MRI Fundamentals

Week 6:
MRI Data Acquisition Strategies

Sung-Hong Park
Bio and Brain Engineering, KAIST


 Contents

2D & 3D Imaging
N
S

Gradient Echo Imaging

N
S

Spin Echo Imaging and Fast Spin Echo Imaging

N
S

Echo Planar Imaging

N
S

Non-Cartesian Imaging
N
S


 2D & 3D Imaging


 Multi-slice imaging (1)
In which order should we fill k-space of multiple slices?
N
S

Two ways to fill the k-spaces

N
S

1. fill all k-space lines in one slice and then move to next slices
TR scan time
TE
① ②
slice 1 ··· NPE*TR
NPE+① NPE+②
slice 2 ··· 2NPE*TR
2NPE+① 2NPE+②
slice 3 ··· 3NPE*TR

• scan time= NPE x NSL x TR x Navg (NPE : number of phase encoding steps, NSL :
number of slices, Navg : number of averages)
• In order to save the scan time, short TR is required.
• Preferred in some gradient echo applications with fast acquisition.


 Multi-slice imaging (2)
Two ways to fill the k-spaces (cont.)
N
S

2. fill the same phase-encoding (PE) line across the slices first and the move to next
PE lines. TR
TE
① ④ ···
slice 1
② ⑤
slice 2 ···
③ ⑥
slice 3 ···

• scan time= NPE x TR x Navg

• NSL (number of slices) does not affect scan time.
• TR should be longer to accommodate multiple slices in one TR.
• Imaging with long TR  signal-to-noise ratio also increases.
• This scheme is preferred in most clinical 2D imaging including T1-, T2-, T2*- and
PD-weighted imaging.


 3D imaging (1)

2D-multislice imaging 3D-volume imaging

Slice excitation by slice selection Volume excitation by slab selection gradient
N

N
S

S
gradient
RF RF

GSS GSS

GPE GPE

GRO GRO

ADC ADC


 3D imaging (2)

2D-multislice imaging 3D-volume imaging

2D K-spaces from multiple slices One single 3D K-space
N

N
S

S
Slice N-1 Slice N Slice N+1

… …

2DFT 2DFT 2DFT 3DFT

Slice N-1 Slice N Slice N+1 Slice N-1 Slice N Slice N+1

… … … …


 3D imaging (3)
Advantage
N
S

- High spatial resolution along the slice direction  high sensitivity for detecting
small lesion
- High signal to noise ratio from volume averaging effects (the excited volume in
3D is much bigger than 2D imaging.)
- 3D gradient echo imaging with extremely short TR can be used after
magnetization preparation to enhance contrast (e.g., inversion recovery for T1
contrast, physiological imaging, etc).
Disadvantage
N
S

- Short TR to maintain clinically reasonable scan time  Limits desired contrast

for certain imaging methods
 In 3D imaging, short TR decreases SNR, which can be compensated by the
volume averaging effects.


 Gradient Echo


 Gradient Echo
 Gradient echo is produced with a single RF pulse in conjunction with prephase and
N
S

frequency encoding gradients

 Pre-phasing gradient with opposite polarity applied first for half the duration
of readout time
 When gradient is reversed afterwards, the spins start to refocus and form an
echo
 Flip angle is usually below 90°
Signal Signal
Amplitude Amplitude

T2* Deca T2* Deca

y y

Time Time
FID Echo

Gradient Gradient


 Gradient Echo Imaging
TR

α α

RF
RF : radiofrequency pulse,
GSS α : flip angle,
GSS : slice-selective
gradient,
GPE GPE : phase-encoding
gradient,
GRO GRO : readout gradient,
TR : repetition time,
ADC TE : echo time.

TE


 Gradient Echo Characteristics
 Used to acquire T1, T2*, proton density (PD) contrast
N
S

 T1-weighted Image
 Short TR or large flip angle (Ernst Angle)
 Short TE

 T2*-weighted Image
 Long TR or small flip angle (<< Ernst Angle)
 Long TE

 PD-weighted Image
 Long TR or small flip angle (<< Ernst Angle)
 Short TE

※ Large flip angle/short TR increases T1 effect and long TE increases T2* effect.

