Brain Functioning
PBL sessions
Emma Leibbrand
Table of Contents
Task 1 – The Imaging Brain (page 2)
Task 2 – Clinical Neuroimaging: What is There to See? (page 12)
Task 3 – Cortical Development and Neurodegeneration (page 21)
Task 4 – Language Representation and Lateralisation (page 34)
Task 5 – Attention to Detail (page 44)
Task 6 – Focal and Diffuse Brain Injury (page 53)
Task 7 – It’s Not a Static Thing! (page 70)
, TASK 1 – IMAGING THE BRAIN
Learning Goals
How does MRI and fMRI work and how can it be used by neuropsychologists to study brain
functioning?
o What are the pros and cons?
o What is BOLD?
What is the Default Mode Network (DMN) and how is it measured?
What are resting-state recordings and how can it be used?
How can the brain network analysis and the including terms in the image be defined?
How can brain network analysis be used to assess brain structure and function?
AMARO: STUDY DESIGN IN FMRI – BASIC PRINCIPLES
Aim = Reviews some aspects of fMRI study design.
MRI Magnetic Resonance Imaging (MRI) A form of structural neuroimaging that involves
applying a combination of magnetic fields and radiofrequency energy waves to the brain
to create detailed images of the brain’s structure and anatomy.
MRI machines use strong magnetic fields to align the protons (hydrogen nuclei) in the
water molecules in the body. These protons have a property called spin.
Radiofrequency (RF) pulses are directed to the aligned protons.
When the radio waves hit the protons, they temporarily disrupt the alignment of the
proton’s spins. Once the radio waves stop, the protons return to their aligned state.
This process is called relaxation time.
As the protons return to their aligned state, they emit radiofrequency signals, which
is detected by the MRI machine.
The MRI computer processes these signals to create detailed images of the body. The
strength and timing of the magnetic fields, as well as the way protons return to their
normal state, vary depending the type of tissue in the body. This variation is used to
create the contrast in MRI images, allowing different tissues to be distinguished.
Magnetic (nuclear magnetic spins) resonance (the matching of frequency between
the RF pulse and the precession of spins) imaging (signal encoded in images).
2
, fMRI Functional Magnetic Resonance Imaging (fMRI) A form of functional neuroimaging
that measures brain activity in real time.
Uses the blood oxygenation level dependent (BOLD) imaging.
Method is based on MR images made sensitive to changes in in the state of
oxygenation of the haemoglobin.
When a particular brain region becomes active during neuronal activity it requires
more oxygen. In response to increased neuronal activity, blood flow to that specific
brain region also increases to deliver more oxygen.
Haemoglobin carries that oxygen and can exist in two states:
o Oxygenated = it behaves as a diamagnetic substance (negative).
o Deoxygenated = it behaves as a paramagnetic substance (positive).
When blood flow increases to an active brain area, it leads to a change in the ratio of
oxygenated to deoxygenated haemoglobin.
BOLD signal = the change in this oxygenation ratio is detected by the fMRI scanner as
the BOLD signal.
o High BOLD response = In brain regions that are actively engaged in a task or
cognitive process. There is increased activity => higher demand for oxygen.
o Low BOLD response = In brain regions that are less active. There is reduced
or baseline neural activity => lower demand for oxygen.
The BOLD response is a dynamic process:
o Initial dip = Increase in deoxygenated haemoglobin concentration = caused
by increased metabolic demand for oxygen before blood flow can fully
respond = results in a brief small decrease of the BOLD signal.
o Increase in the oxy/deoxy-haemoglobin ratio => high MR signal.
o Eventually reaches a plateau if the stimulus is maintained for some time.
o Undershoot = BOLD signal temporarily drops below baseline before returning
to normal.
Summary => subject performs tasks in the scanner while BOLD images of the whole
brain are collected every 1-3s. Images show small changes in the brightness levels of
certain brain areas (related to blood oxygen concentration changes). The areas in
which the brightness changes relative to the task can be used in analyses.
The strategy in an fMRI experiment is based on an intervention in a system (the brain) and
observation of the modulation of the system response (BOLD response) resulting from this
‘provocation’ (cognitive task).
3
, Study Design
Paradigm design Paradigm is defined here as the construction, temporal organisation structure,
and behavioural predictions of cognitive tasks executed by the subject during
an fMRI experiment.
Comparison 1. Substraction => assumes 2 (or more) conditions can be cognitively added.
strategies o Mostly assumption is invalid - it doesn’t allow for interactions.
o BUT can produce useful information, especially in block designs.
2. Factorial => alternative to substraction; cognitive conditions processed in
a factorial manner – THUS allowing for interactions between components.
o Subject performs a task where cognitive components are
intermingled in one moment, and separated in another.
o Relies on an assumption of linearity between BOLD responses.
3. Parametric => method where the cognitive demand associated with a
particular cognitive task is increased (without modifying intrinsic nature).
o Increase in BOLD associated with increase in cognitive demand =
implies heavy link of a particular area to the intrinsic nature of the
parameter being manipulated.
o Allows for separation of these areas from the main cognitive
process, since the BOLD signal in those areas would not depend
on the manipulation of the parameter.
4. Conjuction analysis => subtle deviation from factorial design = at least 2
or more conditions share the cognitive component of interest.
o Whereas other designs are based on detecting differences -> this
approach is based on commonalities between them.
o THUS allows for another angle of analysis.
It is possible to combine these designs obtaining their benefits.
Stimulus 1. Blocked => based on maintaining cognitive engagement in a task by
presentation presenting stimuli sequentially within a condition, alternating this with
strategies other moments (epochs) when a different condition is presented.
o AB block = alternating between 2 conditions; a cycle corresponds
to two epochs of each condition.
