HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis MIT OpenCourseWare

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HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis
Fall 2006
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HST.583: Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006
Harvard-MIT Division of Health Sciences and Technology
Course Director: Dr. Randy Gollub.
MR physics for fMRI
Lawrence L. Wald, Ph.D.
Massachusetts General Hospital
Athinoula A. Martinos Center
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Outline:
1) Review: MR signal
2) Review: MR contrast
3) Image encoding
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
B
protons
Earth’s
Field
N
E
W
compass
S
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Compass needles
Earth’s
Field
υ
z
Main
Field
Bo
North
N
E
W
y
S
x
Freq = γ B
42.58 MHz/T
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Gyroscopic motion
Main
Field
Bo
z
North
• Proton has magnetic moment
M
y
• Proton has spin (angular
momentum)
>>gyroscopic precession
x
Larmor precession freq. = 42.58 MHz/T
υ = γ Bo
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
EXCITATION : Displacing the spins
from Equilibrium (North)
Problem: It must be moving for us to detect it.
Solution: knock out of equilibrium so it oscillates
How? 1) Tilt the magnet or compass suddenly
2) Drive the magnetization (compass needle)
with a periodic magnetic field
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Excitation: Resonance
Why does only one frequency efficiently tip
protons?
Resonant driving force.
It’s like pushing a child on a swing in time with
the natural oscillating frequency.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
z is "longitudinal" direction
x-y is "transverse" plane
Static
Field
z
y
Applied RF
Field
x
Mo
The RF pulse rotates Mo the about applied field
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
The NMR Signal
RF
time
Voltage
(Signal)
time
υ
υo
Bo
z
z
90°
z
y
Mo
y
y
x
x
Wald, fMRI MR Physics
υo
V(t)
x
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Physical Foundations of MRI
NMR: 60 year old phenomena that generates the
signal from water that we detect.
MRI:
using NMR signal to generate an image
Three magnetic fields (generated by 3 coils)
1) static magnetic field Bo
2) RF field that excites the spins B1
3) gradient fields that encode spatial info
Gx, Gy, Gz
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Three Steps in MR:
0) Equilibrium (magnetization points along Bo)
1) RF Excitation (tip magn. away from equil.)
2) Precession induces signal,
dephasing (timescale = T2, T2*).
3) Return to equilibrium (timescale = T1).
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Magnetization vector during MR
RF
encode
time
Voltage
(Signal)
Mz
Mxy
T2*
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Three places in process to make a
measurement (image)
0) Equilibrium (magnetization points along Bo)
1) RF Excitation (tip magn. away from equil.)
2) Precession induces signal, allow to dephase
for time TE.
3) Return to equilibrium (timescale =T1).
proton
density
weighting
T2 or T2*
weighting
T1 Weighting
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
T2*-Dephasing
Wait time TE after excitation before measuring M.
Shorter T2* spins have dephased
z
z
z
y
y
y
vector
sum
x
initially
x
x
at t= TE
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
T2* decay graphs
Transverse Magnetization
1.0
T2* = 200
0.8
Tissue #1
0.6
T2* = 60
0.4
0.2
0.0
0
Wald, fMRI MR Physics
Tissue #2
20
40
60
80
100
Time (milliseconds)
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
T2* Weighting
Phantoms with
four different T2* decay
rates...
There is no contrast
difference immediately
after excitation, must wait
(but not too long!).
Choose TE for max.
inten. difference.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
T1 weighting in MRI
TR
RF
encode
encode
encode
Voltage
(Signal)
Mz
Wald, fMRI MR Physics
grey matter (long T1)
white matter (short T1)
time
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
T1-Weighting
1.0
white matter
T1 = 600
Signal
0.8
grey matter
T1 = 1000
0.6
CSF
T1 = 3000
0.4
0.2
0.0
0
Wald, fMRI MR Physics
1000
2000
3000
TR (milliseconds)
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image contrast summary: TR, TE
Long
Proton
Density
T2
TR
Short
T1
poor!
