Tutorial 1: Create a new protocol

Authors: Francois Tadel, Elizabeth Bock, Sylvain Baillet

How to read these tutorials

The goal of these introduction tutorials is to guide you through most of the features of the software. All the pages use the same example dataset. The results of one section are most of the time used in the following section, so read those pages in the correct order.

Some pages may contain too many details for your level of interest or competence: just skip them for now. You will be able to get back to the theory later if you need.

Please follow first these tutorials with the data we provide. This way you will be able to focus on learning how to use the software. It is better to start with some data that is easy to analyze. After going through all the tutorials, you should be comfortable enough with the software to start analyzing your own recordings.

If you are interested only in EEG or intra-cranial recordings, don't think that an MEG-based tutorial is not adapted for you. Most of the practical aspects of the data manipulation is very similar in EEG and MEG. Start by reading those introduction tutorials, then go through the tutorial "EEG and Epilepsy" to get some more details about the processing steps that are specific for EEG.

Presentation of the experiment

All the introduction tutorials are based on a simple auditory oddball experiment:

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 your first protocol

  1. Menu File > New protocol.

    menuFile.gif

  2. Edit the protocol name and enter: "TutorialAuditory".
    It will automatically update the anatomy and datasets paths.

  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.
    • Default anatomy: (MRI and surfaces)

      • No, use individual anatomy:
        Select when you have individual MRI scans for all the participants of your study.

      • Yes, use default anatomy:
        Select when you do not have individual scans for the participants, and you would like to use one of the anatomy templates available in Brainstorm.

    • Default channel file: (Sensors names and positions)

      • No, use one channel file per condition/run:
        Select this if you may have different sensor positions for one subject. This is usually not the case in EEG, where the electrodes stay in place for all the experiment. In MEG, this is a common setting: one recording session is split in multiple acquisition runs, and the position of the subject's head in the MEG might be different between two runs.

      • Yes, use one channel file per subject:
        This is a common setting for EEG. The electrodes are in the same position for all the files recorded on one subject.

      • Yes, use only one global channel file:
        This is never a recommended setting. It could be used in the case of an EEG study where you use only standard EEG positions on a standard anatomy, but only if you are not doing any advanced source reconstruction. If you share the position of the electrodes between all the subjects, it will also share the source models, which are dependent on the quality of the recordings for each subject. This is complicated to understand at this level, it will make more sense later in the tutorials.

  4. In the context of this study, we are going to use the following settings:

    • No, use individual anatomy: Because we have access to a T1 MRI scan of the subject.

    • No, use one channel file per condition/run: The typical MEG setup.

  5. 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.

Changing the temporary folder

If the amount of storage space you have for your user folder is limited (less than 10Gb), you may have to change the temprorary folder used by Brainstorm. If you work on a centralized network where all the computers are sharing the same resources, the system admins may impose limited disk quotas to all users and encourage them to use local folders instead of the limited and shared user folder.

The default temporary folder of Brainstorm is located in your user folder ($HOME/.brainstorm/tmp/), so when you import recordings or calculate large models, it may fill up quickly your limited quota and at some point block your user account. To prevent this, select the menu File > Edit preferences and set the temporary folder to a folder that is local to your computer, in which you won't suffer from any storage limitation.

Summary








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Tutorials/CreateProtocol (last edited 2015-02-02 16:25:36 by FrancoisTadel)