Introduction: fMRI for Newbies

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IntroductionfMRI for Newbies
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MRI vs. fMRI
Functional MRI (fMRI) studies brain function.
MRI studies brain anatomy.
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Brain Imaging Anatomy
CAT
PET
Photography
MRI
Source modified from Posner Raichle, Images of
Mind
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MRI vs. fMRI
MRI
fMRI
high resolution (1 mm)
low resolution (3 mm but can be better)
one image

fMRI Blood Oxygenation Level Dependent (BOLD)
signal indirect measure of neural activity
many images (e.g., every 2 sec for 5 mins)
? neural activity ? ? blood oxygen ? ?
fMRI signal
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The First Brain Imaging Experiment
and probably the cheapest one too!
Angelo Mosso Italian physiologist (1846-1910)
In Mossos experiments the subject to be
observed lay on a delicately balanced table which
could tip downward either at the head or at the
foot if the weight of either end were increased.
The moment emotional or intellectual activity
began in the subject, down went the balance at
the head-end, in consequence of the
redistribution of blood in his system. --
William James, Principles of Psychology (1890)
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The Rise of fMRI
800
700
600
500
Number of papers (PubMed)
400
300
200
100
0
1990
1995
2000
Year of Publication
Slide modified from Mel Goodale
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fMRI Activation
Flickering Checkerboard OFF (60 s) - ON (60 s)
-OFF (60 s) - ON (60 s) - OFF (60 s)
Brain Activity
Time ?
Source Kwong et al., 1992
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PET and fMRI Activation
Source Posner Raichle, Images of Mind
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fMRI Setup
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Category-Specific Visual Areas
objects
faces
Malach, 2002, TICS

• Parahippocampal Place Area (PPA)
• place-selective
• places gt (objects and faces)
• places gt scrambled images

places

• Fusiform Face Area (FFA) or pFs
• face-selective
• faces gt (objects scenes)
• faces gt scrambled images
• posterior fusiform sulcus (pFs)

• Lateral Occipital (LO)
• object-selective
• objects gt (faces scenes)
• objects gt scrambled images

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A Simple Experiment LO Localizer

• Lateral Occipital Complex
• responds when subject views objects

Blank Screen
Intact Objects
Scrambled Objects
TIME
One volume (12 slices) every 2 seconds for 272
seconds (4 minutes, 32 seconds) Condition
changes every 16 seconds (8 volumes)
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fMRI Experiment Stages Prep

• 1) Prepare subject
• Consent form
• Safety screening
• Instructions and practice trials if appropriate
• 2) Shimming
• putting body in magnetic field makes it
  non-uniform
• adjust 3 orthogonal weak magnets to make
  magnetic field as homogenous as possible
• 3) Sagittals
• Take images along the midline to use to plan
  slices

Note Thats one g, two ts
In this example, these are the functional slices
we want 12 slices x 6 mm
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fMRI Experiment Stages Anatomicals

• 4) Take anatomical (T1) images
• high-resolution images (e.g., 0.75 x 0.75 x 3.0
  mm)
• 3D data 3 spatial dimensions, sampled at one
  point in time
• 64 anatomical slices takes 4 minutes

64 slices x 3 mm
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Slice Terminology
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fMRI Experiment Stages Functionals

• 5) Take functional (T2) images
• images are indirectly related to neural activity
• usually low resolution images (3 x 3 x 6 mm)
• all slices at one time a volume (sometimes
  also called an image)
• sample many volumes (time points) (e.g., 1
  volume every 2 seconds for 136 volumes 272 sec
  432)
• 4D data 3 spatial, 1 temporal

