Read MEG data saved on Yokogawa system and convert it to .meg.mat file.
[usage]
[err] = vb_meg_yokogawa_make_data(proj_root, meg_parm)
[input]
proj_root : <required> Project root directory
meg_parm : <required> <<struct>> structure with following field
: <<fields>>
: .yokogawa_file : <required> <<file>> YOKOGAWA-MEG file
: : .con | .ave | .raw
: .meg_file : <required> Output MEG file.
: : This is used in connecting to proj_root.
: : [proj_root '/' <meg_parm.meg_file>] :
: .pos_file : <optional> <<file>> POS-MAT file
: : the members of which are as follows
: : mri_key - hash key [x1 string]
: : coord_type- coordinate type [x1 string]
: : pos - coordinate [Nch x3 double]
: : name - channel name [Nch x1 string]
: : trans_mri - transform matrix [4x4 double]
: : header - header information <<struct>>
: : .digit_file_name : <optional>
: : .meg_market_id : <optional>
: .ex_ch_gain : <optional> gain of extra channel[]
: .memory_max : <optional> const.DEFAULT_MEMORY_MAX(10000000)
: .saveman : <optional> <<struct>>
: : .data_dir : ['./(name of .meg_file)_bin']
: : - directory where the data will be stored
: : - relative path from the path of .meg_file
: : .precision : ['float64']
: : - precision which is used for fwrite
[output]
err : error code
: 0) success
: not 0) failure
[note]
1) If pos member in POS-MAT file is empty, only import MEG data
2) This function transform coordinates by using trans_mri matrix
3) data format of output file MEG-MAT is as follows
<<MEG-MAT>>
pick(n, 1:3) : position of detector coils.
(n+1:2n, 1:3) : position of conpensation detector coils.
Qpick : vector of pick [Nch x3]
ref_pick : position of reference channels [N_ref_ch x3]
ref_Qpick : vector of ref_pick [N_ref_ch x3]
Measurement : <<string>> measurement code 'MEG'
CoordType : <<string>> coordinate type which all the
: coordinates in MEG-MAT file apply
PositionFile : <<string>> position file (POS-MAT file) name
MEGinfo : <<struct>> with MEG acquisition information
<<MEGinfo>>
.Measurement : <<string>> measurement code 'MEG'
.device : device name (e.g. 'YOKOGAWA')
.sensor_weight : weight to calculate lead field
: sensor_weight = n-th coil weight for m-th sensor channel
: basis(channel,dipole) = sensor_weight * basis(coil,dipole)
.Nchannel : number of active gardiometers
.Nsample : number of sampling data
.Pretrigger : number of sampling data before trigger
.SampleFreq : sampling frequency
.Nrepeat : number of trial
.Trial : <<struct>> trial information [Ntrial x 1]
: .number : trial number (index)
: .sample : [Nsample x 1] sample list
.Vcenter : [3 x 1] origin of sphere model [m]
.MEG_ID : MEG system ID(meg filename with no extension)
.MRI_ID : MRI key (hash key)
.MEGch_name : Active MEG channel name
.MEGch_id : Active MEG channel index
.saveman : <<struct>> saving specifications
.device_info : <<struct>> device dependent information
.sensor_weight_ref:
.TransInfo : <<struct>> transform information
.acq_type : acquisition type
: (e.g.'Continuous_Raw', 'Evoked_Ave', 'Evoked_Raw')
.acq_info : <<struct>> acquisition information
[history]
2007-07-05 (Sako) initial version
2008-03-13 (Sako) thoroughly rewrote according to the new specification
2009-07-14 (Sako) modified to store data as external file inevitably
2010-02-04 (Sako) removed invalid setting of bit_len
2011-02-17 (Sako) changed default value of saveman.data_dir
2011-02-17 (Sako) got rid of old data fields 'bexp' 'bexp_ext', 'refmg'
2011-02-24 (Sako) supported in case ref channels are empty
2011-02-24 (Sako) supported in case memory_max is given but empty
2011-05-26 (Sako) modified according to the new data format
