MRI Physics 2: Contrasts and Protocols

Chris Rorden
Types of contrast: Protocols

Static: T1, T2, PD

Endogenous: T2* BOLD (fMRI), DW
Exogenous: Gadolinium Perfusion
Motion: ASL

www.fmrib.ox.ac.uk/~karla/
www.hull.ac.uk/mri/lectures/gpl_page.html
www.cis.rit.edu/htbooks/mri/chap-8/chap-8.htm
www.e-mri.org/cours/Module_7_Sequences/gre6_en.html

MR Contrast a definition
We

use different MRI

protocols that are dominated
by different contrasts.
Contrasts influence the
brightness of a voxel.
For example, water (CSF) is
relatively dark in a T1weighted scan, but relatively
bright in a T2 scan.
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MR Contrast

Four types of MR contrasts:

1.
2.
3.
4.

Static Contrast: Sensitive to relaxation properties

of the spins (T1, T2)
Endogenous Contrast: Contrast that depends on
intrinsic property of tissue (e.g. fMRI BOLD)
Exogenous contrast: Contrast that requires a
foreign substance (e.g. Gadolinium)
Motion contrast: Sensitive to movement of spins
through space (e.g. perfusion).
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Anatomy of an MRI scan

1.
2.
3.
4.
5.

Place object in strong magnetic field: atoms align to field.

Transmit Radio frequency pulse: atoms absorb energy
Wait
Listen to Radio Frequency emission due to relaxation
Wait, Goto 2
Time between set 2 and 4 is our Echo Time (TE)
Time between step 2 being repeated is our Repetition Time (TR).
TR and TE influence image contrast.
TE

Time

TR

T1 and T2 definitions
T1-Relaxation:

Recovery of longitudinal
orientation.
T1 time refers to interval where
63% of longitudinal magnetization
is recovered.

T2-Relaxation:

Recovery

Dephasing

Loss of transverse magnetization.

T2 time refers to interval where
only 37% of original transverse
magnetization is present.

Contrast: T1 and T2 Effects

Fat: Short T1

CSF: Long T1

0
0

TR (s)

CSF: Long T2

Signal

T1 effects measure recovery of longitudinal magnetization.

T2 refers to decay of transverse magnetization.
T1 and T2 vary for different tissues. For example, fat has very
different T1/T2 than CSF. This difference causes these tissue to
have different image contrast.
T1 is primarily influenced by TR, T2 by TE.
Magnetization

Fat: Short T2

TE (s)

0.2

T1 Effects: get them while their down

Consider very short TR:
Fat has rapid recovery, each RF pulse will
generate strong signal.
Water has slow recovery, little net
magnetization to tip.
Before first pulse:
1H in all tissue
strongly magnetized.

T1 effects explain why we

discard the first few fMRI
scans: the signal has not
saturated, so these scans
show more T1 than
subsequent images.

After several rapid pulses: CSF has little net magnetization,

so these tissue will not generate much signal.

Fat
CSF

Signal Decay Analogy

After

RF transmission, we can detect RF emission

Emission at Larmor frequency.

Emissions amplitude decays over time.
Analogous to tuning fork: frequency constant, amplitude
decays

Relaxation
After

RF absorption ends, protons

begin to release energy

Emission at Larmor frequency.

Emissions amplitude decays over time.
Different tissues show different rates of
decay.
Free Induction Decay (FID).

Strongest

signal immediately after

transmission.
Therefore, do we always want a short
TE?
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TE and T2 contrast
1.
2.
3.

Signals from all tissue decays with time.

Signal decays faster in some tissues than others.
Optimal contrast between tissue when they emit
relatively different signals.

Optimal
GM/WM
contrast

White Matter: Fast Decay

Signal

Signal

Gray Matter: Slow Decay

TE (s)

.2

Contrast: difference
between GM and
WM signal

TE (s)

.2

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Optimal contrast

Optimal

TE will depend on which

tissues you wish to contrast

Gray matter vs White matter

CSF vs Gray matter

Signal

TE (s)

.2

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T2: Dephasing
RF

pulse sets phase.

Initially, everything in phase: maximum signal.

