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## Statistical Parametric Mapping

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### Statistical Parametric Mapping Lecture 3 - Chapter 5 Hardware for functional MRI Textbook: Functional MRI an introduction to methods, Peter Jezzard, Paul Matthews ... – PowerPoint PPT presentation

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Title: Statistical Parametric Mapping

1
Statistical Parametric Mapping
• Lecture 3 - Chapter 5
• Hardware for functional MRI

Textbook Functional MRI an introduction to
methods, Peter Jezzard, Paul Matthews, and
Stephen Smith
Many thanks to those that share their MRI slides
online
2
The Magnetic Field
• Ferrous Bar Similar to Bar Magnet
• Torque align
• Force toward poles

Mostly Force
Mostly Torque
3
Nature of Forces Around Magnet
• Ferromagnetic materials mostly
• Depend on shape of object (longer is worse)
• Increase rapidly with approach to magnet (depends
• Increase approximately with square of B0 (3T vs
1.5T)
• Depends on type of magnet (open, self-shielded,
etc.) (depends on B0 spatial gradient)

4
fMRI Basic Requirements
• Rapid Imaging
• wide bandwidth transceiver
• Stable System
• systematic drift small
• noise small
• High Signal Levels
• high field strength magnet
• RF coil design

EPI T2 demands
Relative to physiological noise
5
Magnetic Susceptibility
• Net B B0 ?B
• ?B is proportional to both field strength (H) and
susceptibility (?). In air ?B 0.
• Macroscopic changes of B induced at different
locations result in spatial gradients in B that
can be significant for EPI.
• For many parts of the brain the macroscopic
susceptibility gradient is small so Larmor
frequencies are similar.
• For areas where the macroscopic susceptibility
gradient is large (e.g. near tissue air
interfaces) Larmor frequencies of nearby voxels
also changes greatly.
• Microscopic changes in susceptibility due to BOLD
effect can be masked when near areas in brain
with large changes in macroscopic susceptibility.

6
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7
EPI style BOLD fMRI -advantages and
• Fast
• Resolve hemodynamic changes, whole head coverage
in 3 seconds or less.
• Freeze subject motion (k-space encode of slice in
lt50ms).
• Encodes full k-space image without RF signal
reset compared to non-EPI imaging (phase errors
accumulate).
• Susceptibility weighted
• Want good signal from microscopic dephasing due
to BOLD induced susceptibility.
• Interference from macroscopic dephasing due to
large extent changes in susceptibility.

8
Problems With Macroscopic Susceptibility
Signal Dropout...
Distortions
All susceptibility effects increase with Bo!!
Wald, Toronto 2005
9
Image Encoding for EPI
All lines in one shot
• Fast (high BW ) in kx.
• Slow (low BW) in ky.
• No reset by RF, so phase errors accumulate.
• Fast (10 slices per second) for 2 mm res.
• Physiological fluctuations modulate overall
intensity
• All k-space NOT treated equally.

dt0.005ms dt0.5ms
Wald, Toronto 2005
10
Temporal Sampling is Asymmetric in EPI 100x
longer in phase direction
ky
• k-space errors due to susceptibility are small in
kx direction because of short time sampling
intervals.
• but can be significant in ky encode direction
(100x longer here).

Note frequency gradient from point 1 to point 2
1
2
kx
Dj Du t dephasing leads to signal loss
frequency map
Wald, Toronto 2005
11
Image encoding strategies EPI
All k-space not treated equally
T2 filtering across k-space increases
• T2 shortens as B0 increases
• Limit total readout time to 2T2

Wald, Toronto 2005
12
EPI and Spiral Scanning of k-space
EPI
Spiral
Gx and Gy 90 degrees phase difference for sprial
Interpolated to regular kx and ky spacing.
Wald, Toronto 2005
13
EPI Spirals Susceptibility distortion, b
lurring, dephasing dephasing Eddy
currents ghosts blurring k 0 is
sampled 1/2 through beginning Corners of
kspace yes no Gradient demands very
high pretty high
Wald, Toronto 2005
14
Normalized SNR vs. Magnetic Strength
• Time fore single Kx (SE,GRE) TAD ltlt T2
• Time for full K-space (EPI) TAD T2
• TAD intermediate for others (FSE, TSE)

