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

Fall 2008

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 HST.583: Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2008
Harvard-MIT Division of Health Sciences and Technology
Course Director: Dr. Randy Gollub.

MR physics and safety

for fMRI

Lawrence L. Wald, Ph.D.

Massachusetts General Hospital

Athinoula A. Martinos Center

Wald, fMRI MR Physics

 Fast MR Imaging
Techniques

• Why, introduction

• How: Review of k-space trajectories

Different techniques (EPI, Spiral)

• Problems from B0 Susceptibility artifacts

Wald, fMRI MR Physics

 Why fast imaging
Capture time course,
(e.g. hemodynamic)
eliminate artifact from motion
(during encode.)

Wald, fMRI MR Physics

 Magnetization vector durning MR
RF encode
time
Voltage
(Signal)

Mz

time

Wald, fMRI MR Physics

 Review of Image encoding,
journey through kspace

Two questions:

1) What does blipping on a gradient do to the

water magnetization.

2) Why does measuring the signal amplitude

after a blip tell you info about the spatial
frequency composition of the image
(k-space).

Wald, fMRI MR Physics

 Aside: Magnetic field gradient

Bo Gx x Bo + Gx x

Uniform magnet Field from Total field

gradient
coils
z

x Gx = ∂Bz ∂x
Wald, fMRI MR Physics
 Step two: encode spatial info.
B along z
in-plane
o

“Frequency encoding”
x
v = γBTOT = γ(Bo + Gx x)
(w/ x gradient)

BTOT = Bo + Gz x
B
o
B Field

x
Signal

υ
Freq. υo
with gradient without gradient
Wald, fMRI MR Physics
 How does blipping on a grad. encode
spatial info?
y Bo
τ
y2 Gy
z
y1
all y locs all y locs
process at process at
(w/ z gradient)

B same freq. same freq.

o
B Field

y spins in
forehead
precess
y1 y2 faster...

υ(y) = γBTOT = γ Bo Δy Gy
θ (y) = υ(y) τ = γ Bo Δy (Gy τ)
Wald, fMRI MR Physics
 How does blipping on a grad. encode
y Bo
spatial info?
y2
y1
z θ (y) = υ(y) τ = γ Bo Δy (Gy τ)

after RF After the blipped y gradient...

z z z z
90°

x y x y x y
x y
υo position y1 position 0 position y2
Wald, fMRI MR Physics
 How does blipping on a grad. encode
spatial info?
y

The magnetization vector

in the xy plane is wound into
a helix directed along y axis.

Phases are ‘locked in’ once

the blip is over.

Wald, fMRI MR Physics

 The bigger the gradient blip area,
the tighter the helix
θ (y) = υ(y) τ = γ Bo Δy (Gy τ)
y Gy

small blip medium blip large blip

Wald, fMRI MR Physics
 What have you measured?
Consider 2 samples:

uniform water
1 cm

no signal observed signal is as big as if no gradient

Wald, fMRI MR Physics
 Measurement intensity at a spatial frequency...

ky
1/1.2mm = 1/Resolution

1/2.5mm
10 mm
1/5mm

1/10 mm

kx

Wald, fMRI MR Physics

 ky Fourier transform
1 / Resx

kx

FOVx = matrix * Resx

Wald, fMRI MR Physics

1 / FOVx
 Sample 3 points in kspace
1/1.2mm = 1/Resolution

1/2.5mm
Gy
1/5mm
t
1/10 mm

Gy kx
t
More efficient!

Frequency and phase encoding are the same principle!

Wald, fMRI MR Physics

 Conventional “Spin-warp” encoding

ky
RF
t
“slice select”Gz
t
“phase enc”Gy
t
“freq. enc”
(read-out)
Gx
a1
a2
t kx
S(t)
t

one excitation, one line of kspace...

Wald, fMRI MR Physics
Image encoding,

“Journey through
kspace”

The Movie…
Wald, fMRI MR Physics
 ky Fourier transform
1 / Resx

kx

FOVx = matrix * Resx

Wald, fMRI MR Physics

1 / FOVx
 Conventional “Spin-warp” encoding
ky
RF
t
“slice select”Gz
t
“phase enc”Gy
t
“freq. enc”
(read-out)
Gx
a1
a2
t kx
S(t)
t

one excitation, one line of kspace...

