Merge pull request #2 from DouweHorsthuis/update_2

update after use
CognitiveNeuroLab · Oct 20, 2021 · a834c20 · a834c20
2 parents f2fa05f + dcf918e
commit a834c20
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diff --git a/README.md b/README.md
@@ -24,15 +24,19 @@ This is still a work in progress. This Repo will contain the full pipeline to an
 
 **Table of Contents**
 1. [About The Project](#about-the-project)  
-2. [Getting started](#getting-started)
+2. [Getting started](#getting-started)  
     - [Prerequisites](#prerequisites)  
-3. [Resting state project](#resting-state-project)
-3. [Pipeline](#pipeline)  
-    - [Raw data to .set and merge](#raw-data-to-.set-and-merge)
-    - [Pre processing](#pre-processing)  
-3. [License](#license)
-3. [Contact](#contact)
-3. [Acknowledgement](#acknowledgement)
+3. [Resting state project](#resting-state-project)  
+3. [Pipeline](#pipeline)
+    - [Raw data to .set and merge](#raw-data-to-.set-and-merge)  
+    - [Pre processing](#pre-processing) 
+3. [Power Frequency Analysis](#power-frequency-analysis)  
+3. [Microstates](#microstates)  
+    - [I_Mictrostates_groups](#i_mictrostates_groups)  
+    - [I_Mictrostates_all](#i_mictrostates_all)    
+3. [License](#license)  
+3. [Contact](#contact)  
+3. [Acknowledgement](#acknowledgement)  
 
 
 
@@ -115,12 +119,17 @@ After that we use the the [pwelch function of Matlab](https://www.mathworks.com/
 
 # add here what channels we use, for now it's just indivual but we will change this to groups and averages of those groups
 
-### Microstates Groups & all
+
+### Microstates
 this script follows the code as descibed in Poulsen, A. T., Pedroni, A., Langer, N., & Hansen, L. K. (2018). Microstate EEGlab toolbox: An introductory guide. [See their guide in bioRxiv for more information.](https://www.biorxiv.org/content/10.1101/289850v1)
 
-In the first part the analysis only focuses on the group level. Since we use both eyes open and eyes closed data, we want to check how many microstates are suggested for both, so we can choose the best (same) amount for both. In the case of patient/control group we would need to compare all 4 the suggestions. Running the whole script would take a lot of time that wasn't needed.
+#### I_Mictrostates_groups
+In the We first focuses on the group level. Since we use both eyes open and eyes closed data, we want to check how many microstates are suggested for both, so we can choose the best (same) amount for both. In the case of patient/control group we would need to compare all 4 the suggestions. Running the whole script would take a lot of time that wasn't needed.
+
+#### J_Microstates_all
+
+The second script will backfit the mictrostates on the individual EEGs (since now you know how many microstates you want). Giving both plots per subject and adds data to the EEG structure to do stats on.  
 
-The second script will do everything again (since now you know how many microstates you want) and backfits it on the individual EEGs. Giving both plots per subject and adds data to the EEG structure to do stats on.
 
 
 ## License

diff --git a/src/A_bdf_merge_sets.m b/src/A_bdf_merge_sets.m
@@ -1,33 +1,35 @@
 % Testing the scr code 6/21/2021
-subject_list = {'10033' '10130' '10131' '10257' '10281' '10293' '10360' '10369' '10385' '10394' '10438' '10446' '10463' '10476' '10526' '10545' '10561' '10562' '10581' '10585' '10616' '10748' '10780' '10784' '10822' '10858' '10906' '10915' '10929' '10935' '12005' '12006' '12007' '12010' '12215' '12328' '12360' '12413' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
+%% extra controls
+subject_list = {'10297' '10331' '10385' '10497' '10553' '10590' '10640' '10867' '10906' '12004' '12006' '12139' '12177' '12188' '12197' '12203' '12206' '12230' '12272' '12415' '12449' '12474' '12482' '12516' '12534' '12549' '12588' '12632' '12735' '12746' '12755' '12770' '12852' '12870'};
+%subject_list = {'10033' '10130' '10131' '10257' '10281' '10293' '10360' '10369' '10385' '10394' '10438' '10446' '10463' '10476' '10526' '10545' '10561' '10562' '10581' '10585' '10616' '10748' '10780' '10784' '10822' '10858' '10906' '10915' '10929' '10935' '12005' '12006' '12007' '12010' '12215' '12328' '12360' '12413' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
 
 %subject_list = {'1106' '1108' '1132' '1134' '1154' '1160' '1173' '1174' '1179' '1190' '1838' '1839' '1874' '11013' '11051' '11056' '11098' '11106' '11198' '11220' '11244' '11293' '11325' '11354' '11369' '11375' '11515' '11560' '11580' '11667' '11721' '11723' '11750' '11852' '11896' '11898' '11913' '11927' '11958' '11965'}; %all the IDs for the indivual particpants
 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\Control\'; %place data is (something like 'C:\data\')
+home_path    = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\'; %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 = 3:length(subject_list)
+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
+    %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
     EEG = pop_saveset( EEG, 'filename',[subject_list{s} '.set'],'filepath',data_path);
 end

diff --git a/src/A_bdf_non_paradigm_merge_sets.m b/src/A_bdf_non_paradigm_merge_sets.m
@@ -1,36 +1,40 @@
 % Testing the scr code 6/21/2021
 % ------------------------------------------------
-%clear variables
-subject_list = {'10158' '10165' '10384' '10407' '10451' '10467' '10501' '10534' '10615' '10620' '10639' '10844' '10956'};
+%% extra controls
+clear variables
+%_closed.bdf
+%_open.bdf
+subject_list = {'10399' '12002' '12122'};
+%subject_list = {'10158' '10165' '10384' '10407' '10451' '10467' '10501' '10534' '10615' '10620' '10639' '10844' '10956'};
 %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\Control\'; %place data is (something like 'C:\data\')
+home_path    = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\'; %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 = 8:length(subject_list)
+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'])
+    disp([data_path  subject_list{s}  '.bdf'])
 
     %loading file 1, adding triggers
-    EEG     = pop_biosig([data_path  subject_list{s} '_' filename '_open.bdf']);
+    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     = 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} '_' filename '_closed.bdf']);
+    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     = 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
@@ -44,6 +48,14 @@
             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

diff --git a/src/B_preprocess1.m b/src/B_preprocess1.m
@@ -8,7 +8,7 @@
 % ------------------------------------------------
 clear variables
 eeglab
-group = {'Aging' 'ASD' 'Control'};%
+group = {'Control'};%
 for g=1:length(group)
     if strcmp(group{g},'ASD')
         subject_list = {'1101' '1164' '1808' '1852' '1855' '11014' '11094' '11151' '11170' '11275' '11349' '11516' '11558' '11583' '11647' '11729' '11735' '11768' '11783' '11820' '11912' '1106' '1108' '1132' '1134' '1154' '1160' '1173' '1174' '1179' '1190' '1838' '1839' '1874' '11013' '11056' '11098' '11106' '11198' '11244' '11293' '11325' '11354' '11369' '11375' '11515' '11560' '11580' '11667' '11721' '11723' '11750' '11852' '11896' '11898' '11913' '11927' '11958' '11965'}; %all the IDs for the indivual particpants
@@ -17,8 +17,11 @@
         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'};
         home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Aging\';
     elseif strcmp(group{g},'Control')
-        subject_list = {'10158' '10165' '10384' '10407' '10451' '10467' '10501' '10534' '10615' '10620' '10639' '10844' '10956' '10033' '10130' '10131' '10257' '10281' '10293' '10360' '10369' '10394' '10438' '10446' '10463' '10476' '10526' '10545' '10561' '10562' '10581' '10585' '10616' '10748' '10780' '10784' '10822' '10858' '10906' '10915' '10929' '10935' '12005' '12007' '12010' '12215' '12328' '12360' '12413' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
-        home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Control\';
+        %% extra controls
+        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' '12449' '12474' '12482' '12516' '12534' '12549' '12588' '12632' '12735' '12746' '12755' '12770' '12852' '12870'};
+        %% aged matched controls
+        %subject_list = {'10158' '10165' '10384' '10407' '10451' '10467' '10501' '10534' '10615' '10620' '10639' '10844' '10956' '10033' '10130' '10131' '10257' '10281' '10293' '10360' '10369' '10394' '10438' '10446' '10463' '10476' '10526' '10545' '10561' '10562' '10581' '10585' '10616' '10748' '10780' '10784' '10822' '10858' '10906' '10915' '10929' '10935' '12005' '12007' '12010' '12215' '12328' '12360' '12413' '12512' '12648' '12651' '12707' '12727' '12739' '12750' '12815' '12898' '12899'};% ------------------------------------------------
+        home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\';
     end
     deleted_channels=zeros(length(subject_list),2);
     wrongconfig_type2 = zeros(1,length(subject_list));
@@ -76,7 +79,7 @@
         old_n_chan = EEG.nbchan;
         EEG = clean_artifacts(EEG, 'FlatlineCriterion',5,'ChannelCriterion',0.8,'LineNoiseCriterion',4,'Highpass','off','BurstCriterion','off','WindowCriterion','off','BurstRejection','on','Distance','Euclidian');
         new_n_chan = EEG.nbchan;
-        deleted_channels{s} = [string(subject_list{s}), old_n_chan-new_n_chan] ;
+        deleted_channels(s,:) = [string(subject_list{s}), old_n_chan-new_n_chan] ;
         EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_exchn.set'],'filepath', data_path);
     end
     %saving matrixes for quality control

diff --git a/src/C_manual_check.m b/src/C_manual_check.m
@@ -3,14 +3,19 @@
 %% ASD
 %subject_list = {'1101' '1164' '1808' '1852' '1855' '11014' '11094' '11151' '11170' '11275' '11349' '11516' '11558' '11583' '11647' '11729' '11735' '11768' '11783' '11820' '11912' '1106' '1108' '1132' '1134' '1154' '1160' '1173' '1174' '1179' '1190' '1838' '1839' '1874' '11013' '11056' '11098' '11106' '11198' '11244' '11293' '11325' '11354' '11369' '11375' '11515' '11560' '11580' '11667' '11721' '11723' '11750' '11852' '11896' '11898' '11913' '11927' '11958' '11965'}; %all the IDs for the indivual particpants
 %home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\ASD\';
-%% ASD controls
+%% aged matched controls
 %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'};% ------------------------------------------------
 %home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Control\';
+%% extra controls
+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' '12449' '12474' '12482' '12516' '12534' '12549' '12588' '12632' '12735' '12746' '12755' '12770' '12852' '12870'};
+% did these again because need extra channels deleted
+% subject_list = {'12139' '10399'};
+home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Remaining_controls\';
 %% MoBI
-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'};             
-% controls and ASD subjects that need to be re-checked because of 160 channel info
-%'10131' '10257' '10369' '10438' '10545' '10585' '12360' '12898' '1808' '1852' '1855' '11345' '1106' '1134' '1154' '1160' '1174' '1179' '1190' '1838' '11106' '11375' '11913'
-home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Aging\';
+% 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'};
+% % controls and ASD subjects that need to be re-checked because of 160 channel info
+% %'10131' '10257' '10369' '10438' '10545' '10585' '12360' '12898' '1808' '1852' '1855' '11345' '1106' '1134' '1154' '1160' '1174' '1179' '1190' '1838' '11106' '11375' '11913'
+% home_path  = 'C:\Users\dohorsth\Desktop\Testing restingstate\Aging\';
 for s=1:length(subject_list)
     clear bad_chan;
     fprintf('\n******\nProcessing subject %s\n******\n\n', subject_list{s});