Title: 10 things you need to know to be a successful fMRI researcher
110 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
2The 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
3The 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
4General Electric 3 Tesla Scanner
5Imaging System Components
Magnet
RF Receiver
Viewing Console
X
Y
Z
RF Transmitter
Scan Controller
Gradient Power Systems
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7To 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
8The 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
9time
Anatomic
Functional
10Echo-Planar Imaging
11Single Shot Imaging
T2 decay
EPI Readout Window
20 to 40 ms
12Imaging System Components
Magnet
RF Receiver
Viewing Console
X
Y
Z
RF Transmitter
Scan Controller
Gradient Power Systems
131991-1992
1992-1999
142 G/cm, 350 T/m/s
4 G/cm, 150 T/m/s
10 G/cm, 1000 T/m/s
15The 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?
16The 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
17Minimum Staff
Physicist (or Engineer) Computer
Specialist Scanning Technologist Researcher and
team -paradigm design -paradigm
construction -processing -interpretation
18The 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
19Imaging 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
20The 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
21A Primary Challenge
...to make progressively more precise inferences
using fMRI without making too many assumptions
about non-neuronal physiologic factors.
22Contrast 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
23Resting Active
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26BOLD 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
27The BOLD Signal
Blood Oxygenation Level Dependent (BOLD) signal
changes
task
task
28Alternating Left and Right Finger Tapping
1992
29Creating a Functional Image
ON
ON
ON
ON
ON
X
Signal Time Course
Reference Function
30Cross Correlation Image
Cross Correlation Image Anatomical Image
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32Perfusion / Flow Imaging
EPISTAR
FAIR
. . .
-
-
-
-
Perfusion Time Series
. . .
33FAIR
EPISTAR
34Resting ASL Signal
35Comparison with Positron Emission Tomography
PET H215O
MRI ASL
36Perfusion Rest Activation
BOLD
37Anatomy
BOLD
Perfusion
38Hemodynamic Specificity
Arterial inflow (BOLD TR lt 500 ms)
Venous inflow (Perf. No VN)
39Hemdodynamic Stress Calibration
5 CO2
12 O2
40CMRO2-related BOLD signal deficit
Hoge, et al.
CBF
BOLD
Simultaneous Perfusion and BOLD imaging during
graded visual activation and hypercapnia
N12
41CBF-CMRO2 coupling
Hoge, et al.
Characterizing Activation-induced CMRO2
changes using calibration with hypercapnia
42Computed CMRO2 changes
Hoge, et al.
40
30
20
10
0
-10
-20
-30
-40
Subject 2
Subject 1
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44The 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
45Hemodynamic Transfer Function
Neuronal
Measured
Activation
fMRI
Signal
Hemodynamics
Physiolologic Factors
46Time (sec)
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50 2 sec
Latency
- 2 sec
Magnitude
51Observed Responses
measured
ideal (linear)
visual stimulation
250 ms
500 ms
1000 ms
2000 ms
motor task
500 ms
1000 ms
2000 ms
4000 ms
52BOLD response is nonlinear
Observed response
Linear response
Short duration stimuli produce larger responses
than expected
53Results visual task
54Sources of this Nonlinearity
- Neuronal
- Hemodynamic
- Oxygen extraction
- Blood volume dynamics
Oxygen Extraction
Flow In
Flow Out
D Volume
55BOLD Correlation with Neuronal Activity
Logothetis et al. Nature, 412, 150-157
Bandettini and Ungerleider, Nature Neuroscience,
4, 864-866
56Motor Cortex
Auditory Cortex
57Logothetis et al. Nature, 412, 150-157
58The 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
59Types 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
60Higher 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
610.25 Hz Breathing at 3T
3ms
Image
26ms
Power Spectra
Respiration map
49ms
0 0.25
0.5 Hz
620.68 Hz Cardiac rate at 3T
3ms
Image
26ms
Power Spectra
Cardiac map
49ms
0 0.68 (aliased) 0.5 Hz
63Temporal 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
64CC Histogram
Continuously Growing Activation Area
Inflection Point
Ziad Saad, et al
65Resting Hemodynamic Autocorrelations
low frequency autocorrelation map
conventional BOLD map
B. Biswal et al., MRM, 34537 (1995)
66The 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
67Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
68Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
69DeYoe et al.
70Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
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720.08 Hz 0.05 Hz
spectral density
c.c. gt 0.5 with spectra
73Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
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76Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
77Detectability constant ISI
SD stimulus duration
ISI inter-stimulus interval
Detectability
0
5
10
15
20
25
30
35
40
Average ISI (s)
78Visual Activation Paradigm 1 , 2, 3 Trials
20 sec
0 sec
0 sec
2 sec
20 sec
0 sec
2 sec
20 sec
4 sec
79Response to Multiple Trials Subject RW
RAW DATA
ESTIMATED RESPONSES
5
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80Detectability 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)
81Speaking - Blocked Trial
82fMRI during tasks that involve brief motion
Blocked Design
motion
BOLD response
task
Event-Related Design
83Overt Word Production
2
3
4
5
6
7
8
9
10
11
12
13
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85Tongue Movement
Jaw Clenching
86Speaking - ER-fMRI
Constant ISI
Expected Response
87Swallowing - Event-Related
88Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
89Example of a Set of Orthogonal Contrasts for
Multiple Regression
90Neuronal Activation Input Strategies
1. Block Design 2. Frequency Encoding 3. Phase
Encoding 4. Single Event 5. Orthogonal Block
Design 6. Free Behavior Design.
91Free Behavior Design
- Use a continuous measure as a reference function
- Task performance
- Skin Conductance
- Heart, respiration rate..
- Eye position
- EEG
92The 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
93Skin 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.
94Brain activity correlated with SCR during Rest
95The 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
96Types of Applications
Clinical presurgical mapping perfusion
mapping correlation with disorders Physiology Basi
c Neuroscience Cognitive Neuroscience Psychiatry P
sychology Pharmacology
97The 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
98Regions of Interest Used for Hemi-Field
Experiment
Left Hemisphere
Right Hemisphere
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100Hemi-field with 500 msec asynchrony
Average of 6 runs Standard Deviations Shown
Percent
MR
Signal
Strength
Time (seconds)
101500 ms
500 ms
Right Hemifield
Left Hemifield
2.5 s
-
0 s
- 2.5 s
102250 ms
250 ms
Right Hemifield
Left Hemifield
2.5 s
-
0 s
- 2.5 s
103Single Shot Imaging
T2 decay
EPI Readout Window
20 to 40 ms
104Multishot Imaging
T2 decay
EPI Window 2
105Multi Shot EPI
Excitations 1 2 4 8 Matrix Size 64 x 64 128
x 128 256 x 128 256 x 256
106Partial k-space imaging
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109ODC 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).
110The 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
111Rules 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
112The 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
113Additional 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
114Functional 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