mri part vi - unibas.ch · diffusion weighted imaging (dwi) diffusion-weighted imaging is an mri...
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Part VI:Advanced Concepts (Selection)
Contents
Cardiovascular magnetic resonance imaging (CMR; cardiac MRI)
Diffusion Imaging(diffusion weighted imaging: DWI, diffusion tensor imaging: DTI)
BOLD (blood oxygenation level dependent) Imaging(functional MRI: fMRI)
MR Angiography (MRA)
MR Spectroscopy (MRS)
Cardiac Imaging
???
ECGECG
Non-invasive assessment of the function and structure of the cardiovascular system.(characterization of heart muscle as normal or abnormal: fat infiltration, oedematous,
iron loaded, acutely infarcted or fibrosed).
ECGECG--gatinggating ((„„prospectiveprospective gatinggating““): multiple ): multiple phasesphases
ECGECG
Segmentof k-space
phase5
Segmentof k-space
phase4
Segmentof k-space
phase3
Segmentof k-space
phase2
Segmentof k-space
phase1
Cardiac ImagingInitial attempts to image the heart were confounded by respiratory and cardiac motion, solved by
using cardiac ECG gating, faster scan techniques and breath hold imaging.
ECGECG--gatinggating ((„„prospectiveprospective gatinggating““): multiple ): multiple phasesphases
Example:GE-Sequence, TR = 10 ms, imaging matrix 128 x 128, heart beat rate 70/min
How long does patient has to hold his breath?
10 ms
ECGECG
Cardiac Imaging
Spins in motion: Diffusion
1 m
Molecular Diffusion of WaterDiffusion probes for dynamic displacements of water on cellular dimensions
and provides a unique insight into tissue structure, microstructure and organization.
1 0 00 1 00 0 1
D
D
In 1956, H.C. Torrey mathematically showed how the Bloch equations for magnetization would change with the addition of diffusion. Torrey modified Bloch's original description of transverse magnetization to include diffusion terms and the application of a spatially varying gradient. The Bloch-Torrey equation neglecting relaxation is:
Isotropic Diffusion
t
10 mT/m
-10 mT/m
t
v=0
with random motion (diffusion)
Diffusion (random walk) generates a randomphase offset after bipolar gradient:
Total signal is reduced depending on strengthof diffusion ands gradient
Diffusion Weighted Imaging (DWI)Diffusion-weighted imaging is an MRI method that produces in vivo magnetic resonance
images of biological tissues weighted with the local characteristics of water diffusion. DWI is a modification of regular MRI techniques, and is an approach which utilizes the
measurement of Brownian motion of molecules.
D: diffusion constant (water = 2.5x10-9m2/s), b: diffusion weighting factor (from gradients)
Example: G = 10 mT/m, = 30 msb ~130 s/mm2
S ~ 0.75 M0
Diffusion (random walk) generates a random phase offset after bipolar gradient
Diffusion Weighted Imaging (DWI)
2 3 223
b G
tG [m
T/m
]
0( , ) bDS b D M e
Signal attenuattion from diffusion:
t
2 2 21( )3
b G
G [m
T/m
]
Restricted Diffusion & Anisotropic Diffusion
Large compartements,high diffusion
cell
small compartements,low diffusion
Detection of affected regions afteracute stroke
Restricted Diffusion
0 00 00 0
DD
D
0 00 00 0
eff
eff
eff
DD
D
>
Nerve bundles: diffusion is higher along than across nerve fibres: Anisotropic diffusion!
Diffusion sensitizing gradients (Bx,Gy,Gz) can be applied independently along all three spatial directions (x,y,z)
This allows to calculate the direction of highest (lowest) diffusion within eachimaging voxel!
Anisotropic Diffusion
1
2
3
0 00 00 0
DD
D
Calculate eigenvectors!
fiber tracks in white matter
Diffusion Tensor Imaging: Tractography
Determine diffusion tensor from at least six measurements with diffusion sensitizing gradients along different directions.
Functional magnetic resonance imaging (fMRI)
Red blood cells containhemoglobine
Heme, part of hemoglobine, contains Iron (Fe)
Hemoglobine can either beparamagnetic or diamagnetic, depending on oxygenationstate
Heme group
hemoglobine
Functional magnetic resonance imaging is a type of specialized MRI scan used to measure the hemodynamic response (change in blood flow) related to neural activity in
the brain. It is one of the most recently developed forms of neuroimaging. Since the early 1990s, fMRI has come to dominate the brain mapping field due to its relatively low
invasiveness, absence of radiation exposure, and relatively wide availability.
Functional magnetic resonance imaging (fMRI)
Hemoglobine can either be paramagnetic or diamagnetic, depending on oxygenation state
magneticmoment
Deoxyhemoglobin
Fe
oo
no magneticmoment
Oxyhemoglobin
Fe
Magnetic field flux
vein
arterie
Functional magnetic resonance imaging (fMRI) BOLD: blood oxygenation level dependent imaging
0
frequency tTEdeox
0
frequency tTEox
Functional magnetic resonance imaging (fMRI) BOLD: blood oxygenation level dependent imaging
BOLD: blood oxygenation level dependent imaging
Firering nerve cells require energyEnergy is provided as oxygen and glucose via capilaries
This locally increases blood flowIncrease of blood flow exceeds demand of oxygen
This locally increases blood oxygenation
Functional magnetic resonance imaging (fMRI)
- normal flow- base level of [Hbr]- base level of CBV
HbO2Hbr
- increased flow- reduced level of [Hbr]- increased CBV
Activated stateResting stateArterioles
Capillaries
Venules
CBV=
cerebral blood volume
BOLD: blood oxygenation level dependent imaging
Functional magnetic resonance imaging (fMRI)
T2* (rest) < T2* (activation)
MR Angiography (MRA)
MRA: Introduction
Characterization of (Human) Vascular System
What is MRA used for?
MRA: Introduction
Vascular abnormalities for MRA?
• Stenosis• Aneurysm
• Arterial Venous Malformation (AVM)• Thrombus
• Plaque• Internal bleeding
• …
MRA: Properties of Blood
Arterial VenousT1 ~ 1200ms @ 1.5TT1 ~ 1500ms @ 3.0T
T1 ~ 1200ms @ 1.5TT1 ~ 1500ms @ 3.0T
T2 ~ 250ms T2 ~ 30ms
Flow Velocity (mean)
100 – 150 cm/sec (3.6 – 5.4 km/h) in abdominal aorta10 – 20 cm/sec (0.36 – 0.72 km/h) in peripheral arteries
Pulsatile: Peak arterial flow @ 150 – 200 ms afterventricular contraction
Relaxation Times
MRA: Techniques
Contrast Enhanced MRA (CE-MRA)
Non-Enhanced (native) MRA (native-MRA)
• high contrast-to-noise ratio (of course!)• fast acquisition dynamic imaging
• No flow induced dephasing of signal loss• Acquisition timing is important (bolus!)
• Gd related NSF is a concern
• can be quantitative• prone to artifacts
• techniques are region specific
CE-MRA
• became popular during 1995 – 1999
Requirements:• High resolution and coverage of large VOI
• Short acquisition times to allowbreath-holding, e.g. for visualization of
abdominal vasculature
Fast 3D Sequences 3D GRE!
CE-MRA: GRE Parameters
TRTE
TR: Repetition timeTE: Echo time: excitation (flip) angle
CE-MRA: GRE Contrast
What do we expect for a GRE acquisition
with short TR/TE (we want to be fast!!!)
and a 90° flip angle?
TR = 3ms << T1, TE ~ 0 ms, = 90°
CE-MRA: GRE Contrast
TR = 6 sec
TR = 3 msec
Signal of blood fora fast 3D GRE?
01(1 )TES S D EP
(1 0)
(1 1)
MRI: Contrast Agents (CA) revisited
2 2, 21/ 1/ [ ]nativT T CA r
Contrast enhancedMRI, cell tracking,SPIOs, USPIOs,…
1 1, 11/ 1/ [ ]nativT T CA r
Paramagnetic agents:
CA
Positive CA:low concentrated Gd-chelates. Predominantly reduction in T1 (electron-proton dipolar coupling).
Positive contrast in T1w-image!
Contrast agents accelerate T1 & T2.
CE-MRA
Gd contrast agents decrease T1 and thereby increase CNR between blood and soft tissue
CE-MRA
TR = 3.54 msTE = 1.38 ms
Flip = 25°1.0 x 1.0 x 0.9 mm
RF spoiled SSFP-FID(FLASH, SPRG, T1-FFE)
heavily T1-weighted
The contrast medium is injected into a vein, and images are acquired during the first pass (bolus) of the agent through the arteries.
