= Paris, France: July 2, 2018 =
Half-day introduction to SEEG/ECOG analysis, as part of the [[https://cuttingeeg.org/|CutingEEG symposium]].

== General information ==
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<<HTML(<TR><TD>)>>'''Where'''<<HTML(</TD><TD>)>>Telecom ParisTech<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''When'''<<HTML(</TD><TD>)>>Monday July 2nd, 2018: 8:30-12:15<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Instructors'''<<HTML(</TD><TD>)>>[[AboutUs/FrancoisTadel|Francois Tadel]] (Grenoble Institute of Neuroscience)<<BR>>[[https://www.linkedin.com/in/anne-sophie-dubarry-6a8a4a33/?locale=en_US|Anne-Sophie Dubarry]](Aix-Marseille University)<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Audience'''<<HTML(</TD><TD>)>>Users interested in analyzing sEEG/EEG/ECoG/MEG recordings using Brainstorm.<<BR>>Teaching in English. <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>'''Slides'''<<HTML(</TD><TD>)>>[[http://neuroimage.usc.edu/brainstorm/WorkshopCambridge2017?action=AttachFile&do=get&target=cambridge2017_slides_tadel.pdf|Introduction]] <<HTML(</TD></TR>)>>

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== Program ==
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<<HTML(<TR><TD>)>>8:30-9:15<<HTML(</TD><TD>)>>Onsite assistance in installing the material for the training session <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>9:15-9:45<<HTML(</TD><TD>)>>'''Lecture: Brainstorm overview (Tadel''')

Software structure, typical data workflow <<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:00-10:45<<HTML(</TD><TD>)>>'''Practice'''

Database explorer

MRI volumes, surfaces and anatomical atlases<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>10:45-11:00<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>11:00-12:30<<HTML(</TD><TD>)>>'''Practice'''

Registration EEG/MRI

Review of continuous EEG recordings

Montages and management of event markers

Frequency filters

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<<HTML(<TR><TD>)>>12:30-13:30<<HTML(</TD><TD>)>>''Lunch''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>13:30-14:30<<HTML(</TD><TD>)>>'''Practice'''

Artifact  detection

Artifact correction with ICA

Averaging<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>14:30-15:00<<HTML(</TD><TD>)>>'''Lecture: Source modeling (Baillet)'''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:00-15:30<<HTML(</TD><TD>)>>''Coffee break''<<HTML(</TD></TR>)>>

<<HTML(<TR><TD>)>>15:30-17:30<<HTML(</TD><TD>)>>'''Practice'''

Head modeling, cortical source reconstruction

Regions of interest (ROIs)

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= Prepare your laptop for the workshop (optional) =
Computers will be available with Matlab and Brainstorm installed, however we recommend participants to bring a laptop. Setting up the software environment is an important part of the training and would be a good preparation step to this workshop. Follow the instructions below if you are insterested in following the hands-on session on your own laptop.

== Important notes ==
 * Working  with MEG/EEG/SEEG recordings involves a lot of computational resources and  large display windows. Therefore we recommend that you bring a laptop  with a decent processing capacity, '''4Gb RAM''', a '''64bit''' operating system, and a '''screen larger than 13"'''.
 * You  would add to your comfort by bringing an '''external mouse'''.   Most of  the manipulations are done with the mouse, and some involve  an  intensive  use of the mouse wheel/scrolling.
 * Don't forget your '''power adapter'''!

== Installation instructions ==
Before   coming to the workshop, you  need to download  the software and the   tutorial dataset from the  Brainstorm website  (220Mb). To streamline  troubleshooting during the  session, please save all the  downloaded  files '''__on your Desktop__'''.

