FMRI – Week 1 – Introduction Scott Huettel, Duke University
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FMRI – Week 1 – Introduction Scott Huettel, Duke University
An Introduction to Functional MRI
FMRI Undergraduate Course (PSY 181F) FMRI Graduate Course (NBIO 381, PSY
362)
Dr. Scott Huettel, Course Director
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Some Introductions: People
Course Director (Both Courses):
Scott Huettel Associate Professor, Psychiatry, BIAC, CCN Research Interests: Decision making, neuroeconomics
Teaching Assistants (Undergraduate Course):
Simon Davis Graduate Student, Psychology & Neuroscience Research Interests: Memory, neural connectivityMelissa Libertus Graduate Student, Psychology & Neuroscience Research Interests: Development of numerical cognition
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Some Introductions: Places
Duke-UNC Brain Imaging & Analysis Center (BIAC)
www.biac.duke.edu
MRI Scanners (3T, 4T), Duke Hospital
Offices and Analysis Laboratory, Bell Building
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Overview of the Course(s)
• Lectures– Wednesdays 3-4:30pm– Room: 3031 Purple Zone, Duke
Clinics
• Readings– Functional Magnetic Resonance
Imaging (Huettel, Song, McCarthy)– Original papers, posted to website
• Laboratories– Introduction: Wed. 4:30-5:30pm– Other times arranged with TAs
• Grading Basis– Attendance – Weekly laboratory exercises
(group)– Short Quizzes– Mid-term examination– Project presentation (group)– Project final report (individual)
Undergraduate Graduate
• Lectures– Wednesdays 3-4:30pm– Room: 3031 Purple Zone, Duke
Clinics
• Readings– Functional Magnetic Resonance
Imaging (Huettel, Song, McCarthy)– Original papers, posted to website
• Laboratories– Times arranged with TAs and
instructor (group)
• Grading Basis– Attendance– Weekly laboratory exercises (group)– Self-assessment exercises– Mid-term examination– Project presentation (group)
Course auditors are welcome to attend lectures!
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Course Textbook
• First edition (2004): Required – Available at bookstore
• Selected chapters from new edition (2008) will be provided by instructor
• Self-assessment questions available on accompanying CD– Graduates: Required– Undergrads: Highly
recommended
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Each week has lecture and laboratory components
Labs start next week and run from Thursday to Tuesday; TAs will schedule.
We will introduce the analysis package FSL in a combined session in this room.
The midterm for both classes is on 10/17. Different exams, same time. Auditors welcome to take it for fun.
In late October, you will form small groups for your fMRI projects. We’ll go over the project phase of the course in great detail around then.
The last undergraduate session is a panel discussion; it is optional for graduate students.
More info about the project presentations forthcoming.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Course logistics… or “What you need to do!”
1. Get a BIAC account and laboratory access– TAs need your name, DukeID, etc.– Gives you access to BIAC computer labs and servers
2. Arrange laboratory times with TAs– Undergrads: Give them your schedule, and they will
coordinate the groups and laboratories– Graduates: Sort into groups of up to 4, pick a day and time,
and then ask the TAs about availability– These times will also be used for data collection and analysis
on your projects
3. Download course materials from the class website: http://www.biac.duke.edu/education/courses/fall07/fmri/(all materials will also be available on BlackBoard)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Any questions?
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Outline for Today
• Lecture: Introducing fMRI– What is fMRI?– History– Key concepts – Parts of a MR scanner– MR safety
• Laboratory: Scanner Visit (Dr. Jim Voyvodic)– Scanner hardware– Stimulus presentation and recording hardware– Demonstration of real-time fMRI
Note: I will post all slides to the course web page!
FMRI – Week 1 – Introduction Scott Huettel, Duke University
1. What is fMRI ?
FMRI – Week 1 – Introduction Scott Huettel, Duke University
1. What is fMRI ?isn’t
FMRI – Week 1 – Introduction Scott Huettel, Duke University
fMRI is not bumpology
FMRI – Week 1 – Introduction Scott Huettel, Duke University
• Phrenology claimed that bumps on the skull reflected exaggerated functions/traits
• It lacked any mechanism underlying its claims.
