Principles of Neuroimaging A - 2014: Difference between revisions
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Principles of Neuroimaging A, Fall, 2014 - Class Schedule and Syllabus | Principles of Neuroimaging A, Fall, 2014 - Class Schedule and Syllabus | ||
=THIS IS A DOCUMENT IN PREPARATION | =THIS IS A DOCUMENT IN PREPARATION UPDATED 11/10/14= | ||
==='''Neuroimaging journal Club (''required for NITP certificate'')'''=== | ==='''Neuroimaging journal Club (''required for NITP certificate'')'''=== | ||
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:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.] | :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.] | ||
==''Wednesday 10/15/ | ==''Wednesday 10/15/14''== | ||
=== - Circuits II. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | === - Circuits II. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
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=Week 3 Circuits and Noise= | =Week 3 Circuits and Noise= | ||
==''Monday 10/20/ | ==''Monday 10/20/14'' - Circuits (cont'd)== | ||
=== Circuits. [mailto:cdrodriguez@ucla.edu Cameron Rodriguez]=== | === Circuits. [mailto:cdrodriguez@ucla.edu Cameron Rodriguez]=== | ||
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Cameron will continue with the basic circuits material, moving on to demos and real-world active circuits. This will continue with the previously uploaded slide set. | Cameron will continue with the basic circuits material, moving on to demos and real-world active circuits. This will continue with the previously uploaded slide set. | ||
==''Wednesday 10/22/ | ==''Wednesday 10/22/14'' - Noise- == | ||
===- Noise. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ===- Noise. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
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=Week 4: Circuits III & Optics= | =Week 4: Circuits III & Optics= | ||
==''Monday 10/27/ | ==''Monday 10/27/14''== | ||
=== Class Project Design === | === Class Project Design === | ||
==''Wednesday 10/29/ | ==''Wednesday 10/29/14''== | ||
===OUCH! Class canceled for personal reasons=== | ===OUCH! Class canceled for personal reasons=== | ||
My sincere apologies | My sincere apologies | ||
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=Week 5: Optics II & Finding Data in the Noise= | =Week 5: Optics II & Finding Data in the Noise= | ||
==''Monday 11/3/ | ==''Monday 11/3/14''== | ||
=== | === In class EEG project build === | ||
:*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering]. | :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering]. | ||
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:*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete]; | :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete]; | ||
==''Wednesday 11/ | ==''Wednesday 11/5/14''== | ||
=== In class EEG project build and demo === | |||
==''Monday 11/10/14''== | |||
=== Sick day for the instructor === | |||
Mid-term distributed by email. | |||
==''Wednesday 11/12/14''== | |||
===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | |||
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts. | |||
[[Image:MeasureForMeasure.jpg|right]] | |||
:*[[media: CohenClassIntroStats11_25_13.pdf | Slides used in class (set 1)]] | |||
''Review of'': | |||
:*Descriptive Statistics: mean, mode, variance, standard deviation | |||
:*Statistical Inference. The Binomial and Normal Distribution | |||
:*Basic Tests: t-test, linear correlation | |||
:*Modeling and non-linear relations | |||
:*Bayes rule | |||
Suggested reading | |||
:*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')] | |||
:*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new] | |||
:The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures | |||
:'''Problem Set 5 - Statistics in matlab''' | |||
::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]] | |||
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]] | |||
==''Monday 11/17/14''== | |||
===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | |||
==''Wednesday 11/19/14''== | |||
===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | |||
==''Monday 11/24/14''== | |||
===EEG in Neuroscience I. "Speaker": [http://alenarto.bol.ucla.edu Agatha Lenartowicz]=== | |||
==''Wednesday 11/26/14''== | |||
===Thanksgiving break, no class!!!=== | |||
==''Monday 12/1/14''== | |||
===EEG in Neuroscience II. "Speaker": [http://alenarto.bol.ucla.edu Agatha Lenartowicz]=== | |||
===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]=== | ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]=== | ||
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''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
