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Title: 10 things you need to know to be a successful fMRI researcher


1
10 things you need to know to be a successful
fMRI researcher
  • Peter A. Bandettini, Ph.D
  • Unit on Functional Imaging Methods
  • 3T Neuroimaging Core Facility
  • Laboratory of Brain and Cognition
  • National Institute of Mental Health

2
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
3
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
4
General Electric 3 Tesla Scanner
5
Imaging System Components
Magnet
RF Receiver
Viewing Console
X
Y
Z
RF Transmitter
Scan Controller
Gradient Power Systems
6
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7
To perform an MRI Experiment
1. Place patient in magnet 2. Send in a radio
frequency (RF) wave 3. Turn off the RF wave. 4.
Patients emits a signal 5. Image is reconstructed
8
The Concept of Contrast (or Weighting)
  • Contrast difference in RF signals emitted by
    water protons between different tissues
  • Example gray-white contrast is possible because
    T1 is different between these two types of tissue

9
time
Anatomic
Functional
10
Echo-Planar Imaging
11
Single Shot Imaging
T2 decay
EPI Readout Window
20 to 40 ms
12
Imaging System Components
Magnet
RF Receiver
Viewing Console
X
Y
Z
RF Transmitter
Scan Controller
Gradient Power Systems
13
1991-1992
1992-1999
14
2 G/cm, 350 T/m/s
4 G/cm, 150 T/m/s
10 G/cm, 1000 T/m/s
15
The use of fMRI to Investigate Brain Function
Where? When? How much? --- How to get the brain
to do what we want it to do in the context of an
fMRI experiment?
16
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
17
Minimum Staff
Physicist (or Engineer) Computer
Specialist Scanning Technologist Researcher and
team -paradigm design -paradigm
construction -processing -interpretation
18
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
19
Imaging and Processing Steps
  • Shimming
  • Localizer
  • High resolution anatomical image
  • Functional time series collection
  • Image reconstruction
  • Time series analysis
  • Registration
  • Correlation, Regression, t-test, etc..
  • Statistical threshold
  • Display
  • Image normalization
  • Multiple subject comparison
  • Interpretation

20
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
21
A Primary Challenge
...to make progressively more precise inferences
using fMRI without making too many assumptions
about non-neuronal physiologic factors.
22
Contrast in Functional MRI
  • Blood Volume
  • Contrast agent injection and time series
    collection of T2 or T2 - weighted images
  • BOLD
  • Time series collection of T2 or T2 - weighted
    images
  • Perfusion
  • T1 weighting
  • Arterial spin labeling
  • CMRO2
  • BOLD and Perfusion w/
  • Normalization to Global Perfusion Change

23
Resting Active
24
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25
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26
BOLD Contrast in the Detection of Neuronal
Activity
Cerebral Tissue Activation
Local Vasodilation
Oxygen Delivery Exceeds Metabolic Need
Increase in Cerebral Blood Flow and Volume
Increase in Capillary and Venous Blood Oxygenation
Deoxy-hemoglobin paramagnetic Oxy-hemoglobin
diamagnetic
Decrease in Deoxy-hemoglobin
Decrease in susceptibility-related intravoxel
dephasing
Increase in T2 and T2
Local Signal Increase in T2 and T2 - weighted
sequences
27
The BOLD Signal
Blood Oxygenation Level Dependent (BOLD) signal
changes
task
task
28
Alternating Left and Right Finger Tapping
1992
29
Creating a Functional Image
ON
ON
ON
ON
ON
X
Signal Time Course
Reference Function

30
Cross Correlation Image
Cross Correlation Image Anatomical Image
31
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32
Perfusion / Flow Imaging
EPISTAR
FAIR