2011-06-22 (Sako) changed the order of load_calibinfo
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function [err] = vb_meg_yokogawa_make_data(proj_root, meg_parm) 0002 % Read MEG data saved on Yokogawa system and convert it to .meg.mat file. 0003 % 0004 % [usage] 0005 % [err] = vb_meg_yokogawa_make_data(proj_root, meg_parm) 0006 % 0007 % [input] 0008 % proj_root : <required> Project root directory 0009 % meg_parm : <required> <<struct>> structure with following field 0010 % : <<fields>> 0011 % : .yokogawa_file : <required> <<file>> YOKOGAWA-MEG file 0012 % : : .con | .ave | .raw 0013 % : .meg_file : <required> Output MEG file. 0014 % : : This is used in connecting to proj_root. 0015 % : : [proj_root '/' <meg_parm.meg_file>] : 0016 % : .pos_file : <optional> <<file>> POS-MAT file 0017 % : : the members of which are as follows 0018 % : : mri_key - hash key [x1 string] 0019 % : : coord_type- coordinate type [x1 string] 0020 % : : pos - coordinate [Nch x3 double] 0021 % : : name - channel name [Nch x1 string] 0022 % : : trans_mri - transform matrix [4x4 double] 0023 % : : header - header information <<struct>> 0024 % : : .digit_file_name : <optional> 0025 % : : .meg_market_id : <optional> 0026 % : .ex_ch_gain : <optional> gain of extra channel[] 0027 % : .memory_max : <optional> const.DEFAULT_MEMORY_MAX(10000000) 0028 % : .saveman : <optional> <<struct>> 0029 % : : .data_dir : ['./(name of .meg_file)_bin'] 0030 % : : - directory where the data will be stored 0031 % : : - relative path from the path of .meg_file 0032 % : : .precision : ['float64'] 0033 % : : - precision which is used for fwrite 0034 % 0035 % [output] 0036 % err : error code 0037 % : 0) success 0038 % : not 0) failure 0039 % 0040 % [note] 0041 % 1) If pos member in POS-MAT file is empty, only import MEG data 0042 % 0043 % 2) This function transform coordinates by using trans_mri matrix 0044 % 0045 % 3) data format of output file MEG-MAT is as follows 0046 % <<MEG-MAT>> 0047 % pick(n, 1:3) : position of detector coils. 0048 % (n+1:2n, 1:3) : position of conpensation detector coils. 0049 % Qpick : vector of pick [Nch x3] 0050 % ref_pick : position of reference channels [N_ref_ch x3] 0051 % ref_Qpick : vector of ref_pick [N_ref_ch x3] 0052 % Measurement : <<string>> measurement code 'MEG' 0053 % CoordType : <<string>> coordinate type which all the 0054 % : coordinates in MEG-MAT file apply 0055 % PositionFile : <<string>> position file (POS-MAT file) name 0056 % MEGinfo : <<struct>> with MEG acquisition information 0057 % 0058 % <<MEGinfo>> 0059 % .Measurement : <<string>> measurement code 'MEG' 0060 % .device : device name (e.g. 'YOKOGAWA') 0061 % .sensor_weight : weight to calculate lead field 0062 % : sensor_weight = n-th coil weight for m-th sensor channel 0063 % : basis(channel,dipole) = sensor_weight * basis(coil,dipole) 0064 % .Nchannel : number of active gardiometers 0065 % .Nsample : number of sampling data 0066 % .Pretrigger : number of sampling data before trigger 0067 % .SampleFreq : sampling frequency 0068 % .Nrepeat : number of trial 0069 % .Trial : <<struct>> trial information [Ntrial x 1] 0070 % : .number : trial number (index) 0071 % : .sample : [Nsample x 1] sample list 0072 % .Vcenter : [3 x 1] origin of sphere model [m] 0073 % .MEG_ID : MEG system ID(meg filename with no extension) 0074 % .MRI_ID : MRI key (hash key) 0075 % .MEGch_name : Active MEG channel name 0076 % .MEGch_id : Active MEG channel index 0077 % .saveman : <<struct>> saving specifications 0078 % 0079 % .device_info : <<struct>> device dependent information 0080 % .sensor_weight_ref: 0081 % .TransInfo : <<struct>> transform