• It used anecdotal, rather than scientific, evidence.
• Nevertheless, its central idea persisted: Localization of FunctionFranz Joseph
Gall (1758-1828)
Johann Spurzheim
(1776-1832)
from Gall (c. 1810)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
fMRI is not mind-reading
This is not a thought.This is not a thought.
This is not a thought.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
fMRI is not a window on the brain
“Mirror neuron activity in the right posterior inferior frontal gyrus –
indicating identification and empathy - while watching the Disney/NFL ad.”
rIFG
“Ventral striatum activity – indicating reward processing - while watching the Disney/NFL
ad.”
ventStr
[Citations omitted to protect the offenders.]
FMRI – Week 1 – Introduction Scott Huettel, Duke University
fMRI is not invasivePositron Emission Tomography (PET)
Intracranial Stimulation /
Recording
FMRI – Week 1 – Introduction Scott Huettel, Duke University
FMRI is… a technique for measuring metabolic correlates of neuronal
activity
• Uses a standard MRI scanner • Acquires a series of images (numbers)• Measures changes in blood oxygenation• Use non-invasive, non-ionizing radiation• Can be repeated many times; can be used for a
wide range of subjects• Combines good spatial and reasonable temporal
resolution
FMRI – Week 1 – Introduction Scott Huettel, Duke University
fMRI is a Measurement Technique…
BRAIBRAINN
BEHAVIBEHAVIOROR
Measurement TechniquesfMRI, PET, EEG
Manipulation Techniques
Lesions, TMS, Stimulation
FMRI – Week 1 – Introduction Scott Huettel, Duke University
… that provides information about a wide range of topics.
Cheng, Waggoner, & Tanaka (2001) Neuron Berns et al. (2006) Science
From what we see… (ocular dominance
columns)
… to what we feel. (the dread of an upcoming shock)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
2. History of fMRI
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Timeline of MR Imaging
1920 1930 1940 1950 1960 1970 1980 1990 2000
1924 - Pauli suggests that
nuclear particles may have angular momentum (spin).
1937 – Rabi measures magnetic moment of
nucleus. Coins “magnetic resonance”.
1944 – Rabi wins Nobel prize in
Physics.
1946 – Purcell shows that matter absorbs energy at a resonant
frequency.
1946 – Bloch demonstrates that nuclear precession can
be measured in detector coils.
1952 – Purcell and Bloch share Nobel prize in Physics.
1972 – Damadian patents idea for large
NMR scanner to detect malignant
tissue.
1959 – Singer measures blood flow
using NMR (in mice).
1973 – Lauterbur publishes method for
generating images using NMR gradients.
1973 – Mansfield independently
publishes gradient approach to MR.
1975 – Ernst develops 2D-Fourier transform for MR.
NMR becomes MRI
MRI scanners become clinically
prevalent.
1990 – Ogawa and colleagues create functional images using endogenous, blood-oxygenation
contrast.
1985 – Insurance reimbursements for MRI exams begin.
M R
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Early Uses of NMR
• Most early NMR was used for chemical analysis– No medical applications
• 1971 – Damadian publishes and patents idea for using NMR to distinguish healthy and malignant tissues– “Tumor detection by nuclear magnetic resonance”, Science– Proposes using differences in relaxation times– No image formation method proposed
• 1973 – Lauterbur describes projection method for creating NMR images– Mansfield (1973) independently describes similar approach
FMRI – Week 1 – Introduction Scott Huettel, Duke University
The First ZMR NMR Image
Lauterbur, P.C. (1973). Image formation by induced local interaction: Examples employing nuclear magnetic resonance. Nature, 242, 190-191.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Early Human MR Images
(Damadian)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Mink5 Image – Damadian (1977)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Digression: 2003 Nobel Controversy
Paul LauterburPaul Lauterbur Peter MansfieldPeter Mansfield
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Raymond DamadianRaymond Damadian
FMRI – Week 1 – Introduction Scott Huettel, Duke University
New York Times October 9, 2003
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Nobel Press Release October 6, 2003
SummaryImaging of human internal organs with exact and non-invasive methods is very important for medical diagnosis, treatment and follow-up. This year's Nobel Laureates in Physiology or Medicine have made seminal discoveries concerning the use of magnetic resonance to visualize different structures. These discoveries have led to the development of modern magnetic resonance imaging, MRI, which represents a breakthrough in medical diagnostics and research. …
This year's Nobel Laureates in Physiology or Medicine are awarded for crucial achievements in the development of applications of medical importance. In the beginning of the 1970s, they made seminal discoveries concerning the development of the technique to visualize different structures. These findings provided the basis for the development of magnetic resonance into a useful imaging method.
