= MEG / Brainstorm Workshop (UQAM summer school) =
== General information ==
* '''When''': Wednesday, July 11, 2012 (9am - 6pm)''' '''
* '''Where: '''UdeM, room D-427 of the [[http://www.umontreal.ca/plancampus/pavillons/pav03.html|Marie-Victorin Building located at 90 Vincent d'Indy Street]], right next to the metro station "Edouard-Montpetit".
== Program ==
'''Morning: Introduction to Magnetoencephalography'''
* 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
'''Afternoon: Brainstorm hands-on session'''
* 13h30 - 14h15 : Introduction to Brainstorm (Francois Tadel, !McGill)
* 14h15 - 15h30 : Database explorer, reviewing continuous recordings, artifact correction, filtering and epoching, averaging, observation of a typical somatosensory evoked response
* 15h45 - 16h00 : Coffee break
* 16h00 - 17h00 : Head modeling, cortical source reconstruction, definition of ROIs, tracking the processing of the sensory information millisecond by millisecond at the cortex level
* 17h00 - 18h00 : Introduction to advanced features, depending on the audience specific requests: Frequency and time-frequency analysis, group analysis, anatomical atlases, advanced scripting interface, ...
== Requirements ==
==== The workshop ====
* Bring your own laptop:
* Any operating system, with or without Matlab installed,
* Relatively recent hardware (some of the tutorial steps require a lot of computation power and could be too long on older laptops),
* '''Brainstorm must be installed''' (version of '''July 2nd''' or later, see instructions below),
* The '''sample dataset must be downloaded''' (see instructions below)
* Make sure you have at least '''5 Gb of free space''' on your hard drive
* 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 (300 to 650Mb). 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 (260 Mb)
* '''Matlab Component Runtime (MCR)''': ONLY if you do __not__ have Matlab installed (350 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<
>But '''do not unzip the file Workshop.zip''' in the folder sample_workshop_uqam.zip
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_uqam''': 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 ''brainstorm3.command'' is executable:<
>=> ''chmod a+x brainstorm3.command ''
* run ''./brainstorm3.command''
* __MacOS__: Double-click on ''brainstorm3.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 read and follow at least the first three online tutorials:
* [[Tutorials/BstFolders|0. Brainstorm architecture]]
* [[Tutorials/TutFirstSteps|1. First steps]]
* [[Tutorials/TutImportAnatomy|2. Importing individual anatomy]]
The slides presented during the workshop are available here:
* [[attachment:Training/120428_worshop_boston.pdf|Francois Tadel]]
== Troubleshooting ==
For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )