Estimate current time course by using inverse filter.
(VBMEG public function)
[syntax]
[Zact,Jinfo,Jext] = vb_job_current(curr_parm)
[Zact,Jinfo,Jext] = vb_job_current(proj_root,curr_parm) [old style]
[input]
proj_root: <<string>> VBMEG project root directory.
curr_parm: <<struct>> Current estimation parameters.
--- fields of curr_parm
bayesfile : <<string>> Model parameter filename (.bayes.mat). This
file is required for current estimation and obtained by
vb_job_vb before running this function.
currfile : <<string>> Cortical current filename (.curr.mat),
specifying the file to which current estimation result
is saved.
area_key : <optional> <<string>> Area ID on which cortical current
is estimated. This parameter will be useful if you have
some knowledge about region of interested.
areafile : <optional> <<string>> Rquired if cortical area is
specified by field 'area_key'.
trial_average: <optional> <<bool>> If true (default), cortical current
averaged across all trials. If false, cortical current
is estimated for all trials.
jactdir : <optional> <<string>> Directory for saving trial
current files. This is the relative path from the
cortical current file. If trial_average == false &
jactdir is specified, current for each trial is saved
as trial current file.
dsampf : <optional> <<int>> Specify frequency of
downsampling. This value must be smaller than the
original sampling frequency of M/EEG data.
tsubsmpl : <obsolete> <optional> <<int vector>> Specify subsampled
time index. If 'tsubsmpl' is empty or not given, time
subsampling is not done. Instead of this, 'dsampf'
parameter is recommended for downsampling.
overlap_mode : <optional> <<bool>> If false (default), cortical
current is averaged over overlapped time
windows. Otherwise, current is not averaged over
overlapped time windows; current time series of each
time windows are concatenated sequentially for spectral
analysis.
If following fields are given, these values are used instead of
bayes_parm field in result file (see vb_job_vb):
basisfile
megfile
twin_meg
Tperiod
Tnext
extra.basisfile (for extra dipole)
---
[output]
Zact : <<float matrix>> Z-current.
Zact(n,t,:) is the current at the vertex 'ix_act(n)' & the time 't'.
Zact(Nact,Nsample) for trial_average = true.
Zact(Nact,Nsample,Ntrials) for trial_average = false.
Nact : # of active region,
Nsample : # of time sample,
Ntrials : # of trials in all session]
Jinfo: <<struct>> Information of cortical current.
Jext : <<double matrix>> Extra dipole current.
[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
2008/07/01 M. Sato
alpha is scaled back by bsnorm before saving in new vb_job_vb
Then, current is calculated by using leadfield without normalization
Leadfield different from that used in VB estimation can be used
2008-08-19 Taku Yoshioka
Extended dipole was supported.
2009-04-02 Taku Yoshioka
Parameter name changed within this code for readability
(just replacing 'resultfile' to bayesfile)
2009-03-01 rhayashi
bugfix(ix_area was not given to vbmeg_reconstruct functions)
2010-12-03 taku-y
[trivial] Comment modified.
[trivial] Struct 'curr_parm' available without field 'areafile'.
2010-12-06 taku-y
[trivial] Comment modified.
2011-05-11 taku-y
[minor] 'vbmeg_current_reconstruct_z(_tr)' was replaced by
'vb_current_reconstruct_z(_tr)', which is the same excepting
Jinfo.Tmsec corresponds to overlaped time windows.
