= Brainstorm Training Workshop at UQAM =
== General information ==
 * '''When''': Wednesday, July 11, 2012  (9am - 6pm)''' '''
 * '''Where: '''MIT [[http://whereis.mit.edu/?go=32|Building 32]] (Stata Center) Room 141

== Program ==
Schedule: , 9am to 6pm
9h00 : Welcome & Introduction (Pierre Jolicoeur, UdeM)
9h15 - 10h00 : Principles of MEG: practical aspects in data collection and experimental set-ups (Elizabeth Bock, McGill)
10h00 - 11h00 : MEG signal extraction and source imaging crash-course: concepts & methodology (Esther Florin, McGill)
11h00 - 11h15 : Coffee break
11h15 - 12h15 :MEG applied to cognitive neuroscience (Pierre Jolicoeur, UdeM)
12h15 - 13h30 : Lunch break
13h30 - 18h00 : Hands-on software training using Brainstorm (Francois Tadel, McGill)

== Requirements ==
==== The workshop ====
 * Bring your own laptop (any operating system, with or without Matlab installed)
  * with Brainstorm installed (version of '''July 2nd''' or later),
  * with the sample dataset downloaded (see instructions below).
 * Power plugs will be available at each desk.
 * Participants who do not follow the instruction on this page before the workshop will not be able to follow the afternoon hands-on session

==== The software ====
Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX:

 * An open-source Matlab application (Matlab required)
  * Necessary: Matlab version R2006a''' '''(7.2), or later
  * Optional: Signal Processing Toolbox (for frequency filtering and resampling)
 * A stand-alone Java executable (Matlab not required)
  * Requires the free download of the Matlab runtime library
  * To check if your operating system is supported: [[http://www.mathworks.com/support/sysreq/current_release/index.html|visit this page]]

== Installation instructions ==
Before coming to the workshop, you  need to download the software and the tutorial dataset from the  Brainstorm website (approximately 400Mb). It requires a free  registration for demographics purposes. To streamline troubleshooting and instructions during the session, please save all the downloaded files '''__on your Desktop__'''.

 1. From the Brainstorm [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] page, log in or create a Brainstorm account (registration is free)
 1. You will then be able to download the following files to '''your Desktop''' '''folder''':
  * '''Brainstorm software''': brainstorm_YYMMDD.zip  (45 Mb)
  * '''Tutorial dataset''': sample_workshop_uqam.zip (240 Mb)
  * '''Matlab Component Runtime (MCR)''': ONLY if you do not have Matlab installed (300 Mb)
 1. Note: if you already have Brainstorm installed, make sure that the  version was released''' after July 2nd'''.
 1. Unzip all the zip files
 1. If you are using the stand-alone version (__without__ Matlab), install the MCR library:
  * __Windows__: Double-click on the .exe and follow the instructions
  * __Linux__: From a terminal, unzip .zip, then run ./install
  * __MacOS__: Click on the zip file to unzip it, then click on "InstallForMacOSX"
 1. Delete the zip files / the installation files
 1. Create a folder "'''brainstorm_db'''" on your '''Desktop '''folder
 1. Final check: you should have now 3 folders on your Desktop:
  * '''brainstorm3''': Program folder, with the Matlab source code and the compiled executable
  * '''brainstorm_db''': Folder for the Brainstorm database (empty)
  * '''sample_workshop''': Example dataset to be used during the training session
 1. Now run Brainstorm, to make sure it starts fine (read carefully the following section)

== Running Brainstorm for the first time ==
==== With Matlab ====
 1. Start Matlab
 1. '''DO''' '''NOT '''add the ''brainstorm3'' folder to your path: Brainstorm will take care of that,
 1. Go to the ''brainstorm3'' folder from the Matlab command window,
 1. Type "''brainstorm''" in the Matlab command window and press ''enter,''
 1. When asked for the location of the Brainstorm database folder, pick the  folder "brainstorm_db" you have just created on the Desktop.

==== Without Matlab ====
 1. Run the executable file located in ''brainstorm3/bin/R2012a/ ''
  * __Windows__: Double-click on ''brainstorm3.bat''
  * __Linux__: From a terminal, ''cd brainstorm3/bin/R2012a/''
   * Make sure that the file ''brainstorm.command'' is executable:<<BR>>=> ''chmod a+x brainstorm.command ''
   * run ''./brainstorm.command''
  * __MacOS__: Double-click on ''brainstorm.command''
 1. When  you start Brainstorm for the first time on Linux or MacOS, you will be  prompted to select the folder where you installed the MCR
 1. When asked for the location of the Brainstorm database folder, pick the  folder ''brainstorm_db'' on your Desktop.

== Getting ready for the workshop ==
In order to make sure that Brainstorm works properly, and to get more familiar with the software, we recommend that you follow at least the first half of the the online tutorials:

 * [[Tutorials/BstFolders|0. Brainstorm architecture]]
 * [[Tutorials/TutFirstSteps|1. First steps]]
 * [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]]
 * [[Tutorials/TutImportRecordings|3. Importing MEG recordings]]
 * [[Tutorials/TutExploreRecodings|4. Exploring the recordings]]

The slides presented during the workshop are available here:

 * Sylvain Baillet
 * [[attachment:Training/120428_worshop_boston.pdf|Francois Tadel]]

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