Principles of Neuroimaging A - 2011: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
m (42 revisions)
 
(38 intermediate revisions by one other user not shown)
Line 1: Line 1:
Principles of Neuroimaging A, Fall, 2011 - Class Schedule and Syllabus
Principles of Neuroimaging A, Fall, 2011 - Class Schedule and Syllabus
=THIS IS A DOCUMENT IN PREPARATION AS OF 9/12/11=
=THIS IS A DOCUMENT IN PREPARATION AS OF 9/20/11=
== This schedule ''will'' change!==
== This schedule ''will'' change!==
:'''[[Principles_of_Neuroimaging_-_2010-2011 | Back to main course page for Principles of Neuroimaging]]'''
 
:'''[[Principles_of_Neuroimaging_-_2011-2012 | Back to main course page for Principles of Neuroimaging]]'''


:'''[[Principles_of_Neuroimaging_B_-_2012 | M284B Principles of Neuroimaging B]]'''
:'''[[Principles_of_Neuroimaging_B_-_2012 | M284B Principles of Neuroimaging B]]'''
Line 9: Line 10:


=Week 1: Orientation to Neuroimaging, Neurons, Brains=
=Week 1: Orientation to Neuroimaging, Neurons, Brains=
==''Friday 9/23/11'' - Orientation & Neurons. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
 
==''Friday 9/23/11'' ==
===- Orientation & Neurons. ''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''
''Required Readings'' - Please complete these readings prior to class.
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[http://www.ccn.ucla.edu/wiki/images/8/81/The_Active_Brain.pdf The Active Brain]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
:*[[media:NeuronFunction+AnatomyNITP.pdf‎| Neuron function slides shown in class]]
Line 24: Line 28:
:*[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]


==''Wednesday 9/28/11'' - The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]==
=Week 2: Intro to linear systems / Orientation to Neuroimaging, Neurons, Brains=
'''A probe mail was sent this afternoon to all students in the class. If you did not receive this (subject, "A Probing Question"), let [mailto:mscohen@ucla.edu 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''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''


[[media:PNIA2010-PS1.pdf|'''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 [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
==''Wednesday 9/28/11''==
----
===- Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
We will be studying linear systems next week. This coming week until Friday 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: [[Media: MathematicalTools.pdf | 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:
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
:Modeling of Neural Systems
Line 63: Line 44:
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.
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 [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer on imaginary numbers] that might be a helpful review.
Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.


==''Friday 9/30/11'' - Transforms and the Convolution Theorem. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].


''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: Mathematical_tools.pdf|Mathematical Tools]] - updated 10/4/10 after class
:*[[media:MathematicalTools.pdf | Mathematical Tools]] - updated 9/27/11 before class


''Suggested Further Reading''
''Suggested Further Reading''
Line 81: Line 62:
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.


==''Wednesday 10/5/11'' - Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
==''Friday 9/30/11''==
[[Image:xkcd_fourier.jpg|right]]
===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===
*Example transform derivations
 
*The Convolution theorem
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:
*Oddness (and Even-ness)
*Phylogenetic Layering
*The Fourier Shift Theorem
*Functional Specialization
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]
*Principles Divisions of the Brain
*Brain Systems
 
''Required Readings''
:*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]
:*[[media:NITPanatomy-Bookheimer.pdf | Slides shown in Class]]
''Suggested Further Reading''
 
[[media:PNIA2010-PS1.pdf|'''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 [mailto:mscohen@ucla.edu Mark] and to [mailto:alheadbme@ucla.edu Austin].
 
=Week 3: Optics=
 
==''Wednesday 10/5/11''==
===- Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===


Optional Readings:
[[Image:Reflection.jpg|right]]
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 5 through 9
The overall goal of this lecture is to establish that:
**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.
''- 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.)''''


'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
'''Outline:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:* Constitutive parameters (ε, μ, η, n, etc.)
:*[http://www.dspguide.com/CH6.PDF Convolution]
:* Plane wave basics
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:* Plane waves at boundaries
:''Note: These chapters are lite on math and try to focus on a conceptual understanding''
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.


