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From MRI physic to fMRI BOLD:From MRI physic to fMRI BOLD:

An introduction to the bases of functional An introduction to the bases of functional

magnetic resonance imagingmagnetic resonance imaging

Cyril PernetCyril Pernet

SFC SFC BrainBrain Imaging Imaging ResearchResearch CenterCenter

DCN, DCN, UniversityUniversity of Edinburghof Edinburgh

OverviewOverview

Magnetic Resonance physicsMagnetic Resonance physics

�� Quick tour in particle physicsQuick tour in particle physics

�� Magnetic ResonanceMagnetic Resonance

�� WhatWhat’’s happening in the magnets happening in the magnet

Magnetic Resonance ImagingMagnetic Resonance Imaging

�� How do we make an image?How do we make an image?

�� What is a contrast image?What is a contrast image?

Blood Oxygen Level Dependant contrastBlood Oxygen Level Dependant contrast

�� Where is the signal coming from?Where is the signal coming from?

�� Why is this functional imaging?Why is this functional imaging?


Quick tour in particle physicsQuick tour in particle physics

WhatWhat’’s an atom?s an atom?

It is a fundamental piece of matter. Everything in the It is a fundamental piece of matter. Everything in the universe, except energy, being made of matter, universe, except energy, being made of matter, everything in the universe is made of atoms.everything in the universe is made of atoms.

An atom itself is made up of three tiny kinds of particles An atom itself is made up of three tiny kinds of particles called subatomic particles: called subatomic particles: protonsprotons, , neutronsneutrons, and , and

electronselectrons..

The protons and the neutrons The protons and the neutrons make up the centre of the atom make up the centre of the atom called the nucleus and the called the nucleus and the electrons fly around above the electrons fly around above the nucleus in a small cloud. The nucleus in a small cloud. The electrons carry a negative charge electrons carry a negative charge and the protons carry a positive and the protons carry a positive charge.charge.

Some atomic propertiesSome atomic properties

An element is defined by itAn element is defined by it’’s number of protons s number of protons –– for for

instance hydrogen as 1 proton (isotopes are atoms with instance hydrogen as 1 proton (isotopes are atoms with

the same number of protons but different number of the same number of protons but different number of

neutrons, e.g. deuterium 1 proton 1 neutron)neutrons, e.g. deuterium 1 proton 1 neutron)


MassMass: the large majority of an atom's mass comes from : the large majority of an atom's mass comes from the protons and neutrons, the total number of these the protons and neutrons, the total number of these particles in an atom is called the particles in an atom is called the mass numbermass number

SizeSize: the dimensions are usually described in terms of : the dimensions are usually described in terms of the distances between two nuclei when the two atoms the distances between two nuclei when the two atoms are joined in a are joined in a chemical bondchemical bond. The radius varies with the . The radius varies with the location of an atom on the atomic chart, the type of location of an atom on the atomic chart, the type of chemical bond, the number of neighbouring atoms and chemical bond, the number of neighbouring atoms and itit’’s s spinspin (see after)(see after)

Energy levelsEnergy levels: When an electron is bound to an atom, it : When an electron is bound to an atom, it has a has a potential energypotential energy that is inversely proportional to its that is inversely proportional to its distance from the nucleus. This is measured by the distance from the nucleus. This is measured by the amount of energy needed to unbind the electron from the amount of energy needed to unbind the electron from the atom. In the quantum mechanical model, a bound atom. In the quantum mechanical model, a bound electron can only occupy a set of states centred on the electron can only occupy a set of states centred on the nucleus, and each state corresponds to a specific energy nucleus, and each state corresponds to a specific energy level. Similarly, nuclei posses their own energy levels.level. Similarly, nuclei posses their own energy levels.


Magnetic moment and spin Magnetic moment and spin ((Wolfgang PauliWolfgang Pauli in 1924.in 1924.): ): particles possess an intrinsic quantum mechanical particles possess an intrinsic quantum mechanical property known as property known as spinspin. . We can think in terms of We can think in terms of classical physicclassical physic that atoms are like spinning tops. These that atoms are like spinning tops. These tops can spin at only given frequencies and exert tops can spin at only given frequencies and exert particular magnetic forces.particular magnetic forces. The magnetic moment The magnetic moment corresponds to the field produced by electric charges corresponds to the field produced by electric charges (proton/electron) which are spinning.(proton/electron) which are spinning.


