Brainstorm Workshop (Biomag 2012)

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_biomag.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 August 17th.

4. Unzip all the zip files
   But do not unzip the file Workshop.zip in the folder sample_workshop_biomag.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_biomag: 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 )