Paul Lauterbur discovered that introduction of gradients in the magnetic field made it possible to create two-dimensional images of structures that could not be visualized by other techniques. In 1973, he described how addition of gradient magnets to the main magnet made it possible to visualize a cross section of tubes with ordinary water surrounded by heavy water. No other imaging method can differentiate between ordinary and heavy water.
Peter Mansfield utilized gradients in the magnetic field in order to more precisely show differences in the resonance. He showed how the detected signals rapidly and effectively could be analysed and transformed to an image. This was an essential step in order to obtain a practical method. Mansfield also showed how extremely rapid imaging could be achieved by very fast gradient variations (so called echo-planar scanning). This technique became useful in clinical practice a decade later.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Timeline of MR Imaging
1920 1930 1940 1950 1960 1970 1980 1990 2000
1924 - Pauli suggests that nuclear particles
may have angular momentum (spin).
1937 – Rabi measures magnetic moment of
nucleus. Coins “magnetic resonance”.
1944 – Rabi wins Nobel prize in
Physics.
1946 – Purcell shows that matter absorbs energy at a resonant
frequency.
1946 – Bloch demonstrates that nuclear precession can be
measured in detector coils.
1952 – Purcell and Bloch share Nobel prize in Physics.
1972 – Damadian patents idea for large
NMR scanner to detect malignant
tissue.
1959 – Singer measures blood flow
using NMR (in mice).
1973 – Lauterbur publishes method for
generating images using NMR gradients.
1973 – Mansfield independently
publishes gradient approach to MR.
1975 – Ernst develops 2D-Fourier transform for MR.
NMR becomes MRI
MRI scanners become clinically
prevalent.
1990 – Ogawa and colleagues create functional images using endogenous, blood-oxygenation
contrast.
1985 – Insurance reimbursements for MRI exams begin.
M R I f
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Physiology (BOLD Contrast)
Blood-Oxygenation-Level
Dependent contrast
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Using MRI to Study Brain Function
Kwong, et al., 1992 Visual Cortex
FMRI – Week 1 – Introduction Scott Huettel, Duke University
0 200 400 600 800 1000 1200 1400
2004
2003
2002
2001
2000
1999
1998
1997
1996
1995
1994
1993
1992
1991
1990
Growth in fMRI : Published Studies
Medline search on “functional magnetic resonance”, “functional MRI”, and “fMRI”.
Year 2004 = ~1500; Years 2005+ > 2000
…
FMRI – Week 1 – Introduction Scott Huettel, Duke University
3. Key Concepts
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Key Concepts
• Contrast• Spatial Resolution• Temporal Resolution• Functional Resolution
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Contrast: Conceptual Overview
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Contrast: Anatomical
Contrast: 1) An intensity difference between quantities: “How much?” 2) The quantity being measured: “What?”
Contrast-to-noise: The magnitude of the intensity difference between quantities divided by the variability in their measurements.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Contrast: Functional
Contrast-to-noise is critical for fMRI: How effectively can we decide whether a given brain region has property X or property
Y?
