The Neurophysiological Biomarker Toolbox (NBT)

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tutorial:tutorial_dipoles [2012/01/16 09:58]
gherrero created
tutorial:tutorial_dipoles [2013/12/06 09:58] (current)
Klaus Linkenkaer-Hansen
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 ====== Tutorial: Simulating and estimating EEG sources ====== ====== Tutorial: Simulating and estimating EEG sources ======
 +
 +Approximate time needed to complete the tutorial: 2 hours.
  
 In this tutorial we will learn how simple intracerebral current sources can  In this tutorial we will learn how simple intracerebral current sources can 
 generate complicated patterns of EEG potentials at the scalp. generate complicated patterns of EEG potentials at the scalp.
 We will then see how, under certain conditions, the underlying We will then see how, under certain conditions, the underlying
-_EEG sources_ can be effectively localized from the scalp measurements. +//EEG sources// can be effectively localized from the scalp measurements. 
 However, the tutorial also aims to illustrate how the solution to  However, the tutorial also aims to illustrate how the solution to 
-the _inverse EEG problem_ can be easily confounded e.g. by the presence of +the //inverse EEG problem// can be easily confounded e.g. by the presence of 
 noisy background EEG activity.  noisy background EEG activity. 
  
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 the topic of this tutorial: the topic of this tutorial:
  
-{{http://www.kasku.org/tutorials/tutorial_dipoles/slides.pdf|Download the slides}}+[[http://sourceforge.net/projects/nbtoolbox/files/pdf/sourcemodel.pdf/download|Download the slides]]
  
  
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 Please download the  Please download the 
-{{http://www.kasku.org/tutorials/tutorial_dipoles/tutorial_dipoles.zip|tutorial files}}+[[http://sourceforge.net/projects/nbtoolbox/files/Tutorials/Scripts/tutorial_dipoles.zip/download|tutorial files]]
  and uncompress the .zip  file. Then simply add directory ''tutorial_dipoles'' and all its   and uncompress the .zip  file. Then simply add directory ''tutorial_dipoles'' and all its 
 subdirectories to your MATLAB's path. To add a directory and all its subdirectories to subdirectories to your MATLAB's path. To add a directory and all its subdirectories to
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 following freely available MATLAB toolboxes: following freely available MATLAB toolboxes:
  
-{{http://fieldtrip.fcdonders.nl/|Fieldtrip MATLAB toolbox}}+[[http://fieldtrip.fcdonders.nl/|Fieldtrip MATLAB toolbox]]
  
  
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 The tutorial makes use of  The tutorial makes use of 
-{{http://www.mathworks.nl/help/techdoc/matlab_oop/brh2rgw.html|MATLAB's classes}}.  +[[http://www.mathworks.nl/help/techdoc/matlab_oop/brh2rgw.html|MATLAB's classes]].  
-Do not get get intimidated by the term. A class is just a _user-defined data type_.+Do not get get intimidated by the term. A class is just a //user-defined data type//.
  MATLAB comes with lots of built-in data types. For instance ''double'' and ''single''  MATLAB comes with lots of built-in data types. For instance ''double'' and ''single''
 are two types that can store numeric data: are two types that can store numeric data:
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  x = 5;  x = 5;
  
-The variable ''x'' above is now an _instance_ (also called  +The variable ''x'' above is now an //instance// (also called  
-an _object_) of class ''double''. You can find out the classes of the variables+an //object//) of class ''double''. You can find out the classes of the variables
 in your MATLAB's workspace using the command ''whos''. The result could be in your MATLAB's workspace using the command ''whos''. The result could be
 something like this: something like this:
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 have defined specifically for the purposes of this tutorial.  have defined specifically for the purposes of this tutorial. 
  
-It is important to realize the difference between a _class_ and an _object_+It is important to realize the difference between a //class// and an //object//
 In the example above, ''x'' and ''y'' are two different objects of the same class. In the example above, ''x'' and ''y'' are two different objects of the same class.
  
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 One of the great advantages of using objects with MATLAB is that it allows you One of the great advantages of using objects with MATLAB is that it allows you
-to {{http://en.wikipedia.org/wiki/Function_overloading|overloading}}+to [[http://en.wikipedia.org/wiki/Function_overloading|overloading]]
  function names. For instance, if you run the   function names. For instance, if you run the 
 command: command:
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  plot(myHead);   plot(myHead);
   
-MATLAB will first check whether a specialized _method_ ''plot()'' has been defined+MATLAB will first check whether a specialized //method// ''plot()'' has been defined
  for class ''head.mri''. If such method exists then it will run that method  for class ''head.mri''. If such method exists then it will run that method
  instead of MATLAB's built-in function ''plot()''. A ''head.mri'' object contains a   instead of MATLAB's built-in function ''plot()''. A ''head.mri'' object contains a 
 head model and a ''double'' object contains just numbers. Indeed, plotting such head model and a ''double'' object contains just numbers. Indeed, plotting such
  different data types involve very different operations. Thus, it makes sense  different data types involve very different operations. Thus, it makes sense
-that different versions of ''plot'' are called, depending on the _class_ of what+that different versions of ''plot'' are called, depending on the //class// of what
  you want to be plotted. Remember: the specialized version of ''plot()'' that  you want to be plotted. Remember: the specialized version of ''plot()'' that
- takes care of plotting ''mri.head'' objects is called a _method_ of class + takes care of plotting ''mri.head'' objects is called a //method// of class 
  ''mri.head''.  ''mri.head''.
    
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 built-in ''plot()'' instead of corresponding to method ''plot()'' of class  built-in ''plot()'' instead of corresponding to method ''plot()'' of class 
 ''mri.head''. Only if you read until the end of the help that is displayed you ''mri.head''. Only if you read until the end of the help that is displayed you
-will see a section that reads ''Overloaded methods:'' and that lists several+will see a section that reads ''Overloaded methods'' and that lists several
 other functions that are also called ''plot()'', and that will be called  other functions that are also called ''plot()'', and that will be called 
 instead of the built-in, depending on the type of the input argument.  instead of the built-in, depending on the type of the input argument. 
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 This tutorial has been prepared for the course  This tutorial has been prepared for the course 
 [[courses:advanced_human_neurophysiology|Advanced Human Neurophysiology]], [[courses:advanced_human_neurophysiology|Advanced Human Neurophysiology]],
- given at the {{http://www.vu.nl/en/|VU University}}, and organized by  + given at the [[http://www.vu.nl/en/|VU University]], and organized by  
-{{http://www.bio.vu.nl/enf/linkenkaer/|Klaus Linkenkaer-Hansen}}. The author of the tutorial is  +Klaus Linkenkaer-Hansen. The author of the tutorial is  
-{{http://www.kasku.org|German Gomez-Herrero}}+[[http://www.kasku.org|German Gomez-Herrero]]
  
 As both code and documentation has been made from scratch for the  As both code and documentation has been made from scratch for the 
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 so that I can improve it.  so that I can improve it. 
  
 +====== Tutorial steps ====== 
 +
 +The tutorial consists of three parts. Follow the links below to each of those parts:
 +
 +
 +  - [[tutorial:tutorial_dipoles:head_model|Building a realistic head model]]
 +  - [[tutorial:tutorial_dipoles:eeg_sources|Simulating EEG sources]]
 +  - [[tutorial:tutorial_dipoles:source_localization|Localizing EEG sources]]
  
tutorial/tutorial_dipoles.1326707894.txt.gz · Last modified: 2012/01/16 09:58 by gherrero
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