Wald, fMRI MR Physics
 “Echo-planar” encoding
ky
RF t
Gz t
Gy t
Gx
etc...
kx
S(t) T2*
(no t
grads)

T2*

one excitation, many lines of kspace...

Wald, fMRI MR Physics
 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)

The phase error (and thus distortions) are kx

in the phase encode direction.

Wald, fMRI MR Physics

 Characterization of EPI performance
length of readout train for given resolution
or echo spacing (esp) or freq of readout…

RF t
Gz t
Gy t
Gx

‘echo spacing’ (esp)

esp = 500 us for whole body grads, readout length = 32 ms
esp = 270us for head gradients, readout length = 17 ms
Wald, fMRI MR Physics
 What is important in EPI performance?

Short image encoding time.

Parameters related to total encoding time:

1) echo spacing.
2) frequency of readout waveform.
Key specs for achieving short encode times:
1) gradient slew rate.
2) gradient strength.
3) ability to ramp sample.

Good shimming (second order shims)

Wald, fMRI MR Physics

 Susceptibility in MR

The good.

The bad.

The ugly.
Wald, fMRI MR Physics
 Enemy #1 of EPI:
local susceptibility gradients

Bo field maps in the head

Wald, fMRI MR Physics
 Enemy #1 of EPI:
local susceptibility gradients

Bo field maps in the head

Wald, fMRI MR Physics
 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

 Ping-pong ball in water…

Susceptibility effects occur

near magnetically dis-similar
materials

Field disturbance around

air surrounded by water
(e.g. sinuses) Bo

Field map
(coronal image)
Wald, fMRI MR Physics 1.5T
 Bo map in head: it’s the air tissue
interface…

Sagittal Bo field maps at 3T

Wald, fMRI MR Physics
 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 3T 7T
Wald, fMRI MR Physics
 Other Sources of Susceptibility You
Should Be Aware of…

Those fillings might be a problem…

Wald, fMRI MR Physics
 Local susceptibility
gradients: 2 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 in-plane gradients.

Wald, fMRI MR Physics

 1) Non-uniform Local Field
Causes Local Dephasing
Sagittal Bo field map at 3T 5 water
protons in
different
parts of the
voxel…

z z
90°
y slowest

x fastest
T=0 T = TE
Wald, fMRI MR Physics
 Local susceptibility gradients:
thru-plane dephasing in grad echo EPI
Bad for thick slice above frontal sinus…

Wald, fMRI MR Physics

3T
 Solution: high resolution

1mm isotropic
TE=30ms, GRAPPA =2
6/8 part-Fourier

Minimal OFC drop-out issues with 3T 1mm isotropic

3T 32ch EPI

Wald, Zhengzhou 2008

 Thru-plane dephasing gets worse at
longer TE

3T, TE = 21, 30, 40, 50, 60ms

Wald, fMRI MR Physics
 Problem #2 Susceptibility Causes
Image Distortion in EPI

To encode the image, we control

phase evolution as a function of
y position with applied gradients.
Field near
sinus
Local suscept. Gradient causes
unwanted phase evolution.
y The phase encode error builds up
with time. Δθ = γ Blocal Δt

Wald, fMRI MR Physics

Susceptibility Causes Image Distortion

y
Field near
sinus

Conventional grad. echo,

Δθ α encode time α 1/BW
Wald, fMRI MR Physics
 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…

3T whole body gradients

Wald, fMRI MR Physics
 Susceptibility Causes Image Distortion

Echoplanar Image,
Δθ α encode time α 1/BW

3T head gradients
Field near
sinus Encode time = 34, 26, 22, 17ms
Wald, fMRI MR Physics
 ky
ky
EPI and Spirals

kx
kx

Gx
Gx

Gy Gy

Wald, fMRI MR Physics

 EPI Spirals
Susceptibility: distortion, blurring,
dephasing 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

 Nasal Sinus

B0

Wald, fMRI MR Physics

 Nasal Sinus + mouth shim

B0

Wald, fMRI MR Physics

 Effect of Ear & Mouth Shim on EPI

B0

Courtesy of Peter Jezzard. Used with permission.

