FREE H1 BIO

PSYCH
Presented by Sana, Falak and Dharani
W1: Lecture 1: TMS

Pre-session activity (4 minutes):

Draw a mind map that includes:
Why we use TMS?
How TMS works?
What are the different types of TMS?
List example research applications of TMS:
 W1: Lecture 1: Introduction
TMS: transcranial magnetic
stimulation
Good spatial and temporal
resolution: limited area of
effect (superficial)
It’s the primary focus of
the lab report, so it is
important to understand.
‘Neural noise’ or
‘temporary lesions’ -
causation
There are trade offs

What is the relationship between TMS

and this image?
W1: Lecture 2: TMS
Applications

Overview:
Inection of neural noise approach with single-pulse TMS
Virtual lession approach with repetitive TMS
Probing excitability approach with single-pulse TMS
Probing information transfer approach with paired-pulse
TMS
W1: Lecture 2: TMS applications
What happened in the experiment when they
moved the coil left and right? Up and Down?

Why did they want to test this?

 W1: Lecture 2: TMS applications
1. TMS zap
2. Neurons fire, causing motor function movement
3. Muscle activity is recorded

We prove an area to see how reactive

(excitable) it is to stimulation
We measure the Motor evoked potentials
(muscle reaction)
 W1: Lecture 2: TMS applications
Does it depend on what type of object?
Does it need to be something the hand can
do?

Probing information transfer approach

with paired-pulse TMS:
Sub-threshold vs Supra-threshold
W2: Lecture 1: Stats 1: T-
test

Pre-session activity (1 minute):

2 main questions:
Why do we use t-tests?
Why do we use effect sizes?
Pre-activity answers:

Why t-tests? Why effect sizes?

To see if the difference between To test how much of the difference

groups is due to chance or not = between groups is due to the
statistically significant experimental condition (i.e. how
effective the experimental
condition is)
 W2: Lecture 1: Stats 1: T-tests:
Different types of experimental
designs:

Single sample design Independent measures design Paired sample design

Scores of one sample compared to Scores from 2 samples of One sample is exposed to 2 conidtions
another value (e.g. population mean) different populations are and the results of each condition are
to test if the difference is due to compared to see if the difference compared to see if they occured due
chance or not is due to chance or not to chance or not
 W2: Lecture 1: Stats 1: T-tests:
One sample design: T-test
Formulas:

Example:

Variance:
 W2: Lecture 1: Stats 1: T-tests:
One sample design: T-test

Previous example: Once we have our t-empirical we compare it

to our t-critical via a statistical appendix:
 W2: Lecture 1: Stats 1: T-tests:
Directional hypothesis = one tailed Non-directional hypothesis = two tailed
W2: Lecture 2: Stats 2: T-
test & Effect sizes

Overview:
Independent measures
Paired sample
Effect sizes: Cohen's D and r^2
W2: Lecture 2: Stats 1: Effect sizes: Independent measures: T-test

Example:
W2: Lecture 2: Stats 1: Effect sizes: Paired samples: T-test

Example: All that has changed is that all our data comes
from the difference between conditions
W2: Lecture 2: Stats 1: Effect sizes:
Cohen's D: r^2 (Variance explained by the
experimental condition):

For Cohen's D and

r^2, Identify the
effect size rules of
thumn:

Either can be used

Repeated measures Cohen's D is effectively the same as single sample Cohen's D
W2: Lecture 2: Stats 1: Effect sizes:
Cohen's D: r^2 (Variance explained by the
experimental condition):

For Cohen's D and

r^2, Identify the
effect size rules of
thumn:

Either can be used

Repeated measures Cohen's D is effectively the same as single sample Cohen's D
W3: Lecture 1: EEG:

Overview:
EEG methods
What is EEG? Strengths, Weaknesses and requirements
Making raw EEG data useable
Neurophysiology of EEGs
Orientation of neurons
 W3: Lecture 1: EEG:
Quick overview of EEG:
Non-invasive use of electrodes on the scalp to measure the electrical activity of
neurons in specific brain regions
We must filter raw EEG data for 'noise', then we can make correlational inferences
about cognitive processes and brain regions
Benefits:
Cheaper and relatively easier to conduct
Higher temporal resolution
Disadvantages:
Lower spatial resolution

EEG requirements:
Ground electrode
Reference electrode
GE readings - RE readings = Brain activity
 W3: Lecture 1: EEG:
Active recall question (30 seconds):
What factors prevent researchers from
making immediate inferences with raw EEG
data? How are these resolved?
 W3: Lecture 1: EEG:
Irrelevant noise: Initial signal is too small
Band-pass filters: Needs to be amplified from 10 - 100
Signals that are too large (>35 - 70Hz) and too small (<0.5 - microvolts by approx 1000 - 100000 x
1 Hz) are removed because they don't represent brain Strong temporal resolution inferences
activity can be made around 256 - 1024Hz =
Notch filters: Sample frequency range
Line noise (signals from technology in the room @ approx.
50 - 60Hz) need to be removed
Artefacts:
Eye-blink artefacts:
Strong dipole + fine motor muscles = lots of electrical
activity
Easy to detect and removed through automated
software (ICA)
Muscle artefacts:
Contracted and tense muscles = electrical activity
Relaxation and choosing appropriate tasks
Skin potential artefacts:
Sweat and moisture = permanent damage to results
Relax participants and reduce stress levels
 W3: Lecture 1: EEG:
How is the electrical activity, which
we measure in EEG, actually
produced?
The pre-synaptic neuron sends chemical
or electrical excitatory
neurotransmitters across the synpatic
gap to excite the dendrites of the post
synaptic neuron
Dendrites of the post synaptic neuron
activate and ion channels open
Sodium ions flow into the cell membrane
and potassium ions flow out, causing a
change in resting membrane potential
from slightly negative to positive
This change in potential travels down the
axon as an action potential and re-starts
the process at the axon terminal
 W3: Lecture 1: EEG:
Active recall question (30 seconds):
Why is the orientation of neurons an important
consideration?
How many neurons do we require to be in the same
orientation to get an EEG signal?
 W3: Lecture 1: EEG:
Why is the orientation of neurons an How many neurons do we
important consideration? require to be in the same
orientation for us to measure
Electrical signals from individual an EEG signal?
neurons are too weak to be detected.
We require them to be grouped We need >= 10000 neurons
together and aligned towards the oriented in the same direction
electrodes on the scalp to actually get towards an electrode and
a signal. grouped together to get a signal

An analogy of neuron orientation:

Condition 1 = group of students shouting random words at the same time and in different directions of an
audience
Condition 2 = group of students shouting the same words in the same direction as the audience
W3: Lecture 2: ERP
Methods:

Pre-session activity (3 minutes):

Draw a mind map in your table group that includes:
A definition of ERPs
5 Key assumptions in their use
Definitions of polarity and order
A major problem associated with them
How we make them measurable in time
W3: Lecture 2: ERP methods:
 W3: Lecture 2: ERP methods:
Describe the experiment from Stephen Luck's textbook (2005), where
researchers studied how the brain reacts to frequent stimuli vs rare
stimuli
They had a screen where the letters X and O were
presented to participants. Xs were presented more
frequently than Os and researchers wanted to
understand how the brain would react differently to
Xs (which participants would more frequently expect)
and Os (less expected)

The EEG data didn’t show a clear difference

where meaningful results could be identified.
This was due to noise in the data
 W3: Lecture 2: ERP methods:
How did Op de Beeck & Nakatani (2019) solve the noise issue identified
by the experiment in Stephen Luck's textbook (2005)?
They averaged across all X trials and all O trails
(isolated each through time-locking). This method
averages out the noise (only when noise has a
mean of 0)
Bumps in averaged data are ERPs, these
are denoted by Polarity and Order
(Positive or negative direction of results
and in when they occur compared to other
ERPs).
We see significant difference at P3, hence,
we can infer that that’s when the brain
differentiates frequent and infrequent
events
 W3: Lecture 2: ERP methods:
Why do we pay so much attention to amplitude in EEG data?
Draw a mind map that lists the different types of amplitude techniques and how they are used:

EEG amplitudes are the dependent variable we are trying to measure. We compare the peaks in
data to infer correlations between brain regions and cognitive processes
 W3: Lecture 2: ERP methods:
Describe the study conducted by Ghering and Colleagues (1993):
Aim: To study cognitive processes behind the detection and compensation of errors
Gehring and Colleagues assumed that the detection and compensation mechanism was so
quick and automatic that they couldn’t directly study it, hence, they used error-related
negativities (ERN).
ERN = component of ERP that is a negative deflection of up to 10 microvolts (uV) which is
measured at central electrodes on the scalp. Measurement occurs around 80-100 ms
after an error
Called ’O shit response’ due to how fast it occurs after an error

Key results:
When participants cared about being accurate they measured greater ERN activity = error
detection mechanism was more active
High ERN was correlated with lower response force when pressing a button = participants were
correcting for errors
High ERN was correlated with longer time to complete next task = participants were being more
careful
Higher ERN was correlated with higher likelihood of getting the next task right = participants were
learning from mistakes
W4: Lecture 1: MRI Basics:

Overview:
Proton and magnetic field interaction
Importance of RF pulse
T1 and T2 decay
Reconstruction of brain images
W4: Lecture 1: MRI Basics:
Active recall question (30 seconds):
Describe the initial interaction between protons and
magnetic fields
How do RF pulses enable us to image the brain?
W4: Lecture 1: MRI Basics:
Describe the initial interaction between protons and magnetic fields
+ How do RF pulses enable brain imagining?
Initially exposed = aligns in that direction
Protons are now parallel to the B0 field and in different phases
of precession (time point of spin). Right now we can't
differentiate the signals from the brain and the MRI machine
Why? Because neurons emit energy and we use that to
differentiate brain regions. If the protons are in the same
direction as B0 then they are effectively the same
We hit the protons with an RF pulse to transversally magnetize
them. They become perpendicular to B0 (transversal/horizontal
axis) and have an aligned phase of precession
The RF pulse matches the precession frequency of these
protons and uses that to get them spinning at the same time
Larmor frequency = frequency of precession (proton spin)
 W4: Lecture 1: MRI Basics:
Draw a mind map that
identifies:
The 2 initial issues
that protons have
when in a magnetic
field
How we use RF
pulses to fix that
The subsequent
issue with RF pulses
The consequences
that arise as due to
the solution of the
RF pulse issue
 W4: Lecture 1: MRI Basics:
How do we figure out where our signals came from in the brain?
Via reconstruction of brain images = manipulating the magnetic field strength,
via gradient coils, in specific locations of the brain across 3 dimensions
Slice selecting gradient:
Change magnetic field strength in a specific slice of the brain
Increases the precession frequency of protons in that slice. We know this
new precession frequency and its different from the rest of the protons in
the brain
We hit this region with a specific RF pulse that matches the new precession
frequency (resonance) and get signals from only this region
Phase encoding gradient:
The entire slice emits the same frequency. However, we want there to be a
slight difference in parts of the slice so we can tell where the signal is
coming from within the slice
Apply another RF pulse to specific protons in the slice to de-phase them
from the others. I.e. some protons will spin at different rates than the others
The difference in precession tells us about their location by changing the
frequency of the signal they emit
Frequency encoding gradient:
We apply the phase encoding gradient again but during the entire read-out
phase to get an even more accurate idea of where our signals come from
W4: Lecture 2: fMRI
Methods:

