Principles of Neuroimaging A - 2016: Difference between revisions
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==''Monday 9/26/16'' == | ==''Monday 9/26/16'' == | ||
===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
''Required Readings'' - Please complete these readings prior to class. | |||
:*[[media:M284AImages-intro.pdf | Lecture Slides Images]] | |||
==''Wednesday 9/28/16''== | ==''Wednesday 9/28/16''== | ||
===- Neurons & Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ===- Neurons & Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen 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. | 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. | ||
[[Image:Neurons.jpg|right]] | [[Image:Neurons.jpg|right]] | ||
''Required Readings'' - Please complete these readings prior to class. | ''Required Readings'' - Please complete these readings prior to class. | ||
:*[[media:TheActiveBrain.pdf | The Active Brain]] | :*[[media:TheActiveBrain.pdf | The Active Brain]] | ||
:*[[media: | :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]] | ||
:*[http://www.science.smith.edu/departments/neurosci/courses/bio330/squid.html Videos of giant squid experiments] | |||
''Suggested Further Reading'' | |||
:*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging] | :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging] | ||
:*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999] | :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf "If Neuroimaging is the Answer, What is the Question?" Kosslyn, 1999] | ||
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning] | :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning] | ||
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:This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry] | :This paper, by Malhi, is a nice orientation in methods of neuroimaging. *[http://www.ccn.ucla.edu/wiki/images/f/f2/Malhi2007.pdf Making sense of neuroimaging in psychiatry] | ||
:*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions] | :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions] | ||
=Week 2: Linear Systems, Convolution, Fourier Transforms= | =Week 2: Linear Systems, Convolution, Fourier Transforms= | ||
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''Required Readings'' | ''Required Readings'' | ||
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1 | :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1 | ||
:*[[media: | :*[[media:MathematicalTools2016.pdf | Mathematical Tools]] | ||
''Suggested Further Reading'' | ''Suggested Further Reading'' | ||
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''Slides shown in class'' | ''Slides shown in class'' | ||
:[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]] | :[[media:LinearityM284A-2016.pdf | Linearity and the Fourier Transform]] | ||
Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo] | Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html 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. | 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. | ||
=Week 3: Math & Circuits I= | =Week 3: Math & Circuits I= | ||
==''Monday 10/10/16''== | ==''Monday 10/10/16''== | ||
=== - Circuits I. | === - Circuits I. Speaker: Cameron Rodriguez === | ||
:*[[media:Circuits_2016.pdf | Circuit slides shown in class]] | |||
==''Wednesday 10/12/ | ==''Wednesday 10/12/16''== | ||
=== - Circuits II. | === - Circuits II. ''Speaker'': Cameron Rodriguez === | ||
Why circuits? | Why circuits? | ||
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Readings: | Readings: | ||
:*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds] | :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds] | ||
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10 | :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10 | ||
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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.] | ||
Other | Other | ||
:*[http://www.youtube.com/watch?feature=player_embedded&v=7uHfjpU3OH0#! Getting Started with Arduino] | :*[http://www.youtube.com/watch?feature=player_embedded&v=7uHfjpU3OH0#! Getting Started with Arduino] | ||
=Week 4 Signal Processing= | =Week 4 Signal Processing= | ||
==''Monday 10/17/16''== | ==''Monday 10/17/16''== | ||
=== - Signal Processing. | === - Signal Processing. ''Speaker'': Cameron Rodriguez === | ||
:*[[media:Signals1-PreProcessing1_2016.pdf | Signal Pre Processing Slide Set 1 shown in class]] | |||
==''Wednesday 10/19/ | |||
=== - Noise | ==''Wednesday 10/19/16''== | ||
=== - Noise ''Speaker'': Cameron Rodriguez === | |||
:*[[media:OneD_signal_Filter_Ex.pdf | Matlab Signal Tutorial printout]] | |||
It is what you ''don't'' want - usually - but things change in quantized systems | It is what you ''don't'' want - usually - but things change in quantized systems | ||
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:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4 | :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4 | ||
:*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides] | :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides] | ||
=Week 5 - Information & Statistical Theory = | =Week 5 - Information & Statistical Theory = | ||
==''Monday 10/ | ==''Monday 10/24/16 - in C8-177''== | ||
===Information Theory | === Noise Cont' & Information Theory Speakers: Cameron Rodriguez & John Villasenor=== | ||
==''Wednesday 10/ | ==''Wednesday 10/26/16''== | ||
===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]=== | ||
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts. | We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts. | ||
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=Week 6 - Neurophysiology= | =Week 6 - Neurophysiology= | ||
==''Monday 10/31/ | ==''Monday 10/31/16''== | ||
=== | === Electrophysiology I ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] === | ||
