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DouweHorsthuisDouweHorsthuis
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Adding Microstate script
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‎src/I_Microstates.m‎

Lines changed: 61 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -3,53 +3,67 @@
33

44
clear variables
55
eeglab
6-
home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Control\';
7-
save_path = [home_path 'figures\Microstates\'];
8-
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' };% ------------------------------------------------
9-
for s=1:length(subject_list)
10-
data_path = [home_path subject_list{s} ''];% Path to the folder containing the current subject's data
11-
% Load original dataset
12-
fprintf('\n\n\n**** %s: Loading dataset ****\n\n\n', subject_list{s});
13-
EEG = pop_loadset('filename', [subject_list{s} '_inter.set'], 'filepath', data_path);
14-
[ALLEEG, EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
15-
end
16-
%this creates a grouped dataset using the standard values
17-
[EEG, ALLEEG] = pop_micro_selectdata( EEG, ALLEEG, 'datatype', 'spontaneous', 'avgref', 1, 'normalise', 0, 'MinPeakDist', 10, 'Npeaks', 1000, 'GFPthresh', 1, 'dataset_idx', 1:length(ALLEEG) );
18-
%[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
19-
eeglab redraw
20-
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, length(ALLEEG)-1,'retrieve',length(ALLEEG),'study',0); %this should select the last one, but not sure how to make it do that for sure
21-
eeglab redraw
22-
EEG = pop_micro_segment( EEG, 'algorithm', 'modkmeans', 'sorting', 'Global explained variance', 'normalise', 0, 'Nmicrostates', 2:8, 'verbose', 1, 'Nrepetitions', 50, 'fitmeas', 'CV', 'max_iterations', 1000, 'threshold', 1e-06, 'optimised', 0 );
23-
24-
[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
25-
figure;MicroPlotTopo( EEG, 'plot_range', [] ); %plotting microstates
26-
print([save_path 'Group_microstate'], '-djpeg');
276

28-
EEG = pop_micro_selectNmicro( EEG ); % only select CV and GEV, look for where GEV doesn't increase significantly
29-
[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
30-
%errors are coming, line 83 of pop_micro_fit Dot indexing is not supported for variables of this type
31-
for s=1:length(subject_list)
32-
%[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 60,'retrieve',s,'study',0);
33-
fprintf('Importing prototypes and backfitting for dataset %i\n',i)
34-
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,'retrieve',s,'study',0);
35-
EEG = pop_micro_import_proto( EEG, ALLEEG, length(ALLEEG));
36-
%% 3.6 Back-fit microstates on EEG
37-
EEG = pop_micro_fit( EEG, 'polarity', 0 );
38-
%% 3.7 Temporally smooth microstates labels
39-
EEG = pop_micro_smooth( EEG, 'label_type', 'backfit', ...
40-
'smooth_type', 'reject segments', ...
41-
'minTime', 30, ...
42-
'polarity', 0 );
43-
%% 3.9 Calculate microstate statistics
44-
EEG = pop_micro_stats( EEG, 'label_type', 'backfit', ...
45-
'polarity', 0 );
7+
Group = {'Aging' 'ASD' 'Control'};%'Control'
8+
name_paradigm = 'restingstate'; % this is needed for saving the table at the end
9+
for g=1:length(Group)
10+
switch Group{g}
11+
case 'Control'
12+
home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Control\';
13+
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' };% ------------------------------------------------
14+
case 'ASD'
15+
home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\ASD\';
16+
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;
17+
case 'Aging'
18+
home_path = 'C:\Users\dohorsth\Desktop\Testing restingstate\Aging\';
19+
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'};
20+
end
21+
save_path = [home_path 'figures\Microstates\'];
22+
for s=1:length(subject_list)
23+
data_path = [home_path subject_list{s} ''];% Path to the folder containing the current subject's data
24+
% Load original dataset
25+
fprintf('\n\n\n**** %s: Loading dataset ****\n\n\n', subject_list{s});
26+
EEG = pop_loadset('filename', [subject_list{s} '_inter.set'], 'filepath', data_path);
27+
[ALLEEG, EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
28+
end
29+
%this creates a grouped dataset using the standard values
30+
[EEG, ALLEEG] = pop_micro_selectdata( EEG, ALLEEG, 'datatype', 'spontaneous', 'avgref', 1, 'normalise', 0, 'MinPeakDist', 10, 'Npeaks', 1000, 'GFPthresh', 1, 'dataset_idx', 1:length(ALLEEG) );
31+
%[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
32+
eeglab redraw
33+
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, length(ALLEEG)-1,'retrieve',length(ALLEEG),'study',0); %this should select the last one, but not sure how to make it do that for sure
34+
eeglab redraw
35+
EEG = pop_micro_segment( EEG, 'algorithm', 'modkmeans', 'sorting', 'Global explained variance', 'normalise', 0, 'Nmicrostates', 2:8, 'verbose', 1, 'Nrepetitions', 50, 'fitmeas', 'CV', 'max_iterations', 1000, 'threshold', 1e-06, 'optimised', 0 );
36+
4637
[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
47-
end
48-
for s=1:length(subject_list)
49-
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,'retrieve',s,'study',0);
50-
figure('units','normalized','outerposition',[0 0 1 1]);[t]=title(subject_list(s));t.FontSize = 35; MicroPlotSegments( EEG, 'label_type', 'backfit', ...
51-
'plotsegnos', 'first', 'plot_time', [4200 5700], 'plottopos', 1 );
52-
print([save_path subject_list{s} '_microstate'], '-djpeg');
53-
close all
54-
EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_microstate.set'],'filepath', data_path);
38+
figure;MicroPlotTopo( EEG, 'plot_range', [] ); %plotting microstates
39+
print([save_path 'Group_microstate'], '-djpeg');
40+
41+
EEG = pop_micro_selectNmicro( EEG ); % only select CV and GEV, look for where GEV doesn't increase significantly
42+
[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
43+
%errors are coming, line 83 of pop_micro_fit Dot indexing is not supported for variables of this type
44+
for s=1:length(subject_list)
45+
%[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 60,'retrieve',s,'study',0);
46+
fprintf('Importing prototypes and backfitting for dataset %i\n',i)
47+
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,'retrieve',s,'study',0);
48+
EEG = pop_micro_import_proto( EEG, ALLEEG, length(ALLEEG));
49+
%% 3.6 Back-fit microstates on EEG
50+
EEG = pop_micro_fit( EEG, 'polarity', 0 );
51+
%% 3.7 Temporally smooth microstates labels
52+
EEG = pop_micro_smooth( EEG, 'label_type', 'backfit', ...
53+
'smooth_type', 'reject segments', ...
54+
'minTime', 30, ...
55+
'polarity', 0 );
56+
%% 3.9 Calculate microstate statistics
57+
EEG = pop_micro_stats( EEG, 'label_type', 'backfit', ...
58+
'polarity', 0 );
59+
[ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);
60+
end
61+
for s=1:length(subject_list)
62+
[ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,'retrieve',s,'study',0);
63+
figure('units','normalized','outerposition',[0 0 1 1]);[t]=title(subject_list(s));t.FontSize = 35; MicroPlotSegments( EEG, 'label_type', 'backfit', ...
64+
'plotsegnos', 'first', 'plot_time', [4200 5700], 'plottopos', 1 );
65+
print([save_path subject_list{s} '_microstate'], '-djpeg');
66+
close all
67+
EEG = pop_saveset( EEG, 'filename',[subject_list{s} '_microstate.set'],'filepath', data_path);
68+
end
5569
end

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