NEUROIMAGING I
INTRODUCTORY LECTURE – Nils Kohn
Overview Course
Goal: Provide Knowledge for research in neuroimaging
→ 3 parts: Electrophysiology, MRI acquisition & fMRI analysis
-> Mini-exam after each part (20% of the final grade of that part)
-> Final exam contains open questions on factual knowledge, simple facts and deeper
understanding (possibilities and limitations) and apply acquired knowledge
Introduction
Brain anatomy
Brain metabolism
• Neural activity consumes energy -> brain represents 2% of the body weight, but receives 15% of
cardiac output, 20% of body oxygen consumption and 25% body glucose utilization
• Glutamate most dominant excitatory neurotransmitter
• The energy demands of glutamatergic neurons account for 80-90% of total cortical glucose usage
Goal of cognitive neuroscience
• Map the information-processing structure of the human mind onto the physical organization of
the brain
• Nowadays more integrated approach, not only localization to one structure
,Emergence of cognitive neuroimaging
Mental work versus Cortical work
• Mental work is cognition, what is being done consciously
• Cortical work is underlying brain activity
• Neuroscience aims at disentangling cortical and mental work to understand both
• Focus on one while controlling the other can help to discern one from the other
Modern blood flow-based measurement
• PET: Positron emission tomography
• Most biological molecules are made up of hydrogen, carbon, nitrogen and/or oxygen
• PET uses radionuclides (that have fixed half-lives) to measure the related metabolism of these
molecules
• Principles of fMRI using deoxygenation of blood
o PET images, oxygen utilization is not correlated to blood flow
o Veins (containing larger proportion of deoxyhemoglobin) are low in fMRI signal (if animal
breathed on 100% oxygen veins disappear)
o In an experiment, increase in blood flow leads to higher oxygenation of blood, leads to less
disturbed signal, leads to signal increase, leads to blobs
Functional imaging
Functional imaging: Temporal and Spatial resolution
• Temporal resolution: ability to measure changes in brain activity over time
• Spatial resolution: ability to distinguish between different locations in the brain
,Functional principles
Spontaneous vs evoked brain activity
• Cannot say that one represents mental work and the
other cognitive work, although that is how people
think about it (deducting noise/background)
• No such thing as simple cognition, where only one
area is active
• Most areas might not be highly specialized but get
activated in multiple tasks
→ Maybe it is just about states of network e.g. degree of activation or combination → Both brain
activities are essential for understanding cognition, neither map should be viewed as representing all
mental or cognitive work on its own
PART 1: MRI ACQUISITION
BUILDING BLOCKS MRI: HARDWARE AND EXCITATION – David Norris
Introductory electromagnetism
What is a field?
• A field is where a force operates
• There are many kinds of forces and fields
• A field has a magneto and direction
• Any object with non-zero mass experiences gravitational attraction of the gravitational field
• Gravity is the weakest force, the next strongest are the electrical and magnetic forces
Field of a bar magnet
• Ferromagnet -> in this course: magnetic fields arise from currents flowing in wires
• Magnetic field generated by magnet is depicted by lines around it
o Lines give you the direction of the field at a particular point
o The closer the lines are the stronger the field
• SI unit of magnetic field strength is the Tesla (T)
o Typical bar magnet field: 0.01 T
o Earth’s magnetic field: 50 µT
The magnetic field of a current
• Electrical currents (I) generate magnetic fields (B)
• If the strength of the current varies in time, then so does the strength of the field
o Problem: strength of field decreases with distance and the fields is around the wire
• Depending on the current flow, the field has a different shape
• We can shape the magnetic field by shaping the wire. We use this effect to generate all the
magnetic fields used in MRI
, Faraday’s law
• A change in the magnetic environment of a wire loop (i.e. the field lines from a
magnet moving through the coil) will give rise to a voltage across its terminals and a
current will flow
o Think of a bicycle dynamo! -> magnet rotates -> magnetic field through coil
varies -> induces voltage -> drives an electric current -> powering lights
• MRI: Distributed magnetisation in your tissue -> spinning magnetization -> cutting
magnetic fields lines -> voltage -> change can be detected by MRI
MRI system components
To perform MRI, we need 3 different forms of magnetic field:
• The magnet which generates the main magnetic field, denoted by (B0). The orientation of the
main magnetic field is by convention along the z-axis (along length of your body; longitudinal).
