https://www.ccn.ucla.edu/wiki/api.php?action=feedcontributions&feedformat=atom&user=Mscohen 2026-05-06T03:24:46Z User contributions MediaWiki 1.43.6 https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3187 2016-10-03T23:28:48Z

<p>Mscohen: /* - Linear Systems II. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://www.science.smith.edu/departments/neurosci/courses/bio330/squid.html Videos of giant squid experiments]<br /> ''Suggested Further Reading''<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2016.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A-2016.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/24/16 - in C8-177''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/26/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16 - in C8-177''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:LinearityM284A-2016.pdf&diff=3186 2016-10-03T23:27:47Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:MathematicalTools2016.pdf&diff=3185 2016-10-03T23:24:27Z

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Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:MathematicalTools2016.pdf&diff=3184 2016-10-03T21:07:11Z

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Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3183 2016-10-03T20:56:46Z

<p>Mscohen: /* Wednesday 10/5/16 */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://www.science.smith.edu/departments/neurosci/courses/bio330/squid.html Videos of giant squid experiments]<br /> ''Suggested Further Reading''<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2016.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/24/16 - in C8-177''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/26/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16 - in C8-177''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:MathematicalTools2016.pdf&diff=3182 2016-10-03T20:56:24Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3181 2016-09-28T20:38:56Z

<p>Mscohen: /* - Neurons &amp; Signaling. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://www.science.smith.edu/departments/neurosci/courses/bio330/squid.html Videos of giant squid experiments]<br /> ''Suggested Further Reading''<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/24/16 - in C8-177''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/26/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16 - in C8-177''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3180 2016-09-28T19:46:13Z

<p>Mscohen: /* - Neurons &amp; Signaling. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://www.science.smith.edu/departments/neurosci/courses/bio330/squid.html | Videos of giant squid experiments]<br /> ''Suggested Further Reading''<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/24/16 - in C8-177''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/26/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16 - in C8-177''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:NeuronFunctionM284-2016_SM.pdf&diff=3179 2016-09-28T19:31:00Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3178 2016-09-28T19:30:42Z

<p>Mscohen: /* - Neurons &amp; Signaling. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunctionM284-2016_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> ''Suggested Further Reading''<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/24/16 - in C8-177''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/26/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16 - in C8-177''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3174 2016-09-26T20:30:17Z

<p>Mscohen: /* - Images. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro.pdf | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunction+AnatomyM284-2015_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> ''Suggested Further Reading''<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/26/16''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/28/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3173 2016-09-26T20:29:33Z

<p>Mscohen: /* - Images. Speaker: Mark Cohen */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284AImages-intro | Images]]<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunction+AnatomyM284-2015_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> ''Suggested Further Reading''<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/26/16''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/28/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3172 2016-09-26T20:28:52Z

<p>Mscohen: /* Week 1: Orientation to Neuro-imaging, Neurons, Brains */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284Amages-intro | Images]]<br /> <br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunction+AnatomyM284-2015_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> ''Suggested Further Reading''<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/26/16''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/28/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:M284AImages-intro.pdf&diff=3171 2016-09-26T20:27:55Z

<p>Mscohen: On the nature on the images, with an emphasis on neuroimaging</p> <hr /> <div>On the nature on the images, with an emphasis on neuroimaging</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_A_-_2016&diff=3170 2016-09-26T20:26:21Z