:'''Problem Set 2B modeling in matlab'''
''Required Readings''
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
''Suggested Further Reading''


[[Media: ProblemSet3A.pdf|Problem Set 2A]] and
==''Friday 10/7/11''==
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 2B]
===- Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===


----
Practice using the Fourier transform:
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').]
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]
----


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 :
''Required Readings''


:''Matrices as solutions to linear equations - determinants and inverses''
''Suggested Further Reading''
:''Matrix multiplication''


For these, I can recommend the Hefferon text noted above.
=Week 4: Finding Data in the Noise=


=Week 3: Noise and Basic Statistics=
It is what you ''don't'' want - usually - but things change in quantized systems
==''Friday 10/7/11'' - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
It is what you ''don't'' want.
:Additive noise
:Additive noise
:White Noise
:White Noise
Line 140: Line 135:
:'''Problem set 3 - properties of noise'''
:'''Problem set 3 - properties of noise'''


==''Wednesday 10/12/11'' - Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
==''Wednesday 10/12/11''==
=== - Noise. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
=Week4: Statistics for Imaging=
==''Friday 10/14/11''==
===- 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.
We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.
[[Image:MeasureForMeasure.jpg|right]]
[[Image:MeasureForMeasure.jpg|right]]


:*[[media: CohenClassIntroStats10_13_10.pdf | Slides used in class (set 1)]]
:*[[media: CohenClassIntroStats10_14_11.pdf | Slides used in class (set 1)]]


''Review of'':
''Review of'':
Line 162: Line 163:
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]
::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]


=Week4: Statistics for Imaging=
==''Wednesday 10/19/11''==
==''Friday 10/14/11'' - Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
===- Statistics for Imaging I. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===
 
#Outline
#Outline
[[image:BVTradeoff.jpg|right]]
[[image:BVTradeoff.jpg|right]]
''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: CohenClassSlides10_18_10.pdf | Slides used in class (set 2)]]
:*[[media: CohenClassSlides10_19_11post.pdf | Slides used in class (set 2)]]


:*The General Linear Model
:*The General Linear Model
Line 176: Line 178:
''Suggested Further Reading''
''Suggested Further Reading''


==''Wednesday 10/19/11'' - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]==
=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'': [http://www.npistat.com/about.asp Catherine Sugar]===
*Fixed and Random Effects
*Fixed and Random Effects
*Repeated measures
*Repeated measures
Line 189: Line 194:
''Suggested Further Reading''
''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.
==''Friday 10/21/11'' - Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
[[Image:Reflection.jpg|right]]
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:'''
==''Wednesday 10/26/11''==
:* Constitutive parameters (ε, μ, η, n, etc.)
===- Fourier Transform Properties. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
:* Plane wave basics
:* Plane waves at boundaries
:* Lenses
:* Advanced imaging properties of lenses
:* Point spread function.


''Required Readings''
[[Image:xkcd_fourier.jpg|right]]
Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].
*Example transform derivations
''Suggested Further Reading''
*The Convolution theorem
*Oddness (and Even-ness)
*The Fourier Shift Theorem
Please see [http://www.brainmapping.org/NITP/PNA/html/ShowConvolutions.html MATLAB demo of Fourier transforms and convolution]


==''Wednesday 10/26/11'' - Optics II. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]==
Optional Readings:
:*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description 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.


''Required Readings''
'''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''
:*[http://www.dspguide.com/CH5.PDF Linear Systems]
:*[http://www.dspguide.com/CH6.PDF Convolution]
:*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]
:''Note: These chapters are light on math and try to focus on a conceptual understanding''


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


Time and Frequency / Spectral Filters


=Week 6: Optical Neuroimaging=
[[Media: ProblemSet3A.pdf|Problem Set 3A]] and
== MIDTERM POSTED ==
[http://www.brainmapping.org/NITP/PNA/html/TwoDimensions.html Problem Set 3B]
:Click [[media:MidTermFall2010.pdf‎ | here for the Midterm. Due in class Mon. 11/8]]


==''Friday 10/28/11'' - Optical Applications. ''Speaker'': tbd==
----
 
Practice using the Fourier transform:
''Required Readings''
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').]
 
