sortElectrodes.m

function elecmatrix=sortElectrodes2
%   Created by:
%
%     Copyright (C) 2009  D. Hermes, Dept of Neurology and Neurosurgery, University Medical Center Utrecht
% 
%     This program is free software: you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published by
%     the Free Software Foundation, either version 3 of the License, or
%     (at your option) any later version.
% 
%     This program is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License for more details.
% 
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <http://www.gnu.org/licenses/>.
    
%   Version 1.1.0, released 26-11-2009% 

% DH - fixed bug with waitforbuttonpress Matlab version > 2007

%% load electrodes file

[data1.elecName]=spm_select(1,'image','select image with electrodes');
data1.elecStruct=spm_vol(data1.elecName);
% from structure to data matrix 
data1.elec=spm_read_vols(data1.elecStruct);
[x,y,z]=ind2sub(size(data1.elec),find(data1.elec>1.5));
% from indices 2 native
data1.elecXYZ=([x y z]*data1.elecStruct.mat(1:3,1:3)')+repmat(data1.elecStruct.mat(1:3,4),1,length(x))';


%%
temp.X=data1.elecXYZ(:,1);
temp.Y=data1.elecXYZ(:,2);
temp.Z=data1.elecXYZ(:,3);

figure;
plot3(temp.X,temp.Y,temp.Z,'.','MarkerSize',20);
axis equal;
xlabel('x'); ylabel('y'); zlabel('z');
hold on;
h=datacursormode;

%%
elecNr=0;
startckeck=0;
disp('specify total number of electrodes')
r=input('');
totalnrElec=r;
elecmatrix=zeros(totalnrElec,3);
disp('press 1 to start')
r=input('');
if r==1
    while elecNr<totalnrElec
        disp(['select electrode nr ' int2str(elecNr+1)])
        next_el=input('');
        if isempty(next_el) % pressed enter 
            info_struct = getCursorInfo(h);
            if elecNr>0 % if second click, check whether ok
                if ismember(info_struct.Position,elecmatrix,'rows')
                    disp('same position as a previous electrode, try again');
                else
                    elecNr=elecNr+1;
                    elecmatrix(elecNr,:)=info_struct.Position;
                    disp(['electrode ' int2str(elecNr) ' position ' int2str(elecmatrix(elecNr,:))]);
%                     plot3(info_struct.Position(1),info_struct.Position(2),info_struct.Position(3),'r.','MarkerSize',20);
                    text(info_struct.Position(1)*1.01,info_struct.Position(2)*1.01,info_struct.Position(3)*1.01,num2str(elecNr),'FontSize',12,'HorizontalAlignment','center','VerticalAlignment','middle')
                end
            else % first click, always add an electrode
                elecNr=elecNr+1;
                elecmatrix(elecNr,:)=info_struct.Position;
                disp(['electrode ' int2str(elecNr) ' position ' int2str(elecmatrix(elecNr,:))]);
%                 plot3(info_struct.Position(1),info_struct.Position(2),info_struct.Position(3),'r.','MarkerSize',20);
                text(info_struct.Position(1)*1.01,info_struct.Position(2)*1.01,info_struct.Position(3)*1.01,num2str(elecNr),'FontSize',12,'HorizontalAlignment','center','VerticalAlignment','middle')
            end 
        end
    end
end

%% save electrode matrix

outputdir= spm_select(1,'dir','select directory to save locations matrix');
    
for filenummer = 1:100
    outputnaam = fullfile(outputdir,['electrodes_loc' int2str(filenummer) '.mat']);
    if ~exist(outputnaam,'file')>0
        disp(strcat(['saving ' outputnaam]));
        save(outputnaam,'elecmatrix');
        break
    end
end