<p>Mscohen: /* Week 1: Orientation to Neuro-imaging, Neurons, Brains */</p> <hr /> <div>Principles of Neuroimaging A, Fall, 2016 - Class Schedule and Syllabus<br /> <br /> <br /> ==='''Neuroimaging journal Club (''required for NITP certificate'')'''===<br /> Contact: Katherine Lawrence (katherine.E.Lawrence@ucla.edu) or Janelle Liu (janelle.j.liu@ucla.edu), Faculty Sponsor: Jamie Feusner (JFeusner@mednet.ucla.edu)<br /> <br /> ==This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2016-2017 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> :'''Coming up next!: [[Principles_of_Neuroimaging_B_-_2017 | M284B Principles of Neuroimaging B]]'''<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> <br /> =Week 1: Orientation to Neuro-imaging, Neurons, Brains=<br /> <br /> ==''Monday 9/26/16'' ==<br /> ===- Images. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 9/28/16''==<br /> ===- Neurons &amp; Signaling. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284Amages-IntrIo | Images]]<br /> <br /> 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.<br /> [[Image:Neurons.jpg|right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:TheActiveBrain.pdf | The Active Brain]]<br /> :*[[media:NeuronFunction+AnatomyM284-2015_SM.pdf | Neuron function slides shown in class]]<br /> :*[http://ccn.ucla.edu/wiki/images/5/5a/CAVEAT_LECTOR.pdf Caveat Lector - the misuse of neuroimaging]<br /> ''Suggested Further Reading''<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Protected/Kosslyn1999.pdf &quot;If Neuroimaging is the Answer, What is the Question?&quot; Kosslyn, 1999]<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[http://www.amazon.com/Fundamental-Neuroscience-Second-Larry-Squire/dp/0126603030 Squire, Fundamentals of Neuroscience]<br /> :*[http://www.amazon.com/Principles-Neural-Science-Eric-Kandel/dp/0838577016 Kandel, et al., &quot;Principles of Neural Science&quot;]<br /> :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]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359308/pdf/jphysiol01232-0142.pdf Replacement of the axoplasm of giant nerve fibres with artificial solutions]<br /> <br /> =Week 2: Linear Systems, Convolution, Fourier Transforms=<br /> ==''Wednesday 10/3/16''==<br /> <br /> ===- Linear Systems I. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 10/5/16''==<br /> ===- Linear Systems II. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> 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:<br /> :Modeling of Neural Systems<br /> :Extraction of Signal from Noise<br /> :Design of Circuits<br /> :Image Enhancement<br /> :Understanding of Image artifacts, and others.<br /> <br /> 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. <br /> <br /> 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.<br /> <br /> Here is [http://www.brainmapping.org/NITP/PNA/Readings/ImaginaryNumbers.pdf A primer I wrote on imaginary numbers] that might be a helpful review.<br /> <br /> There is a nice [http://en.wikibooks.org/wiki/Calculus Wikibook on Calculus].<br /> <br /> ''Required Readings''<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 1<br /> :*[[media:MathematicalTools2014.pdf | Mathematical Tools]]<br /> <br /> ''Suggested Further Reading''<br /> :'''Introduction to matlab'''<br /> <br /> ''Slides shown in class''<br /> :[[media:LinearityM284A.pdf | Linearity and the Fourier Transform]]<br /> <br /> Please see [http://www.brainmapping.org/NITP/PNA/html/Linearity.html MATLAB linearity demo]<br /> <br /> 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.<br /> <br /> <br /> =Week 3: Math &amp; Circuits I=<br /> <br /> ==''Monday 10/10/16''==<br /> === - Circuits I. Speaker: Cameron Rodriguez ===<br /> We will continue with the linear systems lecture and move to circuits<br /> <br /> ==''Wednesday 10/12/16''==<br /> === - Circuits II. ''Speaker'': Cameron Rodriguez ===<br /> <br /> Why circuits?<br /> :(Virtually) Every device you use in your research is electronic. You access your primary data only indirectly<br /> :The device you ''really'' want in your lab doesn't exist. You very well may have to make it.<br /> :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).<br /> <br /> :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&amp;client=safari&amp;rls=en-us&amp;ei=uVSPSfaxE5nMsAPf-tmSCQ&amp;resnum=1&amp;q=art+of+electronics&amp;um=1&amp;ie=UTF-8&amp;cid=8820839049329255765#ps-sellers &quot;Horowitz and Hill: ''The Art of Electronics.''&quot;] 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...) <br /> <br /> Readings:<br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> :*[http://www.ti.com/lit/an/sloa093/sloa093.pdf Filter Design in 30 Seconds]<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapter 2 and 10<br /> :*[https://www.circuitlab.com/ Circuit Lab ] A Free Circuit Web Base Simulator<br /> **You may or may not find this comprehensible without chapters 5 through 9.<br /> <br /> We will discuss:<br /> :*Passive Circuit Elements: Resistors, Capacitors, Inductors<br /> :*Gain<br /> :*Transformers<br /> :*Rectifiers<br /> :*Active Elements<br /> ::- ''Amplifiers''<br /> ::- ''Transistors''<br /> ::- ''Op Amps''<br /> :*Solutions with Matrices<br /> ''Suggested Further Reading''<br /> :*[http://video.google.com/videoplay?docid=5645396659673218353&amp;q=Physics+for+Future+Presidents+Electricity&amp;total=5&amp;start=0&amp;num=10&amp;so=0&amp;type=search&amp;plindex=0#0h20m30s Video intro lecture on charge, current and voltage].