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# transform

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

### Function Synopsis

    varargout = transform(varargin)

### Help Text

    TRANSFORM - Transform coordinates between PCS and MRI
     function varargout = transform(varargin)
        TRANSFORM('callback_name', ...) invoke the named callback.
     Callbacks are pcs2mri, mri2pcs, rap2mri,

     for example,
      Xmri = transform('pcs2mri',Xpcs,R,T)
     where
      Xpcs is
      R is
      T is
     Output
     Xmri is

### Cross-Reference Information

This function is called by

    mri_read_tool                      C:\BrainStorm_2001\Toolbox\mri_read_tool.m
    results_visualization              C:\BrainStorm_2001\Toolbox\results_visualization.m

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

    function varargout = transform(varargin)
    %TRANSFORM - Transform coordinates between PCS and MRI
    % function varargout = transform(varargin)
    %    TRANSFORM('callback_name', ...) invoke the named callback.
    % Callbacks are pcs2mri, mri2pcs, rap2mri,
    %
    % for example,
    %  Xmri = transform('pcs2mri',Xpcs,R,T)
    % where
    %  Xpcs is
    %  R is
    %  T is
    % Output
    % Xmri is

    %<autobegin> ---------------------- 26-May-2004 11:34:40 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Utility - Numeric
    %
    % Subfunctions in this file, in order of occurrence in file:
    %   Xmri = pcs2mri(Xpcs,R,T);
    %   Xpcs = mri2pcs(Xmri,R,T)
    %   Y = rap2mri(Xrap,PCS)
    %
    % At Check-in: $Author: Mosher $  $Revision: 11 $  $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 11:34:40 -----------------------

    % Alex Ossadtchi, University of Southern California
    % John C. Mosher, Ph.D., Los Alamos National Laboratory

    % --------------------- history ----------------
    % AOS June 2002     First designs
    % AOS 12-June-2002  individual subfunctions
    % JCM 12-July-2002  feval switchyard designed for subfunctions
    % AOS               update of calling routines for new FEVAL switchyard
    % ----------------------------------------------

    [varargout{1:nargout}] = feval(varargin{:}); % FEVAL switchyard

    % ------------------ subfunctions --------------------------
    % ------------- CONVERT FROM PCS to MRI COORDINATES
    function Xmri = pcs2mri(Xpcs,R,T);
        if(nargin==3)
            Xmri = R*Xpcs+repmat(T,1,size(Xpcs,2));
        elseif(nargin==2)
            Xmri = R.R*Xpcs+repmat(R.t,1,size(Xpcs,2));
        else
            disp('incorrect number of arguments in ClearPCS2MRI');
            Xmri = [];
            return;
        end;

    % ------------- FROM MRI to PCS ---------------------
    function Xpcs = mri2pcs(Xmri,R,T)
       if(nargin==3)
            Xpcs = inv(R)*(Xmri - repmat(T,1,size(Xmri,2)));
        elseif(nargin==2)
            Xpcs = inv(R.R)*(Xmri - repmat(R.t,1,size(Xmri,2)));
        else
            disp('incorrect number of arguments in ClearMRI2PCS');
            Xpcs = [];
            return;
        end;

    % ---------------- SCALE RAP MUSIC RESULTS, THEN CONVERT --------------
    function Y = rap2mri(Xrap,PCS)
        X = 1000*Xrap;
        Y = PCS.R*X+repmat(PCS.t,1,size(X,2));

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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