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iCAPs/packages/spm12/external/fieldtrip/forward/ft_headmodel_concentricspheres.m
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ft_headmodel_concentricspheres.m
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function headmodel = ft_headmodel_concentricspheres(mesh, varargin)
% FT_HEADMODEL_CONCENTRICSPHERES creates a volume conduction model
% of the head based on three or four concentric spheres. For a 3-sphere
% model the spheres represent the skin surface, the outside of the
% skull and the inside of the skull For a 4-sphere model, the surfaces
% describe the skin, the outside-skull, the inside-skull and the inside of the
% cerebro-spinal fluid (CSF) boundaries.
%
% The innermost surface is sometimes also referred to as the brain
% surface, i.e. as the outside of the brain volume.
%
% This function takes as input a single headshape described with
% points and fits the spheres to this surface. If you have a set of
% points describing each surface, then this function fits the spheres
% to all individual surfaces.
%
% Use as
% headmodel = ft_headmodel_concentricspheres(mesh, ...)
%
% Optional input arguments should be specified in key-value pairs and can
% include
% conductivity = vector with the conductivity of each compartment
% fitind = vector with indices of the surfaces to use in fitting the center of the spheres
%
% See also FT_PREPARE_VOL_SENS, FT_COMPUTE_LEADFIELD
% Copyright (C) 2012-2013, Donders Centre for Cognitive Neuroimaging, Nijmegen, NL
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip 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.
%
% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% get the optional input arguments
conductivity = ft_getopt(varargin, 'conductivity'); % default is determined below
fitind = ft_getopt(varargin, 'fitind', 'all');
if any(strcmp(varargin(1:2:end), 'unit')) || any(strcmp(varargin(1:2:end), 'units'))
% the geometrical units should be specified in the input mesh
ft_error('the ''unit'' option is not supported any more');
end
if isnumeric(mesh) && size(mesh,2)==3
% assume that it is a Nx3 array with vertices
% convert it to a structure, this is needed to determine the units further down
mesh = struct('pos', mesh);
elseif isstruct(mesh) && isfield(mesh,'bnd')
% take the triangulated surfaces from the input structure
mesh = mesh.bnd;
end
% replace pnt with pos
mesh = fixpos(mesh);
if ~isstruct(mesh) || ~isfield(mesh, 'pos')
ft_error('the input mesh should be a set of points or a single triangulated surface')
end
% start with an empty volume conductor
headmodel = [];
% ensure that the mesh has units, estimate them if needed
mesh = ft_determine_units(mesh);
% copy the geometrical units into the volume conductor
headmodel.unit = mesh(1).unit;
if isequal(fitind, 'all')
fitind = 1:numel(mesh);
end
% concatenate the vertices of all surfaces
pos = {mesh.pos};
pos = cat(1, pos{:});
% remove double vertices
pos = unique(pos, 'rows');
npos = size(pos, 1);
% fit a single sphere to all combined headshape points
[single_o, single_r] = fitsphere(pos);
fprintf('initial sphere: number of unique surface points = %d\n', npos);
fprintf('initial sphere: center = [%.1f %.1f %.1f]\n', single_o(1), single_o(2), single_o(3));
fprintf('initial sphere: radius = %.1f\n', single_r);
% fit the radius of each concentric sphere to the corresponding surface points
for i = 1:numel(mesh)
npos = size(mesh(i).pos,1);
dist = sqrt(sum(((mesh(i).pos - repmat(single_o, npos, 1)).^2), 2));
headmodel.r(i) = mean(dist);
end
headmodel.o = single_o; % specify the center of the spheres
headmodel.cond = conductivity; % specify the conductivity of the spheres, can be empty up to here
headmodel.type = 'concentricspheres';
% sort the spheres from the smallest to the largest
[headmodel.r, indx] = sort(headmodel.r);
if isempty(headmodel.cond)
% it being empty indicates that the user did not specify a conductivity, use a default instead
if length(headmodel.r)==1
headmodel.cond = 1; % brain
elseif length(headmodel.r)==3
headmodel.cond = [0.3300 0.0042 0.3300]; % brain, skull, skin
elseif length(headmodel.r)==4
headmodel.cond = [0.3300 1 0.0042 0.3300]; % brain, csf, skull, skin
else
ft_error('conductivity values should be specified for each tissue type');
end
else
% the conductivity as specified by the user should be in the same order as the geometries
% sort the spheres from the smallest to the largest ('insidefirst' order)
headmodel.cond = headmodel.cond(indx);
end
for i=1:numel(mesh)
fprintf('concentric sphere %d: radius = %.1f, conductivity = %f\n', i, headmodel.r(i), headmodel.cond(i));
end
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