%% read mri
if ispc
datadir = 'H:';
else
datadir = '/home';
end
mri = ft_read_mri(strcat(datadir,'/common/matlab/fieldtrip/data/Subject01.mri'));
%% segmentation
cfg = [];
cfg.output = {'gray', 'white', 'csf','skull','scalp'};
segmentedmri = ft_volumesegment(cfg,mri);
%% mesh
cfg = [];
cfg.shift = 0.3;
cfg.method = 'hexahedral';
mesh = ft_prepare_mesh(cfg,segmentedmri);
%% volume conductor
cfg = [];
cfg.method = 'simbio';
cfg.conductivity = [0.33 0.14 1.79 0.01 0.43];
vol = ft_prepare_headmodel(cfg,mesh);
%% electrode alignment
elec = ft_read_sens(strcat(datadir,'/common/matlab/fieldtrip/template/electrode/standard_1020.elc'));
mri = ft_read_mri(strcat(datadir,'/common/matlab/fieldtrip/data/Subject01.mri'));
nas = mri.hdr.fiducial.head.nas;
lpa = mri.hdr.fiducial.head.lpa;
rpa = mri.hdr.fiducial.head.rpa;
fiducials.chanpos = [nas; lpa; rpa];
fiducials.label = {'Nz','LPA','RPA'};
fiducials.unit = 'mm';
cfg = [];
cfg.method = 'fiducial';
cfg.template = fiducials;
cfg.elec = elec;
cfg.fiducial = {'Nz', 'LPA', 'RPA'};
elec_align = ft_electroderealign(cfg);
% add 12 mm to x-axis
n=size(elec_align.chanpos,1);
for i=1:n
elec_align.chanpos(i,1)=elec_align.chanpos(i,1)+12;
elec_align.elecpos(i,1)=elec_align.elecpos(i,1)+12;
end
% figure;
% ft_plot_sens(elec_align,'style','sr','label','label');
% hold on;
% ft_plot_mesh(mesh,'edgeonly','yes','vertexcolor','none','facecolor',[0.5 0.5 0.5],'facealpha',1,'edgealpha',0.1)
%% make grid (sourcemodel):
% At the moment the sourcemodel is defined prior
% to the leadfield because ft_prepare_sourcemodel does not automatically create
% a sourcemodel based on a hexahedral vol.
cfg = [];
cfg.mri = mri;
cfg.sourceunits = vol.unit;
grid = ft_prepare_sourcemodel(cfg);
cfg = [];
cfg.vol = vol;
cfg.elec = elec_align;
cfg.grid = grid;
lf = ft_prepare_leadfield(cfg);
% plot the leadfield for a few representative locations: points around
% z-axis with increasing z values
plotpos = [];
positions=[];
n=size(lf.pos,1);
p=1;
for i = 1:n
if lf.pos(i,1)==-0.1 && lf.pos(i,2)==-0.2
plotpos(p)=i;
positions(p,:)=lf.pos(i,:);
p=p+1;
end
end
positions;
%n=length(plotpos);
figure;
for i=1:20
subplot(4,5,i);
ft_plot_topo3d(lf.cfg.elec.chanpos,lf.leadfield{plotpos(i)}(:,3));
%view([0 0]);
end