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# make_default_subject

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

### Function Synopsis

    make_default_subject(SUBJECT);

### Help Text

    MAKE_DEFAULT_SUBJECT - Make a brainstormsubject and simulated MRI in a folder
     function make_default_subject(SUBJECT);

     Creates a brainstormsubject complete with simulated spherical MRI in the
     SUBJECT folder, such as the default_subject folder.
     SUBJECT should be a referential name, called from the current subject root
      location.

     See also MAKE_DEFAULT_DATABASE, MAKE_DEFAULT_STUDY

### Cross-Reference Information

This function calls

    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m
    mri_read_tool                      C:\BrainStorm_2001\Toolbox\mri_read_tool.m
    simulator_mri                      C:\BrainStorm_2001\Toolbox\simulator_mri.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_subject.m

    function make_default_subject(SUBJECT);
    %MAKE_DEFAULT_SUBJECT - Make a brainstormsubject and simulated MRI in a folder
    % function make_default_subject(SUBJECT);
    %
    % Creates a brainstormsubject complete with simulated spherical MRI in the
    % SUBJECT folder, such as the default_subject folder.
    % SUBJECT should be a referential name, called from the current subject root
    %  location.
    %
    % See also MAKE_DEFAULT_DATABASE, MAKE_DEFAULT_STUDY

    %<autobegin> ---------------------- 26-May-2004 11:30:52 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Database Management
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_message_window.m
    %   toolbox\get_user_directory.m
    %   toolbox\simulator_mri.m
    %
    % Application data and their calls in this file:
    %   set(getappdata(0,'BrainStormMessageWindow'),'pointer','arrow');
    %   set(getappdata(0,'BrainStormMessageWindow'),'pointer','watch');
    %
    % At Check-in: $Author: Mosher $  $Revision: 16 $  $Date: 5/26/04 9:59a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 24-May-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> ------------------------ 26-May-2004 11:30:52 -----------------------

    % History ---------------------------------
    % JCM 06-Nov-2002  First design
    % JCM 11-Sep-2003  Updating to be consistent with make_default_database
    % JCM 26-Apr-2003  Updating to work with Baillet bst_mriviewer instead of
    %                  mri_read_tool (AOS version).
    % ---------------------------------

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

    fig = simulator_mri; % generate the MRI simulator
    handles = guihandles(fig); % get all of its handles

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

    set(handles.edit_folder_name,'String',SUBJECT); % the name of the Default Subject folder
    set(handles.edit_file_name,'String','sphere'); % name of the subject

    % activate as if the button was pushed
    simulator_mri('pushbutton_generate_Callback',handles.pushbutton_generate,[],handles,[]);
    % the sphere_subjectimage is now created in the SUBJECT folder of the current database

    % Now we establish the SCS by using the existing routines
    % New Baillet system is easy, no need to recompute
    if 0 % AOS MRI Read tool routines
        % now get this MRI into the existing BrainStorm coordinate system
        % open the MRI Read Tool
        fig_mri = mri_read_tool;
        fig_mri_handles = guihandles(fig_mri);
        % Load in the image
        mri_read_tool('readbs_Callback',fig_mri_handles.Hloadbsformat,[],fig_mri_handles,...
            fullfile('default_subject',filesep,'sphere_subjectimage.mat'));
        % Define the PCS in CTF using the 4 2 1 points as Nasion, Left PA, Right PA
        mri_read_tool('definepcs_Callback',fig_mri_handles.definepcs,[],fig_mri_handles,...
            [4 1 2]',1)
        % Now save it out
        FNAME = fullfile(pwd,'sphere_subjectimage.mat');
        mri_read_tool('savemrscans_Callback',fig_mri_handles.savemrscans,[],fig_mri_handles,FNAME);
        % now close the mri read tool
        close(fig_mri);
    end

    % make the brainstormsubject file
    Tesselation = []; % keep empty
    Anatomy = fullfile(SUBJECT,'sphere_subjectimage.mat');
    Comments = 'MRI of a sphere';
    DateOfAcquisition = datestr(now);
    DateOfModification = datestr(now);
    Name = 'Default Spherical Subject';

    User = get_user_directory;

    cd(User.SUBJECTS) % the root location of the data
    cd(SUBJECT) % the requested subject folder
    save('sphere_brainstormsubject.mat','Tesselation','Anatomy',...
       'Comments','DateOfAcquisition','DateOfModification','Name');

    % clear the windows and watch
    close(fig); % clear the simulator fig
    set(getappdata(0,'BrainStormMessageWindow'),'pointer','arrow');

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