Skip to content

Commit 7edfcc2

Browse files
DouweHorsthuisDouweHorsthuis
committed
adding interpolation
1 parent 7b6ea63 commit 7edfcc2

File tree

1 file changed

+33
-17
lines changed

1 file changed

+33
-17
lines changed

‎src/E_preprocces3.m‎

Lines changed: 33 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
% Restingstate pipepline (2021)
22
% Final version of SRC code 12/6/2021
33
% this script allows for re-reference (which we skip)
4+
% this script interpolates the bad channels
45
% does an average reference
56
% does ICA (using pop_runica) setting a PCA, of all chans minus 1. This is
67
% not great. So it's changed to pca = rank(EEG.data), which also takes care of bridged channels)
@@ -14,12 +15,12 @@
1415
for g=1:length(Group)
1516
switch Group{g}
1617
case 'Control'
17-
% home_path = '\\data.einsteinmed.org\users\Filip Ana Douwe\Resting state data\Control\';
18+
home_path = '\\data.einsteinmed.org\users\Filip Ana Douwe\Resting state data\Control\';
1819
%% aged matched controls
19-
%subject_list = {'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' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
20+
subject_list = {'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' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
2021
%% extra controls
21-
subject_list = {'10297' '10331' '10385' '10399' '10497' '10553' '10590' '10640' '10867' '10906' '12002' '12004' '12006' '12122' '12139' '12177' '12188' '12197' '12203' '12206' '12230' '12272' '12415' '12474' '12482' '12516' '12534' '12549' '12588' '12632' '12735' '12746' '12755' '12770' '12852' '12870'};
22-
home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\';
22+
%subject_list = {'10297' '10331' '10385' '10399' '10497' '10553' '10590' '10640' '10867' '10906' '12002' '12004' '12006' '12122' '12139' '12177' '12188' '12197' '12203' '12206' '12230' '12272' '12415' '12474' '12482' '12516' '12534' '12549' '12588' '12632' '12735' '12746' '12755' '12770' '12852' '12870'};
23+
% home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\';
2324
% did these again because need extra channels deleted
2425
% subject_list = {'12139' '10399'};
2526
% home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\';
@@ -33,7 +34,8 @@
3334
end
3435
figure_path = [home_path 'figures\'];
3536
participant_info = num2cell(zeros(length(subject_list),9));
36-
deleted_data = num2cell(zeros(length(subject_list), 2));
37+
%deleted_data = num2cell(zeros(length(subject_list), 2));
38+
participant_data_qt = string(zeros(length(subject_list), 4)); %prealocationg space for speed
3739
components = num2cell(zeros(length(subject_list), 8)); %prealocationg space for speed
3840
refchan = { }; %if you want to re-ref to a channel add the name of the channel here, if empty won't re-ref to any specific channel
3941
for s=1:length(subject_list)
@@ -42,7 +44,20 @@
4244
data_path = [home_path subject_list{s} '\\'];
4345
fprintf('\n\n\n**** %s: Loading dataset ****\n\n\n', subject_list{s});
4446
EEG = pop_loadset('filename', [subject_list{s} '_triggerfix.set'], 'filepath', data_path);
45-
%re-referencing, if refchan is empty this get's skipped
47+
%% setting PCA for ICA (amount of ICs you want to be created)
48+
pca = EEG.nbchan-1; %the PCA part of the ICA needs stops the rank-deficiency % pre 12/6/2021 , is not accurate but so far the best we can do. Does not take bridging in account, but neither would the normal ICA function, which misses the avg ref sometimes
49+
%% interpolation
50+
EEGinter = pop_loadset('filename', [subject_list{s} '_info.set'], 'filepath', data_path);%loading participant file with 64 channels