This is the most common MRA method
Visualization:
Images (source is 3D) are displayed as 2D MIPs
(screen is 2D)
12 sec4 sec 16 sec 20 sec 24 sec8 sec 28 sec 32 sec
MRA: MIPs
MIP imaging was invented for use in Nuclear Medicine by Jerold Wallis, MD, in 1988
Maximum Intensity Projection
The highest intensity signal along each ray of is mapped onto the projection image
Cou
rtesy
of S
. Wet
zel,
Uni
vers
ity H
ospi
tal B
asel
Time-of-Flight (TOF) MRA
Remember: This is a native MRA technique!There is no contrast agent
…slice being imaged
TOF-MRA: Principle
Remember: This is a native MRA technique!There is no contrast agent
Short TR! SATURATION!
NO SIGNAL FROM TISSUE!
TOF-MRA: Principle
flow velocitystatic slow fast
saturationmaximum medium minimum
The effective T1 is reduced due to inflow
TOF-MRA: Principle
Inflow of venous blood
Elimination of venous signal?
TOF-MRA: Principle
flow velocitystatic slow fast
saturationmaximum medium minimum
saturated venous phase!
TOF-MRA (2D, 3D)
Inflow(flow-related enhancement)
Seqential 2D
MIP
Inflow related transient signal
Saturated background
RF spoiled SSFP-FID(FLASH, SPRG, T1-FFE)
(native) MR Angiography
TR ~ 50 msTE ~ 10 ms
Flip = 25
CE-MRA & TOF-MRA: Issues
The same sequence (FLASH) is used for TOF and CE-MRA and images rely on high CNR between blood and tissue (hyperintensesignal from blood):
Thus, the absence or reduction of the bloodsignal is related to the presence of somedisease…
Artifactual Signal Loss
2D-TOF/3D-TOF CE-MRA
• In-plane, slow or retrograde flow• Intravoxel dephasing (turbulent
flow, e.g., after stenosis)
• Improper bolus timing• T2* dephasing
Phase Contrast (PC) MRA
+=
variabel
transverse magnetization
M stationary
longitudinal magnetization
Signal Amplitude
Signal Phase
+
Amplitude Image
Phase Image
=
( )
( )
z z
z
v t G t dt
venct G t dt
Gra
dien
t fie
ldst
reng
th
Gradient waveform over time:
z
t
PC-MRA: PrincipleP
hase
imag
es m
easu
re th
e ve
loci
ty!
static
flow
+
φ
PC-MRA
TR ~ 50 msTE ~ 10 msFlip = 25°
flow encoding gradients
phase contrast MRAflow quantification
flow encoded(phase contrast)
RF spoiled SSFP-FID(FLASH, SPRG, T1-FFE)
Courtesy of F. Santini, Radiological Physics,Basel
3D PC MRA
PC-MRA
Courtesy of F. Santini, Radiological Physics,Basel
PC-MRA: Issues
• slow method: 1D: 1 flow, 1 reference, 3D: 3 flow, 1 reference
• long acquisition time (time for PC-MRA >> TOF-MRA)
• phase wraps & poor SNR: proper venc selection
• intravoxel dephasing:turbulent flow, diffusion, longer TE from flow-encoding
The strength of the PC-MRA technique is that in addition to imaging the
flowing blood, quantitative measurements of blood
flow occur at the same time.
MR Spectroscopy (MRS)
In Bloch’s classical description of the phenomenon, polarized nuclei precess about the direction of the main magnetic
field B0 with a frequency that is a product of the gyromagnetic ratio of the nucleus and the strength of the magnetic field at the nucleus B:
Nuclear Magnetic Resonance (NMR)
MRS and MRI arise from the same principle, nuclear magnetic resonance NMR,
first observed by Bloch and Purcell in 1946.
Larmor Equation:
: Larmor frequency, i.e., the resonance frequency: gyromagnetic ratio
In principle, all nuclei with show nuclear magnetic resonance.High natural abundance required to result in sufficient NMR signal.
Biological tissue: 1H is most abundant in water and fat.
Nuclear Magnetic Resonance (NMR)
Nuclear Magnetic Resonance (NMR)
Changes in the resonant frequency gives rise to the information content of both MRI and MRS!
In MRI, the resonant frequency is modified by gradients G imposed on the main magnetic field B0.