 Advantage: fast acquisition speed

N
S

 Disadvantage: Susceptible to magnetic field inhomogeneity

N
S


 Spoiled Gradient Echo (1)
 If TR is short, transverse magnetization from one RF excitation may remain
N
S

when the next RF pulse is applied.

 Two main classes of GRE sequences exist, depending on how this residual
N
S

transverse magnetization is managed:

 Nulling of residual transverse magnetization (Spoiling)

 Conservation of residual transverse magnetization (Steady-state)

 We will talk about spoiled gradient echo imaging here.

N
S

(the steady-state gradient echo sequences will not be discussed in this course.)


 Spoiled Gradient Echo (2)
TR

α α

RF RF : radiofrequency pulse,
α : flip angle,
GSS GSS : slice-selective
gradient,
GPE : phase-encoding
GPE gradient,
GRO : readout gradient,
GRO TR : repetition time,
TE : echo time.
ADC

TE


 Spoiled Gradient Echo (3)
 Long TR : Transverse magnetization de-phases over time.
N
S

 RF spoiling : Phase offsets added to each RF pulse to suppress acquisition of

N
S

effects from residual transverse magnetization

 Gradients spoiling : Application of gradients to de-phase the transverse

N
S

magnetization

 RF pulses or gradients used to de-phase the transverse magnetization are

N
S

called “spoilers”

 Applications:
N
S

 T1-weighted Anatomical Imaging

 MR Angiography (Time-of-Flight, Contrast Enhanced, Phase Contrast MRA)
 T2*-weighted imaging or Susceptibility Weighted Imaging (SWI)


 Spoiled Gradient Echo (4)

• Spoiled Gradient Echo Images acquired in human brain at 3T

T1-weighting T2*-weighting PD-weighting


 Spin Echo


 Spin Echo (1)
z Z Z’
’ ’
90 Protons lose phase coherence
˚

y y y’
’ ’
X X X
’ Z’ ’ ’ 180˚ RF
Z Z pulse to
’ ’ X’ axis
Protons gain phase coherence
Echo formation

y’ y y
’ ’
X’ X X
’ ’
After 90˚ excitation, spins in the transverse plane lose phase coherence by
random dephasing (spin‐spin relaxation, T2) and progressive dephasing
(magnetic field inhomogeneity, T2’ or T2*)
Progressive dephasing can be recovered by applying an 180˚ RF along X’-axis.


 Spin Echo (2)
z Z Z’
’ ’
90 Protons lose phase coherence
˚

y y y’
’ ’
X X X
’ Z’ ’ ’ 180˚ RF
Z Z pulse to
’ ’ Y’ axis
Protons gain phase coherence
Echo formation

y’ y y
’ ’
X’ X X
’ ’
Progressive dephasing can be recovered by applying an 180˚ RF along Y’-axis
too.
Note that the echo is formed along Y’ axis (rather than Y’ axis), the same
polarity as that of FID after 90RF.


 Spin Echo Pulse Sequence

1 2 3 4
K-space
180˚ Trajectory
90˚
RF
3
2
SS Phase
Encoding 1
PE (PE)

Readou 4
t
T2 ADC Readout
decay (Frequency Encoding)
ADC

FID Echo


 Fast Spin Echo (FSE) (1)
Z’ Z Z’
’
After 1st Echo Protons lose phase coherence
formation

y’ y y’
’
X’ X X
’ ’ 180˚ RF
Z’ Z Z pulse to
’ ’ Y’ axis
Protons gain phase coherence
2nd Echo formation

y’ y y
’ ’
X’ X X
’ ’
After 1st echo formation, spins lose phase coherence again and application of another
180 pulse generates another echo.
The above procedure can be repeated to generate multiple echoes.
The echo intensity of the multiple echoes decreases exponentially with time constant
T2.


 Fast Spin Echo (FSE) (2)
180 180 180 18 180
90˚ ˚ ˚ ˚ 0˚ ˚
RF K-space
S
S
PE

Readou PE
t
T2
Echo decay
(ADC)

Multiple 180° RF pulses allow us to get multiple spin echoes. Readout

Each echo fills different phase encoding line.
The echo filling the k-space center region determines the image contrast and thus the
effective echo time.
FSE is favorable for T2-weighted imaging (what TR and TE values should be used for T2-
weighted imaging?)
FSE is also used for T1-weighted imaging (scan time reduction).
The most important imaging sequence in clinical diagnosis.


