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adding all the matlab code for the analysis
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| % Restingstate pipepline (2021) | ||
| % Final version of SRC code 12/6/2021 | ||
| % Merging script to create .set file | ||
| clear all | ||
| %subject_list = {'2202' '2204' '2207' '2212' '2216' '2222' '2229' '2231' '2243' '2256' '2257' '2261' '2267' '2270' '2274' '2281' '2284' '2286' '2292' '2295'}; | ||
| %subject_list = {'7003' '7007' '7019' '7025' '7046' '7049' '7051' '7054' '7058' '7059' '7061' '7064' '7065' '7073' '7075' '7078' '7089' '7092' '7094' '7123' '7556' '7808'}; | ||
| subject_list = {'10293' '10561' '10562' '10581' '10616' '10748' '10822' '10858' '10935' '12004' '12010' '12139' '12177' '12188' '12197' '12203' '12206' '12215' '12272' '12413' '12415' '12449' '12482' '12512' '12588' '12632' '12648' '12651' '12707' '12727' '12739' '12746' '12750' '12755' '12770' '12815' '12852' '12870'}; | ||
| filename = 'restingstate'; % if your bdf file has a name besides the ID of the participant (e.g. oddball_paradigm) | ||
| home_path = '\\data.einsteinmed.org\users\Filip Ana Douwe\Resting state data\'; %place data is (something like 'C:\data\') | ||
| blocks = 1; % the amount of BDF files. if different participant have different amounts of blocks, run those participant separate | ||
| for s = 1:length(subject_list) | ||
| clear ALLEEG | ||
| eeglab | ||
| close all | ||
| data_path = [home_path subject_list{s} '\']; | ||
| disp([data_path subject_list{s} '_' filename '.bdf']) | ||
|
|
||
| if blocks == 1 | ||
| %if participants have only 1 block, load only this one file | ||
| EEG = pop_biosig([data_path subject_list{s} '_' filename '.bdf']); | ||
| else | ||
| for bdf_bl = 1:blocks | ||
| %if participants have more than one block, load the blocks in a row | ||
| %your files need to have the same name, except for a increasing number at the end (e.g. id#_file_1.bdf id#_file_2) | ||
| EEG = pop_biosig([data_path subject_list{s} '_' filename '_' num2str(bdf_bl) '.bdf']); | ||
| [ALLEEG, ~] = eeg_store(ALLEEG, EEG, CURRENTSET); | ||
| end | ||
| %since there are more than 1 files, they need to be merged to one big .set file. | ||
| EEG = pop_mergeset( ALLEEG, 1:blocks, 0); | ||
| end | ||
| [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 0,'setname', [subject_list{s} ' restingstate paradigm'],'gui','off'); %adds a name to the internal .set file | ||
| %save the bdf as a .set file | ||
| mkdir( ['D:\restingstate\data\' subject_list{s}]) | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '.set'],'filepath',['D:\restingstate\data\' subject_list{s}]); | ||
| end | ||
|
|
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| % Restingstate pipepline (2021) | ||
| % Final version of SRC code 12/6/2021 | ||
| % Merging script to create .set file for files that were collected without | ||
| % using paradigm (particpant was told to close eyes or stare at the center | ||
| % of a black screen) | ||
| % ------------------------------------------------ | ||
