1

MRI Physics 2: Contrasts and Protocols

Chris Rorden, Paul Morgan 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.htmlwww.cis.rit.edu/htbooks/mri/chap-8/chap-8.htmwww.e-mri.org/cours/Module_7_Sequences/gre6_en.html

2

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 T1-weighted scan, but relatively bright in a T2 scan.

3

MR Contrast

Four types of MR contrasts:1. Static Contrast: Sensitive to relaxation properties

of the spins (T1, T2)

2. Endogenous Contrast: Contrast that depends on intrinsic property of tissue (e.g. fMRI BOLD)

3. Exogenous contrast: Contrast that requires a foreign substance (e.g. Gadolinium)

4. Motion contrast: Sensitive to movement of spins through space (e.g. perfusion).

4

Anatomy of an MRI scan

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

2. Transmit Radio frequency pulse: atoms absorb energy

3. Wait

4. Listen to Radio Frequency emission due to relaxation

5. 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.

Time

TRTE

5

T1 and T2 definitions

T1-Relaxation: Recovery– Recovery of longitudinal

orientation.– ‘T1 time’ refers to interval where

63% of longitudinal magnetization is recovered.

T2-Relaxation: Dephasing– Loss of transverse magnetization.– ‘T2 time’ refers to interval where

only 37% of original transverse magnetization is present.

60.2

Contrast: T1 and T2 Effects

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.

CSF: Long T1

Fat: Short T1

Ma

gn

etiz

atio

n

TR (s)0 30

1CSF: Long T2

Fat: Short T2Sig

na

l

TE (s)00

1

7

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.

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.

Before first pulse:1H in all tissue strongly magnetized.

CSF

Fat

After several rapid pulses: CSF has little net magnetization, so these tissue will not generate much signal.

8

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

9

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.– Most signal with short TE.– Why not always use short TE?

10

TE and T2 contrast

1. Signals from all tissue decays with time.2. Signal decays faster in some tissues than others.3. Optimal contrast between tissue when they emit

relatively different signals.

Gray Matter: Slow Decay

White Matter: Fast Decay

Sig

na

l

TE (s)0 .2

Contrast: difference between GM and WM signal

Sig

na

l

TE (s)0 .2

Opt

imal

G

M/W

M

cont

rast

11

Optimal contrast

Optimal TE will depend on which tissues you wish to contrast– Gray matter vs White matter– CSF vs Gray matter

Sig

na

l

TE (s)0 .2

12

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.

Time

CSF

Fat

…

13

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

– T2-weighted images use long TE and long TR: they are dominated by the T2 Fat dark (rapid dephasing), water bright (slow dephasing).

– Proton density images use short TE and long TR: reflect hydrogen concentration. A mixture of T1 and T2

14

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).

Due to these artifacts, Larmor frequency varies between locations.

T2* leads to rapid loss of signal: images with long TE with have little coherent signal.

0.2S

ign

al

TE (s)00

1

T2

T2*

MSM TTTT 2

1

2

1

2

1

2

1*

15

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 (Gd)– Weakly attracted: slightly increases field.

Diamagnetic (H2O)– Weakly repelled: slightly decreases field.

16

Tissue Susceptibility

Due to spin-spin interactions, hydrogen’s 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.

17

Field Inhomogeneity Artifacts

When we put an object (like someone’s 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.

18

Spin Echo Sequence

Spin echo sequences apply a 180º refocusing pulse half way between initial 90º pulse and measurement.

This pulse eliminates phase differences due to artifacts, allowing measurement of pure T2.

Spin echo dramatically increases signal.

Sig

na

l

Time

0

1

T2

T2*

0.5 TE 0.5 TE

Actual Signal

19

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*

20

Analogy for Spin Echo

Consider two clocks.– Clock 1: minute hand takes 70 minutes to make a

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

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

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

– Minute hands now differ: out of phase. Reverse direction of each clock (~ send in 180º

RF pulse). Wait precisely one hour

– Minute hands now identical: both read noon.– They are briefly back in phase

Min

ute

hand

rot

atio

n

0

420º

1 hour 1 hour

21

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

22

BOLD effect

Deoxyhemoglobin (Hbr) acts as contrast agentFrequency spread causes signal loss over timeEffect increases with delay (TE = echo time)But, overall signal

reduces with TE.Optimal BOLD TE

~60ms for 1.5T, ~30ms at 3T.Fera et al. (2004) J MRI 19, 19-26

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

Low HighFrequency

0.2TE (s)

0

23

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.

BOLDNon-BOLD www.fmrib.ox.ac.uk/~karla/

24

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’

25

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

26

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?

27

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. Use very short TR, so signal in slice is saturated. External spins flowing into slice have full magnetization.

2. Conduct a Spin Echo Scan: 90º and 180º inversion pulses applied to different slices. Only nuclei that travel between slices show coherent signal.

Saturated Spins

Unsaturated Spins

SLIC

E

Flow

28

Arterial Spin Labelling

ASL 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?

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

inversionslab

imagingplane

excitation

inversion

xy

z (=B0)

bloodblood

white matter = low perfusionGray matter = high perfusion

29

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.

30

Advanced Physics Notes

We described 2D images using a 90º 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.

31

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.

1.5T Scanner

3.0T Scanner

Sig

na

l

TE (s)0 .2

Ma

gn

etiz

atio

n

0 30

1

TR (s)