Introduction to fMRI

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1. Introduction to fMRI
2. Basic fMRI Physics
3. Data Analysis
4. Localisation
5. Cortical Anatomy
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Introduction to fMRI
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MRI vs. fMRI
Functional MRI (fMRI) studies brain function.
MRI studies brain anatomy.
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Brain Imaging Anatomy
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
active neurons shed oxygen and become more
magnetic increasing the fMRI signal
many images (e.g., every 2 sec for 5 mins)
? neural activity ? ? blood oxygen ? ?
fMRI signal
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fMRI Activation
Flickering Checkerboard OFF (60 s) - ON (60 s)
-OFF (60 s) - ON (60 s) - OFF (60 s)
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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fMRI Experiment Stages Prep

• 1) Prepare subject
• Consent form
• Safety screening
• Instructions
• 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
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fMRI Experiment Stages Anatomicals

• 4) Take anatomical (T1) images
• high-resolution images (e.g., 1x1x2.5 mm)
• 3D data 3 spatial dimensions, sampled at one
  point in time
• 64 anatomical slices takes 5 minutes

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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 (3x3x5 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 150 volumes 300 sec
  5 minutes)
• 4D data 3 spatial, 1 temporal

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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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2. Basic fMRI Physics
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Recipe for MRI

• 1) Put subject in big magnetic field (leave him
  there)
• 2) Transmit radio waves into subject about 3
  ms
• 3) Turn off radio wave transmitter
• 4) Receive radio waves re-transmitted by subject
• Manipulate re-transmission with magnetic fields
  during this readout interval 10-100 ms MRI
  is not a snapshot
• 5) Store measured radio wave data vs. time
• Now go back to 2) to get some more data
• 6) Process raw data to reconstruct images
• 7) Allow subject to leave scanner (this is
  optional)

Source Robert Coxs web slides
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History of NMR
NMR nuclear magnetic resonance Felix Block and
Edward Purcell 1946 atomic nuclei absorb and
re-emit radio frequency energy 1952 Nobel prize
in physics nuclear properties of nuclei of
atoms magnetic magnetic field required resonance
interaction between magnetic field and radio
frequency
Bloch
Purcell
NMR ? MRI Why the name change?
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History of fMRI
MRI -1971 MRI Tumor detection (Damadian) -1973
Lauterbur suggests NMR could be used to form
images -1977 clinical MRI scanner
patented -1977 Mansfield proposes echo-planar
imaging (EPI) to acquire images
faster fMRI -1990 Ogawa observes BOLD effect
with T2 blood vessels became more visible as
blood oxygen decreased -1991 Belliveau observes
first functional images using a contrast
agent -1992 Ogawa et al. and Kwong et al.
publish first functional images using BOLD signal
Ogawa
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Necessary Equipment
4T magnet
RF Coil
gradient coil (inside)
Magnet
Gradient Coil
RF Coil
Source Joe Gati, photos
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The Big Magnet
Very strong
Continuously on
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Magnet Safety
The whopping strength of the magnet makes safety
essential. Things fly Even big things!
Source www.howstuffworks.com
Screen subjects carefully Make sure you and all
your students staff are aware of
hazzards Develop stratetgies for screening
yourself every time you enter the magnet
Source http//www.simplyphysics.com/ flying_objec
ts.html
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Subject Safety

• Anyone going near the magnet subjects, staff
  and visitors must be thoroughly screened
• Subjects must have no metal in their bodies
• pacemaker
• aneurysm clips
• metal implants (e.g., cochlear implants)
• interuterine devices (IUDs)
• some dental work (fillings okay)
• Subjects must remove metal from their bodies
• jewellery, watch, piercings
• coins, etc.
• wallet
• any metal that may distort the field (e.g.,
  underwire bra)
• Subjects must be given ear plugs (acoustic noise
  can reach 120 dB)

This subject was wearing a hair band with a 2 mm
copper clamp. Left with hair band. Right
without. Source Jorge Jovicich
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Protons align with field
Outside magnetic field

