plotDTI.m

function plotDTI(D,delta)
%-fanDTasia ToolBox------------------------------------------------------------------
% This Matlab script is part of the fanDTasia ToolBox: a Matlab library for Diffusion 
% Weighted MRI (DW-MRI) Processing, Diffusion Tensor (DTI) Estimation, High-order 
% Diffusion Tensor Analysis, Tensor ODF estimation, Visualization and more.
%
% A Matlab Tutorial on DW-MRI can be found in:
% http://www.cise.ufl.edu/~abarmpou/lab/fanDTasia/tutorial.php
%
%-CITATION---------------------------------------------------------------------------
% If you use this software please cite the following work:
% A. Barmpoutis, B. C. Vemuri, T. M. Shepherd, and J. R. Forder "Tensor splines for 
% interpolation and approximation of DT-MRI with applications to segmentation of 
% isolated rat hippocampi", IEEE TMI: Transactions on Medical Imaging, Vol. 26(11), 
% pp. 1537-1546 
%
%-DESCRIPTION------------------------------------------------------------------------
% This function plots a 2D field of 3D tensors as ellipsoidal glyphs. The 3D tensors 
% must be in the form of 3x3 symmetric positive definite matrices. The field can 
% contain either a single tensor, or a row of tensors or a 2D field of tensors.
%
% NOTE: This function plots only 2nd-order tensors (i.e. traditional DTI). For higher
% order tensors (such as 4th-order tensor visualization) please use the plotTensors.m
%
%-USE--------------------------------------------------------------------------------
% example 1: plotDTI(D)
% where D is of size 3x3 or 3x3xN or 3x3xNxM
%
% example 2: plotDTI(D,delta)
% where delta is a scalar that controls the size 
% of a voxel in the field. Default: delta=1
%
%-DISCLAIMER-------------------------------------------------------------------------
% You can use this source code for non commercial research and educational purposes 
% only without licensing fees and is provided without guarantee or warrantee expressed
% or implied. You cannot repost this file without prior written permission from the 
% authors. If you use this software please cite the following work:
% A. Barmpoutis, B. C. Vemuri, T. M. Shepherd, and J. R. Forder "Tensor splines for 
% interpolation and approximation of DT-MRI with applications to segmentation of 
% isolated rat hippocampi", IEEE TMI: Transactions on Medical Imaging, Vol. 26(11), 
% pp. 1537-1546 
%
%-AUTHOR-----------------------------------------------------------------------------
% Angelos Barmpoutis, PhD
% Computer and Information Science and Engineering Department
% University of Florida, Gainesville, FL 32611, USA
% abarmpou at cise dot ufl dot edu
%------------------------------------------------------------------------------------


if nargin==1
    delta=1;
end

sz=size(D);
if length(sz)==2
    nx=1;ny=1;
elseif length(sz)==3
    nx=sz(3);ny=1;
elseif length(sz)==4
    nx=sz(3);ny=sz(4);
end


n=size(D,3);
for i=1:nx
    for j=1:ny
        %if(D(3,3,i,j) ~= 0) %skips if the tensor is zero
            [v,l]=eig(D(:,:,i,j));
            [X,Y,Z]=ellipsoid(0,0,0,l(1,1),l(2,2),l(3,3),10);
            sz=size(X);
            for x=1:sz(1)
                for y=1:sz(2)
                    A=[X(x,y) Y(x,y) Z(x,y)]';
                    A=(v/delta)*A; %added the /delta to reduce the sizes of the ellipsoids without changing the axis'
                    X(x,y)=A(1);Y(x,y)=A(2);Z(x,y)=A(3);
                end
            end
            X=X+i; %*delta*2 in original script
            Y=Y+j; %*delta*2 in original script
            %h(i)=
            if i==1 && j==1
                hold
            end
            surf(X,Y,Z);
        %end
    end
end
axis equal
view([0 90]);
set(gca,'GridLineStyle','none')
%set(gca,'XTick',[])
%set(gca,'YTick',[])
%set(gca,'ZTick',[])
shading interp
%colormap([0.8 0.8 0.8])
lighting phong
light('Position',[0 0 1],'Style','infinite','Color',[ 1.000 0.584 0.000]);
hold

fprintf(1,'\nIf you use plotDTI.m please cite the following work:\n');
fprintf(1,'A. Barmpoutis, B. C. Vemuri, T. M. Shepherd, and J. R. Forder "Tensor splines for\n');
fprintf(1,'interpolation and approximation of DT-MRI with applications to segmentation of\n');
fprintf(1,'isolated rat hippocampi", IEEE TMI: Transactions on Medical Imaging, Vol. 26(11),\n');
fprintf(1,'pp. 1537-1546\n');