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# warp_everything_bst

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

### Function Synopsis

    warp_everything(lm_real, lm_phantom, surface_file, mr_file, warped_surface_file,warped_mr_file)

### Help Text

    WARP_EVERYTHING - (summary line here)
     function warp_everything(lm_real, lm_phantom, surface_file, mr_file, warped_surface_file,warped_mr_file)

     inputs:
     lm_real = landmarks in real head coordinates, i.e. from a Polhemus or
       Zebris 3D localizer. Units must be scaled to mm! format is n x 3 (n=#
       landmarks). The first three entries MUST be Nasion, Left PreAuricular
       Point and Right preauricular Point in this order!
       lm_phantom = landmarks in phantom coordinates. see lm_real.
       surface_file = file name of the surface file to be warped. This MUST be
       the filename only without the directory name. It is assumed that this
       function is already in the appropriate directory when called!
     mr_file = mr file name. see surface file for details.
     warped_surface_file = output surface file containing the warped surfaces
     warped_mr_file = output mr file containing the warped MR structure

### Cross-Reference Information

This function calls

    save_fieldnames                    C:\BrainStorm_2001\Toolbox\save_fieldnames.m

This function is called by

    tess_align_tool                    C:\BrainStorm_2001\Toolbox\tess_align_tool.m

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

    function warp_everything(lm_real, lm_phantom, surface_file, mr_file, warped_surface_file,warped_mr_file)
    %WARP_EVERYTHING - (summary line here)
    % function warp_everything(lm_real, lm_phantom, surface_file, mr_file, warped_surface_file,warped_mr_file)
    %
    % inputs:
    % lm_real = landmarks in real head coordinates, i.e. from a Polhemus or
    %   Zebris 3D localizer. Units must be scaled to mm! format is n x 3 (n=#
    %   landmarks). The first three entries MUST be Nasion, Left PreAuricular
    %   Point and Right preauricular Point in this order!
    %   lm_phantom = landmarks in phantom coordinates. see lm_real.
    %   surface_file = file name of the surface file to be warped. This MUST be
    %   the filename only without the directory name. It is assumed that this
    %   function is already in the appropriate directory when called!
    % mr_file = mr file name. see surface file for details.
    % warped_surface_file = output surface file containing the warped surfaces
    % warped_mr_file = output mr file containing the warped MR structure

    %<autobegin> ---------------------- 12-Oct-2004 12:02:51 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Visualization
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\save_fieldnames.m
    %
    % Subfunctions in this file, in order of occurrence in file:
    %   [W,A,e]=warp_transform(p,q)
    %   [rw]=warp_lm(r,A,W,p)
    %
    % At Check-in: $Author: Mosher $  $Revision: 2 $  $Date: 10/12/04 10:24a $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 12-Oct-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> ------------------------ 12-Oct-2004 12:02:51 -----------------------

    % /---Script Author--------------------------------------\
    % |                                                      |
    % | *** Felix Darvas, Ph.D                               |
    % | University of Southern California                    |
    % |                                                      |
    % \------------------------------------------------------/

    % ----------------------------- Script History ---------------------------------
    % 08-Oct-2004 DP  Change input output arguments to integrate into BrainStorm
    % JCM 11-Oct-2004 commenting header
    % ----------------------------- Script History ---------------------------------

    [W,A,e]=warp_transform(lm_phantom,lm_real); % compute warp transform parameters

    surf_in=load(surface_file);
    surf_out=surf_in;

    for i=1:length(surf_in.Vertices) % warp all surfaces
        surf_out.Comment{i}=['warped ' surf_in.Comment{i}];
        surf_out.Vertices{i}=(warp_lm(surf_in.Vertices{i}',A,W,lm_phantom)+surf_in.Vertices{i}')';
    end
    mr_in=load(mr_file);

    R=mr_in.SCS.R;
    T=mr_in.SCS.T;

    lm_phan_mr=(inv(R)*(lm_phantom'*1000-T*ones(1,size(lm_phantom,1))))'; % transform landmarks into MR coordinates
    lm_real_mr=(inv(R)*(lm_real'*1000-T*ones(1,size(lm_real,1))))';

    [Wmr,Amr]=warp_transform(lm_phan_mr,lm_real_mr); % compute warp transform in MR coordinates

    ixc=find(mr_in.Cube>0); % get voxel coordinates. This part is quite memory intensive
    [xv,yv,zv]=ind2sub(size(mr_in.Cube),ixc);
    rv=[xv';yv';zv'];
    clear xv yv zv
    val=uint8(mr_in.Cube(ixc));
    clear ixc;
    sts=10000; % warp only sts coordinates at a time. Doing all at once costs too much memory, doing only 1 at a time costs too much time
    rpcw=zeros(size(rv));
    kk=0;
    hh=waitbar(0,'transforming coordinates');
    ix0=1;
    for i=1:ceil(size(rv,2)/sts)
        ix1=ix0-1+sts;
        if(ix1>size(rv,2))
            ix1=size(rv,2);
        end
        kk=kk+1;
        if(kk>ceil(size(rv,2)/sts)/100)
            kk=0;
            waitbar(i/ceil(size(rv,2)/sts));
        end
        rpcw(:,ix0:ix1)=(warp_lm(rv(:,ix0:ix1)',Amr,Wmr,lm_phan_mr)+rv(:,ix0:ix1)')';
        ix0=ix1+1;
    end
    close(hh)
    rpcw=ceil(rpcw);

    for i=1:3
        ix=find(rpcw(i,:)<1);
        rpcw(i,ix)=1;
    end
    % set up new MR structure for BrainStorm
    %newCube=uint8(zeros(size(mr_in.Cube)));
    newCube=uint8(zeros(max(rpcw')));

    ixn=sub2ind(size(newCube),rpcw(1,:)',rpcw(2,:)',rpcw(3,:)');
    newCube(ixn)=val;
    newMr=mr_in;
    newMr.Cube=double(newCube);
    clear newCube;
    clear ixn;
    clear rpcw;
    clear rv;
    newfid=lm_real_mr(1:3,:)';
    origin=(newfid(:,2)+newfid(:,3))/2;
    newMr.SCS.mmCubeFiducial=[newfid origin];
    save_fieldnames(newMr,warped_mr_file);
    save_fieldnames(surf_out,warped_surface_file);

    function [W,A,e]=warp_transform(p,q)
    % [W,A,e]=warp_transform(p,q)
    % calculates nonlinear transformatin coefficents see Ermer's Thesis
    % p... = Landmarks in system 1
    % q... = landmarks in system 2
    % e =warp energy
    K=zeros(size(p,1),size(p,1));
    for i=1:size(K,1)
        for j=1:size(K,2)
            K(i,j)=norm(p(i,:)-p(j,:));
        end
    end
    P=[p ones(size(p,1),1)];
    L=[K P;P' zeros(4,4)];
    D=[q-p;zeros(4,3)];
    H=L\D;
    W=H(1:size(p,1),:);
    A=H(size(p,1)+1:end,:);
    e=sum(diag(W'*K*W));

    function [rw]=warp_lm(r,A,W,p)
    % function [rw]=warp_lm(r,A,W,p)
    % performs warp transformation with linear 3D RFB see Ermer's Thesis
    rw=r*A(1:3,1:3)+repmat(A(4,:),size(r,1),1);
    for i=1:size(p,1)
      U=sqrt(sum((r-repmat(p(i,:),size(r,1),1)).^2,2));
      rw=rw+U*W(i,:);
    end

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