|
Size: 1678
Comment:
|
Size: 6413
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Installation = == Installation steps == 1. Get the latest BrainStorm package avaiable at: 1. Unzip the brainstorm3_xxxxxx.zip package 1. If you chose to download the anatomy templates, unzip them in the same directory <<BR>> Example : the files for template "collin27" should be in .../brainstorm3/templates/anatomy/collin27/ 1. Create a folder to store the BrainStorm database anywhere in your home directory (ex: "Protocols" or "brainstorm_protocols")<<BR>> Note: make sure you will have enough disk space avaiable to store all your recordings and analysis files in the folder, ie. some gigabytes... 1. "Protocols" or "brainstorm_protocols" somewhere |
= Installation & Updates = == Requirements == Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX: * 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: '''R2013b (8.2)''' * __Windows__: Any version * __Linux__: Ubuntu 12.04+, RH 6.x, Debian 6.x, SUSE 11.3+ * __MacOS__: MacOSX 10.7.4+ (Lion), 10.8 (Mountain Lion), 10.9 (Mavericks) * For older systems, or if this version doesn't work: [[InstallationR2012b|Read this page]] * More details: [[http://www.mathworks.com/support/sysreq/current_release/index.html?sec=mac|Mathworks website]] 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". 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. == Installation == 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 * __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 == Start Brainstorm == ==== With Matlab ==== |
| Line 9: | Line 38: |
| 1. Go in the .../brainstorm3/ directory 1. Type "brainstorm" at the Matlab command prompt |
1. Do '''NOT '''add brainstorm3 folder to your path: this will be done automatically 1. Go to the brainstorm3 folder 1. Type "brainstorm" in the command window 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. |
| Line 12: | Line 44: |
| == BrainStorm directories == BrainStorm needs three different directories: |
==== Without Matlab ==== 1. Download the '''MCR R2013b (8.2)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]] |
| Line 15: | Line 47: |
| * '''Program directory "brainstorm3"'''<<BR>>It contains all the Matlab .m script files, and has the following architecture: * developers/ : Personal directories of BrainStorm developers. More details... * doc/ : * java/ : * plugins/ : * templates/eeg/ : * templates/anatomy/ : * toolbox/ * '''User directory ".brainstorm"'''<<BR>>Created automatically at BrainStorm startup, in the user directory (home directory under linux, "C:\Documents and Settings\username" under 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 * '''Protocol directory'''<<BR>>Created by the user. Contains all the BrainStorm database files. |
1. Follow the instructions to 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. On MacOSX, if you get errors installing the MCR, you may have to install Oracle Java 7 manually: * Google "download java 7" and follow the instructions * Google "download jdk 7" and follow the instructions (you need both the JRE and JDK) * Open a terminal, cd to the MCR installation folder, and run manually the install program:<<BR>>cd ~/Downloads/MCR_R2013b_maci64_installer/<<BR>>./install -javadir /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home -v * Thank Apple Inc. for making non-Apple platforms so complicated to install 1. Run the program in brainstorm3/bin/R2013b/ * __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/R2013b/ * Make sure that the file "''brainstorm3.command''" is executable:<<BR>>=> chmod a+x brainstorm3.command * Run: ''./brainstorm3.command '' * If nothing happen, run: ''./brainstorm3.command MCR_DIR ''<<BR>>MCR_DIR is where the MCR 8.2 is installed (ex: /Applications/MATLAB/MCR/v82) 1. MacOSX despaired users: if nothing works, you may try running the MCR 2012b: [[http://neuroimage.usc.edu/brainstorm/InstallationR2012b|Read this page]] 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. == 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 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...) * Restart Matlab after updating the software. * Manual updates (Matlab version only): * Menu '''Help ''''''> 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. * Stand-alone 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) * Dowload the latest release of the Brainstorm version * Follow the installation instructions (see above) |
Installation & Updates
Requirements
Brainstorm is available in two distinct forms, both available for Windows, Linux and MacOSX:
- 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: R2013b (8.2)
Windows: Any version
Linux: Ubuntu 12.04+, RH 6.x, Debian 6.x, SUSE 11.3+
MacOS: MacOSX 10.7.4+ (Lion), 10.8 (Mountain Lion), 10.9 (Mavericks)
For older systems, or if this version doesn't work: Read this page
More details: Mathworks website
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".
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.
Installation
Go to the Download page, complete the quick and free registration process
(it helps us keep track of our users' demographics)- Download the latest brainstorm_....zip archive
Unzip it somewhere on your computer, for example:
Windows: Program Files\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
With Matlab
- Start Matlab
Do NOT add brainstorm3 folder to your path: this will be done automatically
- Go to the brainstorm3 folder
- Type "brainstorm" in the command window
- When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created
We recommend you visit the Tutorials pages to learn how to use most features of the software.
Without Matlab
Download the MCR R2013b (8.2) for your operating system: Mathworks website
- Follow the instructions to 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".
- On MacOSX, if you get errors installing the MCR, you may have to install Oracle Java 7 manually:
- Google "download java 7" and follow the instructions
- Google "download jdk 7" and follow the instructions (you need both the JRE and JDK)
Open a terminal, cd to the MCR installation folder, and run manually the install program:
cd ~/Downloads/MCR_R2013b_maci64_installer/
./install -javadir /Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home -v- Thank Apple Inc. for making non-Apple platforms so complicated to install
- Run the program in brainstorm3/bin/R2013b/
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/R2013b/
Make sure that the file "brainstorm3.command" is executable:
=> chmod a+x brainstorm3.commandRun: ./brainstorm3.command
If nothing happen, run: ./brainstorm3.command MCR_DIR
MCR_DIR is where the MCR 8.2 is installed (ex: /Applications/MATLAB/MCR/v82)
MacOSX despaired users: if nothing works, you may try running the MCR 2012b: Read this page
- 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
- When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created
Visit the Tutorials section to learn how to use most features of the software.
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 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...)
- Restart Matlab after updating the software.
- Manual updates (Matlab version only):
Menu Help > 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.
- Stand-alone 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)
- Dowload the latest release of the Brainstorm version
- Follow the installation instructions (see above)