51+
%saving the original amount of total channels
52+
labels_all = {EEGinter.chanlocs.labels}.'; %stores all the labels in a new matrix
53+
%interpolating for 64 channels
54+
labels_good = {EEG.chanlocs.labels}.'; %saves all the channels that are in the excom file
55+
disp(EEG.nbchan); %writes down how many channels are there
56+
EEG = pop_interp(EEG, EEGinter.chanlocs, 'spherical');%interpolates the data
57+
EEG = eeg_checkset( EEG );
58+
EEG = pop_saveset( EEG, 'filename', [subject_list{s} '_inter.set'], 'filepath', data_path); %saves data
59+
disp(EEG.nbchan)
60+
%% re-referencing, if refchan is empty this get's skipped
4661
if isempty(refchan)~=1 %if no re-reference channels chose this gets skipped
4762
for j=1:length(EEG.chanlocs)
4863
if strcmp(refchan{1}, EEG.chanlocs(j).labels)
@@ -60,8 +75,9 @@
6075
EEG = pop_reref( EEG, [ref1 ref2]); %re-references to the average of 2 channels
6176
end
6277
end
63-
EEG = eeg_checkset( EEG );
64-
%another re-ref to the averages as suggested for the ICA
78+
79+
80+
%% Avg re-reference as suggested for the ICA
6581
EEG = pop_reref( EEG, []);
6682
EEG = eeg_checkset( EEG );
6783
EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_ref.set'],'filepath', data_path);
@@ -75,7 +91,7 @@
7591
end
7692
%Independent Component Analysis
7793
EEG = eeg_checkset( EEG );
78-
pca = EEG.nbchan-1; %the PCA part of the ICA needs stops the rank-deficiency % pre 12/6/2021 , is not accurate but so far the best we can do. Does not take bridging in account, but neither would the normal ICA function, which misses the avg ref sometimes
94+
7995
EEG = pop_runica(EEG, 'extended',1,'interupt','on','pca',pca); %using runica function, with the PCA part
8096
EEG = eeg_checkset( EEG );
8197
EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_ica.set'],'filepath', data_path);
@@ -135,16 +151,16 @@
135151
delete([figure_path subject_list{s} '_remaining_ICs_topos.png'])
136152
close all
137153
EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_excom.set'],'filepath', data_path);%save
138-
%% extra cleaning %was uses before 12/6/2021 for all projects, not needed after update to cleaning function
139-
%orig_length=EEG.xmax;
140-
%EEG = pop_rejcont(EEG, 'elecrange',[1:EEG.nbchan] ,'freqlimit',[20 40] ,'threshold',8 ,'epochlength',0.5,'contiguous',4,'addlength',0.25,'taper','hamming');
141-
%clean_length=EEG.xmax;
142-
%EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_clean.set'],'filepath', data_path);%save
143154
%% saving structures
144-
deleted_data(s,:)=[subject_list(s), 100-(clean_length/orig_length)*100];
145155
subj_comps=[subject_list(s), num2cell(brain_ic), num2cell(muscle_ic), num2cell(eye_ic), num2cell(hearth_ic), num2cell(line_noise_ic), num2cell(channel_ic), num2cell(other_ic)];
146-
components(s,:)=[subj_comps];
156+
lables_del = setdiff(labels_all,labels_good); %only stores the deleted channels
157+
All_bad_chan = strjoin(lables_del); %puts them in one string rather than individual strings
158+
ID = string(subject_list{s});%keeps all the IDs
159+
data_subj = [ID, length(lables_del), All_bad_chan, EEG.nbchan]; %combines IDs and Bad channels, total channels at the end
160+
participant_data_qt(s,:) = data_subj;%combine new data with old data
161+
components(s,:) =[subj_comps];
162+
clear EEG_temp EEGinter
147163
end
148164
save([home_path 'components_' Group{g} ], 'components');
149-
save([home_path 'deleted_data_' Group{g}], 'deleted_data');
165+
save([home_path 'deleted_data_' Group{g}], 'participant_data_qt');
150166
end

0 commit comments

Comments
 (0)