Differences between revisions 7 and 18 (spanning 11 versions)

Aarhus, Denmark: December 10, 2013

Important notes

Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommand that you bring a laptop with a decent processing capacity and a screen larger than 12".
You would also add to your comfort by bringing an external mouse. 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.
Don't forget your power adapter...

Requirements

Before installing Brainstorm, you need to install either Matlab or the Matlab Compiler Runtime (MCR) library.

With a Matlab license: No operating system restrictions, any Matlab version >= R2007b (7.5)
Without Matlab: You need to be able to install the MCR R2012b (8.2):
- 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: Mathworks website

For installing the MCR, those operating systems constrains can be very annoying. Please consider this problem in advance because you may need to upgrade your system before coming to the workshop. If you can't install the MCR on your laptop, you can chose between:

Upgrading MacOSX or your Linux distribution,
Installing Matlab (any version),
Borrowing another laptop for the workshop.

Installation instructions

Before coming to the workshop, you need to download the software and the tutorial dataset from the Brainstorm website (300 to 650Mb). It requires a free registration for demographics purposes. To streamline troubleshooting and instructions during the session, please save all the downloaded files on your Desktop.

From the Brainstorm Download page, log in or create a Brainstorm account (registration is free)
You will then be able to download the following files to your Desktop folder:
- Brainstorm software: brainstorm_YYMMDD.zip (45 Mb)
- Tutorial dataset: sample_workshop_fullday.zip (250 Mb)
Note: if you already have Brainstorm installed, make sure that the version was released
after November 25th.
Unzip the two zip files
Delete the zip files / the installation files
Create a folder "brainstorm_db" on your Desktop folder
Final check: you should have now 3 folders on your Desktop:
- brainstorm3: Program folder, with the Matlab source code and the compiled executable
- brainstorm_db: Folder for the Brainstorm database (empty)
- sample_workshop_fullday: Example dataset to be used during the training session
Now run Brainstorm, to make sure it starts fine (read carefully the following section)

Running Brainstorm for the first time

With Matlab

Start Matlab
DO NOT add the brainstorm3 folder to your path: Brainstorm will take care of that,
Go to the brainstorm3 folder from the Matlab command window,
Type "brainstorm" in the Matlab command window and press enter,
When asked for the location of the Brainstorm database folder, pick the folder "brainstorm_db" you have just created on the Desktop.

Without Matlab

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".
  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 (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.
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:
    => chmod a+x brainstorm3.command
  - Run: ./brainstorm3.command
  - If nothing happens, run: ./brainstorm3.command MCR_DIR
    MCR_DIR is where the MCR 8.0 is installed (ex: /Applications/MATLAB/MCR/v80)
If you can't get to run properly the compiled version, you can try with the MCR 2013b version.
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 on your Desktop.

Getting ready for the workshop

In order to make sure that Brainstorm works properly, and to get more familiar with the software, we recommend that you read and follow at least the first three online tutorials:

?Brainstorm architecture
?First steps
?Importing individual anatomy

Troubleshooting

For any technical problem, please contact Francois Tadel ( francois.tadel@mcgill.ca )

-  ⇤ ← Revision 7 as of 2013-11-22 15:40:16 → 
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+   ← Revision 18 as of 2016-10-26 19:46:00 → ⇥
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  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
- * You would also add to your comfort by bringing an '''external mouse'''. 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.
+ * You would also add to your comfort by bringing an '''external mouse'''. 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.
 Line 10:
- * '''With a Matlab license''': No operating system restrictions, any Matlab version >= '''R2006b '''(7.3)
 * '''Without Matlab''': You need to be able to install the '''MCR R2013b''' (8.2):
+ * '''With a Matlab license''': No operating system restrictions, any Matlab version >= '''R2007b '''(7.5)
 * '''Without Matlab''': You need to be able to install the '''MCR R2012b''' ('''8.2'''):
 Line 13:
-  * __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)
  * Note that Linux and MacOSX need '''recent systems '''
  * More details: [[http://www.mathworks.com/support/sysreq/current_release/index.html?sec=mac|See the Mathworks website]]
+  * __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/current_release/index.html?sec=mac|Mathworks website]]
-Line 31:
+Line 30:
-. Note: if you already have Brainstorm installed, make sure that the  version was released<<BR>><<HTML(<FONT color=red>)>>'''after November 23th'''<<HTML(</FONT>)>>.
+. Note: if you already have Brainstorm installed, make sure that the  version was released<<BR>><<HTML(<FONT color=red>)>>'''after November 25th'''<<HTML(</FONT>)>>.
-Line 50:
+Line 49:
-. Download the '''MCR R2013b (8.2)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]]
 1. Follow the instructions to install the MCR:
+. Download the '''MCR R2012b (8.0)''' for your operating system: [[http://www.mathworks.com/products/compiler/mcr/|Mathworks website]]

 1. Install the MCR:
 Line 54:
-  * __MacOS__: Click on the zip file to unzip it, then click on "InstallForMacOSX"
 1. Run the executable file located in ''brainstorm3/bin/R2013b/ ''
  * __Windows__: Double-click on ''brainstorm3.bat''
  * __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''
  * __MacOS__: Double-click on ''brainstorm3.command'' and wait for instructions.
+  * __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]].

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