This script calculates estimated current time courses for each trial
---
USAGE:
function vb_job_current_tr(proj_root,parm)
or
function vb_job_current_tr(parm)
--- Input parameters
- parm.bayesfile : Current variance file (.bayes.mat)
- parm.currfile : Average current is saved.
Infomation of current file are also saved.
current of each trials are saved into 'jactdir' directory
.curr.mat file
- parm.jactdir : output directory of current files for each trial
relative path from proj_root
do not include '/' or '\' in the end of string
If 'jactdir' is not given, jactdir = 'temp'
---- Optional (default)
- parm.areafile ([]) --> focal window
.area.mat file.
- parm.area_key ([])
ID of interested area.
- parm.tsubsmpl ([]) --> whole time points
Time points where currents are calculated. For example,
if tsubsmpl = [1:5:100], currents are calculated at only every 5 sample
point.
- parm.overlap_mode
= 0 : current is averaged over overlapped time window
= 1 : current is not averaged for overlapped window
current time series of each time windows
are concatenated sequentially for spectral analysis
* Parameters saved in output file (.curr.mat)
- Jact
- Jbck
- ix_act
- ix_bck
- Lact
- Lbck
- Varact
- bayes_parm
- vb_parm
* Example
>> proj_root = '.'
>> parm.areafile = 'NG/data/100009d.area.mat';
>> parm.bayesfile = 'NG/result/result3_col.bayes.mat';
>> parm.trial_average = OFF;
>> parm.area_key = 'fMTl';
>> parm.currfile = 'result/result3_col_fMTl_1.curr.mat';
>> parm.jactdir = 'temp';
>> vb_job_current_tr(proj_root,parm);
2005-03-31 Taku Yoshioka
2005/08/22 O. Yamashita ver.30b
2005/08/24 O. Yamashita Modified
2006/03/24 M. Sato Modified
Eliminate zero variance point in current reconstruction
2006/04/06 D. Kawawaki modified
'project root' problem was solved.
2006/07/19 O. Yamashita Modified
2006/09/01 M. Sato
2009-04-02 Taku Yoshioka
Parameter name changed within this code for readability
(just replacing 'resultfile' to bayesfile)
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [Jact,ix_act,Jbck,ix_bck,Varact] = vb_job_current_tr(varargin) 0002 % This script calculates estimated current time courses for each trial 0003 % 0004 % --- 0005 % USAGE: 0006 % function vb_job_current_tr(proj_root,parm) 0007 % or 0008 % function vb_job_current_tr(parm) 0009 % 0010 % --- Input parameters 0011 % - parm.bayesfile : Current variance file (.bayes.mat) 0012 % - parm.currfile : Average current is saved. 0013 % Infomation of current file are also saved. 0014 % current of each trials are saved into 'jactdir' directory 0015 % .curr.mat file 0016 % - parm.jactdir : output directory of current files for each trial 0017 % relative path from proj_root 0018 % do not include '/' or '\' in the end of string 0019 % If 'jactdir' is not given, jactdir = 'temp' 0020 % ---- Optional (default) 0021 % - parm.areafile ([]) --> focal window 0022 % .area.mat file. 0023 % - parm.area_key ([]) 0024 % ID of interested area. 0025 % - parm.tsubsmpl ([]) --> whole time points 0026 % Time points where currents are calculated. For example, 0027 % if tsubsmpl = [1:5:100], currents are calculated at only every 5 sample 0028 % point. 0029 % - parm.overlap_mode 0030 % = 0 : current is averaged over overlapped time window 0031 % = 1 : current is not averaged for overlapped window 0032 % current time series of each time windows 0033 % are concatenated sequentially for spectral analysis 0034 % 0035 % * Parameters saved in output file (.curr.mat) 0036 % 0037 % - Jact 0038 % - Jbck 0039 % - ix_act 0040 % - ix_bck 0041 % - Lact 0042 % - Lbck 0043 % - Varact 0044 % - bayes_parm 0045 % - vb_parm 0046 % 0047 % * Example 0048 % 0049 % >> proj_root = '.' 