M ACHINE L EARNING ON N EUROIMAGING D ATA L ECTURE 1: N EUROIMAGING T - - PowerPoint PPT Presentation

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M ACHINE L EARNING ON N EUROIMAGING D ATA L ECTURE 1: N EUROIMAGING T ECHNIQUES Ilya Kuzovkin AACIMP, August 2014 T HE COURSE L1 P1 N EUROIMAGING D ATA T HE COURSE L1 L2 P1 P2 N EUROIMAGING M ACHINE + D ATA L EARNING T HE COURSE L1 L2 P1

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SLIDE 1

MACHINE LEARNING ON NEUROIMAGING DATA

Ilya Kuzovkin

AACIMP, August 2014

LECTURE 1: NEUROIMAGING TECHNIQUES

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SLIDE 2

THE COURSE

NEUROIMAGING DATA

L1 P1

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SLIDE 3

THE COURSE

NEUROIMAGING DATA MACHINE LEARNING

L1 P1 L2 P2

+

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SLIDE 4

THE COURSE

NEUROIMAGING DATA MACHINE LEARNING BRAIN-COMPUTER INTERFACE

L1 P1 L2 P2 P3

+ =

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SLIDE 5

PART I INTRACORTICAL

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SLIDE 6

NEURONS

http://biomedicalengineering.yolasite.com

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SLIDE 7

NEURONS

http://biomedicalengineering.yolasite.com

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SLIDE 8

SPIKE

http://faculty.tcc.edu/mmitchell/142/ap-graph1.jpg

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SLIDE 9

SPIKE

http://faculty.tcc.edu/mmitchell/142/ap-graph1.jpg

How can voltage be negative?

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SLIDE 10

http://newton.umsl.edu/tsytsarev_files/neuron_electrode.JPG

ELECTRODES

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SLIDE 11

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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SLIDE 12

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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SLIDE 13

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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SLIDE 14

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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SLIDE 15

For each measured neuron we record the time moments when it spiked

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SLIDE 16

RASTER PLOT

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SLIDE 17

RASTER PLOT

What is on the X axis?

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SLIDE 18

RASTER PLOT

Time

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SLIDE 19

RASTER PLOT

What is on the Y axis? Time

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SLIDE 20

RASTER PLOT

Time Neurons

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SLIDE 21

RASTER PLOT

Time Neurons

rastrum

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SLIDE 22

PSTH

Post-Stimulus Time Histogram

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SLIDE 23

PSTH

Post-Stimulus Time Histogram

Neurons \ Trials

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SLIDE 24

PSTH

Post-Stimulus Time Histogram

Neurons \ Trials 100 ms

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SLIDE 25

PSTH

Post-Stimulus Time Histogram

Neurons \ Trials 100 ms 100 ms

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SLIDE 26

PSTH

Post-Stimulus Time Histogram

Neurons \ Trials 100 ms 100 ms 100 ms 100 ms

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SLIDE 27

PSTH

Post-Stimulus Time Histogram

Neurons \ Trials 100 ms 100 ms 100 ms 100 ms 31 spikes 34 spikes 27 spikes 218 spikes 33 spikes

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SLIDE 28

PSTH

Time Neurons \ Trials

Post-Stimulus Time Histogram

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SLIDE 29

PSTH

Time Neurons \ Trials

Post-Stimulus Time Histogram What is on the Y axis?

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SLIDE 30

PSTH

Time Neurons \ Trials

Post-Stimulus Time Histogram

Spikes per 100 ms

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SLIDE 31

PSTH

Time Neurons \ Trials

Post-Stimulus Time Histogram

Spikes per 100 ms

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SLIDE 32

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

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SLIDE 33

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

45

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SLIDE 34

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

45

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SLIDE 35

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz)

45

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SLIDE 36

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz)

45

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SLIDE 37

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz) 7 spikes per second (7 Hz)

45

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SLIDE 38

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz) 7 spikes per second (7 Hz)

45

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SLIDE 39

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz) 7 spikes per second (7 Hz)

45

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SLIDE 40

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

  • n this plot?

45

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SLIDE 41

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz) 7 spikes per second (7 Hz)

45

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SLIDE 42

TUNING CURVE

http://www.beatricebiologist.com/2012/11/types-of-cells.html

40 spikes per second (40 Hz) 7 spikes per second (7 Hz)

45

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SLIDE 43

SUMMARY

  • High spatial resolution

(up to single neuron)

  • High temporal resolution
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SLIDE 44

SUMMARY

  • High spatial resolution

(up to single neuron)

  • High temporal resolution

What does “spatial resolution” mean?