 1. From the Brainstorm [[http://neuroimage.usc.edu/bst/download.php|Download]] page, log in or create a Brainstorm account
 1. Download the following files to '''your Desktop''' '''folder''':
  * '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>>   (70 Mb)
  * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>tutorial_epimap.zip<<HTML(</FONT>)>>  (150 Mb)
 1. If you already have Brainstorm, make sure that the  version was released <<HTML(<FONT color=red>)>>'''after June 18th'''<<HTML(</FONT>)>>.
 1. Unzip the two downloaded files on your desktop
 1. Delete the two downloaded zip files
 1. Create a folder "'''brainstorm_db'''" on your '''Desktop '''
 1. Final check: you should have now 3 folders on your desktop:
  * '''brainstorm3''': Program folder, with the source code and the compiled executable
  * '''brainstorm_db''': Brainstorm database (empty)
  * '''tutorial_epimap''': Example dataset used during the training session
 1. Run Brainstorm, to make sure it works correctly on your computer (read the following section)

== Running Brainstorm for the first time ==
==== With Matlab ====
 1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible
 1. Start Matlab
 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically
 1. Go to the brainstorm3 folder
 1. Type "brainstorm" in the command window
 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created

==== Without Matlab ====
 1. The instructions below are valid for the following operating systems:
  * '''Windows''': Any version ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Windows.pdf|details]])
  * '''Linux''': Ubuntu 14.04+, RedHat 6.x+, Debian 7.x, SUSE 11.3+  ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Linux.pdf|details]])
  * '''MacOS''': 10.9.5 (Mavericks), 10.10 (Yosemite) ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Macintosh.pdf|details]])
  * If your system is not listed here, try with another version: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]], [[InstallationR2016a|2016a]], ...
 1. Download the '''MCR R2015b (9.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]]
 1. Install the MCR:
  * __Windows__: Double-click on the .exe and follow the instructions
  * __MacOS__: Click on the zip file to unzip it, then click on "InstallForMacOSX"
  * __Linux__: From a terminal, unzip .zip, then run ./install
 1. Run the program in brainstorm3/bin/R2015b/
  * __Windows__: Double-click on ''brainstorm3.bat''
  * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions
  * __Linux__: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2015b/''<<BR>>''./brainstorm3.command ''
 1. Troubleshooting for MacOS or Linux:
  * On  recent versions of MacOS, you may get an error message "Application  can't be opened because it is from an unidentified developer". This  message would appear for all the programs that were not downloaded from  the Apple app-store. To go around this verification: right-click on the  application > Open, then click on the Open button.
  * From a terminal, make sure that the file "''brainstorm3.command''" is executable:<<BR>>''chmod a+x brainstorm3.command''
  * If nothing happens, run: <<BR>>''./brainstorm3.command MCR_DIR''<<BR>>MCR_DIR is the MCR 9.0 folder (ex: /Applications/MATLAB/MCR/v90)
  * Try with another binary release: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]][[http://neuroimage.usc.edu/brainstorm/InstallationR2016a|, 2016a]], ...
 1. Troubleshooting for Windows:
  * Your  current user may not have the necessary privileges. If you are an  administrator for your computer, you can do the following: right-click  on ''brainstorm3.bat'' > Run as administrator.
  * If  you are not the administrator of your computer and Matlab or the MCR  are not installed in the standard paths, Brainstorm may have trouble  finding them. To specify manually the path of the MCR or Matlab folder,  right-click on ''brainstorm3.bat'' > Edit. Fill the second line of  the script (Example: @SET MATLABROOT="C:\Program Files\MATLAB\R2015b"),  save the file, and try to execute it again.
 1. On Linux or MacOS, you may be asked to select the folder where you installed the MCR.
 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.

== Make sure it works ==
In order to check if Brainstorm works properly or your computer, please follow these instructions:

 * Create a new protocol: Menu File > New protocol.<<BR>>Set the name to "Test", don't change the other default options.
 * In the folder "Default anatomy", double-click successively on the files: MRI, head, cortex_15002V
 * It should open the figures below, make sure they work correctly:
  * Click in the MRI Viewer to move the slices
  * Click+move your mouse in the 3D figure to rotate
  * Zoom in/out with the mouse wheel or the two-finger scroll on MacBook pads
  * The head surface should be transparent, with the brain visible through it
 {{attachment:test_bst.gif}}

== Troubleshooting ==
For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )