Calculate leadfield matrix and create leadfiled file (.basis.mat).
(VBMEG public function)
This function can calculate leadfield matrix for using the following
numerical methods:
MEG Sphere model (Sarvas equation)
MEG 1-shell BEM (boundary element method)
MEG Spherical harmonics expansion
EEG 3-shell Sphere model
EEG 3-shell BEM
[syntax]
vb_job_leadfield(proj_root, basis_parm)
[input]
proj_root : <<string>> VBMEG project root directory.
basis_parm: <<struct>> Parameters for leadfield calculation.
--- fields of basis_parm
brain_file : <<string>> Cortical surface model file (.brain.mat).
area_file : <<string>> Cortical area file (.area.mat).
meg_file : <<string>> MEG-MAT or EEG-MAT file (.meg.mat).
basis_file : <<string>> Leadfield file (.basis.mat).
bem_mode : <<int>> Specify numerical method for calculating
leadfield.
=0: MEG Sphere model (Sarvas equation).
=1: MEG 1-shell BEM (boundary element method).
=2: MEG Spherical harmonics expansion.
=3: EEG 3-shell Sphere model.
=4: EEG 3-shell BEM.
head_file : <optional><<string>> Head model file (.head.mat). This
parameter is referred if the lead field is calculated by
BEM or spherical harmonics expansion (see 'bem_mode').
expansion
Basis_mode : <<int>> Degree of freedom of current direction. Not only
the DOF, but also the direction of current dipoles at each
vertex is also specified by this parameter. Currently
VBMEG supports Basis_mode=1 (1st June, 2010).
=1: Single dipole perpendicular to the cortical surface.
=2: Double dipoles tangental to the cortical surface.
=3: Triple dipoles parallel to three axes (x, y, z).
Vcenter : <<vector>> Coordinate value of the head center (1x3 on
SPM_Right_m).
func_order : <<int?>> Order of spherical harmonics function. This
parameter is effective when employing spherical harmonics
expansion (see 'bem_mode').
sigma : <<vector>> Conductivity from innermost to outermost.
radius : <<vector>> Relative radius of sphere from innermost to
outermost.
area_key : <optional><<string>>
normal_mode: <optional><int>
Recalc : <optional>
---
[output]
Leadfield file (.basis.mat) is created with filename specified by
'basis_file' field. If BEM is used, head model file (.head.mat) is
updated with a matrix, which depends only on the head model, not on the
cortical surface model. So, if size of .head.mat file become large, it
is not an error.
[note]
This function call the following sub-functions in accordance with
basis_parm.bem_mode:
vb_job_leadfield_meg_sphere
vb_job_leadfield_meg_bem
vb_job_leadfield_meg_harmonics
vb_job_leadfield_eeg_sphere
vb_job_leadfield_eeg_bem
'vbmeg_inst' structure have constants for specifying the numerical
method and model related to leadfield calculation. Those constants are
recommended to specify parameters for readability of your program.
--- Constants for 'basis_parm.bem_mode'
vbmeg_inst.const.BASIS_MEG_SPHERE = 0
vbmeg_inst.const.BASIS_MEG_BEM = 1
vbmeg_inst.const.BASIS_MEG_HARMONICS = 2
vbmeg_inst.const.BASIS_MEG_SPHERE = 3
vbmeg_inst.const.BASIS_MEG_BEM = 4
--- Constants for 'basis_parm.Basis_mode'
vbmeg_inst.const.CURRENT_NORMAL = 1
vbmeg_inst.const.CURRENT_TANGENT = 2
vbmeg_inst.const.CURRENT_3D = 3
--- Constants for 'basis_parm.normal_mode
vbmeg_inst.const.NORMAL_ADJACENT_MEAN = 0
vbmeg_inst.const.NORMAL_NEIGHBOR_MEAN = 1
---
[history]
2007-01-26 (Sako) reworked the architecture
2008-10-15 Taku Yoshioka
Support '.sensortype' parameter (argument check)
2010-05-?? Taku Yoshioka
Minor change (verbose level support)