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [Zact, Jinfo, Jext] = vb_job_current(varargin) 0002 % Estimate current time course by using inverse filter. 0003 % (VBMEG public function) 0004 % 0005 % [syntax] 0006 % [Zact,Jinfo,Jext] = vb_job_current(curr_parm) 0007 % [Zact,Jinfo,Jext] = vb_job_current(proj_root,curr_parm) [old style] 0008 % 0009 % [input] 0010 % proj_root: <<string>> VBMEG project root directory. 0011 % curr_parm: <<struct>> Current estimation parameters. 0012 % --- fields of curr_parm 0013 % bayesfile : <<string>> Model parameter filename (.bayes.mat). This 0014 % file is required for current estimation and obtained by 0015 % vb_job_vb before running this function. 0016 % currfile : <<string>> Cortical current filename (.curr.mat), 0017 % specifying the file to which current estimation result 0018 % is saved. 0019 % area_key : <optional> <<string>> Area ID on which cortical current 0020 % is estimated. This parameter will be useful if you have 0021 % some knowledge about region of interested. 0022 % areafile : <optional> <<string>> Rquired if cortical area is 0023 % specified by field 'area_key'. 0024 % trial_average: <optional> <<bool>> If true (default), cortical current 0025 % averaged across all trials. If false, cortical current 0026 % is estimated for all trials. 0027 % jactdir : <optional> <<string>> Directory for saving trial 0028 % current files. This is the relative path from the 0029 % cortical current file. If trial_average == false & 0030 % jactdir is specified, current for each trial is saved 0031 % as trial current file. 0032 % dsampf : <optional> <<int>> Specify frequency of 0033 % downsampling. This value must be smaller than the 0034 % original sampling frequency of M/EEG data. 0035 % tsubsmpl : <obsolete> <optional> <<int vector>> Specify subsampled 0036 % time index. If 'tsubsmpl' is empty or not given, time 0037 % subsampling is not done. Instead of this, 'dsampf' 0038 % parameter is recommended for downsampling. 0039 % overlap_mode : <optional> <<bool>> If false (default), cortical 0040 % current is averaged over overlapped time 0041 % windows. Otherwise, current is not averaged over 0042 % overlapped time windows; current time series of each 0043 % time windows are concatenated sequentially for spectral 0044 % analysis. 0045 % If following fields are given, these values are used instead of 0046 % bayes_parm field in result file (see vb_job_vb): 0047 % basisfile 0048 % megfile 0049 % twin_meg 0050 % Tperiod 0051 % Tnext 0052 % extra.basisfile (for extra dipole) 0053 % --- 0054 % 0055 % [output] 0056 % Zact : <<float matrix>> Z-current. 0057 % Zact(n,t,:) is the current at the vertex 'ix_act(n)' & the time 't'. 0058 % Zact(Nact,Nsample) for trial_average = true. 0059 % Zact(Nact,Nsample,Ntrials) for trial_average = false. 0060 % Nact : # of active region, 0061 % Nsample : # of time sample, 0062 % Ntrials : # of trials in all session] 0063 % Jinfo: <<struct>> Information of cortical current. 0064 % Jext : <<double matrix>> Extra dipole current. 0065 % 0066 % [example] 0067 % >> parm.areafile = './NG/data/100009d.area.mat'; 0068 % >> parm.bayesfile = './NG/result/result3_col.bayes.mat'; 0069 % >> parm.trial_average = OFF; 0070 % >> parm.area_key = 'fMTl'; 0071 % >> parm.currfile = './result/result3_col_fMTl_1.curr.mat'; 0072 % >> vb_job_current(parm); 0073 % 0074 % 2005-03-31 Taku Yoshioka 0075 % 2005/08/22 O. Yamashita ver.30b 0076 % 2005/08/24 O. Yamashita Modified 0077 % 2006/03/24 M. Sato Modified 0078 % Eliminate zero variance point in current reconstruction 0079 % 2006/04/06 D. Kawawaki modified 0080 % 'project root' problem was solved. 