information 0082 % .acq_type : acquisition type 0083 % : (e.g.'Continuous_Raw', 'Evoked_Ave', 'Evoked_Raw') 0084 % .acq_info : <<struct>> acquisition information 0085 % 0086 % [history] 0087 % 2007-07-05 (Sako) initial version 0088 % 2008-03-13 (Sako) thoroughly rewrote according to the new specification 0089 % 2009-07-14 (Sako) modified to store data as external file inevitably 0090 % 2010-02-04 (Sako) removed invalid setting of bit_len 0091 % 2011-02-17 (Sako) changed default value of saveman.data_dir 0092 % 2011-02-17 (Sako) got rid of old data fields 'bexp' 'bexp_ext', 'refmg' 0093 % 2011-02-24 (Sako) supported in case ref channels are empty 0094 % 2011-02-24 (Sako) supported in case memory_max is given but empty 0095 % 2011-05-26 (Sako) modified according to the new data format 0096 % 2011-06-22 (Sako) changed the order of load_calibinfo 0097 % 0098 % Copyright (C) 2011, ATR All Rights Reserved. 0099 % License : New BSD License(see VBMEG_LICENSE.txt) 0100 0101 % --- CHECK ARGUMENTS --- % 0102 if ~exist('proj_root', 'var'), proj_root = []; end 0103 if ~exist('meg_parm', 'var'), meg_parm = []; end 0104 [proj_root, meg_parm, ykgwfile, posfile, out_file, meg_info] = ... 0105 inner_check_arguments(proj_root, meg_parm); 0106 0107 % --- MAIN PROCEDURE --------------------------------------------------------- % 0108 % 0109 err = 0; % success 0110 0111 % --- new spec - meg_info has acqfile field 0112 [meg_info] = vb_meginfo_set_acqfile(meg_info, ykgwfile); 0113 % <at this moment> determined fields of meg_info are ... 0114 % device_info.acq_info.data_file % acquisition file path 0115 0116 0117 [pick, Qpick, ref_pick, ref_Qpick, CoordType, meg_info] = ... 0118 vb_ykgwfile_load_meg_channel_info(ykgwfile, meg_info); 0119 % only load hardware coordinate here 0120 % later, apply appropriate coordinate system 0121 % <at this moment> determined fields of meg_info are ... 0122 % MEGch_id % Active MEG channel index 0123 % MEGch_name % Active MEG channel name 0124 % Nchannel % number of active axialmeters 0125 % nch0 % number of axialmeters 0126 % sensor_weight % coil weight 0127 % ActiveChannel % active channel flag 0128 0129 0130 [meg_info] = vb_ykgwfile_load_header(ykgwfile, meg_info); 0131 % <at this moment> newly determined fields of meg_info are ... 0132 % MEG_ID % MEG filename (non extention) 0133 % device % 'YOKOGAWA' <-- hard-coded 0134 % coord_type 0135 % acq_type 0136 % Nsample % sampling number of measurement 0137 % Pretrigger % number of sample before trigger 0138 % SampleFreq % sampling frequency 0139 % Nrepeat % repeat number 0140 % Trial % struct of trial information 0141 0142 0143 [meg_info] = vb_ykgwfile_load_extra_channel_info(ykgwfile, meg_info); 0144 % <at this moment> newly determined fields of meg_info are ... 0145 % ExtraChannelInfo % <<struct>> extra channels' information 0146 0147 0148 [meg_info] = vb_info_add_posfile_info(meg_info, posfile); 0149 % <at this moment> fields of meg_info which may be newly determined are ... 0150 % Vcenter 0151 % Vradius 0152 % MRI_ID 0153 % TransInfo 0154 0155 0156 % --- load calibrate and separate data 0157 [out_path] = vb_get_file_parts(out_file); 0158 [meg_info] = vb_ykgwfile_load_data(ykgwfile, meg_info, out_path); 0159 % <at this moment> fields of meg_info which may be newly determined are ... 0160 % MEGch_id 0161 0162 0163 % --- convert information struct ---> MEGinfo 0164 [MEGinfo] = vb_meginfo_convert_raw2vbmeg(meg_info); 0165 0166 0167 % --- affine transform 'pick', 'Qpick', 'ref_pick', 'ref_Qpick' 0168 if ~isempty(ref_pick) && ~isempty(ref_Qpick) 0169 [ref_pick, ref_Qpick] = ... 