Sydney, Australia: December 11-12, 2019

Important notes

Installation instructions

Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (330Mb). To streamline troubleshooting 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. Download the following files to your Desktop folder:

    • Brainstorm software: (75 Mb)

    • Tutorial dataset: (330 Mb)

  3. If you already have Brainstorm, make sure that the version was released after November 18th.

  4. Unzip the two downloaded files on your desktop
  5. Delete the two downloaded zip files
  6. Create a folder "brainstorm_db" on your Desktop

  7. Final check: you should have now 3 folders on your desktop:
    • brainstorm3: Program folder, with the source code and the compiled executable

    • brainstorm_db: Brainstorm database (empty)

    • sample_introduction: Example dataset used during the training session

  8. Start Brainstorm (see following section)
  9. Select the menu Help > Workshop preparation.

  10. Follow the instructions: when you see the 3D figure, make sure you see both a transparent head surface and a brain surface. Try to rotate the view with your mouse, and zoom in and out with the mouse wheel.


Running Brainstorm for the first time

  1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible

  2. Start Matlab
  3. Do NOT add brainstorm3 folder to your Matlab path: this will be done automatically

  4. Go to the brainstorm3 folder
  5. Type "brainstorm" in the command window
  6. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created

Without Matlab

  1. The instructions below are valid for the following operating systems:
  2. Download the MCR R2015b (9.0) for your operating system: Mathworks website

  3. Install the MCR:
    • Windows: Double-click on the .exe and follow the instructions

    • MacOS: Click on the zip file to unzip it, then click on "InstallForMacOSX"

    • Linux: From a terminal, unzip .zip, then run ./install

  4. Run the program in brainstorm3/bin/R2015b/
    • Windows: Double-click on brainstorm3.bat

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

    • Linux: From a terminal, run:
      cd brainstorm3/bin/R2015b/

  5. Troubleshooting for MacOS or Linux:
    • On recent versions of MacOS, you may get an error message "Application can't be opened because it is from an unidentified developer". This message would appear for all the programs that were not downloaded from the Apple app-store. To go around this verification: right-click on the application > Open, then click on the Open button.

    • From a terminal, make sure that the file "brainstorm3.command" is executable:
      chmod a+x brainstorm3.command

    • If nothing happens, run:
      ./brainstorm3.command MCR_DIR
      MCR_DIR is the MCR 9.0 folder (ex: /Applications/MATLAB/MCR/v90)

    • Try with another binary release: 2012b, 2013b, 2014b, 2016a, 2016b, 2017a...

  6. Troubleshooting for Windows:
    • Your current user may not have the necessary privileges. If you are an administrator for your computer, you can do the following: right-click on brainstorm3.bat > Run as administrator.

    • If you are not the administrator of your computer and Matlab or the MCR are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the MCR or Matlab folder, right-click on brainstorm3.bat > Edit. Fill the second line of the script (Example: @SET MATLABROOT="C:\Program Files\MATLAB\R2015b"), save the file, and try to execute it again.

  7. On Linux or MacOS, you may be asked to select the folder where you installed the MCR.
  8. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.


For any technical problem, please contact Martin Cousineau ( )

WorkshopSydney2019Install (last edited 2019-11-20 19:56:07 by ?MartinCousineau)