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LEYLA ISIK: So I'm
going to just go over

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some very basic neuroscience,
mostly terminology, just

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for people who have very little
to no neuroscience background.

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When you hear the rest of the
talks, you would think like,

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what does it mean that they're
talking about spiking activity?

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Or what is fMRI measuring?

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So that's like the
level at which this is.

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So my disclaimers are one, like
I said, that it's very basic.

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And two, that it will be
CBMM and vision centric,

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because the goal is to
get you ready for the rest

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of this course.

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So please don't think that
this is an exhaustive,

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or what I think
is an exhaustive,

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summary of basic neuroscience.

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So just to give you
a brief outline,

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first we'll talk about
the basics of neurons,

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and their firing.

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Basic brain anatomy.

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How people measure neural
activity in the brain,

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both invasively
and non invasively.

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And then a brief rundown
of the visual system.

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This is a neuron.

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And it has dendrites and
axons, and the signal

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is propagated along
the axon, and the axon

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terminates on another cell.

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And when one neuron
terminates on another neuron,

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they form what's
called the synapse.

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So here are some pictures.

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Sorry, it's hard to see on the
projector, of neurons synapsing

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on other neurons.

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And that is how
neurons communicate.

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They send electrical
activity down their axon,

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and it reaches the next cell.

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And the synapse is both
an electrical and chemical

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phenomenon.

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We're not going to get
into the details of that,

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but if you're interested, I
encourage you to Wikipedia it.

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Neurons have a ion
gradient across them.

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So there is a
different concentration

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of certain types of ions
inside and outside of the cell.

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And there are ion
channels along the cell.

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And these ion channels
are voltage gated.

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So what happens is when
these ion channels open,

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the voltage inside
the cell changes,

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and that eventually
leads a neuron to fire.

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And they fire what is known
as an action potential.

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So it's possible for neurons'
voltage to change a little bit,

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and that is known
as potentiation.

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So they can get either
excitatory and inhibitory

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potentiation.

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So that means either higher or
lower activity, as shown here.

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And then once it reaches
a certain threshold,

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they fire what's known
as an action potential.

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So action potentials
are all or none firing,

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and that's what is referred
to as neural firing,

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or neural spiking.

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It's this actual
spike in the voltage.

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That is all you need
to know, like when

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people are talking
about neural spiking,

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they're talking about the
actual action potential.

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But oftentimes, we're
not measuring things

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at the level of single spikes.

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So I'll get into
it in a little bit,

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about what people are
actually measuring,

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and what they're
talking about when

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they're talking about
different recording techniques.

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So some basic brain anatomy.

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This is a slice of the cortex,
and just to orient you,

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I'm going to put
these online, just

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so you know the terminologies.

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But there are different lobes.

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The occipital lobe is
in the back, that's

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where early visual cortex is.

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Temporal lobe, parietal
lobe, and frontal lobe.

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And if people are talking about
the inferior part of the brain,

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they mean the bottom,
superior top, et cetera.

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And this is a rough layout
of where different sensory--

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can people see that?

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Kind of, different
sensory and motor

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cortexes, where they
land on the cortex.

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So Nancy is going to give
a really nice introduction

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to the functional
specialization of the brain.

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This is just some
basic anatomical terms

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to familiarize you all.

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Right, so neural recordings.

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So when we're talking about
invasive neural recordings,

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the first type that we'll talk
about is electrophysiology.

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So single and
multi-unit recordings.

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And what that means is that
somebody actually sticks

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an electrode into the
brain of an animal

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and records their
neural activity.

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So this can either
be a single unit

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recording, which means you are
recording from a single neuron.

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And either by sticking
the electrode inside or on

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top of the neuron, or
very close to the neuron.

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And that means that you're
close enough that you're only

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picking up the changes
in electrical activity

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from that one neuron.

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But what's more
commonly measured now

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is multi-unit activity.

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That means that you stick
an electrode in the brain,

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and it's picking up
activity from a bunch

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of neurons around it.

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So you can either
take that data,

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and get what's known as
the local field potentials.

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So that is the
changes in potential,

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in general, in that
whole group of neurons.

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And people often
analyze that data.

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Or, you can do some
sort of preprocessing

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to figure out how many
neural spikes you're getting.