Wald, fMRI MR Physics

 With fast gradients, add parallel imaging
2π
Δk =
FOV

Acquisition: { Reduced k-space

sampling
SMASH

SENSE
Folded images in
each receiver channel

Reconstruction:

Folded datasets
+
Coil sensitivity
maps
Wald, fMRI MR Physics
 Using the detector array to encode image

Wald, RSNA 2007 A.A. Martinos Center, MGH Radiology

90 Channel
Uncombined
Images

Wald, RSNA 2007 A.A. Martinos Center, MGH Radiology

 Parallel acquisition: noise penalties
Calculating the g-factor map
SNR full − k
SNRaccel =
G R
map of 1/G

noise correlation matrix

Rate = 4
coil sensitivity profiles Gmax=2.17
Wald, RSNA 2007
 1/G-factor Maps, 3 Tesla
R=2 R=3 R=4 R=5 R=6 1.0

0.9

MGH 0.8
96 Ch
Gmax=1.01 Gmax=1.04 Gmax=1.17 Gmax=1.42 Gmax=1.86
0.7

0.6

0.5
MGH
32 Ch 0.4

Gmax=1.02 Gmax=1.26 Gmax=2.6 Gmax=4.1 Gmax=6.0

0.3

0.2

0.1
12 Ch

Wald, RSNA 2007 0

Gmax=1.1 Gmax=1.52 Gmax=2.67 Gmax=4.78 Gmax=6.6
 1/G-factor, 2D Acceleration
2X2 2X3 4X3 4X4 5X4 1.0

0.9

MGH 0.8
96 Ch
Gmax=1.02 Gmax=1.05 Gmax=1.4 Gmax=1.6 Gmax=2.0 0.7

0.6

0.5
MGH
32 Ch 0.4
Gmax=1.05 Gmax=1.3 Gmax=2.3 Gmax=3.6 Gmax=8.6
0.3

0.2

0.1
12 Ch
0
Wald, RSNA 2007 Gmax=1.26 Gmax=2.8 Gmax=36
 3D encoding power of the array:
eigenmodes of the sensitivity maps

Analysis following:
Univ. Würzburg
Breuer et al.
ISMRM 2005 p2668
MGH brain arrays

The 90ch coil

still has significant
components over 32ch.

Wald, RSNA 2007 A.A. Martinos Center, MGH Radiology

 (iPAT) GRAPPA for EPI
susceptibility

3T Trio, MRI Devices Inc. 8 channel array

b=1000 DWI images

iPAT (GRAPPA) = 0, 2x, 3x

Fast gradients are the foundation, but EPI
still suffers distortion
Wald, fMRI MR Physics
 Encoding with RF…
4 fold acceleration of single shot sub-
millimeter 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

Extending the phased array to more
channels:
23 channel “Bucky” array for 1.5T
 9 Fold GRAPPA acceleration 3D
FLASH
9 minute scan down to 1 minute…

23 Channel array at 1.5T

Can speed up encoding by
an order of magnitude!

3D Flash, 1mm x 1mm x 1.5mm, 256x256x128

Wald, fMRI MR Physics
 32 channel coil improves fMRI

12 channel coil 32 channel coil

1 run 3 run 5 run 1 run

3T Retinotopic mapping
Triantafyllou, Hinds, MIT
Wald, Beijing 2008
 90 ch 1.5T 96 ch 3T

Graham Wiggins

Wald, Boston 2008 A.A. Martinos Center, MGH Radiology

 3T SNR Maps
150

96 Ch

100

32 Ch

50

12 Ch

0
 3T SNR Profiles

agn Order of
magnitude!
SNR

Position
Wald, Munich 2008
 Questions, comments to:

Larry Wald

Wald, fMRI MR Physics