. . .
-
-
-
-
Perfusion Time Series
. . .
33
FAIR
EPISTAR
34
Resting ASL Signal
35
Comparison with Positron Emission Tomography
PET H215O
MRI ASL
36
Perfusion Rest Activation
BOLD
37
Anatomy
BOLD
Perfusion
38
Hemodynamic Specificity
Arterial inflow (BOLD TR lt 500 ms)
Venous inflow (Perf. No VN)
39
Hemdodynamic Stress Calibration
5 CO2
12 O2
40
CMRO2-related BOLD signal deficit
Hoge, et al.
CBF
BOLD
Simultaneous Perfusion and BOLD imaging during
graded visual activation and hypercapnia
N12
41
CBF-CMRO2 coupling
Hoge, et al.
Characterizing Activation-induced CMRO2
changes using calibration with hypercapnia
42
Computed CMRO2 changes
Hoge, et al.
40
30
20
10
0


-10
-20
-30
-40
Subject 2
Subject 1
43
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44
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
45
Hemodynamic Transfer Function
Neuronal
Measured
Activation
fMRI
Signal
Hemodynamics
Physiolologic Factors
46
Time (sec)
47
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48
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49
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50
2 sec
Latency
- 2 sec
Magnitude
51
Observed Responses
measured
ideal (linear)
visual stimulation
250 ms
500 ms
1000 ms
2000 ms
motor task
500 ms
1000 ms
2000 ms
4000 ms
52
BOLD response is nonlinear
Observed response
Linear response
Short duration stimuli produce larger responses
than expected
53
Results visual task
54
Sources of this Nonlinearity
  • Neuronal
  • Hemodynamic
  • Oxygen extraction
  • Blood volume dynamics

Oxygen Extraction
Flow In
Flow Out
D Volume
55
BOLD Correlation with Neuronal Activity
Logothetis et al. Nature, 412, 150-157
Bandettini and Ungerleider, Nature Neuroscience,
4, 864-866
56
Motor Cortex
Auditory Cortex
57
Logothetis et al. Nature, 412, 150-157
58
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
59
Types of Artifacts Nature of Noise
  • Drift (scanner and/or subject)
  • Stimulus correlated motion
  • Cardiac, respiratory motion
  • Bo changes (mouth movement, etc..)
  • Eye movement
  • Equipment in scanner room (RF interference)
  • Scanner spiking

60
Higher Signal to Noise in a single image does not
necessarily translate to higher Signal to Noise
over time.
Temporal vs. Spatial SNR- 3T
26ms
49ms
26ms
49ms
SPIRAL
27ms
50ms
27ms
50ms
EPI
61
0.25 Hz Breathing at 3T
3ms
Image
26ms
Power Spectra
Respiration map
49ms
0 0.25
0.5 Hz
62
0.68 Hz Cardiac rate at 3T
3ms
Image
26ms
Power Spectra
Cardiac map
49ms
0 0.68 (aliased) 0.5 Hz
63
Temporal S/N vs. Image S/N
PHANTOMS
SUBJECTS
1400 1200 1000 800 600 400 200
Temporal S/N
Temporal S/N
0 200 400 600 800
1000 1200 1400
Image S/N
Image S/N
N. Petridou
64
CC Histogram
Continuously Growing Activation Area
Inflection Point
Ziad Saad, et al
65
Resting Hemodynamic Autocorrelations
low frequency autocorrelation map
conventional BOLD map
B. Biswal et al., MRM, 34537 (1995)
66
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
67
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
68
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
69
DeYoe et al.
70
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
71
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72
0.08 Hz 0.05 Hz
spectral density
c.c. gt 0.5 with spectra
73
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
74
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76
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
77
Detectability constant ISI
SD stimulus duration
ISI inter-stimulus interval
Detectability
0
5
10
15
20
25
30
35
40
Average ISI (s)
78
Visual Activation Paradigm 1 , 2, 3 Trials
20 sec
0 sec
0 sec
2 sec
20 sec
0 sec
2 sec
20 sec
4 sec
79
Response to Multiple Trials Subject RW
RAW DATA
ESTIMATED RESPONSES
5
5
4
4
T
H
R
E
E
-
T
R
I
A
L
3
3
T
W
O
-
T
R
I
A
L
2
2
1
1
O
N
E
-
T
R
I
A
L
0
0
-
1
-
1
0
1
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1
0
1
1
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T
I
M
E