Short
Wald, fMRI MR Physics
Long
TE
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Basis of fMRI: BOLD contrast
Qualitative Changes during activation
Observation of Hemodynamic Changes
• Direct Flow effects
• Blood oxygenation effects
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Blood cell magnetization and Oxygen State
Bo
M =0
Oxygenated Red Cell
M = χB
de-Oxygenated Red Cell
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Addition of paramagnetic compound
to blood: T2* effect
Bo
Local field is heterogeneous
• Water is dephased
• T2* shortens, S goes down on EPI
H2 O
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Addition of paramagnetic compound
to blood
Figure by MIT OpenCourseWare.
Bo
Signal from water is dephased
T2* shortens, S goes down
on T2* weighted image
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Neuronal Activation . . .
Produces local hemodynamic changes
(Roy and Sherrington, 1890)
Increases local blood flow
Increases local blood volume
BUT, relatively little change in oxygen
consumption
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Deoxy. Heme Conc. goes down when flow goes up
1 sec
1 sec
Venous out
flow (4 balls/ sec.)
consumption =
3 balls/sec.
1 sec
1 sec
Venous out
flow (6 balls/ sec.)
Wald, fMRI MR Physics
consumption =
3 balls/sec.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Activation
• Increases blood flow (F )
⇓
⇓
• Increases blood volume (V )
• Small increase in oxygen consumption
So:
⇓
venous O2
deoxy Hb concentration ⇓
less magnetic stuff
less dephasing
MR signal increases on T2* weighted image
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
MR pulse sequences to see BOLD
Considerations:
Signal increase = 0 to 5% (small)
Motion artifact on conventional image is 0.5% - 3%
=> need to “freeze motion”
Need to see changes on timescale of hemodynamic
changes (seconds)
Requirement:
Fast, “single shot” imaging,
image in 80ms, set of slices every 1-3 seconds.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Magnetic field gradient:
the key to image encoding
Bo
Gx x
Uniform magnet
z
x
Field from
gradient coils
Bo + Gx x
Total field
Gx = ∂Bz ∂x
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Gradient field for MR encoding
B(z)
The magnet’s field is
homogeneous.
Bo
z
A gradient coil is a spool of
wire designed to provide a
linear “trim” field.
B(z)
z
0
z=0
B(z)
Gradient coil in magnet
B0
Wald, fMRI MR Physics
z=0
z
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
A gradient causes a spread of frequencies
Bo
y
MR frequency of the protons in
a given location is proportional to
the local applied field.
Wald, fMRI MR Physics
B o + Gz z
Bo
# of spins
υo
υ
B Field
v = γBTOT = γ(Bo + Gz z)
z
z
υ
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Step one: excite a slice
Bo
y
While the grad. is on,
excite only band of
frequencies.
B o + Gz z
z
B
RF
o
t
Signal inten.
B Field
(w/ z gradient)
z
Wald, fMRI MR Physics
Gz
t
Δv
v
Why?
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Step two:
encode spatial info. in-plane
y
“Frequency encoding”
Bo along z
x
B
BTOT = Bo + Gz x
Signal
x
υ
Wald, fMRI MR Physics
with gradient
υo
υ
without gradient
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
‘Pulse sequence’ so far
RF
t
“slice select”
Gz
“freq. encode”
(read-out)
Gx
t
t
S(t)
Sample points
t
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
“Phase encoding”
RF
“slice select”
“phase encode”
“freq. encode”
(read-out)
Gz
Gy
Gx
t
t
t
t
S(t)
t
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
How does blipping on a grad. encode
spatial info?
Bo
y
τ
Gy
y2
z
B Field
(w/ z gradient)
y1
all y locs
process at
same freq.
B
all y locs
process at
same freq.
o
y
y1
y2
υ(y) = γ BTOT = γ (Bo +Δy Gy)
Δθ (y) = Δυ(y) t = γ Δy (Gy t)
spins in
forehead
precess
faster...
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
How does blipping on a grad. encode
spatial info?
y
B
o
y2
θ (y) = υ(y) τ = γ Gy Δy τ
after RF
z
y1
After the blipped y gradient...
z
z
z
z
90°
x
υo
y
Wald, fMRI MR Physics
x
position y2
y
x
y
x
position 0 position y1
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
y
How does blipping on a grad. encode
spatial info?
y
The magnetization
in the xy plane is wound into
a helix directed along y axis.
