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HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis
Fall 2006
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HST.583: Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006
Harvard-MIT Division of Health Sciences and Technology
Course Director: Dr. Randy Gollub.
Laboratory 2: Introduction to
fMRI Data and Analysis
September 18, 2006
HST.583
Divya Bolar
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
What is functional MRI?
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Broad sense: fMRI refers to any MR technique
that goes beyond anatomy to measure aspects
of local physiology.
Specific sense: fMRI refers to MR techniques
that investigate changes in brain function over
time.
Brain function/ information processing results
from the activity of ensembles of neurons.
Primary goal of fMRI is to detect signal changes
corresponding to neuronal activity.
Buxton RB. Introduction to Functional Magnetic Resonance Imaging, 2002.
Huettel S, Song AW, McCarthy G. Funcitonal Magnetic Resonance Imaging, 2004.
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
How do we measure neuronal
activity with MRI?
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Currently not possible to directly measure neural
activity (i.e. firing of action potentials) with MRI
Can visualize downstream correlates of neural
activity
Simplified Flowchart
Neural
Activity
Cellular
Metabolism
Blood
Flow
Venous
deoxyHb
Blood oxygen level
dependence (BOLD)
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
BOLD Imaging
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Neural activation increases local blood flow
Increased blood flow delivers fresh, oxygenated
hemoglobin, and washes out deoxygenated
hemoglobin (dHb)
Venous dHb content decreases, leading to an
increase in MRI signal (dHb attenuates MRI
signal)
MRI signal thus increases with increased brain
activity*
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
BOLD Imaging: Timing
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BOLD effect is dependent on so-called
“hemodynamic response”
Hemodynamic response describes how
blood flow changes over time, in response
to neural activation
Hemodynamic response does not
instantaneously follow neural activity; it
occurs with delay and dispersion
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Example Hemodynamic Response
(impulse response)
1.2
Impulse
Ensemble Neural Firing
Hemodynamic Response
Delay
1
Amplitude
0.8
0.6
Dispersion
0.4
0.2
0
-0.2
0
2
4
6
8
10
12
14
16
18
20
Time (s)
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Figure by MIT OpenCourseWare. After Hubel, 1995.
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Sample fMRI paradigm:
Simple visual task; flashing circle checkerboard (8 Hz)
See supplemental video clip #1
1 min
OFF
ON
OFF
ON
OFF
ON
Total task/ scan time: 6 minutes
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Time series fMRI data of
visual cortex voxel
matches paradigm
•
Indicates a positive BOLD
effect; i.e. decreased dHb
content as a result of
neural activation
•
This is fMRI!
Screenshots courtesy of NeuroLens.org.
Used with permission.
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Goals of laboratory 2:
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Goal 1: Get familiar with sample fMRI data set
from visual hemifield stimulation task
(Neurolens1 tutorial, exercises 1 and 2)
Goal 2: Successfully analyze data set and show
appropriate activations (Neurolens tutorial,
exercises 3 and 4)
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Goal 3: Answer laboratory questions and do
exercises on handout (graded)
Bonus: Neurolens tutorial, exercises 5 and 6
1. Hoge RD, www.neurolens.org, 2006.
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Visual Task:
Interleaved left
and right
visual field
stimulation
(8 Hz flashing
checkerboard)
See supplemental video clip #2
Visual stimulus seen by subject
Left
hemifield
32 sec
Right
hemifield
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Visual Field Pathway
Courtesy of Merck & Co., Inc. Used
with permission. From The Merck
Manual of Medical Information – Second
Home Edition, edited by Robert S. Porter.
Copyright 2006 by Merck & Co., Inc.,
Whitehouse Station, NJ. Available at:
http://www.merck.com/mmhe.
Accessed September 4, 2008.
So where should we expect activation??
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
So where should we expect activation?
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Primary activation should be in
contralateral visual cortex
Will be slight activation in ipsilateral visual
cortex, due to some crosstalk. In other
words, the flashing checkerboard
stiumulus does not completely isolate L/R
visual fields
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.
Image removed due to copyright restrictions.
“Visual Pathways.” Images #202 & 203 from
Hanaway, Woolsey, Gado and Roberts. The Brain
Atlas: A Visual Guide to the Human Central
Nervous System. Fitzgerald Science Press, 1998.
Cite as: Divya S. Bolar, HST.583 Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2006. (Massachusetts Institute of
Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed MM DD, YYYY). License: Creative Commons BY-NC-SA.