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SLIDE 45

SUMMARY

  • Requires surgery
  • Localized

What does “temporal resolution” mean?

  • High spatial resolution

(up to single neuron)

  • High temporal resolution
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SLIDE 46
  • High spatial resolution

(up to single neuron)

  • High temporal resolution

SUMMARY

  • Requires surgery
  • Localized
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SLIDE 47
  • 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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SLIDE 48

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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SLIDE 49

NUCLEAR MAGNETIC RESONANCE

Physical phenomenon in which nucleus

  • f an atom can absorb or reemit

electromagnetic radiation if placed in a magnetic field

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SLIDE 50

NUCLEAR MAGNETIC RESONANCE

Physical phenomenon in which nucleus

  • f an atom can absorb or reemit

electromagnetic radiation if placed in a magnetic field

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SLIDE 51

NUCLEAR MAGNETIC RESONANCE

Physical phenomenon in which nucleus

  • f an atom can absorb or reemit

electromagnetic radiation if placed in a magnetic field

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SLIDE 52

NUCLEAR MAGNETIC RESONANCE

Physical phenomenon in which nucleus

  • f an atom can absorb or reemit

electromagnetic radiation if placed in a magnetic field.

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SLIDE 53

SPIN

Spin-UP +1/2 Spin-DOWN

  • 1/2

http://www.markusehrenfried.de/science/physics/hermes/whatisspin.html

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SLIDE 54

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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SLIDE 55

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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SLIDE 56

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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SLIDE 57

MAGNETIC MOMENT

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SLIDE 58

MAGNETIC MOMENT

Particle with non-zero nuclear spin is like a small magnet.

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SLIDE 59

MAGNETIC MOMENT

  • r ?

Particle with non-zero nuclear spin is like a small magnet.

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SLIDE 60

MAGNETIC MOMENT

  • r ?

Particle with non-zero nuclear spin is like a small magnet.

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SLIDE 61

MAGNETIC MOMENT

Particle with non-zero nuclear spin is like a small magnet.

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SLIDE 62

IN A MAGNETIC FIELD

What happens to a magnet if you put it in a magnetic field?

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SLIDE 63

IN A MAGNETIC FIELD

What happens to a magnet if you put it in a magnetic field?

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SLIDE 64

IN A MAGNETIC FIELD

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SLIDE 65

IN A MAGNETIC FIELD

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SLIDE 66

IN A MAGNETIC FIELD

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SLIDE 67

IN A MAGNETIC FIELD

Stronger field — larger energy gap

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SLIDE 68

Nuclear Magnetic Resonance

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SLIDE 69

Nuclear Magnetic Resonance

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SLIDE 70

Nuclear Magnetic Resonance

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SLIDE 71

?

Nuclear Magnetic Resonance

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SLIDE 72

RADIO FREQUENCY PULSE

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SLIDE 73

RADIO FREQUENCY PULSE

We can give energy to a particle and move it to a higher energy level

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SLIDE 74

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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SLIDE 75

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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SLIDE 76

RELAXATION

Now we stop the pulse

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SLIDE 77

RELAXATION

Now we stop the pulse

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SLIDE 78

RELAXATION

Nucleus will give out same amount of energy in the form of electromagnetic radiation.

Now we stop the pulse

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SLIDE 79

Nuclear Magnetic Resonance Imaging

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SLIDE 80

Nuclear Magnetic Resonance Imaging

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SLIDE 81

Nuclear Magnetic Resonance Imaging

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SLIDE 82

HYDROGEN

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SLIDE 83

HYDROGEN

Possible spin states +1/2 or -1/2

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SLIDE 84

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

HYDROGEN IN A MAGNETIC FIELD

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SLIDE 85

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

HYDROGEN IN A MAGNETIC FIELD

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SLIDE 86

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

RF PULSE

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SLIDE 87

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

RF PULSE

What will happen?