<br /> :*[[media:Electricity_Basics.pdf‎ | Well organized text on electrical concepts by Tony R. Kuphaldt]]<br /> :*[http://en.wikibooks.org/wiki/Circuit_Theory Circuit Theory - Wikibook]<br /> <br /> '''Suggested, Optional Readings from [http://www.dspguide.com DSPguide.com]:'''<br /> :*[http://www.dspguide.com/CH5.PDF Linear Systems]<br /> :*[http://www.dspguide.com/CH6.PDF Convolution]<br /> :*[http://www.dspguide.com/CH8.PDF Discrete Fourier Transform (DFT)]<br /> :''Note: These chapters are light on math and try to focus on a conceptual understanding''<br /> <br /> Time and Frequency / Spectral Filters<br /> <br /> ----<br /> Practice using the Fourier transform:<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvolutionWorksheet.pdf Fourier transform and Convolution Worksheet]. &lt;!-- [http://www.brainmapping.org/NITP/PNA/ConvFThtml/ConvFT.html (''Solutions'').] --&gt;<br /> :[http://www.brainmapping.org/NITP/PNA/ConvFThtml/Something.wav Sound file for worksheet above.]<br /> <br /> :*[[Media: Circuits.pdf|Circuits 1 &amp; 2]]<br /> Other<br /> :*[http://www.youtube.com/watch?feature=player_embedded&amp;v=7uHfjpU3OH0#! Getting Started with Arduino]<br /> <br /> <br /> =Week 4 Signal Processing=<br /> <br /> ==''Monday 10/17/16''==<br /> === - Signal Processing. ''Speaker'': Cameron Rodriguez ===<br /> <br /> <br /> ==''Wednesday 10/19/16''==<br /> === - Noise ''Speaker'': Cameron Rodriguez ===<br /> <br /> It is what you ''don't'' want - usually - but things change in quantized systems<br /> :Additive noise<br /> :White Noise<br /> :Boltzmann noise<br /> :Colored Noise<br /> :Gaussian Noise<br /> :Coherent noise<br /> :Sampling Errors<br /> :Aliasing<br /> :Quantization noise<br /> :Spectral filtering<br /> <br /> 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.<br /> <br /> Readings:<br /> :*[http://www.elsevier.com/wps/find/bookdescription.cws_home/710026/description#description van Drongelen:] Chapters 2 through 4<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Noise.pdf Noise Slides]<br /> <br /> <br /> =Week 5 - Information &amp; Statistical Theory =<br /> <br /> ==''Monday 10/26/16''==<br /> === Noise Cont' &amp; Information Theory Speakers: Cameron Rodriguez &amp; John Villasenor===<br /> <br /> ==''Wednesday 10/28/16''==<br /> ===Statistical Theory ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> We will consider the general problems of statistical inference, with a concentration on developing an intuitive understanding of statistical concepts.<br /> [[Image:MeasureForMeasure.jpg|right]]<br /> <br /> Suggested reading<br /> :*[http://www.statsoft.com/textbook/stbasic.html Statsoft online text (''free'')]<br /> :*[http://www.amazon.com/Cartoon-Guide-Statistics-Larry-Gonick/dp/0062731025 The Cartoon Guide to Statistics - Gonick $17.95 new]<br /> :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<br /> <br /> :'''Problem Set 3 - Statistics in matlab'''<br /> ::[[media: Problem_Set_1.doc|Problem set using stats and MATLAB]]<br /> ::[[media: Problem_Set_1B.doc|More practice with stats and MATLAB]]<br /> <br /> <br /> =MIDTERM=<br /> <br /> <br /> =Week 6 - Neurophysiology=<br /> ==''Monday 10/31/16''==<br /> === Midterm Review ===<br /> <br /> ==''Wednesday 11/2/16''==<br /> === Electrophysiology ''Speaker'': [http://alenarto.bol.ucla.edu Agatha Lenartowicz] ===<br /> We will examine our first imaging modality, EEG (and MEG).<br /> <br /> <br /> =Week 7 - Neurophysiology =<br /> ==''Monday 11/7/16''==<br /> ===EEG Signal Processing ''Speaker'': Agatha Lenartowicz, Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/9/16''==<br /> ===Intracranial Recordings ''Speaker'': Nanthia Sultana ===<br /> <br /> <br /> =Week 8 - Practical Neurophysiology=<br /> ==''Monday 11/14/16''==<br /> ===Building an EEG System - Circuit 1 ''Speaker'': Cameron Rodriguez===<br /> <br /> ==''Wednesday 11/16/16''==<br /> ===Building an EEG System - Circuit 2 ''Speaker'': Cameron Rodriguez===<br /> <br /> :*[https://learn.sparkfun.com/tutorials/how-to-solder Through holesoldering].<br /> :*[https://learn.sparkfun.com/tutorials/pcb-basics Printed Circuit Board Basics].<br /> :*[https://learn.sparkfun.com/tutorials/how-to-install-and-setup-eagle Installing and Setting Up Eagle].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-schematic Using Eagle Schematic].<br /> :*[https://learn.sparkfun.com/tutorials/using-eagle-board-layoutc Using Eagle Board Layout].<br /> <br /> :*[https://www.sparkfun.com/videos#pete/NJKZZArjdg8 PCB Layout 1 - According to Pete];<br /> :*[https://www.sparkfun.com/videos#pete/JANZsjRiM3w PCB Layout 2 - According to Pete];<br /> <br /> <br /> =Week 9 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/21/16''==<br /> ===MR Signal Origin ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesday 11/23/16''==<br /> ===Thankgiving Wed - No Class ===<br /> <br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> OUTLINE<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> <br /> ''Suggested Further Reading''<br /> [[image:PSatSeq.jpg|right]]<br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> <br /> =Week 10 - Magnetic Resonance Fundamentals =<br /> ==''Monday 11/28/16''==<br /> ===MR Physics ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ==''Wednesady 11/30/16''==<br /> ===TBD/Q&amp;A===<br /> <br /> <br /> =Week 11 - Finals Week=<br /> ==''Monday 11/5/16''==<br /> ===Final Exam===<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!