| clear variables | ||
| subject_list = {'2260' '2201'}; | ||
| %subject_list = {'1101' '1164' '1808' '1852' '1855' '11014' '11094' '11151' '11170' '11275' '11349' '11516' '11558' '11583' '11647' '11729' '11735' '11768' '11783' '11820' '11912'}; | ||
| filename = 'restingstate'; % if your bdf file has a name besides the ID of the participant (e.g. oddball_paradigm) | ||
| home_path = '\\data.einsteinmed.org\users\Filip Ana Douwe\Resting state data\'; %place data is (something like 'C:\data\') | ||
| wrongconfig = zeros(1,length(subject_list)); %there are 160channel files that have a wrong config file, this is to save them | ||
| for s = 1:length(subject_list) | ||
| clear ALLEEG | ||
| eeglab | ||
| close all | ||
| data_path = [home_path subject_list{s} '\']; | ||
| disp([data_path subject_list{s} '.bdf']) | ||
|
|
||
| %loading file 1, adding triggers | ||
| EEG = pop_biosig([data_path subject_list{s} '_open.bdf']); | ||
| first = 1; %where the trigger will happen | ||
| second = 10; | ||
| TRIG = [first 0; second 50]; %script doesn't like only one trigger so adding 2 (first one can be ignored) | ||
| %%%% Import All events back into the EEG data structure | ||
| EEG = pop_importevent( EEG, 'event', TRIG, 'fields',{'latency','type'},'timeunit',NaN,'append','no'); | ||
| EEG = pop_editeventvals(EEG,'delete',1); %deleting the extra event | ||
| EEG = eeg_checkset(EEG); | ||
| [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); | ||
| %loading file 2, adding triggers | ||
| EEG = pop_biosig([data_path subject_list{s} '_closed.bdf']); | ||
| first = 1; %where the trigger will happen | ||
| second = 10; | ||
| TRIG = [first 0; second 51]; %script doesn't like only one trigger so adding 2 (first one can be ignored) | ||
| %%%% Import All events back into the EEG data structure | ||
| EEG = pop_importevent( EEG, 'event', TRIG, 'fields',{'latency','type'},'timeunit',NaN,'append','no'); | ||
| EEG = pop_editeventvals(EEG,'delete',1); %deleting the extra event | ||
| EEG = eeg_checkset(EEG); | ||
| [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); | ||
| EEG = pop_mergeset( ALLEEG, 1:2, 0);%merging into one | ||
| %merging files | ||
| [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 0,'setname', [subject_list{s} ' restingstate non-paradigm'],'gui','off'); %adds a name to the internal .set file | ||
| %some files have been collected with a wrong config file, need to rename the first 64 channels to fit the 160 channel names. | ||
| if strcmp(EEG.chanlocs(1).labels,'Fp1') && strcmp(EEG.chanlocs(65).labels,'C1') | ||
| correct_160_chan={'A1' 'A2' 'A3' 'A4' 'A5' 'A6' 'A7' 'A8' 'A9' 'A10' 'A11' 'A12' 'A13' 'A14' 'A15' 'A16' 'A17' 'A18' 'A19' 'A20' 'A21' 'A22' 'A23' 'A24' 'A25' 'A26' 'A27' 'A28' 'A29' 'A30' 'A31' 'A32' 'B1' 'B2' 'B3' 'B4' 'B5' 'B6' 'B7' 'B8' 'B9' 'B10' 'B11' 'B12' 'B13' 'B14' 'B15' 'B16' 'B17' 'B18' 'B19' 'B20' 'B21' 'B22' 'B23' 'B24' 'B25' 'B26' 'B27' 'B28' 'B29' 'B30' 'B31' 'B32'}; | ||
| for n=1:64 | ||
| EEG.chanlocs(n).labels = correct_160_chan{n}; | ||
| wrongconfig(:,s)=string(subject_list(s)); | ||