0081 % 2006/07/19 O. Yamashita Modified 0082 % 2006/09/01 M. Sato 0083 % 2008/07/01 M. Sato 0084 % alpha is scaled back by bsnorm before saving in new vb_job_vb 0085 % Then, current is calculated by using leadfield without normalization 0086 % Leadfield different from that used in VB estimation can be used 0087 % 2008-08-19 Taku Yoshioka 0088 % Extended dipole was supported. 0089 % 2009-04-02 Taku Yoshioka 0090 % Parameter name changed within this code for readability 0091 % (just replacing 'resultfile' to bayesfile) 0092 % 2009-03-01 rhayashi 0093 % bugfix(ix_area was not given to vbmeg_reconstruct functions) 0094 % 2010-12-03 taku-y 0095 % [trivial] Comment modified. 0096 % [trivial] Struct 'curr_parm' available without field 'areafile'. 0097 % 2010-12-06 taku-y 0098 % [trivial] Comment modified. 0099 % 2011-05-11 taku-y 0100 % [minor] 'vbmeg_current_reconstruct_z(_tr)' was replaced by 0101 % 'vb_current_reconstruct_z(_tr)', which is the same excepting 0102 % Jinfo.Tmsec corresponds to overlaped time windows. 0103 % 0104 % Copyright (C) 2011, ATR All Rights Reserved. 0105 % License : New BSD License(see VBMEG_LICENSE.txt) 0106 0107 % 0108 % check input arguments 0109 % 0110 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0111 if length(varargin) == 1 0112 proj_root = []; 0113 curr_parm = varargin{1}; 0114 elseif length(varargin) == 2 0115 proj_root = varargin{1}; 0116 curr_parm = varargin{2}; 0117 else 0118 error('Error: invalid usage of job_current.'); 0119 end 0120 0121 proj_root = vb_rm_trailing_slash(proj_root); 0122 0123 if ~isfield(curr_parm,'trial_average'), 0124 curr_parm.trial_average = true; 0125 end 0126 0127 if ~isfield(curr_parm,'areafile'), 0128 curr_parm.areafile = []; 0129 end 0130 0131 % 0132 % set absolute path 0133 % 0134 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0135 if ~isempty(proj_root) 0136 bayesfile = [proj_root filesep curr_parm.bayesfile]; % bayes file 0137 currfile = [proj_root filesep curr_parm.currfile]; % current file 0138 if isfield(curr_parm, 'areafile') 0139 areafile = [proj_root filesep curr_parm.areafile]; % vb_get_area 0140 end 0141 else 0142 bayesfile = curr_parm.bayesfile; 0143 currfile = curr_parm.currfile; 0144 if isfield(curr_parm, 'areafile') 0145 areafile = curr_parm.areafile; 0146 end 0147 end 0148 0149 % 0150 % Current estimation 0151 % 0152 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0153 vb_disp('Start current estimation') 0154 0155 if ~isempty(areafile) ... 0156 & isfield(curr_parm, 'area_key') & ~isempty(curr_parm.area_key), 0157 Area = vb_get_area(areafile, curr_parm.area_key); 0158 ix_area = Area.Iextract; 0159 else 0160 ix_area = []; 0161 end 0162 0163 parm = curr_parm; 0164 parm.ix_area = ix_area; 0165 if curr_parm.trial_average == false ... 0166 && isfield(curr_parm,'jactdir') && ~isempty(curr_parm.jactdir) 0167 [Zact, Jinfo, bayes_parm, vb_parm, MEGinfo, Jext, Pointlist] ... 0168 = vb_current_reconstruct_z_tr(proj_root, parm); 0169 else 0170 [Zact, Jinfo, bayes_parm, vb_parm, MEGinfo, Jext, Pointlist] ... 0171 = vb_current_reconstruct_z(proj_root, parm); 0172 end; 0173 0174 % load brain vertex number 0175 brain_file = fullfile(proj_root, bayes_parm.brainfile); 0176 Nvertex = vb_load_cortex_info(brain_file); 0177 0178 0179 % 0180 % Save result 0181 % 0182 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0183 vb_disp(sprintf('--- Save estimated current: %s\n',currfile)); 0184 vb_fsave(currfile,'Zact','Jinfo','MEGinfo','bayes_parm','vb_parm',... 0185 'Jext','Pointlist', 'curr_parm', 'Nvertex'); 0186 0187 % 0188 % project_file save 0189 % 0190 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0191 proj_file = get_project_filename; 0192 if isempty(proj_file) 0193 return; 0194 end 0195 0196 project_file_mgr('load', proj_file); 0197 project_file_mgr('add', 'current_parm', curr_parm); 0198 0199 return;