--<br /> SPARE CONTENT / PREVIOUS YEARS<br /> <br /> =Week 3: Stats begins!=<br /> <br /> ==''Monday 10/12/15''==<br /> <br /> ===- Statistical Fundamentals. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> :*[[media: CohenClassIntroStats11_25_13.pdf‎ | Slides used in class (set 1)]]<br /> <br /> ''Review of'':<br /> :*Descriptive Statistics: mean, mode, variance, standard deviation<br /> :*Statistical Inference. The Binomial and Normal Distribution<br /> :*Basic Tests: t-test, linear correlation<br /> :*Modeling and non-linear relations<br /> :*Bayes rule<br /> <br /> <br /> ==''Wednesday 10/14/15''==<br /> ===- Statistical Fundamentals II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> =Week 4 - Stats and circuits=<br /> ==''Monday 10/19/15''==<br /> ===- Statistical Fundamentals III. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> ==''Wednesday 10/21/15''==<br /> ===Circuits continued: Active devices. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ===Optics I. ''Speaker'': [mailto:zdeis@seas.ucla.edu Zachary Taylor]===<br /> [[Image:Reflection.jpg|right]]<br /> The overall goal of this lecture is to establish that:<br /> ''- Physical constants have tangible meanings''<br /> ''- Plane waves form a physically unrealizable but extremely good approximation to real systems''<br /> ''- Boundaries bend light''<br /> ''- Physical constants, plane wave mechanics, and boundaries can be used to describe the operation of a lens''<br /> ''- The PSF gives a good indication of the overall performance of an imaging system''<br /> ''- All of these concepts have analogues in other areas of engineering (ie circuits, mechanical vibrations, etc.)''''<br /> <br /> '''Outline:'''<br /> :* Constitutive parameters (ε, μ, η, n, etc.)<br /> :* Plane wave basics<br /> :* Plane waves at boundaries<br /> :* Lenses<br /> :* Advanced imaging properties of lenses<br /> :* Point spread function.<br /> <br /> ''Required Readings''<br /> Zach has very kindly agreed to post his [http://www.brainmapping.org/NITP/PNA/Readings/OpticsTaylor3-10-10.pdf Optics lecture notes].<br /> ''Suggested Further Reading''<br /> <br /> <br /> <br /> <br /> ==''Wednesday 11/19/14''== <br /> ===Optogenetics. ''Speaker'': [http://faculty.neuroscience.ucla.edu/institution/personnel?personnel_id=47031 Tom Otis]===<br /> <br /> <br /> =Week 8: =<br /> ==''Monday 12/1/14 ''==<br /> ===- Statistics for Imaging. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> <br /> [[image:BVTradeoff.jpg|right]]<br /> ''Required Readings''<br /> :*[[media: Mumford_stat_modeling.pdf | Statistical Modeling and Inference (pdf)]]<br /> :*[[media: CohenClassSlides12_2_13.pdf | Slides used in class 12/2/14 and 12/4/14]]<br /> <br /> :*The General Linear Model<br /> *Linear Algebra applied to Statistical Solutions<br /> :*Analysis of Variance<br /> <br /> ==''Wednesday 11/20/14 ...''==<br /> === - Statistics for Imaging II. ''Speaker'': [http://www.npistat.com/about.asp Catherine Sugar]===<br /> *Fixed and Random Effects<br /> *Repeated measures<br /> :*Bonferroni and Other Corrections<br /> *Non-Parametric Methods<br /> *Autocorrelation<br /> *Unknown Distributions<br /> <br /> ''Required Readings''<br /> :*[[media: CohenClassSlides12_2_13.pdf‎ | same as 12/2/14]]<br /> <br /> ''Suggested Further Reading''<br /> <br /> :*[http://ccn.ucla.edu/media/PNI20121121.mp4 Lecture Video - To be Posted Shortly - Please Right Click and Save rather than Stream - Thank you Alan and Edward!]<br /> <br /> =Week 9: =<br /> ==''Monday 11/25/14''==<br /> === - TBD. [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> ==''Wednesday 11/27/14''==<br /> ===- The Organization of the Human Brain. ''Speaker'': [http://ccn.ucla.edu/bmcweb/bmc_bios/SusanBookheimer/ Susan Bookheimer]===<br /> <br /> 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:<br /> *Phylogenetic Layering<br /> *Functional Specialization<br /> *Principles Divisions of the Brain<br /> *Brain Systems<br /> <br /> ''Required Readings''<br /> :*[http://da.biostr.washington.edu:80/cgi-bin/DA/PageMaster?atlas:NeuroSyllabus+ffpathIndex/Splash^Page^Syllabus+2 Neuroanatomy Programmed Learning]<br /> :*[[media:Cognitive_science_and_neuro_2012.pdf | Slides shown in Class UPDATED 2012/10/17]]<br /> ''Suggested Further Reading''<br /> <br /> :*[[media:PNIA_2012_PS1_Soln.pdf‎ | Solution to Problem Set 1]]<br /> ===- Human Electrophysiology ''Speakers'': [http://greenlab.npih.ucla.edu/ROSTER.html Agatha Lenartowicz], [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]===<br /> <br /> ''Evoked Responses'' - Guest Lecturer: [http://greenlab.npih.ucla.edu/ROSTER.html Jonathan Wynn]<br /> *A look at real EEG data<br /> *Preprocessing:<br /> **filtering<br /> **artifact detection/removal<br /> *averaging<br /> *single events<br /> *interpretation<br /> <br /> ''Clinical EEG'' - Guest Lecturer: [http://dgsom.healthsciences.ucla.edu/institution/personnel?personnel_id=9140 John Stern]<br /> *Normal and Abnormal EEG<br /> *EEG as a marker for brain state<br /> **sleep staging<br /> **alpha and relaxation<br /> *Neurofeedback??? --&gt;</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3104 2016-03-10T00:08:36Z

