Pulse Sequences

Field trip: Tuesday, Feb 5th

Hardware tour of VUIIIS Philips 3T
Meet here at regular class time (11.15)
Complete MRI screening form!

Chuck Nockowski
Philips Service Engineer

Reminder: Project/Presentation
Pick a special topic of interest to you:

Clinical (e.g., cancer, stroke, Alzheimers disease)

Technical (e.g., parallel imaging, k-space, novel acquisition)
Hardware (e.g., coils, gradients, radiofrequency transmission)
NOTE: if you are actively working on an imaging research
project (Ph.D., etc.) you must choose something different from
your thesis topic! I must approve all topics: just email or talk to me.

Prepare written report

10-20 pgs; double-spaced; font=12 pt; margins=1
Present summary to class
15 min (~10 slides)

What do we know so far about how

MR imaging works?
When we place a brain, body, etc. in MRI
scanner, spins of protons on water
molecules will align, on average, with the
main magnetic field
Main field is in z-direction
This occurs due to Zeeman effect
Lower energy state for alignment of spins with, vs.
against, B0 z

What do we know so far about how

MR imaging works?
After magnetization (M) reaches equilibrium
with main magnetic field B0 (few seconds), we
can apply a rotating field B1 to cause M to move
into the transverse (x-y) plane
Frequency of pulse given by ( B )
The duration of the pulse determines the flip
angle
e.g., if 5 ms pulse gives 45 degree flip angle
10 ms pulse gives 90 degree flip angle

What do we know so far about how

MR imaging works?
If we turn off the B1 pulse, M will revert to its
equilibrium orientation because of relaxation
Longitudinal component (Mz) re-aligns with z
according to time constant T1
Transverse component (Mxy) decays to zero with
time constant T2(*)

T1 and T2 are (i) independent and (ii) unique for

different tissue types.
Sources of two different contrasts in MRI!

What do we know so far about how

MR imaging works?
We detect oscillations from M by using a coil
Oscillating magnetic field will induce current in a coil
Faraday induction

We discern spatial information from sample by:

Applying a gradient during signal acquisition
This generates a spatially varying phase for the M vectors
(i.e., the gradient encodes spatial information)

Perform Fourier transform of acquired signal to obtain

estimate of spin density function (i.e., image)
Generally, we do this in 2-D and consider spatial frequencies.

Signal Detection
B0

Changing magnetic field introduces a current in a wire

Precessing magnetization detected with a coil tuned to the
appropriate frequency
Important: can only detect components in transverse (x-y)
plane
Movie courtesy of William Overall

Going further
We know basics of MRI physics, slice selection,
and image formation
How do we use this information to generate
contrast?
How do we obtain T1, T2, T2*, diffusion, flow, etc.
weightings?
Need to understand pulse sequence variants and
parameters

How do we represent pulse

sequences?
When we turn on receiver
i.e., detect signal

Gradient strength
(mT / meter)

Our B1 pulses
RF = radiofrequency
(T)

Time ( ~ ms )

Pulse sequence timing

What is a pulse sequence?

Time description of RF, gradients and data acquisition

Or, a sequence of RF, gradient and acquisition timings

Important sequence timing parameters

TE: echo time, or the time between B1 excitation and the

center of k-space
TR: repetition time, or the time between repeated
excitations of the same slice
TI: inversion time, or the time between inversion and
excitation

Complete description of what the scanner is doing,

sufficient info to predict what images will look like!

Most important parameters of MRI

pulse sequence
Acquire

Excita'on

Echo 'me (TE)

Repe''on 'me (TR)

Introduction to pulse sequences

What influences signal level?
Proton density, T1, T2, T2*

Simple pulse sequences

Gradient echo, spin echo and inversion
recovery

Readout trajectory and considerations

Bandwidth, SNR, artifacts, and time

Excitation
Tip magnetization vector from being
aligned with the magnetic field (B0) so that
it is in the x-y (transverse) plane
Do this with radiofrequency (RF) excitation
pulse

The flip angle of the RF excitation can be

more or less than 90 degrees
So long as some magnetization is in
transverse plane

Excitation Pulse

Laboratory reference frame (e.g., sitting at the

scanner console)

Movie courtesy of William Overall

Excitation Pulse

Rotating reference frame of B1 (e.g., riding on B1)

Rotating at angular frequency ( = -0)

Movie courtesy of William Overall

Turn off the RF pulse

Excitation pulse moves some component of
the magnetization vector into the transverse
plane
After this, we turn off the RF pulse
The excited magnetization will relax back
to its original state

The speed of this relaxation is determined by two

time constants:
Transverse plane: T2
Longitudinal plane: T1
T2 and T1 are completely independent!

What happens after we turn off the

RF excitation pulse?

Mz returns to alignment with main magnetic field

T1 describes this relaxation time

Movie courtesy of William Overall

What happens after we turn off the

RF excitation pulse?

