written by Ki-Young Jung, MD
ENSLab. Neuroscience Research Institute
Seoul National University College of Medicine
last updated  July 12, 2019
 

This tutorial is made using a ERP data published in following paper.
 
Byun J-I, Lee BU, Kim M, Sunwoo J-S, Lim J-A, Moon J, Lee S-T, Jung K-H,
Chu K, Kim M-H, Jeong MH, Cha KS, Choi JW, Kim KH, Lee SK, Jung K-Y.
Reduced P300 amplitude during a visuospatial attention task in idiopathic
rapid eye movement % sleep behavior disorder. Sleep Medicine 2017;38:78-84.
https://www.sciencedirect.com/science/article/abs/pii/S1389945717303155  
 

Contents

flow of ERP analysis

load data

clc; clear all;

load rbd_erp_data.mat;

whos

% help whos

  Name      Size               Bytes  Class     Attributes

  EEG       1x1             18244950  struct    global    

EEG structure

EEG

data = EEG.data;
time = EEG.times;
srate = EEG.srate;

size(data) % 60 ch, 1200 data point, 120 epochs

EEG = 

             setname: ''
            filename: 'RBD_3_Invalid1000.set'
            filepath: 'C:\Users\jky\Dropbox\0713\매트랩...'
             subject: ''
               group: ''
           condition: ''
             session: []
            comments: ''
              nbchan: 60
              trials: 63
                pnts: 1200
               srate: 400
                xmin: -1.6000
                xmax: 1.3975
               times: [1x1200 double]
                data: [60x1200x63 single]
              icaact: []
             icawinv: []
           icasphere: []
          icaweights: []
         icachansind: []
            chanlocs: [1x60 struct]
          urchanlocs: []
            chaninfo: [1x1 struct]
                 ref: 'common'
               event: []
             urevent: []
    eventdescription: {}
               epoch: []
    ... .... ....

ans =

          60        1200          63

data extraction

% 특정 채널, 에폭, 시간대 데이터 뽑아내기
% epch 10, 20 만 추출
data_10 = data(:,:,10)  ;
data_20 = data(:,:,20)  ;

% channel 10 추출
data_ch10 = data(10, :, :);

data merge, divide

% 합치기
data_2D = [data_10 data_20]; % 가로 배열 붙이기

% cat 명령어로 A와 B를 2nd dimension 에서 붙인다.
data_30 = cat(2,data_10,data_20) ;       % 서로 다른 데이터를 붙이기

% 3. 2차원 데이터 두개를 합쳐서 3차원 데이터로 만들기
data_3D(:,:,1) = data_10 ;
data_3D(:,:,2) = data_20 ;

% reshape
data_sum = reshape(data_2D, 60, 1200, []);

% data 차원 순서 바꾸기
aa = permute(data, [2, 3,1]);  % time, epoch, channel 로 변경

find specific time period

% 특정 time index 찾기
[junk, tim_idx] = min(abs(time - 0)); % time 0 --> 640

% p300 구간대: 300 -500 ms
[junk, tim1] = min(abs(time - 400))
[junk, tim2] = min(abs(time - 600))

data_p300 = data(:, [tim1:tim2], :);

junk =

     0


tim1 =

   801


junk =

     0


tim2 =

   881

make ERP

% make ERP data: epoch을 평균시킴. 3D --> 2D
data_erp = mean(data, 3); % epoch을 평균냄

% p300 amplitude 구하기
data_erp_p300 = mean(data_erp(:, [tim1:tim2]), 2);

data_erp_p300 = squeeze(data_erp_p300);

% P300 amplitude at Pz channel
chan_idx = find(strcmpi({EEG.chanlocs.labels}, {'Fz'}))
chan_idx = find(strcmpi({EEG.chanlocs.labels}, {'Cz'}))
chan_idx = find(strcmpi({EEG.chanlocs.labels}, {'Pz'}))

data_erp_p300_Pz = data_erp_p300(48)

chan_idx =

    12


chan_idx =

    30


chan_idx =

    48


data_erp_p300_Pz =

    1.2367

plot erp

% plot all channels: butterfly plot
figure;
plot(time, data_erp)

% plot Pz channel
figure;
plot(time, data_erp(48, :))
xlim([-400, 800])
ylim([-4, 4])

% plot several channels
figure;
for k = 1:10
subplot(5,2,k); plot(time, data_erp(k, :));
end

% plot major 9 channels
chan_list = [10 12 14 28 30 32 46 48 50]; % frontal, centra, parietal
figure;
for k = 1:9
subplot(3,3,k);
plot(time, data_erp(chan_list(k), :));
axis([-200 1000 -4 4]);
hold on; plot([0 0], [-4 4])
end

save figure and variable into file

% saveas :
saveas(gcf, 'rbd_erp_plot', 'jpg');

% print명령을 사용
print( gcf, '-djpeg', 'rbd_erp_plot1');


% 여러 파일이름들을 자동으로 변수로 할당하기
list = dir('*.mat')
name1 = list(1).name(1:end-4)
% name2 = list(2).name(1:end-4)


% 위 할당 변수를 이용하여 저장하기
save([list(1).name(1:end-4) '_data'], 'data', '-v7.3');


% end of file. Enjoy!   by JKY

list = 

2x1 struct array with fields:

    name
    date
    bytes
    isdir
    datenum


name1 =

rbd_erp_data

Published with MATLAB® R2015a