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function vb_job_leadfield(proj_root, basis_parm) 0002 % Calculate leadfield matrix and create leadfiled file (.basis.mat). 0003 % (VBMEG public function) 0004 % 0005 % This function can calculate leadfield matrix for using the following 0006 % numerical methods: 0007 % MEG Sphere model (Sarvas equation) 0008 % MEG 1-shell BEM (boundary element method) 0009 % MEG Spherical harmonics expansion 0010 % EEG 3-shell Sphere model 0011 % EEG 3-shell BEM 0012 % 0013 % [syntax] 0014 % vb_job_leadfield(proj_root, basis_parm) 0015 % 0016 % [input] 0017 % proj_root : <<string>> VBMEG project root directory. 0018 % basis_parm: <<struct>> Parameters for leadfield calculation. 0019 % --- fields of basis_parm 0020 % brain_file : <<string>> Cortical surface model file (.brain.mat). 0021 % area_file : <<string>> Cortical area file (.area.mat). 0022 % meg_file : <<string>> MEG-MAT or EEG-MAT file (.meg.mat). 0023 % basis_file : <<string>> Leadfield file (.basis.mat). 0024 % bem_mode : <<int>> Specify numerical method for calculating 0025 % leadfield. 0026 % =0: MEG Sphere model (Sarvas equation). 0027 % =1: MEG 1-shell BEM (boundary element method). 0028 % =2: MEG Spherical harmonics expansion. 0029 % =3: EEG 3-shell Sphere model. 0030 % =4: EEG 3-shell BEM. 0031 % head_file : <optional><<string>> Head model file (.head.mat). This 0032 % parameter is referred if the lead field is calculated by 0033 % BEM or spherical harmonics expansion (see 'bem_mode'). 0034 % expansion 0035 % Basis_mode : <<int>> Degree of freedom of current direction. Not only 0036 % the DOF, but also the direction of current dipoles at each 0037 % vertex is also specified by this parameter. Currently 0038 % VBMEG supports Basis_mode=1 (1st June, 2010). 0039 % =1: Single dipole perpendicular to the cortical surface. 0040 % =2: Double dipoles tangental to the cortical surface. 0041 % =3: Triple dipoles parallel to three axes (x, y, z). 0042 % Vcenter : <<vector>> Coordinate value of the head center (1x3 on 0043 % SPM_Right_m). 0044 % func_order : <<int?>> Order of spherical harmonics function. This 0045 % parameter is effective when employing spherical harmonics 0046 % expansion (see 'bem_mode'). 0047 % sigma : <<vector>> Conductivity from innermost to outermost. 0048 % radius : <<vector>> Relative radius of sphere from innermost to 0049 % outermost. 0050 % area_key : <optional><<string>> 0051 % normal_mode: <optional><int> 0052 % Recalc : <optional> 0053 % --- 0054 % 0055 % [output] 0056 % Leadfield file (.basis.mat) is created with filename specified by 0057 % 'basis_file' field. If BEM is used, head model file (.head.mat) is 0058 % updated with a matrix, which depends only on the head model, not on the 0059 % cortical surface model. So, if size of .head.mat file become large, it 0060 % is not an error. 0061 % 0062 % [note] 0063 % This function call the following sub-functions in accordance with 0064 % basis_parm.bem_mode: 0065 % vb_job_leadfield_meg_sphere 0066 % vb_job_leadfield_meg_bem 0067 % vb_job_leadfield_meg_harmonics 0068 % vb_job_leadfield_eeg_sphere 0069 % vb_job_leadfield_eeg_bem 0070 % 0071 % 'vbmeg_inst' structure have constants for specifying the numerical 0072 % method and model related to leadfield calculation. Those constants are 0073 % recommended to specify parameters for readability of your program. 0074 % --- Constants for 'basis_parm.bem_mode' 0075 % vbmeg_inst.const.BASIS_MEG_SPHERE = 0 0076 % vbmeg_inst.const.BASIS_MEG_BEM = 1 0077 % vbmeg_inst.const.BASIS_MEG_HARMONICS = 2 0078 % vbmeg_inst.const.BASIS_MEG_SPHERE = 3 0079 % vbmeg_inst.const.BASIS_MEG_BEM = 4 0080 % --- Constants for 'basis_parm.Basis_mode' 0081 % vbmeg_inst.const.CURRENT_NORMAL = 1 0082 % vbmeg_inst.const.CURRENT_TANGENT = 2 0083 % vbmeg_inst.const.CURRENT_3D = 3 0084 % --- Constants for 'basis_parm.normal_mode 0085 % vbmeg_inst.const.NORMAL_ADJACENT_MEAN = 0 0086 % vbmeg_inst.const.NORMAL_NEIGHBOR_MEAN = 1 0087 % --- 0088 % 0089 % [history] 0090 % 2007-01-26 (Sako) reworked the architecture 0091 % 2008-10-15 Taku Yoshioka 0092 % Support '.sensortype' parameter (argument check) 0093 % 2010-05-?? Taku Yoshioka 0094 % Minor change (verbose level support) 0095 % 0096 % Copyright (C) 2011, ATR All Rights Reserved. 