Figure 5.3 from textbook.
15
Total SNR vs Thermal SNR
Data from 1.5T (triangles) and 3.0T systems
(squares)
Physiological
Signal - S Thermal and system noise -
?0 Physiological sources - ?p Total noise - ?
1.
3.
2.
Figure 5.4 from textbook.
16
Schematic of MRI System
Same or different transmit and receive coil.
A/P - Array Processor RF, Shim, Gradient Coils
inside magnet All but Host, RAM, and A/P in
equipment room
Figure 5.1b from textbook.
17
RF Coil Uniformity and SNR
B1 directions indicated by color arrows.
(1) two surface coils on opposite sides in
phase. (2) two surface coils out of phase. (3)
single surface coil on right side. (largest
SNR) (4) head coil. (most uniform SNR)
Figure 5.7 from textbook.
18
Surface Coils
19
Surface Coil Orientations
B0
Surface coils are like loops for detecting B1
which is precessing about B0 which is parallel to
the z-axis
• Best orientation is with plane of coil
perpendicular to B0 which for the brain in normal
orientation leads to following as best sites
• Left or right side
• Anterior of posterior

Figure 5.8 from textbook.
20
Tissue Heating During RF Transmit
• Concerns are total body and localized heating
• Not practical to monitor increase in temperature
except in phantoms
• Specific Absorption Rate (SAR) used to estimate
temperature increase
• 1 SAR 1 W/kg
• 1 SAR would increase temperature of an insulated
slab by 1? C/hr
• SAR also used in monitoring RF for cell phones

21
Scanner Software Estimates SAR
• Runs a calibration routine
• Determines energy for RF pulses
• Adds up energy from all RF pulses per TR and
divides by TR
• Divides by tissue weight to get total body or
regional SAR
• Requires height and weight for algorithm
• If limits are exceeded operator must alter pulse
sequence

22
RF - FDA Limits
• Integrated SAR limits
• Trunk SAR 120 W-min/kg
• Extremeties SAR 180 W-min/kg
• SAR rates
• Head (38 C) SAR3.2 W/kg
• Trunk (39 C) SAR 8 W/kg
• Extremities (40 C) SAR 12 W/kg
• Other
• Infants, pregnancy, cardiocirculatory or cerebral
vascular impairment (1.5 W/kg)

23
SAR Pulse Sequence Impact
• Minimal for EPI acquisition (1-2 RF pulses per
plane)
• Higher for 3D anatomical scan GRE (1 RF pulse per
• High for T1W spin echo (one 90º and one 180º RF
pulse per kx line) with slice geometry same as
GRE
• Within pulse sequence effects
• Increasing TR without increasing of RF pulses
reduces SAR
• Reducing number of slices per TR (in multislice
SE)
• Partial Fourier imaging reduces number of phase
encodes with RF for each (in multislice SE)

24
Figure 5.5
Figure 5.6 from textbook.
25
c
a
d
b
• a. gradient current supplied (short rise time
induces eddy currents)
• b. eddy currents oppose changing field w/o
compensation
• c. gradient current supplied with eddy current
compensation
• d. potential field vs time with eddy current
compensation

Jerry Allison.
26
dB/dt Effect (more eddy currents) Peripheral
Nerve Stimulation
• dB/dt --gt dE/dt
• dt is gradient ramp time
• dB/dt largest near ends of gradient coils
• spatial gradient of dE/dt important

27
dB/dt / E-Field Characteristics of Stimulation
• Not dependent on B0
• Gradients - 40mT/m (larger Bmax for longer
coil)
• Gradient Coil Differences - strength (increases
dB) and length (head vs. body determines site)
• Rise Time - shorter rise time means shorter dt
and therefore larger dB/dt
• Other
• Disruption of nearby medical electronic devices
• Subject Instructions
• Dont clasp hands - closed circuit, lower
threshold
• Report tingling, muscle twitching, painful
sensations