0170 vb_meg_transform_coordinate(ref_pick, ref_Qpick, CoordType, posfile); 0171 end 0172 0173 [pick, Qpick, CoordType] = ... 0174 vb_meg_transform_coordinate(pick, Qpick, CoordType, posfile); 0175 0176 % store data 0177 % !!! if you use vb_save, it is very slower than using vb_fsave !!! 0178 Measurement = 'MEG'; 0179 MEGinfo.Measurement = Measurement; 0180 PositionFile = posfile; 0181 bexp = []; 0182 bexp_ext = []; 0183 0184 vb_fsave(out_file, 'pick', 'Qpick', ... 0185 'ref_pick', 'ref_Qpick', 'CoordType', ... 0186 'Measurement', 'PositionFile', ... 0187 'MEGinfo', 'bexp', 'bexp_ext', 'meg_parm'); 0188 0189 fprintf('---\n--- make %s\n---\n', out_file); 0190 return; 0191 % 0192 % --- END OF MAIN PROCEDURE -------------------------------------------------- % 0193 0194 % --- INNER FUNCTIONS -------------------------------------------------------- % 0195 % 0196 % --- inner_check_arguments() 0197 % 0198 function [proj_root, meg_parm, ykgwfile, posfile, outfile, meginfo] = ... 0199 inner_check_arguments(proj_root, meg_parm) 0200 func_ = mfilename; 0201 0202 const = vb_define_yokogawa; 0203 0204 % --- check parameters 0205 if isempty(meg_parm) 0206 error('(%s)meg_parm is a required parameter', func_); 0207 end 0208 0209 % --- check fields of file 0210 if ~isfield(meg_parm, 'yokogawa_file') 0211 error('(%s)yokogawa_file is a required field of meg_parm', func_); 0212 end 0213 0214 if ~isfield(meg_parm, 'pos_file') 0215 meg_parm.pos_file = ''; 0216 % error('(%s)pos_file is a required field of meg_parm', func_); 0217 end 0218 0219 % --- check files 0220 if exist(meg_parm.yokogawa_file, 'file') ~= 2 0221 error('(%s)cannot find yokogawa_file : %s', func_, meg_parm.yokogawa_file); 0222 end 0223 0224 if ~isempty(meg_parm.pos_file) && exist(meg_parm.pos_file, 'file') ~= 2 0225 error('(%s)cannot find pos_file : %s', func_, meg_parm.pos_file); 0226 end 0227 0228 ykgwfile = meg_parm.yokogawa_file; 0229 posfile = meg_parm.pos_file; 0230 0231 % --- MEGinfo 0232 meginfo = []; 0233 0234 % --- EEG GAIN 0235 if isfield(meg_parm, 'ex_ch_gain') 0236 meginfo = vb_meginfo_set_extra_ch_gain(meginfo, meg_parm.ex_ch_gain); 0237 else 0238 meginfo = vb_meginfo_set_extra_ch_gain(meginfo, []); 0239 end 0240 0241 % --- OUTPUT FILE 0242 outfile = fullfile(proj_root, meg_parm.meg_file); 0243 0244 % --- SAVING SPECIFICATION 0245 DEFAULT_PRECISION = 'float64'; 0246 0247 real_dir = ''; 0248 0249 % --- check and fill saveman if necessary 0250 if ~isfield(meg_parm, 'saveman') ... 0251 || isempty(meg_parm.saveman) 0252 0253 meg_parm.saveman = struct; 0254 end 0255 0256 if ~isfield(meg_parm.saveman, 'data_dir') ... 0257 || isempty(meg_parm.saveman.data_dir) 0258 0259 [DEFAULT_DATA_DIR, real_dir] = vb_device_make_data_dir(outfile); 0260 meg_parm.saveman.data_dir = DEFAULT_DATA_DIR; 0261 end 0262 0263 if ~isfield(meg_parm.saveman, 'precision') ... 0264 || isempty(meg_parm.saveman.precision) 0265 0266 meg_parm.saveman.precision = DEFAULT_PRECISION; 0267 end 0268 0269 if isempty(real_dir) 0270 base_dir = vb_get_file_parts(outfile); 0271 real_dir = fullfile(base_dir, meg_parm.saveman.data_dir); 0272 end 0273 0274 % --- check real directory 0275 if exist(real_dir, 'dir') ~= 7 0276 vb_mkdir(real_dir); 0277 end 0278 0279 meginfo.saveman = meg_parm.saveman; 0280 0281 if isfield(meg_parm, 'memory_max') && ~isempty(meg_parm.memory_max) 0282 meginfo.memory_max = meg_parm.memory_max; 0283 else 0284 meginfo.memory_max = const.DEFAULT_MEMORY_MAX; 0285 end 0286 return; 0287 % 0288 % --- end of inner_check_arguments() 0289 % 0290 % --- END OF INNER FUNCTIONS ------------------------------------------------- % 0291 0292 %--- END OF FILE ---%