analysis:rhythms
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| ~~DISCUSSION~~ | ~~DISCUSSION~~ | ||
| - | Welcome! This is the home page for the optional hands-on (heads-on) 2016 edition of the "Rhythmic Brain" course. | + | Welcome! This is the home page for the optional hands-on (heads-on) 2020 edition of the "Rhythmic Brain" course. |
| - | ==== Contents ==== | + | ==== Getting started with Emotiv headsets ==== |
| - | * [[analysis:rhythms:step1|Step 1: from zero to loading and plotting Emotiv data]] | + | * Using the course laptops, launch the Emotiv Xavier Control Panel using the Desktop icon. |
| + | * Click "Continue without Cloud Services" | ||
| + | * Type an username ("TestUser" works fine) | ||
| + | * Follow the instructions on the screen. | ||
| - | === Getting started with MATLAB === | + | |
| + | ==== Analysis modules ==== | ||
| + | |||
| + | * [[analysis:rhythms:step1|Module 1: Setting up, loading and plotting Emotiv data]] | ||
| + | * [[analysis:rhythms:step3|Module 2: Signal processing, basics of sampling (aliasing, Nyquist)]] | ||
| + | * [[analysis:rhythms:step2|Module 3: Signal processing, Fourier analysis and power spectra]] | ||
| + | |||
| + | (more advanced modules can be found [[analysis:nsb2018|here]].) | ||
| + | |||
| + | ==== Getting started with MATLAB ==== | ||
| Depending on your background and programming experience you might find the following resources helpful: | Depending on your background and programming experience you might find the following resources helpful: | ||
| - | * Textbook: {{:analysis:wallisch_matlabforneuro.pdf|Wallisch, MATLAB for Neuroscientists}} | + | * Textbook chapter: {{:analysis:wallisch_ch2.pdf|Wallisch, "MATLAB for Neuroscientists"}} |
| * [[http://www.mathworks.com/help/matlab/getting-started-with-matlab.html?s_cid=learn_doc|"Getting Started with MATLAB" Primer]]. | * [[http://www.mathworks.com/help/matlab/getting-started-with-matlab.html?s_cid=learn_doc|"Getting Started with MATLAB" Primer]]. | ||
| * [[http://www.mathworks.com/matlabcentral/about/cody/ | Cody]], a continually expanding set of problems with solutions to work through, with a points system to track your progress | * [[http://www.mathworks.com/matlabcentral/about/cody/ | Cody]], a continually expanding set of problems with solutions to work through, with a points system to track your progress | ||
| - | If you are unsure, take a look at the table of contents of the MATLAB Primer in the link above. If there are things you don't recognize, use the Primer itself, or Chapter 2 of the MATLAB for Neuroscientists book to get up to speed. If you've never used MATLAB, definitely start with the steps in the Primer. | + | If you are unsure, take a look at the table of contents of the MATLAB Primer in the link above. If there are things you don't recognize, use the Tutorials in the Primer itself, and/or Chapter 2 of the MATLAB for Neuroscientists book to get up to speed. If you've never used MATLAB, I recommend you start with the Tutorials in the Primer, and refer to the book chapter if you'd like a change of pace or a different way of explaining the same things. |
| Regardless of your MATLAB abilities, some great ways to keep learning are: | Regardless of your MATLAB abilities, some great ways to keep learning are: | ||
| Line 22: | Line 34: | ||
| * [[http://stackoverflow.com/questions/tagged/matlab | MATLAB questions on StackOverflow]], a Q&A site where you can browse previous questions and add new ones | * [[http://stackoverflow.com/questions/tagged/matlab | MATLAB questions on StackOverflow]], a Q&A site where you can browse previous questions and add new ones | ||