• randomly oriented

Inside magnetic field

• spins tend to align parallel or anti-parallel to
  B0
• net magnetization (M) along B0
• spins precess with random phase
• no net magnetization in transverse plane
• only 0.0003 of protons/T align with field

M
longitudinal axis
Longitudinal magnetization
transverse plane
Source Mark Cohens web slides
M 0
Source Robert Coxs web slides
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fMRI Basics The functional magnetic resonance
imaging technique measures the amount of oxygen
in the blood in small regions of the brain.
These regions are called voxels. Neural activity
uses up oxygen and the vasculature responds by
providing more highly oxygenated blood to local
brain regions. Thus a change in amount of oxygen
in the blood is measured, and this is taken as a
proxy for the amount of local neural activity.
The measured signal is often called the BOLD
signal (Blood Oxygen Level Dependent). Because
neural activity is not measured directly, one
needs to think about what the indirect signal
really tells us, and how its spatial and
temporal resolution are limited. Certainly,
however,the BOLD signal tells us something about
localization of neural activity in the brain.
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BOLD signal
Blood Oxygen Level Dependent signal

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

Mxy Signal
Mo sin?
T2 task
T2 control
Stask
?S
Scontrol
time
TEoptimum
Source fMRIB Brief Introduction to fMRI
Source Jorge Jovicich
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BOLD signal
Source Doug Nolls primer
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3. DATA ANALYSIS
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Hypotheses vs. Data

• Hypothesis-driven
• Examples t-tests, correlations, general linear
  model (GLM)
• a priori model of activation is suggested
• data is checked to see how closely it matches
  components of the model
• most commonly used approach
• Data-driven
• Independent Component Analysis (ICA)
• no prior hypotheses are necessary
• multivariate techniques determine the patterns
  in the data that account for the most variance
  across all voxels
• can be used to validate a model (see if the math
  comes up with the components you wouldve
  predicted)
• can be inspected to see if there are things
  happening in your data that you didnt predict
• can be used to identify confounds (e.g., head
  motion)
• need a way to organize the many possible
  components
• new and upcoming

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Comparing the two approaches

• Region of Interest (ROI) Analyses
• Gives you more statistical power because you do
  not have to correct for the number of comparisons
  
• Hypothesis-driven
• ROI is not smeared due to intersubject averaging
• Easy to analyze and interpret
• Neglects other areas which may play a fundamental
  role
• Popular in North America

• Whole Brain Analysis
• Requires no prior hypotheses about areas involved
  
• Includes entire brain
• Can lose spatial resolution with intersubject
  averaging
• Can produce meaningless laundry lists of areas
  that are difficult to interpret
• Depends highly on statistics and threshold
  selected
• Popular in Europe

NOTE Though different experimenters tend to
prefer one method over the other, they are NOT
mutually exclusive. You can check ROIs you
predicted and then check the data for other areas.
Source Tootell et al., 1995
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Why do we need statistics?

• MR Signal intensities are arbitrary
• -vary from magnet to magnet, coil to coil, within
  a coil (especially surface coil), day to day,
  even run to run
• -may also vary from area to area (some areas may
  be more metabolically active)
• We must always have a comparison condition within
  the same run
• We need to know whether the eyeball tests of
  significance are real.
• Because we do so many comparisons, we need a way
  to compensate.

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Two approaches ROI

• A. ROI approach
• Do (a) localizer run(s) to find a region (e.g.,
  show moving rings to find MT)
• Extract time course information from that region
  in separate independent runs
• See if the trends in that region are
  statistically significant
• Because the runs that are used to generate the
  area are independent from those used to test the
  hypothesis, liberal statistics can be used

Example study Tootell et al, 1995, Motion
Aftereffect
Source Tootell et al., 1995
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4. LOCALISATION
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BRAIN LOCALIZATION AND ANATOMYwith an emphasis
on cortical areas

• Why so corticocentric?
• cortex forms the bulk of the brain
• subcortical structures are hard to image (more
  vulnerable to motion artifacts) and resolve with
  fMRI
• cortex is relevant to many cognitive processes
• neuroanatomy texts typically devote very little
  information to cortex

• Caveats of corticocentrism
• other structures like the cerebellum are
  undoubtedly very important (contrary to popular
  belief it not only helps you walk and chew gum
  at the same time but also has many cognitive
  functions) but unfortunately are poorly
  understood as yet
• need to remember there may be lots of subcortical
  regions were neglecting

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How can we define regions?

