Tutorial 1: Create a new protocol

Authors: Francois Tadel, Sylvain Baillet

Brainstorm folders

Brainstorm needs different directories to work properly. If you put everything in the same folder, you would run into many problems. Try to understand this organization before creating a new database.


1. Program directory: "brainstorm3"


2. Database directory: "brainstorm_db"


3. User directory: ".brainstorm"


4. Original data files:

Starting Brainstorm for the first time

  1. If you haven't read in the installation instructions, do it now: Installation.

  2. Start Brainstorm from Matlab or with the compiled executable.

    BST> Starting Brainstorm:
    BST> =================================
    BST> Version: 28-Jan-2015
    BST> Checking internet connectivity... ok
    BST> Compiling main interface files...
    BST> Emptying temporary directory...
    BST> Deleting old process reports...
    BST> Loading configuration file...
    BST> Initializing user interface...
    BST> Starting OpenGL engine... hardware
    BST> Reading plugins folder...
    BST> Loading current protocol...
    BST> =================================
  3. Read and accept the license file.
  4. Select your Brainstorm database directory (brainstorm_db).
  5. If you do something wrong and don't know how to go back, you can always re-initialize Brainstorm by typing "brainstorm reset" in the Matlab command window, or by clicking on [Reset] in the software preferences (menu File > Edit preferences).

Main interface window

main_window.gif

Database structure

Brainstorm allows you to organize your recordings and analysis with three levels of definition:

Database files

Create first protocol

  1. Click on the File menu, and select, and select New protocol.

    menuFile.gif

  2. Edit the protocol name and enter: "TutorialFirstSteps". It will automatically update the paths (Anatomy path and Datasets path).

  3. Default properties for the subjects:

    • These are the default settings that are used when creating new subjects. It is then possible to override those settings for each subject individually.
    • Our objective is to create one subject that uses the default anatomy Colin27, so select the option "Yes, use protocol's default anatomy".

    • The option Default channel file is a bit more complicated to understand. It defines at what level we want to define the sensors information (position, orientation, name...) in the database. To make you data management more efficient, you can in some cases use the same channel file for all the subjects, or for all the folders within one subject. For more information on this option, click on the Help button.

    • In this specific case, this option is not relevant because we are not going to import any recordings.
  4. Once you get something like the following figure, click on Create.

    createNewProtocol.gif

Protocol exploration

The protocol is created and you can now see it in the database explorer. It is represented by the top-most node in the tree.

Summary








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Tutorials/CreateProtocol (last edited 2015-01-28 23:05:03 by FrancoisTadel)