Signals gradually dephase = signal is reduced.
Some tissue shows more rapid dephasing than other tissue.

Fat

CSF
Time

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T1 and T2 contrasts

Every scan is influenced by both T1 and T2.

However, by adjusting TE and TR we can determine which effect dominates:

T1-weighted images use short TE and short TR.

T2-weighted images use long TE and long TR: they are dominated by the T2

Fat bright (fast recovery), water dark (slow recovery)

Fat dark (rapid dephasing), water bright (slow dephasing).

Proton density images use short TE and long TR: reflect hydrogen concentration.

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T2 vs T2*
T2

only one reason for dephasing:

Pure T2 dephasing is intrinsic to sample

(e.g. different T2 of CSF and fat).
T2* dephasing includes true T2 as well
as field inhomogeneity (T2m) and tissue
susceptibility (T2ms).
to these artifacts, Larmor frequency
varies between locations.

1
1
1
1

*
T 2 T 2 T 2 M T 2 MS

Due

T2*

T2
Signal

leads to rapid loss of signal:

images with long TE with have little
coherent signal.

T2*

0
0

TE (s)

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0.2

Susceptibility artifacts
Magnet

fields interact with material.

Ferromagnetic (iron, nickel, cobalt)

Strongly attracted: dramatically increases

magnetic field.
all steel has Iron (FE), but not all steel is
ferromagnetic (try putting a magnet on a
austenitic stainless steel fridge).

Paramagnetic

Weakly attracted: slightly increases field.

Diamagnetic

(Gd)

(H2O)

Weakly repelled: slightly decreases field.

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Tissue Susceptibility
Due

to spin-spin interactions, hydrogens

resonance frequency differs between
materials.

E.G. hydrogen in water and fat resonate at slightly

different frequencies (~220 Hz; 1.5T).
Macroscopically:

These effects can lead spatial distortion

(e.g. fat shift relative to water) and signal dropout.
Microscopically: field gradients at boundaries of different
tissues causes dephasing and signal loss.

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Field Inhomogeneity Artifacts

When we put an object (like someones head)

inside a magnet, the field becomes non-uniform.
When the field is inhomogeneous, we will get
artifacts: resonance frequency will vary across
image.
Prior to our first scans, the scanner is shimmed to
make the field as uniform as possible.
Shimming is difficult near air-tissue boundaries
(e.g., sinuses).
Shimming artifacts more intense at higher fields.

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Spin Echo Sequence

echo sequences apply a
180 refocusing pulse half
way between initial 90 pulse
and measurement.
This pulse eliminates phase
differences due to artifacts,
allowing measurement of
pure T2.
Spin echo dramatically
increases signal.

Actual Signal

T2
Signal

Spin

T2*

0.5 TE

0.5 TE

Time

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Spin Echo Sequences

The refocusing pulse allows us to recover true T2.
Image from

www.e-mri.org/cours/Module_4_Signal/contraste1_en.html
Web site includes interactive adjustment of T1/T2

T2
T2*

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Analogy for Spin Echo

Consider two clocks.

Simultaneously,set both clocks to read 12:00. (~

420
send in 90 RF pulse).
Wait precisely one hour

Clock 1: minute hand takes 70 minutes to make a

revolution.
Clock 2: minute hand takes 55 minutes to make a
revolution.

Minute hands now differ: out of phase.

Minute hand rotation

Reverse direction of each clock (~ send in 180 RF

pulse).
Wait precisely one hour

Minute hands now identical: both read noon.

They are briefly back in phase

1 hour

1 hour

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T2*: fMRI Signal is an artifact

fMRI

is Blood Oxygenation Level Dependent

measure (BOLD).
Brain regions become oxygen rich after
activity: ratio of Hbr/HbrO2 decreases

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BOLD effect
Deoxyhemoglobin

(Hbr) acts as contrast agent

Frequency spread causes signal loss over time
Effect increases with delay (TE = echo time)
But, overall signal
www.fmrib.ox.ac.uk/~karla/
reduces with TE.
Optimal BOLD TE
~60ms for 1.5T,
0
~30ms at 3T.
TE (s)

0.2

Fera et al. (2004) J MRI 19, 19-26

Low

Frequency

High

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BOLD artifacts
fMRI

is a T2* image we will have all the artifacts

that a spin-echo sequence attempts to remove.
Dephasing near air-tissue boundaries (e.g.,
sinuses) results in signal dropout.

