neuroimaging: intracortical, fmri, eeg
DESCRIPTION
Introductory lecture on neuroimaging techniques: intracortical, fMRI, EEG. Tends to explain the ideas of the technologies on a good level of intuition. Presented at AACIMP'14 (http://summerschool.ssa.org.ua/program/42-program/ns-2014/442-machine-learning-on-neuroimaging-data)TRANSCRIPT
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MACHINE LEARNING ON NEUROIMAGING DATA
Ilya Kuzovkin
AACIMP, August 2014
LECTURE 1: NEUROIMAGING TECHNIQUES
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THE COURSE
NEUROIMAGING DATA
L1
P1
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THE COURSE
NEUROIMAGING DATA
MACHINE LEARNING
L1
P1
L2
P2+
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THE COURSE
NEUROIMAGING DATA
MACHINE LEARNING
BRAIN-COMPUTER INTERFACE
L1
P1
L2
P2 P3+ =
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PART I INTRACORTICAL
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SPIKE
http://faculty.tcc.edu/mmitchell/142/ap-graph1.jpg
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SPIKE
http://faculty.tcc.edu/mmitchell/142/ap-graph1.jpg
How can voltage be negative?
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http://newton.umsl.edu/tsytsarev_files/neuron_electrode.JPG
ELECTRODES
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THE SIGNAL
• Local Field Potential
http://www.frontiersin.org/files/Articles/414/fnins-02-037/image_m/fnins-02-037-g001.jpg http://lifesciences.ieee.org/images/stories/life-sciences/2012-01-spike-01_l.png
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THE SIGNAL • Multi-unit spikes
• Local Field Potential
http://www.frontiersin.org/files/Articles/414/fnins-02-037/image_m/fnins-02-037-g001.jpg http://lifesciences.ieee.org/images/stories/life-sciences/2012-01-spike-01_l.png
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THE SIGNAL • Multi-unit spikes
• Local Field Potential
Spike sorting
http://www.frontiersin.org/files/Articles/414/fnins-02-037/image_m/fnins-02-037-g001.jpg http://lifesciences.ieee.org/images/stories/life-sciences/2012-01-spike-01_l.png
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THE SIGNAL
http://www.frontiersin.org/files/Articles/414/fnins-02-037/image_m/fnins-02-037-g001.jpg http://lifesciences.ieee.org/images/stories/life-sciences/2012-01-spike-01_l.png
• Multi-unit spikes
• Local Field Potential
• Single-unit spikes
Spike sorting
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For each measured neuron we record the time moments when it spiked
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RASTER PLOT
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RASTER PLOT
What is on the X axis?
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RASTER PLOT
Time
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RASTER PLOT
What is on the Y axis?
Time
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RASTER PLOT
Time
Neu
rons
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RASTER PLOT
Time
Neu
rons
rastrum
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PSTHPost-Stimulus Time Histogram
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PSTHPost-Stimulus Time Histogram
Neu
rons
\ Tr
ials
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PSTHPost-Stimulus Time Histogram
Neu
rons
\ Tr
ials
100
ms
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PSTHPost-Stimulus Time Histogram
Neu
rons
\ Tr
ials
100
ms
100
ms
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PSTHPost-Stimulus Time Histogram
Neu
rons
\ Tr
ials
100
ms
100
ms
100
ms
100
ms
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PSTHPost-Stimulus Time Histogram
Neu
rons
\ Tr
ials
100
ms
100
ms
100
ms
100
ms
31 s
pike
s
34 s
pike
s
27 s
pike
s
218
spik
es
33 s
pike
s
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PSTH
Time
Neu
rons
\ Tr
ials
Post-Stimulus Time Histogram
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PSTH
Time
Neu
rons
\ Tr
ials
Post-Stimulus Time Histogram
What is on the Y axis?
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PSTH
Time
Neu
rons
\ Tr
ials
Post-Stimulus Time Histogram
Spik
es p
er 1
00 m
s
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PSTH
Time
Neu
rons
\ Tr
ials
Post-Stimulus Time Histogram
Spik
es p
er 1
00 m
s
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)
What do you expect to see on this plot?0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)0
45
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TUNING CURVE
http://www.beatricebiologist.com/2012/11/types-of-cells.html
40 spikes per second (40 Hz)
7 spikes per second (7 Hz)0
45
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SUMMARY
• High spatial resolution (up to single neuron)
!• High temporal resolution
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SUMMARY
• High spatial resolution (up to single neuron)
!• High temporal resolution
What does “spatial resolution” mean?
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SUMMARY
• Requires surgery !• Localized
What does “temporal resolution” mean?
• High spatial resolution (up to single neuron)
!• High temporal resolution
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• High spatial resolution (up to single neuron)
!• High temporal resolution
SUMMARY
• Requires surgery !• Localized
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• High spatial resolution (up to single neuron)
!• High temporal resolution
SUMMARY
• Requires surgery !• Localized
Very informative and precise, but not applicable to general
audience due to surgery.