<p>Mscohen: </p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_Woods.pdf‎ | Dr. Woods' slides]]<br /> <br /> ''Suggested Further Reading''<br /> :[http://www.ncbi.nlm.nih.gov/pubmed/12667854 *RP Woods, “Characterizing volume and surface deformations in an atlas framework: theory, applications, and implementation.” Neuroimage, 18(3): p. 769-788. 2003]<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_AThomas030216.pdf‎ | Dr. Thomas' slides]]<br /> ''Suggested Further Reading''<br /> :* [http://www.ncbi.nlm.nih.gov/pubmed/23292856 SA Wijtenburg, LM Rowland, RA Edden and PB Barker, “Reproducibility of brain spectroscopy at 7T using conventional localization and spectral editing techniques.” J Magn Reson Imaging, 38(2): p. 460-467. 2013. PMCID: PMC3620961]<br /> :* [http://www.ncbi.nlm.nih.gov/pubmed/20574964 S Lipnick, G Verma, S Ramadan, J Furuyama and MA Thomas, “Echo planar correlated spectroscopic imaging: implementation and pilot evaluation in human calf in vivo.” Magn Reson Med, 64(4): p. 947-956. 2010. PMCID: PMC2946523]<br /> :* [http://www.ncbi.nlm.nih.gov/pubmed/22505247 JK Furuyama, NE Wilson, BL Burns, R Nagarajan, DJ Margolis and MA Thomas, “Application of compressed sensing to multidimensional spectroscopic imaging in human prostate.” Magn Reson Med, 67(6): p. 1499-1505. 2012.]<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> [[Image:Kinship.png | right]]<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*[[media:Carter-Genomics.pdf | ''Enhancing the Informativeness and Replicability of Imaging Genomics Studies'' Carter et al.]]<br /> :*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:M284B_AThomas030216.pdf&diff=3103 2016-03-09T23:59:20Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3102 2016-03-09T23:56:04Z