Now look at just the transverse (Mx,y) component

Dephasing!
T2 / T2* describes this time

Movie courtesy of William Overall

Transverse magnetization
T2 = 25 ms
T2 = 50 ms
T2 = 100 ms

Mx,y = e-TE/T2

Longitudinal magnetization

T1 = 800 ms
T1 = 1200 ms
T1 = 4300 ms

Mz = 1-e-TR/T1

We can add pulses before the

excitation pulse too!
Acquire

Excita'on

Inversion 'me (TI)

Echo 'me (TE)

Longitudinal magnetization in
inversion recovery experiment

T1 = 800 ms
T1 = 1200 ms
T1 = 4300 ms
Inversion Mme (TI; ms)

Mz = 1-(2e-TI/T1-e-TR/T1)

MRI signal
T2 = 25 ms
T2 = 50 ms
T2 = 100 ms

T1 = 800 ms
T1 = 1200 ms
T1 = 4300 ms

Signal ~ C Mx,y(TE) Mz(TR,TI)

Water density
Specific to tissue
We dont change this

Transverse magnetization
Manipulate magnitude by
varying TE

Longitudinal magnetization
Manipulate magnitude by
varying TR

What are T1 and T2 values?

Depends on field strength. T1 increases with field strength whereas
T2 decreases with field strength
T2 times at 3 Tesla

White matter ~ 110 ms

Gray matter ~ 80 ms
Cerebrospinal fluid ~ 600 ms

T1 times at 3 Tesla

White matter ~ 800 ms

Gray matter ~ 1200 ms
Cerebrospinal fluid ~ 4300 ms

Unique T1/T2 for other tissue types as well (e.g., tumor, blood,
edema, etc.)
Unique T1/T2 provides contrast between tissues
More to come on this next week!

One additional relaxation time: T2*

Dephasing of spins in transverse plane
causes magnetization vectors to oppose
each other.
Net signal is lower due to dephasing
Leads to apparent decrease in T2.

This is called effective T2, or T2*

T2 = relaxation due to field inhomogeneity

1
1 1
* =
' +
T2 T2 T2

Relaxation times thus far

T1: relaxation time in longitudinal plane
T2*: effective relaxation time in transverse
plane.

Includes dephasing from controllable

inhomogeneities (e.g., imperfect scanner
shielding, magnetic objects/implants, etc.)
Also includes dephasing from uncontrollable
interactions (e.g., local interactions of molecules
in voxel)

T2: Relaxation time in transverse plane only

from uncontrollable spin-spin effects

How can we obtain T2 and/or T2*

contrast?
Gradient echo (GRE): Fundamentally T2*weighted
Spin echo (SE): Fundamentally T2-weighted
Note: we can vary pulse sequence
parameters to make these sequences T1weighted instead (more to come on this next
time)

Fundamentals of gradient echo

(GRE)
What does signal look like after the
excitation?
RF
Free induction decay (FID)
Well-defined frequency
(Modulated by decaying exponential)

Signal

Gradient echo (GRE) pulse sequence

Gradient echo can be used with different k-space
trajectories
e.g., GRE spinwarp, GRE spiral, GRE radial

Many structural, fMRI, susceptibility scans utilize

GRE contrast
Vendor-speak

Philips:
Fast Field Echo (FFE)
Siemens:
Fast Low Angle Shot (FLASH)
GE:
SPoiled Gradient Recall (SPGR)

Fundamentals of gradient echo

(GRE)
Apply Gx gradient with half the area
sequentially with slice-select gradient
Causes an echo: spins within the slice will
be in-phase at time TE
RF
Gz
Gx
Signal

TE

Fundamentals of gradient echo (GRE)

BUT: We can choose TE to be anything we
want
This may reduce absolute signal
However may increase T2* contrast
RF
Gz
Gx
Signal

TE

TE-choose

Fundamentals of gradient echo (GRE)

Optimum TE has most signal
TE-choose has most contrast!

Best choice may depend on application

BOLD fMRI: choose TE to maximize contrast in
and around venous blood water

RF
Gz
Gx
Signal

TE

TE-choose

Problem: dephasing of spins quite

short, especially at high field
At 7 Tesla, venous blood water T2* < 5 ms
At 7 Tesla, tissue water T2* ~ 25 ms
At 3 Tesla, these numbers are longer (15 40
ms)
Difficult to fill our k-space when the signal
decays so quickly. Can we do better?

Can we do anything to lengthen the

time it takes for spins to dephase?
Yes, apply an RF pulse to transverse
magnetization

Movie courtesy of William Overall

Spin echo (SE) signal

SE can refocus only part of the signal decay
T2 refers to part that can be refocused
(1/T2*=1/T2+1/T2)

Without refocusing, signal will have T2* contrast

Even spin echo signal experiences some

decay
T2 refers to signal decay that cannot be refocused
With refocusing, signal will have T2 contrast

T2* < T2

Gradient vs. spin echo sequences

Gradient echo (GRE)

T2* decay
Fast!