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Anatomic Slices Corresponding to Functional Slices
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Time Courses
Arbitrary signal varies from voxel to voxel, day
to day, subject to subject
MR SIGNAL (ARBITRARY UNITS)
TIME
To make the y-axis more meaningful, we usually
convert the signal into units of
change 100(x - baseline)/baseline Changes are
typically in the order of 0.5-4 .
MR SIGNAL ( Change)
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Activation Statistics
Functional images
Time
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Statistical Maps Time Courses
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2D ? 3D
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Design Jargon Runs
session all of the scans collected from one
subject in one day
run (or scan) one continuous period of fMRI
scanning (5-7 min)
experiment a set of conditions you want to
compare to each other
Note Terminology can vary from one fMRI site to
another (e.g., some places use scan to refer to
what weve called a volume).
A session consists of one or more
experiments. Each experiment consists of several
(e.g., 1-8) runs More runs/expt are needed when
signalnoise is low or the effect is weak. Thus
each session consists of numerous (e.g., 5-20)
runs (e.g., 0.5 3 hours)
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Design Jargon Paradigm
paradigm (or protocol) the set of conditions and
their order used in a particular run
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fMRI Equipment
Gradient Coil
Magnet (4T)
4T magnet
RF Coil
gradient coil (inside)
Head Coil
Surface Coil
Source Joe Gati, photos
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What Does fMRI Measure?

• Big magnetic field
• protons (hydrogen molecules) in body become
  aligned to field
• RF (radio frequency) coil
• radio frequency pulse
• knocks protons over
• as protons realign with field, they emit energy
  that coil receives (like an antenna)
• Gradient coils
• make it possible to encode spatial information
• MR signal differs depending on
• concentration of hydrogen in an area (anatomical
  MRI)
• amount of oxy- vs. deoxyhemoglobin in an area
  (functional MRI)

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BOLD signal
Blood Oxygen Level Dependent signal

• neural activity ? ? blood flow ? ? oxyhemoglobin
  ? ? T2 ? ? MR signal

Source fMRIB Brief Introduction to fMRI
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Percent Signal Change
505
500
205
200
Slide from Duke course
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Stats on Anatomical
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Susceptibility Artifacts
T1-weighted image
T2-weighted image

• -artifacts occur near junctions between air and
  tissue
• sinuses, ear canals

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BOLD Correlations

• Local Field Potentials (LFP)
• reflect post-synaptic potentials
• similar to what EEG (ERPs) and MEG measure
• Multi-Unit Activity (MUA)
• reflects action potentials
• similar to what most electrophysiology measures
• Logothetis et al. (2001)
• combined BOLD fMRI and electrophysiological
  recordings
• found that BOLD activity is more closely related
  to LFPs than MUA

Source Logothetis et al., 2001, Nature
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Comparing Electrophysiolgy and BOLD
Data Source Disbrow et al., 2000, PNAS Figure
Source, Huettel, Song McCarthy, Functional
Magnetic Resonance Imaging
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fMRI Measures the Population Activity

• population activity depends on
• how active the neurons are
• how many neurons are active
• manipulations that change the activity of many
  neurons a little have a show bigger activation
  differences than manipulations that change the
  activation of a few neurons a lot
• attention
• ? activity
• learning
• ? activity
• fMRI may not
• match single neuron
• physiology results

Raichle Posner, Images of Mind cover image
Ideas from Scannell Young, 1999, Proc Biol Sci
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More Caveats

• brain vs. vein debate
• source of signal affects spatial resolution
• scientists havent agreed on a single theory to
  explain the relationship between oxygen, glucose
  metabolism and blood flow
• no one really understands how neurons trigger
  increased blood flow
• neural synchrony may be a factor

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Bottom Line

• Despite all the caveats, questions and concerns,
  BOLD imaging is well-correlated with results from
  other methods
• BOLD imaging can resolve activation at a fairly
  small scale (e.g., retinotopic mapping)
• PSPs and action potentials are correlated so
  either way, its getting at something meaningful
• even if BOLD activation doesnt correlate
  completely with electrophysiology, that doesnt
  mean its wrong
• may be picking up other processing info (e.g.,
  PSPs, synchrony)