Phases are ‘locked in’ once
the blip is over.
θ (y) = υ(y) τ = γ Gy Δy τ
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Big gradient blip area means tighter helix
y
small blip
medium blip
θ (y) = υ(y) τ
= γ Gy Δy τ
= γ Δy (Gy τ)
large blip
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Signal after the blip: Consider 2 samples:
y
uniform water
y
no signal observed
1 cm
signal is as big as if no gradient
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
You’ve measured:
intensity at a spatial frequency...
ky
1/1.2mm = 1/Resolution
y
1/2.5mm
10 mm
1/5mm
1/10 mm
kx
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Fourier transform
ky
1 / Resx
kx
FOVx = matrix * Resx
Wald, fMRI MR Physics
1 / FOVx
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Frequency encoding revisited
RF
t
Gz
Gx
t
t
S(t)
t
Kspace, the movie...
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
“Spin-warp” encoding
ky
RF
“slice select”
Gz
“phase enc”
Gy
“freq. enc”
(read-out)
Gx
t
t
t
a2
a1
kx
t
S(t)
t
one excitation, one line of kspace...
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
TE
One shot per readout line…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies:
FLASH
One shot per readout line…
TE
RF
Gz
Gx
Gy
Sample
Wald, fMRI MR Physics
• High BW in readout.
• new excitation every
PE line (“reboot”).
• Lenghty (~5 s per slice)
for 2mm res, TR=50ms
• Physiol. fluctuations/ motion
modulate phase/amplitude
across kspace.
• Strong inflow effects.
• All readouts same polarity.
• All kspace treated equally.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Fourier transform
ky
1 / Resx
kx
FOVx = matrix * Resx
Wald, fMRI MR Physics
1 / FOVx
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Fourier transform
ky
kx
kspace (magnitude)
Image space (magnitude)
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
esp
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
esp
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
esp
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
esp
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
All lines in one shot…
ky
RF
Gz
esp
Gx
kx
Gy
Sample
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
Performance is parameterized by ESP
for a given resolution
BW in PE = 1/esp
gives image distortion in mm.
ESP
esp
Gx
3mm EPI:
Total readout length:
gives image distortion in pixel
units.
esp = 500 us for whole body grads, readout length = 32 ms
esp = 270us for head gradients, readout length = 17 ms
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Bandwidth is asymmetric in EPI
(Distortion is 100x more in phase direction)
ky
The phase error (and thus
distortions) are in the phase
encode direction.
υ1 υ2
ϕ = Δυ τ
kx
δt=0.5ms
Wald, fMRI MR Physics
δt=0.005ms
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: EPI
Packing in the slices…
fat sat
TE
start next
slice
1/2 of EPI
readout
RF
t
Gz
t
t
Gy
bottom half
Gx
top half
t
15ms
30ms
15ms
5ms
Total = 65ms => 15 slices per second
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: Spirals
All kspace in one shot…
TE
ky
RF
Gz
kx
Gx
Gy
Sample
Wald, fMRI MR Physics
“spiral out”
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: Spiral
All kspace in one shot…
ky
kx
Wald, fMRI MR Physics
δt=0.005ms
δt=0.5ms
• Fast (high BW ) in azimuthal k.
• Slow (low BW) in radial k.
• No “reboot”, phase error
accumulates.
• Fast (~10 slices per second)
for 2mm res.
• Physiological fluctuations
modulate overall intensity
• Readouts alternating polarity.
• All kspace NOT treated equally.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image encoding strategies: Spirals
TE
Two problems:
1) deadtime.
2) kspace filtering
RF
Gz
If TE = T2* (BOLD max)
then signal down ~3 fold
by first sample.
Gx
dead time
Gy
exp(-t/T2*)
High kspace is severely
filtered.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
“Spin-warp” encoding mathematics
Keep track of the phase...
Phase due to readout:
θ(t) = ωo t + γ Gx x t
Phase due to P.E.