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Spatial Resolution: Voxels
Voxel: A small rectangular prism that is the basic sampling unit of fMRI. Typical anatomical voxel: (1.5mm)3. Typical functional voxel: (4mm)3.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Spatial Resolution: Examples
~8mm~8mm22 ~4mm~4mm22 ~2mm~2mm22
~1.5mm~1.5mm22 ~1mm~1mm22
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Temporal Resolution• Determining factors
– Sampling rate, usually repetition time (TR)– Dependent variable, usually BOLD response
• BOLD response is sluggish, taking 2-3 seconds to rise above baseline and 4-6 seconds to peak
– Experimental design
• Most FMRI studies have temporal resolution on the order of a few seconds– With specialized designs and data acquisition, this can be
improved to ~100ms
FMRI – Week 1 – Introduction Scott Huettel, Duke University
FMRI – Week 1 – Introduction Scott Huettel, Duke University
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Functional Resolution
The ability of a measurement technique to identify the relation between underlying
neuronal activity and a cognitive or behavioral phenomenon.
Functional resolution is limited both by the intrinsic properties of our brain measure and by
our ability to manipulate the experimental design to allow variation in the phenomenon of
interest.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
4. MRI Scanners
FMRI – Week 1 – Introduction Scott Huettel, Duke University
GE 3T Scanner (cf. BIAC’s)GE 3T Scanner (cf. BIAC’s)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Siemens 3T ScannerSiemens 3T ScannerPhillips 3T Scanner (Vanderbilt)Phillips 3T Scanner (Vanderbilt)
Phillips 0.6T Open ScannerPhillips 0.6T Open Scanner FONAR 0.6T MR FONAR 0.6T MR Operating RoomOperating Room
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Main Components of a Scanner
1. Magnetic: Static Magnetic Field Coils2. Resonance: Radiofrequency Coil3. Imaging: Gradient Field Coils
• Shimming Coils• Data transfer and storage computers• Physiological monitoring, stimulus
display, and behavioral recording hardware
FMRI – Week 1 – Introduction Scott Huettel, Duke University
1. Magnetic: Static Field Coils
The scanner contains large parallel coilings of wires.
These generate the main magnetic field (B0), which gives the scanner its field strength
(e.g., 3T).
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Surface Coil Volume Coil
2. Resonance: Radiofrequency Coils
Electronic coils tuned to radio signals send
energy into the brain and record
an emitted “echo”.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
3. Imaging: Gradient Coils
Three gradient coils are used, one in each
of the cardinal directions.
These allow spatial encoding of the MR
signal.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
The scanner is controlled by a pulse sequence.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Pulse Sequences
• Recipes for controlling scanner hardware• Allow MR to be extremely flexible
T1
T2
FMRI – Week 1 – Introduction Scott Huettel, Duke University
5. MRI Safety
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Hospital NightmareBoy, 6, Killed in Freak MRI Accident
July 31, 2001 — A 6-year-old boy died after undergoing an MRI exam at a New York-area hospital when the machine's powerful magnetic field jerked a metal oxygen tank across the room, crushing the child's head. …
ABCNews.com
FMRI – Week 1 – Introduction Scott Huettel, Duke University
MR Incidents• Pacemaker malfunctions leading to death
– At least 5 as of 1998 (Schenck, JMRI, 2001)– E.g., in 2000 an elderly man died in Australia after being twice
asked if he had a pacemaker
• Blinding due to movements of metal in the eye– At least two incidents (1985, 1990)
• Dislodgment of aneurysm clip (1992)
• Projectile injuries (most common incident type)– Injuries (e.g., cranial fractures) from oxygen canister (1991, 2001)– Scissors hit patient in head, causing wounds (1993)
• Gun pulled out of policeman’s hand, hitting wall and firing– Rochester, NY (2000)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Issues in MR Safety• Known acute risks
– Projectiles, rapid field changes, RF heating, claustrophobia, acoustic noise, etc.
• Potential acute/chronic risks– Current induction in tissue at high fields?– Changes in the developing brain?
