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Copy pathnr_htkmatstruct_ipad.m
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nr_htkmatstruct_ipad.m
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function nr_htkmatstruct_ipad(htk_dir,htkmatstruct_otpt_filename,M1_ch1,M1_ch2,ipad_filename,aux_lbl,htkmatstruct_file_dir,anl_dir)
cd(htk_dir)
ecog = struct('chan',{});
aux = struct('chan',{});
aux(1).chan(1).raw=[];
aux(1).chan(2).raw=[];
aux(1).chan(3).raw=[];
emg = struct('chan',{});
X = struct('chan',{});
signal = struct('chan',{});
gain=1e6;
Fs=1000; % sampling freq after downsampling
files = dir('*.htk');
%% load the data and store processed Aux chan data into structure array
for abc =1 : length(files)
if ~isempty(strfind(files(abc).name,'htk'))
% load the data and convert in mat.file
file_name=files(abc).name;
[d,fs,dt,tc,t]=nr_readhtk(file_name);
%store the downsampled data in structure arrays
if ~isempty(strfind(file_name,'ipad.htk'))
aux(1).chan(1).raw=resample(d,2^10,(5^5)*8);
elseif ~isempty(strfind(file_name,'accel.htk'))
aux(1).chan(2).raw=resample(d,2^10,(5^5)*8);
elseif ~isempty(strfind(file_name,'trig.htk'))
aux(1).chan(3).raw=resample(d,2^10,(5^5)*8);
elseif ~isempty(strfind(file_name,'emg.htk'))
emg(1).chan(1).raw=resample(d,2^10,(5^5)*8);
elseif ~isempty(strfind(file_name,'emg2.htk'))
emg(1).chan(2).raw=resample(d,2^10,(5^5)*8);
elseif ~isempty(strfind(file_name,'signal.htk'))
signal(1).chan(1).raw=resample(d,2^10,(5^5)*8);
else
ecog(1).contact_pair(tc).raw_ecog_signal=resample(d,2^10,5^5)*gain;
end
abc
length(ecog(1).contact_pair)
end
end
C2 = 1e6; % constant to convert ecog/lfp channel voltage level from V->microV to match GL4k system
Glfp = 25000; % LFP channel gain
if ~isempty(signal)
ecog(1).contact_pair(29).raw_ecog_signal=signal(1).chan(1).raw*C2/Glfp;
end
%% notch filter around 60Hz, 120Hz and 180Hz
% butterworth notch filter - model order, [low/(Fs/2) high/(Fs/2)]
[n1_b, n1_a]=butter(3,2*[57 63]/Fs,'stop'); %60hz
[n2_b, n2_a]=butter(3,2*[117 123]/Fs,'stop'); %120hz
[n3_b, n3_a]=butter(3,2*[177 183]/Fs,'stop'); %180hz
[n4_b, n4_a]=butter(3,2*[237 243]/Fs,'stop'); %240hz
[n5_b, n5_a]=butter(3,2*[297 303]/Fs,'stop'); %300hz
[n6_b, n6_a]=butter(3,2*[357 363]/Fs,'stop'); %360hz
% [n7_b, n7_a]=butter(3,2*[88 94]/Fs,'stop'); %180hz
for k=1:length(ecog(1).contact_pair)
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n1_b, n1_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 60
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n2_b, n2_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 120
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n3_b, n3_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 180
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n4_b, n4_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 60
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n5_b, n5_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 120
ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n6_b, n6_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 180
% ecog(1).contact_pair(k).raw_ecog_signal=filtfilt(n7_b, n7_a, ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 180
end
%% remove DC offset
for k=1:length(ecog(1).contact_pair)
ecog(1).contact_pair(k).raw_ecog_signal=ecog(1).contact_pair(k).raw_ecog_signal-mean(ecog(1).contact_pair(k).raw_ecog_signal); %notch out at 60
end
for k=1:length(aux.chan)
aux.chan(k).raw=aux.chan(k).raw-mean(aux.chan(k).raw);
end
% %% contact to remove
%
% unused=input('unused contacts');