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PART II FMRI
http://www.csulb.edu/~cwallis/482/fmri/fmri.h3.gif http://neuro.mediasauce.com/images/fmri_machine.png
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NUCLEAR MAGNETIC RESONANCE
Physical phenomenon in which nucleus of an atom can absorb or reemit
electromagnetic radiation if placed in a magnetic field
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NUCLEAR MAGNETIC RESONANCE
Physical phenomenon in which nucleus of an atom can absorb or reemit
electromagnetic radiation if placed in a magnetic field
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NUCLEAR MAGNETIC RESONANCE
Physical phenomenon in which nucleus of an atom can absorb or reemit
electromagnetic radiation if placed in a magnetic field
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NUCLEAR MAGNETIC RESONANCE
Physical phenomenon in which nucleus of an atom can absorb or reemit
electromagnetic radiation if placed in a magnetic field.
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SPIN
Spin-UP +1/2
Spin-DOWN -1/2
http://www.markusehrenfried.de/science/physics/hermes/whatisspin.html
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SPIN
Spin-UP +1/2
Spin-DOWN -1/2
http://www.markusehrenfried.de/science/physics/hermes/whatisspin.html
Nothing actually spins in there. No analogy in classical mechanics.
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SPIN
Spin-UP +1/2
Spin-DOWN -1/2
Nothing actually spins in there. No analogy in classical mechanics.
But why call it spin then?http://www.markusehrenfried.de/science/physics/hermes/whatisspin.html
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
NOT A JOKE
Six known types of quarks and their official names. So spin is not that bad.
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MAGNETIC MOMENT
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MAGNETIC MOMENT
Particle with non-zero nuclear spin is like a
small magnet.
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MAGNETIC MOMENT
or ?
Particle with non-zero nuclear spin is like a
small magnet.
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MAGNETIC MOMENT
or ?
Particle with non-zero nuclear spin is like a
small magnet.
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MAGNETIC MOMENT
Particle with non-zero nuclear spin is like a
small magnet.
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IN A MAGNETIC FIELD
What happens to a magnet if you put it in a magnetic field?
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IN A MAGNETIC FIELD
What happens to a magnet if you put it in a magnetic field?
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IN A MAGNETIC FIELD
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IN A MAGNETIC FIELD
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IN A MAGNETIC FIELD
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IN A MAGNETIC FIELD
Stronger field — larger energy gap
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Nuclear Magnetic Resonance
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Nuclear Magnetic Resonance
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Nuclear Magnetic Resonance
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?Nuclear Magnetic Resonance
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RADIO FREQUENCY PULSE
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RADIO FREQUENCY PULSE
We can give energy to a particle
and move it to a higher energy level
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RADIO FREQUENCY PULSE
We can give energy to a particle
and move it to a higher energy level
To do that we send an electromagnetic wave
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RADIO FREQUENCY PULSE
We can give energy to a particle
and move it to a higher energy level
Nucleus will absorb energy only if frequency of the wave is correct for
• the nucleus we work with • strength of the magnetic field
To do that we send an electromagnetic wave
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RELAXATION
Now we stop the pulse
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RELAXATION
Now we stop the pulse
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RELAXATION
Nucleus will give out same amount of energy in the form of electromagnetic radiation.
Now we stop the pulse
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Nuclear Magnetic Resonance Imaging
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Nuclear Magnetic Resonance Imaging
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Nuclear Magnetic Resonance Imaging
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HYDROGEN
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HYDROGEN
Possible spin states +1/2 or -1/2
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
HYDROGEN IN A MAGNETIC FIELD
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
HYDROGEN IN A MAGNETIC FIELD
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
RF PULSE
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
RF PULSE
What will happen?
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
RF PULSE
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
RELAXATION
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
RELAXATION
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For different tissues the time of relaxation
is different
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http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
NUCLEI SEND SIGNALS
One large piece is still missing…
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GRADIENT COILS
http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
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GRADIENT COILS
http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
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GRADIENT COILS
http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
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GRADIENT COILS
http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
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GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
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GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
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GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
![Page 100: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/100.jpg)
GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
![Page 101: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/101.jpg)
GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
![Page 102: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/102.jpg)
GRADIENT COILS
http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html
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FMRI F FOR FUNCTIONAL*
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FMRI F FOR FUNCTIONAL*
*MRI signals associated with functional brain activity
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BOLDBLOOD-OXYGEN-LEVEL DEPENDENT
Active neuron Passive neuron
I need oxygen and
glucose!I need nothing…
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FMRI
Have different magnetic resonance
Distinguishable by MRI
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FMRI DATA
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• High spatial resolution !• No surgery! !• Records whole brain
SUMMARY
• Low temporal resolution !• Cost !• Size
Still pretty informative and precise, does not require a surgery, but is huge and costs a lot.
