Principles of Neuroimaging A - 2010

Principles of Neuroimaging A, Fall, 2010 - Class Schedule and Syllabus

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M284B Principles of Neuroimaging B

Lecture Videos

• Monday 10-18-10 - Statistics for Imaging I. Speaker Catherine Sugar
• Wednesday 10-20-10 - Statistics for Imaging II. Speaker Catherine Sugar
• Wednesday 10-27-10 - Optics II. Speaker Zachary Taylor
• Wednesday 11-03-10 - Noise Speaker Mark Cohen
• Monday 11-8-10 - Wide field Optical imaging. Speaker Nader Pouratian
• Wednesday 11-10-10 - Circuits I. Mark Cohen
• Wednesday 11-17-10 - Human Electrophysiology Speaker John Stern
• Monday 11-22-10 - Design of an EMG Preamp. Speaker Mark Cohen
• Wednesday 12-1-10 - review Speaker Mark Cohen

Week 1: Orientation to Neuroimaging, Neurons, Brains

Monday 9/27/10 - 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.

File:Neurons.jpg

Required Readings

• The Active Brain
• Neuron function slides shown in class
• Caveat Lector - the misuse of neuroimaging

Suggested Further Reading

• "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999
• Neuroanatomy Programmed Learning
• Squire, Fundamentals of Neuroscience
• Kandel, et al., "Principles of Neural Science"

This paper, by Malhi, is a nice orientation in methods of neuroimaging. *Making sense of neuroimaging in psychiatry

• Replacement of the axoplasm of giant nerve fibres with artificial solutions

Wednesday 9/29/10 - The Organization of the Human Brain. Speaker: Susan Bookheimer

A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let me know

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

• Neuroanatomy Programmed Learning
• Slides shown in Class

Suggested Further Reading

Problem Set 1 Neuroanatomy. Due in class 10/6. Please remember that the preferred way for us to receive problem sets is via email to Mark and to Austin.

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We will be studying linear systems next week. This coming week until Monday would be a good time to review your calculus fundamentals:

Derivatives of Polynomials

Integrals of polynomials

Basic trig + derivatives and integrals of sine and cosine functions

When we start on the linear systems section, we will be using these fundamentals to develop the LaPlace and Fourier transforms, which involve the use of imaginary numbers. The math content for that section is largely contained in this link: Mathematical Tools.

Please let me know by email or other means if this material looks too difficult.

You will need to have matlab installed and running to do the next problem set.

Week 2: Linear Systems

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 on imaginary numbers that might be a helpful review.

Monday 10/4/10 - Transforms and the Convolution Theorem. Speaker: Mark Cohen

Required Readings

• van Drongelen: Chapter 1
• Mathematical Tools - updated 10/4/10 after class

Suggested Further Reading

Problem Set 2A - Introduction to matlab

Slides shown in class

Linearity and the Fourier Transform - updated 10/4/10 after 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.

Wednesday 10/6/10 - Fourier Transform Properties. Speaker: Mark Cohen

File:Xkcd fourier.jpg

• Example transform derivations
• The Convolution theorem
• Oddness (and Even-ness)
• The Fourier Shift Theorem

Please see MATLAB demo of Fourier transforms and convolution

Optional Readings:

• van Drongelen: Chapters 5 through 9

• • Note: This reading may be heavy going. I will not be going into nearly this much detail in class, but your time on this will be very well spent. We will be revisiting this material later in the course in week 5.

Suggested, Optional Readings from DSPguide.com:

• Linear Systems
• Convolution
• Discrete Fourier Transform (DFT)

Note: These chapters are lite on math and try to focus on a conceptual understanding

Problem Set 2B modeling in matlab

Problem Set 2A and Problem Set 2B

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Practice using the Fourier transform:

Fourier transform and Convolution Worksheet. (Solutions).

Sound file for worksheet above.

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I suggest very strongly that you brush up on linear algebra during this week in anticipation of Dr. Sugar's lectures in statistics. In particular, I would like you to have an understanding of :

Matrices as solutions to linear equations - determinants and inverses

Matrix multiplication

For these, I can recommend the Hefferon text noted above.