• Talairach coordinates
• Anatomical localization
• Functional localization
• Region of interest (ROI) analyses

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Talairach Coordinate System
Individual brains are different shapes and sizes
How can we compare or average brains?
Note Thats TalAIRach, not TAILarach!
Source Brain Voyager course slides
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Rotate brain into ACPC plane
Find anterior commisure (AC)
Find posterior commisure (PC)
ACPC line horizontal axis
Note official Tal sez use top of AC and bottom
of PC
Source Duvernoy, 1999
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Deform brain into Talairach space

• Mark 8 points in the brain
• anterior commisure
• posterior commisure
• front
• back
• top
• bottom (of temporal lobe)
• left
• right

Extract 3 coordinates
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Left is what?!!!
Note Make sure you know what your magnet and
software are doing before publishing left/right
info!
Note If youre really unsure which side is
which, tape a vitamin E capsule to the one side
of the subjects head. It will show up on the
anatomical image.
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How to Talairach

• For each subject
• Rotate the brain to the ACPC Plane (anatomical)
• Deform the brain into the shoebox (anatomical)
• Perform the same transformations on the
  functional data
• For the group
• Either
• Average all of the functionals together and
  perform stats on that
• Perform the stats on all of the data (GLM) and
  superimpose the statmaps on an averaged
  anatomical (or for SPM, a reference brain)

Averaged anatomical for 6 subjects
Averaged functional for 7 subjects
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Talairach Atlas
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Brodmanns Areas
Brodmann (1905) Based on cytoarchitectonics
study of differences in cortical layers between
areas Most common delineation of cortical
areas More recent schemes subdivide Brodmanns
areas into many smaller regions Monkey and human
Brodmanns areas not necessarily homologous
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Talairach Pros and Cons

• Advantages
• widespread system
• allows averaging of fMRI data between subjects
• allows researchers to compare activation foci
• easy to use

• Disadvantages
• based on the squished brain of an elderly
  alcoholic woman (how representative is that?!)
• not appropriate for all brains (e.g., Japanese
  brains dont fit well)
• activation foci can vary considerably other
  landmarks like sulci may be more reliable

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Anatomical LocalizationSulci and Gyri
pial surface
gray/white border
SULCUS
FISSURE
GYRUS
Source Ludwig Klingler, 1956 in Tamraz
Comair, 2000
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Variability of Sulci
Variability of Sulci
Source Szikla et al., 1977 in Tamraz Comair,
2000
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Variability of Functional Areas
Watson et al., 1995 -functional areas (e.g., MT)
vary between subjects in their Talairach
locations -the location relative to sulci is more
consistent
Source Watson et al. 1995
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Cortical Surfaces
segment gray-white matter boundary
inflate cortical surface
render cortical surface
sulci concave dark gray gyri convex light
gray

• Advantages
• surfaces are topologically more accurate
• alignment across sessions and experiments allows
  task comparisons