4
PBL sessions
Emma Leibbrand
Table of Contents
Task 1 – The Imaging Brain (page 2)
Task 2 – Clinical Neuroimaging: What is There to See? (page 12)
Task 3 – Cortical Development and Neurodegeneration (page 21)
Task 4 – Language Representation and Lateralisation (page 34)
Task 5 – Attention to Detail (page 44)
Task 6 – Focal and Diffuse Brain Injury (page 53)
Task 7 – It’s Not a Static Thing! (page 70)
, TASK 1 – IMAGING THE BRAIN
Learning Goals
How does MRI and fMRI work and how can it be used by neuropsychologists to study brain
functioning?
o What are the pros and cons?
o What is BOLD?
What is the Default Mode Network (DMN) and how is it measured?
What are resting-state recordings and how can it be used?
How can the brain network analysis and the including terms in the image be defined?
How can brain network analysis be used to assess brain structure and function?
AMARO: STUDY DESIGN IN FMRI – BASIC PRINCIPLES
Aim = Reviews some aspects of fMRI study design.
MRI Magnetic Resonance Imaging (MRI) A form of structural neuroimaging that involves
applying a combination of magnetic fields and radiofrequency energy waves to the brain
to create detailed images of the brain’s structure and anatomy.
MRI machines use strong magnetic fields to align the protons (hydrogen nuclei) in the
water molecules in the body. These protons have a property called spin.
Radiofrequency (RF) pulses are directed to the aligned protons.
When the radio waves hit the protons, they temporarily disrupt the alignment of the
proton’s spins. Once the radio waves stop, the protons return to their aligned state.
This process is called relaxation time.
As the protons return to their aligned state, they emit radiofrequency signals, which
is detected by the MRI machine.
The MRI computer processes these signals to create detailed images of the body. The
strength and timing of the magnetic fields, as well as the way protons return to their
normal state, vary depending the type of tissue in the body. This variation is used to
create the contrast in MRI images, allowing different tissues to be distinguished.
Magnetic (nuclear magnetic spins) resonance (the matching of frequency between
the RF pulse and the precession of spins) imaging (signal encoded in images).
2
, fMRI Functional Magnetic Resonance Imaging (fMRI) A form of functional neuroimaging
that measures brain activity in real time.
Uses the blood oxygenation level dependent (BOLD) imaging.
Method is based on MR images made sensitive to changes in in the state of
oxygenation of the haemoglobin.
When a particular brain region becomes active during neuronal activity it requires
more oxygen. In response to increased neuronal activity, blood flow to that specific
brain region also increases to deliver more oxygen.
Haemoglobin carries that oxygen and can exist in two states:
o Oxygenated = it behaves as a diamagnetic substance (negative).
o Deoxygenated = it behaves as a paramagnetic substance (positive).
When blood flow increases to an active brain area, it leads to a change in the ratio of
oxygenated to deoxygenated haemoglobin.
BOLD signal = the change in this oxygenation ratio is detected by the fMRI scanner as
the BOLD signal.
o High BOLD response = In brain regions that are actively engaged in a task or
cognitive process. There is increased activity => higher demand for oxygen.
o Low BOLD response = In brain regions that are less active. There is reduced
or baseline neural activity => lower demand for oxygen.
The BOLD response is a dynamic process:
o Initial dip = Increase in deoxygenated haemoglobin concentration = caused
by increased metabolic demand for oxygen before blood flow can fully
respond = results in a brief small decrease of the BOLD signal.
o Increase in the oxy/deoxy-haemoglobin ratio => high MR signal.
o Eventually reaches a plateau if the stimulus is maintained for some time.
o Undershoot = BOLD signal temporarily drops below baseline before returning
to normal.
Summary => subject performs tasks in the scanner while BOLD images of the whole
brain are collected every 1-3s. Images show small changes in the brightness levels of
certain brain areas (related to blood oxygen concentration changes). The areas in
which the brightness changes relative to the task can be used in analyses.
The strategy in an fMRI experiment is based on an intervention in a system (the brain) and
observation of the modulation of the system response (BOLD response) resulting from this
‘provocation’ (cognitive task).
3
, Study Design
Paradigm design Paradigm is defined here as the construction, temporal organisation structure,
and behavioural predictions of cognitive tasks executed by the subject during
an fMRI experiment.
Comparison 1. Substraction => assumes 2 (or more) conditions can be cognitively added.
strategies o Mostly assumption is invalid - it doesn’t allow for interactions.
o BUT can produce useful information, especially in block designs.
2. Factorial => alternative to substraction; cognitive conditions processed in
a factorial manner – THUS allowing for interactions between components.
o Subject performs a task where cognitive components are
intermingled in one moment, and separated in another.
o Relies on an assumption of linearity between BOLD responses.
3. Parametric => method where the cognitive demand associated with a
particular cognitive task is increased (without modifying intrinsic nature).
o Increase in BOLD associated with increase in cognitive demand =
implies heavy link of a particular area to the intrinsic nature of the
parameter being manipulated.
o Allows for separation of these areas from the main cognitive
process, since the BOLD signal in those areas would not depend
on the manipulation of the parameter.
4. Conjuction analysis => subtle deviation from factorial design = at least 2
or more conditions share the cognitive component of interest.
o Whereas other designs are based on detecting differences -> this
approach is based on commonalities between them.
o THUS allows for another angle of analysis.
It is possible to combine these designs obtaining their benefits.
Stimulus 1. Blocked => based on maintaining cognitive engagement in a task by
presentation presenting stimuli sequentially within a condition, alternating this with
strategies other moments (epochs) when a different condition is presented.
o AB block = alternating between 2 conditions; a cycle corresponds
to two epochs of each condition.
4
