Skip to content

Commit 8ae7db6

Browse files
DouweHorsthuisDouweHorsthuis
committed
pwelch update
1 parent adb17a5 commit 8ae7db6

File tree

3 files changed

+140
-109
lines changed

3 files changed

+140
-109
lines changed

‎README.md‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -105,7 +105,12 @@ After that we use [pop_rejcont](https://github.com/wojzaremba/active-delays/blob
105105
This script loads a file with all the original channels, deletes the externals and uses these file locations to interpolate the channels of the corresponding's subjects data.
106106
In the case of 160 channel data, it uses the [transform_n_channels](https://github.com/CognitiveNeuroLab/Interpolating_160ch_to_64ch_eeglab) function to interpolate the remaining channels not to the original 160, but to 64 channel data so that it is the same as all the other data. For this to work Matlab needs to know the location of 2 things, the trannsform_n_channel.m file and the EEG files called 64.set and 64.fdt.
107107

108+
### Power Frequency Analysis
109+
In the G_PSD_pwelsh script, we first make sure that the triggers are still in the right place. Due to the extra cleaning we did with the pop_rejcont function in [E_preprocces3](#e_preprocces3) it is possible that the triggers got deleted if the corresponding continues data were too noisy. If they got deleted, the scripts calculates what the time of the onset of that deleted part of data was and uses that instead as the latency of the trigger.
108110

111+
After that we use the the [pwelch function of Matlab](https://www.mathworks.com/help/signal/ref/pwelch.html) and a log tranformation of the results to get the power frequency results.
112+
113+
#add here what channels we use, for now it's just indivual but we will change this to groups and averages of those groups
109114