28
Acoustic Noise Levels
Ouch
front row RR band
• Noise Reduction Rating
• 25-30 dB
• Combined 5 dB more

Tomoyuki et al, Toshiba
29
Acoustic Noise
• Lorentz forces acting on gradient coils
• Forces gradient noise level increases with both
• Levels for EPI fMRI
• Peak 130 dB _at_ 3T, 110 dB _at_ 1.5T
• Average 90-117 dB(A)
• Frequency content varies by sequence
• EPI higher average frequency (more read and phase
• 3D GRE probably next (short TR)
• Spin Echo (depends on TE and TR slices per TR,
etc.)

30
Acoustic Noise
• Lorentz forces acting on gradient coils
• Gradient noise level increases with both B0 and
• Levels for EPI fMRI
• Peak 130 dB _at_ 3T, 110 dB _at_ 1.5T
• Average 90-117 dB(A)
• Frequency content varies by sequence
• EPI higher average frequency (more read and phase
• 3D GRE probably next (short TR)
• Spin Echo (depends on TE and TR slices per TR,
etc.)

31
• Experimental Designs
• Reduce intra- acquisition noise
• Reduce inter-acquisition noise
• Reduce Noise at source
• Hardware changes
• Passive and Active Noise Reduction
• Earplugs, mufflers

Covered in later lectures.
32
• Amplitude of sound transmitted to the ear by bone
conduction is frequency dependent and maximal at
2 kHz.
• Active noise cancellation systems may be more
useful for 1.5T and 2T systems that produce
sounds below 1 kHz.
• Some 3T scanners produce strong sounds in the
1.5-2.5 kHz frequency range.

33
34
Video Projection Approaches
LCD Projector, Mirror, Screen
Mirror on RF coil Screen
35
Stimulus Presentation / Monitoring
36
E-Prime
• Software
• Time-Line
• Control Stimulus
• Monitor Response
• Synchronize timing with MRI

37
• Hardware
• Stimulation
• Visual
• Motor
• Auditory
• Response
• Visual
• Motor
• Auditory

38
fMRI Personnel
• Patient or Volunteer Support
• Family
• Nurse, physician
• MRI Operation
• Board Certified Tech
• Research Group
• PI collaborators
• Associated Equipment Tech
• Stimulus presentation, monitoring, etc.
• Analysis
• PI
• Post doc, research assistant, etc.

I know this is not following the theme of this
chapter, but important.
39
fMRI Study Time
4 hr (one instance)
• New Design
• Scanning
• Setup
• Scans
• Take down
• Preprocessing
• Statistical Analysis

1-1.5 hr/subject
15-20 min
45 min to 1 hr
15 min
lt2 hr/ subject
?
variable
40
fMRI Study Raw Data
• Localizer image lt 1 MByte
• Anatomy image
• Same resolution (2562 x 25) gt 3 MByte
• 3D high resolution (2563) gt 30 MByte
• Event Related fMRI study
• 20 slices/image x 15 images/event x 20
repetitions
• x 128x128 images 200 mByte
• Reorganizing data into volumes indexed by time
200 mByte

41
fMRI Study All Data
• Raw Data 200 mBytes
• Motion Correction 180 mBytes
• Other Corrections 180 mBytes each possibly
• Spatial Normalization 30 mBytes
• Statistical Analysis
• Statistical Parametric Image (128x128x20) lt 1
MByte
• Statistical Parametric Map (2x SPI) gt 1 MByte

Total Data per subject can be 0.5-1.0 gBytes
42
Statistical Parametric Mapping
• Lecture 3 - Chapter 5
• Hardware for functional MRI

Textbook Functional MRI an introduction to
methods, Peter Jezzard, Paul Matthews, and
Stephen Smith
Many thanks to those that share their MRI slides
online