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| = Installation = | = Installation & Updates = |
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| Brainstorm is written in Matlab code only, thus it can run on any operating system supported by Matlab (including Windows, Linux, MacOS...). | Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX: |
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| If you have a Matlab licence: | * An open-source Matlab application (Matlab license required) * Necessary: Any Matlab version >= '''R2006b (7.3) ''' * No specific operating system requirements * Optional: Signal Processing Toolbox (for frequency filtering and resampling) * A stand-alone Java executable (Matlab license not required) * Requires the free download of the Matlab Compiler Runtime library ('''MCR''') * MCR version: '''R2012b (8.0)''' * __Windows__: Any version * __Linux__: Ubuntu 11.10 & 12.04, RH 5.x and 6.x, Debian 6.x, SUSE 11.1+ * __MacOS__: MacOSX 10.6.4+ (Snow Leopard), 10.7 (Lion), 10.8 (Mountain Lion) * More details: [[http://www.mathworks.com/support/sysreq/current_release/index.html?sec=mac|Mathworks website]] |
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| * 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) |
Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommand that you use a computer with a decent processing capacity and a screen larger than 13". |
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| If you do not have a Matlab licence: | 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. |
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| * 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 |
== Installation == 1. Go to the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] page, complete the quick and free registration process <<BR>>(it helps us keep track of our users' demographics) 1. Download the latest brainstorm_....zip archive 1. Unzip it somewhere on your computer, for example:<<BR>> * __Windows__: Program Files\brainstorm3 * __Linux__: /usr/local/brainstorm3 (or ~/brainstorm3 if you are not admin) * __MacOS__: Applications/brainstorm3 |
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| == 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 [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] section, create an account, and follow the indications. 1. Download the latest bst_src_....zip archive 1. Unzip it somewhere you usually put your program files. For example: * __Windows__: C:\Program Files\brainstorm3 * __Linux__: /home/username/brainstorm3 * __MacOS__: Documents/brainstorm3 1. Create an empty folder "'''brainstorm_db'''" to store your Brainstorm database. For example: * __Windows__: C:\Program Files\brainstorm_db |
1. Create a new folder "'''brainstorm_db'''" for the Brainstorm database, for example: * __Windows__: My documents\brainstorm_db |
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| 1. 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 1. 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. 1. Visit the [[Tutorials/TutFirstSteps|Tutorials]] section to learn what to do next. |
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| == Updating your existing installation (Sources) == Brainstorm is improving every day. It is recommended to update the software regularly. |
== Start Brainstorm == ==== With Matlab ==== 1. Start Matlab 1. Do '''NOT '''add brainstorm3 folder to your path: this will be done automatically 1. Go to the brainstorm3 folder 1. Type "brainstorm" in the command window 1. When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created 1. We recommend you visit the [[Tutorials]] pages to learn how to use most features of the software. |
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| * Newest versions of Brainstorm do that automatically. When you start Brainstorm, it checks online if your version is older than a month.<<BR>>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. |
==== Without Matlab ==== 1. Download the '''MCR R2012b (8.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] |
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| == Installation steps (Binaries) == 1. Visit the [[http://neuroimage.usc.edu/brainstorm3_register/download.php|Download]] section, create an account, and follow the indications. 1. Download the two binaries bst_bin...zip archive for your operating system. <<BR>> * 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 [[http://neuroimage.usc.edu/forums/|Forum]], we will do our best to make it available. 1. Unzip the bst_bin..._MCR.zip file, and execute the MCRInstaller<<BR>> * This will install the Matlab Runtime Component (MCR) on your computer. * Read more about the MCR: [[http://www.mathworks.com/access/helpdesk/help/toolbox/compiler/f12-999353.html|Matlab website]] 1. Unzip the bst_bin...zip file somewhere you usually put your program files. For example:<<BR>> * Windows: C:\Program Files\brainstorm3 * Linux: /home/username/brainstorm3 1. Run brainstorm executable:<<BR>> * Windows: brainstorm3/bin/brainstorm.exe * Linux: brainstorm3/bin/run_brainstorm3.sh 1. Visit the [[Tutorials/TutFirstSteps|Tutorials]] section to learn what to do next. |
