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# mri2scs

## (Toolbox/mri2scs.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [transf,varargout] = mri2scs(MRI,varargin);

### Help Text

    MRI2SCS - Compute the transform to move form the MRI coordinate system (in mm) to the SCS
     function [transf,varargout] = mri2scs(MRI,varargin);
     function [transf] = mri2scs(MRI);
      MRI - a proper BrainStorm MRI structure (i.e. from any subjectimage file, with fiducial points
            and SCS system properly defined)
      transf - a structure specifying the transform that is applied to the MRI mm coordinates
      Definition of the transform is the following:
      Xscs = transf.R Xmri + transf.T ;
      (Xmri in mm)
      transf.Origin is the location of the SCS origin in MRI coordinates

      function [transf,scsCoord] = mri2scs(MRI,mriCoord);
      mriCoord - a 3xN matrix of point coordinates in the MRI system (in mm)
      scsCoord - a 3xN matric of corresponding point coordinates in the SCS system (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\mri2scs.m

    function [transf,varargout] = mri2scs(MRI,varargin);
    %MRI2SCS - Compute the transform to move form the MRI coordinate system (in mm) to the SCS
    % function [transf,varargout] = mri2scs(MRI,varargin);
    % function [transf] = mri2scs(MRI);
    %  MRI - a proper BrainStorm MRI structure (i.e. from any subjectimage file, with fiducial points
    %        and SCS system properly defined)
    %  transf - a structure specifying the transform that is applied to the MRI mm coordinates
    %  Definition of the transform is the following:
    %  Xscs = transf.R Xmri + transf.T ;
    %  (Xmri in mm)
    %  transf.Origin is the location of the SCS origin in MRI coordinates
    %
    %  function [transf,scsCoord] = mri2scs(MRI,mriCoord);
    %  mriCoord - a 3xN matrix of point coordinates in the MRI system (in mm)
    %  scsCoord - a 3xN matric of corresponding point coordinates in the SCS system (in mm)

    %<autobegin> ---------------------- 08-Jun-2004 15:11:31 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - Numeric
    %
    % At Check-in: $Author: Mosher $  $Revision: 12 $  $Date: 6/08/04 1:38p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 28-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> ------------------------ 08-Jun-2004 15:11:31 -----------------------

    % /---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

    % Fiducial coordinates in mm
    % Nasion
    NAS = MRI.SCS.mmCubeFiducial(:,1);%MRI.SCS.LookUpFiducials(1));
    % MRI.SCS.Label{LookUpFiducials(1)} = 'Nasion';
    % LPA
    LPA = MRI.SCS.mmCubeFiducial(:,2);%MRI.SCS.LookUpFiducials(2));
    % MRI.SCS.Label{LookUpFiducials(2)} = 'LEFT Preauricular';
    % RPA
    RPA = MRI.SCS.mmCubeFiducial(:,3);%MRI.SCS.LookUpFiducials(3));
    % MRI.SCS.Label{LookUpFiducials(3)} = 'RIGHT Preauricular';

    % Move to SCS
    % Definition:
    % Xscs = R Xmri + T ; Xmri in mm

    switch(MRI.SCS.System)

    case 'CTF'
        transf.Origin = .5*(LPA+RPA); % in mm
        %     nLR = cross(NAS-RPA,LPA-RPA);  % Vector normal to the NLR plane, pointing upwards
        %     nLR = nLR/norm(nLR);

        vx = (NAS-transf.Origin)/norm((NAS-transf.Origin));
        %     vy = inv([vx,nLR,cross(vx,nLR)])*[0 0 1]'; % y direction
        %     vy = vy/norm(vy);

        vz = cross(vx, LPA-RPA); vz = vz/norm(vz);  % Vector normal to the NLR plane, pointing upwards
        vy = cross(vz,vx); vy = vy/norm(vy);

        transf.R = inv([vx,vy,vz]); % Rotation
        transf.T = - transf.R * transf.Origin;

        %rot = [0 1 0;1 0 0;0 0 1]*inv([vx,vy,cross(vx,vy)]);
        %rot = [0 1 0;-1 0 0;0 0 1]* rot;

    case 'NEUROMAG' % Warning - need to be re-checked !

        LR = LPA - RPA; % Left\Right Vector
        LR = LR/norm(LR);
        LRp = [0 -1 0;1 0 0;0 0 0]* LR; % A vector orthogonal to LR that will define a plane perpendicular to the NLR plane
        LRp = LRp/norm(LRp);
        % note: The LR line is defined according to the intersection between 2 orthogonal planes.

        OR = dot(RPA-NAS,RPA-LPA)/dot(RPA-LPA,RPA-LPA) * (RPA-LPA);
        Origin = RPA - OR;
        vx = OR/norm(OR);
        vy = (NAS-Origin)/norm(NAS - Origin);
        vz = cross(vx,vy);

        transf.R = inv([vx,vy,vz]); % Rotation
        transf.T = - transf.R * Origin; % Translation
        transf.Origin = Origin;
    end

    if nargin == 2 % User has specified point coordinates to transform
        if nargout == 2 % ... and wants to get them back in SCS

            varargout{1} = [transf.R, transf.T] * [varargin{1};ones(1,size(varargin{1},2))]; % Compact form of RX+T
            %varargout{1} = transf.R * varargin{1} + repmat(transf.T,1,size(varargin{1},2)); % Compact form of RX+T

        end
    end

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