 Fast Spin Echo (FSE) (3)
echo train

180 180 180 18 180 180 18 180

90˚
˚ ˚ ˚ 0˚ ˚ ˚ 0˚ ˚
RF

PE

The number of 180° RF pulses = turbo factor or echo train length

Short echo train length
Short effective TE
Increase T1 weighting
Longer scan time
More slices per TR
Less image blurring
long echo train length
Long effective TE
Increase T2 weighting
Shorter scan time
Less slices per TR
More image blurring


 Fast Spin Echo (FSE) (4)
Advantages
Reduce scan times significantly
High-resolution matrices and multiple number of excitation (NEX)can
be used
Improve image quality
More T2 information

Disadvantages
Increase some flow and motion effects
Bright fat signals on T2 weighted images
Image blurring with very long echo trains


 T1-, T2-, and PD-weighted Imaging Sequences
For T1, T2, and PD-weighted imaging, RF Excitation and corresponding acquisition
of one PE line are typically performed across multiples slices within one TR.
T1-weighted imaging
- Short TR (~tissue T1 values, 400-1000ms) and short TE (as short as possible)
- The short TR usually accommodates all the slices necessary for clinical
diagnosis of a target region (e.g. brain) (1525 slices) using spin echo or
gradient echo imaging.
- When number of slices are small (e.g. sagittal spine imaging,  11 slices), fast
spin echo with short echo train length is also used to reduce scan time.
T2- and PD-weighted imaging
- Long TR ( 2 times tissue T1 values,  2000 msec)
- Fast spin echo with long TE (~ tissue T2 values, 60 100 msec) or short TE (as
short as possible) (PD-w) determined by k-space center echo (effective TE).
- Multiple slices can be excited and encoded in one TR because of the long TR.
- Spin echo T2-w imaging is used when bright fat and/or blurring is not desired.


 Echo Planar Imaging (EPI)


 Sequence Diagram (Non-EPI vs EPI)
Non-EPI (basic gradient echo) Single-shot EPI
α TR α α

RF RF

GS GS
S S
Phase encoding blip
GP GP
E E
GR GR
O O

Signa Signa
l T l
E T
Echo Planar Imaging is the fastest MR imaging sequence E
N
S

Multiple echoes from alternating frequency encoding gradients

N
S

Phase encoding blips to fill the whole K-space region.

N
S

Acquiring a whole image typically with one RF excitation

N
S


 Echo Planar Imaging (EPI)
Non-EPI Single-shot EPI
𝑘𝑦 𝑘𝑦

𝑘𝑥 𝑘𝑥

TR

5~20 𝑚𝑠 300~650 𝜇𝑠

Both readout and phase encoding prephase gradients move the k-space position
N
S

from the center to the lower left corner.

The alternating frequency encoding gradients fill the data from left to right and
N
S

then from right to left repeatedly.

Phase encoding blips shift the k-space location step by step.
N
S


 GE-EPI vs SE-EPI
Two types of EPI sequences : Gradient-echo EPI (GE-EPI) and Spin-echo EPI (SE-EPI)
N
S

α 90° 180°

R R
F F
GS GS
S S
GP GP
E E
GR GR
O O
Sign Signa
al l

TE TE/ TE/
2 2
GE-EPI SE-EPI
In terms of pulse sequencing, the only difference between GE-EPI and SE-EPI is the
N
S

existence of 180 RF and change in polarities of readout and phase encoding prephase
gradients.


 GE-EPI vs SE-EPI

GE-EPI SE-EPI
Flip angle Any flip angle Only 90°
K-space Center Echo Gradient echo Spin echo
Readout Gradient echo Gradient echo
Scan time Short Short
Compensation of
No Yes
field inhomogeneity


 Segmented EPI (Multi-shot EPI)
Segmented EPI utilizes multiple RF excitations to fill one whole k-space compared to
N
S

single-shot EPI which utilizes one RF excitation.  Higher SNR

α α α α 𝑘𝑦

RF

GS
S
GP ... ... ...
... ... ... 𝑘𝑥
E
GR
O

Signa ... ... ...

l
Sequence diagram of segmented EPI (# of segment = 4)
# of lines per segment
Total phase encoding lines are divided into multiple segments
N
S