<p>Mscohen: /* - Brain Morphometry. Speaker: Roger Woods: */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_Woods.pdf‎ | Dr. Woods' slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*RP Woods, “Characterizing volume and surface deformations in an atlas framework: theory, applications, and implementation.” Neuroimage, 18(3): p. 769-788. 2003 http://www.ncbi.nlm.nih.gov/pubmed/12667854<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> [[Image:Kinship.png | right]]<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*[[media:Carter-Genomics.pdf | ''Enhancing the Informativeness and Replicability of Imaging Genomics Studies'' Carter et al.]]<br /> :*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:M284B_Woods.pdf&diff=3101 2016-03-09T23:53:06Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3100 2016-03-07T22:20:28Z

<p>Mscohen: /* Monday 3/7/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> [[Image:Kinship.png | right]]<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*[[media:Carter-Genomics.pdf | ''Enhancing the Informativeness and Replicability of Imaging Genomics Studies'' Carter et al.]]<br /> :*[[media:Flint_and_Geschwind.pdf | ''Genetics and genomics of psychiatric disease'' Flint and Geschwind]]<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Flint_and_Geschwind.pdf&diff=3099 2016-03-07T22:17:36Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Carter-Genomics.pdf&diff=3098 2016-03-07T22:17:02Z

<p>Mscohen: Enhancing the Informativeness and Replicability of Imaging Genomics Studies</p> <hr /> <div>Enhancing the Informativeness and Replicability of Imaging Genomics Studies</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3097 2016-03-07T17:43:58Z

<p>Mscohen: /* Week 10: Multimodal Methods / Course wrap up */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> [[Image:Kinship.png | right]]<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3096 2016-03-07T17:43:33Z

<p>Mscohen: /* Monday 3/7/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> [[Image:Kinship.png | right]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3095 2016-03-07T17:42:56Z

<p>Mscohen: /* Week 10: Multimodal Methods */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods / Course wrap up=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> [[Image:Kinship.png]]<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Bearden_NITP2_2016-3-4.pdf | Dr. Bearden's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Course wrap up and review. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Kinship.png&diff=3094 2016-03-07T17:41:26Z

<p>Mscohen: Mscohen uploaded a new version of &amp;quot;File:Kinship.png&amp;quot;</p> <hr /> <div>Illustration from Bearden</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Bearden_NITP2_2016-3-4.pdf&diff=3093 2016-03-07T17:37:29Z

<p>Mscohen: Bearden Lecture 2016</p> <hr /> <div>Bearden Lecture 2016</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Kinship.png&diff=3092 2016-03-07T17:36:24Z

<p>Mscohen: Illustration from Bearden</p> <hr /> <div>Illustration from Bearden</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:ONeill2016Spectro.pdf&diff=3091 2016-03-02T23:10:59Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3090 2016-03-02T23:10:35Z

