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FMRI – Week 1 – Introduction Scott Huettel, Duke University

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An Introduction to Functional MRI

FMRI Undergraduate Course (PSY 181F) FMRI Graduate Course (NBIO 381, PSY

362)

Dr. Scott Huettel, Course Director


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


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


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!


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


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.


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)

http://www.biac.duke.edu/education/courses/fall07/fmri/


Any questions?


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!


1. What is fMRI ?


1. What is fMRI ?isn’t


fMRI is not bumpology


• 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 is not mind-reading

This is not a thought.This is not a thought.

This is not a thought.


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 is not invasivePositron Emission Tomography (PET)

Intracranial Stimulation /

Recording


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 is a Measurement Technique…

BRAIBRAINN

BEHAVIBEHAVIOROR

Measurement TechniquesfMRI, PET, EEG

Manipulation Techniques

Lesions, TMS, Stimulation


… 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)


2. History of fMRI


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


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


The First ZMR NMR Image

Lauterbur, P.C. (1973). Image formation by induced local interaction: Examples employing nuclear magnetic resonance. Nature, 242, 190-191.


Early Human MR Images

(Damadian)


Mink5 Image – Damadian (1977)


Digression: 2003 Nobel Controversy

Paul LauterburPaul Lauterbur Peter MansfieldPeter Mansfield


Raymond DamadianRaymond Damadian


New York Times October 9, 2003


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.



1920 1930 1940 1950 1960 1970 1980 1990 2000

1924 - Pauli suggests that nuclear particles

may have angular momentum (spin).




Physics.


frequency.

1946 – Bloch demonstrates that nuclear precession can be

measured in detector coils.




tissue.








NMR becomes MRI


prevalent.


contrast.


M R I f


Physiology (BOLD Contrast)

Blood-Oxygenation-Level

Dependent contrast


Using MRI to Study Brain Function

Kwong, et al., 1992 Visual Cortex


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

…


3. Key Concepts


Key Concepts

• Contrast• Spatial Resolution• Temporal Resolution• Functional Resolution


Contrast: Conceptual Overview


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.


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?


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.


Spatial Resolution: Examples

~8mm~8mm22 ~4mm~4mm22 ~2mm~2mm22

~1.5mm~1.5mm22 ~1mm~1mm22


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


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.


4. MRI Scanners


GE 3T Scanner (cf. BIAC’s)GE 3T Scanner (cf. BIAC’s)


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


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


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).


Surface Coil Volume Coil

2. Resonance: Radiofrequency Coils

Electronic coils tuned to radio signals send

energy into the brain and record

an emitted “echo”.


3. Imaging: Gradient Coils

Three gradient coils are used, one in each

of the cardinal directions.

These allow spatial encoding of the MR

signal.


The scanner is controlled by a pulse sequence.


Pulse Sequences

• Recipes for controlling scanner hardware• Allow MR to be extremely flexible

T1

T2


5. MRI Safety


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


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)


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)


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!


Any questions?


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



1920 1930 1940 1950 1960 1970 1980 1990 2000

1924 - Pauli suggests that

nuclear particles may have angular momentum (spin).




Physics.


frequency.

1946 – Bloch demonstrates that nuclear precession can

be measured in detector coils.




tissue.








NMR becomes MRI


prevalent.


contrast.



Rabi and the Measurement of the Nuclear Magnetic Moment (1937)


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



1920 1930 1940 1950 1960 1970 1980 1990 2000

1924 - Pauli suggests that nuclear particles

may have angular momentum (spin).




Physics.


frequency.

1946 – Bloch demonstrates that nuclear precession can be

measured in detector coils.


1972 – Damadian patents idea for

large NMR scanner to detect malignant

tissue.








NMR becomes MRI


prevalent.


contrast.


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