(
S
E
C
)
T
I
M
E

(
S
E
C
)
80
Detectability vs. Average ISI
SD 4000 s.
Detectability
SD 1000 ms.
SD 250 ms.
0
5
10
15
20
25
30
35
40
average ISI (s)
81
Speaking - Blocked Trial
82
fMRI during tasks that involve brief motion
Blocked Design
motion
BOLD response
task
Event-Related Design
83
Overt Word Production
2
3
4
5
6
7
8
9
10
11
12
13
84
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85
Tongue Movement
Jaw Clenching
86
Speaking - ER-fMRI
Constant ISI
Expected Response
87
Swallowing - Event-Related
88
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
89
Example of a Set of Orthogonal Contrasts for
Multiple Regression
90
Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
91
Free Behavior Design
  • Use a continuous measure as a reference function
  • Task performance
  • Skin Conductance
  • Heart, respiration rate..
  • Eye position
  • EEG

92
The Skin Conductance Response (SCR)
Ventromedial PFC
Orbitofrontal Cortex
Amygdala
Hypothalamus
Sympathetic Nervous System
Resistance change across two electrodes induced
by changes in sweating.
Sweat Gland
93
Skin Conductance Dynamics
1 - 3 sec 1 - 3 sec 8 - 14 sec
  • Boucsein, Wolfram (1992). Electrodermal Activity.
    Plenum Press, NY
  • Venables, Peter, (1991). Autonomic Activity
    ANYAS 620191-207.

94
Brain activity correlated with SCR during Rest
95
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
96
Types of Applications
Clinical presurgical mapping perfusion
mapping correlation with disorders Physiology Basi
c Neuroscience Cognitive Neuroscience Psychiatry P
sychology Pharmacology
97
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
98
Regions of Interest Used for Hemi-Field
Experiment
Left Hemisphere
Right Hemisphere
99
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100
Hemi-field with 500 msec asynchrony
Average of 6 runs Standard Deviations Shown
Percent
MR
Signal
Strength
Time (seconds)
101
500 ms
500 ms
Right Hemifield
Left Hemifield
2.5 s

-
0 s
- 2.5 s
102
250 ms
250 ms
Right Hemifield
Left Hemifield
2.5 s

-
0 s
- 2.5 s
103
Single Shot Imaging
T2 decay
EPI Readout Window
20 to 40 ms
104
Multishot Imaging
T2 decay
EPI Window 2
105
Multi Shot EPI
Excitations 1 2 4 8 Matrix Size 64 x 64 128
x 128 256 x 128 256 x 256
106
Partial k-space imaging
107
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108
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109
ODC Maps using fMRI
1 cm
calcarine
  • Identical in size, orientation, and appearance
    to those obtained by optical imaging1 and
    histology3,4.

1Malonek D, Grinvald A. Science 272, 551-4
(1996). 3Horton JC, Hocking DR. J Neurosci 16,
7228-39 (1996). 4Horton JC, et al. Arch
Ophthalmol 108, 1025-31 (1990).
110
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
111
Rules of Thumb
Signal Dropout shimming limits Image
Warping Resolution Repetition Time (TR) Echo Time
(TE) Time necessary for a slice Amount of
averaging necessary Smoothing? (spatial,
temporal) RF coils Comparisons within/across
subjects
112
The 10 Things
1. The Scanning Technique (MRI) 2. Necessary
Technical skills and/or People 3. Imaging and
Processing steps 4. Types of Functional Contrast
5. Details of Functional Contrast 6. Types of
Artifacts 7. Methods to Bypass or Remove
Artifacts 8. Types of Applications 9. Limits of
Techniques and Applications 10. Some rules of
thumb
113
Additional Thanks To
Eric Wong, UCSD Robert Savoy, MGH Richard Hoge,
MGH Randy Buckner, Wash. U. Ted DeYoe, MCW Sue
Courtney, Johns Hopkins U. Rasmus Birn, NIH Ziad
Saad, NIH Patrick Bellgowan, NIH
114
Functional Imaging Methods / 3T Group
Staff Scientists Sean Marrett Jerzy Bodurka Post
Docs Rasmus Birn Patrick Bellgowan Ziad
Saad Graduate Student Natalia Petridou Summer
Student Dan Kelley Program Assistant Kay Kuhns
August, 2000
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