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# make_default_study

## (Toolbox/make_default_study.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    make_default_study(STUDY,SUBJECT);

### Help Text

    MAKE_DEFAULT_STUDY - Create simulated default data and link to a simulated subject
     function make_default_study(STUDY,SUBJECT);

     Invokes the simulator and stores a simulated data set in the STUDY folder,
      linked to an assumed default data set in the SUBJECT folder.
     STUDY and SUBJECT should be referential to the current database

     See also MAKE_DEFAULT_DATABASE, MAKE_DEFAULT_SUBJECT

### Cross-Reference Information

This function calls

    bst_headmodeler                    C:\BrainStorm_2001\Toolbox\bst_headmodeler.m
    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m
    hanning_window                     C:\BrainStorm_2001\Toolbox\hanning_window.m
    simulator                          C:\BrainStorm_2001\Toolbox\simulator.m

This function is called by

    make_default_database              C:\BrainStorm_2001\Toolbox\make_default_database.m

### Listing of function C:\BrainStorm_2001\Toolbox\make_default_study.m

    function make_default_study(STUDY,SUBJECT);
    %MAKE_DEFAULT_STUDY - Create simulated default data and link to a simulated subject
    % function make_default_study(STUDY,SUBJECT);
    %
    % Invokes the simulator and stores a simulated data set in the STUDY folder,
    %  linked to an assumed default data set in the SUBJECT folder.
    % STUDY and SUBJECT should be referential to the current database
    %
    % See also MAKE_DEFAULT_DATABASE, MAKE_DEFAULT_SUBJECT

    %<autobegin> ---------------------- 12-Oct-2004 01:11:23 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Database Management
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_headmodeler.m
    %   toolbox\bst_message_window.m
    %   toolbox\get_user_directory.m
    %   toolbox\hanning_window.m
    %   toolbox\simulator.m
    %
    % Application data and their calls in this file:
    %   'SourceLoc'
    %   'SourceOrientation'
    %   'TimeSeries'
    %
    %   setappdata(fig,'SourceLoc',SourceLoc);
    %   setappdata(fig,'SourceOrientation',SourceOrientation);
    %   setappdata(fig,'TimeSeries',TimeSeries);
    %
    %   set(getappdata(0,'BrainStormMessageWindow'),'pointer','arrow');
    %   set(getappdata(0,'BrainStormMessageWindow'),'pointer','watch');
    %
    % At Check-in: $Author: Mosher $  $Revision: 16 $  $Date: 10/11/04 11:33p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 23-Sep-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 12-Oct-2004 01:11:23 -----------------------

    % ----------------------------- Script History ---------------------------------
    % JCM 06-Nov-2002  First design
    % JCM 11-Sep-2003  updating to be consistent with make_default_database
    % JCM 11-Oct-2004  changed hanning to be BST function hanning_window
    % ----------------------------- Script History ---------------------------------

    bst_message_window('append','WAIT: Generating simulated data . . .');

    fig = simulator; % create the simulator GUI
    handles = guihandles(fig); % get all of the handles to it

    set(fig,'pointer','watch');
    set(getappdata(0,'BrainStormMessageWindow'),'pointer','watch');
    drawnow

    % set the app data in the simulator, it handles the rest
    % Default cortex is 75 - 79 mm.
    SourceLoc = {[0 0 75]'/1000,[20 20 70]'/1000,[-20 -20 70]'/1000};
    SourceOrientation = {[1 0 0]',[1 -1 0]'/norm([1 1 0]) [-1 1 0]'/norm([-1 1 0])};
    TimeSeries = [[hanning_window(50);zeros(50,1)], [zeros(25,1);hanning_window(50);zeros(25,1)], ...
          [zeros(50,1);hanning_window(50)]] * 10e-9; % A-m

    setappdata(fig,'SourceLoc',SourceLoc);
    setappdata(fig,'SourceOrientation',SourceOrientation);
    setappdata(fig,'TimeSeries',TimeSeries);

    % reinitialize the simulator with the above locations
    simulator('initialize_gui',fig, [], handles);

    % set the location
    set(handles.edit_data_folder_name,'string',STUDY);
    set(handles.edit_data_root_name,'string','sphere_');

    % activate as if the button was pushed
    simulator('pushbutton_generate_Callback',handles.pushbutton_generate,[],handles,[]);

    % data are now created in the current database, in the STUDY folder.

    % make the brainstormstudy file
    % SUBJECT should be referential to the current database
    BrainStormSubject = fullfile(SUBJECT,'sphere_brainstormsubject.mat');
    Session = 'Simulated Sphere Data';
    DateOfStudy = datestr(now);
    DateOfModification = datestr(now);
    Name = 'Default Data';

    User = get_user_directory;

    cd(User.STUDIES) % the root location of the data
    cd(STUDY) % the requested folder
    save('sphere_brainstormstudy.mat','Session','BrainStormSubject',...
       'DateOfStudy','DateOfModification','Name');

    % clear the windows and watch
    close(fig); % clear the simulator fig

    % make a headmodel

    bst_message_window('wrap',{...
          'Computing head model for study: ',...
          'sphere_brainstormstudy',...
          'with default parameters',...
       });

    OPTIONS.HeadModelFile = 'Default';
    bst_headmodeler(fullfile(STUDY,'sphere_brainstormstudy.mat'),OPTIONS);

    set(getappdata(0,'BrainStormMessageWindow'),'pointer','arrow');

Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Nov 2 16:17:59 2004
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