Installation

Requirements

Brainstorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...).

If you have a Matlab licence:

• You can download and run directly the Brainstorm source scripts,

• Using the source distribution will be make the application much easier to install
• Minimum Matlab version: 7.1 (= R14-SP3)
• Minimum Java VM version: 1.5 (To check that: type "ver" at Matlab command prompt)

If you do not have a Matlab licence:

• You can download the Brainstorm binaries corresponding to your operating system.
• The executables are build using the Matlab Compiler (mcc)
• This will require that you also install the Matlab Component Runtime (MCR) on your computer, a freely redistributable library
• MCR is available for download on the website

Sources or binaries ?

You have Matlab installed: download the source code.

You don't have Matlab installed: try to install the MCR and the binaries.

Installation steps (Sources)

1. Visit the Download section, create an account, and follow the indications.

2. Download the latest bst_src_....zip archive
3. Unzip it somewhere you usually put your program files. For example:

   • Windows: C:\Program Files\brainstorm3

   • Linux: /home/username/brainstorm3

   • MacOS: Documents/brainstorm3

4. Create an empty folder "brainstorm_db" to store your Brainstorm database. For example:

   • Windows: C:\Program Files\brainstorm_db

   • Linux: /home/username/brainstorm_db

   • MacOS: Documents/brainstorm_db

5. Read carfully these recommandations about the brainstorm_db folder:

   • Do not create the brainstorm_db folder in the brainstorm3 program folder

   • Never put your original data files in this directory
   • All the data in Brainstorm database need to be imported via the user interface
   • This directory is managed completely automatically by the application, do not move or delete the files it contains by yourself
6. Start Matlab, go to the brainstorm3 directory, and type "brainstorm" in the Matlab command window.

   • Note: Do not add brainstorm3 and subdirectories to your Matlab path, this will be done automatically.

7. Visit the ?Tutorials section to learn what to do next.

Updating your existing installation (Sources)

Brainstorm is improving every day. It is recommended to update the software regularly.

• Newest versions of Brainstorm do that automatically. When you start Brainstorm, it checks online if your version is older than a month.
  To enable / disable those automatic updates, edit the software preferences (File > Set preferences...)

• You can update Brainstorm manually by selecting the menu File > Update Brainstorm, in the main Brainstorm window.

• In case those automatic updates do not work, just delete the old brainstorm3 folder, and follow the installations steps again (previous section).
• Warning: On Linux / Unix / MacOS systems, if the automatic update fails, check that you have the rights to modify the files in brainstorm3 folder.

Installation steps (Binaries)

1. Visit the Download section, create an account, and follow the indications.

2. Download the two binaries bst_bin...zip archive for your operating system.
   

   • One file is the Matlab Component Runtime (MCR)
   • The other file is the compiled application itself.

   • If your operating system is not listed: post a message on the Forum, we will do our best to make it available.

3. Unzip the bst_bin..._MCR.zip file, and execute the MCRInstaller
   

   • This will install the Matlab Runtime Component (MCR) on your computer.

   • Read more about the MCR: Matlab website

4. Unzip the bst_bin...zip file somewhere you usually put your program files. For example:
   

   • Windows: C:\Program Files\brainstorm3
   • Linux: /home/username/brainstorm3

5. Run brainstorm executable:
   

   • Windows: brainstorm3/bin/brainstorm.exe
   • Linux: brainstorm3/bin/run_brainstorm3.sh

6. Visit the ?Tutorials section to learn what to do next.

Brainstorm folders

Some more explanations about files and folders.
Brainstorm needs different directories, please try not to put everything at the same place, it won't work:

• Program directory: "brainstorm3"

  • Contains all the program files: Matlab scripts, Java archives, documentation...
  • No user data in this folder: you can delete it and replace it with a new version, your data will be safe
  • Recommended location:

    • Windows: C:\Program Files\brainstorm3

    • Linux: /home/username/brainstorm3

    • MacOS: Documents/brainstorm3

• Database directory: "brainstorm_db"

  • Created by user.
  • Contains all the Brainstorm database files.
  • Managed automatically by the application: do not move, delete or add files by yourself.
  • Recommended location:

    • Windows: C:\Program Files\brainstorm_db

    • Linux: /home/username/brainstorm_db

    • MacOS: Documents/brainstorm_db

• User directory: ".brainstorm"

  • Created automatically at Brainstorm startup.
  • Contains the database structure and the temporary folders
  • Typical location:

    • Windows: C:\Documents and Settings\username\.brainstorm

    • Linux: /home/username/.brainstorm

  • Contains:

    • brainstorm.mat: Matlab matrix where the Brainstorm options and database structure are stored.

    • tmp/: temporary directory used by some of the Brainstorm functions. Cleaned each time Brainstorm is started

• Original data files:

  • Recordings and anatomies you acquired and you want to process with Brainstorm.

  • Put them wherever you want but not in any of the previous folders.