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So that's typically trying
to look at the neural firing.

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So from that activity,
you can either

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get the spiking pattern,
or what people refer to

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as the local field potential.

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And then you probably
heard, you will

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hear a lot about ECoG data, from
Gabriel and others this time.

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So this is really exciting.

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It's the opportunity to record
from inside the human brain.

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From patients who have
pharmacologically intractable

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epilepsy.

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So sorry this is kind of gross.

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But when people are
having seizures,

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if surgeons want to
resect that area,

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they first have to
map very carefully

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where the seizures
are coming from,

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and what else is around there,
to make sure that they're

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helping the patient.

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So to do that, they place a grid
of electrodes on the surface

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of the subject's cortex.

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And then leave that
there often for a week,

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for several days, while they
do different types of mapping

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in that area.

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So this provides the opportunity
for scientists like Gabriel

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to then go and test the neural
activity in those humans.

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Which is a very rare opportunity
to be able to record invasively

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from humans.

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And again, since we're on
the surface of the brain,

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this is not single
unit activity.

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So you get something that is
more similar to the LFP type

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signal.

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And then what I and many
other people in the center do

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is also neuroimaging.

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So this is noninvasive,
often in humans.

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Although people also do
it in animals as well.

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And the main types you'll
probably hear about

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at this course are
MEG and EEG, which

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are very similar,
and functional MRI.

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So when many neurons
fire synchronously,

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so the neurons in your
cortex have the nice property

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that they're all aligned
in the same orientation.

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So when they fire
at the same time,

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you actually get a weak
electrical current.

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And that electrical
current causes

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a change in both the electric
and magnetic fields around it.

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And EEG and MEG measure
the changes in electric e,

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and magnetic m, fields
from those neural firings.

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But it's usually on
the order of like tens

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of millions of neurons
that need to be firing.

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So we're now at a
much larger scale

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than we were with the
invasive recordings.

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And because the neurons all have
to be firing at the same time,

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usually they're not all
firing an action potential.

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Because if you remember, it
was just this very brief spike.

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You're just measuring
kind of the changes

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in the potentiation
of that whole group

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of cortical neurons.

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So this is a very
coarse measure,

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but it's a direct
measure of neural firing.

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So it has very good
temporal resolution.

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So the question
was about, I don't

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know if everyone heard,
the temporal scale of MEG.

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So it's a millisecond
temporal resolution.

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I think you can maybe
even get higher.

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fMRI, on the other hand, usually
has a temporal resolution

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of seconds, a couple of seconds.

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But this spatial
resolution of fMRI

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is on the order of
millimeters, whereas it's

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more like centimeters in MEG.

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And actually, so the
problem in MEG and EEG

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is you're recording from--

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here's a picture of the MEG,
scanner subject sits in,

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and there's this helmet
that goes around their head.

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And that helmet has 306 sensors.

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If it was an EEG, they
would be wearing a cap.

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You've probably seen
an EEG cap before,

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and the electrodes would
be directly contacting

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their scalp.

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So you're measuring activity
from 100 to 300 sensors,

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and often you're trying
to estimate the activity

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in the cortex underneath.

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And so that is on the order
of like 10,000 sources.

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And so it's a very
ill posed problem,

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meaning that there is
not a unique solution

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to go from sensors to cortex.

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And so because of that,
we don't actually-- that's

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why they say that the
spatial scale is so poor.

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But actually it's not
a well-defined problem.

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So it's hard to even know where
the activity is originating

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from.

00:08:57.310 --> 00:08:59.260
But that's a very
active area of research

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for how you can constrain
that problem with anatomy,

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and other measurements,
to get better resolution.

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But still, I think
people typically

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think of it as being on
the order of centimeters.

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So the other main type of
noninvasive neuroimaging we'll

00:09:14.350 --> 00:09:15.910
talk about is functional MRI.

00:09:15.910 --> 00:09:18.740
So here's a picture
of an FMRI scanner.

00:09:18.740 --> 00:09:20.134
Subject's laying
there, and often

00:09:20.134 --> 00:09:21.550
if we're doing a
visual task, they

00:09:21.550 --> 00:09:26.570
look at stimuli on a mirror that
reflects from a screen where

00:09:26.570 --> 00:09:28.820
we're presenting the stimuli.

