Title: MRI Physics 2: Contrasts and Protocols
1MRI 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.htm
l
2MR 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.
3MR Contrast
- 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).
4Anatomy 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
5T1 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.
6Contrast 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
0
0.2
0
0
3
TR (s)
TE (s)
7T1 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 pulse1H in all tissue strongly
magnetized.
After several rapid pulses CSF has little net
magnetization, so these tissue will not generate
much signal.
Fat
CSF
8Signal 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
9Relaxation
- 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?
10TE 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
0
.2
0
.2
TE (s)
TE (s)
11Optimal contrast
- Optimal TE will depend on which tissues you wish
to contrast - Gray matter vs White matter
- CSF vs Gray matter
Signal
0
.2
TE (s)
12T2 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
13T1 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.
14T2 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
0
0
0.2
TE (s)
15Susceptibility 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.
16Tissue 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.
17Field 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.
18Spin 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
0.5 TE
0.5 TE
Time
19Spin 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
20Analogy 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 1200. (
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
420º
Minute hand rotation
0
1 hour
1 hour
21T2 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
22BOLD 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
www.fmrib.ox.ac.uk/karla/
0.2
0
TE (s)
Low High
Frequency
23BOLD 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.
BOLD
www.fmrib.ox.ac.uk/karla/
24Optimal 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 r2, TE35ms, TR 2100ms - Typical 1.5T 3x3x3mm 64x64 matrix, 36 slcies,
TE60ms, TR 3500ms.
- Shorter TR yields better SNR
- Diminishing returns
- G.H. Glover (1999) On Signal to Noise Ratio
Tradeoffs in fMRI
25Diffusion 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
26Gadolinium 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?
27Time 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. Except, 90º and 180º
inversion pulses applied to different slices.
Only nuclei that travel between slices show
coherent signal.
Saturated Spins
Flow
Unsaturated Spins
SLICE
28Arterial Spin Labelling
www.fmrib.ox.ac.uk/karla/
z (B0)
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?
29Common 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.
30Advanced 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.
31Advanced 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
0
0
.2
0
3
TE (s)
TR (s)