:[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]
''Suggested Further Reading''
 
 
==''Wednesday 11/2/11'' - Optical and flourescence methods in dynamic neural systems. ''Speaker'': [mailto:kmcevoy@ucla.edu Kevin McEvoy]==
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]
 
=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Friday 11/4/11'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==


''Required Readings''
==''Friday 10/28/11''==
=== - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]===


''Suggested Further Reading''
==''Wednesday 11/9/11'' - Circuits I. [http://www.brainmapping.org/MarkCohen Mark Cohen]==
Why circuits?
Why circuits?
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
:(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly
Line 250: Line 235:
: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).
: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, [[Media:Electricity.pdf|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 [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "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...)  
:If you have not had any of this background, you might want to have a look at this handout, [[Media:Electricity.pdf|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 [http://www.allaboutcircuits.com/ Online Books: All About Circuits] ''IF'' you want practical hands-on knowledge about this material, my all-time favorite text is [http://www.google.com/products/catalog?hl=en&client=safari&rls=en-us&ei=uVSPSfaxE5nMsAPf-tmSCQ&resnum=1&q=art+of+electronics&um=1&ie=UTF-8&cid=8820839049329255765#ps-sellers "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 [http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s intro lecture on charge, current and voltage].


Readings:
Readings:
Line 270: Line 253:
::- ''Op Amps''
::- ''Op Amps''
:*Solutions with Matrices
:*Solutions with Matrices
''Suggested Further Reading''
:*[http://video.google.com/videoplay?docid=5645396659673218353&q=Physics+for+Future+Presidents+Electricity&total=5&start=0&num=10&so=0&type=search&plindex=0#0h20m30s Video intro lecture on charge, current and voltage].
:*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]
:*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]
=Week 6: Optical Neuroimaging=
== MIDTERM POSTED ==
:Click [http://www.brainmapping.org/NITP/tests/PNIA2010Midterm.pdf | 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. [http://www.brainmapping.org/MarkCohen Mark Cohen]===
#Outline
''Required Readings''
:*[http://ccn.ucla.edu/wiki/images/d/d3/NeuroimagingCellularLevel_KMcEvoy_2010.pdf Lecture Slides]
=Week 7: Optical Intrinsic Imaging, Beginning Circuits=
==''Friday 11/4/11'' - Wide field Optical imaging. ''Speaker'': [http://www.uclahealth.org/body.cfm?xyzpdqabc=0&id=479&action=detail&ref=95328 Nader Pouratian]==
''Required Readings''
''Suggested Further Reading''
''Suggested Further Reading''
==''Wednesday 11/9/11'' - ==
TBD


==''Friday 11/11/11'' - Veteran's Day==
==''Friday 11/11/11'' - Veteran's Day==


=Week 8: Electricity and Electronics. Human Electrophysiology=
=Week 8: Electricity and Electronics. Human Electrophysiology=
==''Wednesday 11/16/11'' - Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
==''Wednesday 11/16/11''==
===- Electricity and Electronics. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
[[Image:Opamp.jpg|right]]
[[Image:Opamp.jpg|right]]
*Laplace transform analysis
*Laplace transform analysis
Line 287: Line 308:
Please note that I have the components we used for the class demos available for you to play with at your leisure.
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'': [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]==
==''Friday 11/18/11''==
===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===
 
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]
*A look at real EEG data
*A look at real EEG data
Line 307: Line 330:
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.
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'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
==''Wednesday 11/23/11''==
===- Design of an EMG Preamp. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
#Outline
#Outline


Line 319: Line 344:
==''Friday 11/25'' - NO CLASS - Thanksgiving Holiday
==''Friday 11/25'' - NO CLASS - Thanksgiving Holiday


==''Wednesday 11/30/11'' - Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
==''Wednesday 11/30/11''==
===- Building and Using Electronic Devices: ''EMG''. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
#Outline
#Outline


Line 328: Line 355:


=Week 10: Filters=
=Week 10: Filters=
==''Friday 12/2/11'' - Circuits, cont'd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==
===''Friday 12/2/11''==
===- Circuits, cont'd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===
 
 
==''Wednesday 12/3/11''==
===- Autocorrelation, Filters and Color/Course review. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===


==''Wednesday 12/3/11'' - Autocorrelation, Filters and Color/Course review. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]==


''Required Readings''
''Required Readings''
Line 338: Line 369:




==''Friday 12/5/11'' - '''Final distributed electronically'''
==''Friday 12/5/11''==
===- '''Final distributed electronically'''===

Latest revision as of 03:46, 16 January 2014

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.

File:Neurons.jpg

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

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

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.

File:MeasureForMeasure.jpg

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
File:BVTradeoff.jpg

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

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:

    • 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

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.

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

Retrieved from "https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2011&oldid=1877"