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Signal and Noise in fMRI

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Signal and Noise in fMRI John VanMeter, Ph.D. Center for Functional and Molecular Imaging Georgetown University Medical Center Outline Definition of SNR and CNR in ... – PowerPoint PPT presentation

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Title: Signal and Noise in fMRI


1
Signal and Noise in fMRI John VanMeter,
Ph.D. Center for Functional and Molecular
Imaging Georgetown University Medical Center
2
Outline
  • Definition of SNR and CNR in context of anatomic
    imaging
  • Definition of functional SNR
  • Sources of noise in MRI
  • Source of noise in fMRI
  • Changes in MRI SNR and functional SNR with
    increased magnetic field strength

3
MRI Signal and Noise
  • Signal is primarily dependent on number of
    protons in the voxel
  • Noise can come from RF energy leaking into the
    scanner room, random fluctuations in electrical
    current, etc.
  • The body creates noise in the MR signal via
    changes in current in the body producing small
    changes in the magnet field breathing can change
    homogeneity

4
Measuring MRI Signal-to-Noise Ratio (SNR)
  • Signal is the intensity (brightness) of one or
    more pixels in the object of interest.
  • Noise is the intensity of one or more pixels in
    the air (i.e. outside the object of interest).
  • SNR Signal (low SNR grainy, fuzzy images)
  • Noise
  • Fundamental measure of image quality

5
MRI SNR Example 1
  • S 700
  • N 20
  • SNR 700 / 20
  • 35

6
MRI SNR Example 2
  • S 300
  • N 50
  • SNR 300 / 50
  • 6

7
MRI SNR - Side-by-Side
SNR 35 SNR 6
8
SNR in Terms of fMRI
  • MRI SNR is not the most important issue with
    regard to functional MRI
  • Functional SNR is contingent on ability to detect
    changes in BOLD signal between conditions (across
    time)
  • Underlying MRI SNR still important in terms of
    providing base for signal in functional SNR but
    several other factors affect signal and noise in
    fMRI data

9
Affect of MRI SNR on Functional SNR
  • Increase in MRI signal due to BOLD affect rides
    on top of signal of in MRI scan
  • Imagine 2 increase in signal between these two
    fMRI scans
  • In which image will the 2 change be more
    detectable?

10
Changes in BOLD Signal are Small
  • Visual and sensorimotor areas percent change
    might be as high 5
  • For most other cortical areas expected percent
    change is on the order of 1-3

11
Measuring Percent Signal Change
12
MRI Contrast-to-Noise Ratio (CNR)
  • Measure of separation in terms of average
    intensity between two tissues of interest
  • Defined as difference between the SNR of the two
    tissues (A B)
  • CNR SignalA SignalB
  • Noise

13
MRI CNR Example 1
  • SW 700, SG 200
  • N 20
  • CNRWG (700 200) / 20
  • 25

14
MRI CNR Example 2
  • SW 200, SG 100
  • N 50
  • CNRWG (200 100) / 50
  • 2

15
MRI CNR Side-by-Side
CNRWG 35 CNRWG 6
16
Functional CNR vs Functional SNR
  • Generally CNR is unimportant in fMRI as there is
    little contrast between tissues
  • Some researchers refer to difference between On
    and Off as dynamic CNR or functional CNR
  • Probably more accurate to refer to ability to
    detect changes related to activity as functional
    SNR

17
  • Functional SNR is a dependent on differences in
    signal across time
  • Ability to distinguish differences between
    different conditions - effect size

18
Differences Between Two Conditions
  • Typically compare BOLD signal in the same area
    under different conditions
  • Example fusiform face area responds to both
    faces and tools but about 0.2 more to faces

19
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20
Sources of Noise in fMRI Data
  • System noise
  • Thermal noise
  • Signal drift
  • Subject dependent noise
  • Physiological noise
  • Variability in BOLD response
  • Variability across sessions within subject
  • Variability across subjects

21
Thermal Noise
  • Intrinsic noise due to thermal motion of
    electrons
  • In subject
  • In RF equipment
  • Increases with temperature - atoms move faster
    more collisions greater loss of energy
  • Unfortunately increases with field strength
    approximately linearly
  • Effects limited to temporal fluctuations and is
    equally likely to add or subtract thus roughly
    Gaussian (i.e. normally) distributed

22
Signal Drift Across Time
  • Magnetic field has slight drifts in strength over
    time produces drift in signal
  • Gradually, over time the MRI signal in a voxel
    drifts
  • This drift can vary from one voxel to the next
    both in degree and direction!

