Home > functions > job > vb_job_grandaverage.m

vb_job_grandaverage

PURPOSE ^

Calculate intersubject average of estimated cortical current.

SYNOPSIS ^

function vb_job_grandaverage(proj_root,avr_parm)

DESCRIPTION ^

 Calculate intersubject average of estimated cortical current.
 (VBMEG public function)

 [syntax]
 vb_job_current_grandaverage(proj_root,avr_parm)

 [input]
 proj_root: <<string>> VBMEG project root directory. 
 avr_parm : <<struct>> Parameters for intersubject averaging. 
 --- fields of avr_parm
  curr_file    : <<cell>> Cortical current files. 
  brain_file   : <<cell>> Cortical surface model files. 
  key          : <<cell>> ID of coregistration matrix for each subjects
                 corresponding to brain files. In common, coregistration
                 matrix from the subject to a template cortical model is
                 specified. 
  reduce       : <optional> <<double>> Reduction ratio of vertices of
                 the cortical surface model on which grandaverage is
                 taken. 
  tbrain_file  : <optional> <<string>> Filename of cortical surface
                 model on which grandaverage is taken. This file is used
                 to reduce the number of vertices. 
  curr_file_out: <<string>> Filename of cortical current file. 
 ---

 [output]
 Cortical current file (.curr.mat) on the template cortical surface
 model (curr_file_out).

 [example]
 >> avr_parm.curr_file = {'./subjects/0001/result/0001_LR.curr.mat', ...
                          './subjects/0002/result/0002_LR.curr.mat', ...
                          './subjects/0003/result/0003_LR.curr.mat', ...
                          './subjects/0004/result/0004_LR.curr.mat'};
 >> avr_parm.brain_file ...
     = {'./subjects/0001/brain/0001.brain.mat', ...
        './subjects/0002/brain/0002.brain.mat', ...
        './subjects/0003/brain/0003.brain.mat', ...
        './subjects/0004/brain/0004.brain.mat'};
 >> avr_parm.key = {'fsaverage.sphere.reg','fsaverage.sphere.reg', ...
                    'fsaverage.sphere.reg','fsaverage.sphere.reg'};
 >> avr_parm.tbrain_file = './subjects/fsaverage/fsaverage.brain.mat';
 >> avr_parm.curr_file_out ...
     = './subjects/fsaverage/result/fsaverage_LR.curr.mat';
 >> vb_job_grandaverage(proj_root,avr_parm);

 [history]
 2010-12-01 Taku Yoshioka
 2011-01-27 taku-y
  [minor] 'reduce' parameter supported. If reduce is not given or
  reduce==1.0, this function give the same result with that of the
  previous version. 
 2011-11-15 taku-y
  [minor] Bug fixed for insufficient number of current dipoles, due to
  small number of Z-current dipoles not covering whole cortex. 
 2012-02-08 taku-y
  [minor] Bug fixed for insufficient number of current dipoles, due to
  small number of Z-current dipoles not covering whole cortex (first
  loop). 

