Seattle: June 21, 2013

Important notes

Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommand that you bring a laptop with a decent processing capacity and a screen larger than 12".

You would also 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 scrolling operation. A mouse wheel or the "two-finger move" on MacBooks are perfect for this, but this operation is not always easy to perform on some laptops.

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

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_fullday.zip (241 Mb)

3. Note: if you already have Brainstorm installed, make sure that the version was released
   after June 10th.

4. Unzip the two zip files
5. Delete the zip files / the installation files

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

7. 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_fullday: Example dataset to be used during the training session

8. 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. Download the Matlab Compiler Runtime (MCR), version R2012b, corresponding to your operating system. This is a set of libraries that will let you run Brainstorm on your computer without Matlab.
   Click here: Link to the Mathworks website.

2. Important note for Mac users:
   It is not clear on the Mathworks website, but the current MCR requires a version of MacOSX >= 10.6.4 (Snow Leopard), with Apple Java installed (see link).
   If you can't install the MCR on your Mac, you can chose between: updating MacOS, installing Matlab, or borrowing another laptop for the workshop.

3. Follow the instructions to install the MCR:

   • 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"

4. Run the executable file located in brainstorm3/bin/R2012b/

   • Windows: Double-click on brainstorm3.bat

   • Linux: From a terminal, cd brainstorm3/bin/R2012b/

     • Make sure that the file brainstorm3.command is executable:
       => chmod a+x brainstorm3.command

     • run ./brainstorm3.command

   • MacOS: Double-click on brainstorm3.command and wait for instructions.

5. 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

6. 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:

1. ?Brainstorm architecture

2. ?First steps

3. ?Importing individual anatomy

Troubleshooting

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