This script calculates estimated current time courses in a
specified area.
---
USAGE:
function vb_job_current(proj_root,parm)
or
function vb_job_current(parm)
--- Input parameters
- parm.currfile
.curr.mat file into which estimated current time courses are
saved.
- parm.bayesfile
.bayes.mat file.
---- Optional (default)
- parm.areafile ([]) --> focal window
.area.mat file.
- parm.area_key ([])
ID of interested area.
- parm.trial_average (ON)
ON: Average current over all sessions.
OFF: Current for each session. This option is needed for time
frequency analysis.
- 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)
- Zact
- Zbck
- ix_act
- ix_bck
- Lact
- Lbck
- Varact
- bayes_parm
- vb_parm
- Jinfo
* Example
>> 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';
>> vb_job_current(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 [Zact,ix_act,Zbck,ix_bck,Varact] = vb_job_current_z(varargin) 0002 % This script calculates estimated current time courses in a 0003 % specified area. 0004 % 0005 % --- 0006 % USAGE: 0007 % function vb_job_current(proj_root,parm) 0008 % or 0009 % function vb_job_current(parm) 0010 % 0011 % --- Input parameters 0012 % - parm.currfile 0013 % .curr.mat file into which estimated current time courses are 0014 % saved. 0015 % - parm.bayesfile 0016 % .bayes.mat file. 0017 % 0018 % ---- Optional (default) 0019 % - parm.areafile ([]) --> focal window 0020 % .area.mat file. 0021 % - parm.area_key ([]) 0022 % ID of interested area. 0023 % - parm.trial_average (ON) 0024 % ON: Average current over all sessions. 0025 % OFF: Current for each session. This option is needed for time 0026 % frequency analysis. 0027 % - parm.tsubsmpl ([]) --> whole time points 0028 % Time points where currents are calculated. For example, 0029 % if tsubsmpl = [1:5:100], currents are calculated at only every 5 sample 0030 % point. 0031 % - parm.overlap_mode 0032 % = 0 : current is averaged over overlapped time window 0033 % = 1 : current is not averaged for overlapped window 0034 % current time series of each time windows 0035 % are concatenated sequentially for spectral analysis 0036 % 0037 % * Parameters saved in output file (.curr.mat) 0038 % 0039 % - Zact 0040 % - Zbck 0041 % - ix_act 0042 % - ix_bck 0043 % - Lact 0044 % - Lbck 0045 % - Varact 0046 % - bayes_parm 0047 % - vb_parm 0048 % - Jinfo 0049 % * Example 0050 % 0051 % >> parm.areafile = './NG/data/100009d.area.mat'; 0052 % >> parm.bayesfile = './NG/result/result3_col.bayes.mat'; 0053 % >> parm.trial_average = OFF; 0054 % >> parm.area_key = 'fMTl'; 0055 % >> parm.currfile = './result/result3_col_fMTl_1.curr.mat'; 0056 % >> vb_job_current(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.'); 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 ~isempty(parm.areafile) ... 0104 & isfield(parm, 'area_key') & ~isempty(parm.area_key), 0105 Area = vb_get_area(areafile,parm.area_key); 0106 ix_area = Area.Iextract; 0107 else 0108 ix_area = []; 0109 end 0110 0111 if isfield(parm,'trial_average') 0112 trial_average = parm.trial_average; 0113 else 0114 trial_average = ON; 0115 end 0116 if isfield(parm,'tsubsmpl') 0117 tsubsmpl = parm.tsubsmpl; 0118 else 0119 tsubsmpl = []; 0120 end 0121 if isfield(parm,'overlap_mode') 0122 overlap_mode = parm.overlap_mode; 0123 else 0124 overlap_mode = 0; 0125 end 0126 if ~isfield(parm,'flag') 0127 parm.flag = 0; 0128 end 0129 0130 fprintf('Start current estimation\n') 0131 0132 % Current estimation 0133 %[Jact, ix_act, Jbck, ix_bck, Varact] ... 0134 0135 [Zact ,ix_act, Zbck, ix_bck, Varact, Jinfo] ... 0136 = vbmeg_current_reconstruct_z(proj_root, parm.bayesfile,... 0137 ix_area, trial_average, tsubsmpl, overlap_mode); 0138 0139 %%%%%% load result file 0140 load(bayesfile, 'bayes_parm','vb_parm'); 0141 0142 if ~isempty(proj_root) 0143 megfile = [proj_root filesep bayes_parm.megfile{1}]; 0144 else 0145 megfile = bayes_parm.megfile{1}; 0146 end 0147 0148 % Time window 0149 if isempty(tsubsmpl) 0150 Jinfo.Tstart = bayes_parm.twin_meg(1); 0151 Jinfo.Tend = bayes_parm.twin_meg(2); 0152 Jinfo.Tsample = Jinfo.Tstart:Jinfo.Tend; 0153 else 0154 Jinfo.Tstart = tsubsmpl(1) + bayes_parm.twin_meg(1) - 1; 0155 Jinfo.Tend = tsubsmpl(end) + bayes_parm.twin_meg(1) - 1; 0156 Jinfo.Tsample = tsubsmpl + bayes_parm.twin_meg(1) - 1; 0157 end 0158 0159 % MEG information 0160 MEGinfo = vb_load_meg_info(megfile); 0161 0162 % Save result 0163 fprintf(' --- Save estimated current: %s\n',currfile) 0164 vb_fsave(currfile,'Zact','Zbck','Jinfo','Varact', ... 0165 'MEGinfo','bayes_parm','vb_parm'); 0166 0167 %vb_fsave(currfile,'Jact','Jbck','ix_act','ix_bck','Varact','MEGinfo', ... 0168 % 'Tsample','Tstart','Tend','Lact','Lbck','bayes_parm','vb_parm'); 0169 0170 % project_file save 0171 proj_file = get_project_filename; 0172 if isempty(proj_file) 0173 return; 0174 end 0175 0176 project_file_mgr('load', proj_file); 0177 project_file_mgr('add', 'current_parm', parm); 0178