MRI without gating

Inversion Recovery

One method for manipulating contrast is called Inversion-Recovery.

An Inversion-Recovery consists in applying a 180 inversion pulse at the

beginning of the sequence.

The 180 inversion pulse changes the direction of the longitudinal

magnetization vector to its opposite. Then, the longitudinal magnetization is
going to recover as defined by T1 relaxation.

At time TI (inversion time), a regular spin echo (or gradient recalled echo or
echo planar) sequence is performed, starting with an excitation pulse.



The TI is defined so that the longitudinal magnetization of a chosen

tissue is null.
Consequently, this tissue will have a null transverse magnetization
after the excitation pulse, resulting in a signal suppression of this
tissue.
The optimal TI for eliminating the signal of a given tissue depends
on the tissue's characteristic T1 time.
The displayed image usually shows the magnitude of the signal,
which corresponds to the absolute value of the signal instead of the
signed value
Tissues with no magnetization appear in dark and tissues with
magnetization (positive or negative) appear in gray or bright.
Inversion-Recovery allows to eliminate the signal of tissues
according to their T1 time by choosing an appropriate TI.

Inversion Recovery
Fat Signal Suppression

STIR

Fat : T1 time is short,

And hence fat signal can be eliminated by
an inversion-recovery with a short TI time
(about 140 milliseconds).

STIR

Pros:
Fat signal suppression

Cons:
Increased scan time
Clinical use:
MSK SYSTEM

Water Signal Suppression

FLAIR

In the same way, with a TI time about 2000

ms, water signal is eliminated (water T1 is
long).

FLAIR

Pros:
Elimination of CSF signal
Useful with T2-weighted images (edema)
Cons:
Long scan time
Clinical use:
Neuroradiology

4. Gradient Echo

Two major differences distinguish the gradient echo

technique from the spin echo technique:

An excitation pulse with a flip angle lower than 90

No 180 rephasing pulse

A flip angle lower than 90 (partial flip angle) decreases

the amount of magnetization tipped into the transverse
plane.
The consequence of a low-flip angle excitation is a
faster recovery of longitudinal magnetization that allows
shorter TR/TE and decreases scan time.
The advantages of low-flip angle excitations and GRE
techniques are faster acquisitions, new contrasts
between tissues and a stronger MR signal in case of
short TR.

In the following eg., there differences in longitudinal and transversal

magnetization after a 90 excitation pulse and a 30 excitation pulse. With
partial flip angle excitation, the decrease in longitudinal magnetization is
very low (only a 13 percent loss) but the transverse magnetization is half
of its maximum value (sin 30).

Gradient Echo

The flip angle determines the fraction of magnetization tipped

in the transverse plane (which will produce the NMR signal)
and the quantity of magnetization left on the longitudinal axis.
If the flip angle decreases, the residual longitudinal
magnetization will be higher and the recovery of
magnetization for a given T1 and TR will be more complete.
On the other hand, the result of a lower flip angle excitation
is a lower tipped magnetization.



Gradient Echo
The actual decay of the transverse magnetization is due to
several factors:

spin-spin tissue-specific relaxation (T2) which is random

B0 field inhomogeneities and magnetic susceptibility,
which are static

As GE techniques use a single RF pulse and no 180

rephasing pulse, the relaxation due to fixed causes is not
reversed and the loss of signal results from T2* effects (pure
T2 + static field inhomogeneities).



Gradient Echo
Signal weighting in GE imaging lies on 3 parameters:
TR
TE
Flip angle
The resulting contrast in basic GE sequences is a variable mix of
T1 and T2*:
the higher the flip angle chosen, the more T1-weighted the image
will be
the shorter the TE obtained, the less T2*-weighted the image will be



Gradient Echo
There is an optimal combination between the TR and
the flip angle so that the NMR signal is maximal.
The optimal flip angle is called the Ernst angle.
It is calculated from the TR value and the T1-tissue
specific value to give the best flip angle to choose if we
want to obtain the maximal signal for a given tissue.

Gradient Echo

If you compare it to an SE sequence diagram, you

can note that a GE sequence is simpler, with a
single RF pulse, which allows for shorter TR and
TE and faster acquisition.
Data is acquired during the gradient echo, created
by the bipolar readout gradient (with a dephasing
lobe).
Note this is the same principle with data
acquisition in SE sequences (but the spin echo
and the gradient reading echo match)

Gradient Echo

Pros:
fast technique

Cons:

T2*-weighted images instead of T2

More sensitive to magnetic susceptibility artifacts

Clinical use:
eg. Hemorrhage , calcification

5. Advanced Gradient Echo

Steady-state
The GE technique allows for very short TR and TE.
The TR can be so short that the spins on the slice plane do not
have enough time to dephase completely the MR signal never
decays completely. These sequences are called steady-state.
They require that TR is less than T2*.
The steady-state technique produces T2*-weighted images very
fast (in less than 1 second with TRs < 10 msec).
The contrast between tissues and fluids is very high and images
have a good signal to noise ratio.
As TEs are also very short, blood generally appears bright as it
does not have enough time to move out of the slice plane.

