Installation and updates

Brainstorm is available in two forms: an open-source Matlab application (Matlab license required) and a standalone Java executable (free). Both are available for download in the same package.

Requirements

With Matlab

• Matlab >= R2009b (7.9)

• Optional toolboxes:
  • Image Processing
  • Optimization
  • Parallel Computing
  • Signal Processing
  • Statistics and Machine Learning
  • Wavelet Toolbox

• For smoother graphics, we recommend Matlab >= R2014b:
  
  

Without Matlab

• Matlab Runtime: R2023a (9.14)

  • Download for free from the Mathworks website

  • Supported operating systems: Windows, Linux, MacOS

• If your OS is not supported, Brainstorm is available for other versions of the Matlab Runtime:

  • Recommend versions: 2022b, 2020a or 2015b

  • See all the versions available at the bottom of the Download page

Hardware recommendations

• Screen: Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommend that you use a computer with a decent processing capacity and a screen larger than 13".

• Mouse: You would also add to your comfort by using an external mouse instead of your laptop pad. 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.

• Memory: Brainstorm can work with a limited amount of memory, it will only restrict the loading of larger files. However, you are strongly advised to work with a 64bit operating system. Computers running a Windows 32bit system may run into a lot of "Out of memory" errors.

New Desktop for Matlab (Matlab > R2023a)

• Since release R2023a, Matlab it is possible to use a beta version of a new Desktop Matlab (this is not the default, it needs to be added as Add-On). This new Desktop has not been fully tested in Brainstorm and could lead to slower figures and graphic bugs.
  For the moment, we recommend the use of the "old" Desktop in Matlab.

Apple Silicon (Matlab > R2023b)

• From release R2023b, Matlab provides native support for Apple Silicon. However when Brainstorm runs on Apple silicon, some functions and plugins may not not supported yet.
  For Apple systems with M1/M2/M3 chips, we recommend to use Matlab < 2023b.

• Also, for Matlab with native support for Apple Silicon, you may need to install Java8, and setup Matlab to use this version of Java. See the steps in this post: https://neuroimage.usc.edu/forums/t/46848/2

Installation

1. Go to the Download page, complete the quick and free registration process.

2. If you don't receive the confirmation email, please check your spam folder.

3. Download one of the latest archive:

   • Source: brainstorm_yymmdd_src.zip - For execution within Matlab

   • Binary: brainstorm_yymmdd_bin.zip - Compiled version with no Matlab license required

   • Source + binary: brainstorm_yymmdd.zip - Everything in the same zip file

4. 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

5. 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

   • Warning: Never create this folder inside the program folder (brainstorm3), it would get deleted when updating Brainstorm.

6. Set up a regular backup for your brainstorm_db folder, like you would do for any work you do on your computer. Losing hundreds of hours of work because of a wrong manipulation or a disk failure is common, but easy to avoid.

Start Brainstorm

With Matlab

1. Start Matlab

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

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

6. Follow all the introduction tutorials in the section "Get started": Tutorials

Without Matlab

1. Download the Runtime R2023a (9.14) for your operating system: Mathworks website

2. Install the Matlab Runtime:

   • 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

3. Run the program in brainstorm3/bin/R2023a/

   • Windows: Double-click on brainstorm3.bat

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

   • Linux: From a terminal, run:
     

     • cd brainstorm3/bin/R2023a/
       ./brainstorm3.command

4. Troubleshooting for MacOS:

   • 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. It is now saved as an exception to your security settings, and you can open it at any time by double-clicking on it.

   • Other MacOS issues are discussed on the forum: Support for MacOS BigSur.

5. Troubleshooting for MacOS or Linux:

   • Some Linux Mint users have reported having interface issues, changing the graphical theme of their OS fixed this problem.

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

     • Some MacOS users have reported the error message "The file brainstorm3.command could not be executed because you do not have appropriate access privileges." Running the command above should solve it.

   • If nothing happens, run:
     ./brainstorm3.command MATLABROOT
     MATLABROOT being the Matlab Runtime 2023a folder (ex: /Applications/MATLAB/MATLAB_Runtime/R2023a)

   • Try with another binary release: See at the bottom of the Download page

6. Troubleshooting for Windows:

   • Your current user may not have the necessary privileges. If 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 Runtime are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the Runtime or Matlab folder, right-click on brainstorm3.bat > Edit. Fill the second line of the script (Example: @SET "MATLABROOT=C:\Program Files\MATLAB\MATLAB Runtime\R2023a"), save the file, and try to execute it again.

7. If the startup process seems very long, try pressing ENTER after clicking on the terminal window.
8. On Linux or MacOS, you may be asked to select the folder where you installed the Runtime.
9. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.

10. Follow all the introduction tutorials in the section "Get started": Tutorials

No internet access

For some specific tasks, Brainstorm needs to download and install additional files and plugins. On a computer with no internet connectivity (e.g. at a hospital), you need to download manually these extra files on a different computer, then copy them to the computer where Brainstorm is installed.

SPM linear normalization

• Original tutorial: Import the subject anatomy

• Download: SPM_TPM.zip

• Unzip it to: $HOME/.brainstorm/defaults/spm

Anatomy templates

• Original tutorial: Default anatomy

• Go to the Download page

• Download the zip corresponding to the template you need
• Copy it without unzipping it to the folder: $HOME/.brainstorm/defaults/anatomy

Plugins

• Original tutorial: Plugins

• Check the list of available plugins in the tutorial, try to download it manually from the reference website.

• If you can't find any way to download the plugin, check directly for the field URLzip in the function bst_plugin.m.

• Unzip the downloaded file anywhere outside of the Brainstorm folders.

• In the Plugins menu, select the menu Custom install > Select installation folder. See example.

Proxy configuration

• In some cases, the workstation has access to the internet, but it appears that Matlab and Brainstorm don't. If the workstation accesses the web through a proxy, you may have to configure Matlab manually to use it.

• Matlab documentation: https://www.mathworks.com/help/matlab/import_export/proxy.html

Managing emails

After creating a new account, you will start receiving by email a weekly digest of the activity on the Brainstorm forum: questions from users, methodological discussions and bug reports.

If you would like to stop receiving these emails, log into the forum, go to your email preferences, and disable the option "When I don’t visit here, send me an email summary of popular topics and replies".

If instead you would like to receive a copy of all the messages posted on the forum, select the option "Enable mailing list mode".

Updates

Brainstorm is quickly improving and evolving. We have chosen not to go through a stable-release policy but rather, we established a quick and easy way to update the software seamlessly for you. Although this approach has its shares of risks of possibly seeing new bugs emerging from the most recent update, it has the great advantage of being dynamic and of rapidly disseminating new, important features. We encourage our users to report bugs through our forum, and our experience shows fixes are completed quickly enough to avoid disruptive downtime to our users.

For these reasons, we recommend that you update Brainstorm regularly using the following options:

• Automatic updates (Matlab version only):
  • When Brainstorm starts, it checks online if a version newer than a month-old is available.

  • To disable the automatic updates, edit the software preferences (File > Edit preferences)

  • Restart Matlab after updating the software.
• Manual updates (Matlab version only):

  • Menu Update > Update Brainstorm, in the main application window.

  • If it doesn't work: check that you have the rights to write in the brainstorm3 folder.
  • Restart Matlab after updating the software.
• Standalone version (or in case the above methods do not work for you)
  • Delete the brainstorm3 folder (it will not delete your database, which is in your user folder)
  • Download the latest release of Brainstorm
  • Follow the installation instructions (see above)