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PART III EEG
http://infantlab.psych.sc.edu/PWREEGDemoBaby
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NEURONS
http://biomedicalengineering.yolasite.com
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NEURONS
http://www.conncad.com/gallery/single_cells.html
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NEURONS
http://en.wikipedia.org/wiki/Neural_oscillation
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NEURONS
http://en.wikipedia.org/wiki/Neural_oscillation
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NEURONS
http://en.wikipedia.org/wiki/Neural_oscillation
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NEURONS
http://en.wikipedia.org/wiki/Neural_oscillation
What is the frequency in this example?
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BRAINWAVES
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BRAINWAVESDelta 0-4 Hz
Theta 4-7 Hz
Alpha 7-14 Hz
Mu 8-13 Hz
Beta 15-30 Hz
Gamma 30-100 Hz
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BRAINWAVESDelta 0-4 Hz
Theta 4-7 Hz
Alpha 7-14 Hz
Mu 8-13 Hz
Beta 15-30 Hz
Gamma 30-100 Hz
slow wave sleep, babies, lesions
children, drowsiness, meditation, relaxed
closed eyes, relaxed
motor neuron in rest, mirror neurons
motor activity, anxious thinking, concentration
networking between populations of neurons
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EEG
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EEG
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EEG
TIME
CH
ANN
ELS
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EEG
TIME
CH
ANN
ELS
![Page 125: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/125.jpg)
EEG
Alpha 7-14 Hz
Beta 15-30 Hz
Gamma 30-100 Hz
?TIME
CH
ANN
ELS
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EEG
Alpha 7-14 Hz
Beta 15-30 Hz
Gamma 30-100 Hz
?TIME
CH
ANN
ELS
Jean Baptiste Joseph Fourier 1768 — 1830
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FOURIER TRANSFORM*
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FOURIER TRANSFORM*
*discrete
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FOURIER TRANSFORM*
*discrete
=
![Page 130: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/130.jpg)
FOURIER TRANSFORM*
*discrete
signal at time t frequency complex number
=
![Page 131: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/131.jpg)
FOURIER TRANSFORM*
*discrete
signal at time t frequency complex number
=
Amplitude of the component with
frequency k
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FOURIER TRANSFORM*
*discrete
signal at time t frequency complex number
=
Amplitude of the component with
frequency k
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EEG DATA
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EEG DATA
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EEG DATA
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TIME-FREQUENCY DOMAIN
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Are we done?
EEG DATA
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Are we done?
Hint:
EEG DATA
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300 MS
EEG DATA
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300 MS
EEG DATA
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300 MS
EEG DATA
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300 MS
EEG DATA
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300 MS
10 channels 50 frequencies 3 seconds of data 300 ms window
EEG DATA
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300 MS
10 channels 50 frequencies 3 seconds of data 300 ms window
• How many numbers to describe 1 reading of 300 ms?
EEG DATA
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300 MS
• How many numbers to describe 1 reading of 300 ms?
• How many numbers to describe all 3 seconds of data?
10 channels 50 frequencies 3 seconds of data 300 ms window
EEG DATA
![Page 146: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/146.jpg)
• High temporal resolution !• No surgery! !• Mobile
!• Cheap
SUMMARY
• Low spatial resolution
Available to wide audience, but measurements are approximate.
![Page 147: Neuroimaging: Intracortical, fMRI, EEG](https://reader033.vdocument.in/reader033/viewer/2022051111/556b04b5d8b42ae47d8b459e/html5/thumbnails/147.jpg)
SUMMARY OF NEUROIMAGING TECHNIQUESTechnology Electrical Magnetic Optical
Name EEG ECoG Intracortical MEG fMRI fNIRS
Invasive !
Portable !
Cost From $100 to $30,000+ $1000 grid
$2000 per array $1 mln $2-3
mln $200,000
Temporal resolution 50 ms 3 ms 3 ms 50ms 1-2 s 1 s
Spatial resolution 1+ cm 1 mm 0.5 mm -
0.05 mm 5 mm 1 mm voxels 5 mm
Pattern!classification VEP ERD/
ERS P300
Performance2 class 90% 3 class 80%
4 class ?
Large number
of targets2 cls 90%
Large number
of targets8 cls 90% High*
~ same as EEG based
4 cls 90%
2 cls 90%
Technology Electrical Magnetic Optical
Name EEG ECoG Intracortical MEG fMRI fNIRS
Invasive !
Portable !
Cost From $100 to $30,000+ $1000 grid
$2000 per array $1 mln $2-3
mln $200,000
Temporal resolution 50 ms 3 ms 3 ms 50ms 1-2 s 1 s
Spatial resolution 1+ cm 1 mm 0.5 mm -
0.05 mm 5 mm 1 mm voxels 5 mm
Pattern!classification VEP ERD/
ERS P300
Performance2 class 90% 3 class 80%
4 class ?
Large number
of targets2 cls 90%
Large number
of targets8 cls 90% High*
~ same as EEG based
4 cls 90%
2 cls 90%