Advanced Gradient Echo

Steady-state

In order to maintain the steady-state, the phase
shifts from one excitation to the next must
remain constant.

This is done by applying a phase-encoding
rewinder gradient after the signal readout.

The rewinder gradient is of equal amplitude but
opposite sign of the phase-encoding gradient.

It restores the original phase state before phaseencoding, which is needed for spatial localization. Such
sequences are called steady-state GRE.

Image contrast resulting from steady-state is a complex

mix of T1 and T2* so that steady-state can be harmful if
we want to obtain T1-weighted images.
In these cases, a spoiler gradient or RF is used to
destroy the transverse steady-state. These sequences
are called spoiled GRE sequences.

Advanced Gradient Echo

Steady-state

Commercial name: FISP (Siemens), FFE (Philips), GRASS (GE).

Pros:
Accentuated signal form liquids
Very good contrast between liquids and soft tissues
Very fast (breath-hold sequences, dynamic cine imaging)
Cons:
Image contrast and sensitivity to motion very complex depending
on TR, TE and flip angle
Clinical use:
urinary tract and biliary explorations



Advanced Gradient Echo

Enhanced Steady-state

Commercial name: True-FISP (Siemens), Balanced - FFE

(Philips), FIESTA (GE).

Using a fully-balanced gradient waveform, the stationary spin

returns to the same phase it had before the gradients were
applied.
This pulse sequence produces images with increased signal from
fluid.
True FISP is a reliable technique, very fast and relatively motion
insensitive, with very good contrast between liquids and soft
tissues.

Pros:

Increased signal from fluid

Very good contrast between liquids and soft tissues
Very fast (motion imaging)

Clinical use:
urinary tract, pelvic and biliary explorations
Pediatrics and antenatal imaging ++
Cardiac and vascular imaging ++

Advanced Gradient Echo

Spoiled gradient echo

Commercial name :SPGR (GE), FLASH (Siemens), FFE T1 (Philips).

Pros:

T1 weighted anatomic imaging

Short scan time, volume acquisitions, breath-hold sequences
MR angiography

Cons:
Magnetic susceptibility artifacts
Clinical use:
Cardio-vascular MRI

Image quality and artifacts

The quality of an MR image depends on several factors:

1.

Spatial resolution and image contrast

Signal to noise ratio (and contrast to noise ratio)
Artifacts
An MR exploration is a compromise between scan time and
image quality.
An MR exploration protocol and its sequence parameters
will have to be optimized in function of the organs and
pathology.

2.
3.

Spatial resolution

Spatial resolution corresponds to the size

of the smallest detectable detail.
The smaller the voxels are, the higher the
potential spatial resolution will be.
Voxel volume is determined by the matrix
size (256 x 256 or 512 x 512 etc..), the field
of view (10 cm, 20 cm, etc....), and slice
thickness.

FOV 25

FOV 35

FOV 50

MATRIX SIZE (128 X 128)

MATRIX SIZE (256 X 256 )

MATRIX SIZE (512 X512)

Signal and Noise

Noise is like interferences which present as a irregular

granular pattern.
This random variation in signal intensity degrades image
information.
The main source of noise in the image is the patient's body
(RF emission due to thermal motion).
The whole measurement chain of the MR scanner (coils,
electronics...) also contributes to the noise.
This noise corrupts the signal coming from the transverse
magnetization variations of the intentionally excited spins (on
the selected slice plane).
The signal to noise ratio (SNR) is equal to the ratio of the
average signal intensity over the standard deviation of the
noise.

INCREASING NOISE



Signal and Noise

The signal to noise ratio depends both on some factors that
are beyond the operator's control (the MR scanner
specifications and pulse sequence design) and on factors
that the user can change:
Fixed factors : static field intensity, pulse sequence design,
tissue characteristics
Factors under the operator's control

RF coil to be used

Sequence parameters :
voxel size (limiting spatial resolution), number of
averagings, receiver bandwidth

Surface coil

The smaller the sensitive volume of a coil,

the lower the noise from the adjacent
structures of the selected slice plane which
it can detect, and the better the signal to
noise ratio will be.
A local coil, or better, a surface coil have a
higher signal to noise ratio than a body coil.



Signal and Noise

The signal comes from the excited protons on the selected
slice plane. The number of spins in parallel state in excess is
proportional to the static magnetic field intensity. The larger
the field intensity is, the higher the excess number of spins in
parallel state (available to make the MR signal) will be. Thus,
the signal intensity varies almost linearly with the main field
intensity.
Assuming a uniform proton density, the number of excited
spins is proportional to the voxel size and so is the signal
intensity. The signal goes up linearly with the voxel size.