<p>Mscohen: /* Week 9: MR Spectroscopy */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> No class<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> === Spectroscopy fundamentals. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:ONeill2016Spectro.pdf‎ | Dr. O'Neill's slides]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3089 2016-03-02T23:07:58Z

<p>Mscohen: /* N.B. First draft 1-6-16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3044 2016-02-17T22:09:45Z

<p>Mscohen: /* - Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani: */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Methods slides]]<br /> :*[[media:PeymanResearchTalk.pdf | Dr. Golshani's Research slides]]<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:PeymanResearchTalk.pdf&diff=3043 2016-02-17T22:08:49Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3042 2016-02-17T20:11:23Z

<p>Mscohen: /* - Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani: */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshani's Handout]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3041 2016-02-17T20:10:30Z

<p>Mscohen: /* - Optical Neuroimaging and Optogenetics. Speaker: Peyman Golshani: */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:Golshani_NITP_2016.pdf | Dr. Golshanai's Handout]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Golshani_NITP_2016.pdf&diff=3040 2016-02-17T20:09:47Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3039 2016-02-09T23:53:24Z

<p>Mscohen: /* Week 6: Brain Stimulation and Ultrasound */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:US_Imaging_Systems_1.pdf | Ultrasound Slides (2016)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:US_Imaging_Systems_1.pdf&diff=3038 2016-02-09T23:51:44Z

<p>Mscohen: George Saddik Ultrasound talk</p> <hr /> <div>George Saddik Ultrasound talk</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3037 2016-02-09T17:48:52Z

<p>Mscohen: /* Wednesday 1/27/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled.===<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3036 2016-02-09T17:47:00Z

<p>Mscohen: /* Wednesday 2/10/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010.pdf | A review of tissue substitutes for ultrasound imaging ]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3035 2016-02-09T17:46:37Z

<p>Mscohen: /* Wednesday 2/10/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :* [[media:Culjat2010 | A review of tissue substitutes for ultrasound imaging ]]<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:Culjat2010.pdf&diff=3034 2016-02-09T17:46:05Z

<p>Mscohen: A review of tissue substitutes for ultrasound imaging</p> <hr /> <div>A review of tissue substitutes for ultrasound imaging</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3033 2016-02-09T17:41:58Z

<p>Mscohen: /* TMS. Speaker: Allan Wu */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016'''<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3032 2016-02-09T17:41:45Z

<p>Mscohen: /* Monday 2/8/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2016-02-08-distribution_SM.pdf | Wu Lecture slides 2016]] '''&lt;- modified 2-9-2016<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:NITP-talk-2016-02-08-distribution_SM.pdf&diff=3031 2016-02-09T17:41:12Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3030 2016-02-09T17:39:05Z

<p>Mscohen: /* Wednesday 2/3/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-3-16.pdf | Dr. Edythe London PET Slides]] &lt;-- '''Modified 2-3-16'''<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2015-03-04-distribution_SM.pdf | Wu Lecture slides 2015]]<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=File:NITP_PET_2-3-16.pdf&diff=3029 2016-02-09T17:37:54Z

<p>Mscohen: </p> <hr /> <div></div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3028 2016-02-01T23:20:17Z

<p>Mscohen: /* Monday 3/7/16 */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-23-15_SM.pdf | Dr. Edythe London PET Slides]]<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2015-03-04-distribution_SM.pdf | Wu Lecture slides 2015]]<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Speaker'': [http://www.semel.ucla.edu/bearden-lab Carrie Bearden]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3027 2016-02-01T23:19:27Z

<p>Mscohen: /* - Optical Neuroimaging and Optogenetics. Peyman Golshani: */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-23-15_SM.pdf | Dr. Edythe London PET Slides]]<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2015-03-04-distribution_SM.pdf | Wu Lecture slides 2015]]<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. ''Speaker'': [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Carrie Bearden'': ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen https://www.ccn.ucla.edu/wiki/index.php?title=Principles_of_Neuroimaging_B_-_2016&diff=3026 2016-02-01T23:18:59Z