| end | ||
| disp('fixed configuration') | ||
| if strcmp(subject_list{s},'10399') %collected data with 160chn config but only data in 64 ch | ||
| EEG = pop_select( EEG, 'channel',{'A1','A2','A3','A4','A5','A6','A7','A8','A9','A10','A11','A12','A13','A14','A15','A16','A17','A18','A19','A20','A21','A22','A23','A24','A25','A26','A27','A28','A29','A30','A31','A32','B1','B2','B3','B4','B5','B6','B7','B8','B9','B10','B11','B12','B13','B14','B15','B16','B17','B18','B19','B20','B21','B22','B23','B24','B25','B26','B27','B28','B29','B30','B31','B32'}); | ||
| correct_64_chan={'Fp1' 'AF7' 'AF3' 'F1' 'F3' 'F5' 'F7' 'FT7' 'FC5' 'FC3' 'FC1' 'C1' 'C3' 'C5' 'T7' 'TP7' 'CP5' 'CP3' 'CP1' 'P1' 'P3' 'P5' 'P7' 'P9' 'PO7' 'PO3' 'O1' 'Iz' 'Oz' 'POz' 'Pz' 'CPz' 'Fpz' 'Fp2' 'AF8' 'AF4' 'AFz' 'Fz' 'F2' 'F4' 'F6' 'F8' 'FT8' 'FC6' 'FC4' 'FC2' 'FCz' 'Cz' 'C2' 'C4' 'C6' 'T8' 'TP8' 'CP6' 'CP4' 'CP2' 'P2' 'P4' 'P6' 'P8' 'P10' 'PO8' 'PO4' 'O2'}; | ||
| for n=1:64 | ||
| EEG.chanlocs(n).labels = correct_64_chan{n}; | ||
| wrongconfig(:,s)=string(subject_list(s)); | ||
| end | ||
| end | ||
| EEG = eeg_checkset(EEG); | ||
| end | ||
| %save the bdf as a .set file | ||
| mkdir( ['D:\restingstate\data\' subject_list{s}]) | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '.set'],'filepath',['D:\restingstate\data\' subject_list{s}]); | ||
| end | ||
| save([home_path 'participants_with_wrong_config'], 'wrongconfig'); | ||
|
|
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| % Restingstate pipepline (2021) | ||
| % Final version of SRC code 12/6/2021 | ||
| % fixing channel names for people with 160 config file with only 64 channels | ||
| % downsample | ||
| % exclude externals | ||
| % 1hz and 50hz filter | ||
| % channel info | ||
| % exclude channels | ||
| % ------------------------------------------------ | ||
| clear variables | ||
| eeglab | ||
| group = { 'Control' '22q' 'schiz'};% | ||
| lowpass_filter_hz=50; %50hz filter | ||
| highpass_filter_hz=1; %1hz filter | ||
| script_location= 'D:\restingstate\scripts\'; | ||
|
|
||
| for g=1:length(group) | ||
| if strcmp(group{g},'22q') | ||
| subject_list = {'2201' '2202' '2204' '2207' '2212' '2216' '2222' '2229' '2231' '2243' '2256' '2257' '2260' '2261' '2267' '2270' '2274' '2281' '2284' '2286' '2292' '2295'}; | ||
| home_path = 'D:\restingstate\data\'; | ||
| elseif strcmp(group{g},'schiz') | ||
| subject_list = {'7003' '7007' '7019' '7025' '7046' '7049' '7051' '7054' '7058' '7059' '7061' '7064' '7065' '7073' '7075' '7078' '7089' '7092' '7094' '7123' '7556' '7808'}; | ||
| home_path = 'D:\restingstate\data\'; | ||
| elseif strcmp(group{g},'Control') | ||
| subject_list = {'10293' '10561' '10562' '10581' '10616' '10748' '10822' '10858' '10935' '12004' '12010' '12139' '12177' '12188' '12197' '12203' '12206' '12215' '12272' '12413' '12415' '12449' '12482' '12512' '12588' '12632' '12648' '12651' '12707' '12727' '12739' '12746' '12750' '12755' '12770' '12815' '12852' '12870'}; | ||
| home_path = 'D:\restingstate\data\'; | ||
| end | ||
| deleted_channels=zeros(length(subject_list),2); | ||
