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Scripts_Sharing/ISFC toolbox/Utilities/Plotting/show_FSmesh.m
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show_FSmesh.m
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function myH=show_FSmesh(hemi,meshType,varargin)
% SHOW_FSMESH show a freesurfer 3-dimensional hemisphere mesh
%
% IN:
% hemi - a char array containing 'l','r', or 'lr', indicating which hemi-
% sphere to display
% meshtype - a char array containing mesh type ('white')
% 'faceColor': ColorSpec - colour for the faces of the brain mesh
% triangles
% 'faceAlpha': scalar between 0 and 1 - alpha transparency value to
% use for brain mesh triangles (0: fully transparent, 1: fully
% opaque)
% 'edgeColor': ColorSpec - colour for the edges of the brain mesh
% triangles
% 'edgeAlpha': scalar between 0 and 1 - alpha transparency value to
% use for brain mesh triangle edges (0: fully transparent, 1: fully
% opaque)
% 'reducePatchVal': scalar, fraction of patches to keep - increasing
% from the default value may crash Matlab due to a bug in Matlab.
% OUT:
% myH: a vector of handles to patch objects
%
% v1.0 Nov 2009 Jonas Richiardi
% - inital release based on read_surf/trisurf snippet by Markus Gschwind
% v1.1 2009 Dec 10 Jonas Richiardi
% - code clean up
% - fix for alpha values crashing in 2-hemispheres display (known bug
% 484445): use subdivision algorithm to "downsample" Delaunay triangulation
% This is a better solution in this case than those suggested in
% http://www.mathworks.com/support/bugreports/484445
% v1.2 2010 Jul Jonas Richiardi
% - fix a bug due to reducepatch does not setting CData and FaceVertexCData
% after reducing the vertex and face count (despite the doc saying it does
% not set the Faces and Vertices properties). Now CData and FaceVertexCData
% are in sync.
[createFigure,FaceColor,EdgeColor,FaceAlpha,EdgeAlpha,useConvexHull,...
reducePatchVal]=process_options(varargin,...
'createFigure',true,'FaceColor',[0.8 0.8 0.8],'EdgeColor',[0.5 0.5 0.5],...
'FaceAlpha',0.2,'EdgeAlpha',0.05,'useConvexHull',false,'reducePatchVal',...
0.015);
%% sanity check
hemiSupported={'l','r','lr'};
meshTypeSupported={'white'};
if all(cellfun('isempty',strfind(hemiSupported,hemi)))
error(['Unsupported hemi type: ' hemi]);
end
if all(cellfun('isempty',strfind(meshTypeSupported,meshType)))
error(['Unsupported mesh type: ' meshType]);
end
%% setup host-specific options and paths
location=whereAmIRunning;
if strcmp(location,'jmac')
% set root path to FreeSurfer application
FSROOTPATH='/Applications/freesurfer/';
else
error('Please modify whereAmIRunning.m for your own settings');
end
% generate path where to find the surface mesh files
FSSURFPATH=fullfile(FSROOTPATH,'subjects','fsaverage','surf');
if exist('read_surf')~=2
addpath(fullfile(FSROOTPATH,'matlab'));
end
if (createFigure==true)
figure;
end
hold on;
%% load surfaces
% surfaces are encoded by Delaunay triangulation (region-adjacency graph
% of Voronoi tesselation - Delaunay graph is the dual of the Voronoi
% diagram (Okabe et al 200))
% faces is the m x 3 triangulation matrix - the set of simplices (triangle)
% that make the triangulation. Each row (in simplex-vertex format) encodes
% the three vertices a triangular face via indexing into a matrix containing
% the 3D space location of vertices
% e.g. 1 4 2 says that this triangles is made up of vertices 1, 4, and 2,
% whose 3D spatial locations are found in the vertices matrix.
myH=zeros(numel(hemi),1);
for h=1:numel(hemi)
if strcmp(hemi(h),'r')
f_surf=['rh.' meshType];
elseif strcmp(hemi(h),'l')
f_surf=['lh.' meshType];
else
error('Wrong hemi specification. How on earth did you trigger this code path?');
end
% read surface using freesurfer function
% note we could access matlab functionality for the TriRep class via
% trirep(faces+,vertices(:,1)... etc)
[vertices,faces]=read_surf(fullfile(FSSURFPATH,f_surf));
vertices=single(vertices); % save memory
nVertices = size(vertices,1);
if (useConvexHull==true)
disp('Computing convex hull...');
myConvHull = convhulln(double(vertices));
myH(h)=trisurf(myConvHull+1,vertices(:,1),vertices(:,2),vertices(:,3),...
'FaceColor',FaceColor,'EdgeColor',EdgeColor);
%disp('Doing mesh subdivision...');
%reducepatch(myH(h),0.05);
else
% plot Delaunay triangulated mesh
myH(h)=trisurf(faces+1,vertices(:,1),vertices(:,2),vertices(:,3),...
ones(nVertices,1),'FaceColor',FaceColor,'EdgeColor',EdgeColor);
% do subdivision to reduce number of faces
% another solution would be to set(gca,'DrawMode','Fast'); as per
% 484445 bug report
%disp('Doing mesh subdivision...');
reducepatch(myH(h),reducePatchVal); % higher may cause crash, still too many faces
% CData and FaceVertexCData are now desynchronised, so fix them
% manually
nf=get(myH(h),'Faces');
nv=get(myH(h),'Vertices');
% 1) fix CData to be 3xsize(Faces,1), all ones or actually FaceColor
set(myH(h),'CData',repmat(FaceColor,3,size(nf,1)));
% 2) fix FaceVertexCData to be nVertices x 1
set(myH(h),'FaceVertexCData',repmat(FaceColor,size(nv,1),1));
end
xlabel('left-right'); ylabel('posterior-anterior'); zlabel('ventral-dorsal');
clear vertices faces;
if (h==1)
axis equal;
view(0,90);
end
end
%set(gca,'DrawMode','Fast');
% set transparency now, with reduced number of faces (does not crash)
for h=1:numel(hemi)
set(myH(h),'EdgeAlpha',EdgeAlpha,'FaceAlpha',FaceAlpha,...
'DiffuseStrength',1,'SpecularStrength',0);
end
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