00:09:28.820 --> 00:09:31.660
So fMRI measures the
changes in blood flow

00:09:31.660 --> 00:09:34.420
that happen when neurons fire.

00:09:34.420 --> 00:09:37.610
And so as a result, this
is not a direct measure.

00:09:37.610 --> 00:09:40.810
So this is not a direct measure
of the actual neural firing.

00:09:40.810 --> 00:09:44.590
So it has a longer latency
for the blood flow effects

00:09:44.590 --> 00:09:46.150
to occur.

00:09:46.150 --> 00:09:48.520
And so that's why it has
the temporal scale that's

00:09:48.520 --> 00:09:50.560
more like a couple of seconds.

00:09:50.560 --> 00:09:53.450
But it has quite good
spatial resolution.

00:09:53.450 --> 00:09:55.600
There's structural MRI,
which if any of you

00:09:55.600 --> 00:09:59.140
have ever been injured,
you may have had an MRI,

00:09:59.140 --> 00:10:04.774
and that measures the actual--

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it doesn't measure
the blood flow,

00:10:06.190 --> 00:10:10.260
it measures the actual
structures underneath.

00:10:10.260 --> 00:10:13.420
I mean, often people will do
an MRI and a functional MRI,

00:10:13.420 --> 00:10:15.280
and co register the
two, so you have

00:10:15.280 --> 00:10:18.390
a very precise anatomical
image that you can then

00:10:18.390 --> 00:10:20.610
put the brain activity on.

00:10:27.570 --> 00:10:28.070
OK.

00:10:28.070 --> 00:10:29.270
So I got into this a bit.

00:10:29.270 --> 00:10:35.049
So invasive electrophysiology
is the highest resolution data,

00:10:35.049 --> 00:10:36.590
both spatial and
temporally, I think,

00:10:36.590 --> 00:10:39.620
that most scientists collect.

00:10:39.620 --> 00:10:40.830
But it has some advantages.

00:10:40.830 --> 00:10:41.829
One, that it's invasive.

00:10:41.829 --> 00:10:44.810
So it's hard to test
questions in humans.

00:10:44.810 --> 00:10:47.950
And just more
difficult in general.

00:10:47.950 --> 00:10:50.600
And two, you're limited
by brain coverage.

00:10:50.600 --> 00:10:53.000
So you can only stick
a grid or an electrode

00:10:53.000 --> 00:10:55.470
in a couple of brain
regions at once.

00:10:55.470 --> 00:10:57.710
So you really can't
get information

00:10:57.710 --> 00:11:00.140
from across the whole
brain, at this resolution

00:11:00.140 --> 00:11:02.950
with the technologies
we currently have.

00:11:02.950 --> 00:11:05.870
fMRI, on the other hand, has
broad coverage and good spatial

00:11:05.870 --> 00:11:08.330
resolution, but lower
temporal resolution.

00:11:08.330 --> 00:11:10.515
And EEG and MEG have
high temporal resolution,

00:11:10.515 --> 00:11:13.587
broad brain coverage, but
low spatial information.

00:11:18.260 --> 00:11:20.440
All right.

00:11:20.440 --> 00:11:23.150
So a bit about visual
processing in the brain.

00:11:23.150 --> 00:11:25.690
So this is a diagram.

00:11:25.690 --> 00:11:27.390
Can you see the colors?

00:11:27.390 --> 00:11:28.510
OK.

00:11:28.510 --> 00:11:30.240
A little, sorry.

00:11:30.240 --> 00:11:33.440
Of roughly what people
think of as visual cortex.

00:11:33.440 --> 00:11:37.150
So the blue in the back is
primary visual cortex, or V1,

00:11:37.150 --> 00:11:39.190
that's the earliest
cortical stage that where

00:11:39.190 --> 00:11:42.100
visual signals originate.

00:11:42.100 --> 00:11:44.980
And then there is what's known
as the ventral stream, which

00:11:44.980 --> 00:11:46.720
is often called
the what pathway,

00:11:46.720 --> 00:11:49.679
or where people roughly believe
object recognition occurs.