We will examine our first imaging modality, EEG (and MEG). | |||
::[[media: EEGNeurophys_161102.pdf|Slides for Neurophysiology Lectures]] | |||
==''Wednesday 11/2/16''== | |||
=== Electrophysiology II ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] === | |||
Continuing with neurophysiology. ERPs & Source Localization. | |||
=Week 7 - Neurophysiology = | =Week 7 - Neurophysiology = | ||
==''Monday 11/7/ | ==''Monday 11/7/16''== | ||
=== | === Electrophysiology III ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] === | ||
Continuing with neurophysiology. Connectivity & Oscillations. | |||
==''Wednesday 11/9/ | ==''Wednesday 11/9/16''== | ||
===Intracranial Recordings | ===Intracranial Recordings ''Speaker'': [http://neurosurgery.ucla.edu/neuromodulation-neuroimaging-lab Nanthia Suthana]=== | ||
::[[media: Suthana.pdf|Slides for Intracranial Lecture]] | |||
::[[media: LachauxIntracranial.pdf|Lachaux et al Reading]] | |||
::[[media: HarrisIntracranial.pdf|Harris et al Reading]] | |||
=Week 8 - Practical Neurophysiology= | =Week 8 - Practical Neurophysiology= | ||
==''Monday 11/14/ | ==''Monday 11/14/16''== | ||
===Building an EEG System - Circuit 1 | ===Building an EEG System - Circuit 1 - Going over circuit ''Speaker'': Cameron Rodriguez=== | ||
:*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering]. | :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering]. | ||
Line 227: | Line 230: | ||
:*[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 11/16/16''== | |||
===Data Processing Hands On ''Speaker'': Cameron Rodriguez=== | |||
=Week 9 - | =Week 9 - Data Acquisition = | ||
==''Monday 11/21/ | ==''Monday 11/21/16 - in C8-177''== | ||
=== | ===Data Acquisition ''Speaker'': Agatha Lenartowicz=== | ||
Please meet in CCN suite. | |||
==''Wednesday 11/23/ | ==''Wednesday 11/23/16''== | ||
===Thankgiving Wed - No Class === | ===Thankgiving Wed - No Class!! === | ||
Happy Thanksgiving! | |||
=Week 10 - Data Processing = | |||
*Please complete class evaluations via [https://my.ucla.edu/ '''MyUCLA''']. | |||
*Also we have an inhouse feedback form regarding the course syllabus: [https://docs.google.com/forms/d/e/1FAIpQLSd8xn340PxZRWb3-GQ__ZisYwFWoSgmYrcwyjvyBY5JV_mxnQ/viewform '''Feedback Form'''] | |||
: | |||
'' | |||
'' | |||
Your feedback is invaluable to us!! | |||
==''Monday 11/28/16''== | |||
==''Monday 11/28/ | ===Midterm Review, Data Processing ''Speaker'': Agatha Lenartowicz=== | ||
=== | Hands on practice with EEG data, in Matlab using EEGLAB. Lab materials distributed by email 11/27/16. | ||
==''Wednesady 11/30/ | ==''Wednesady 11/30/16''== | ||
=== | ===Data Processing ''Speaker'': Agatha Lenartowicz=== | ||
Hands on practice with EEG data, in Matlab using EEGLAB. | |||
=Week 11 - Finals Week= | =Week 11 - Finals Week= | ||
==''Monday 11/5/ | Final will be distributed 11/2/16. | ||
==''Monday 11/5/16''== | |||
===Final Exam=== | ===Final Exam=== | ||
Latest revision as of 04:04, 29 November 2016
Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus
Neuroimaging journal Club (required for NITP certificate)
Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)
This schedule will change!
- Coming up next!: M284B Principles of Neuroimaging B
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 Neuro-imaging, Neurons, Brains
Monday 9/26/16
- Images. Speaker: Mark Cohen
Required Readings - Please complete these readings prior to class.
Wednesday 9/28/16
- Neurons & Signaling. 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: Linear Systems, Convolution, Fourier Transforms
Wednesday 10/3/16
- Linear Systems I. Speaker: Mark Cohen
Wednesday 10/5/16
- Linear Systems II. 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.
Week 3: Math & Circuits I
Monday 10/10/16
- Circuits I. Speaker: Cameron Rodriguez
Wednesday 10/12/16
- Circuits II. Speaker: Cameron Rodriguez
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:
- 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:
Other
Week 4 Signal Processing
Monday 10/17/16
- Signal Processing. Speaker: Cameron Rodriguez
Wednesday 10/19/16
- Noise Speaker: Cameron Rodriguez
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
- Noise Slides
Week 5 - Information & Statistical Theory
Monday 10/24/16 - in C8-177
Noise Cont' & Information Theory Speakers: Cameron Rodriguez & John Villasenor
Wednesday 10/26/16
Statistical Theory Speaker: Mark Cohen
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
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 3 - Statistics in matlab
MIDTERM
Week 6 - Neurophysiology
Monday 10/31/16
Electrophysiology I Speaker: Agatha Lenartowicz
We will examine our first imaging modality, EEG (and MEG).
Wednesday 11/2/16
Electrophysiology II Speaker: Agatha Lenartowicz
Continuing with neurophysiology. ERPs & Source Localization.
Week 7 - Neurophysiology
Monday 11/7/16
Electrophysiology III Speaker: Agatha Lenartowicz
Continuing with neurophysiology. Connectivity & Oscillations.
Wednesday 11/9/16
Intracranial Recordings Speaker: Nanthia Suthana
Week 8 - Practical Neurophysiology
Monday 11/14/16
Building an EEG System - Circuit 1 - Going over circuit Speaker: Cameron Rodriguez
Wednesday 11/16/16
Data Processing Hands On Speaker: Cameron Rodriguez
Week 9 - Data Acquisition
Monday 11/21/16 - in C8-177
Data Acquisition Speaker: Agatha Lenartowicz
Please meet in CCN suite.
Wednesday 11/23/16
Thankgiving Wed - No Class!!
Happy Thanksgiving!
Week 10 - Data Processing
- Please complete class evaluations via MyUCLA.
- Also we have an inhouse feedback form regarding the course syllabus: Feedback Form
Your feedback is invaluable to us!!
Monday 11/28/16
Midterm Review, Data Processing Speaker: Agatha Lenartowicz
Hands on practice with EEG data, in Matlab using EEGLAB. Lab materials distributed by email 11/27/16.
Wednesady 11/30/16
Data Processing Speaker: Agatha Lenartowicz
Hands on practice with EEG data, in Matlab using EEGLAB.
Week 11 - Finals Week
Final will be distributed 11/2/16.