| deleted_data=zeros(length(subject_list),2); | ||
| wrongconfig_type2 = zeros(1,length(subject_list)); | ||
| % Loop through all subjects | ||
| for s=1:length(subject_list) | ||
| fprintf('\n******\nProcessing subject %s\n******\n\n', subject_list{s}); | ||
| data_path = [home_path subject_list{s} '\\']; | ||
| % Load original dataset (created by previous script) | ||
| fprintf('\n\n\n**** %s: Loading dataset ****\n\n\n', subject_list{s}); | ||
| EEG = pop_loadset('filename', [subject_list{s} '.set'], 'filepath', data_path); | ||
| %the following people have had a wrong config file that saved 160 channels even though only 64 have data | ||
| if strcmp(subject_list{s},'1101' ) || strcmp(subject_list{s},'11583')|| strcmp(subject_list{s},'10501') | ||
| EEG = pop_select( EEG, 'channel',{'A1' 'A2' 'A3' 'A4' 'A5' 'A6' 'A7' 'A8' 'A9' 'A10' 'A11' 'A12' 'A13' 'A14' 'A15' 'A16' 'A17' 'A18' 'A19' 'A20' 'A21' 'A22' 'A23' 'A24' 'A25' 'A26' 'A27' 'A28' 'A29' 'A30' 'A31' 'A32' 'B1' 'B2' 'B3' 'B4' 'B5' 'B6' 'B7' 'B8' 'B9' 'B10' 'B11' 'B12' 'B13' 'B14' 'B15' 'B16' 'B17' 'B18' 'B19' 'B20' 'B21' 'B22' 'B23' 'B24' 'B25' 'B26' 'B27' 'B28' 'B29' 'B30' 'B31' 'B32'}); | ||
| correct_64_chan={'Fp1' 'AF7' 'AF3' 'F1' 'F3' 'F5' 'F7' 'FT7' 'FC5' 'FC3' 'FC1' 'C1' 'C3' 'C5' 'T7' 'TP7' 'CP5' 'CP3' 'CP1' 'P1' 'P3' 'P5' 'P7' 'P9' 'PO7' 'PO3' 'O1' 'Iz' 'Oz' 'POz' 'Pz' 'CPz' 'Fpz' 'Fp2' 'AF8' 'AF4' 'AFz' 'Fz' 'F2' 'F4' 'F6' 'F8' 'FT8' 'FC6' 'FC4' 'FC2' 'FCz' 'Cz' 'C2' 'C4' 'C6' 'T8' 'TP8' 'CP6' 'CP4' 'CP2' 'P2' 'P4' 'P6' 'P8' 'P10' 'PO8' 'PO4' 'O2'}; | ||
| for n=1:64 | ||
| EEG.chanlocs(n).labels = correct_64_chan{n}; | ||
| wrongconfig_type2(:,s)=string(subject_list(s)); | ||
| end | ||
| disp('fixed configuration') | ||
| EEG = eeg_checkset(EEG); | ||
| end | ||
| if strcmp(subject_list{s},'12851') %this file was the only mobi BDF file and needs not used channels deleted | ||
| EEG = pop_select( EEG, 'nochannel',{'F1' 'F2' 'F3' 'F4' 'F5' 'F6' 'F7' 'F8' 'F9' 'F10' 'F11' 'F12' 'F13' 'F14' 'F15' 'F16' 'F17' 'F18' 'F19' 'F20' 'F21' 'F22' 'F23' 'F24' 'F25' 'F26' 'F27' 'F28' 'F29' 'F30' 'F31' 'F32' 'G1' 'G2' 'G3' 'G4' 'G5' 'G6' 'G7' 'G8' 'G9' 'G10' 'G11' 'G12' 'G13' 'G14' 'G15' 'G16' 'G17' 'G18' 'G19' 'G20' 'G21' 'G22' 'G23' 'G24' 'G25' 'G26' 'G27' 'G28' 'G29' 'G30' 'G31' 'G32' 'H1' 'H2' 'H3' 'H4' 'H5' 'H6' 'H7' 'H8' 'H9' 'H10' 'H11' 'H12' 'H13' 'H14' 'H15' 'H16' 'H17' 'H18' 'H19' 'H20' 'H21' 'H22' 'H23' 'H24' 'H25' 'H26' 'H27' 'H28' 'H29' 'H30' 'H31' 'H32' 'EXG1' 'EXG2' 'EXG3' 'EXG4' 'EXG5' 'EXG6' 'EXG7' 'EXG8' 'GSR1' 'GSR2' 'Erg1' 'Erg2' 'Resp' 'Plet' 'Temp'}); | ||
| end | ||
| EEG = eeg_checkset( EEG ); | ||
| %downsample | ||
| EEG = pop_resample( EEG, 256); %downsample to 256hz | ||
| EEG = eeg_checkset( EEG ); | ||
| %deleting externals | ||
| EEG = pop_select( EEG,'nochannel',{'EXG1','EXG2','EXG3','EXG4','EXG5','EXG6','EXG7','EXG8' 'GSR1' 'GSR2' 'Erg1' 'Erg2' 'Resp' 'Plet' 'Temp'}); | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_exext.set'],'filepath', data_path); | ||
| %filtering | ||