00:11:49.679 --> 00:11:51.220
And the dorsal
stream, which is often

00:11:51.220 --> 00:11:52.960
known as the where
pathway, which is

00:11:52.960 --> 00:11:58.040
thought to be more implicated
in spatial information.

00:11:58.040 --> 00:12:00.650
However, this is an
extreme oversimplification.

00:12:00.650 --> 00:12:03.490
I think Tommy put up this
wiring diagram the other day.

00:12:03.490 --> 00:12:07.210
This is still a simplification,
but a more realistic box

00:12:07.210 --> 00:12:09.310
diagram of all the
different-- each box

00:12:09.310 --> 00:12:10.900
represents a different
visual region.

00:12:10.900 --> 00:12:13.720
You can see that
there's connections

00:12:13.720 --> 00:12:16.780
between all of them, between
the ventral and dorsal stream.

00:12:16.780 --> 00:12:19.420
And while we roughly think
of it as feedforward,

00:12:19.420 --> 00:12:22.540
which means that the input
from, the output from one layer

00:12:22.540 --> 00:12:24.670
serves as input to the
next, often there's

00:12:24.670 --> 00:12:25.810
feedback connections.

00:12:25.810 --> 00:12:29.620
Meaning that information
can flow between areas.

00:12:29.620 --> 00:12:32.620
So that's why it's been
so challenging to probe

00:12:32.620 --> 00:12:33.520
with physiology.

00:12:36.592 --> 00:12:38.300
OK, so like I said,
there are many layers

00:12:38.300 --> 00:12:40.133
and they are thought
to be roughly organized

00:12:40.133 --> 00:12:44.880
hierarchically into the first
level primary visual cortex.

00:12:44.880 --> 00:12:47.460
In that area, you have
cells that respond

00:12:47.460 --> 00:12:50.070
to oriented lines and edges.

00:12:50.070 --> 00:12:51.810
So a cell will--

00:12:51.810 --> 00:12:53.520
I'll show an example
of this, but fire

00:12:53.520 --> 00:12:56.490
for stimuli that it sees, that
are in a certain orientation,

00:12:56.490 --> 00:12:58.410
in a certain place.

00:12:58.410 --> 00:13:02.810
And that is known as the
cell's receptive field.

00:13:02.810 --> 00:13:05.460
And so it's often thought
of as an edge detector.

00:13:05.460 --> 00:13:07.530
It's very analogous to
a lot of edge detection

00:13:07.530 --> 00:13:11.044
algorithms in computer
vision, for example.

00:13:11.044 --> 00:13:12.960
But then at what's thought
to be the top layer

00:13:12.960 --> 00:13:16.380
of the ventral stream,
inferior temporal cortex,

00:13:16.380 --> 00:13:19.530
cells fire in response
to whole objects.

00:13:19.530 --> 00:13:22.121
And it's not just a specific
orientation that they like.

00:13:22.121 --> 00:13:24.120
They will see this-- they
will fire whether they

00:13:24.120 --> 00:13:26.310
see this object at
different positions,

00:13:26.310 --> 00:13:29.310
and also have some tolerance
to viewpoint and scale as well.

00:13:34.620 --> 00:13:36.690
So a lot of what we know
about the visual system

00:13:36.690 --> 00:13:39.920
stem from Hubel and Wiesel's
seminal work in the 1960s,

00:13:39.920 --> 00:13:44.760
looking at cells and cat V1.

00:13:44.760 --> 00:13:47.870
This is the stimulus that
they're showing to the cat.

00:13:47.870 --> 00:13:49.880
It's an anesthesized cat,
and they're recording.

00:13:49.880 --> 00:13:52.440
So you'll hear a
popping, and those pops

00:13:52.440 --> 00:13:55.514
are the neural activity
that they're recording.

00:13:55.514 --> 00:13:58.470
[POPPING NOISES]

00:13:58.470 --> 00:14:01.020
So they're recording from
a single cell right now.

00:14:01.020 --> 00:14:02.700
So you see, you can
hear anytime they

00:14:02.700 --> 00:14:05.430
present that light bar,
in that specific position,

00:14:05.430 --> 00:14:06.120
the cell fires.

00:14:11.260 --> 00:14:13.330
And then as soon as they
move it out of the bar,

00:14:13.330 --> 00:14:14.450
the cells stop firing.