Source Jody Culham
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Cortical Inflation Movie
Movie unfoldorig.mpeg http//cogsci.ucsd.edu/ser
eno/unfoldorig.mpg Source Marty Serenos web
page
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Cortical Flattening
2) make cuts along the medial surface (Note,
one cut typically goes along the fundus of the
calcarine sulcus though in this example the cut
was placed below)
1) inflate the brain
3) unfold the medial surface so the cortical
surface lies flat
4) correct for the distortions so that the true
cortical distances are preserved
Source Brain Voyager Getting Started Guide
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Spherical Averaging
Future directions of fMRI Use cortical surface
mapping coordinates Inflate the brain into a
sphere Use sulci and/or functional areas to match
subjects data to template Cite latitude
longitude of spherical coordinates
Movie brain2ellipse.mpeg http//cogsci.ucsd.edu/
sereno/coord1.mpg Source Marty Serenos web page
Source Fischl et al., 1999
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Spherical Averaging
Source MIT HST583 online course notes
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5. CORTICAL ANATOMY
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14 Major Sulci

• Main sulci are formed early in development
• Fissures are really deep sulci
• Typically continuous sulci
• Interhemispheric fissure
• Sylvian fissure
• Parieto-occipital fissure
• Collateral sulcus
• Central sulcus
• Calcarine Sulcus
• Typically discontinuous sulci
• Superior frontal sulcus
• Inferior frontal sulcus
• Postcentral sulcus
• Intraparietal sulcus
• Superior temporal sulcus
• Inferior temporal sulcus
• Cingulate sulcus

Source Ono, 1990
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Interhemispheric Fissure
-hugely deep (down to corpus callosum) -divides
brain into 2 hemispheres
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Sylvian Fissure
-hugely deep -mostly horizontal -insula (purple)
is buried within it -separates temporal lobe from
parietal and frontal lobes
Sylvian Fissure
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Parieto-occipital Fissure and Calcarine Sulcus
Cuneus (pink) -visual areas on medial side above
calcarine (lower visual field)
Parieto-occipital fissure (red) -very deep -often
Y-shaped from sagittal view, X-shaped in
horizontal and coronal views
Lingual gyrus (yellow) -visual areas on medial
side below calcarine and above collateral sulcus
(upper visual field)
Calcarine sulcus (blue) -contains V1
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Collateral Sulcus
-divides lingual (yellow) and parahippocampal
(green) gyri from fusiform gyrus (pink)
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Cingulate Sulcus
-divides cingulate gyrus (turquoise) from
precuneus (purple) and paracentral lobule (gold)
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Central, Postcentral and Precentral Sulci
Central Sulcus (red) -usually freestanding (no
intersections) -just anterior to ascending
cingulate
Precentral Sulcus (red) -often in two parts
(superior and inferior) -intersects with superior
frontal sulcus (T-junction) -marks anterior end
of precentral gyrus (motor strip, yellow)
Postcentral Sulcus (red) -often in two parts
(superior and inferior) -often intersects with
intraparietal sulcus -marks posterior end of
postcentral gyrus (somatosensory strip, purple)
ascending band of the cingulate
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Intraparietal Sulcus
-anterior end usually intersects with inferior
postcentral (some texts call inferior postcentral
the ascending intraparietal sulcus) -posterior
end usually forms a T-junction with the
transverse occipital sulcus (just posterior to
the parieto-occipital fissure) -IPS divides the
superior parietal lobule from the inferior
parietal lobule (angular gyrus, gold, and
supramarginal gyrus, lime)
POF
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Slice Views
inverted omega hand area of motor cortex
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Superior and Inferior Temporal Sulci
Superior Temporal Sulcus (red) -divides superior
temporal gyrus (peach) from middle temporal gyrus
(lime) Inferior Temporal Sulcus (blue) -not
usually very continuous -divides middle temporal
gyrus from inferior temporal gyrus (lavender)
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Superior and Inferior Frontal Sulci
Superior Frontal Sulcus (red) -divides superior
frontal gyrus (mocha) from middle frontal gyrus
(pink) Inferior Frontal Sulcus (blue) -divides
middle frontal gyrus from inferior frontal gyrus
(gold) orbital gyrus (green) and frontal pole
(gray) also shown
Frontal Eye fields lie at this junction
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Medial Frontal
-superior frontal gyrus continues on medial
side -frontal pole (gray) and orbital gyrus
(green) also shown