emse_write_wfr - write mesh to EMSE wireframe (.wfr)
emse_write_wfr(file,vertex,face,meshtype)
Write a .wfr file, in minor revision 3 format (ascii).
See the EMSE website at http://www.sourcesignal.com
for more information on file formats.
This function assumes the vertex coordinate axes are
+X anterior, +Y left, +Z superior
vertex - Nx3 matrix of XYZ values (in meters)
face - Nx3 matrix of vertex indices for triangulation
meshtype - a string, with values of:
'unknown',
'scalp',
'outer skull',
'inner skull',
'cortex',0001 function emse_write_wfr(file,vertex,face,meshtype) 0002 0003 % emse_write_wfr - write mesh to EMSE wireframe (.wfr) 0004 % 0005 % emse_write_wfr(file,vertex,face,meshtype) 0006 % 0007 % Write a .wfr file, in minor revision 3 format (ascii). 0008 % See the EMSE website at http://www.sourcesignal.com 0009 % for more information on file formats. 0010 % 0011 % This function assumes the vertex coordinate axes are 0012 % +X anterior, +Y left, +Z superior 0013 % 0014 % vertex - Nx3 matrix of XYZ values (in meters) 0015 % face - Nx3 matrix of vertex indices for triangulation 0016 % meshtype - a string, with values of: 0017 % 0018 % 'unknown', 0019 % 'scalp', 0020 % 'outer skull', 0021 % 'inner skull', 0022 % 'cortex', 0023 % 0024 0025 0026 % $Revision: 1.1 $ $Date: 2005/01/21 04:33:18 $ 0027 0028 0029 % Copyright (C) 2004 Darren L. Weber 0030 % 0031 % This program is free software; you can redistribute it and/or 0032 % modify it under the terms of the GNU General Public License 0033 % as published by the Free Software Foundation; either version 2 0034 % of the License, or (at your option) any later version. 0035 % 0036 % This program is distributed in the hope that it will be useful, 0037 % but WITHOUT ANY WARRANTY; without even the implied warranty of 0038 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 0039 % GNU General Public License for more details. 0040 % 0041 % You should have received a copy of the GNU General Public License 0042 % along with this program; if not, write to the Free Software 0043 % Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 0044 % USA. 0045 0046 0047 % History: 12/2004 Darren.Weber_at_radiology.ucsf.edu 0048 % - created function from mesh_emse2matlab 0049 % 0050 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0051 0052 ver = '$Revision: 1.1 $ $Date: 2005/01/21 04:33:18 $'; 0053 fprintf('\nEMSE_WRITE_WFR [v%s]\n',ver(11:15)); 0054 0055 [path,name,ext] = fileparts(file); 0056 ext = '.wfr'; 0057 file = fullfile(path,[name ext]); 0058 fprintf('...writing to: %s\n',file); 0059 0060 fid = fopen(file,'w','ieee-le'); 0061 0062 if(fid == -1), 0063 msg = sprintf('...could not open file: %s',file); 0064 error(msg); 0065 else 0066 0067 % Write prolog 0068 fprintf(fid,'3\t4000\n'); 0069 fprintf(fid,'3\n'); 0070 0071 % Write mesh type 0072 type = lower(meshtype); 0073 switch type, 0074 case 'unknown', fprintf(fid, '0\n'); 0075 case 'scalp', fprintf(fid, '40\n'); 0076 case 'outer skull', fprintf(fid, '80\n'); 0077 case 'inner skull', fprintf(fid,'100\n'); 0078 case 'cortex', fprintf(fid,'200\n'); 0079 case 'pial', fprintf(fid,'200\n'); % cortex variant 0080 case 'white', fprintf(fid,'200\n'); % cortex variant 0081 case 'smoothwm', fprintf(fid,'200\n'); % cortex variant 0082 otherwise, fprintf(fid, '0\n'); 0083 fprintf('\n...WARNING, unknown meshtype!\n\n'); 0084 end 0085 0086 0087 % EMSE Voxel Coordinates 0088 % Voxel coordinates measure location in terms of the voxels inherent in 0089 % the given volumetric set. The origin is the bottom (inferior) axial 0090 % slice, the posterior row and in the rightmost column. This coordinate 0091 % system is right-handed (although, internally, the origin is in the 0092 % anterior row, and thus is left-handed; this representation is not 0093 % available to the user). The order of the displayed coordinates is 0094 % (slice#, row#, column#). 0095 % 0096 % EMSE MRI Coordinates 0097 % MRI coordinates share the same origin as internal voxel coordinates, 0098 % but differ from the latter in two ways: first, the coordinates 0099 % are measured in millimeters, not voxels. Secondly, the origin is that 0100 % of the internal representation; that is, the inferior slice, anterior 0101 % row and rightmost column. As mentioned above, this internal representation 0102 % is left-handed. To correct for this, the row axis is numbered in the 0103 % opposite direction, making the displayed coordinate system right-handed. 0104 % The order of the displayed coordinates is (x, y, z). 0105 0106 % Given a point P(x,y,z) in head frame (the activation point on the 0107 % cortical mesh) and you want to find the corresponding voxel in the 0108 % vmi file. Symbolically you have P(head) and you want to find P(voxel). 0109 % 0110 % 1. The registration file contains the matrix HeadToImage, 0111 % so P(MRI-mm) = HeadToImage*P(head), where P(MRI-mm) is the 0112 % point in MRI coordinates. 0113 % 2. From the voxel size, you can find P(MRI-voxel), which 0114 % is the MRI coordinates expressed in voxels 0115 % 3. Use the offset between the MRI coordinate frame and 0116 % the Image coordinate frame to find P(voxel). 0117 % 0118 %Demetrios Voreades, Ph.D. 0119 %Applications Engineer, Source Signal Imaging 0120 % 0121 0122 0123 % Rotate -90 degrees around Z, given that emse coordinates 0124 % have +X through Nasion and +Y through left ear. 0125 fprintf('...assuming coordinate axes are +X anterior, +Y left, +Z superior\n'); 0126 %vertex = rz(vertex,-90,'degrees'); 0127 0128 % Write vertex data 0129 for v = 1:size(vertex,1), 0130 fprintf(fid,'v\t%12.8f\t%12.8f\t%12.8f\n',vertex(v,1),vertex(v,2),vertex(v,3)); 0131 end 0132 0133 % matlab vertex indices start at one, 0134 % not zero, so we subtract one from matlab values 0135 fprintf('...subtracting 1 from face indices, so they start at zero\n'); 0136 face = face - 1; 0137 for t = 1:size(face,1), 0138 fprintf(fid,'t\t%d\t%d\t%d\t\n',face(t,1),face(t,2),face(t,3)); 0139 end 0140 0141 fclose(fid); 0142 0143 end 0144 0145 return