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

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function vb_job_grandaverage(proj_root,avr_parm)
0002 % Calculate intersubject average of estimated cortical current.
0003 % (VBMEG public function)
0004 %
0005 % [syntax]
0006 % vb_job_current_grandaverage(proj_root,avr_parm)
0007 %
0008 % [input]
0009 % proj_root: <<string>> VBMEG project root directory.
0010 % avr_parm : <<struct>> Parameters for intersubject averaging.
0011 % --- fields of avr_parm
0012 %  curr_file    : <<cell>> Cortical current files.
0013 %  brain_file   : <<cell>> Cortical surface model files.
0014 %  key          : <<cell>> ID of coregistration matrix for each subjects
0015 %                 corresponding to brain files. In common, coregistration
0016 %                 matrix from the subject to a template cortical model is
0017 %                 specified.
0018 %  reduce       : <optional> <<double>> Reduction ratio of vertices of
0019 %                 the cortical surface model on which grandaverage is
0020 %                 taken.
0021 %  tbrain_file  : <optional> <<string>> Filename of cortical surface
0022 %                 model on which grandaverage is taken. This file is used
0023 %                 to reduce the number of vertices.
0024 %  curr_file_out: <<string>> Filename of cortical current file.
0025 % ---
0026 %
0027 % [output]
0028 % Cortical current file (.curr.mat) on the template cortical surface
0029 % model (curr_file_out).
0030 %
0031 % [example]
0032 % >> avr_parm.curr_file = {'./subjects/0001/result/0001_LR.curr.mat', ...
0033 %                          './subjects/0002/result/0002_LR.curr.mat', ...
0034 %                          './subjects/0003/result/0003_LR.curr.mat', ...
0035 %                          './subjects/0004/result/0004_LR.curr.mat'};
0036 % >> avr_parm.brain_file ...
0037 %     = {'./subjects/0001/brain/0001.brain.mat', ...
0038 %        './subjects/0002/brain/0002.brain.mat', ...
0039 %        './subjects/0003/brain/0003.brain.mat', ...
0040 %        './subjects/0004/brain/0004.brain.mat'};
0041 % >> avr_parm.key = {'fsaverage.sphere.reg','fsaverage.sphere.reg', ...
0042 %                    'fsaverage.sphere.reg','fsaverage.sphere.reg'};
0043 % >> avr_parm.tbrain_file = './subjects/fsaverage/fsaverage.brain.mat';
0044 % >> avr_parm.curr_file_out ...
0045 %     = './subjects/fsaverage/result/fsaverage_LR.curr.mat';
0046 % >> vb_job_grandaverage(proj_root,avr_parm);
0047 %
0048 % [history]
0049 % 2010-12-01 Taku Yoshioka
0050 % 2011-01-27 taku-y
0051 %  [minor] 'reduce' parameter supported. If reduce is not given or
0052 %  reduce==1.0, this function give the same result with that of the
0053 %  previous version.
0054 % 2011-11-15 taku-y
0055 %  [minor] Bug fixed for insufficient number of current dipoles, due to
0056 %  small number of Z-current dipoles not covering whole cortex.
0057 % 2012-02-08 taku-y
0058 %  [minor] Bug fixed for insufficient number of current dipoles, due to
0059 %  small number of Z-current dipoles not covering whole cortex (first
0060 %  loop).
0061 %
0062 % Copyright (C) 2011, ATR All Rights Reserved.
0063 % License : New BSD License(see VBMEG_LICENSE.txt)
0064 
0065 
0066 %
0067 % Input arguments
0068 %
0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0070 vb_struct2vars(avr_parm,{'curr_file','brain_file','key','reduce', ...
0071                     'tbrain_file','curr_file_out'});
0072 
0073 if isempty(reduce),
0074   reduce = 1.0;
0075 end
0076 
0077 %
0078 % Load first file
0079 %
0080 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0081 [Jinfo,J] = vb_load_current(curr_file{1},0,true);
0082 C         = vb_load_cortex_pmat(brain_file{1},key{1});
0083 
0084 % added by taku-y 2012-02-08
0085 Jtmp = zeros(size(C,2),size(J,2));
0086 Jtmp(Jinfo.ix_act_ex,:) = J;
0087 J = Jtmp;
0088 
0089 if reduce==1.0, 
0090   Javr = C*J;
0091 else
0092   brain_file_tmp = tbrain_file;
0093   
0094   % Reduce vertex of the cortical surface model
0095   V = vb_load_cortex(brain_file_tmp);
0096   ix_act = vb_reduce_cortex(brain_file_tmp,1:size(V,1),reduce);
0097   I = length(ix_act);
0098   
0099   % Calculate mean distance between reduced vertices to determine
0100   % smoothing filter size
0101   R = 0.0;
0102   N = 0;
0103   [nextDD,nextIX] = vb_load_cortex_neighbour(brain_file_tmp);
0104   for i=1:length(ix_act)
0105     [tmp,ixx] = union(nextIX{ix_act(i)},ix_act);
0106     R = R+sum(nextDD{ix_act(i)}(ixx));
0107     N = N+length(ixx);
0108   end
0109   R = R/N;
0110   
0111   % Calculate smoothing filter. It will be used for displaying purpose,
0112   % not affect further analysis.
0113   [W,ix_act_ex] ...
0114       = vb_spatial_gauss_filter(brain_file_tmp,R,2*R,ix_act,1,-1,1);
0115   W = W./repmat(sum(W,2),[1 size(W,2)]);
0116   
0117   % Load average current and map onto the template cortical surface
0118   C    = vb_load_cortex_pmat(brain_file{1},key{1});
0119   I    = size(C,2);
0120   T    = size(J,2);
0121   Jtmp = zeros(I,T);
0122   
0123   Jtmp(Jinfo.ix_act_ex,:) = J;
0124   Jtmp                    = C*Jtmp; % current on the template brain
0125   Zavr                    = Jtmp(ix_act,:);
0126 end
0127 
0128 %
0129 % Load subsequent files and calculate intersubject average
0130 %
0131 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0132 for i=2:length(curr_file)
0133   [Jinfo,J] = vb_load_current(curr_file{i},0,true);
0134   C         = vb_load_cortex_pmat(brain_file{i},key{i});
0135   
0136   % added by taku-y 2011-11-15
0137   Jtmp = zeros(size(C,2),size(J,2));
0138   Jtmp(Jinfo.ix_act_ex,:) = J;
0139   J = Jtmp;
0140   
0141   if reduce==1.0
0142     Javr = Javr+C*J;
0143   else
0144     % Map current onto the template cortical surface
0145     I    = size(C,2);
0146     Jtmp = zeros(I,T);
0147     
0148     Jtmp(Jinfo.ix_act_ex,:) = J;
0149     Jtmp                    = C*Jtmp; % current on the template brain
0150     Zavr                    = Zavr+Jtmp(ix_act,:);
0151   end
0152 end
0153 
0154 %
0155 % Variables to be saved
0156 %
0157 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0158 Jinfo = vb_load_current(curr_file{1},0,true);
0159 Jinfo.Ntrial = 1;
0160 
0161 if reduce==1.0
0162   NJact = size(C,1);
0163   Jinfo.ix_act     = 1:NJact;
0164   Jinfo.ix_act_ex  = 1:NJact;
0165   Jinfo.NJact      = NJact;
0166   Jinfo.Wact       = speye(NJact);
0167 
0168   load(curr_file{1},'bayes_parm');
0169   Jinfo.patch_norm = bayes_parm.patch_norm;
0170   
0171   Zact = Javr./length(curr_file);
0172 else
0173   Jinfo.ix_act    = ix_act;
0174   Jinfo.ix_act_ex = ix_act_ex;
0175   Jinfo.NJact     = length(ix_act_ex);
0176   Jinfo.Wact      = W;
0177   
0178   load(curr_file{1},'bayes_parm');
0179   Jinfo.patch_norm = bayes_parm.patch_norm;
0180   
0181   Zact = Zavr./length(curr_file);
0182 end
0183   
0184 %
0185 % Save result
0186 %
0187 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0188 vb_fsave(curr_file_out,'Zact','Jinfo');
0189 
0190 %
0191 % Save project file
0192 %
0193 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0194 proj_file = get_project_filename;
0195 if isempty(proj_file), 
0196   return;
0197 end;
0198 
0199 project_file_mgr('load', proj_file);
0200 project_file_mgr('add', 'avr_parm', avr_parm);
0201 
0202 return;

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