1. 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".<<BR>>It is not clear on the Mathworks website, but the current MCR requires a version of<<BR>>MacOSX >= 10.6.4 (Snow Leopard), with Apple Java installed ([[http://www.mathworks.com/support/sysreq/current_release/macintosh.html|see link]]).<<BR>>If you can't install the MCR on your Mac, you can chose between: updating MacOSX or installing a full copy of the Matlab environment. 1. Run the program in brainstorm3/bin/R2012b/ * __Windows__: Double-click on brainstorm3.bat * __Linux__: From a terminal, cd brainstorm3/bin/R2012b/ * Make sure that the file "''brainstorm3.command''" is executable:<<BR>>=> chmod a+x brainstorm3.command * run ''./brainstorm3.command '' * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions 1. If you can't get to run properly the compiled version, you can try with the [[InstallationR2013b|MCR 2013b version]]. 1. When you start Brainstorm for the first time on Linux or MacOS, you will be prompted to select the folder where you installed the MCR 1. When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created 1. Visit the [[Tutorials]] section to learn how to use most features of the software. |
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| == Brainstorm folders == Some more explanations about files and folders.<<BR>>Brainstorm needs '''different directories''', please try not to put everything at the same place, it won't work: |
== 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 [[http://neuroimage.usc.edu/forums|forum]], and our experience shows fixes are completed quickly enough to avoid disruptive downtime to our users. |
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| * '''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__'''. |
For these reasons, we recommend that you update Brainstorm regularly using the following options: * Automatic updates (Matlab version only): * When Brainstorm starts, it automatically checks online if a version newer than a month-old is available. * To disable the automatic updates, edit the software preferences accordingly (File > Set preferences...) * Restart Matlab after updating the software. * Manual updates (Matlab version only): * Menu '''Help ''''''> 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. * Stand-alone 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) * Dowload the latest release of the Brainstorm version * Follow the installation instructions (see above) |
Installation & Updates
Requirements
Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX:
- An open-source Matlab application (Matlab license required)
Necessary: Any Matlab version >= R2006b (7.3)
- No specific operating system requirements
- Optional: Signal Processing Toolbox (for frequency filtering and resampling)
- A stand-alone Java executable (Matlab license not required)
Requires the free download of the Matlab Compiler Runtime library (MCR)
MCR version: R2012b (8.0)
Windows: Any version
Linux: Ubuntu 11.10 & 12.04, RH 5.x and 6.x, Debian 6.x, SUSE 11.1+
MacOS: MacOSX 10.6.4+ (Snow Leopard), 10.7 (Lion), 10.8 (Mountain Lion)
More details: Mathworks website
Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommand that you use a computer with a decent processing capacity and a screen larger than 13".
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.
Installation
Go to the Download page, complete the quick and free registration process
(it helps us keep track of our users' demographics)- Download the latest brainstorm_....zip archive
Unzip it somewhere on your computer, for example:
Windows: Program Files\brainstorm3
Linux: /usr/local/brainstorm3 (or ~/brainstorm3 if you are not admin)
MacOS: Applications/brainstorm3
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
With Matlab
- Start Matlab
Do NOT add brainstorm3 folder to your path: this will be done automatically
- Go to the brainstorm3 folder
- Type "brainstorm" in the command window
- When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created
We recommend you visit the Tutorials pages to learn how to use most features of the software.
Without Matlab
Download the MCR R2012b (8.0) for your operating system: Mathworks website
- 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".
It is not clear on the Mathworks website, but the current MCR requires a version of
MacOSX >= 10.6.4 (Snow Leopard), with Apple Java installed (see link).
If you can't install the MCR on your Mac, you can chose between: updating MacOSX or installing a full copy of the Matlab environment.
- Run the program in brainstorm3/bin/R2012b/
Windows: Double-click on brainstorm3.bat
Linux: From a terminal, cd brainstorm3/bin/R2012b/
Make sure that the file "brainstorm3.command" is executable:
=> chmod a+x brainstorm3.commandrun ./brainstorm3.command
MacOS: Double-click on brainstorm3.command and wait for instructions
If you can't get to run properly the compiled version, you can try with the MCR 2013b version.
- When you start Brainstorm for the first time on Linux or MacOS, you will be prompted to select the folder where you installed the MCR
- When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created
Visit the Tutorials section to learn how to use most features of the software.
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 automatically checks online if a version newer than a month-old is available.
To disable the automatic updates, edit the software preferences accordingly (File > Set preferences...)
- Restart Matlab after updating the software.
- Manual updates (Matlab version only):
Menu Help > 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.
- Stand-alone 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)
- Dowload the latest release of the Brainstorm version
- Follow the installation instructions (see above)