prepare_leadfield_eeg

 Prepare leadfield matrix

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

0001 function prepare_leadfield_eeg(p)
0002 % Prepare leadfield matrix
0003 %
0004 % Copyright (C) 2011, ATR All Rights Reserved.
0005 % License : New BSD License(see VBMEG_LICENSE.txt)
0006 
0007 disp(mfilename);
0008 
0009 % Make directory to save leadfield
0010 leadfield_dir = fullfile(p.proj_root, p.eeg_dirname, p.leadfield_dirname);
0011 if exist(leadfield_dir, 'dir') ~= 7
0012     mkdir(leadfield_dir);
0013 end
0014 
0015 %% Construct 3-shell surface model
0016 
0017 % Set input files
0018 % (Relative path from proj_root)
0019 head_parm.brain_file = fullfile(p.brain_dirname, [p.struct_name, '.brain.mat']);
0020 % (Absolute path)
0021 head_parm.analyze_file = fullfile(p.proj_root, p.t1_dirname, ['m' p.struct_name '.nii']);
0022 freesurfer_dir = fullfile(p.proj_root, p.fs_dirname, p.struct_name);
0023 head_parm.fs_scalp_file = fullfile(freesurfer_dir, 'bem', 'outer_skin_surface.asc');
0024 head_parm.freesurf_file = fullfile(freesurfer_dir, 'bem', 'inner_skull_surface.asc');
0025 head_parm.gray_file = fullfile(p.proj_root, p.t1_dirname, ['c1m' p.struct_name '.nii']);
0026 
0027 % Set output file (Relative path from proj_root)
0028 head_parm.head_file = fullfile(p.eeg_dirname, p.leadfield_dirname, [p.struct_name '.head.mat']);
0029 head_parm.Nsurf = 3;%  3-shell head model in the case of EEG data
0030 
0031 % Construct 3-shell surface model
0032 vb_job_head_3shell(p.proj_root, head_parm);
0033 
0034 
0035 %% Make leadfield matrix
0036 
0037 % Set input files (relative path from proj_root)
0038 basis_parm.brain_file = head_parm.brain_file;
0039 basis_parm.area_file  = '';
0040 basis_parm.head_file  = head_parm.head_file;
0041 basis_parm.device = 'BRAINAMP';% EEG device name
0042 basis_parm.bem_mode   = 4;% EEG 3-shell BEM
0043 basis_parm.Basis_mode = 1;% Single dipole perpendicular to the cortical surface
0044 basis_parm.meg_file = fullfile(p.eeg_dirname, p.trial_dirname, 'crri_all.info.mat');
0045 
0046 % Set output file (Relative path from proj_root)
0047 basis_parm.basis_file = fullfile(p.eeg_dirname, p.leadfield_dirname, [p.struct_name '.basis.mat']);
0048 
0049 % Make leadfield matrix
0050 vb_job_leadfield(p.proj_root, basis_parm)
0051 
0052 % Take common average
0053 basis_file = fullfile(p.proj_root, basis_parm.basis_file);
0054 load(basis_file, 'basis')
0055 for v = 1:size(basis, 1);
0056     basis(v, :) = basis(v, :)-mean(basis(v,:), 2);
0057 end
0058 vb_save(basis_file, 'basis');
0059 
0060