𝑁𝑃𝐸
(the number of lines per segment = ~𝐸𝑇𝐿 𝑖𝑛 𝑓𝑎𝑠𝑡 𝑠𝑝𝑖𝑛 𝑒𝑐ℎ𝑜)
# 𝑜𝑓 𝑠𝑒𝑔𝑚𝑒𝑛𝑡𝑠


 Ghost artifacts in EPI
Before phase correction After phase correction

20
Readout gradient 20
Even echoes = 𝐹𝑂𝑉/2
40 40
60 60
Odd echoes 80 80
100 100 = 𝐹𝑂𝑉/2
Due to eddy current
120 120
a b c
20 40 60 80 100 120 20 40 60 80 100 120
Ghost artifacts
• Ghost artifacts can be induced in EPI
N
S

Before phase correction After phase correction

- Due to gradient imperfections (e.g. eddy currents) which cause mismatch between
N
S

phase-encoding lines from 20 odd and even echoes 20

- The phase error between40even and odd echoes results40in signal displacement along the
N
S

phase encoding direction.60 60

- If there are N pixels across80the FOV, this aliased ghost appears at the position shifted by
N

80
S

N/2 pixels relative to the100

original location. (also called100 Nyquist N/2 ghost artifacts)
- The artifact can be suppressed by phase map acquired120with the same EPI scan without
N

120
S

phase encoding blips, which is20called

40 60 a reference
80 100 120scan. 20 40 60 80 100 120


 Advantages and Disadvantages of EPI
Advantages
N
S

- The fastest MR imaging sequence

- Whole brain images can be acquired in a few seconds.
- Applicable to functional MRI, physiological MRI (perfusion, diffusion, etc)

Disadvantages
N
S

- Severe distortions
- Signal dropouts
- Ghost artifacts (needs phase correction)
- Low spatial resolution due to low signal-to-ratio (SNR)


 Non-Cartesian Imaging


 Non-Cartesian Imaging
Cartesian imaging sequence: Acquired data points are directly stored in a Cartesian
grid, so Fourier transform directly generates the image.

Noncartetian imaging sequence: K-space trajectory is not on a Cartesian grid.

Cartesian Spiral Radial

The K-space trajectory can be manipulated by modifying the frequency

encoding and the phase encoding gradients. (Class in Week 4)


 Non-Cartesian Imaging
Most anatomical contrast of an image is determined by the low spatial
frequency components (i.e. central portion of the K-space).
Sampling more at the low spatial frequency offers a better image quality.
Non-cartesian imaging is one of the efficient ways.

Advantage
• Faster acquisition => Can fill K-space with fewer excitation. Generally used
in cardiac MR imaging.
• Robust for motion => K-space center is sampled every TR, providing
average effect.
• No ghost artifact which occurs in EPI imaging.

Disadvantage
• Blurring effect due to undersampling of the high spatial frequency
components and gradient imperfections (if not compensated well).
• The reconstruction is difficult because 2DFT is not directly applicable. There
are many algorithms for reconstruction of images with various complexity.


 Spiral K-space sampling

RF

𝐺𝑆𝑆 Single trajectory Multiple trajectories

K-space can be acquired using single

𝐺𝑃𝐸
trajectory or interleaved multiple trajectories.
Single trajectory is more time efficient but is
𝐺𝑅𝑂 susceptible to artifacts from field
inhomogeneity.
K-space corners are sometimes ignored
Sampling
ADC
because the corners hardly contribute to the
final image.


 Radial K-space sampling

RF

𝐺𝑆𝑆
Radial trajectory

Historically, radial K-space sampling is the

𝐺𝑃𝐸
first data acquisition method used in MRI
imaging, like backprojection reconstruction
𝐺𝑅𝑂 in X-ray Computed Tomography.
K-space center can be continuously updated.
Sampling
Reasonable for dynamic MRI imaging (heart,
ADC
lung, etc).
Streaking artifacts when number of samples
is not large enough.


 Reconstruct of Non-Cartesian K-space
Representative methods
1. Previously known methods in CT image
reconstruction.
• Filtered backprojection

2. Resampling the noncartesian K-space into 𝑘𝑦

Cartesian grid and then using 2DFT.

• Interpolation Interpolation for
resampling on
Cartesian grid

𝑘𝑥