{{attachment:pittsburgh.gif}}

<<BR>>

= Pittsburgh, USA: March 24-25 =
== Important notes ==
 * Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore we recommend that you bring a laptop with a decent processing capacity, '''4Gb RAM''', a '''64bit''' operating system, and a '''screen larger than 13"'''.
 * We strongly discourage the use of any Windows 32bit computer. The limitations of the memory management may result in lots of "Out of memory" errors that will make the training difficult to follow.
 * You  would 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 Apple MacBooks are perfect for this, but this operation is not always easy to perform on some laptops.
 * Don't forget your '''power adapter'''!
 * Prepare a '''personal dataset''' that you would like to process with Brainstorm during the second day.

== Installation instructions ==
Before  coming to the workshop, you  need to download  the software and the  tutorial dataset from the  Brainstorm website  (150Mb). To streamline troubleshooting during the  session, please save all the  downloaded files '''__on your Desktop__'''.

 1. From the Brainstorm [[http://neuroimage.usc.edu/bst/download.php|Download]] page, log in or create a Brainstorm account
 1. Download the following files to '''your Desktop''' '''folder''':
  * '''Brainstorm software''': <<HTML(<FONT color=red>)>>brainstorm_YYMMDD.zip<<HTML(</FONT>)>>   (60 Mb)
  * '''Tutorial dataset''': <<HTML(<FONT color=red>)>>workshop_pittsburgh.zip<<HTML(</FONT>)>>  (74 Mb)
 1. If you already have Brainstorm, make sure that the  version was released <<HTML(<FONT color=red>)>>'''after March 8th'''<<HTML(</FONT>)>>.
 1. Unzip the two downloaded files on your desktop
 1. Delete the two downloaded zip files
 1. Create a folder "'''brainstorm_db'''" on your '''Desktop '''
 1. Final check: you should have now 3 folders on your desktop:
  * '''brainstorm3''': Program folder, with the source code and the compiled executable
  * '''brainstorm_db''': Brainstorm database (empty)
  * '''workshop_pittsburgh''': Example dataset used during the training session
 1. Run Brainstorm, to make sure it works correctly on your computer (read the following section)

== Running Brainstorm for the first time ==
==== With Matlab ====
 1. Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible
 1. Start Matlab
 1. Do '''NOT '''add brainstorm3 folder to your Matlab path: this will be done automatically
 1. Go to the brainstorm3 folder
 1. Type "brainstorm" in the command window
 1. When asked for the Brainstorm database folder, pick the "brainstorm_db" you have just created

==== Without Matlab ====
 1. The instructions below are valid for the following operating systems:
  * '''Windows''': Any version ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Windows.pdf|details]])
  * '''Linux''': Ubuntu 14.04+, RedHat 6.x+, Debian 7.x, SUSE 11.3+  ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Linux.pdf|details]])
  * '''MacOS''': 10.9.5 (Mavericks), 10.10 (Yosemite) ([[http://www.mathworks.com/support/sysreq/files/SystemRequirements-Release2015b_Macintosh.pdf|details]])
  * If your system is not listed here, try with another version: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]]
 1. Download the '''MCR R2015b (9.0)''' 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
  * __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/R2015b/
  * __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/R2015b/''<<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 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.
  * 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 9.0 folder (ex: /Applications/MATLAB/MCR/v90)
  * Try with another binary release: [[InstallationR2012b|2012b]], [[InstallationR2013b|2013b]], [[InstallationR2014b|2014b]]
 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 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\R2015b"), 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.

== Make sure it works ==
In order to check if Brainstorm works properly or your computer, please follow these instructions:

 * Create a new protocol: Menu File > New protocol.<<BR>>Set the name to "Test", don't change the other default options.
 * In the folder "Default anatomy", double-click successively on the files: MRI, head, cortex_15002V
 * It should open the figures below, make sure they work correctly:
  * Click in the MRI Viewer to move the slices
  * Click+move your mouse in the 3D figure to rotate
  * Zoom in/out with the mouse wheel or the two-finger scroll on MacBook pads
  * The head surface should be transparent, with the brain visible through it
 {{http://neuroimage.usc.edu/brainstorm/WorkshopToronto2015Install?action=AttachFile&do=get&target=test_bst.gif|test_bst.gif|class="attachment"}}

== Bring your own data ==
The second  day will be mostly dedicated to the processing of your own  recordings.  We encourage you to prepare some EEG/MEG/ECoG/sEEG data you would  be  interested in processing in Brainstorm. If you are coming with colleagues, try to organize small groups with similar interests (2-4 people).

The list of file formats that can be read by Brainstorm is available on the [[http://neuroimage.usc.edu/brainstorm/Introduction#Supported_file_formats|Introduction page]]. Please contact us in advance if you are not sure your dataset can be imported in Brainstorm.

If  you are interested in using the subject's MRI for more realistic source  estimation, you would have to process it in advance. You could try  using the following programs: [[Tutorials/LabelFreeSurfer|FreeSurfer]], [[Tutorials/SegBrainVisa|BrainVISA]], [[Tutorials/SegBrainSuite|BrainSuite]]

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