==''Monday 11/10/ | ==''Monday 11/10/14''== | ||
==''Wednesday 11/12/ | ==''Wednesday 11/12/14''== | ||
===Circuits review. "Speaker": Cameron Rodriguez=== | ===Circuits review. "Speaker": Cameron Rodriguez=== | ||
=="Monday 11/17/ | =="Monday 11/17/14"== | ||
===EEG in Neuroscience. "Speaker": [http://alenarto.bol.ucla.edu Agatha Lenartowicz]=== | ===EEG in Neuroscience. "Speaker": [http://alenarto.bol.ucla.edu Agatha Lenartowicz]=== | ||
==''Wednesday 11/19/ | ==''Wednesday 11/19/14''== | ||
===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]=== | ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]=== | ||
==''Monday 11/24/ | ==''Monday 11/24/14''== | ||
==''Wednesday 11/26/ | ==''Wednesday 11/26/14''== | ||
===No Class - Thanksgiving=== | ===No Class - Thanksgiving=== | ||
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=Week 8: = | =Week 8: = | ||
==''Monday 12/1/ | ==''Monday 12/1/14 ''== | ||
===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | ||
Line 267: | Line 291: | ||
''Required Readings'' | ''Required Readings'' | ||
:*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]] | :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]] | ||
:*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/ | :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]] | ||
:*The General Linear Model | :*The General Linear Model | ||
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''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
==''Wednesday 11/20/ | ==''Wednesday 11/20/14 ...''== | ||
=== - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]=== | ||
*Fixed and Random Effects | *Fixed and Random Effects | ||
Line 285: | Line 309: | ||
''Required Readings'' | ''Required Readings'' | ||
:*[[media: CohenClassSlides12_2_13.pdf | same as 12/2/ | :*[[media: CohenClassSlides12_2_13.pdf | same as 12/2/14]] | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
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=Week 9: = | =Week 9: = | ||
==''Monday 11/25/ | ==''Monday 11/25/14''== | ||
=== - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
==''Wednesday 11/27/ | ==''Wednesday 11/27/14''== | ||
===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]=== | ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]=== | ||
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=Week 10: Optical Neuroimaging= | =Week 10: Optical Neuroimaging= | ||
==''Monday 12/2/ | ==''Monday 12/2/14''== | ||
=== - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
==''Wednesday 12/4/ | ==''Wednesday 12/4/14''== | ||
=== - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
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=Week 11: Human Electrophysiology= | =Week 11: Human Electrophysiology= | ||
==''Monday 12/9/ | ==''Monday 12/9/14''== | ||
FINALS WEEK | FINALS WEEK | ||
Revision as of 18:50, 10 November 2014
Principles of Neuroimaging A, Fall, 2014 - Class Schedule and Syllabus
THIS IS A DOCUMENT IN PREPARATION UPDATED 11/10/14
Neuroimaging journal Club (required for NITP certificate)
This schedule will change!
- Coming up next!: M284B Principles of Neuroimaging B
Lecture Videos
- Hopefully, we can start recording the class sessions for those who cannot make a few lectures.
Course Reading
Required Reading
- Signal Processing for Neuroscientists by Wim van Drongelen
- This can be found as a PDF on scribd.com, for a small fee of $8.99
Supplemental Reading
- Matlab for Neuroscientists
- Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists
- Cartoon Guide to Statistics
- Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics
- NOTE: if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.
Week 1: Orientation to Neuroimaging, Neurons, Brains; Linear Systems
Monday 10/6/14
- Orientation & Neurons. Speaker: Mark Cohen
In this first class we will review the basics of neurophysiology with an eye towards what signals of brain function might be visible to the neuroimager. We will discuss information coding, energetics, size and time scales.
Required Readings - Please complete these readings prior to class.
Suggested Further Reading
- This paper, by Malhi, is a nice orientation in methods of neuroimaging. *Making sense of neuroimaging in psychiatry
Wednesday 10/8/14
Transforms and the Convolution Theorem. Speaker: Mark Cohen
Why the emphasis on Linear Systems? Because they are actually easy (as compared to non-linear systems, which are not.) As we go through this course, we will see many ways in which linear systems theory is applied to:
- Modeling of Neural Systems
- Extraction of Signal from Noise
- Design of Circuits
- Image Enhancement
- Understanding of Image artifacts, and others.