110115

111116
## License

‎src/G_PSD_pwelch.m‎

Lines changed: 135 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,135 @@
1+
clear variables
2+
eeglab
3+
len = 256;
4+
Fs = 256;
5+
nfft = 512; %should be power of 2
6+
%noverlap = 0; %we'll do 50% overlap, better b/c welch uses hamming window
7+
8+
9+
group= {'Aging' }%'Control' 'ASD'};
10+
11+
for group_count = 1:length(group)
12+
if strcmp(group{group_count},'Aging')
13+
subject_list = {'12022' '12023' '12031' '12081' '12094' '12188' '12255' '12335' '12339' '12362' '12364' '12372' '12376' '12390' '12398' '12407' '12408' '12451' '12454' '12457' '12458' '12459' '12468' '12478' '12498' '12510' '12517' '12532' '12564' '12631' '12633' '12634' '12636' '12665' '12670' '12696' '12719' '12724' '12751' '12763' '12769' '12776' '12790' '12806' '12814' '12823' '12830' '12847' '12851' '12855' '12856' '12857' '12859' '12871' '12872' '12892'};
14+
people_no_trigger = [];
15+
people_no50_trigger = [];
16+
people_no51_trigger = [];
17+
trigger50_51_same = [];
18+
elseif strcmp(group{group_count},'ASD')
19+
subject_list = {'1101' '1164' '1808' '1852' '1855' '11014' '11094' '11151' '11170' '11275' '11349' '11516' '11558' '11583' '11647' '11729' '11735' '11768' '11783' '11820' '11912' '1106' '1132' '1134' '1154' '1160' '1173' '1174' '1179' '1190' '1838' '1839' '1874' '11013' '11056' '11098' '11106' '11198' '11244' '11293' '11325' '11354' '11375' '11515' '11560' '11580' '11667' '11721' '11723' '11750' '11852' '11896' '11898' '11913' '11927' '11958' '11965'}; %all the IDs for the indivual particpants;
20+
people_no_trigger = [];
21+
people_no50_trigger = [];
22+
people_no51_trigger = [];
23+
trigger50_51_same = [];
24+
elseif strcmp(group{group_count},'Control')
25+
subject_list = {'12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899' '10033' '10130' '10131' '10158' '10165' '10257' '10281' '10293' '10360' '10369' '10384' '10394' '10407' '10438' '10446' '10451' '10463' '10467' '10476' '10501' '10526' '10534' '10545' '10561' '10562' '10581' '10585' '10616' '10615' '10620' '10639' '10748' '10780' '10784' '10822' '10858' '10906' '10915' '10929' '10935' '10844' '10956' '12005' '12007' '12010' '12215' '12328' '12360' '12413' };% ------------------------------------------------
26+
people_no_trigger = [];
27+
people_no50_trigger = [];
28+
people_no51_trigger = [];
29+
trigger50_51_same = [];
30+
end
31+
path_1 = ['C:\Users\dohorsth\Desktop\Testing restingstate\' group{group_count} '\'];
32+
33+
for subject_list_count = 1:length(subject_list)
34+
path = [path_1 subject_list{subject_list_count} '\'];
35+
EEG = pop_loadset('filename',[subject_list{subject_list_count} '_inter.set'],'filepath', path );
36+
%% separate EO from EC
37+
info = [];
38+
for i = 1:length(EEG.event)
39+
if strcmp(EEG.event(i).type, 'boundary') % in there because of manual artefact rejection
40+
continue
41+
elseif isfield(EEG.event,'edftype') %isempty(EEG.event(i).edftype)~=1
42+
info(i,1) = string(EEG.event(i).edftype);
43+
elseif isfield(EEG.event,'type') %isempty(EEG.event(i).type)~=1
44+
info(i,1) = string(EEG.event(i).type);
45+
end
46+
info(i,2) = EEG.event(i).latency;
47+
end
48+
if size(info,1)==2 && length(info)==2 %because there were no boundries, the data is in a 2x2 matrix instead of a 1x4)
49+
info(3,1)=0; %we add a zero, so it does the same
50+
end
51+
info(info==0) = []; %delete all zeros
52+
53+
if isempty(info)%if there are no triggers, we are going to choose the data ourselves but take less to be safe
54+
durations=0;
55+
%when 1 or more triggers are missing, this loop happens. using the latencies + durations of the boundaries in EEG.event to reproduce the original continues data.
56+
%calculating which boundary is the one that would have included the trigger and using there latency to instead of the missing trigger's
57+
for ii= 1:length(EEG.event)
58+
durations=durations+EEG.event(ii).duration; %this will sum all the durations of the deleted data
59+
if EEG.event(ii).latency+durations-EEG.event(ii).duration-1<EEG.urevent(1).latency && EEG.event(ii).latency+durations+1>EEG.urevent(1).latency %if the start of the boundry is before the latency of the original 50 and the duration last until after) (-1 and +1 just to prevent rounding up/down issues)
60+
info=[50, 51, EEG.event(ii).latency]; %keeps the 2 correct ones from info, but uses the start of the boundry event for the first trigger
61+
people_no50_trigger = [people_no50_trigger, subject_list(subject_list_count)];
62+