The frequency thus becomes a function of the position r and in this way, spatial information is extracted and images are created.
Introduction: Spectroscopy (MRS)
The origin of MRS dates to 1951 when Albert described small changes in resonant frequency of protons due to the local chemical
bonding environment. (protons are shielded from the full applied magnetic field Bo by surrounding electrons)
where the shift imparted by the local bonding environment is given the symbol and is called the chemical shift.
The frequency of resonance of a nuclei in a molecule is given by
In MRS, the resonance offset is normalized to the operating frequency of the magnet and further referenced to a standard to minimize confusion when comparing results from laboratories
using different field strengths.
Resonance positions are then reported in parts per million (ppm)
Introduction: Spectroscopy (MRS)
Electronegative atoms such as oxygen (O) or chlorine (Cl) attract electrons and cause deshielding of nearby hydrogen.
Each type of hydrogen has a unique position of absorption (called the chemical shift) in the NMR spectrum
Introduction: Spectroscopy (MRS)
Based on this standard, protons in water resonate at 4.8 ppm
regardless of magnetic field strength.
OH
H
C C C CH H H H
H H H H
0
3.5 ppm
H2O
Fat
[ppm]1.34.8
1 ppm = 64Hz @ 1.5 T1 ppm = 128Hz @ 3.0 T1 ppm = 298Hz @ 7.0 T
For 1H spectroscopy, the standard is the methyl proton resonance of
tetramethyl silane which was chosen to be 0 ppm.
The resonance of the methyleneprotons in adipose tissue is 1.3 ppm.
The shift between water and fat remains 3.5 ppm, regardless of field
strength, although the frequency difference in hertz changes!
Theoretical Background: Fourier Transform
Water and Fat generate a…
water: Aw
fat: Af
exp( 2iw t )
exp( 2if t )
…time varying signal response S(t):
Awexp(2iw t ) + Af exp(2if t )
…a time varying signal response: S(t)=Awexp(2iw t ) + Af exp(2if t )
…
21( ) ( )2
i vtF v S t e dt
…and its Fourier transform:
0
3.5 ppm
[ppm]1.34.8
Aw
Af
Theoretical Background: Fourier Transform
The „peak height“ in the spectrum relates to the amplitude
Theoretical Background: Line-Width
FFT
ppm0…
…
dirac-delta function (-0)
……ppm0
FFT~ T2
FWHMLorentzian function
……
Shifted Lorentzian functiondamped decay
x
=
=
ppm0
FFT
The „area under the peak“ in the spectrum relates to the amplitude
Theoretical Background: Line-Width
……damped decay
FFT
phase
oscillation
damping
Go for the real part of the Fourier transform of the signal!
FFT
Theoretical Background: Phase Shifting
However, proper phasing of the FFT signal is required
Theoretical Background: Truncation
*0 2
0
0
2 / , ( ) ~0 ,
i t t Tie e e t ts tt t
… …
Be aware: Truncation of the signal may cause
Fourier wiggles!
truncated damped decay
A filter (exponential envelope) can be appliedto smooth the truncation
(which removes thewiggles but not withoutbroadening the line).
Theoretical Background: Line Broadening
The main magnetic field B0 isperturbed by local susceptibility
changes on the macroscopic(e.g., air/bone – tissue interface), mesoscopic (e.g., vessels) and
microsopic (e.g., cells) level.
For brain @ 1.5T (64MHz), macroscopic susceptibility effectsinduce frequency changes in the
range of 30Hz ~ 0.5 ppm.
Macroscopic susceptibility effectscan be reduced by proper
shimming!
Proper and accurate shimming of the ROI is elementary!
ppm
Frequencydistribution ()
causingline-broadening
0 ppm
CA CB O H
H
H
H
H
H
Theoretical Background: J-Coupling
[ppm]
…fully decoupled
With increasing B0, the dispersion (difference in resonance frequency
in Hertz) between singletresonances increases linearly.
Closely spaced singlets become thus more distinct with increasing B0 (although the difference in ppm
remains the same.
[ppm]
…coupled
1 3 3 11 2 1
However, many of these resonances are not singlets (i.e., a single
resonance line), but multiplets.
Nuclei with different chemical shifts may exchange energy through the
bonding electron clouds in the molecule (J-coupling, being
independent on B0).
