= Installation =
== Sources or binaries ? ==
The distribution of Brainstorm is available in two formats: Matlab source code (.m scripts), and compiled binaries.

If you have a Matlab installation running on your computer or if you can get a licence easily, you should download the source distribution. It will be much easier to make it work, to update, to fix, and you will be able to use the rich Matlab environment to perform custom computation or visualization operations.

If you don't have Matlab, you can use a compiled version if you find one corresponding to your operating system in the ''Download ''section. "Compiled" means processed with the Matlab Compiler Toolbox. It does not produce real native executable code, but requires the Matlab Component Runtime, a library which is freely redistributable and included in the binary distributions. This explains why the compiled version of Brainstorm is over 200Mb.

== Installation steps (Sources) ==
 1. Visit the Register section, create an account, and then go the Download section.
 1. Download the toolbox sources archive.
 1. Unzip it somewhere you usually put program files.
 1. Somewhere else, create an empty folder to store your Brainstorm database (for instance "''brainstorm_database''", or "''brainstorm_protocols''").
  * Do '''not '''create this folder in the '''brainstorm3 program folder'''
  * This directory will be managed completely automatically by Brainstorm
  * '''Never put your original data files''' in this directory: it could prevent Brainstorm to manage it efficiently
  * All the data in Brainstorm database need to be imported via the GUI
 1. Start Matlab, go to the brainstorm3 directory, and type "brainstorm" in the Matlab command window.
  * Do '''not '''add brainstorm3 and subdirectories to your Matlab path, this will be managed automatically.

 1. It should display a nice splash screen and then ask you several things.
 1. Visit the Tutorials section to learn what to do.

== Updating your existing installation (Sources) ==
Brainstorm is improving every day. It is recommended to update the software regularly.

 * Newest versions of Brainstorm should do that automatically. When you start Brainstorm, it checks online if your version is older than a month.<<BR>>To enable / disable those automatic updates, edit the software preferences (File > Set preferences...)
 * You can update Brainstorm manually by selecting the menu '''File > Update Brainstorm''', in the main Brainstorm window.
 * In case those automatic updates do not work, just delete the old brainstorm3 folder, and follow the installations steps again (previous section).
 * Warning: On Linux / Unix / MacOS systems, if the automatic update fails, check that you have the rights to modify the files in brainstorm3 folder.

== Installation steps (Binaries) ==
Coming soon

== Brainstorm folders ==
Some more explanations about files and folders.<<BR>>Brainstorm needs '''different directories''', please try not to put everything at the same place, it won't work:

 * '''Program directory: "brainstorm3"'''<<BR>>It contains all the Matlab .m script files, and has the following architecture:
  * '''doc'''/ :
  * '''java'''/ :
  * '''plugins'''/ :
  * '''defaults/eeg'''/ :
  * '''defaults/anatomy'''/ :
  * '''toolbox'''/:
 * '''Database directory'''<<BR>>Created by the user. Contains all the Brainstorm database files.
 * '''User directory: ".brainstorm"'''<<BR>>Created automatically at Brainstorm startup, in the user directory (home directory on linux, "C:\Documents and Settings\username" on 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
 * '''Original data files''', recordings and anatomies: you can put them wherever you want but not in any of the previous folders.