| - | If you have no formal training in computer programming (i.e. you have never taken a "Intro to Computer Science" or "Introductory Programming" type course) a great introduction to the "Zen of programming" is to do the pen-and-paper exercises in this [[http://sites.tufts.edu/rodrego/files/2011/03/Secrets-of-Computer-Power-Revealed-2008.pdf | short chapter]] by Daniel Dennett ("The Secrets of Computer Power Revealed") before you embark on the MATLAB primer linked to above. Most people find it frustrating at first, but rewarding if they stick with it for a few hours. | + | If you have no training or experience in computer programming (i.e. you have never taken a "Intro to Computer Science" or "Introductory Programming" type course) a great introduction to the "Zen of programming" is to do the pen-and-paper exercises in this [[http://sites.tufts.edu/rodrego/files/2011/03/Secrets-of-Computer-Power-Revealed-2008.pdf | short chapter]] by Daniel Dennett ("The Secrets of Computer Power Revealed") before you embark on the MATLAB primer linked to above. Most people find it frustrating at first, but rewarding if they stick with it for a few hours. |
| - | === Resources === | + | ==== Resources ==== |
| - | The following textbooks provide more in-depth treatment of some of the topics we touch on in the course: | + | Emotiv documentation: |
| - | * Textbook: {{:analysis:leis_dspusingmatlab.pdf|Leis, Digital Signal Processing using MATLAB for Students and Researchers}} | + | * {{:analysis:quickstartguide2014.pdf|Quick Start Guide}} |
| - | * Textbook: {{:analysis:johnstonwu.pdf|Johnston and Wu, Foundations of Cellular Neurophysiology}} | + | * {{:analysis:emotiv_epoc_specifications_2014.pdf|Specification Sheet}} |
| - | * Textbook: {{:analysis:dayanabbott_theoneuro.pdf|Dayan & Abbott, Theoretical Neuroscience}} | + | * {{:analysis:epocusermanual2014.pdf|Manual}} |
| + | * {{:analysis:testbench_manual.pdf|TestBench (Emotiv software) manual}} | ||
| + | * [[https://www.emotiv.com/knowledge-base/electrode-oxidation/|Cleaning instructions]] | ||
| - | These are selected modules from a graduate course I teach on neural data analysis: | + | The following textbooks provide more in-depth treatment of some of the topics we touch on in the course: |
| - | * [[analysis:nsb2015:week0|Principles of (neural) data analysis]] | + | * Textbook: Leis, Digital Signal Processing using MATLAB for Students and Researchers |
| - | * [[analysis:course-w16:week1|Module 1: Setting up (MATLAB, paths, GitHub, accessing data; Week 1)]] | + | * Textbook: Johnston and Wu, Foundations of Cellular Neurophysiology |
| - | * [[analysis:course-w16:week2|Module 2: Introduction to neural data formats and preprocessing (Week 2)]] | + | * Textbook: Dayan & Abbott, Theoretical Neuroscience |
| - | * [[analysis:course-w16:week3long|Module 3: Visualizing raw neural data in MATLAB (Week 3)]] | + | |
| - | * [[analysis:course-w16:week4|Module 4: Anatomy of time series data, sampling theory (Week 4)]] | + | |
| - | * [[analysis:course-w16:week5|Module 5: Fourier series, transforms, power spectra (Week 4)]] | + | |
| - | * [[analysis:course-w16:week6|Module 6: Filtering: filter design, use, caveats (Week 5)]] | + | |
| - | * [[analysis:course-w16:week7|Module 7: Time-frequency analysis: spectrograms (Week 5)]] | + | |
| - | * [[analysis:course-w16:week11|Module 11: Interactions between multiple signals: coherence, Granger causality, and phase-slope index (Week 8)]] | + | |
| - | * [[analysis:course-w16:week12|Module 12: Time-frequency analysis II: cross-frequency coupling (Week 9)]] | + | |
| - | * [[analysis:course-w16:week13|Module 13: Spike-field relationships: spike-triggered average, phase locking, phase precession (Week 10)]] | + | |
| - | === Note for Linux users === | + | Some tasks to try to generate specific brain rhythms: |
| - | The lab codebase is set up for machines running 64-bit Windows 7 or Mac %%OS%% X. If you want to use Linux or some other %%OS%% you will probably need to compile some of the low-level loading functions yourself. Some pointers for this are provided in subsequent modules when loading is introduced. | + | * Occipital-parietal alpha (10 Hz): eyes-open vs eyes-closed contrast |
| + | * Frontal alpha: negative high arousal picture viewing, or mentally counting backwards from a large number in steps of 7 or 13 | ||
| + | * Drawing a stick figure (see for yourself what happens, take care to avoid moving artifacts) | ||
analysis/rhythms.1459274612.txt.gz · Last modified: 2018/07/07 10:19 (external edit)
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