MEG / Brainstorm Workshop (UQAM summer school)

General information

• When: Wednesday, July 11, 2012 (9am - 6pm)

• Where: UdeM, room D-427 of the 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: 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 Download page, log in or create a Brainstorm account (registration is free)

2. 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)

3. Note: if you already have Brainstorm installed, make sure that the version was released after July 2nd.

4. Unzip all the zip files
   But do not unzip the file Workshop.zip in the folder sample_workshop_uqam.zip

5. 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"

6. Delete the zip files / the installation files

7. Create a folder "brainstorm_db" on your Desktop folder

8. 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

9. 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

2. DO NOT add the brainstorm3 folder to your path: Brainstorm will take care of that,

3. Go to the brainstorm3 folder from the Matlab command window,

4. Type "brainstorm" in the Matlab command window and press enter,

5. 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

2. 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

3. 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:

• ?0. Brainstorm architecture

• ?1. First steps

• ?2. Importing individual anatomy

The slides presented during the workshop are available here:

• Francois Tadel

Troubleshooting

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