| EEG.filter=table(lowpass_filter_hz,highpass_filter_hz); %adding it to subject EEG file | ||
| EEG = pop_eegfiltnew(EEG, 'locutoff',highpass_filter_hz); | ||
| EEG = eeg_checkset( EEG ); | ||
| EEG = pop_eegfiltnew(EEG, 'hicutoff',lowpass_filter_hz); | ||
| close all | ||
| EEG = eeg_checkset( EEG ); | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_downft.set'],'filepath', data_path); | ||
| EEG = pop_editset(EEG, 'chanlocs', [script_location 'Functions and files\BioSemi64.sfp']); %need to first load any sort of sfp file with the correct channels (the locations will be overwritten to the correct ones later) | ||
| %adding channel location | ||
| EEG=pop_chanedit(EEG, 'lookup',[fileparts(which('eeglab')) '\plugins\dipfit\standard_BESA\standard-10-5-cap385.elp']); %make sure you put here the location of this file for your computer | ||
|
|
||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_info.set'],'filepath', data_path); | ||
| old_n_chan = EEG.nbchan; | ||
| old_samples=EEG.pnts; | ||
| %old way, only channel rejection - used for Aging and ASD: | ||
| %EEG = clean_artifacts(EEG, 'FlatlineCriterion',5,'ChannelCriterion',0.8,'LineNoiseCriterion',4,'Highpass','off','BurstCriterion','off','WindowCriterion','off','BurstRejection','on','Distance','Euclidian'); | ||
| %new way, also bad data (bursts) rejection: | ||
| % the only thing to double check is if it will still reject eye | ||
| % components in ICA or if these are pre-deleted now (which they shouldn't) | ||
| %EEG = pop_clean_rawdata(EEG, | ||
| %'FlatlineCriterion',5,'ChannelCriterion',0.8,'LineNoiseCriterion',4,'Highpass','off','BurstCriterion','off','WindowCriterion','off','BurstRejection','off','Distance','Euclidian');%doesn't delete bad periods | ||
| %first at 'BurstCriterion',20, this caused too much data to be | ||
| %deleted, second time at 'BurstCriterion',50, this caused too few data to be | ||
| EEG = pop_clean_rawdata(EEG, 'FlatlineCriterion',5,'ChannelCriterion',0.8,'LineNoiseCriterion',4,'Highpass','off','BurstCriterion',35,'WindowCriterion','off','BurstRejection','on','Distance','Euclidian'); % deletes bad chns and bad periods | ||
| EEG.deleteddata_wboundries=100-EEG.pnts/old_samples*100; | ||
| new_n_chan = EEG.nbchan; | ||
| deleted_sample=EEG.pnts; | ||
| if ~isempty(EEG.event) %at least 1 participant with no events | ||
| %adding one boundary at the end to stop issues, will delete later | ||
| for i=1:length(EEG.event) | ||
| EEG.event(i).time=EEG.event(i).latency/EEG.srate | ||
| end | ||
| EEG.event(length(EEG.event)+1)=EEG.event(length(EEG.event)); EEG.event(length(EEG.event)).type='temp';% EEG.event(length(EEG.event)).latency=EEG.event(length(EEG.event)).latency+100;EEG.event(length(EEG.event)).duration=EEG.event(length(EEG.event)).duration+100; | ||
|
|
||
| for i = length(EEG.event)-1:-1:1%12139 caused issue | ||
| if strcmp(EEG.event(i).type, 'boundary') && strcmp(EEG.event(i+1).type, 'boundary') && EEG.event(i+1).latency/EEG.srate-EEG.event(i).latency/EEG.srate < 2 %following event is also a boundary and less then 2 seconds of "good" data between them | ||
