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| = Installation = | = 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. <<TableOfContents(2,2)>> |
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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...). | ==== With Matlab ==== * Matlab >= '''R2009b (7.9)''' * Optional toolboxes: Signal Processing, Parallel Processing * For smoother graphics, we recommend Matlab >=''' R2014b''': <<BR>><<BR>> {{attachment:matlab_version_render.gif}} |
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| If you have a Matlab licence: | ==== Without Matlab ==== * Matlab Runtime: '''R2020a (9.8)''' * Download for free from the [[https://www.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]] * Supported operating systems: [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2020a-windows.pdf|Windows]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2020a-linux.pdf|Linux]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2020a-macintosh.pdf|MacOS]] * If your OS is not supported, Brainstorm is available for older versions of the Matlab Runtime: * Recommend version: [[InstallationR2015b|2015b]] * See all the versions available at the bottom of the [[https://neuroimage.usc.edu/bst/download.php|Download]] page |
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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) |
==== 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. |
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| If you do not have a Matlab licence: | == Installation == 1. Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page, complete the quick and free registration process. 1. If you don't receive the confirmation email, please check your '''spam folder'''. 1. 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 |
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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 |
1. Unzip it somewhere on your computer, for example:<<BR>> * __Windows__: My documents\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. |
1. 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. 1. 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. |
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| You don't have Matlab installed: try to install the MCR and the binaries. | == Start Brainstorm == ==== With Matlab ==== 1. Start Matlab 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be automatically done 1. Go to the brainstorm3 folder 1. Type "brainstorm" in the command window 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created 1. Follow all the introduction tutorials in the section "Get started": [[Tutorials]] |
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| == 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 sources .zip archive. 1. Unzip it somewhere you usually put your program files. For example: |
==== Without Matlab ==== 1. Download the '''Runtime R2020a (9.8)''' for your operating system: [[https://fr.mathworks.com/products/compiler/matlab-runtime.html|Mathworks website]] 1. 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 1. Run the program in brainstorm3/bin/R2020a/ * __Windows__: Double-click on ''brainstorm3.bat'' * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions * __Linux__: From a terminal, run:<<BR>>''cd brainstorm3/bin/R2020a/''<<BR>>''./brainstorm3.command '' 1. 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. * Other MacOS issues are discussed on the forum: [[https://neuroimage.usc.edu/forums/t/support-for-macos-bigsur/26890|Support for MacOS BigSur]]. 1. 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:<<BR>>''chmod a+x brainstorm3.command'' * If nothing happens, run: <<BR>>''./brainstorm3.command MCR_DIR''<<BR>>MCR_DIR being the MCR 9.8 folder (ex: /Applications/MATLAB/MCR/v98) * Try with another binary release: See at the bottom of the [[https://neuroimage.usc.edu/bst/download.php|Download]] page 1. 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\R2020a"), save the file, and try to execute it again. 1. If the startup process seems very long, try pressing ENTER after clicking on the terminal window. 1. On Linux or MacOS, you may be asked to select the folder where you installed the Runtime. 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created. 1. Follow all the introduction tutorials in the section "Get started": [[Tutorials]] |
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| * Windows: C:\Program Files\brainstorm3 * Linux: /home/username/brainstorm3 * MacOS: Documents/brainstorm3 |
== 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. |
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| 1. 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 * 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. |
If you would like to stop receiving these emails, log into the [[https://neuroimage.usc.edu/forums/|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"''. |
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| 1. It should display a nice splash screen and then ask you several things. 1. Visit the Tutorials section to learn what to do. |
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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| == Updating your existing installation (Sources) == Brainstorm is improving every day. It is recommended to update the software regularly. |
<<HTML(<CENTER>)>> {{attachment:email_pref1.gif||width="388",height="91"}} |
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| * Newest versions of Brainstorm should 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. |
{{attachment:email_pref2.gif||width="457",height="461"}} <<HTML(</CENTER>)>> |
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| == Installation steps (Binaries) == Coming soon |
== 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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| == 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: |
For these reasons, we recommend that you update Brainstorm regularly using the following options: |
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| * '''Program directory: "brainstorm3"'''<<BR>>It contains all the Matlab .m script files, and has the following architecture: * '''doc'''/ : * '''java'''/ : * '''plugins'''/ : * '''defaults/eeg'''/ : * '''defaults/anatomy'''/ : * '''toolbox'''/: * '''Database directory'''<<BR>>Created by the user. Contains all the Brainstorm database files. * '''User directory: ".brainstorm"'''<<BR>>Created automatically at Brainstorm startup, in the user directory (home directory on linux, "C:\Documents and Settings\username" on Windows). * 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 can put them wherever you want but not in any of the previous folders. |
* 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) |
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: Signal Processing, Parallel Processing
For smoother graphics, we recommend Matlab >= R2014b:
Without Matlab
Matlab Runtime: R2020a (9.8)
Download for free from the Mathworks website
- If your OS is not supported, Brainstorm is available for older versions of the Matlab Runtime:
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.
Installation
Go to the Download page, complete the quick and free registration process.
If you don't receive the confirmation email, please check your spam folder.
- 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
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
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.
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
- Start Matlab
Do NOT add brainstorm3 folder to your Matlab path: this will be automatically done
- Go to the brainstorm3 folder
- Type "brainstorm" in the command window
- When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created
Follow all the introduction tutorials in the section "Get started": Tutorials
Without Matlab
Download the Runtime R2020a (9.8) for your operating system: Mathworks website
- 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
- Run the program in brainstorm3/bin/R2020a/
Windows: Double-click on brainstorm3.bat
MacOS: Double-click on brainstorm3.command and wait for instructions
Linux: From a terminal, run:
cd brainstorm3/bin/R2020a/
./brainstorm3.command
- 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.
Other MacOS issues are discussed on the forum: Support for MacOS BigSur.
- 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.commandIf nothing happens, run:
./brainstorm3.command MCR_DIR
MCR_DIR being the MCR 9.8 folder (ex: /Applications/MATLAB/MCR/v98)Try with another binary release: See at the bottom of the Download page
- 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\R2020a"), save the file, and try to execute it again.
- If the startup process seems very long, try pressing ENTER after clicking on the terminal window.
- On Linux or MacOS, you may be asked to select the folder where you installed the Runtime.
- When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.
Follow all the introduction tutorials in the section "Get started": Tutorials
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)