Neuroimaging: Intracortical, fMRI, EEG
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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)
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Neuroimaging: Intracortical, fMRI, EEG
- 1. MACHINE LEARNING ON NEUROIMAGING DATA Ilya Kuzovkin AACIMP, August 2014 LECTURE 1: NEUROIMAGING TECHNIQUES
- 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
- 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
- 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
- 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
- 15. For each measured neuron we record the time moments when it spiked
- 16. RASTER PLOT
- 17. RASTER PLOT What is on the X axis?
- 18. RASTER PLOT Time
- 19. RASTER PLOT What is on the Y axis? Time
- 29. PSTH Time NeuronsTrials Post-Stimulus Time Histogram What is on the Y axis?
- 35. TUNING CURVE http://www.beatricebiologist.com/2012/11/types-of-cells.html 40 spikes per second (40 Hz)45
- 36. TUNING CURVE http://www.beatricebiologist.com/2012/11/types-of-cells.html 40 spikes per second (40 Hz) 0 45
- 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)0 45
- 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)0 45
- 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)0 45
- 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 on this plot? 0 45
- 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)0 45
- 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)0 45
- 43. SUMMARY • High spatial resolution (up to single neuron) ! • High temporal resolution
- 44. SUMMARY • High spatial resolution (up to single neuron) ! • High temporal resolution What does “spatial resolution” mean?
- 45. SUMMARY • Requires surgery ! • Localized What does “temporal resolution” mean? • High spatial resolution (up to single neuron) ! • High temporal resolution
- 46. • High spatial resolution (up to single neuron) ! • High temporal resolution SUMMARY • Requires surgery ! • Localized
- 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.
- 49. NUCLEAR MAGNETIC RESONANCE Physical phenomenon in which nucleus of an atom can absorb or reemit electromagnetic radiation if placed in a magnetic field
- 50. NUCLEAR MAGNETIC RESONANCE Physical phenomenon in which nucleus of an atom can absorb or reemit electromagnetic radiation if placed in a magnetic field
- 51. NUCLEAR MAGNETIC RESONANCE Physical phenomenon in which nucleus of an atom can absorb or reemit electromagnetic radiation if placed in a magnetic field
- 52. NUCLEAR MAGNETIC RESONANCE Physical phenomenon in which nucleus of an atom can absorb or reemit electromagnetic radiation if placed in a magnetic field.
- 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.
- 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
- 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.
- 57. MAGNETIC MOMENT
- 58. MAGNETIC MOMENT Particle with non-zero nuclear spin is like a small magnet.
- 59. MAGNETIC MOMENT or ? Particle with non-zero nuclear spin is like a small magnet.
- 60. MAGNETIC MOMENT or ? Particle with non-zero nuclear spin is like a small magnet.
- 61. MAGNETIC MOMENT Particle with non-zero nuclear spin is like a small magnet.
- 62. IN A MAGNETIC FIELD What happens to a magnet if you put it in a magnetic field?
- 63. IN A MAGNETIC FIELD What happens to a magnet if you put it in a magnetic field?
- 64. IN A MAGNETIC FIELD
- 65. IN A MAGNETIC FIELD
- 66. IN A MAGNETIC FIELD
- 67. IN A MAGNETIC FIELD Stronger field — larger energy gap
- 73. RADIO FREQUENCY PULSE We can give energy to a particle and move it to a higher energy level
- 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
- 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
- 76. RELAXATION Now we stop the pulse
- 77. RELAXATION Now we stop the pulse
- 78. RELAXATION Nucleus will give out same amount of energy in the form of electromagnetic radiation. Now we stop the pulse
- 79. Nuclear Magnetic Resonance Imaging
- 80. Nuclear Magnetic Resonance Imaging
- 81. Nuclear Magnetic Resonance Imaging
- 82. HYDROGEN
- 83. HYDROGEN Possible spin states +1/2 or -1/2
- 84. http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html HYDROGEN IN A MAGNETIC FIELD
- 85. http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html HYDROGEN IN A MAGNETIC FIELD
- 91. For different tissues the time of relaxation is different
- 92. http://www.howequipmentworks.com/physics/medical_imaging/mri/magnetic_resonance_imaging.html NUCLEI SEND SIGNALS One large piece is still missing…
- 93. GRADIENT COILS http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
- 94. GRADIENT COILS http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
- 95. GRADIENT COILS http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
- 96. GRADIENT COILS http://www.howtolearn.com/HTL/media/Visualisations-in-Medicine-MRI-Hi-Res-Crop1.jpg
- 104. FMRI F FOR FUNCTIONAL* *MRI signals associated with functional brain activity
- 105. BOLD BLOOD-OXYGEN-LEVEL DEPENDENT Active neuron Passive neuron I need oxygen and glucose! I need nothing…
- 106. FMRI Have different magnetic resonance Distinguishable by MRI
- 107. FMRI DATA
- 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.
- 117. NEURONS http://en.wikipedia.org/wiki/Neural_oscillation What is the frequency in this example?
- 118. BRAINWAVES
- 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
- 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
- 121. EEG
- 122. EEG
- 123. EEG TIME CHANNELS
- 124. EEG TIME CHANNELS
- 125. EEG Alpha 7-14 Hz Beta 15-30 Hz Gamma 30-100 Hz ?TIME CHANNELS
- 126. EEG Alpha 7-14 Hz Beta 15-30 Hz Gamma 30-100 Hz ?TIME CHANNELS Jean Baptiste Joseph Fourier 1768 — 1830
- 127. FOURIER TRANSFORM*
- 130. FOURIER TRANSFORM* *discrete signal at time t frequency complex number =
- 131. FOURIER TRANSFORM* *discrete signal at time t frequency complex number = Amplitude of the component with frequency k
- 132. FOURIER TRANSFORM* *discrete signal at time t frequency complex number = Amplitude of the component with frequency k
- 133. EEG DATA
- 134. EEG DATA
- 135. EEG DATA
- 137. Are we done? EEG DATA
- 138. Are we done? Hint: EEG DATA
- 139. 300 MS EEG DATA
- 140. 300 MS EEG DATA
- 141. 300 MS EEG DATA
- 142. 300 MS EEG DATA
- 143. 300 MS 10 channels 50 frequencies 3 seconds of data 300 ms window EEG DATA
- 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
- 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
- 146. • High temporal resolution ! • No surgery! ! • Mobile ! • Cheap SUMMARY • Low spatial resolution Available to wide audience, but measurements are approximate.
- 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 of targets 2 cls 90% Large number of 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 of targets 2 cls 90% Large number of targets 8 cls 90% High* ~ same as EEG based 4 cls 90% 2 cls 90%