Magnetic ResonanceMagnetic Resonance

Nuclear Magnetic ResonanceNuclear Magnetic Resonance

IsidorIsidor RabiRabi (1938, Phys Rev 53) showed that when an (1938, Phys Rev 53) showed that when an

external magnetic field oscillates at the same frequency external magnetic field oscillates at the same frequency

as some atomic nuclei, these ones absorb the energy as some atomic nuclei, these ones absorb the energy

from the field. This is called from the field. This is called magnetic resonancemagnetic resonance. .

The frequency of the field has to match the spin The frequency of the field has to match the spin

frequency, and this match corresponds to the frequency, and this match corresponds to the resonance resonance

frequencyfrequency. (1944 Nobel Prize in physics). (1944 Nobel Prize in physics)

NMR was discovered independently byNMR was discovered independently by Felix BlockFelix Block

(1946, (1946, PhysiolPhysiol Rev, 70) Rev, 70) and and Edward PurcellEdward Purcell (1946, (1946,

PhysiolPhysiol Rev, 69)Rev, 69)..

They showed that atomic nuclei of bulk matter placed They showed that atomic nuclei of bulk matter placed

in a magnetic field absorb and in a magnetic field absorb and rere--emitemit radio waves, a radio waves, a

phenomenon called nuclear inductionphenomenon called nuclear induction or or nuclear nuclear

magnetic resonancemagnetic resonance. . (1952 Nobel Prize in physics)(1952 Nobel Prize in physics)

This phenomenon turned out to be very This phenomenon turned out to be very

useful for studying physical, chemical, and useful for studying physical, chemical, and

biological properties of matterbiological properties of matter

Nuclear Magnetic ResonanceNuclear Magnetic Resonance


WhatWhat’’s happening in the magnets happening in the magnet

We have seen that atomic nuclei (protons + neutrons) We have seen that atomic nuclei (protons + neutrons)

have spins and magnetic momentshave spins and magnetic moments

♦ Magnetic field strengths are measured

in units of Gauss (G) and Tesla (T).

♦ Earth's magnetic field = 0.5G

♦ 1T= 10 000G

♦ Scanner 3T = 60,000 times Earth’s MF

�� Outside a magnetic field, spins of different nuclei are Outside a magnetic field, spins of different nuclei are

randomly oriented whereas inside a magnetic field, randomly oriented whereas inside a magnetic field,

spins of nuclei tend to be aligned with the magnetic spins of nuclei tend to be aligned with the magnetic

fieldfield

NMR: magnetismNMR: magnetism

B0

=

At 1.5T, for every oneAt 1.5T, for every one--

million nuclei, there is million nuclei, there is

about one extra spin about one extra spin

aligned with the aligned with the BB00 field! field!

♦♦ For a magnetic field For a magnetic field BB00, the alignment of spins , the alignment of spins

corresponds to low and high energetic states of the corresponds to low and high energetic states of the

nuclei (spins are said aligned or counternuclei (spins are said aligned or counter--aligned). aligned).

Because Because the parallel alignment of atomsthe parallel alignment of atoms’’ spin with B0 spin with B0

is energetically more favourableis energetically more favourable, it exists a net , it exists a net

(macroscopic) magnetization (macroscopic) magnetization MM00 for all the nuclei.for all the nuclei.


Small Small BB00 produces small produces small MM00 and large and large BB00 produces large produces large MM00


In addition to the alignment of spins and the In addition to the alignment of spins and the

orientation of the magnetic moment, there also orientation of the magnetic moment, there also

exists a rotation of exists a rotation of MM0 0 around around BB0 0 ,,this is the this is the

precessionprecession

MM00rotates (precesses) at a frequency ω, proportional

to the size of BB00B0

M0

ω = γ. BB00

γ is the gyro-magnetic

ratio which varies

according to the type

of nucleus (Larmor

Frequency)

Video ☺


Summary 1Summary 1

People like the rest of the universe are made of atomsPeople like the rest of the universe are made of atoms

Atoms are themselves composed of protons, neutrons Atoms are themselves composed of protons, neutrons and electrons and electrons –– atoms have an intrinsic property called atoms have an intrinsic property called spin ; in addition protons and electrons possess electric spin ; in addition protons and electrons possess electric charges so that atoms spinning produces a small charges so that atoms spinning produces a small magnetic fieldmagnetic field

If we apply an external magnetic field then i) spins get If we apply an external magnetic field then i) spins get aligned to the field ii) because the parallel alignment of aligned to the field ii) because the parallel alignment of atomsatoms’’ spin is energetically more favourablespin is energetically more favourable, it exists a , it exists a net macroscopic magnetization and iii) net macroscopic magnetization and iii) this macroscopic this macroscopic magnetization vector magnetization vector precessesprecesses at a frequency which is at a frequency which is proportional to the strength of the field and depends on proportional to the strength of the field and depends on the type of elements.the type of elements.