Spin echo (SE)

T2 decay
T2 > T2*

Gradient and spin echo sequences can have

different k-space readout trajectories
Cartesian

Spiral

Examples of different MRI sequences

Gradient echo (T2*-weighted depending on TE)
Blood oxygenation level-dependent (BOLD)
functional MRI (fMRI)
Susceptibility weighted imaging

Spin echo (T2-weighted depending on TE)

Fluid attenuated inversion recovery (FLAIR)

Diffusion weighted imaging

Inversion recovery (inversion prepulse followed

by GRE or SE)
FLAIR
Arterial spin labeling (ASL)
Vascular space occupancy (VASO)

Introduction to pulse sequences

Basic image contrast
Proton density, T1, T2, T2*

Simple pulse sequences

Gradient echo and spin echo

Readout trajectory and considerations

Bandwidth
Signal-to-noise ratio (SNR)

Gradient and spin echo sequences can have

different k-space readout trajectories
Cartesian

Spiral

Remember:
Low frequencies describe basic object structure
High frequencies contain ne structure informa'on
Best readout choice oOen depends on applica'on

Radial

Objects and frequencies

Object

Object
Frequency = 0

Object

Object

Low frequency

Remember:
Low frequencies describe basic object structure
High frequencies contain ne structure informa'on
Best readout choice oOen depends on applica'on

High frequency

Frequencies in images
High frequency
High frequency

Low frequency
Cornelius
Vanderbilt
1794-1877

Low frequency

Signal to noise ratio (SNR)

Image quality frequency evaluated in terms of signalto-noise ratio (SNR)
SNR: signal / noise ()
Signal is easy to characterize: just the net signal we
detect
Noise is more difficult, with multiple contributions:

Thermal noise: noise due to hardware, outside RF

interference, etc.
Physiological noise: fluctuations secondary to biological
changes (e.g., cardiac fluctuations, respiratory fluctuations,
spontaneous brain activity
Should keep track of which noise you are interested in

Thinking about thermal and

physiological noise
In simplest cases (single coil, absence of
parallel imaging), the thermal noise can be
quan'ed from the signal outside the brain

Physiological noise can be thought of

as varia'on in signal over 'me

Time

More to come on these later

What influences SNR? Voxel size

1 x 1 x 1 mm
Volume = 1 mm3

Larger voxels have signal

contribution from more spins
Signal proportional to voxel
volume

Note: reducing voxel size by n

along each m dimensions costs
nm in signal
2 x 2 x 1 mm
Volume = 4 mm3

For example, changing from

1x1x1 mm to 2x2x1 mm
increases signal by four-fold

What influences SNR? Bandwidth

Bandwidth

Frequencies of Object
Noise

Bandwidth: the range of frequencies

sampled
Determined by strength of gradient field

What influences SNR? Bandwidth

Bandwidth

Frequencies of Object
Noise

High bandwidth = high noise

Low bandwidth = low noise

Bandwidth and the readout

Tshot
Gradient Strength
Gx

Tshot
Increasing the readout
bandwidth reduces total time
required to obtain signal
(Tshot ~ 1/Gx)

Gx

What influences SNR?

Multiple acquisitions
Each time additional measurement is
acquired, signal adds but random noise
does not
Each line in multi-line readout
Every plane in 3D acquisition
Any repetition or averaging of acquisition

What influences SNR?

Multiple acquisitions
Longer acquisitions generally lead to
higher SNR
There are diminishing returns however.
Increases scale with square root.

Noise

Nshot = NPE x N3D x Nave

1/ ~ Nshot
Nshot

What influences SNR?

Imaging time
Good rule of thumb: SNR is higher for longer
scan times
For multi-shot acquisitions, where multiple
excitations and readouts are used to acquire a
single slice of data, the total time time (Ttot) is the
product of the number of shots (Nshot) and the
time of each shot (Tshot):
Ttot = Nshot x Tshot

1/ ~ [Nshot x Tshot] = TTot

Noise in images

1. Smaller voxel sizes

2. Fewer averages
3. Lower Mxy
4. Lower Mz
5. Higher bandwidth
6. Lower B0

Pulse sequence summary

Pulse sequence variants:
Gradient echo (GRE)
Spin echo (SE)

Gradient echo refocuses signal decay with bipolar gradient

(negative refocusing component with half the area of sliceselect positive component)
Fundamentally T2*-weighted
Fast signal decay

Spin echo refocuses signal decay with 180-degree refocusing

RF pulse
Fundamentally T2-weighted
Slower signal decay

Pulse sequence summary

Acquire

Excita'on

Echo 'me (TE)

Repe''on 'me (TR)

Noise in images

1. Smaller voxel sizes

2. Fewer averages
3. Lower Mxy
4. Lower Mz
5. Higher bandwidth
6. Lower B0

Coming up
Thursday: Contrast manipulation + example
problems
Tuesday: Jay Moore: RF pulses / hardware
Thursday: Jay Moore: RF pulses / hardware
Tuesday: Chuck Nockowski: Hardware tour
Mid-term exam: 19 Feb (not 14 Feb)