Cognitive Neuroscience
MRI vs. fMRI
MRI studies brain anatomy.
Functional MRI (fMRI)
studies brain function.
Source: Jody Culham’s fMRI for Dummies web site
Brain Imaging: Anatomy
CAT
Photography
PET
MRI
Source: modified from Posner & Raichle, Images of Mind
The major methods
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•
•
•
Single-unit recording
Lesion studies
Transcranial magnetic stimulation (TMS)
Neurosurgery-related methods
– Direct cortical stimulation
– Split-brain
– WADA
• Functional imaging
– Electromagnetic: EEG, MEG
– Hemodynamic: PET, fMRI
Single unit recording
•
•
Used extensively in animal studies
A microelectrode is inserted into brain tissue and recordings of action
potentials can be made from nearby neurons, ideally a single neuron.
– Recordings are typically extracellular
•
•
•
The animal can then be presented with various sensory stimuli, or
trained to perform some task, and the effects on neural activity can be
monitored
Advantages: great spatial and temporal resolution
Disadvantages: sampling only a very small fraction of a functional
neural system
Lesion studies
• Correlation of functional deficits with regions of
damage
• Both human and animal studies
– In animals, lesions can be made experimentally
– In humans, lesions are causes by “experiments of
nature”
Lesion studies (con’t)
•
Common types of lesions in humans
– Stroke (A “brain attack”)
• Ischemic: blockage of blood flow in an artery
• Hemmorrhagic: rupture of an artery
– Trauma
• Open vs. closed head injury
– Tumor
– Degenerative disease (e.g., alzheimers disease)
•
In general, the more focal the lesion, the easier it is to link the site of
damage to a behavioral deficit
Transcranial Magnetic Stimulation
• A method for producing temporary focal brain “lesion”
(disruption), via stimulation with a strong magnetic
field.
• With milder fields, can produce “excitation” or
facilitation effects.
Neurosurgery Methods
•
Direct cortical stimulation
– Delivery of a small electric current directly on the cortical surface
– Causes temporary disruption or facilitation of function in cortex being
stimulated
– Used clinically to map function, so that critical regions can be avoided
during tissue resection
– Can be done intra-operatively, or more commonly now, via chronically
implanted electrode grids
Neurosurgery methods (con’t)
• Split-brain
– Sectioning of corpus callosum as a treatment for medically
intractable epilepsy
– Can study the separate contributions of the left and right
hemispheres to various abilities/tasks
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Neurosurgery methods (con’t)
• WADA procedure
– Injection of sodium amytal (a barbituate), into one and then
the other carotid artery temporarily (5-10min) puts half the
brain to sleep allowing neurologists to assess function in the
awake hemisphere
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Neurosurgery methods (con’t)
• General considerations
– Advantages: better experimental control in some situations,
e.g., temporary lesions can be very focal and reversible
– Disadvantages: all subjects in these subjects are undergoing
these procedures because they have a neurological
disorder, therefore it is not clear how generalizable the
results are.
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PET and fMRI Activation
Source: Posner & Raichle, Images of Mind
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• PET scans = Positron Emission
Tomography scans
• Rely upon electrical activity calling for
local increase in oxygen and energy
• Based upon detected photons emitted
from electron-positron annihilations.
• Slow, some risk, costly
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fMRI Setup
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
Note: That’s one g, two t’s
Take images along the midline to use to plan slices
Source: Jody Culham’s fMRI for Dummies web site
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
Source: Jody Culham’s fMRI for Dummies web site
Slice Terminology
VOXEL
(Volumetric Pixel)
Slice Thickness
e.g., 6 mm
In-plane resolution
e.g., 192 mm / 64
= 3 mm
3 mm
6 mm
SAGITTAL SLICE
IN-PLANE SLICE
Number of Slices
e.g., 10
Matrix Size
e.g., 64 x 64
Field of View (FOV)
e.g., 19.2 cm
Source: Jody Culham’s fMRI for Dummies web site
3 mm
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
…
first volume
(2 sec to acquire)
Source: Jody Culham’s fMRI for Dummies web site
Activation Statistics
Functional images
~2s
ROI Time
Course
fMRI
Signal
(% change)
Time
Condition
Statistical Map
superimposed on
anatomical MRI image
Time
Region of interest (ROI)
~ 5 min
Source: Jody Culham’s fMRI for Dummies web site
Statistical Maps & Time Courses
Use stat maps to pick regions
Then extract the time course
Source: Jody Culham’s fMRI for Dummies web site
2D  3D
Source: Jody Culham’s fMRI for Dummies web site
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
condition: one set of stimuli or one task
Note: Terminology can vary from one fMRI site
to another (e.g., some places use “scan” to refer
to what we’ve called a volume).
4 stimulus conditions
+ 1 baseline condition (fixation)
A session consists of one or more experiments.
Each experiment consists of several (e.g., 1-8) runs
More runs/expt are needed when signal:noise is low or the effect is weak.