• Epidemiological studies of chronic risks– Extended exposure to magnetic fields does not cause harm
• Difficulty in assessing subjective experience– In one study, 45% of subjects exposed to a 4T scanner reported
unusual sensations (Erhard et al., 1995)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Projectile Effects: External
“Large ferromagnetic objects that were reported as having been drawn into the MR equipment include a defibrillator, a wheelchair, a respirator, ankle weights, an IV pole, a tool box, sand bags containing metal filings, a vacuum cleaner, and mop buckets.”
-Chaljub et al., (2001) AJR Chaljub (2001)
Chaljub (2001)
Schenck (1996)
The The Scanner is Scanner is Never Off!Never Off!
FMRI – Week 1 – Introduction Scott Huettel, Duke University
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Any questions?
FMRI – Week 1 – Introduction Scott Huettel, Duke University
BIAC Scanner Tour
• Dr. Jim Voyvodic will demonstrate real-time fMRI– We will see the 3T BIAC scanner in action– Go through the mock scanner
• You’ll go through low-field areas of the MR center– Anyone with pacemaker, other implanted metal
(shunts, clips, etc.) should tell instructor– Fillings, piercings fine (for console room)– Please be considerate while walking through the
hospital!
• We’ll travel in groups– Undergraduates: Go now with Simon Davis– Graduates: Go with Melissa Libertus momentarily– Auditors: Go with Scott Huettel, after the other
groups
FMRI – Week 1 – Introduction Scott Huettel, Duke University
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Timeline of MR Imaging
1920 1930 1940 1950 1960 1970 1980 1990 2000
1924 - Pauli suggests that
nuclear particles may have angular momentum (spin).
1937 – Rabi measures magnetic moment of
nucleus. Coins “magnetic resonance”.
1944 – Rabi wins Nobel prize in
Physics.
1946 – Purcell shows that matter absorbs energy at a resonant
frequency.
1946 – Bloch demonstrates that nuclear precession can
be measured in detector coils.
1952 – Purcell and Bloch share Nobel prize in Physics.
1972 – Damadian patents idea for large
NMR scanner to detect malignant
tissue.
1959 – Singer measures blood flow
using NMR (in mice).
1973 – Lauterbur publishes method for
generating images using NMR gradients.
1973 – Mansfield independently
publishes gradient approach to MR.
1975 – Ernst develops 2D-Fourier transform for MR.
NMR becomes MRI
MRI scanners become clinically
prevalent.
1990 – Ogawa and colleagues create functional images using endogenous, blood-oxygenation
contrast.
1985 – Insurance reimbursements for MRI exams begin.
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Rabi and the Measurement of the Nuclear Magnetic Moment (1937)
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Discovery of Nuclear Magnetic Resonance Absorption (1946)
• Bloch and Purcell independently discovered how to measure nuclear moment of bulk matter (1946)
• They showed that energy applied at a resonant frequency was absorbed by matter, and the re-emission could be measured in detector coils
• They shared the 1952 Nobel Prize in Physics
Felix Bloch
Edward Purcell
FMRI – Week 1 – Introduction Scott Huettel, Duke University
Timeline of MR Imaging
1920 1930 1940 1950 1960 1970 1980 1990 2000
1924 - Pauli suggests that nuclear particles
may have angular momentum (spin).
1937 – Rabi measures magnetic moment of
nucleus. Coins “magnetic resonance”.
1944 – Rabi wins Nobel prize in
Physics.
1946 – Purcell shows that matter absorbs energy at a resonant
frequency.
1946 – Bloch demonstrates that nuclear precession can be
measured in detector coils.
1952 – Purcell and Bloch share Nobel prize in Physics.
1972 – Damadian patents idea for
large NMR scanner to detect malignant
tissue.
1959 – Singer measures blood flow
using NMR (in mice).
1973 – Lauterbur publishes method for
generating images using NMR gradients.
1973 – Mansfield independently
publishes gradient approach to MR.
1975 – Ernst develops 2D-Fourier transform for MR.
NMR becomes MRI
MRI scanners become clinically
prevalent.
1990 – Ogawa and colleagues create functional images using endogenous, blood-oxygenation
contrast.
1985 – Insurance reimbursements for MRI exams begin.