mesh_bet2matlab - Read FSL BET tesselation (.coo/.dat)
USEAGE: [FV] = mesh_bet2matlab(fileprefix)
This function will load ascii files created by the FSL
BET function, see http://www.fmrib.ox.ac.uk/fsl
When used with the -x option, the FSL BET function can
output the tesselation of the brain surface (ie, only
a fairly smooth, non-detailed, surface), eg:
bet T1 T1_brain -x
The brain tesselation is output into two files, eg:
T1_brain.coo
T1_brain.dat
The T1_brain.coo file contains the co-ordinates of the
vertices, and the .dat file contains the details of
the links between vertices (each line corresponds to
each vertex in the .coo file, and the 1's correspond
to which other vertices they are connected to).
The returned FV struct contains the 'vertices' and
'faces' matrices, which can be input to the patch
command, eg:
Hpatch = patch('Vertices',FV.vertices,'Faces',FV.faces,...
'EdgeColor',[.8 .8 .8],...
'FaceColor',[0.9 0.9 0.9]);
This will plot the mesh as a patch object. See the patch
command and matlab help for more information on coloring
this object.
See also: mesh_freesurfer2matlab0001 function [FV] = mesh_bet2matlab(fileprefix) 0002 0003 % mesh_bet2matlab - Read FSL BET tesselation (.coo/.dat) 0004 % 0005 % USEAGE: [FV] = mesh_bet2matlab(fileprefix) 0006 % 0007 % This function will load ascii files created by the FSL 0008 % BET function, see http://www.fmrib.ox.ac.uk/fsl 0009 % 0010 % When used with the -x option, the FSL BET function can 0011 % output the tesselation of the brain surface (ie, only 0012 % a fairly smooth, non-detailed, surface), eg: 0013 % 0014 % bet T1 T1_brain -x 0015 % 0016 % The brain tesselation is output into two files, eg: 0017 % 0018 % T1_brain.coo 0019 % T1_brain.dat 0020 % 0021 % The T1_brain.coo file contains the co-ordinates of the 0022 % vertices, and the .dat file contains the details of 0023 % the links between vertices (each line corresponds to 0024 % each vertex in the .coo file, and the 1's correspond 0025 % to which other vertices they are connected to). 0026 % 0027 % The returned FV struct contains the 'vertices' and 0028 % 'faces' matrices, which can be input to the patch 0029 % command, eg: 0030 % 0031 % Hpatch = patch('Vertices',FV.vertices,'Faces',FV.faces,... 0032 % 'EdgeColor',[.8 .8 .8],... 0033 % 'FaceColor',[0.9 0.9 0.9]); 0034 % 0035 % This will plot the mesh as a patch object. See the patch 0036 % command and matlab help for more information on coloring 0037 % this object. 0038 % 0039 % See also: mesh_freesurfer2matlab 0040 % 0041 0042 % $Revision: 1.1 $ $Date: 2004/11/12 01:32:35 $ 0043 0044 % Licence: GNU GPL, no implied or express warranties 0045 % History: 03/02 Darren.Weber_at_radiology.ucsf.edu 0046 % 0047 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0048 0049 if ~exist('fileprefix','var'), 0050 error('No input fileprefix'); 0051 end 0052 0053 if findstr('.coo',fileprefix), 0054 fprintf('MESH_BET2MATLAB: Removing .coo extension from ''%s''\n',fileprefix); 0055 fileprefix = strrep(fileprefix,'.coo',''); 0056 end 0057 if findstr('.dat',fileprefix), 0058 fprintf('MESH_BET2MATLAB: Removing .dat extension from ''%s''\n',fileprefix); 0059 fileprefix = strrep(fileprefix,'.dat',''); 0060 end 0061 0062 FV.vertices = readCOO(fileprefix); 0063 0064 Nvertices = size(FV.vertices,1); 0065 0066 edgematrix = readDAT(fileprefix,Nvertices); 0067 0068 FV.faces = edge2face(FV.vertices,edgematrix); 0069 0070 return 0071 0072 0073 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0074 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0075 function faces = edge2face(vertices,edgematrix) 0076 0077 Nvertices = size(vertices,1); 0078 0079 plot3(vertices(:,1),vertices(:,2),vertices(:,3),'b.'), hold on 0080 0081 for i = 1:Nvertices, 0082 0083 % Get current vertex XYZ coordinates 0084 v = vertices(i,:); 0085 0086 plot3(v(:,1),v(:,2),v(:,3),'go'); 0087 0088 % Get neighbouring vertex XYZ coordinates 0089 vn = vertices(find(edgematrix(i,:)),:); 0090 0091 plot3(vn(:,1),vn(:,2),vn(:,3),'ro'); 0092 0093 0094 faces = tri([v;vn]); 0095 0096 0097 0098 0099 return 0100 0101 0102 0103 0104 0105 end 0106 0107 faces = []; 0108 0109 return 0110 0111 0112 function faces = tri(V) 0113 0114 % Must identify angle of rotation from 0115 % central vertex, V(1,:), to all other vertices 0116 % in a counterclockwise direction 0117 0118 % First translate all vertices to an origin 0119 % given by the central vertex 0120 Vo = V - repmat(V(1,:),size(V,1),1); 0121 0122 % Find direction cosines for line from centre to vertex 0123 d = zeros(size(Vo,1),1); 0124 l = zeros(size(Vo,1),1); 0125 m = zeros(size(Vo,1),1); 0126 n = zeros(size(Vo,1),1); 0127 0128 for i = 1:length(Vo), 0129 0130 x = Vo(i,1); y = Vo(i,2); z = Vo(i,3); 0131 0132 d(i) = sqrt( (x)^2 + (y)^2 + (z)^2 ); 0133 0134 if d(i) > 0, 0135 l(i) = x/d(i); % cos alpha 0136 m(i) = y/d(i); % cos beta 0137 n(i) = z/d(i); % cos gamma 0138 end 0139 end 0140 0141 0142 faces = []; 0143 0144 0145 %hold off 0146 %plot3(Vo(:,1),Vo(:,2),Vo(:,3),'b.'), view(2), hold on 0147 0148 0149 return 0150 0151 0152 0153 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0154 function vertices = readCOO(fileprefix) 0155 0156 [path,name,ext] = fileparts(strcat(fileprefix,'.coo')); 0157 file = fullfile(path,[name ext]); 0158 0159 fid = fopen(file,'r'); 0160 0161 if isequal(fid,-1), 0162 S=sprintf('Could not open file: "%s"',file); 0163 error(S); 0164 else 0165 fprintf('...Reading BET vertices...'); 0166 tic; 0167 0168 % Read vertices 0169 vertices = fscanf(fid,'%s%f%f%f',[4,inf]); 0170 fclose(fid); 0171 0172 % remove last row (all zeros) and translate 0173 vertices = vertices(2:4,:)'; 0174 0175 t = toc; 0176 fprintf('...done (%6.2f sec).\n',t); 0177 end 0178 0179 return 0180 0181 0182 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0183 function edgematrix = readDAT(fileprefix,Nvertices) 0184 0185 [path,name,ext] = fileparts(strcat(fileprefix,'.dat')); 0186 file = fullfile(path,[name ext]); 0187 0188 fid = fopen(file,'r'); 0189 0190 if isequal(fid,-1), 0191 S=sprintf('Could not open file: "%s"',file); 0192 error(S); 0193 else 0194 fprintf('...Reading BET edge matrix...'); 0195 tic; 0196 0197 % Read faces 0198 edgematrix = fscanf(fid,'%1d',[Nvertices,Nvertices]); 0199 fclose(fid); 0200 0201 t = toc; 0202 fprintf('...done (%6.2f sec).\n',t); 0203 end 0204 return