Week 3: Noise and Basic Statistics

Monday 10/11/10 - Noise. Speaker: Mark Cohen

It is what you don't want.

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

• Slides used in Class:

Noise Slides

Problem set 3 - properties of noise

Wednesday 10/13/10 - 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.

File:MeasureForMeasure.jpg

• 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

• Statsoft online text (free)
• 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

Problem set using stats and MATLAB

More practice with stats and MATLAB

Week4: Statistics for Imaging

Monday 10/18/10 - Statistics for Imaging I. Speaker: Catherine Sugar

1. Outline

File:BVTradeoff.jpg

Required Readings

• Statistical Modeling and Inference (pdf)
• Slides used in class (set 2)

• The General Linear Model

• Linear Algebra applied to Statistical Solutions

• Analysis of Variance

Suggested Further Reading

Wednesday 10/20/10 - 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

• Slides used in class (set 3)

Suggested Further Reading

Week 5: Optics

The prototypical imaging means: Direct visualization. These lectures will cover the principles of light transmission, refraction, reflection and dispersion and will develop a quantitative approach to the analysis of optical systems. We will cover the theory of lenses, imperfections in focus, such as chromatic aberration, and a model of optical devices that builds on our understanding of convolution.

Monday 10/25/10 - Optics I. Speaker: Zachary Taylor

File:Reflection.jpg

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

Wednesday 10/27/10 - Optics II. Speaker: Zachary Taylor

Required Readings

Suggested Further Reading

Week 6: Optical Neuroimaging

MIDTERM POSTED

Click here for the Midterm. Due in class Mon. 11/8

Monday 11/1/10 - Optical Applications. Speaker: tbd

Required Readings

Suggested Further Reading

Wednesday 11/3/10 - Optical and flourescence methods in dynamic neural systems. Speaker: Kevin McEvoy

1. Outline

Required Readings

• Lecture Slides

Week 7: Optical Intrinsic Imaging, Beginning Circuits

Monday 11/8/10 - Wide field Optical imaging. Speaker: Nader Pouratian

Required Readings

Suggested Further Reading

Wednesday 11/10/10 - Circuits I. Mark Cohen

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...)

I found a nice intro lecture on charge, current and voltage.

Readings:

• Circuits 1 & 2
• Slides shown in class (revised 10:30pm 1/28/2010)
• van Drongelen: Chapter 2 and 10

• • 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

Week 8: Electricity and Electronics. Human Electrophysiology

Monday 11/15/10 - Electricity and Electronics. Speaker: Mark Cohen

File:Opamp.jpg

• Laplace transform analysis
• Op Amp Circuits
• Active Filters
• Noise Control

Required Readings

Suggested Further Reading Please note that I have the components we used for the class demos available for you to play with at your leisure.

Wednesday 11/17/10 - Human Electrophysiology Speakers: Jonathan Wynn, 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???

Week 9: Practical Electronic Circuits

This week we will design, build and test a practical device for recording of human electrical potentials: The electromyogram, or EMG. This device must manage the many challenges of interfacing with small biological signals: Sensitivity, Gain, Noise, Linearity, Filtering. The recording we (hopefully) will make will demonstrate issues of linearity and neural coding.

Monday 11/22/10 - Design of an EMG Preamp. Speaker: Mark Cohen

1. Outline

Required Readings

Suggested Further Reading

Problem Set on circuits - Due Monday 11/30

Circuits problem set

Wednesday 11/24/10 - Building and Using Electronic Devices: EMG. Speaker: Mark Cohen

1. Outline

Required Readings

Suggested Further Reading

Week 10: Filters

Wednesdat 12/3/10 - Autocorrelation, Filters and Color/Course review. Speaker: Mark Cohen

Required Readings Most of what we will look at today is in chapter 7 & 8 of Van Drongelen.

Suggested Further Reading

==Monday 12/8/10 - Final distributed electronically