o Tesla area
o You need big changes in magnetic field strengths to see differences in resolution
• The gradient set, which generates switched magnetic field gradients in (Bz). There are three
gradient fields giving a gradient in Bz along the x, y, and z-axes. These are denoted Gx, Gy, Gz;
longitudinal, sagittal and transversal.
o Milli Tesla per meter
• The radio-frequency system consisting of:
(a) Transmitter and resonator which together generate a rotating field known as the (B1) field.
(b) Receiver coil or coils which detect and amplify the weak MR signal.
All three of these fields have markedly different characteristics -> Know the different characteristics!!
1. Magnets
• Main magnetic field
• Goal is to have a magnet with a very homogeneous magnetic field in the region
where you are imaging.
• An infinite solenoid will do this (a finite solenoid is shown). However, this is not a
practical design, and compromises have to be made to restrict the dimensions and
allow access.
o Finite solenoid: magnet field is concentrated into a nearly uniform field in the center of a
long solenoid. The field outside is weak and divergent
Direction of the static magnetic field for the new MRI system is from head to
foot, because coils are aligned like that. In the old MRI system, the direction
is vertical. The old one you can switch on/off, you don’t see that todays.
What is the most dangerous aspect of MRI? Projectiles: attract ferromagnetic
objects with a great force
Characteristics of the main magnetic field
• This is the strongest of the magnetic fields, with a strength in Teslas
• In a superconducting system the magnet is always on
o And hence it is always pulling magnetic objects into it
• The field should be stable in time
• It should also be homogeneous over the imaging volume
On homogeneity and shims
• It is impossible in practice to build a magnet with a perfectly homogeneous field. Furthermore,
the presence of an object will distort the field.
INTRODUCTORY LECTURE – Nils Kohn
Overview Course
Goal: Provide Knowledge for research in neuroimaging
→ 3 parts: Electrophysiology, MRI acquisition & fMRI analysis
-> Mini-exam after each part (20% of the final grade of that part)
-> Final exam contains open questions on factual knowledge, simple facts and deeper
understanding (possibilities and limitations) and apply acquired knowledge
Introduction
Brain anatomy
Brain metabolism
• Neural activity consumes energy -> brain represents 2% of the body weight, but receives 15% of
cardiac output, 20% of body oxygen consumption and 25% body glucose utilization
• Glutamate most dominant excitatory neurotransmitter
• The energy demands of glutamatergic neurons account for 80-90% of total cortical glucose usage
Goal of cognitive neuroscience
• Map the information-processing structure of the human mind onto the physical organization of
the brain
• Nowadays more integrated approach, not only localization to one structure
,Emergence of cognitive neuroimaging
Mental work versus Cortical work
• Mental work is cognition, what is being done consciously
• Cortical work is underlying brain activity
• Neuroscience aims at disentangling cortical and mental work to understand both
• Focus on one while controlling the other can help to discern one from the other
Modern blood flow-based measurement
• PET: Positron emission tomography
• Most biological molecules are made up of hydrogen, carbon, nitrogen and/or oxygen
• PET uses radionuclides (that have fixed half-lives) to measure the related metabolism of these
molecules
• Principles of fMRI using deoxygenation of blood
o PET images, oxygen utilization is not correlated to blood flow
o Veins (containing larger proportion of deoxyhemoglobin) are low in fMRI signal (if animal
breathed on 100% oxygen veins disappear)
o In an experiment, increase in blood flow leads to higher oxygenation of blood, leads to less
disturbed signal, leads to signal increase, leads to blobs
Functional imaging
Functional imaging: Temporal and Spatial resolution
• Temporal resolution: ability to measure changes in brain activity over time
• Spatial resolution: ability to distinguish between different locations in the brain
,Functional principles
Spontaneous vs evoked brain activity
• Cannot say that one represents mental work and the
other cognitive work, although that is how people
think about it (deducting noise/background)
• No such thing as simple cognition, where only one
area is active
• Most areas might not be highly specialized but get
activated in multiple tasks
→ Maybe it is just about states of network e.g. degree of activation or combination → Both brain
activities are essential for understanding cognition, neither map should be viewed as representing all
mental or cognitive work on its own
PART 1: MRI ACQUISITION
BUILDING BLOCKS MRI: HARDWARE AND EXCITATION – David Norris
Introductory electromagnetism
What is a field?
