-
Notifications
You must be signed in to change notification settings - Fork 7
/
bdf2mat_main.m
156 lines (150 loc) · 6.1 KB
/
bdf2mat_main.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
function [eeg_data, emg_data, fs, varargout] = bdf2mat_main(trl_num, elec_num, emg_ch, eeg_ch, filename, varargin)
%
% [eeg_data, emg_data, fs] = bdf2mat_main(trl_num, elec_num, emg_ch, eeg_ch, filename)
% [eeg_data, emg_data, fs, emg_onset_sampl, emg_onset_time] = bdf2mat_main(trl_num, elec_num, emg_ch, eeg_ch, filename, drift_flag, onset_flag)
%
% *************************************************************************
% * Reading EEG/EMG signal from bdf files, preprocessing and conditioning *
% *************************************************************************
%
% Usage: [eeg_data, emg_data, fs] = bdf2mat_main(trl_num, elec_num, emg_ch, eeg_ch, filename)
% [eeg_data, emg_data, fs, emg_onset_sampl, emg_onset_time] = bdf2mat_main(trl_num, elec_num, emg_ch, eeg_ch, filename, drift_flag, onset_flag)
% inputs:
% 'trl_num': number of trials
% 'elec_num': number of electrodes used to record EEG
% 'emg_ch': EMG channel of interest
% 'eeg_ch': scalar or double vector of EEG channels of interest
% 'filename': file name format as a string
% (opt) 'drift_flag': baseline drift rejection flag, available options:
% 'drift', 'nodrift'(default: drift_flag = 'drift')
% (opt) 'onset_flag': onset detection flag, available options: 1, 0
% (default = 1)
% outputs:
% 'eeg_data': preprocessed EEGs of the selected channel from all
% trials
% 'emg_data': preprocessed EMGs of the selected channel from all
% trials
% 'fs': sampling frequency
% 'emg_onset_sampl': sample number of the movement onset
% 'emg_onset_time': corresponding time of movement onset
% Note:
% an empty bracket [] Must be assigned to not-specified values
%
% This program is provided by ESMAEIL SERAJ. Please make sure to cite BOTH
% the original studies and the User Manual to help others find these items.
%
% Authors:
% Esmaeil Seraj, Karthiga Mahalingam
% Websites:
% https://github.com/EsiSeraj/ERP_Connectivity_EMG_Analysis
% http://oset.ir/category.php?dir=Tools
%
% Copyright (C) <2018> <ESMAEIL SERAJ (eseraj3@gatech.edu)>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/> or
% write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth
% Floor, Boston, MA 02110-1301, USA.
%
%% Checking inputs and assigning default values
if nargin < 5
error('***wrong number of input arguments. Refer to Manual for details***')
elseif nargin == 5
drift_flag = 'drift';
onset_flag = 1;
elseif nargin > 5
if size(varargin, 2) ~= 2
error('***an empty bracket [] Must be assigned to not-specified values***')
else
if isempty(varargin{1})
drift_flag = 'drift';
else
drift_flag = varargin{1};
end
if isempty(varargin{2})
onset_flag = 1;
else
onset_flag = varargin{2};
end
end
end
if (~(isscalar(trl_num) && isscalar(elec_num) && isscalar(onset_flag)))
error('***trial and electrode numbers have to be a scalar***')
end
if (~(isa(emg_ch, 'double') && isa(eeg_ch, 'double')))
error('***EMG and EEG channels of interest have to be a doubles (i.e. integer or vector of indices)***')
end
if (~(ischar(filename) && ischar(drift_flag)))
error('***filename and drift_flag have to be strings***')
else
if (~(strcmp(drift_flag, 'drift') || strcmp(drift_flag, 'nodrift')))
error('***typo in your specified drift_flag string***')
end
end
%% *.bdf to *.mat transformation
emg_data = cell(1, trl_num);
eeg_data = cell(1, trl_num);
emg_onset_sampl = zeros(1, trl_num);
emg_onset_time = zeros(1, trl_num);
L = [700, 500]; % time window needed here has to be about 1-2 sec
approach = 'mn';
for i=1:trl_num
% reading data and separating EEG & EMG signals
% [data,numChan,labels,txt,fs,gain,prefiltering,ChanDim] = eeg_read_bdf(sprintf(filenameformat, i), 'all', 'n');
[data, ~, ~, ~, fs, ~, ~, ~] = eeg_read_bdf(sprintf(filename, i), 'all', 'n');
eeg_all = data(1:elec_num ,:);
if (isscalar(eeg_ch) || isscalar(emg_ch))
emg = data(emg_ch, :);
eeg = eeg_all(eeg_ch, :);
elseif (isa(eeg_ch, 'double') || isa(emg_ch, 'double'))
[~, nn] = size(data);
emg = zeros(length(emg_ch), nn);
eeg = zeros(length(eeg_ch), nn);
for lll=1:length(emg_ch)
emg(lll, :) = data(emg_ch(lll), :);
end
for ll=1:length(eeg_ch)
eeg(ll, :) = eeg_all(eeg_ch(ll), :);
end
end
% ref = mean(data(1:16, :));
% ref = (data(271, :) + data(272, :))/2;
% eeg = eeg-ref;
if (strcmp(drift_flag, 'drift'))
% preprocessing the data: BaseLineWander Removal
emg = drift_reject(emg, L(1), L(2), approach);
eeg = drift_reject(eeg, L(1), L(2), approach);
elseif (strcmp(drift_flag, 'nodrift'))
emg = drift_reject(emg, L(1), L(2), approach);
if onset_flag == 1
window = 30;
[emg_onset_sampl(i), emg_onset_time(i)] = emg_onset(emg, fs, window);
end
else
error('You need to choose an option to deal with DRIFT')
end
% EMG onset estimation
if onset_flag == 1
window = 30;
[emg_onset_sampl(i), emg_onset_time(i)] = emg_onset(emg, fs, window, i);
end
% saving EEG & EMG signal
emg_data{i} = emg;
eeg_data{i} = eeg;
eeg = [];
end
if onset_flag == 1
varargout{1} = emg_onset_sampl;
varargout{2} = emg_onset_time;
end
end