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| = Installation: MCR 2012b = On MacOSX, the transition between Apple Java and Oracle Java is a terrible mess. It makes it very difficult to run correctly the compiled version of Brainstorm. This page provides instructions for running it with Matlab 2012b, to ensure the compatibility with older MacOSX systems that run Apple Java 6. |
= Binary installation: R2012b = This stand-alone version is currently not distributed in the main package.<<BR>>You can download it separately: [[http://neuroimage.usc.edu/bst/download.php|bst_bin_R2012b_YYMMDD.zip]] |
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| Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX: | ==== Operating system ==== * '''Windows''': Any version ([[http://www.mathworks.com/support/sysreq/release2012b/index.html|details]]) * '''Linux''': Ubuntu 11.10 & 12.04, !RedHat 5.x and 6.x, Debian 6.x, SUSE 11.1+ ([[http://www.mathworks.com/support/sysreq/release2012b/linux.html|details]]) * '''MacOS''': 10.6.4+ (Snow Leopard), 10.7 (Lion), 10.8 (Mountain Lion) ([[http://www.mathworks.com/support/sysreq/release2012b/macintosh.html|details]]) |
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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 free download of the Matlab Compiler Runtime library ('''MCR''') * MCR version: '''R2012b (8.0)''' * Windows: Any version * Linux: Ubuntu 11.10 & 12.04, RH 5.x and 6.x, Debian 6.x, SUSE 11.1+ * MacOS: MacOSX 10.6.4+ (Snow Leopard), 10.7 (Lion), 10.8 (Mountain Lion) * More details: [[http://www.mathworks.com/support/sysreq/release2012b/macintosh.html|Mathworks website]] |
==== Matlab Compiler Runtime ==== * '''MCR version''': R2012b (8.0) * Download for free from the [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] == Installation == 1. Download the latest bst_bin_R2012b_....zip archive 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 |
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| ==== Without Matlab ==== 1. Download the '''Matlab Compiler Runtime (MCR)''' corresponding to your operating system, version '''2012b''' (v8.0). This is a set of libraries that will let you run Brainstorm on your computer without Matlab. Click here: [[http://www.mathworks.com/products/compiler/mcr/index.html|Link to the Mathworks website]]. |
1. Download the '''MCR R2012b (8.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] 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" 1. Run the program in brainstorm3/bin/R2012b/ * __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/R2012b/''<<BR>>''./brainstorm3.command '' 1. Troubleshooting for MacOS or Linux: * On recent versions of MacOS, you may get an error message "Application can't be opened because it is from an unindentified developer". This message would appear for all the programs that were not downloaded from the Apple appstore. To go around this verification: right-click on the application > Open, then click on the Open button. * 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 is the MCR 8.0 folder (ex: /Applications/MATLAB/MCR/v80) * Try with another binary release: [[InstallationR2013b|Matlab 2013b]], [[InstallationR2014a|Matlab 2014a]], [[InstallationR2014b|Matlab 2014b]] 1. Troubleshooting for Windows: * Your current user may not have the necessary privileges. If are an adminstrator 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 MCR are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the MCR or Matlab folder, right-click on ''brainstorm3.bat'' > Edit. Fill the second line of the script (Example: @SET MATLABROOT="C:\Program Files\MATLAB\R2014b"), save the file, and try to execute it again. 1. On Linux or MacOS, you may be asked to select the folder where you installed the MCR. 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created. 1. Follow all the 12+3 introduction tutorials: [[Tutorials]] |
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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". 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]]). If you can't install the MCR on your Mac, you can chose between: updating MacOSX or installing a full copy of the Matlab environment. 1. Run the program in brainstorm3/bin/R2012b/ * Windows: Double-click on brainstorm3.bat * Linux: From a terminal, cd brainstorm3/bin/R2012b/ * Make sure that the file "''brainstorm3.command''" is executable: => chmod a+x brainstorm3.command * run ''./brainstorm3.command '' * MacOS: Double-click on ''brainstorm3.command ''and wait for instructions 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 [[http://neuroimage.usc.edu/brainstorm/Tutorials|Tutorials]] section to learn how to use most features of the software. |
== Updates == The automatic updates do not work with the stand-alone versions, follow this procedure: * Delete the brainstorm3 folder (don't worry, it will not delete your database) * Download the latest release of the Brainstorm version * Follow the installation instructions (see above) |
Binary installation: R2012b
This stand-alone version is currently not distributed in the main package.
You can download it separately: bst_bin_R2012b_YYMMDD.zip
Requirements
Operating system
Windows: Any version (details)
Linux: Ubuntu 11.10 & 12.04, RedHat 5.x and 6.x, Debian 6.x, SUSE 11.1+ (details)
MacOS: 10.6.4+ (Snow Leopard), 10.7 (Lion), 10.8 (Mountain Lion) (details)
Matlab Compiler Runtime
MCR version: R2012b (8.0)
Download for free from the Mathworks website
Installation
- Download the latest bst_bin_R2012b_....zip archive
- 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
Start Brainstorm
Download the MCR R2012b (8.0) for your operating system: Mathworks website
- Install the MCR:
Windows: Double-click on the .exe and follow the instructions
Linux: From a terminal, unzip .zip, then run ./install
MacOS: Click on the zip file to unzip it, then click on "InstallForMacOSX"
- Run the program in brainstorm3/bin/R2012b/
Windows: Double-click on brainstorm3.bat
MacOS: Double-click on brainstorm3.command and wait for instructions
Linux: From a terminal, run:
cd brainstorm3/bin/R2012b/
./brainstorm3.command
- Troubleshooting for MacOS or Linux:
On recent versions of MacOS, you may get an error message "Application can't be opened because it is from an unindentified developer". This message would appear for all the programs that were not downloaded from the Apple appstore. To go around this verification: right-click on the application > Open, then click on the Open button.
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 is the MCR 8.0 folder (ex: /Applications/MATLAB/MCR/v80)Try with another binary release: Matlab 2013b, ?Matlab 2014a, Matlab 2014b
- Troubleshooting for Windows:
Your current user may not have the necessary privileges. If are an adminstrator 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 MCR are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the MCR or Matlab folder, right-click on brainstorm3.bat > Edit. Fill the second line of the script (Example: @SET MATLABROOT="C:\Program Files\MATLAB\R2014b"), save the file, and try to execute it again.
- On Linux or MacOS, you may be asked to select the folder where you installed the MCR.
- When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created.
Follow all the 12+3 introduction tutorials: Tutorials
Updates
The automatic updates do not work with the stand-alone versions, follow this procedure:
- Delete the brainstorm3 folder (don't worry, it will not delete your database)
- Download the latest release of the Brainstorm version
- Follow the installation instructions (see above)