plotting_source_surface.md

title	tags	redirect_from
Plotting the result of source reconstruction on a cortical mesh	example plotting source	/example/plotting_the_result_of_soruce_reconstructing_on_a_cortical_mesh/

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;