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 directory, the software will not work properly. 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 Matlab, go to brainstorm3 directory, and type "brainstorm" in Matlab command window.

    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 at any moment 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

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.

Fiducials selection (MRI Viewer)

A few more details about the MRI and the fiducials: Right-click on the MRI file > Edit MRI...

MRI visualization

There are many different ways to display the MR volumes. Right click on the T1-MRI in Default anatomy, menu Display. Just click everywhere and try all the options by yourself, it is the best way to learn.

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MRI Viewer

Already introduced in this tutorial
It is the default visualization mode; when you double-click on the MRI file, it brings up the MRI Viewer.

Axial / coronal / sagittal slices

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3D orthogonal slices

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Surfaces visualization

There is only one way to display the surfaces: in 3D figures. To display a surface you can either double-click on it or right-click > Display.

Coordinates tab

Create a subject

If you explored well, you should have found the "New subject" menu in the protocol's popup menu.

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Change the default anatomy

When you create a new protocol, the program makes a copy of the Colin27 anatomy and sets it as the default for the protocol. It means that you will be able to use the Colin27 brain as a substitute for the subjects without an individual MRI, or as the common brain for group analysis.

Other sets of MRI+surfaces are available to replace the Colin27 anatomy. Right-click on (Default anatomy) > Use template. If a package is not currently available on your system, it will be downloaded from the Brainstorm website and saved in $HOME/.brainstorm/templates. The available options are:

They all include the following information:

The atlases will be discussed in the following tutorials. For more information on the interactions between FreeSurfer and Brainstorm: read this tutorial.

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If you click on any of the download options, it downloads it into your $HOME/.brainstorm/templates folder:

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Then the list of files in the (default anatomy) folder is replaced with the new template.

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Modify the default MRI fiducials

The fiducial points (Nasion, LPA, RPA) used in your recordings might not be the same as the ones used in the anatomy templates in Brainstorm (Colin27, ICBM152, FSAverage). By default, the LPA/RPA points are defined at the junction between the tragus and the helix, as represented with the red dot in the Coordinates systems page.

If you want to use an anatomy template but you are using a different convention when digitizing the position of those points, you have to modify the default positions of the template with the MRI Viewer.

Next

Now you know how to create a protocol with a default anatomy, and visualize MR volumes and surfaces.

Next step: how to import an individual anatomy for a subject.





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Tutorials/CreateProtocol (last edited 2015-01-28 22:39:40 by FrancoisTadel)