Differences between revisions 83 and 202 (spanning 119 versions)

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.

Contents

Requirements
Installation
Start Brainstorm
No internet access
Managing emails
Updates

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
- Supported operating systems: Windows, Linux, MacOS
If your OS is not supported, Brainstorm is available for other versions of the Matlab Runtime:
- Recommend versions: ?2020a or 2015b
- See all the versions available at the bottom of the Download page

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.command
- If 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

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)

-  ⇤ ← Revision 83 as of 2013-02-14 15:50:54 → 
  Size: 5583
  Editor: agrippa
  Comment:
+   ← Revision 202 as of 2023-01-27 16:49:21 → ⇥
  Size: 11203
  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= Installation & Updates =
Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX:
+= 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.
 Line 4:
- * An open-source Matlab application (Matlab required)
  * Necessary: Matlab version R2006a''' '''(7.2), or later
  * Optional: Signal Processing Toolbox (for frequency filtering and resampling)
 * A stand-alone Java executable (Matlab not required)
  * Requires the free download of the Matlab runtime library (MCR)
  * __MacOS__: MacOSX version >= 10.6.4 (Snow Leopard), with Apple Java installed ([[http://www.mathworks.com/support/sysreq/current_release/macintosh.html|see link]])
+<<TableOfContents(2,2)>>
-Line 11:
+Line 6:
-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".
+== 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}}
-Line 13:
+Line 12:
-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.
+==== 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/support/requirements/matlab-system-requirements.html|Windows]], [[https://fr.mathworks.com/support/requirements/matlab-linux.html|Linux]], [[https://fr.mathworks.com/support/requirements/matlab-linux.html|MacOS]]
 * If your OS is not supported, Brainstorm is available for other versions of the Matlab Runtime:
  * Recommend versions: [[javascript:void(0);/*1674837668124*/|2020a]] or [[InstallationR2015b|2015b]]
  * See all the versions available at the bottom of the [[https://neuroimage.usc.edu/bst/download.php|Download]] page

==== 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.
-Line 16:
+Line 26:
-. 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
+. 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
-Line 19:
+Line 34:
-  * __Windows__: Program Files\brainstorm3
+  * __Windows__: My documents\brainstorm3
-Line 23:
+Line 38:
-. Create a new folder named e.g., "'''brainstorm_db'''", which will be used by the Brainstorm database. For example:
+. Create a new folder "'''brainstorm_db'''" for the Brainstorm database, for example:
-Line 27:
+Line 42:
+  * '''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.
-Line 31:
+Line 48:
-. Do '''NOT '''add brainstorm3 folder to your path: this will be done automatically
+. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be automatically  done
-Line 34:
+Line 51:
-. 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.
+. 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]]
-Line 38:
+Line 55:
-. Download the '''Matlab Compiler Runtime (MCR)''' corresponding to your operating system. This is a set of libraries that will let you run Brainstorm on your computer without Matlab.<<BR>>Click here: [[http://www.mathworks.com/products/compiler/mcr/index.html|Link to the Mathworks website]].
+. 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]]
-Line 40:
+Line 80:
-. 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 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 MacOS or installing Matlab.
 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 "brainstorm.command" is executable:<<BR>>=> chmod a+x brainstorm.command
   * run ./brainstorm.command
  * __MacOS__: Double-click on brainstorm.command
 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.
+== 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>)>>
-Line 60:
+Line 122:
-  * 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)
-Line 64:
+Line 126:
-  * Menu '''Help ''''''> Update Brainstorm''', in the main application window.
+  * Menu '''Update ''''''> Update Brainstorm''', in the main application window.
-Line 67:
+Line 129:
- * Stand-alone version (or in case the above methods do not work for you)
  * Delete the brainstorm3 folder (it will not delete your database)
  * Dowload the latest release of the Brainstorm executable or its Matlab version
+ * 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

Software

Users

Development

Installation and updates

Requirements

With Matlab

Without Matlab

Hardware recommendations

Installation

Start Brainstorm

With Matlab

Without Matlab

No internet access

SPM linear normalization

Anatomy templates

Plugins

Proxy configuration

Managing emails

Updates