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# scs2mri

## (Toolbox/scs2mri.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [mriCoord] = scs2mri(MRI,scsCoord);

### Help Text

    SCS2MRI - transform SCS point coordinates (in mm) to MRI coordinate system (in mm)
     function [mriCoord] = scs2mri(MRI,scsCoord);
      function [scsCoord] = mri2scs(MRI,mriCoord);
      MRI - a proper BrainStorm MRI structure (i.e. from any subjectimage file, with fiducial points
            and SCS system properly defined)
      scsCoord - a 3xN matric of corresponding point coordinates in the SCS system (in mm)

      mriCoord - a 3xN matrix of point coordinates in the MRI system (in mm)

      Definition of original transform is the following:
      Xscs = MRI.SCS.R Xmri + MRI.SCS.T ;
      (Xmri in mm)

### Cross-Reference Information

This function is called by

    bst_mriviewer                      C:\BrainStorm_2001\Toolbox\bst_mriviewer.m

### Listing of function C:\BrainStorm_2001\Toolbox\scs2mri.m

    function [mriCoord] = scs2mri(MRI,scsCoord);
    %SCS2MRI - transform SCS point coordinates (in mm) to MRI coordinate system (in mm)
    % function [mriCoord] = scs2mri(MRI,scsCoord);
    %  function [scsCoord] = mri2scs(MRI,mriCoord);
    %  MRI - a proper BrainStorm MRI structure (i.e. from any subjectimage file, with fiducial points
    %        and SCS system properly defined)
    %  scsCoord - a 3xN matric of corresponding point coordinates in the SCS system (in mm)
    %
    %  mriCoord - a 3xN matrix of point coordinates in the MRI system (in mm)
    %
    %  Definition of original transform is the following:
    %  Xscs = MRI.SCS.R Xmri + MRI.SCS.T ;
    %  (Xmri in mm)
    %

    %<autobegin> ---------------------- 26-May-2004 11:34:18 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - Numeric
    %
    % At Check-in: $Author: Mosher $  $Revision: 8 $  $Date: 5/26/04 10:02a $
    %
    % 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 11:34:18 -----------------------

    % /---Script Authors-------------------------------------\
    % |  *** Sylvain Baillet, Ph.D.                          |
    % |  Cognitive Neuroscience & Brain Imaging Laboratory   |
    % |  CNRS UPR640 - LENA                                  |
    % |  Hopital de la Salpetriere, Paris, France            |
    % |  sylvain.baillet@chups.jussieu.fr                    |
    % |                                                      |
    % |  *** Alexei Ossadtchi, Ph.D.                         |
    % |  USC - SIPI                                          |
    % |                                                      |
    % \------------------------------------------------------/
    %
    % Script History ---------------------------------------------------------------
    % SB  15-Mar-2004 (BrainStorm v.1 update)
    % Script History ---------------------------------------------------------------

    % Memo
    % FidNames0{1} = 'Nasion';
    % FidNames0{2} = 'LEFT Preauricular';
    % FidNames0{3} = 'RIGHT Preauricular';

    if ~isfield(MRI,'SCS')
        errordlg({'MRI SCS was not defined or subjectimage file is from another version of BrainStorm',...
                'Please re-define the subject coordinate system on this MRI'},'MRI file error')
        return
    end

    mriCoord = ...
        inv(MRI.SCS.R) * (scsCoord - repmat(MRI.SCS.T,1,size(scsCoord,2)));

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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