00:14:14.450 --> 00:14:16.030
So that specific
cell really likes

00:14:16.030 --> 00:14:18.160
this bar in this orientation.

00:14:18.160 --> 00:14:19.750
And they called
this a simple cell.

00:14:22.900 --> 00:14:27.270
We can fast forward
a little bit.

00:14:27.270 --> 00:14:30.312
They also show, OK.

00:14:30.312 --> 00:14:32.895
And then they found that there
are these other types of cells.

00:14:35.585 --> 00:14:38.507
[CAR HONKING]

00:14:42.390 --> 00:14:42.890
Sorry.

00:14:47.280 --> 00:14:49.764
They showed that if you rotate
it, doesn't fire at all.

00:14:49.764 --> 00:14:51.180
And then they show
that there were

00:14:51.180 --> 00:14:53.470
these other types of cells.

00:14:53.470 --> 00:14:55.080
This is maybe not
the movie we want.

00:14:55.080 --> 00:14:57.210
There are other cells
that fire not only

00:14:57.210 --> 00:15:00.810
to that specific position,
but to slight shifts

00:15:00.810 --> 00:15:02.320
in that position as well.

00:15:02.320 --> 00:15:04.620
And so it seems like those
cells formed an aggregate

00:15:04.620 --> 00:15:08.160
over the simple cells, and
they called those cells

00:15:08.160 --> 00:15:09.000
complex cells.

00:15:12.650 --> 00:15:15.800
And then people did similar
things in mostly macaque IT.

00:15:15.800 --> 00:15:17.780
And so they found
that in contrast

00:15:17.780 --> 00:15:20.300
to simple lines and
edges, cells here

00:15:20.300 --> 00:15:21.940
fired in response to hands.

00:15:21.940 --> 00:15:26.260
So this is showing the
cells' response here.

00:15:26.260 --> 00:15:29.450
So this is the number
of spikes over time.

00:15:29.450 --> 00:15:32.870
So it fires a lot to hands.

00:15:32.870 --> 00:15:34.070
And it fires to that hand.

00:15:34.070 --> 00:15:35.600
This cell likes
that hand, no matter

00:15:35.600 --> 00:15:37.910
what position you show it in.

00:15:37.910 --> 00:15:40.430
But it doesn't like these kind
of other more simple objects,

00:15:40.430 --> 00:15:42.950
and this one is not
selective for faces.

00:15:42.950 --> 00:15:46.130
So in IT, there are cells that
are selective for very high,

00:15:46.130 --> 00:15:48.620
you would think of as
high level objects.

00:15:48.620 --> 00:15:50.870
And they're tolerant to
changes in those objects.

00:15:53.790 --> 00:15:56.910
So people have done many
more sophisticated studies.

00:15:56.910 --> 00:16:01.010
This is an example from
Gabriel and Jim DiCarlo,

00:16:01.010 --> 00:16:05.760
and Chou Hung, where they
showed neural decoding.

00:16:05.760 --> 00:16:07.550
So applying a machine
learning algorithm

00:16:07.550 --> 00:16:11.300
to the output of many cells,
that these cells were again

00:16:11.300 --> 00:16:12.890
very specific for
certain objects,

00:16:12.890 --> 00:16:15.330
but invariant to
different transformations.

00:16:15.330 --> 00:16:17.480
So in particular here, they
showed this monkey face

00:16:17.480 --> 00:16:19.040
at different sizes.

00:16:19.040 --> 00:16:26.030
And they showed
that the cell fired.

00:16:26.030 --> 00:16:28.640
There was information present
in the population of neurons

00:16:28.640 --> 00:16:30.890
for this specific
monkey face, regardless

00:16:30.890 --> 00:16:32.690
of what size we showed it at.

00:16:32.690 --> 00:16:35.006
So these cells are
often thought to be--

00:16:35.006 --> 00:16:36.380
so it's often
thought that as you

00:16:36.380 --> 00:16:39.960
move along the visual hierarchy,
cells become more selective.

00:16:39.960 --> 00:16:43.340
So meaning, they like
more specific objects.