| disp(i) | ||
| EEG = pop_select( EEG, 'notime',[EEG.event(i).latency/EEG.srate EEG.event(i+1).latency/EEG.srate] ); | ||
| if strcmp(EEG.event(length(EEG.event)).type, 'boundary') | ||
| EEG.event(length(EEG.event)+1)=EEG.event(length(EEG.event)); EEG.event(length(EEG.event)).type='temp'; | ||
| end | ||
| end | ||
| end | ||
| EEG.event(length(EEG.event)) = []; | ||
| end | ||
| % deleting the event we added before | ||
| new_samples=EEG.pnts; | ||
| EEG.deleteddata=100-EEG.pnts/old_samples*100; | ||
| deleted_channels(s,:) = [string(subject_list{s}), old_n_chan-new_n_chan] ; | ||
| deleted_data(s,:) = [string(subject_list{s}), new_samples/old_samples*100] ; | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_exchn.set'],'filepath', data_path); | ||
| end | ||
| %saving matrixes for quality control | ||
| save([home_path 'wrongconfig_type2_' group{g}], 'wrongconfig_type2'); | ||
| save([home_path 'deleted_channels_' group{g}], 'deleted_channels'); | ||
| save([home_path 'deleted_data_' group{g}] , 'deleted_data'); | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| % Restingstate pipepline (2021) | ||
| % Final version of SRC code 12/6/2021 | ||
| % Load the raw data of each participant to see if they have bad channels | ||
| % Deleting remaining bad channels by eye + seeing if there is something | ||
| % of note going on with the raw data of each person | ||
| clear variables | ||
| %subject_list = {'2201' '2202' '2204' '2207' '2212' '2216' '2222' '2229' '2231' '2243' '2256' '2257' '2260' '2261' '2267' '2270' '2274' '2281' '2284' '2286' '2292' '2295'}; | ||
| %subject_list = {'7003' '7007' '7019' '7025' '7046' '7049' '7051' '7054' '7058' '7059' '7061' '7064' '7065' '7073' '7075' '7078' '7089' '7092' '7094' '7123' '7556' '7808'}; | ||
| subject_list = {'10293' '10561' '10562' '10581' '10616' '10748' '10822' '10858' '10935' '12004' '12010' '12139' '12177' '12188' '12197' '12203' '12206' '12215' '12272' '12413' '12415' '12449' '12482' '12512' '12588' '12632' '12648' '12651' '12707' '12727' '12739' '12746' '12750' '12755' '12770' '12815' '12852' '12870'}; | ||
| home_path = 'D:\restingstate\data\'; | ||
| for s=1:length(subject_list) | ||
| clear bad_chan; | ||
| fprintf('\n******\nProcessing subject %s\n******\n\n', subject_list{s}); | ||
| data_path = [home_path subject_list{s} '\']; | ||
| EEG = pop_loadset('filename', [subject_list{s} '_exchn.set'], 'filepath', data_path); | ||
| pop_eegplot( EEG, 1, 1, 1); | ||
| prompt = 'Delete channels? If yes, input them all as strings inside {}. If none hit enter '; | ||
| bad_chan = input(prompt); % | ||
| if isempty(bad_chan) ~=1 | ||
| EEG = pop_select( EEG, 'nochannel',bad_chan); | ||
| EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_exchn.set'],'filepath', data_path); | ||
| end | ||
| close all | ||
|
|
||
| end | ||
| %2204 a lot of alpha eyes closed | ||
| %7064 muscle artifact, check ICA | ||
| %10561 noisy | ||
| %12449 don't use only 16 chn left | ||
| %12707 check n channels (seems few left) |
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