% used = setdiff(1:length(ecog.contact_pair),unused);
% for i = 1:length(used)
% j=used(i);
% X(1).contact_pair(i).raw_ecog_signal=ecog.contact_pair(j).raw_ecog_signal;
% end
% ecog=X;
%% detection of bad electrodes
% figure;hold on
% for i = 1: 14
% subplot(3,5,i)
% plot(ecog.contact_pair(i).raw_ecog_signal)
% title(num2str(i))
% % ylim([-0.005 0.005])
% end
% figure;hold on
% for i = 15: 28
% subplot(3,5,i-14)
% plot(ecog.contact_pair(i).raw_ecog_signal)
% title(num2str(i))
% % ylim([-25 25])
% end
% bad=input('bad contacts');
%
% close all
%% common reference
if length(ecog.contact_pair) <=30
length_CAR = 28;
elseif length(ecog.contact_pair) <=64
length_CAR = 64;
else
length_CAR = 256;
end
data = nan*ones(length_CAR,length(ecog.contact_pair(1).raw_ecog_signal));
for i = 1: length_CAR
data(i,:) = ecog.contact_pair(i).raw_ecog_signal';
end
car=nanmean(data)/length_CAR;
for i = 1: length_CAR
ecog.contact_pair(i).remontaged_ecog_signal = ecog.contact_pair(i).raw_ecog_signal-car;
% ecog.contact_pair(i).remontaged_ecog_signal=ecog.contact_pair(i).raw_ecog_signal-ecog.contact_pair(i+1).raw_ecog_signal;
end
% ecog.contact_pair(28).remontaged_ecog_signal=ecog.contact_pair(28).raw_ecog_signal;
if size(ecog.contact_pair,2) ==29
ecog.contact_pair(29).remontaged_ecog_signal=ecog.contact_pair(29).raw_ecog_signal;
elseif size(ecog.contact_pair,2) >28 && size(ecog.contact_pair,2) <=32
for ii = 29:size(ecog.contact_pair,2)-1
ecog.contact_pair(ii).remontaged_ecog_signal=ecog.contact_pair(ii).raw_ecog_signal-ecog.contact_pair(ii+1).raw_ecog_signal;
end
end
%% load ipad data
%if ~isempty(strfind(filename,'_ipad')) %evt == 1
% [d,fs,dt,tc,t]=readhtk('trig.htk');
% chan_trig=d;
% % find active and rest periods using the raw signal
% MARGIN = 0.005; % is a very wide range that handles large fluctuations in task voltage. ParseIntraOpEvents uses MARGIN = 0.05
%
% % thresh = max(chan_trig);
% % ACTIVE = [thresh-MARGIN thresh+MARGIN]; %Determine the threshold
% % in1 = inrange(chan_trig,ACTIVE);
% thresh = 4;%mean(chan_trig(find(chan_trig~=0)))
% in1=chan_trig>thresh;
% inds = find(in1);
% [pos,n] = evFindGroups(inds,1,1000); %find active period of 1s minimum
% active_time = inds(pos(1,:))/(fs/1000);
% rest_time = inds(pos(2,:))/(fs/1000);
%
% % save rest/active timestamps in ecog structure array
% ecog(1).rest_time=int32(rest_time);
% ecog(1).active_time=int32(active_time);
% find the begining of each trial using the raw signal
[d,fs,dt,tc,t]=nr_readhtk('ipad.htk');
chan_ipad=d;
plot(d)
hold on
THRESH = input('thresh');
START = 15% input('start');
inds = find(chan_ipad(START:end-15)>=THRESH);
[pos,n] = nr_evFindGroups(inds,500,1);
plot(inds(pos(1,1:end-1))+START,THRESH, '*r')
ipad_ON_time = (inds(pos(1,1:end-1))+START)/(fs/1000);
ipad_OFF_time = (inds(pos(1,2:end))+START)/(fs/1000);
DELETE = input('delete');
GOOD = setdiff([1:length(ipad_ON_time)],DELETE)
ecog(1).ipad_ON_time=int32(ipad_ON_time(GOOD));
ecog(1).ipad_OFF_time= int32(ipad_OFF_time(GOOD));
%else
% ecog(1).rest_time=[];
% ecog(1).active_time=[];
ecog(1).ipad_ON_time=[];
ecog(1).ipad_OFF_time=[];
%end
%% save data
% use filename to create output filename
name = [htkmatstruct_otpt_filename(1:11),'str_',htkmatstruct_otpt_filename(12:end),'_ecog.mat'];
% name=[filename '_ecog'];
% filename=[filename,'_ecog.mat'];
cd(anl_dir)
load(aux_lbl)
cd(htkmatstruct_file_dir)
save(name,'name','ecog','M1_ch1','M1_ch2','aux','emg','Fs','thresh','auxchan_lbl');
%% Add IPAD file info
load(ipad_filename)
save(name ,'description','timestamp','-append');