θ(t) = ωo t + γ Gy y τ
Δθ(t) = ωo t + γ Gx x t + γ Gy y τ
RF
t
Gz
t
Gy
Gx
t
a2
a1
t
S(t)
t
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
“Spin-warp” encoding mathematics
Signal at time t from location (x,y)
S(t) = ρ (x, y)e
iγGx xt+iγ Gy yτ
The coil integrates over object:
S(t) =
∫∫ ρ( x, y)e
iγG x xt +iγ G y yτ
dxdy
object
Substituting kx = -γ Gx t and kx = -γ Gx t :
S(kx , k y ) =
∫∫ ρ(x, y)e
−ik x x−ik y y
dxdy
object
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
“Spin-warp” encoding mathematics
View signal as a matrix in kx, ky…
S(kx , k y ) =
∫∫ ρ(x, y)e
−ik x x−ik y y
dxdy
object
:
Solve for ρ(x,y,)
ρ(x, y) = FT
−1
[S(k x ,k y )]
ρ(x, y) = ∫∫ S(k x ,ky )e
ik x x +ik y y
dk x dk y
kspace
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Drawbacks of Single Shot Imaging
• Require high gradient
performance to eliminate
susceptibility induced
distortions.
• Susceptibility in the
head is worse at 3T than
1.5T.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Enemy #1 of EPI:
local susceptibility gradients
Wald, fMRI MR Physics
Bo field maps in the head
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Susceptibility in MR
Gives us
BOLD
Gives us
dropouts
Wald, fMRI MR Physics
Gives us
distortion.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
What do we mean by
“susceptibility”?
In physics, it refers to a material’s tendency to
magnetize when placed in an external field.
In MR, it refers to the effects of magnetized
material on the image through its local distortion
of the static magnetic field Bo.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
What is the source of susceptibility?
Bo
1) deoxyHeme is paramagnetic
2) Water is diamagnetic (χ = -10-5)
3) Air is paramagnetic (χ = 4x10-6)
Pattern of B field outside
magnetic object in a
uniform field…
The magnet has a spatially uniform field
but your head is magnetic…
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Ping-pong ball in water…
Susceptibility effects occur near
magnetically dis-similar materials
Field disturbance around air
surrounded by water (e.g.
sinuses)
Wald, fMRI MR Physics
Bo
Field map
(coronal image) 1.5T
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Bo map in head: it’s the air tissue
interface…
Wald, fMRI MR Physics
Sagittal Bo field maps at 3T
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Susceptibility field (in Gauss)
increases w/ Bo
Ping-pong ball in H20:
Field maps (ΔTE = 5ms), black lines spaced
by 0.024G (0.8ppm at 3T)
1.5T
Wald, fMRI MR Physics
3T
7T
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
What is the effect of having a non-uniform
field on the MR image?
Sagittal Bo field map at 3T
Local field changes with position.
To the extent the change is linear,
=> local suscept. field gradient.
We expect uniform field and
controllable external
gradients…
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Local susceptibility gradients:
two effects
1) Local dephasing of the signal (signal loss) within a
voxel, mainly from thru-plane gradients
2) Local geometric distortions, (voxel location
improperly reconstructed) mainly from local inplane gradients.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
1) Non-uniform Local Field
Causes Local Dephasing
5 water
protons in
different parts
of the voxel…
Sagittal Bo field map at 3T
z
z
90°
y
slowest
x
Wald, fMRI MR Physics
T=0
fastest
T = TE
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Thru-plane dephasing gets worse
at longer TE
3T, TE = 21, 30, 40, 50, 60ms
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Local susceptibility gradients:
thru-plane dephasing
Bad for thick slice above frontal sinus…
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Partial volume effects: w/ focal
activation, less is more...
1.4mm x 1.4mm x 2mm EPI
SNR is proportional to voxel
volume but contrast?
1.5mm voxel
2.5mm
N. Kanwisher face study
Wald, fMRI MR Physics
Courtesy of Nancy Kanwisher. Used with permission.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Mitigation: thru-plane
dephasing; easy to implement
1) Good shimming. (first and second order)
2) Use thinner slices preferably w/ isotropic voxel.
Drawback: takes more to cover brain.
3) Use shorter TE.
Drawback: BOLD contrast is optimized for TE =
T2*local. Thus BOLD is only optimized for
the poor susceptibility regions.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Mitigation: thru-plane dephasing;
harder to implement
1) Bo correction.
