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.

Contents

  1. Requirements
  2. Installation
  3. Start Brainstorm
  4. No internet access
  5. Managing emails
  6. Updates

Requirements

With Matlab

Without Matlab

Hardware recommendations

New Desktop for Matlab (Matlab > R2023a)

Apple Silicon (Matlab > R2023b)

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

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

Anatomy templates

Plugins

Proxy configuration

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".

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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:

Installation (last edited 2024-12-04 22:06:36 by ChinmayChinara)