ea_reconstruct.m

function [coords,trajvector,trajectory,tramat]=ea_reconstruct(options,side,lnii)
% This function is the heart of Lead-DBS, reconstructing the electrode
% lead trajectory for one side (left/right) of the MR-data. It reads two MR
% images from a folder called 'patientname' and iteratively reconstructs a
% line in 3D-space that best describes the electrode trajectory.
% __________________________________________________________________________________
%
% Inputs:
%           options           Struct containing various options, see e.g.
%                             ea_defaultoptions.m
%           side              which side of the brain shall be
%                             reconstructed. 1 > right hemisphere, 2 > left hemisphere.
% ----------------------------------------------------------------------------------
%
% Outputs:  coords            8x3 vector of electrode coordinates in
%                             mm-representations within MNI-space (if
%                             MR-images have been normalized correctly).
%           trajvector        3 element vector describing the traversing
%                             direction of the lead trajectory.
%           trajectory        nx3 vector describing the fitted line of the
%                             trajectory.
%           tramat            4x4 matrix describing the normalization of
%                             MR-images. This is used to reconstruct the
%                             distances of the electrode contacts in
%                             MNI-space (since the distance has changed
%                             from e.g. 2mm in native space due to
%                             normalization).
%
% __________________________________________________________________________________
% Copyright (C) 2014 Charite University Medicine Berlin, Movement Disorders Unit
% Andreas Horn

options.axiscontrast=3;

trajectory=[]; % empty initialization.
for refine=0:options.refinesteps
    [trajectory,trajvector]=ea_reconstruct_trajectory(trajectory,lnii,side,refine,options);
end

% determine height of last electrode
if options.verbose>1
    di=figure('name','Finding local maxima in diameters...','numbertitle','off');
end

if options.verbose>2
    close(di);
end

% first, calculate distance between contacts. rename matfile to text
tramat=eye(4);
[~,~,dist]=ea_calc_distance(options.elspec.eldist,trajvector,tramat(1:3,1:3),fullfile(options.subj.normDir,'tmp','lpost.nii'));

% zdist is the distance between electrodes in z-direction.
zdist=dist/norm(trajvector);

[coords,goodz]=ea_reconstruct_coords(trajectory,trajvector,options);