Brainstorm Training Workshop at MIT

General information

• When: Saturday, April 28, 2012 (9am - 5pm)

• Where: MIT Building 32 (Stata Center) Room 141

Requirements

The workshop

• Bring your own laptop (any operating system, with or without Matlab installed) with Brainstorm installed (version of April 20th or later), and the sample dataset (see instructions below).

• Power plugs will be available at each desk.

• Participants encountering issues with the installation process are encouraged to visit the laptop clinics that will be held prior to the Brainstorm training session:

  • April 27 / all day: MIT Bldg 46 Atrium (3rd floor) during the MEG symposium,

  • April 28 @ 8am: MIT Bldg 32, outside room 141,

  • Until then, email us with your questions.

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 (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 Download page, login 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.zip (240 Mb)

   • Matlab Component Runtime (MCR): ONLY if you do not have Matlab installed (300 Mb)

3. Note: if you already have Brainstorm installed, make sure that the version was released after April 18th.

4. Unzip all the zip files
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: Example dataset to be used during the training session

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 follow at least the first half of the the online tutorials:

• ?0. Brainstorm architecture

• ?1. First steps

• ?2. Importing individual anatomy

• ?3. Importing MEG recordings

• ?4. Exploring the recordings

The slides presented during the workshop are available here:

• Sylvain Baillet

• Francois Tadel

Troubleshooting

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

For those who need help prior to the meeting, please come to our laptop clinics:

• April 27 / all day: MIT Bldg 46 Atrium (3rd floor) during the McGovern Institute Annual Symposium

• April 28 @ 8am: MIT Bldg 32, outside room 141