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# bstscript_ForwardInverse_basic

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

### Help Text

    BSTSCRIPT_FORWARDINVERSE_BASIC - Basic Head Modelling and Source Imaging BrainStorm Script

     This script is intended to be used without the BrainStorm GUI's.
     A basic spherical headmodel is computed based on the individual scalp envelope.
     Sources are distributed over the cortical surface or white/gray matter interface.
     A minimum-norm estimate of the distribution of source amplitudes is also computed.
     Data and Results are saved in BrainStorm's format (i.e. in Matlab archive .mat files).

     For advanced options to headmodelling and source imaging, please refer to more specific
     scripts such as BST_HEADMODELER.M and BST_SOURCEIMAGING.M in the <BrainStorm>\Toolbox folder.

### Cross-Reference Information

This calls

    bst_headmodeler                    C:\BrainStorm_2001\Toolbox\bst_headmodeler.m
    bst_sourceimaging                  C:\BrainStorm_2001\Toolbox\bst_sourceimaging.m

### Listing of C:\BrainStorm_2001\Toolbox\bstscript_ForwardInverse_basic.m

    %BSTSCRIPT_FORWARDINVERSE_BASIC - Basic Head Modelling and Source Imaging BrainStorm Script
    %
    % This script is intended to be used without the BrainStorm GUI's.
    % A basic spherical headmodel is computed based on the individual scalp envelope.
    % Sources are distributed over the cortical surface or white/gray matter interface.
    % A minimum-norm estimate of the distribution of source amplitudes is also computed.
    % Data and Results are saved in BrainStorm's format (i.e. in Matlab archive .mat files).
    %
    % For advanced options to headmodelling and source imaging, please refer to more specific
    % scripts such as BST_HEADMODELER.M and BST_SOURCEIMAGING.M in the <BrainStorm>\Toolbox folder.

    %<autobegin> ---------------------- 14-Jun-2004 17:09:50 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Inverse Modeling
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_headmodeler.m
    %   toolbox\bst_sourceimaging.m
    %
    % Group : Preference data and their calls in this file:
    %   'BrainStorm' : 'UserDataBase'
    %   'BrainStorm' : 'iUserDataBase'
    %
    %   setpref('BrainStorm','UserDataBase',UserDB);
    %   setpref('BrainStorm','iUserDataBase',1);
    %
    %
    % At Check-in: $Author: Mosher $  $Revision: 8 $  $Date: 6/14/04 3:37p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 14-Jun-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> ------------------------ 14-Jun-2004 17:09:50 -----------------------

    % /---Script Author--------------------------------------\
    % |                                                      |
    % | *** Sylvain Baillet, Ph.D.                           |
    % | Cognitive Neuroscience & Brain Imaging Laboratory    |
    % | CNRS UPR640 - LENA                                   |
    % | Hopital de la Salpetriere, Paris, France             |
    % | sylvain.baillet@chups.jussieu.fr                     |
    % |                                                      |
    % \------------------------------------------------------/

    % Script History----------------------------------------------------
    % SB  09-Mar-2004  : Creation
    % ------------------------------------------------------------------

    % Set-up paths -----------------------------------------------------

    % 1) Add BrainStorm path
    addpath('e:\brainstorm2001\toolbox')  % EDIT

    % 2) Where is your data ? Create a database entry
    % a) Anatomy (i.e. so-called SUBJECTS folder)
    UserDB(1).STUDIES = 'I:\Data\Studies'; % EDIT
    % b) Functional (e.g. MEG/EEG, so-called STUDIES folder)
    UserDB(1).SUBJECTS = 'I:\Data\Subjects'; % EDIT
    UserDB(1).FILELIST = '';

    % Store this information in Matlab's preferences
    setpref('BrainStorm','UserDataBase',UserDB);
    setpref('BrainStorm','iUserDataBase',1);

    % Forward modelling -----------------------------------------------

    % Store arguments to be passed to main script in fwOPTIONS structure
    StudyFile = 'I:\Data\Studies\NDiaye\S10\aud\aud-avTr17_brainstormstudy.mat'; % path to BrainStorm studyfile (i.e. database entry) % EDIT
    fwOPTIONS.Method = {'meg_sphere'}; % MEG spherical head model

    % Use scalp tessellation to fit sphere to head
    fwOPTIONS.Scalp.FileName = 'I:\Data\Subjects\NDiaye\S10\S10_tess.mat';  % EDIT
    fwOPTIONS.Scalp.iGrid = 1; % Location of head envelope in .FileName tessellation cell arrays % EDIT %

    % Use cortex or white/gray interface to distribute sphere to distribute source models
    fwOPTIONS.Cortex.FileName = 'I:\Data\Subjects\NDiaye\S10\S10_tess.mat';  % EDIT
    fwOPTIONS.Cortex.iGrid = 4; % WARNING : for all subjects in this study but S7 where .iGrid = 10 % EDIT %

    % Type HELP BST_HEADMODELER.M for further info on the following arguments
    fwOPTIONS.VolumeSourceGrid = 0;
    fwOPTIONS.HeadModelFile = 'default';
    fwOPTIONS.ImageGridFile = 'default';
    fwOPTIONS.Verbose = 1;

    % Call main function
    [OPTIONS.HeadModelFile, tmp] = bst_headmodeler(StudyFile,fwOPTIONS);
    % -> Done with Forward modelling

    % Inverse modelling ------------------------------------------------------

    % Store arguments to be passed to main script in invOPTIONS structure
    invOPTIONS.DataFile = {'I:\Data\Studies\NDiaye\S10\aud\aud-avTr17_data_trial_1.mat'}; % EDIT % Store MEG-EEG datafile(s) to be processed in a cell array of strings
    invOPTIONS.TimeSegment = [-0.1000 0.2000]; % Time segment to be processed, in seconds
    invOPTIONS.DataTypes = 1; % Process MEG (1); EEG (2) or Fusion of MEG with EEG (3)
    invOPTIONS.HeadModelFile = OPTIONS.HeadModelFile;
    invOPTIONS.Method = 'Minimum-Norm Imaging';
    invOPTIONS.Verbose = 1;

    % Call main function

    [Results, tmp] = bst_sourceimaging(invOPTIONS);
    % -> Done with inverse estimation

Produced by color_mat2html, a customized BrainStorm 2.0 (Alpha) version of mat2html on Tue Oct 12 12:05:14 2004
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