0050 % >> parm.areafile = 'NG/data/100009d.area.mat'; 0051 % >> parm.bayesfile = 'NG/result/result3_col.bayes.mat'; 0052 % >> parm.trial_average = OFF; 0053 % >> parm.area_key = 'fMTl'; 0054 % >> parm.currfile = 'result/result3_col_fMTl_1.curr.mat'; 0055 % >> parm.jactdir = 'temp'; 0056 % >> vb_job_current_tr(proj_root,parm); 0057 % 0058 % 2005-03-31 Taku Yoshioka 0059 % 2005/08/22 O. Yamashita ver.30b 0060 % 2005/08/24 O. Yamashita Modified 0061 % 2006/03/24 M. Sato Modified 0062 % Eliminate zero variance point in current reconstruction 0063 % 2006/04/06 D. Kawawaki modified 0064 % 'project root' problem was solved. 0065 % 2006/07/19 O. Yamashita Modified 0066 % 2006/09/01 M. Sato 0067 % 2009-04-02 Taku Yoshioka 0068 % Parameter name changed within this code for readability 0069 % (just replacing 'resultfile' to bayesfile) 0070 % 0071 % Copyright (C) 2011, ATR All Rights Reserved. 0072 % License : New BSD License(see VBMEG_LICENSE.txt) 0073 0074 %check input arguments 0075 if length(varargin) == 1 0076 proj_root = []; 0077 parm = varargin{1}; 0078 elseif length(varargin) == 2 0079 proj_root = varargin{1}; 0080 parm = varargin{2}; 0081 else 0082 error('Error: invalid usage of job_current_tr.'); 0083 end 0084 0085 proj_root = vb_rm_trailing_slash(proj_root); 0086 0087 %set absolute path 0088 if ~isempty(proj_root) 0089 bayesfile = [proj_root filesep parm.bayesfile]; % curr. var. file 0090 currfile = [proj_root filesep parm.currfile]; % current file 0091 if isfield(parm, 'areafile') 0092 areafile = [proj_root filesep parm.areafile]; % vb_get_area 0093 end 0094 else 0095 bayesfile = parm.bayesfile; 0096 currfile = parm.currfile; 0097 if isfield(parm, 'areafile') 0098 areafile = parm.areafile; 0099 end 0100 end 0101 0102 % set paramater 0103 if isfield(parm,'trial_average') & parm.trial_average == ON; 0104 error('vb_job_current_tr should be used for trial_average = OFF') 0105 end 0106 if ~isempty(parm.areafile) ... 0107 & isfield(parm, 'area_key') & ~isempty(parm.area_key), 0108 Area = vb_get_area(areafile,parm.area_key); 0109 ix_area = Area.Iextract; 0110 else 0111 ix_area = []; 0112 end 0113 0114 if isfield(parm,'tsubsmpl') 0115 tsubsmpl = parm.tsubsmpl; 0116 else 0117 tsubsmpl = []; 0118 end 0119 if isfield(parm,'overlap_mode') 0120 overlap_mode = parm.overlap_mode; 0121 else 0122 overlap_mode = 0; 0123 end 0124 if isfield(parm,'jactdir'), 0125 jactdir = parm.jactdir; 0126 else 0127 jactdir = 'temp'; 0128 end; 0129 0130 % Current estimation 0131 [Jact ,ix_act, Jbck, ix_bck, Varact, JactInfo] = ... 0132 vbmeg_current_reconstruct_tr(proj_root, parm.bayesfile, ... 0133 ix_area, tsubsmpl, jactdir, overlap_mode); 0134 0135 % Dipole component number 0136 if isempty(ix_act) 0137 Lact = 1; 0138 else 0139 Lact = size(Jact,1)/length(ix_act); 0140 end 0141 if isempty(ix_bck) 0142 Lbck = 1; 0143 else 0144 Lbck = size(Jbck,1)/length(ix_bck); 0145 end 0146 0147 %%%%%% load current variance file 0148 load(bayesfile, 'bayes_parm','vb_parm'); 0149 0150 if ~isempty(proj_root) 0151 megfile = [proj_root filesep bayes_parm.megfile{1}]; 0152 else 0153 megfile = bayes_parm.megfile{1}; 0154 end 0155 0156 0157 % Time window 0158 if isempty(tsubsmpl) 0159 Tstart = bayes_parm.twin_meg(1); 0160 Tend = bayes_parm.twin_meg(2); 0161 Tsample = Tstart:Tend; 0162 else 0163 Tstart = tsubsmpl(1) + bayes_parm.twin_meg(1) - 1; 0164 Tend = tsubsmpl(end) + bayes_parm.twin_meg(1) - 1; 0165 Tsample = tsubsmpl + bayes_parm.twin_meg(1) - 1; 0166 end 0167 0168 % MEG information 0169 MEGinfo = vb_load_meg_info(megfile); 0170 0171 % Save result 0172 fprintf(' --- Save estimated current: %s\n',currfile) 0173 vb_fsave(currfile,'Jact','Jbck','ix_act','ix_bck','Varact','MEGinfo', ... 0174 'Tsample','Tstart','Tend','Lact','Lbck','bayes_parm','vb_parm','JactInfo'); 0175 0176 % project_file save 0177 proj_file = get_project_filename; 0178 if isempty(proj_file) 0179 return; 0180 end 0181 0182 project_file_mgr('load', proj_file); 0183 project_file_mgr('add', 'current_parm', parm);