23
Signal Drift
24
Affect of Signal Drift
25
Effect of Nonlinear Drifts
26
Physiological Noise
  • Subject movement during scan
  • Single largest source of noise in fMRI data
  • Extremely problematic if motion is timed with
    task
  • Makes studies with overt speech during the scan
    quite difficult
  • Motion more problematic across time points

27
Subject Motion
28
Pulsatile Motion of Brain
  • Influx of blood into brain induces movement
    especially around base of brain - why there?
  • Short TRs can also pick-up noise due to
    respiration (TRlt2500ms) and cardiac (TRlt500ms)
    cycle

29
  • Map showing standard deviation of intensity over
    time
  • Two sources of noise evident
  • Why do edges of brain show large effect?
  • Often referred to as ringing

30
Power Spectrum
31
Other Sources of Physiological Noise
  • Change in CO2 - hyperventilation produces change
    in O2 content of blood blood flow increases to
    compensate
  • Drug affects - antihistamines, etc
  • Smokers vs. Non-smokers
  • Hypoactivation on attentional task after
    abstaining for 1hr reversed following nicotine
    patch (Lawrence et al, 2002)

32
Genetic Based Differences
  • ApoE risk factor for Alzheimers disease
  • Study of non-symptomatic carriers
  • Reduced activation in hippocampus on a memory
    task for high risk carriers (AS Fleisher, et al,
    Neurobiology of Aging, 2008)

33
Noise from Neural Activity Not of Interest
  • Eye movements - results in activation of the
    frontal eye-fields
  • Noise of the scanner - activates auditory
    cortices
  • Usually not a problem as noise common to both
    conditions
  • Auditory experiments difficult though
  • Other thoughts - whats for dinner, going over a
    to-do list, wondering what the experiment is
    testing (grad students), etc

34
Behavioral and Cognitive Variability
  • Passive tasks are prone to drift in subject
    attention and/or arousal
  • Difficult to identify performance on tasks and
    compare across subjects
  • Tasks with responses can lead to variations in
    reaction/response time
  • Speed-accuracy trade-off
  • Task strategies used can differ
  • Task difficulty especially between groups of
    subjects very problematic

35
Inter-Subject Variability
36
Inter-Session Variability
37
Intra-Session Variability
38
99-Scanning Sessions
  • Same subject participated in 99 identical
    scanning sessions
  • 33 each for motor task, visual task, and a
    cognitive task
  • Everything kept exactly the same
  • Considerable variability was observed

39
33 Motor Sessions
McGonigle, et al., Neuroimage, 2000
40
33 Cognitive Sessions
41
Strategies for Dealing with Noise Improving
Signal
  • MRI Center Steps
  • Measure stability of signal over time
  • Ensure stability of equipment
  • Eliminate RF-noise
  • Researcher
  • Formalize instructions (use scripts)
  • Train subjects ahead of time
  • Instruct subjects to use same strategy
  • Stress importance of staying still, focus, etc.
  • Use better post-processing techniques
  • Increase field strength

42
Post-processing
Pre Post
Smith, et al., Human Brain Mapping, 2005
43
Signal Averaging
  • Averaging across multiple trials greatly helps to
    improve SNR
  • Each graph shows 20 traces of 1 trial, average of
    4 trials, average of 9 trials, etc

44
Increasing MRI Signal with Stronger Magnets
  • Increase magnetic field strength
  • Plus
  • more protons pulled into alignment thus greater
    net magnetization resulting in increased MRI
    signal
  • Minus
  • shortens T2 resulting in larger spatial
    distortions with gradient echo sequences
  • Requires larger RF pulses thus SAR goes up (why?)

45
Susceptibility Distortion Increases with Field
Strength
  • 1.5T
  • 4.0T

46
Rules of Thumb
  • Quadratic increase in MRI signal with increase in
    field strength
  • Thermal noise scales linearly with field strength
  • Raw MRI SNR thus only scales linearly
  • What about functional SNR?

47
Functional SNR Linearly Increases with Field
Strength?
48
Functional SNR vs Field Strength
  • MRI signal goes up quadratically
  • Thermal noise goes up linearly
  • Physiological noise goes up quadratically
  • Eventually functional SNR expected to plateau

49
Upsides to Field Strength for Functional SNR
  • Increase in number of voxels activated and
    presumably detectability
  • T2 of blood much shorter thus signal drops off
    in larger vessels
  • Linear increase in large vessels
  • Quadratic increase in small vessels
  • Thus, spatial specificity increases
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