2) “Z-shimming” Repeat measurement several times with an applied
z gradients that rewind the dephasing, Pick the right gradient
afterward on a pixel by pixel basis. (Drawback: multi shot or
longer encode). MRM 39 p402, 1998.
2) Use special RF pulse with built-in prephasing in just the right
places. (Drawback: long RF pulse, pre-phasing differs from person
to person.)
Glover et al. Proceed. ISMRM p298, 1998.
3) The “mouth shim” diamagnetic material in roof of mouth.
Wilson, Jenkinson, Jezzard, Proceed. ISMRM p205, 2002.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Problem #2 Susceptibility Causes
Image Distortion in EPI
y
Field near
sinus
y
To encode the image, we control
phase evolution as a function of
position with applied gradients.
Local suscept. Gradient causes
unwanted phase evolution.
The phase encode error builds up
with time. Δθ = γ Blocal Δt
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Susceptibility Causes Image Distortion
y
Field near
sinus
y
Wald, fMRI MR Physics
Conventional grad. echo,
Δθ α encode time α 1/BW
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Bandwidth is asymmetric in EPI
ky
• Adjacent points in kx have
short Δt = 5 us (high bandwidth)
• Adjacent points along ky are taken
with long Δt (= 500us). (low
bandwidth)
kx
The phase error (and thus distortions)
are in the phase encode direction.
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Susceptibility Causes Image Distortion
Echoplanar Image,
Δθ α encode time α 1/BW
z
Field near sinus
3T head gradients
Encode time = 34, 26, 22, 17ms
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Characterization of grad. performance
length of readout train for given resolution
or echo spacing (esp) or freq of readout…
RF
Gz
Gy
t
t
t
Gx
‘echo spacing’ (esp)
esp = 500 us for whole body grads, readout length = 32 ms
Wald, fMRI MR
Physics
esp
= 270us for 3T, readout length = 17 ms
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Parallel Imaging: speed up by 2x…
FFT
Folded, but many
kspace,
every other line (under-sampled)
SMASH, GRAPPA
SENSE
FFT
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
4 fold GRAPPA acceleration
sub-millimeter, single shot SE-EPI:
23 channel array
23 Channel array at 1.5T
With and without 4x Accel.
Single shot EPI,
256x256, 230mm FOV
TE = 78ms
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
32ch fMRI
1mm isotropic
TE=30ms EPI
3T, 8ch array,
GRAPPA =2
6/8 part-Fourier
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Susceptibility in EPI can give either
a compression or expansion
Altering the direction kspace is
transversed causes either local
compression or expansion.
choose your poison…
Wald, fMRI MR Physics
3T whole body gradients
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Effect of Ear & Mouth Shim on EPI
B0
Wald, fMRI MR Physics
From P. Jezzard, Oxford
Courtesy of Peter Jezzard. Used with permission.
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Lip
EPI and Spirals
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
EPI
Spirals
Susceptibility:
distortion,
dephasing
blurring,
dephasing
Eddy currents:
ghosts
blurring
k = 0 is sampled:
1/2 through
1st
Corners of kspace:
yes
no
Gradient demands:
very high
pretty high
Wald, fMRI MR Physics
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Dephasing: local field variations
Near low deOxy Hb conc.
S(t)
T2*
FT
S(υ)
Δυ
t
υ
υ
o
Near high deOxy Hb conc.
.
FT
S(t)
t
Wald, fMRI MR Physics
S(υ)
Δυ
υ
υ
o
z
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Contrast/Noise Ratio
and Echo Time (TE)
− Ra t
− Rb t
− So e
Sa = So exp(-Rat) ΔS = So e
Sb = So exp(-Rbt) ΔS = S e− R a t − S e− (Ra−ΔR ) R b t
o
o
ΔS = So e− R t (1 − e ΔRt )
a
t
Ra= 1/T2a*
Rb= 1/T2b*
ΔR = Ra - Rb
Wald, fMRI MR Physics
ΔS = −S o e−R t ΔRt
a
∂
(ΔS) = 0
∂t
t = 1/ Ra
TE = T2a*
Cite as: Lawrence L. Wald, Ph.D, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute
of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
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