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| = Installation & Updates = | = 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 available in two distinct forms, both available for Windows, Linux and MacOSX: | ==== 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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| * 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 install of the Matlab Compiler Runtime library ('''MCR'''): [[http://www.mathworks.com/products/compiler/mcr/|Download from Mathworks]] * 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) * If your system is not listed here, try with packages compiled with other versions of Matlab: * Matlab 2012b: [[InstallationR2012b|See instructions]] * Matlab 2013b: [[InstallationR2013b|See instructions]] |
==== Without Matlab ==== * Matlab Runtime: '''R2023a (9.14)''' * 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-2023a-windows.pdf|Windows]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2023a-linux.pdf|Linux]], [[https://fr.mathworks.com/content/dam/mathworks/mathworks-dot-com/support/sysreq/files/system-requirements-release-2023a-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/InstallationR2022b|2022b]], [[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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| 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". | ==== 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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| 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. | ==== 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. ==== 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. * 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 |
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| 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 |
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 1. Unzip it somewhere on your computer, for example: * __Windows__: My documents\brainstorm3 |
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| * '''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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| 1. Do '''NOT '''add brainstorm3 folder to your path: this will be done automatically | 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be automatically done |
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| 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. |
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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| 1. Download the '''MCR R2012b (8.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] | 1. Download the '''Runtime R2023a (9.14)''' 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/R2023a/ * __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/R2023a/ ./brainstorm3.command }}} |
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| 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 * __MacOS__: Double-click on ''brainstorm3.command ''and wait for instructions * If nothing happens, open a terminal and follow the Linux instructions. * __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 '' * If nothing happens, run: ''./brainstorm3.command MCR_DIR''<<BR>>MCR_DIR is where the MCR 8.0 is installed (ex: /Applications/MATLAB/MCR/v80) 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. |
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. 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: [[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 2023a folder (ex: /Applications/MATLAB/Runtime/R2023a) * 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\R2023a"), 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||height="91",width="388"}} {{attachment:email_pref2.gif||height="461",width="457"}} <<HTML(</CENTER>)>> |
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| * 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...) |
* 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) |
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| * Menu '''Help ''''''> Update Brainstorm''', in the main application window. | * Menu '''Update ''''''> Update Brainstorm''', in the main application window. |
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| * Stand-alone version (or in case the above methods do not work for you) | * Standalone version (or in case the above methods do not work for you) |
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| * Download the latest release of the Brainstorm version | * Download the latest release of Brainstorm |
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: R2023a (9.14)
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 R2023a (9.14) 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/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
- 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.
- 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 2023a folder (ex: /Applications/MATLAB/Runtime/R2023a)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\R2023a"), 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)