0097 % License : New BSD License(see VBMEG_LICENSE.txt) 0098 0099 global vbmeg_inst; 0100 const = vbmeg_inst.const; 0101 0102 % --- CHECK ARGUMENTS --- % 0103 if ~exist('proj_root', 'var'), proj_root = []; end; 0104 if ~exist('basis_parm', 'var'), basis_parm = []; end; 0105 [proj_root, basis_parm] = inner_check_arguments(const, proj_root, basis_parm); 0106 0107 % --- MAIN PROCEDURE --------------------------------------------------------- % 0108 % 0109 switch basis_parm.bem_mode 0110 case const.BASIS_MEG_SPHERE, 0111 [basis, basis_parm] = vb_job_leadfield_meg_sphere(proj_root, basis_parm); 0112 0113 case const.BASIS_MEG_BEM, 0114 [basis, basis_parm] = vb_job_leadfield_meg_bem(proj_root, basis_parm); 0115 0116 case const.BASIS_MEG_HARMONICS, 0117 [basis, basis_parm] = vb_job_leadfield_meg_harmonics(proj_root, basis_parm); 0118 0119 case const.BASIS_EEG_SPHERE, 0120 [basis, basis_parm] = vb_job_leadfield_eeg_sphere(proj_root, basis_parm); 0121 0122 case const.BASIS_EEG_BEM, 0123 [basis, basis_parm] = vb_job_leadfield_eeg_bem(proj_root, basis_parm); 0124 end 0125 0126 inner_terminate(const, proj_root, basis_parm, basis); 0127 % 0128 % --- MAIN PROCEDURE --------------------------------------------------------- % 0129 0130 0131 % --- INNER FUNCTIONS -------------------------------------------------------- % 0132 % 0133 % --- inner_terminate() 0134 % 0135 function inner_terminate(const, proj_root, basis_parm, basis) 0136 0137 % const.BASIS_MEG_SPHERE; % MEG Sphere model (Sarvas) 0138 % const.BASIS_MEG_BEM; % MEG BEM 0139 % const.BASIS_MEG_HARMONICS;% MEG Spherical harmonics expansion 0140 % const.BASIS_EEG_SPHERE; % EEG 3-shell Sphere model 0141 % const.BASIS_EEG_BEM; % EEG 3-shell BEM 0142 0143 bem_name = { ... 0144 'MEG spherical model (Sarvas)'; ... 0145 'MEG BEM 1 shell model'; ... 0146 'MEG spherical harmonics expansion'; ... 0147 'EEG spherical 3 shell model'; ... 0148 'EEG BEM 3 shell model'; ... 0149 }; 0150 0151 switch basis_parm.bem_mode 0152 case const.BASIS_MEG_SPHERE 0153 calc_type = bem_name{1}; 0154 0155 case const.BASIS_MEG_BEM 0156 calc_type = bem_name{2}; 0157 0158 case const.BASIS_MEG_HARMONICS 0159 calc_type = bem_name{3}; 0160 0161 case const.BASIS_EEG_SPHERE 0162 calc_type = bem_name{4}; 0163 0164 case const.BASIS_EEG_BEM 0165 calc_type = bem_name{5}; 0166 0167 otherwise 0168 calc_type = 'unknown calculation type'; 0169 end 0170 0171 vb_disp(sprintf('Leadfield calculation : %s', calc_type)); 0172 vb_disp(sprintf('Current direction = %d',basis_parm.Basis_mode)); 0173 0174 if isfield(basis_parm, 'normal_mode') ... 0175 & basis_parm.normal_mode == const.NORMAL_NEIGHBOR_MEAN, 0176 vb_disp('Normal vector is averaged over neighborhood'); 0177 end 0178 0179 % Output file path 0180 basis_file = [proj_root filesep basis_parm.basis_file]; 0181 vb_disp(sprintf('Save basis file [%s]', basis_file)); 0182 vb_save(basis_file,'basis','basis_parm'); 0183 0184 % project_file save 0185 proj_file = get_project_filename; 0186 if isempty(proj_file) 0187 return; 0188 end 0189 0190 project_file_mgr('load', proj_file); 0191 project_file_mgr('add', 'basis_parm', basis_parm); 0192 % 0193 % --- end of inner_terminate() 0194 0195 0196 % --- inner_check_arguments() 0197 % 0198 function [proj_root, basis_parm] = ... 0199 inner_check_arguments(const, proj_root, basis_parm) 0200 0201 if isempty(proj_root), error('proj_root is a required parameter'); end; 0202 if isempty(basis_parm), error('basis_parm is a required parameter'); end; 0203 0204 proj_root = vb_rm_trailing_slash(proj_root); 0205 0206 % check common fields of basis_parm 0207 if ~isfield(basis_parm, 'normal_mode') 0208 basis_parm.normal_mode = const.NORMAL_ADJACENT_MEAN; 0209 end 0210 0211 if ~isfield(basis_parm,'Recalc'), 0212 % Recalculation force flag 0213 basis_parm.Recalc = OFF; 0214 end 0215 0216 if ~isfield(basis_parm,'DEBUG'), 0217 basis_parm.DEBUG = OFF; 0218 end 0219 0220 if ~isfield(basis_parm,'sensortype'), 0221 basis_parm.sensortype = []; 0222 end 0223 0224 % if you want to check other points, you can do that here 0225 % ... 0226 0227 % 0228 % --- end of inner_check_arguments() 0229 % 0230 % --- END OF INNER FUNCTIONS ------------------------------------------------- % 0231 0232 %%% END OF FILE %%%