Plotting the result of source reconstruction on a cortical mesh
The following function can be used to plot the results of source reconstruction on a cortical surface sheet. It assumes a cortical sheet surf, described by vertices (pnt) and triangles (tri). The vertices can be used as positions in ft_sourceanalysis by specifying cfg.sourcemodel.pos = surf.pnt, and cfg.sourcemodel.tri = surf.tri. The resulting source structure (i.e. obtained after running ft_sourceanalysis) can subsequently be used by ft_sourceanalysis, using cfg.method = ‘surface’. If the source level data also contains a time-dimension, the function ft_sourceplot_interactive can also be used. The below code was written before the already mentioned functionality was implemented in FieldTrip. There is no strict need to use it, nor a guarantee that it will still work.
function [handles] = myownsurfplot(cfg,surf,source)
% function [handles] = myownsurfplot(cfg,surf,source)
%
% allows to plot source results obtained from a cortical mesh
%
% cfg - opacity: specifies the opacities of the vertices e.g., [0,1]
% cfg - colormapping: defines the colorrange of the vertices e.g., [0,1]
% cfg - edgealpha: defines the transparency of the edges for identifying gyri & sulci, e.g., 0.2
% cfg - mask matrix specifying opacity, format: [n,1] for n vertices
if nargin < 3
cfg = struct();
end
cortex_light = [0.781 0.762 0.664];
cortex_dark = [0.781 0.762 0.664]/2;
sourcevals = source.avg.pow(:);
backgcolor = repmat(cortex_light, size(surf.pnt,1), 1);
if ~isfield(cfg,'opacity')
opacmin = min((source.avg.pow(:)));
opacmax = max((source.avg.pow(:)));
else
opacmin = cfg.opacity(1);
opacmax = cfg.opacity(2);
end
if ~isfield(cfg,'colormapping')
fcolmin = min((source.avg.pow(:)));
fcolmax = max((source.avg.pow(:)));
else
fcolmin = cfg.opacity(1);
fcolmax = cfg.opacity(2);
end
if ~isfield(cfg,'edgealpha'), edgealpha = 1; end;
if ~isfield(cfg,'mask'),
maskval = source.avg.pow(:);
else
maskval = cfg.mask;
end
figure;
h1 = patch('Vertices', surf.pnt, 'Faces', surf.tri, 'FaceVertexCData', backgcolor , 'FaceColor', 'interp');
%set(h1, 'EdgeColor', 'none');
set(h1, 'EdgeColor', [0,0,0],'EdgeAlpha',edgealpha);
axis off;
axis vis3d;
axis equal;
h2 = patch('Vertices', surf.pnt, 'Faces', surf.tri, 'FaceVertexCData', sourcevals , 'FaceColor', 'interp');
%set(h2, 'EdgeColor', 'none');
set(h2, 'EdgeColor', [0,0,0],'EdgeAlpha',edgealpha);
set(h2, 'FaceVertexAlphaData', maskval);
set(h2, 'FaceAlpha', 'interp');
set(h2, 'AlphaDataMapping', 'scaled');
alim(gca, [opacmin opacmax]);
caxis(gca,[fcolmin fcolmax]);
lighting gouraud
colorbar;
handles.h1 = h1;
handles.h2 = h2;