Linear systems analysis is one of the great technologies of the 20th and 21st century. It is now the basis for virtually all electronics design, and its extension into the discrete (digital) domain is the basis for most of modern signal processing.
In our specific case, we will use these few basic principles of linear systems to understand both the instruments we use and the neuroimaging signals we collect. When you have mastered this material, you should be in a much better position to model the systems that you study in order to develop an approach to studying them.
Here is A primer I wrote on imaginary numbers that might be a helpful review.
There is a nice Wikibook on Calculus.
Required Readings
- van Drongelen: Chapter 1
- Mathematical Tools
Suggested Further Reading
- Introduction to matlab
Slides shown in class
Please see MATLAB linearity demo
If you are the type who sees beauty in mathematics, the Euler identity may be one of the most beautiful pieces of math in the world.
Problem Set 1. Due by email 10/20/14. Please remember that the preferred way for us to receive problem sets is via email to Mark and to John Dell'Itlalia .
Week 2: Math & Circuits I
Monday 10/13/14
This problem set refers largely to last week's contents: Problem Set 1. Due by email 10/20/14. Please remember that the preferred way for us to receive problem sets is via email to Mark and to John Dell'Itlalia .
- Circuits I. Mark Cohen
We will continue with the linear systems lecture and move to circuits
Why circuits?
- (Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
- The device you really want in your lab doesn't exist. You very well may have to make it.
- There are electronic analogs to most of the linear systems that you have so far studied (and vice versa - the tools you now understand can be used to analyze and predict circuit behavior).
- If you have not had any of this background, you might want to have a look at this handout, Electrical Circuits, in advance. There are near infinite numbers of resources on the web that cover similar material (near enough to infinite that by the time you read all of them, there would be a whole new set.) I have recently come across a link to Online Books: All About Circuits IF you want practical hands-on knowledge about this material, my all-time favorite text is "Horowitz and Hill: The Art of Electronics." The latest edition, however, is dated 1989 and a new third edition is promised. I have therefore stopped short of recommending a purchase unless your need to make circuits is immediate. In this book, you will find an excellent education on the fundamental principles of electrical circuits and an incredible compendium of practical data, such as how to assemble circuit boards, how to make measurements, etc...)
Readings:
- Circuits 1 & 2
- Filter Design in 30 Seconds
- van Drongelen: Chapter 2 and 10
- Circuit Lab A Free Circuit Web Base Simulator
- You may or may not find this comprehensible without chapters 5 through 9.
We will discuss:
- Passive Circuit Elements: Resistors, Capacitors, Inductors
- Gain
- Transformers
- Rectifiers
- Active Elements
- - Amplifiers
- - Transistors
- - Op Amps
- Solutions with Matrices
Suggested Further Reading
Suggested, Optional Readings from DSPguide.com:
- Note: These chapters are light on math and try to focus on a conceptual understanding
Time and Frequency / Spectral Filters
Practice using the Fourier transform:
Wednesday 10/15/14
- Circuits II. Mark Cohen
Other
Week 3 Circuits and Noise
Monday 10/20/14 - Circuits (cont'd)
Circuits. Cameron Rodriguez
Cameron will continue with the basic circuits material, moving on to demos and real-world active circuits. This will continue with the previously uploaded slide set.
Wednesday 10/22/14 - Noise-
- Noise. Mark Cohen
It is what you don't want - usually - but things change in quantized systems
- Additive noise
- White Noise
- Boltzmann noise
- Colored Noise
- Gaussian Noise
- Coherent noise
- Sampling Errors
- Aliasing
- Quantization noise
- Spectral filtering
Noise comes in all shapes and colors. It is present in every measurement we make, from an EEG voltage to an estimate of the effects of dopamine on forebrain signal. Our best weapons are an understanding of the statistical properties of noise, the sources of noise and the ways to control it. Noise in the discrete digital domain is special, as it is both created by digitization and amplified by sampling.