<p>Mscohen: /* Week 9: MR Spectroscopy */</p> <hr /> <div>Principles of Neuroimaging B, Winter, 2016 - Class Schedule and Syllabus<br /> <br /> = N.B. First draft 1-6-16 =<br /> == This schedule ''will'' change!==<br /> <br /> :'''[[Principles_of_Neuroimaging_-_2015-2016 | Back to main course page for Principles of Neuroimaging]]'''<br /> <br /> =Lecture Videos=<br /> : Hopefully, we can start recording the class sessions for those who cannot make a few lectures.<br /> <br /> =Course Reading=<br /> ===Required Reading===<br /> :'''Signal Processing for Neuroscientists''' by ''Wim van Drongelen''<br /> ::This can be found as a PDF on scribd.com, for a small fee of $8.99<br /> <br /> ===Supplemental Reading===<br /> :'''Matlab for Neuroscientists'''<br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/88212458/Matlab-Matlab-for-Neuroscientists<br /> <br /> :'''Cartoon Guide to Statistics''' <br /> ::Link for download found here for a small fee: http://www.scribd.com/doc/148072668/Cartoon-Guide-to-Statistics<br /> <br /> :'''NOTE:''' if you subscribe for a Scribd account for a day, you can download as many documents as you like for one fee.<br /> <br /> =Week 1: Magnetic Resonance Imaging=<br /> ==''Monday 1/4/16'' ==<br /> ===- MRI Contrast. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Magnetic Resonance Imaging (MRI) is probably the most influential and most flexible current means of imaging the human brain. It features a vast number of separable contrast mechanisms, and a near ideal combination of non-invasiveness, safety, resolution and metric accuracy. However, it is extraordinarily expensive and has limited temporal resolution, especially for functional studies<br /> <br /> ''Required Readings''<br /> :*[[media:MRIforPNIB2014_sm.pdf‎ | MRI Slides]]<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.<br /> ''Suggested Further Reading''<br /> :*[http://www.imaios.com/en/e-Courses/e-MRI eMRI] is another excellent online MRI learning resource<br /> :*[http://www.brainmapping.org/NITP/PNA/Readings/Hahn1950.pdf Erwin Hahn - Spin Echoes: ''Essential reading for the MRI community'']<br /> <br /> [[Image:HahnFig1.png | center]]}<br /> &lt;div style=&quot;text-align: center;&quot;&gt;Figure 1 from Hahn, 1950&lt;/div&gt;<br /> <br /> ==''Wednesday 1/6/16'' ==<br /> ===- MRI Image Formation and fMRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> <br /> =Week 2: MRI Techniques=<br /> ==''Monday 1/11/16'' ==<br /> [[Image:ASL.png | right]]<br /> ===- Measurement of Blood Flow by MRI. ''Danny JJ Wang'': [http://www.bri.ucla.edu/people/danny-jiong-jiong-wang-phd]===<br /> Most MRI images in use today are static maps, generally called &quot;structural&quot; images. However, the MRI signal is sensitive to a wide variety of dynamic phenomena. Practitioners typically use the term &quot;functional&quot; to describe images that pick up time-varying signals. The term ''functional MRI'', of course, has been usurped to describe brain activity mapping and, in most cases, refers to BOLD signal effects.<br /> <br /> Measurement of blood ''flow'' in particular is another window into brain activity. Several methods exist to create signal sensitive to blood flow, or blood flow changes. Some label the blood flow based on relaxation effects (Arterial Spin Labeling - ASL - being one important method) and others measure flow by velocity.<br /> <br /> In most cases, MRI is used as a semi quantitative modality. We get accurate spatial metrics but, in general, the image intensities are in arbitrary units. Blood flow is one particular feature that we can measure in native units.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*[http://www.pnas.org/content/89/1/212.long Williams, PNAS 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910230106/abstract;jsessionid=E42CC3817A5B7B6BB12B6BA3562C1913.f03t04 Detre, MRM 1992]<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.21790/epdf Dai, MRM 2008]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/17969096 Wu, MRM 2007]<br /> :*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155947/ Zheng, Neuroimage 2012]<br /> <br /> ==''Wednesday 1/13/16'' ==<br /> ===- More MRI. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> <br /> ''Suggested Further Reading''<br /> <br /> =Week 3: tbd=<br /> ==''Monday 1/18/16'' ==<br /> ===- MLK School Holiday===<br /> <br /> ==''Wednesday 1/20/16'' ==<br /> ===- tbd. ''Speaker'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> Abstract<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 4: Multimodal imaging=<br /> ==''Monday 1/25/16'' ==<br /> ===Multimodal imaging. ''Speaker'': [http://www.brainmapping.org/MarkCohen MarkCohen]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:MultimodalNITP.pdf | slides handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 1/27/16'' ==<br /> ===Class canceled. ''Speaker'': tbd===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 5: Positron Emission Tomography=<br /> [[Image:PET-ring.png | left]]<br /> ==''Monday 2/1/16'' ==<br /> ===Positron Emission Tomography. ''Speaker'': [http://faculty.pharmacology.ucla.edu/institution/personnel?personnel_id=45558 Magnus Dahlboun]===<br /> Handouts distributed in class.<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[media:PET_2016_M284B_SM.pdf | Dr. Dahlbom's PET handout]]<br /> <br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> [[Image:PETfounders.png | right]]<br /> <br /> ==''Wednesday 2/3/16'' ==<br /> ===PET applications. ''Speaker'': [http://www.semel.ucla.edu/profile/edythe-london Edythe London]===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*[[Media:NITP_PET_2-23-15_SM.pdf | Dr. Edythe London PET Slides]]<br /> ''Suggested Further Reading''<br /> <br /> =Week 6: Brain Stimulation and Ultrasound=<br /> ==''Monday 2/8/16'' ==<br /> ===TMS. ''Speaker'': [http://faculty.bri.ucla.edu/institution/personnel?personnel_id=121107 Allan Wu]===<br /> <br /> 'Required Readings''<br /> :* [[media:NITP-talk-2015-03-04-distribution_SM.pdf | Wu Lecture slides 2015]]<br /> :* [[media:TMSSafetyAndEthics-Rossi.pdf | TMS Safety and Ethics - Rossi, 2009]]<br /> :* [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T0J-50CV801-1&amp;_user=4423&amp;_coverDate=01%2F31%2F2011&amp;_rdoc=1&amp;_fmt=high&amp;_orig=search&amp;_origin=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000059605&amp;_version=1&amp;_urlVersion=0&amp;_userid=4423&amp;md5=f9fa3c7d63942dfb3c74e047a1f848bc&amp;searchtype=a | M Sandrini, C Umilta and E Rusconi, “''The use of transcranial magnetic stimulation in cognitive neuroscience: a new synthesis of methodological issues.''” '''Neurosci Biobehav Rev''', '''35'''(3): p. 516-536. 2011]<br /> <br /> ''Suggested Further Reading''<br /> Once upon a time we demonstrated that this sort of magnetic stimulation can take place in the MRI machines:<br /> :*[http://onlinelibrary.wiley.com/doi/10.1002/mrm.1910140226/pdf MS Cohen, RM Weisskoff, RR Rzedzian and HL Kantor, “Sensory stimulation by time-varying magnetic fields.” Magnetic Resonance in Medicine, 14(2): p. 409-414. 1990]<br /> <br /> ==''Wednesday 2/10/16'' ==<br /> [[Image:Cetacean.png | right]]<br /> ===Ultrasound. ''Speaker'': [https://www.linkedin.com/pub/george-saddik/2b/558/49 George Saddik]===<br /> ''Required Readings''<br /> :*[[media:SaddikUltrasound2015.pdf‎ | Ultrasound Slides (2015)]]<br /> <br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 7: Optical neuroimaging and optogenetics=<br /> ==''Monday 2/15/16'' ==<br /> ===- President's Day - School holiday: ===<br /> <br /> ==''Wednesday 2/17/16'' ==<br /> [[Image:PTEN.png | left]]<br /> ===- Optical Neuroimaging and Optogenetics. [http://golshanilab.neurology.ucla.edu Peyman Golshani]: ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 8: Advanced MRI methods=<br /> ==''Monday 2/22/16'' ==<br /> [[Image:DIffusingSpheres.png | left]]<br /> ===- Diffusion Physics ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=18 Ben Ellingson]===<br /> ''Required Readings''<br /> Slides should be up soon.<br /> :*[https://www.dropbox.com/s/0feqz7tlojbfgzl/1_DiffusionMRI_Methods_2015.key.pdf?dl=0 Handouts for class on 1/14/15] ''&lt;- New 1/26-2015''<br /> :*[[media:1_DiffusionMRI_Methods_v1 - 2014.pdf | Ben Ellingson Diffusion Slides]] uploaded 3/14/14<br /> ''Suggested Further Reading''<br /> :*[[media:DTIHageman.pdf | Hageman DTI Slides]]<br /> :*[[media:NICourse_DTILecture4Post_11-01-26.pdf | Hageman DTI Notes 2/26/12]]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/15037456?dopt=Citation Diffusion tensor imaging of cerebral white matter: a pictorial review of physics, fiber tract anatomy, and tumor imaging patterns AJNR Am J Neuroradiol. 2004 Mar;25(3):356-69]<br /> <br /> :Sadly, the library does not have a subscription for the journals below (Mark has copies on reserve in his office):<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/8661285?dopt=Citation Microstructural and physiological features of tissues elucidated by quantitative-diffusion-tensor MRI. J Magn Reson B. 1996 Jun;111(3):209-19]<br /> :*[http://www.ncbi.nlm.nih.gov/pubmed/16950152?dopt=Citation Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron. 2006 Sep 7;51(5):527-39]<br /> <br /> ==''Wednesday 2/25/16'' ==<br /> [[Image:Callosum.png | right]]<br /> ===- Brain Morphometry. ''Speaker'': [http://www.bmap.ucla.edu/about/peopledetails/roger_woods/ Roger Woods]: ===<br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 9: MR Spectroscopy=<br /> ==''Monday 2/29/16'' ==<br /> ===- Clinical Spectroscopy. ''Speaker'': [http://people.healthsciences.ucla.edu/institution/personnel?personnel_id=74852 Joseph O'Neill] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/2/16'' ==<br /> ===- Spectroscopic Methods. ''Speaker'': [http://radiology.ucla.edu/body.cfm?id=48&amp;action=detail&amp;ref=65 Albert Thomas] ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> =Week 10: Multimodal Methods=<br /> ==''Monday 3/7/16'' ==<br /> ===- Imaging Genetics. ''Carrie Bearden'': ===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*<br /> <br /> ==''Wednesday 3/9/16'' ==<br /> ===- Multimodal imaging approaches. ''Mark Cohen'': [http://www.brainmapping.org/MarkCohen Mark Cohen]===<br /> <br /> ''Required Readings'' - Please complete these readings prior to class.<br /> :*<br /> &lt;!--<br /> :*[http://www.cis.rit.edu/htbooks/mri/ These notes] by Joseph Hornak are highly professional and complete coverage of MRI.]<br /> :*[[media:M284B_perfusion-web.pdf‎ | Dr. Wang's Handout]]<br /> [[Image:HahnFig1.png]]<br /> ''above'': Figure 1 from Hahn, 1950<br /> --&gt;<br /> ''Suggested Further Reading''<br /> :*</div>

Mscohen