elseif EEG.event(ii).latency+durations-EEG.event(ii).duration-1<EEG.urevent(2).latency && EEG.event(ii).latency+durations+1>EEG.urevent(2).latency %if the start of the boundry is before the latency of the original 50 and the duration last until after)
63+
info=[info(1), info(2), info(3), EEG.event(ii).latency]; %don't think this is correct, I think this wil
64+
end
65+
end
66+
people_no_trigger = [people_no_trigger, subject_list(subject_list_count)];
67+
elseif length(info)~=4 %if one of the two triggers got deleted by the auto cleaning
68+
if info(1)==50 %trigger 51 is deleted (EC) will find the correct time and add it
69+
durations=0;
70+
for ii= 1:length(EEG.event)
71+
durations=durations+EEG.event(ii).duration; %this will sum all the durations of the deleted data
72+
if EEG.event(ii).latency+durations-EEG.event(ii).duration-1<EEG.urevent(2).latency && EEG.event(ii).latency+durations+1>EEG.urevent(2).latency %if the start of the boundry is before the latency of the original 50 and the duration last until after)
73+
info=[info(1), 51, info(2), EEG.event(ii).latency]; %don't think this is correct, I think this wil
74+
people_no51_trigger = [people_no51_trigger, subject_list(subject_list_count)];
75+
end
76+
end
77+
elseif info(1)==51 %trigger 51 is deleted (EC) will find the correct time and add it
78+
durations=0;
79+
for ii= 1:length(EEG.event)
80+
durations=durations+EEG.event(ii).duration; %this will sum all the durations of the deleted data
81+
if EEG.event(ii).latency+durations-EEG.event(ii).duration-1<EEG.urevent(1).latency && EEG.event(ii).latency+durations+1>EEG.urevent(1).latency %if the start of the boundry is before the latency of the original 50 and the duration last until after) (-1 and +1 just to prevent rounding up/down issues)
82+
info=[50, info(1), EEG.event(ii).latency, info(2)]; %keeps the 2 correct ones from info, but uses the start of the boundry event for the first trigger
83+
people_no50_trigger = [people_no50_trigger, subject_list(subject_list_count)];
84+
end
85+
end
86+
else
87+
breakhere
88+
89+
end
90+
end
91+
if info(4)-info(3)<2 %this looks if trigger 50&51 are at almost the same time 1==1sec/256
92+
info(3)=1000;
93+
trigger50_51_same= [trigger50_51_same; subject_list(subject_list_count)];
94+
end
95+
data_EO = EEG.data(:,info(3):info(4));
96+
data_EO(:,1:2560)=[];%added to delete first 10 sec
97+
if info(4)+(info(4)-info(3))>EEG.pnts
98+
data_EC = EEG.data(:,info(4):end); %if the EC part is shorter then the EO part it would exceed the max pnts value
99+
else
100+
data_EC = EEG.data(:,info(4):info(4)+(info(4)-info(3))); %this makes sure they are both equally long
101+
end
102+
data_EC(:,1:2560)=[];%added to delete first 10 sec
103+
% end
104+
%% Compute Power
105+
CPz = 32;
106+
Pz = 31;
107+
Cz = 48;
108+
109+
[P_EO_CPz freqs] = pwelch(data_EO(CPz,:),len,[],nfft,Fs); %does not produce an image with outputs
110+
P_EO_Pz = pwelch(data_EO(Pz,:),len,[],nfft,Fs); %does not produce an image with outputs
111+
P_EO_Cz = pwelch(data_EO(Cz,:),len,[],nfft,Fs); %does not produce an image with outputs
112+
P_EC_CPz = pwelch(data_EC(CPz,:),len,[],nfft,Fs); %does not produce an image with outputs
113+
P_EC_Pz = pwelch(data_EC(Pz,:),len,[],nfft,Fs); %does not produce an image with outputs
114+
P_EC_Cz = pwelch(data_EC(Cz,:),len,[],nfft,Fs); %does not produce an image with outputs
115+
116+
PSD_EO_CPzlog(:,subject_list_count) = 10*log10(P_EO_CPz);
117+
PSD_EO_Pzlog(:,subject_list_count) = 10*log10(P_EO_Pz);
118+
PSD_EO_Czlog(:,subject_list_count) = 10*log10(P_EO_Cz);
119+
PSD_EC_CPzlog(:,subject_list_count) = 10*log10(P_EC_CPz);
120+
PSD_EC_Pzlog(:,subject_list_count) = 10*log10(P_EC_Pz);
121+
PSD_EC_Czlog(:,subject_list_count) = 10*log10(P_EC_Cz);
122+
123+
end
124+
% save([path_1 'PSD_EO_CPzlog_' group{group_count}], 'PSD_EO_CPzlog')
125+
% save([path_1 'PSD_EO_Pzlog_' group{group_count}], 'PSD_EO_Pzlog')
126+
% save([path_1 'PSD_EO_Czlog_' group{group_count}], 'PSD_EO_Czlog')
127+
% save([path_1 'PSD_EC_CPzlog_' group{group_count}], 'PSD_EC_CPzlog')
128+
% save([path_1 'PSD_EC_Pzlog_' group{group_count}], 'PSD_EC_Pzlog')
129+
% save([path_1 'PSD_EC_Czlog_' group{group_count}], 'PSD_EC_Czlog')
130+
save([path_1 'trigger50_51_same_' group{group_count}], 'trigger50_51_same')
131+
save([path_1 'people_no_trigger_' group{group_count}], 'people_no_trigger')
132+
save([path_1 'people_1_trigger_' group{group_count}], 'people_1_trigger')
133+
134+
end
135+

‎src/I_PSD_pwelch.m‎

Lines changed: 0 additions & 109 deletions
This file was deleted.

0 commit comments

Comments
 (0)