User Tools

Site Tools


analysis:rhythms

====== Differences ====== This shows you the differences between two versions of the page.

Link to this comparison view

analysis:rhythms [2020/01/08 18:34]
analysis:rhythms [2018/04/17 15:20] (current)
Line 1: Line 1:
 +~~DISCUSSION~~
  
 +Welcome! This is the home page for the optional hands-on (heads-on) 2017 edition of the "​Rhythmic Brain" course.
 +
 +==== Contents ====
 +
 +  * [[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 follow below)
 +
 +=== Getting started with MATLAB ===
 +
 +Depending on your background and programming experience you might find the following resources helpful:
 +
 +  * 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/​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 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:
 +
 +  * [[http://​blogs.mathworks.com/​ | Mathworks staff blogs]], especially "Loren on the Art of MATLAB"​ is a treasure trove of tips and tricks
 +  * [[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 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 ===
 +
 +Emotiv documentation:​
 +
 +  * {{:​analysis:​quickstartguide2014.pdf|Quick Start Guide}}
 +  * {{:​analysis:​emotiv_epoc_specifications_2014.pdf|Specification Sheet}}
 +  * {{:​analysis:​epocusermanual2014.pdf|Manual}}
 +  * {{:​analysis:​testbench_manual.pdf|TestBench (Emotiv software) manual}}
 +  * [[https://​emotiv.com/​forum/​forum4/​topic2081/​messages/​|Cleaning instructions]]
 +
 +The following textbooks provide more in-depth treatment of some of the topics we touch on in the course:
 +
 +  * Textbook: Leis, Digital Signal Processing using MATLAB for Students and Researchers
 +  * Textbook: Johnston and Wu, Foundations of Cellular Neurophysiology
 +  * Textbook: Dayan & Abbott, Theoretical Neuroscience
 +
 +These are selected modules from a graduate course I teach on neural data analysis:
 +
 +   * [[analysis:​nsb2015:​week0|Principles of (neural) data analysis]]
 +   * [[analysis:​course-w16:​week1|Module 1: Setting up (MATLAB, paths, GitHub, accessing data)]]
 +   * [[analysis:​course-w16:​week2|Module 2: Introduction to neural data formats and preprocessing]]
 +   * [[analysis:​course-w16:​week3long|Module 3: Visualizing raw neural data in MATLAB]]
 +   * [[analysis:​course-w16:​week4|Module 4: Anatomy of time series data, sampling theory]]
 +   * [[analysis:​course-w16:​week5|Module 5: Fourier series, transforms, power spectra]]
 +   * [[analysis:​course-w16:​week6|Module 6: Filtering: filter design, use, caveats]]
 +   * [[analysis:​course-w16:​week7|Module 7: Time-frequency analysis: spectrograms]]
 +   * [[analysis:​course-w16:​week11|Module 11: Interactions between multiple signals: coherence, Granger causality, and phase-slope index]]
 +   * [[analysis:​course-w16:​week12|Module 12: Time-frequency analysis II: cross-frequency coupling]] ​
 +   * [[analysis:​course-w16:​week13|Module 13: Spike-field relationships:​ spike-triggered average, phase locking, phase precession]]
 +=== Note for Linux users ===
 +
 +The tutorials provided here are 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.