mesh_emse2brainstorm

 mesh_emse2brainstorm - Convert EMSE meshes (.wfr) to brainstorm format

 USEAGE: [Comment,Faces,Vertices] = mesh_emse2brainstorm(fileprefix,meshes)

 This routine calls the mesh_emse_wfr2matlab routine for
 each layer of the subject tesselation required in brainstorm
 (ie, cortex, inner skull, scalp).  It returns the variables
 required by BrainStorm for source modelling.  The EMSE coordinate
 framework is different from that of Neuroscan and Brainstorm, so
 all vertices and faces are rearranged to suit.

 fileprefix should be a string containing the path and subject
 code for the emse meshes to load and convert.  For example:
 'c:\data\c01_'.  If the cell array 'meshes' is given, it should 
 contain the names of the meshes to load.  Only those meshes will 
 be loaded. For example: meshes = {'cortex','innerskull','scalp'} 
 is the default.  This routine then loads the following EMSE meshes:

 c:\data\c01_cortex.wfr
 c:\data\c01_innerskull.wfr
 c:\data\c01_scalp.wfr

 The workspace variables created are saved, in the brainstorm 
 file format, into the file called 'c:\data\c01_subjecttess.mat'.
 The variables from this file can be loaded using the matlab 'load' 
 command. To plot the default cortex, skull & scalp BrainStorm data:

 Hpatch1 = patch('Vertices',Vertices{1}','Faces',Faces{1},...
                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
 Hpatch2 = patch('Vertices',Vertices{2}','Faces',Faces{2},...
                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
 Hpatch3 = patch('Vertices',Vertices{3}','Faces',Faces{3},...
                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);

 See the BrainStorm website at http://neuroimage.usc.edu/brainstorm/
 for more information about the BrainStorm toolbox and the format
 and content of the subjecttess variables.  Also, see the EMSE/MRVU
 website at http://www.sourcesignal.com.

0001 function [Comment,Faces,Vertices] = mesh_emse2brainstorm(file,meshes)
0002 
0003 % mesh_emse2brainstorm - Convert EMSE meshes (.wfr) to brainstorm format
0004 %
0005 % USEAGE: [Comment,Faces,Vertices] = mesh_emse2brainstorm(fileprefix,meshes)
0006 %
0007 % This routine calls the mesh_emse_wfr2matlab routine for
0008 % each layer of the subject tesselation required in brainstorm
0009 % (ie, cortex, inner skull, scalp).  It returns the variables
0010 % required by BrainStorm for source modelling.  The EMSE coordinate
0011 % framework is different from that of Neuroscan and Brainstorm, so
0012 % all vertices and faces are rearranged to suit.
0013 %
0014 % fileprefix should be a string containing the path and subject
0015 % code for the emse meshes to load and convert.  For example:
0016 % 'c:\data\c01_'.  If the cell array 'meshes' is given, it should
0017 % contain the names of the meshes to load.  Only those meshes will
0018 % be loaded. For example: meshes = {'cortex','innerskull','scalp'}
0019 % is the default.  This routine then loads the following EMSE meshes:
0020 %
0021 % c:\data\c01_cortex.wfr
0022 % c:\data\c01_innerskull.wfr
0023 % c:\data\c01_scalp.wfr
0024 %
0025 % The workspace variables created are saved, in the brainstorm
0026 % file format, into the file called 'c:\data\c01_subjecttess.mat'.
0027 % The variables from this file can be loaded using the matlab 'load'
0028 % command. To plot the default cortex, skull & scalp BrainStorm data:
0029 %
0030 % Hpatch1 = patch('Vertices',Vertices{1}','Faces',Faces{1},...
0031 %                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
0032 % Hpatch2 = patch('Vertices',Vertices{2}','Faces',Faces{2},...
0033 %                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
0034 % Hpatch3 = patch('Vertices',Vertices{3}','Faces',Faces{3},...
0035 %                 'EdgeColor',[.6 .6 .6],'FaceColor',[0.9 0.9 0.9]);
0036 %
0037 % See the BrainStorm website at http://neuroimage.usc.edu/brainstorm/
0038 % for more information about the BrainStorm toolbox and the format
0039 % and content of the subjecttess variables.  Also, see the EMSE/MRVU
0040 % website at http://www.sourcesignal.com.
0041 %
0042 
0043 % $Revision: 1.1 $ $Date: 2004/11/12 01:32:35 $
0044 
0045 % Licence:  GNU GPL, no implied or express warranties
0046 % History:  01/02 Darren.Weber_at_radiology.ucsf.edu
0047 %
0048 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0049 
0050 % Check for existence of saved file
0051 brainstormfile = strcat(file,'subjecttess');
0052 
0053 fid = fopen(strcat(brainstormfile,'.mat'),'r');
0054 
0055 if (fid ~= -1),
0056     fclose(fid);
0057     fprintf('\nLoading BrainStorm data from %s',brainstormfile);
0058     fprintf('\nTo reload data from EMSE, first delete/rename BrainStorm data.\n\n');
0059     load(brainstormfile);
0060     return;
0061 else
0062     
0063     if ~exist('meshes','var'),
0064         meshes = {'cortex','innerskull','scalp'};
0065     end
0066     
0067     Comment = meshes;
0068     Faces = cell(size(meshes));
0069     Vertices = cell(size(meshes));
0070     
0071     % Load EMSE data
0072     options = {'vertex','patch'}; % only load vertex & patch data
0073     for i = 1:max(size(meshes)),
0074         fprintf('\nLoading EMSE mesh: %s\n',meshes{i});
0075         inputfile = strcat(file,meshes{i},'.wfr');
0076         [vertices,patches] = mesh_emse2matlab(inputfile,options);
0077         % EMSE vertices are rearranged here, swapping x & y to
0078         % match the coordinate frame of the NeuroScan 3Dspace electrodes.
0079         Vertices{i} = [ vertices.y; vertices.x; vertices.z ]; % 3 x n
0080         % The faces remain the same order as they refer only to the
0081         % vertices as a set of 3D coordinates.
0082         Faces{i} = [ patches.vertex1; patches.vertex2; patches.vertex3 ]'; % m x 3
0083     end
0084     
0085     fprintf('\nSaving BrainStorm data to %s',brainstormfile);
0086     save(brainstormfile, 'Comment', 'Faces', 'Vertices');
0087 end