Thus each session consists of numerous (e.g., 5-20) runs (e.g., 0.5 – 3
hours)
Source: Jody Culham’s fMRI for Dummies web site
Design Jargon: Paradigm
paradigm (or protocol): the set of conditions and their order used in a
particular run
run
epoch: one instance of a
condition
first “objects right” epoch
second “objects right” epoch
volume #1
(time = 0)
Time
epoch
8 vol x 2 sec/vol = 16 sec
volume #105
(time = 105 vol x 2 sec/vol = 210 sec = 3:30)
fMRI Equipment
Magnet (4T)
Gradient Coil
4T magnet
RF Coil
gradient coil
(inside)
Head Coil
Source: Joe Gati, photos
Surface Coil
Source: Jody Culham’s fMRI for Dummies web site
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)
BOLD signal
Blood Oxygen Level Dependent signal
neural activity   blood flow   oxyhemoglobin   T2*   MR signal
Source: fMRIB Brief Introduction to fMRI
Magnet Safety
The whopping strength of the magnet makes safety essential.
Things fly – Even big things!
Source: www.howstuffworks.com
Source: http://www.simplyphysics.com/
flying_objects.html
Source: Jody Culham’s fMRI for Dummies web site
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QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
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
Cognitive Neuroscience Methods
QuickTime™ and a YUV420 codec decompressor are needed to see this picture.
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How can we define regions?
1. Talairach coordinates
2. Anatomical localization
3. Functional localization
• Region of interest (ROI) analyses
• already covered in Design lectures so will not be reconsidered
here
Talairach Coordinate System
Individual brains are different shapes and sizes…
How can we compare or average brains?
Talairach & Tournoux, 1988
• squish or stretch brain into “shoe box”
• extract 3D coordinate (x, y, z) for each
activation focus
Note: That’s TalAIRach, not TAILarach!
Source: Brain Voyager course slides
Rotate brain into ACPC plane
Corpus Callosum
Fornix
Find anterior commisure (AC)
Find posterior commisure (PC)
ACPC line
= horizontal axis
Note: official Tal sez use top of
AC and bottom of PC
Pineal Body
“bent asparagus”
Source: Duvernoy, 1999
Deform brain into Talairach
space
Mark 8 points in the brain:
• anterior commisure
• posterior commisure
• front
• back
• top
• bottom (of temporal lobe)
• left
• right
Squish or stretch brain to fit in “shoebox”
of Tal system
y<0
AC=0
y
y>0
z
y>0
ACPC=0
y<0
x
Extract 3 coordinates
Left is what?!!!
Neurologic (i.e. sensible) convention
• left is left, right is right
L
R
-
Note: Make sure you know what your magnet
and software are doing before publishing
left/right info!
+
x=0
Radiologic (i.e. stupid) convention
• left is right, right is left
R
L
+
x=0
Note: If you’re really unsure which side is
which, tape a vitamin E capsule to the one
side of the subject’s head. It will show up
on the anatomical image.
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
a)
Average all of the functionals together and perform stats on that
b)
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
Talairach Atlas
Brodmann’s Areas
Brodmann (1905):
Based on cytoarchitectonics: study of
differences in cortical layers between areas
Most common delineation of cortical areas
More recent schemes subdivide
Brodmann’s areas into many smaller
regions
Monkey and human Brodmann’s areas not
necessarily homologous
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 don’t fit well)
• activation foci can vary considerably – other landmarks like sulci may
be more reliable
Anatomical Localization
Sulci and Gyri
gray matter
(dendrites & synapses)
BANK
white matter
(axons)
FISSURE
FUNDUS
Source: Ludwig & Klingler, 1956 in Tamraz & Comair, 2000
Variability of Sulci
Source: Szikla et al., 1977 in Tamraz & Comair, 2000
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
Cortical Surfaces
segment gray-white
matter boundary
render cortical surface
inflate 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
Cortical Inflation Movie
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Movie: unfoldorig.mpeg
http://cogsci.ucsd.edu/~sereno/unfoldorig.mpg
Source: Marty Sereno’s web page
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 preseved
Source: Brain Voyager Getting Started Guide
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
subject’s data to template
Cite “latitude” & “longitude” of spherical
coordinates
QuickTime™ and a
YUV420 codec decompressor
are needed to see this picture.
Movie: brain2ellipse.mpeg
http://cogsci.ucsd.edu/~sereno/coord1.mpg
Source: Marty Sereno’s web page
Source: Fischl et al., 1999
Spherical Averaging
Source: MIT HST583 online course notes
Functional imaging
• Electroencephalography (EEG)
– Scalp electrodes measure the summed electrical
activity of large populations of synchronously
active neurons
– Can look at the changes in this signal as a
function of mental activity
• Changes in synchrony of different populations of
neurons
• Changes in morphology of EEG signals that are
time-locked to an event (e.g., a perceptual stimulus),
this is called event-related potentials (ERPs)
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Magnetoencephalography
Magnetoencephalography
Front
Magnetoencephalography
Magnetoencephalography
MEG Results
Right hippocampal
activation during place
learning was observed
in 2/7 children with FA
Right hippocampal
activation during place
learning was observed
in 6/7 controls
Magnetic Resonance Spectroscopy
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