Non-BOLD

BOLD

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www.fmrib.ox.ac.uk/~karla/

Optimal fMRI scans

More observations with shorter TR, but slightly less

signal per observation (due to T1 effects and
temporal autocorrelation).
When you have a single anatomical region of
interest use the fewest slices required for a very
short TR.
For exploratory group study, use a scan that covers
whole brain with minimal spatial distortion (for
good normalization).

Typical 3T: 3x3x3mm 64x64 matrix, 36 slices, SENSE r=2,

TE=35ms, TR= 2100ms
Typical 1.5T: 3x3x3mm 64x64 matrix, 36 slcies, TE=60ms,
TR= 3500ms.

Shorter TR yields better SNR

Diminishing returns
G.H. Glover (1999) On Signal to
Noise Ratio Tradeoffs in fMRI

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Diffusion Imaging
Diffusion

imaging is an endogenous contrast.

Apply two gradients sequentially with
opposite polarity.
Stationary tissue will be both dephased and
rephased, while spins that have moved will
be dephased.
Sensitive to acute stroke (DWI, see lesion
lecture)
Multiple directions can measure white matter
integrity (diffusion tensor imaging, see DTI
lecture)

water diffuses
faster in
unconstrained
ventricles than
in white matter

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Gadolinium Enhancement
Gd

Perfusion scans are an example of an

exogenous contrast.

intravenously-injected.

Gd

not detected by MRI (1H).

Gd has an effect on surrounding 1H.

Gd shortens T1, T2, T2* of surrounding tissue.
makes vessels, highly vascular tissues, and areas of
blood leakage appear brighter.

Very

rare side effect: allergic reaction.

Gd can help measure perfusion.

Useful for clinical studies: how much blood is getting to a

region, how long does it take to get there?

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Time of Flight

ToF is a motion contrast.

In T1 scans, motion of blood between
slices can cause artifacts.
ToF intentionally magnifies flow
artifacts.
Several Protocols of ToF, E.G:
1.

2.

Flow

Unsaturated
Spins

SLICE

Use very short TR, so signal in slice is

saturated. External spins flowing into slice
have full magnetization.
Conduct a Spin Echo Scan. Except, 90
and 180 inversion pulses applied to
different slices. Only nuclei that travel
between slices show coherent signal.

Saturated
Spins

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Arterial Spin Labelling

z (=B0)
excitation
y

www.fmrib.ox.ac.uk/~karla/

inversion
slab
blood

x
inversion
ASL

imaging
plane

white matter = low perfusion

Gray matter = high perfusion

is an example of a motion contrast

IMAGEperfusion = IMAGEuninverted IMAGEinverted

Perfusion is useful for clinical studies: how much blood is getting to
a region, how long does it take to get there?

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Common Neuroimaging Protocols

T1

scans: high resolution, good gray-white matter

contrast: VBM lecture.
T2/DW scans: permanent brain injury: lesion lecture.
Gd scans: acute brain dysfunction: lesion lecture.
DTI scans: white matter fiber tracking: DTI lecture.
T2*/ASL scans: scans for brain activity: most of this
course.

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Advanced Physics Notes

We

described 2D images using a 90 flip angle and

spin echo for refocusing.

The very short TR of our T1 3D sequences use smaller flip

angle with gradient echo refocusing.
Optimal flip angle = Ernst angle. It is calculated from the TR
value and the T1 of tissue.

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Advanced Physics Notes

Field

strength influences T1 and T2.

Optimal TR/TE for contrast will depend on field strength.

Higher Field = Faster T2 decay: Typically, TE decreases as field increases = faster imaging.
Higher Field = Slower T1 recovery: TR must increase with field strength. Influences T1
contrast: e.g. time of flight improves improves with field strength.

3.0T Scanner
Signal

1.5T Scanner

Magnetization

0
0

TE (s)

.2

TR (s)

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