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| = Installation = == Sources or binaries ? == The distribution of Brainstorm is available in two formats: Matlab source code (.m scripts), and compiled binaries. |
= 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. |
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| If you have a Matlab installation running on your computer or if you can get a licence easily, you should download the source distribution. It will be much easier to make it work, to update, to fix, and you will be able to use the rich Matlab environment to perform custom computation or visualization operations. | <<TableOfContents(2,2)>> |
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| If you don't have Matlab, you can use a compiled version if you find one corresponding to your operating system in the ''Download ''section. "Compiled" means processed with the Matlab Compiler Toolbox. It does not produce real native executable code, but requires the Matlab Component Runtime, a library which is freely redistributable and included in the binary distributions. This explains why the compiled version of Brainstorm is over 200Mb. | == Requirements == ==== 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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| == Installation steps (Sources) == 1. Visit the Register section, create an account, and then go the Download section. 1. Download the toolbox sources archive. 1. Unzip it somewhere you usually put program files. 1. Somewhere else, create an empty folder to store your Brainstorm database (for instance "''brainstorm_database''", or "''brainstorm_protocols''"). * Do '''not '''create this folder in the '''brainstorm3 program folder''' * This directory will be managed completely automatically by Brainstorm * '''Never put your original data files''' in this directory: it could prevent Brainstorm to manage it efficiently * All the data in Brainstorm database need to be imported via the GUI 1. Start Matlab, go to the brainstorm3 directory, and type "brainstorm" in the Matlab command window. * Do '''not '''add brainstorm3 and subdirectories to your Matlab path, this will be managed automatically. |
==== Without Matlab ==== * Matlab Runtime: '''R2022b (9.13)''' * 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-2022b-windows.pdf|Windows]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2022b-linux.pdf|Linux]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2022b-macintosh.pdf|MacOS]] * If your OS is not supported, Brainstorm is available for other versions of the Matlab Runtime: * Recommend versions: [[https://neuroimage.usc.edu/brainstorm/InstallationR2020a|2020a]] or [[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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| 1. It should display a nice splash screen and then ask you several things. 1. Visit the Tutorials section to learn what to do. |
==== 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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| == Updating your existing installation (Sources) == Brainstorm is improving every day. It is recommended to update the software regularly. |
==== New Desktop for Matlab (Matlab > R2023a) ==== * Since release R2023a, Matlab it is possible to use [[https://www.mathworks.com/matlabcentral/fileexchange/119593-new-desktop-for-matlab-beta|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.<<BR>>For the moment, we recommend the use of the "old" Desktop in Matlab. |
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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. |
==== Apple Silicon (Matlab > R2023b) ==== * From release R2023b, [[https://blogs.mathworks.com/matlab/2023/06/22/native-apple-silicon-support-in-the-matlab-simulink-r2023b-pre-release/|Matlab provides native support for Apple Silicon]]. However when Brainstorm runs on Apple silicon, some functions and plugins may not not supported yet.<<BR>>For Apple systems with M1/M2/M3 chips, we recommend to use Matlab < 2023b. |
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| == Installation steps (Binaries) == Coming soon |
* 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|https://neuroimage.usc.edu/forums/t/46848/2]] |
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| == BrainStorm directories == 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: |
== 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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| * '''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. |
1. 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 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. == 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]] ==== Without Matlab ==== 1. Download the '''Runtime R2022b (9.13)''' 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/R2022b/ * __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/R2022b/ ./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 MATLABROOT''<<BR>>MATLABROOT being the Matlab Runtime 9.13 folder (ex: /Applications/MATLAB/Runtime/v913) * 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\MATLAB Runtime\R2022b"), 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]] == 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: [[https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_normalization|Import the subject anatomy]] * Download: [[http://neuroimage.usc.edu/bst/getupdate.php?t=SPM_TPM|SPM_TPM.zip]] * Unzip it to: $HOME/.brainstorm/defaults/spm ==== Anatomy templates ==== * Original tutorial: [[https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy#Changing_the_default_anatomy|Default anatomy]] * Go to the [[https://neuroimage.usc.edu/bst/download.php|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: [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|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 [[https://github.com/brainstorm-tools/brainstorm3/blob/master/toolbox/core/bst_plugin.m#L117|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 [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins#Example:_FieldTrip|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 [[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"''. If instead you would like to receive a copy of all the messages posted on the forum, select the option ''"Enable mailing list mode"''. <<HTML(<CENTER>)>> {{attachment:email_pref1.gif||width="388",height="91"}} {{attachment:email_pref2.gif||width="457",height="461"}} <<HTML(</CENTER>)>> == 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. 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) |
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: R2022b (9.13)
Download for free from the Mathworks website
- If your OS is not supported, Brainstorm is available for other 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.
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
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 R2022b (9.13) 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/R2022b/
Windows: Double-click on brainstorm3.bat
MacOS: Double-click on brainstorm3.command and wait for instructions
Linux: From a terminal, run:
cd brainstorm3/bin/R2022b/ ./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 MATLABROOT
MATLABROOT being the Matlab Runtime 9.13 folder (ex: /Applications/MATLAB/Runtime/v913)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\MATLAB Runtime\R2022b"), 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
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)