Binary installation: R2016b

This stand-alone version is currently not distributed in the main package.
You can download it separately:


Operating system

Matlab Compiler Runtime


  1. Download the latest archive
  2. Unzip it somewhere on your computer, for example:
    • Windows: My documents\brainstorm3

    • Linux: /usr/local/brainstorm3 (or ~/brainstorm3 if you are not admin)

    • MacOS: Applications/brainstorm3

  3. Create a new folder "brainstorm_db" for the Brainstorm database, for example:

    • Windows: My documents\brainstorm_db

    • Linux: /home/username/brainstorm_db

    • MacOS: Documents/brainstorm_db

Start Brainstorm

  1. Download the MCR R2016b (9.1) for your operating system: Mathworks website

  2. 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".

  3. Run the program in brainstorm3/bin/R2016b/
    • Windows: Double-click on brainstorm3.bat

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

    • Linux: From a terminal, run:
      cd brainstorm3/bin/R2016b/

  4. 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 unindentified developer". This message would appear for all the programs that were not downloaded from the Apple appstore. 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 9.1 folder (ex: /Applications/MATLAB/MCR/v91)

    • Try with another binary release: 2012b, 2013b, 2014b, 2015b, 2016a, 2017a

  5. Troubleshooting for Windows:
    • Your current user may not have the necessary privileges. If are an adminstrator 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\R2016b"), save the file, and try to execute it again.

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


The automatic updates do not work with the stand-alone versions, follow this procedure:

InstallationR2016b (last edited 2017-06-14 18:04:23 by FrancoisTadel)