Overview:
Relationship between fMRI and oxygenated blood
Haemodynamic response function curve
BOLD signal
Interpreting fMRI images
Quick pre-activity question:
Whats the difference between MRI and fMRI?
W4: Lecture 2: fMRI Basics:
Active recall question (30 seconds):
Describe how fMRI uses oxygenated blood in what it
intends to measure:

MRI vs fMRI
MRI images the brains
structure

fMRI images activation in

the brain with increases in
oxygenated blood
 W4: Lecture 2: fMRI Basics:
Describe how fMRI uses oxygenated blood in what it intends to measure:

fMRI is a haemodynamic neuroimaging

method, which means it indirectly measures
neural activity through the direct
measurement of oxygenated blood flow in
brain tissue.

This process is possible because cognitive

functions require energy to execute. The
primary energy source in cells is ATP
(adenosine triphosphate), which is produced
through glucose metabolism. Glucose
metabolism requires oxygen and therefore
cognitive functions can be identified through
increased oxygen consumption in cells.
HRF Rapid fire
questions: 2. Approx. how
long after stimuli 3. Why isn't
onset does blood BOLD signal
oxygenation worse during
1. Can we compare the HRF of
peak and return neural
different brain regions? to baseline? activation?

4. Why is there an initial dip in

oxygenated blood in the HRF
curve?
HRF Rapid fire
questions: 2. Cognitive
process 3. Peak = 4 - 8
immediately seconds and
1. We can't compare HRFs of consumes some baseline = 16
different brain regions because oxygen reserves seconds
they are slightly different
(different rates of oxygen
consumption)
4. Oversupply of oxygen, which is
diamagnetic, causes better signal
reading
 W4: Lecture 2: fMRI Methods:
What does the BOLD signal measure and what are its
correlations (hint: inputs, outputs and EIN)
 W4: Lecture 2: fMRI Basics:
Identify what the X-axis, Y-axis, each run, each row of every run and each
column of every run, in this image, represents

Each row of the Y-axis (Time) represents an individual

scan of the brain (not a full image)
Each run is a different total brain scan (image of the
brain) that has been seperated by time (takes break
between)
Each column that is identified as a 'cond', represents a
(experimental) condition that is being tested
Every white square is an individual brain scan where the
condition was tested and demonstrated. The other blocs
are non-experimental and irrelevant signals (e.g. head
movement)
Each run can be turned into a brain model that shows
the location in which each condition triggered brain
activity
 W4: Lecture 2: fMRI Basics:
Putting everything together: White spots =
Brain regions
most active
during a task
(BOLD signal)
Each voxel is run through a
t-test and the resulting
points are the most
statistically significant
(most aren't)

Structural brain images are overlaid with

regions from BOLD imagining that passes
statistical tests. Result is an image that
shows locations with the strongest and most
statistically significant brain activity
W5 L1 -> all about
faces and fMRI
Presented by Dharani
W5: Lecture 1: faces and fmri:
W5: Lecture 1: faces and fmri:
W5: Lecture 1: faces and fmri:
W5: Lecture 1: faces and fmri:
W5: Lecture 1: faces and fmri:
W5: Lecture 1: faces and fmri:
W5 L2 -> all about fMRI
limitations
Presented by Dharani
W5: Lecture 2: all about fMRI limitations:
W5: Lecture 2: all about fMRI limitations:
W5: Lecture 2: all about fMRI limitations:
W5: Lecture 2: all about fMRI limitations:
W6 L1 -> all about
audition
Presented by Dharani
W6: Lecture 1: all about audition:
W6: Lecture 1: all about audition:
W6: Lecture 1: all about audition:
 14

Activity??
W6: Lecture 1: all about audition:
W6: Lecture 1: all about audition:
W6: Lecture 1: all about audition:
W6 L2 -> all about
vision
Presented by Dharani
W6: Lecture 2: all about vision:
W6: Lecture 2: all about vision:
W6: Lecture 2: all about vision:
W6: Lecture 2: all about vision:
W6: Lecture 2: all about vision:
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