NMR: RF excitationNMR: RF excitation

Remember that if we apply a magnetic field that Remember that if we apply a magnetic field that

oscillates at the same frequency than atoms they absorb oscillates at the same frequency than atoms they absorb

and reand re--emit radio waves.emit radio waves.

In a scanner, we have a constant magnetic field B0 such In a scanner, we have a constant magnetic field B0 such

as each atom has itas each atom has it’’s spin oriented with the field and s spin oriented with the field and

precessingprecessing at a given frequency at a given frequency ωω..

We then apply magnetic pulses at the frequency We then apply magnetic pulses at the frequency ωω so so

that i) atoms will absorb the energy of the field and thus that i) atoms will absorb the energy of the field and thus

jump into a higher energy level (thus we have a change jump into a higher energy level (thus we have a change

in the spin alignment and decrease of M0) and ii) the in the spin alignment and decrease of M0) and ii) the

precessions of the different atoms become in phaseprecessions of the different atoms become in phase

♦♦ On a macroscopic level, RF exposure causes the net On a macroscopic level, RF exposure causes the net

magnetization magnetization MM to spiral away from the direction of to spiral away from the direction of

the the BB00 fieldfield..

The RF pulse changes the The RF pulse changes the

number of nuclei at high number of nuclei at high

and low energy states (and low energy states (MzMz

decreases) decreases) and puts spins and puts spins

in phase (in phase (Mxy Mxy increases)increases). .

Video ☺


After applying a RF pulse, After applying a RF pulse, Mxy Mxy is like a little magnet is like a little magnet

that rotates. It generates an oscillating voltage that rotates. It generates an oscillating voltage

induced by magnetic field changes and is detected induced by magnetic field changes and is detected

by a coil of wires placed around the subject, this is by a coil of wires placed around the subject, this is

called magnetic called magnetic inductioninduction. . This voltage is the This voltage is the RF RF

signalsignal whose measurements form the raw data for whose measurements form the raw data for

MRIMRI

Free induction decay


Summary 1Summary 1

People like the rest of the universe are made of atomsPeople like the rest of the universe are made of atoms

Atoms are themselves composed of protons, neutrons Atoms are themselves composed of protons, neutrons and electrons and electrons –– atoms have an intrinsic property called atoms have an intrinsic property called spin ; in addition protons and electrons possess electric spin ; in addition protons and electrons possess electric charges so that atoms spinning produces a small charges so that atoms spinning produces a small magnetic fieldmagnetic field

If we apply an external magnetic field then i) spins get If we apply an external magnetic field then i) spins get aligned to the field ii) because the parallel alignment of aligned to the field ii) because the parallel alignment of atomsatoms’’ spin is energetically more favourablespin is energetically more favourable, it exists a , it exists a net macroscopic magnetization and iii) net macroscopic magnetization and iii) this macroscopic this macroscopic magnetization vector magnetization vector precessesprecesses at a frequency which is at a frequency which is proportional to the strength of the field and depends on proportional to the strength of the field and depends on the type of elements.the type of elements.

Summary 2Summary 2

By applying a RF pulse at the frequency of which the net By applying a RF pulse at the frequency of which the net magnetization oscillates, we make the nuclei to change magnetization oscillates, we make the nuclei to change their energy level, i.e. we change the spin alignment = their energy level, i.e. we change the spin alignment = decrease of the signal in the direction of B0 (the static decrease of the signal in the direction of B0 (the static magnetic field).magnetic field).

This also make each atoms to oscillate in phase = This also make each atoms to oscillate in phase = increase of the signal in the direction of B1 (the RF increase of the signal in the direction of B1 (the RF pulse).pulse).

The signal measured in the scanner is then the The signal measured in the scanner is then the oscillation of the net magnetization vector in the direction oscillation of the net magnetization vector in the direction of the pulse which create voltage variations in the coil of of the pulse which create voltage variations in the coil of wires.wires.

Magnetic Resonance ImagingMagnetic Resonance Imaging

How do we make an image?How do we make an image?

We can only detect one dimensional signal, i.e. the We can only detect one dimensional signal, i.e. the

total RF signal from the entire 3D volume inside the total RF signal from the entire 3D volume inside the

““RF coilRF coil”” (the detecting antenna) .. (the detecting antenna) .. How do we make How do we make

an image from that?an image from that?

♦ 1st NMR experiment in 1945, 1st MRI Image in 1972

♦ 2003 Physiology or Medicine Nobel prize: Lauterbur and Mansfield

How to make an image?How to make an image?

from mri physic to fmri bold - university of · pdf filefrom mri physic to fmri bold: ......

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