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

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. Four types of MR contrasts:
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).

4. Anatomy of an MRI scan
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. TR TE
Time

5. T1 and T2 definitions T1-Relaxation: Recovery T2-Relaxation: Dephasing
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.

6. 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.
Fat: Short T1 1 1
CSF: Long T2
Magnetization
Signal
CSF: Long T1
Fat: Short T2
0.2 3
TR (s)
TE (s)

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

8. After RF transmission, we can detect RF emission
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 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.
White Matter: Fast Decay
Optimal GM/WM contrast
Gray Matter: Slow Decay
Contrast: difference between GM and WM signal
Signal
Signal .2 .2
TE (s)
TE (s)

11. Optimal TE will depend on which tissues you wish to contrast
Optimal contrast
Optimal TE will depend on which tissues you wish to contrast
Gray matter vs White matter
CSF vs Gray matter
Signal .2
TE (s)

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.
Fat …
CSF
Time

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. 1 T2
Signal
T2*
TE (s)
0.2

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.
Actual Signal 1 T2
Signal
T2*
0.5 TE
0.5 TE
Time

19. Spin Echo Sequences The refocusing pulse allows us to recover true T2.
Image from
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).
Minute hands now identical: both read noon.
They are briefly back in phase
420º
Minute hand rotation
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. Deoxyhemoglobin (Hbr) acts as contrast agent
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 reduces with TE.
Optimal BOLD TE ~60ms for 1.5T, ~30ms at 3T.
Fera et al. (2004) J MRI 19, 19-26
0.2
TE (s)
Low High
Frequency

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.
Non-BOLD
BOLD

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:
Use very short TR, so signal in slice is saturated. External spins flowing into slice have full magnetization.
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
Flow
Unsaturated Spins
SLICE

28. Arterial Spin Labelling
z (=B0)
inversion
slab
imaging
plane
excitation
blood y x
inversion
white matter = low perfusion
Gray matter = high perfusion
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?

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
3.0T Scanner
1.5T Scanner
Magnetization
Signal .2 3
TE (s)
TR (s)