Readings:
- van Drongelen: Chapters 2 through 4
Week 4: Circuits III & Optics
Monday 10/27/14
Class Project Design
Wednesday 10/29/14
OUCH! Class canceled for personal reasons
My sincere apologies
Week 5: Optics II & Finding Data in the Noise
Monday 11/3/14
In class EEG project build
Wednesday 11/5/14
In class EEG project build and demo
Monday 11/10/14
Sick day for the instructor
Mid-term distributed by email.
Wednesday 11/12/14
- Statistical Fundamentals. Speaker: Catherine Sugar
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
Review of:
- Descriptive Statistics: mean, mode, variance, standard deviation
- Statistical Inference. The Binomial and Normal Distribution
- Basic Tests: t-test, linear correlation
- Modeling and non-linear relations
- Bayes rule
Suggested reading
- The latter teaches stats at what I feel to be the right level - developing intuitions about the kinds of questions that can be answered using stats and about the statistical tests and measures
- Problem Set 5 - Statistics in matlab
Monday 11/17/14
- Statistical Fundamentals II. Speaker: Catherine Sugar
Wednesday 11/19/14
- Statistical Fundamentals III. Speaker: Catherine Sugar
Monday 11/24/14
EEG in Neuroscience I. "Speaker": Agatha Lenartowicz
Wednesday 11/26/14
Thanksgiving break, no class!!!
Monday 12/1/14
EEG in Neuroscience II. "Speaker": Agatha Lenartowicz
Optics I. Speaker: Zachary Taylor
The overall goal of this lecture is to establish that: - Physical constants have tangible meanings - Plane waves form a physically unrealizable but extremely good approximation to real systems - Boundaries bend light - Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens - The PSF gives a good indication of the overall performance of an imaging system - All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''
Outline:
- Constitutive parameters (ε, μ, η, n, etc.)
- Plane wave basics
- Plane waves at boundaries
- Lenses
- Advanced imaging properties of lenses
- Point spread function.
Required Readings Zach has very kindly agreed to post his Optics lecture notes. Suggested Further Reading
Monday 11/10/14
Wednesday 11/12/14
Circuits review. "Speaker": Cameron Rodriguez
"Monday 11/17/14"
EEG in Neuroscience. "Speaker": Agatha Lenartowicz
Wednesday 11/19/14
Optogenetics. Speaker: Tom Otis
Monday 11/24/14
Wednesday 11/26/14
No Class - Thanksgiving
Week 8:
Monday 12/1/14
- Statistics for Imaging. Speaker: Catherine Sugar
- Outline
Required Readings
- The General Linear Model
- Linear Algebra applied to Statistical Solutions
- Analysis of Variance
Suggested Further Reading
Wednesday 11/20/14 ...
- Statistics for Imaging II. Speaker: Catherine Sugar
- Fixed and Random Effects
- Repeated measures
- Bonferroni and Other Corrections
- Non-Parametric Methods
- Autocorrelation
- Unknown Distributions
Required Readings
Suggested Further Reading
Week 9:
Monday 11/25/14
- TBD. Mark Cohen
Wednesday 11/27/14
- The Organization of the Human Brain. Speaker: Susan Bookheimer
We will discuss the general organization of the human brain, and the regional specialization of cortical areas. The emphasis will be on understanding principles of organization:
- Phylogenetic Layering
- Functional Specialization
- Principles Divisions of the Brain
- Brain Systems
Required Readings
Suggested Further Reading
Week 10: Optical Neuroimaging
Monday 12/2/14
- TBD. Mark Cohen
Wednesday 12/4/14
- TBD. Mark Cohen
- Outline
Required Readings
Week 11: Human Electrophysiology
Monday 12/9/14
FINALS WEEK
- Human Electrophysiology Speakers: Agatha Lenartowicz, John Stern
Evoked Responses - Guest Lecturer: Jonathan Wynn
- A look at real EEG data
- Preprocessing:
- filtering
- artifact detection/removal
- averaging
- single events
- interpretation
Clinical EEG - Guest Lecturer: John Stern
- Normal and Abnormal EEG
- EEG as a marker for brain state
- sleep staging
- alpha and relaxation
- Neurofeedback???