00:16:43.340 --> 00:16:45.860
And more invariant,
so more tolerant

00:16:45.860 --> 00:16:48.620
to changes in different
transformations.

00:16:52.176 --> 00:16:54.050
And so the other thing
I wanted to talk about

00:16:54.050 --> 00:16:58.220
was hierarchical feedforward.

00:16:58.220 --> 00:17:00.260
So computational models
of the visual system,

00:17:00.260 --> 00:17:02.360
because Tommy
mentioned this briefly,

00:17:02.360 --> 00:17:06.530
and I think it will tie into
a lot of the computer vision

00:17:06.530 --> 00:17:07.910
work you'll hear about.

00:17:07.910 --> 00:17:10.339
So these are inspired by
Hubel and Wiesel's findings

00:17:10.339 --> 00:17:12.300
in visual cortex.

00:17:12.300 --> 00:17:16.430
So meaning-- and I'm going
to talk both about the HMAX

00:17:16.430 --> 00:17:18.470
model, which is the
model developed by Tommy

00:17:18.470 --> 00:17:22.400
and others in his lab
which is a simpler, more

00:17:22.400 --> 00:17:23.839
biologically faithful model.

00:17:23.839 --> 00:17:25.550
But this sort of
architecture is also

00:17:25.550 --> 00:17:27.650
true of deep learning
systems that you heard a lot

00:17:27.650 --> 00:17:30.500
about recently, and that
have had a lot of success

00:17:30.500 --> 00:17:33.210
in computer vision challenges.

00:17:33.210 --> 00:17:35.750
So if you have an
input image, you

00:17:35.750 --> 00:17:38.150
can then have a set
of simple samples.

00:17:38.150 --> 00:17:41.000
Again, these are inspired by
Hubel and Wiesel's findings,

00:17:41.000 --> 00:17:43.730
so they are oriented
lines and edges.

00:17:43.730 --> 00:17:46.520
So this cell will
fire, if you have

00:17:46.520 --> 00:17:49.052
an edge that's
oriented like this,

00:17:49.052 --> 00:17:50.135
at that part of the image.

00:17:53.650 --> 00:17:57.780
And so again, it's just
a basic edge detector.

00:17:57.780 --> 00:18:00.320
And so these perform
template matching

00:18:00.320 --> 00:18:04.580
between their template, which
is in this case an oriented bar,

00:18:04.580 --> 00:18:07.775
and the input image to
build up selectivity.

00:18:07.775 --> 00:18:09.150
And then there
are complex cells.

00:18:09.150 --> 00:18:14.300
And these complex cells pool, or
take a local aggregate measure,

00:18:14.300 --> 00:18:16.010
to build up invariance.

00:18:16.010 --> 00:18:21.140
And so what that means is if you
have, say this red cell here,

00:18:21.140 --> 00:18:23.760
this complex cell would look
at these four simple cells.

00:18:23.760 --> 00:18:26.360
So you are now selective
to that oriented line,

00:18:26.360 --> 00:18:29.486
not just at this position,
but at all of these positions.

00:18:29.486 --> 00:18:30.860
And that gives
you some tolerance

00:18:30.860 --> 00:18:32.090
to changes in position.

00:18:32.090 --> 00:18:34.140
So you'd be able to
recognize the same object,

00:18:34.140 --> 00:18:35.690
whether it had this feature.

00:18:35.690 --> 00:18:40.435
Whether it was presented at
this corner or in a local area.

00:18:40.435 --> 00:18:41.810
And so the way
you do that is you

00:18:41.810 --> 00:18:45.500
take a max over the response
of all those input cells.

00:18:45.500 --> 00:18:47.390
And then you can repeat
this for many layers

00:18:47.390 --> 00:18:50.090
and, it's essentially
the same thing

00:18:50.090 --> 00:18:54.240
as a multilayer
convolutional neural network.

00:18:54.240 --> 00:18:57.020
And at the end, in
this HMAX model,

00:18:57.020 --> 00:18:59.700
you take a global max over
all scales and positions.

00:18:59.700 --> 00:19:03.320
So, in theory, you have all
these more complex features

00:19:03.320 --> 00:19:05.840
that you can now respond
to, regardless of where

00:19:05.840 --> 00:19:09.040
in the image and how
large they're presented.