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SLIDE 88

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

RF PULSE

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SLIDE 89

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

RELAXATION

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SLIDE 90

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

RELAXATION

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SLIDE 91

For different tissues the time of relaxation is different

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SLIDE 92

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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SLIDE 93

GRADIENT COILS

http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg

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SLIDE 94

GRADIENT COILS

http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg

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SLIDE 95

GRADIENT COILS

http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg

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SLIDE 96

GRADIENT COILS

http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg

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SLIDE 97

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 98

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 99

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 100

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 101

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 102

GRADIENT COILS

http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html

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SLIDE 103

FMRI

F FOR FUNCTIONAL*

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SLIDE 104

FMRI

F FOR FUNCTIONAL*

*MRI signals associated with functional brain activity

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SLIDE 105

BOLD

BLOOD-OXYGEN-LEVEL DEPENDENT

Active neuron Passive neuron

I need

  • xygen and

glucose! I need nothing…

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SLIDE 106

FMRI

Have different magnetic resonance Distinguishable by MRI

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SLIDE 107

FMRI DATA

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SLIDE 108
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SLIDE 109
  • 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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SLIDE 110

https://www.coursera.org/course/fmri

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SLIDE 111

PART III EEG

http://infantlab.psych.sc.edu/PWREEGDemoBaby

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SLIDE 112

NEURONS

http://biomedicalengineering.yolasite.com

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SLIDE 113

NEURONS

http://www.conncad.com/gallery/single_cells.html

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SLIDE 114

NEURONS

http://en.wikipedia.org/wiki/Neural_oscillation

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SLIDE 115

NEURONS

http://en.wikipedia.org/wiki/Neural_oscillation

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SLIDE 116

NEURONS

http://en.wikipedia.org/wiki/Neural_oscillation

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SLIDE 117

NEURONS

http://en.wikipedia.org/wiki/Neural_oscillation

What is the frequency in this example?

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SLIDE 118

BRAINWAVES

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SLIDE 119

BRAINWAVES

Delta

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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SLIDE 120

BRAINWAVES

Delta

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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SLIDE 121

EEG

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SLIDE 122

EEG

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SLIDE 123

EEG

TIME CHANNELS

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SLIDE 124

EEG

TIME CHANNELS

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SLIDE 125

EEG

Alpha

7-14 Hz

Beta

15-30 Hz

Gamma

30-100 Hz

?

TIME CHANNELS

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SLIDE 126

EEG

Alpha

7-14 Hz

Beta

15-30 Hz

Gamma

30-100 Hz

?

TIME CHANNELS

Jean Baptiste Joseph Fourier 1768 — 1830

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SLIDE 127

FOURIER TRANSFORM*

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SLIDE 128

FOURIER TRANSFORM*

*discrete

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SLIDE 129

FOURIER TRANSFORM*

*discrete

=

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SLIDE 130

FOURIER TRANSFORM*

*discrete

signal at time t frequency complex number

=

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SLIDE 131

FOURIER TRANSFORM*

*discrete

signal at time t frequency complex number

=

Amplitude of the component with frequency k

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SLIDE 132

FOURIER TRANSFORM*

*discrete

signal at time t frequency complex number

=

Amplitude of the component with frequency k

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SLIDE 133

EEG DATA

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SLIDE 134

EEG DATA

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SLIDE 135

EEG DATA

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SLIDE 136

TIME-FREQUENCY DOMAIN

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SLIDE 137

Are we done?

EEG DATA

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SLIDE 138

Are we done? Hint:

EEG DATA

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SLIDE 139

300 MS

EEG DATA

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SLIDE 140

300 MS

EEG DATA

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SLIDE 141

300 MS

EEG DATA

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SLIDE 142

300 MS

EEG DATA

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SLIDE 143

300 MS

10 channels 50 frequencies 3 seconds of data 300 ms window

EEG DATA

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SLIDE 144

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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SLIDE 145

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

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SLIDE 146
  • High temporal resolution
  • No surgery!
  • Mobile
  • Cheap

SUMMARY

  • Low spatial resolution

Available to wide audience, but measurements are approximate.

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SLIDE 147

SUMMARY OF NEUROIMAGING TECHNIQUES

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 Performance 2 class 90% 3 class 80% 4 class ? Large number

  • f targets

2 cls 90% Large number

  • f targets

8 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 Performance 2 class 90% 3 class 80% 4 class ? Large number

  • f targets

2 cls 90% Large number

  • f targets

8 cls 90% High* ~ same as EEG based 4 cls 90% 2 cls 90%