Theoretical Background: Summary
The Fourier transform relates the time-domain with the frequency domainand thus the decay of the signal with T2 relates to the line-width
(Lorentzian with FWHM ~ 1/T2)
Only the real part of the spectrum is used(less line broadening, but requires proper phasing)
A dispersion in resonance frequencies, e.g., induced by localsusceptibility changes, causes a broadening of the lines.
(proper shimming required)
Truncation of the FID may induce Fourier wiggles(can be removed by filtering, but broadens the line)
J-coupling may induce the appearance of multiplets(J-coupling is independent on B0, thus multiplets appear closer with increasing fields)
Separation of lines improves with increasing field strength(T2 ~ 100ms 0.050ppm @ 1.5T, 0.025ppm @ 3.0T, 0.011 @ 7.0T)
1H and X-nuclei Spectroscopy
MRS methods can be broadly classified into two categories:
1H MRS X-nuclei MRS
The dominant clinical application is 1H MRS,
since no additional hardware is required.(The same RF coils transmit and receive systems used for MRI are
also applicable to 1H MRS)
Imaging (H2O)
1 x 1 x 1 mm3
SNR ~ 100
MRS (NAA)
13 x 13 x 13 mm3
SNR ~ 100
[H2O] : [NAA] = 72 : 0.03 (Molar)
SNRH2O : SNRNAA 133 : 1
1H Spectroscopy: Sensitivity
…the problem with the water…
The dispersion of the 1H spectrum is small, with all the resonances of interest in the human within 5 ppm of the
water resonance (0 – 4.8 ppm).
The line shape of the water resonance in vivo yields a large base line signal,
overwhelming the resonances of interest.
RememberSNRH2O : SNRNAA 133 : 1
Water suppression required!Baseline correction required!
Sample of a 1H spectrum
4 3 2 1 ppm
PCr
GABA
GABA
Ala
Lac
Glc
PE
GSHGSHCr
Asp
MM
Cr + PCr
NAA
NAA
Glu GluGln
Gln
myo- Ins
GluGln Cho
scyllo-Ins
myo-Ins
Tau
High-resolution proton spectroscopy at 9.4 TAfter: Accurate Shimming
Water suppresionBaseline correctionPhase correction
1H Spectroscopy: Single Voxel Excitation
How can we select a small volume (~1 cm3)?
Localizedvolume
Methods:PRESS = Point-resolved spectroscopySTEAM = Stimulated echo acquisition mode
1H Spectroscopy: Localization Methods
A slice-selective 90o and two slice-selective 180° pulses form a spin echo from a single voxel.
Point-resolved spectroscopy: PRESSAchieves localization within a single acquisition
1H Spectroscopy: Localization Methods
TE/2
90° 90° 90°
TE/2TM
RF
Gx
Gy
Gz
Three slice-selective 90o pulses form a stimulated echo from a single voxel.
Only half of the available signal is obtained
Can achieve shorter TE than PRESS
Stimulated echo acquisition mode: STEAMAchieves localization within a single acquisition
2D-1H Spectroscopy: Chemical Shift Imaging
Chemical Shift Imaging (CSI)
Similar to MRI. The FID of a single voxel (i.e., its 1D-1H spectrum) is encoded with a phase (via gradients). Thisencoding has to be donealong every direction.
Thus, for a 32x32 imagingmatrix 1024 phase-encoded1D-1H-spectra are recorded…
The same principles apply as with 1D-1H MRS…
1H Spectroscopy: Summary
4 3 2 ppm
1
9
8
5
4
3
12,13
1717
6,7,182
10
1,2
16
16
6
6,77
20
14,15
2111,20
19
Energy metabolism:1: phosphcreatine (PCr)2: creatine (Cr)3: glucose (Glc)4: lactate (Lac)5: alanine (Ala)
Neurotransmission:6: glutamate (Glu)7: glutamine (Gln)8: GABA9: N-acetyl-aspartyl-glutamate (NAAG)10: aspartate (Asp)11: glycine (Gly)12: serine (Ser)
Membrane metabolism:13: phospho-ethanolamine (PE)14: phosphocholine (PC)15: glycerophosphocholine (GPC)16: N-acetyl-aspartate (NAA)
Antioxidants/osmolytes:17: glutathione (GSH)18: vitamin C (Asc)19: taurine (Tau)20: myo-inositol (Ins)21: scyllo-inositol (s-Ins)
1