Principles of Neuroimaging A - 2011

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Principles of Neuroimaging A, Fall, 2011 - Class Schedule and Syllabus

THIS IS A DOCUMENT IN PREPARATION AS OF 9/20/11

This schedule will change!

Back to main course page for Principles of Neuroimaging
M284B Principles of Neuroimaging B

Lecture Videos

Week 1: Orientation to Neuroimaging, Neurons, Brains

Friday 9/23/11

- 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

Week 2: Intro to linear systems / Orientation to Neuroimaging, Neurons, Brains

Wednesday 9/28/11

- 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

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.

Friday 9/30/11

- 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

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.

Week 3: Optics

Wednesday 10/5/11

- 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

Friday 10/7/11

- Optics II. Speaker: Zachary Taylor

Required Readings

Suggested Further Reading

Week 4: Finding Data in the Noise

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:

  • Slides used in Class:
Noise Slides
Problem set 3 - properties of noise

Wednesday 10/12/11

- Noise. Speaker: Mark Cohen

Week4: Statistics for Imaging

Friday 10/14/11

- 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
Problem set using stats and MATLAB
More practice with stats and MATLAB

Wednesday 10/19/11

- Statistics for Imaging I. Speaker: Catherine Sugar

  1. Outline

Required Readings

  • The General Linear Model
  • Linear Algebra applied to Statistical Solutions
  • Analysis of Variance

Suggested Further Reading

Week 5: Optics / Linear Systems - reprieve

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.

Friday 10/21/11

- 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


Wednesday 10/26/11

- Fourier Transform Properties. Speaker: Mark Cohen

  • 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:

    • 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:

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

THE FOLLOWING PROBLEM SETS ARE ASSIGNED AS OF 10-25-11 (valid at 3:30p 10/25/11)

Time and Frequency / Spectral Filters

Problem Set 3A and Problem Set 3B


Practice using the Fourier transform:

Fourier transform and Convolution Worksheet. (Solutions).
Sound file for worksheet above.

Friday 10/28/11

- 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...)

Readings:

    • 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 6: Optical Neuroimaging

MIDTERM POSTED

Click | here for the Midterm. Due in class Wed. 11/16

- Optical Applications. Speaker: tbd

Required Readings

Suggested Further Reading

Wednesday 11/2/11

- Circuits II. Mark Cohen

  1. Outline

Required Readings

Week 7: Optical Intrinsic Imaging, Beginning Circuits

Friday 11/4/11 - Wide field Optical imaging. Speaker: Nader Pouratian

Required Readings

Suggested Further Reading


Wednesday 11/9/11 -

TBD

Friday 11/11/11 - Veteran's Day

Week 8: Electricity and Electronics. Human Electrophysiology

Wednesday 11/16/11

- Electricity and Electronics. Speaker: Mark Cohen

  • 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.

Friday 11/18/11

- 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???

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.

Wednesday 11/23/11

- Design of an EMG Preamp. Speaker: Mark Cohen

  1. Outline

Required Readings

Suggested Further Reading

Problem Set on circuits - Due Friday 11/30
Circuits problem set

==Friday 11/25 - NO CLASS - Thanksgiving Holiday

Wednesday 11/30/11

- Building and Using Electronic Devices: EMG. Speaker: Mark Cohen

  1. Outline

Required Readings

Suggested Further Reading


Week 10: Filters

=Friday 12/2/11

- Circuits, cont'd. Speaker: Mark Cohen

Wednesday 12/3/11

- 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


Friday 12/5/11

- Final distributed electronically