• A field is where a force operates
• There are many kinds of forces and fields
• A field has a magneto and direction
• Any object with non-zero mass experiences gravitational attraction of the gravitational field
• Gravity is the weakest force, the next strongest are the electrical and magnetic forces
Field of a bar magnet
• Ferromagnet -> in this course: magnetic fields arise from currents flowing in wires
• Magnetic field generated by magnet is depicted by lines around it
o Lines give you the direction of the field at a particular point
o The closer the lines are the stronger the field
• SI unit of magnetic field strength is the Tesla (T)
o Typical bar magnet field: 0.01 T
o Earth’s magnetic field: 50 µT
The magnetic field of a current
• Electrical currents (I) generate magnetic fields (B)
• If the strength of the current varies in time, then so does the strength of the field
o Problem: strength of field decreases with distance and the fields is around the wire
• Depending on the current flow, the field has a different shape
• We can shape the magnetic field by shaping the wire. We use this effect to generate all the
magnetic fields used in MRI
, Faraday’s law
• A change in the magnetic environment of a wire loop (i.e. the field lines from a
magnet moving through the coil) will give rise to a voltage across its terminals and a
current will flow
o Think of a bicycle dynamo! -> magnet rotates -> magnetic field through coil
varies -> induces voltage -> drives an electric current -> powering lights
• MRI: Distributed magnetisation in your tissue -> spinning magnetization -> cutting
magnetic fields lines -> voltage -> change can be detected by MRI
MRI system components
To perform MRI, we need 3 different forms of magnetic field:
• The magnet which generates the main magnetic field, denoted by (B0). The orientation of the
main magnetic field is by convention along the z-axis (along length of your body; longitudinal).
o Tesla area
o You need big changes in magnetic field strengths to see differences in resolution
• The gradient set, which generates switched magnetic field gradients in (Bz). There are three
gradient fields giving a gradient in Bz along the x, y, and z-axes. These are denoted Gx, Gy, Gz;
longitudinal, sagittal and transversal.
o Milli Tesla per meter
• The radio-frequency system consisting of:
(a) Transmitter and resonator which together generate a rotating field known as the (B1) field.
(b) Receiver coil or coils which detect and amplify the weak MR signal.
All three of these fields have markedly different characteristics -> Know the different characteristics!!
1. Magnets
• Main magnetic field
• Goal is to have a magnet with a very homogeneous magnetic field in the region
where you are imaging.
• An infinite solenoid will do this (a finite solenoid is shown). However, this is not a
practical design, and compromises have to be made to restrict the dimensions and
allow access.
o Finite solenoid: magnet field is concentrated into a nearly uniform field in the center of a
long solenoid. The field outside is weak and divergent
Direction of the static magnetic field for the new MRI system is from head to
foot, because coils are aligned like that. In the old MRI system, the direction
is vertical. The old one you can switch on/off, you don’t see that todays.
What is the most dangerous aspect of MRI? Projectiles: attract ferromagnetic
objects with a great force
Characteristics of the main magnetic field
• This is the strongest of the magnetic fields, with a strength in Teslas
• In a superconducting system the magnet is always on
o And hence it is always pulling magnetic objects into it
• The field should be stable in time
• It should also be homogeneous over the imaging volume
On homogeneity and shims
• It is impossible in practice to build a magnet with a perfectly homogeneous field. Furthermore,
the presence of an object will distort the field.
