Epoch EEG data using a script

1

Hello,

I am trying to epoch EEG raw data using my script and keep getting the following error message. I suspect this is related to the 'datafile' option, but can't figure out why. Can you help?

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image883×483 9.65 KB

% Script generated by Brainstorm (25-Jul-2019)
cd 'G:\My Drive\EEG\Dissertation\Analaysis_Script\Data_Analysis'
load('Subj_list.mat');

% Input files
sFiles = ;
SubjectNames = Subj_Names;

% Create RawFiles
RawFiles1 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{1});
RawFiles2 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{2});
RawFiles3 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{3});
RawFiles4 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{4});
RawFiles5 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{5});
RawFiles6 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{6});
RawFiles7 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{7});
RawFiles8 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{8});
RawFiles9 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{9});
RawFiles10 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{10});
RawFiles11 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{11});
RawFiles12 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{12});
RawFiles13 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{13});
RawFiles14 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{14});
RawFiles15 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{15});
RawFiles16 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{16});
RawFiles17 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{17});
RawFiles18 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{18});
RawFiles19 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{19});
RawFiles20 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{20});
RawFiles21 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{21});
RawFiles22 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{22});
RawFiles23 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{23});
RawFiles24 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{24});
RawFiles25 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{25});
RawFiles26 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{26});
RawFiles27 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{27});
RawFiles28 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{28});
RawFiles29 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{29});
RawFiles30 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{30});
RawFiles31 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{31});
RawFiles32 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{32});
RawFiles33 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{33});
RawFiles34 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{34});
RawFiles35 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{35});
RawFiles36 = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{36});

RawFiles = {RawFiles1,RawFiles2,RawFiles3,RawFiles4,RawFiles5,RawFiles6,RawFiles7,RawFiles8,RawFiles9,RawFiles10,...
RawFiles11,RawFiles12,RawFiles13,RawFiles14,RawFiles15,RawFiles16,RawFiles17,RawFiles18,RawFiles19,RawFiles20,...
RawFiles21,RawFiles22,RawFiles23,RawFiles24,RawFiles25,RawFiles26,RawFiles27,RawFiles28,RawFiles29,RawFiles30,...
RawFiles31,RawFiles32,RawFiles33,RawFiles34,RawFiles35,RawFiles36};

for i = 1:1
% for i = 1:length(SubjectNames)
% Start a new report
bst_report('Start', sFiles);

% Process: Import MEG/EEG: Events
sFiles = bst_process('CallProcess', 'process_import_data_event', sFiles, , ...
'subjectname', SubjectNames{1}, ...
'condition', '', ...
'datafile', {RawFiles{1},'SET'}, ...
'eventname', 'correct', ...
'timewindow', , ...
'epochtime', [0.9, 1.5], ...
'createcond', 1, ...
'ignoreshort', 1, ...
'channelalign', 1, ...
'usectfcomp', 1, ...
'usessp', 1, ...
'freq', , ...
'baseline', [0.9, 1]);

% Process: Set comment: CRT_900-1500ms
sFiles = bst_process('CallProcess', 'process_set_comment', sFiles, [], ...
    'tag',           'CRT_900-1500ms', ...
    'isindex',       1);
    
% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
%bst_report('Export', ReportFile, ExportDir);

end

2

The problem is the type of the data in "datafile" indeed. It is expected to be a list of file (cell array), not a single file name as you did (char). Use "RawFiles(i)" instead of "RawFiles{i}" and it should work.

You could also maybe replace all the creation of your RawFiles variable with a short loop:

RawFiles = cell(1,36);
for i = 1:36
    RawFiles{i} = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{i});
end
3

Thanks Francois! As you suggest, I made changes, but got the following error message.

image
image869×462 8.92 KB

% Script generated by Brainstorm (25-Jul-2019)
cd 'G:\My Drive\EEG\Dissertation\Analaysis_Script\Data_Analysis'
load('Subj_list.mat');

% Input files
sFiles = ;
SubjectNames = Subj_Names;

RawFiles = cell(1,36);
for i = 1:36
RawFiles{i} = sprintf('F:\Dissertation\Clean_v4\%s_Cleaned_v4.set',SubjectNames{i});
end

for i = 1:1
% for i = 1:length(SubjectNames)
% Start a new report
bst_report('Start', sFiles);

% Process: Import MEG/EEG: Events
sFiles = bst_process('CallProcess', 'process_import_data_event', sFiles, , ...
'subjectname', SubjectNames{1}, ...
'condition', '', ...
'datafile', {RawFiles(1),'SET'}, ...
'eventname', 'correct', ...
'timewindow', , ...
'epochtime', [0.9, 1.5], ...
'createcond', 1, ...
'ignoreshort', 1, ...
'channelalign', 1, ...
'usectfcomp', 1, ...
'usessp', 1, ...
'freq', , ...
'baseline', [0.9, 1]);

% Process: Set comment: CRT_900-1500ms
sFiles = bst_process('CallProcess', 'process_set_comment', sFiles, [], ...
    'tag',           'CRT_900-1500ms', ...
    'isindex',       1);
    
% Save and display report
ReportFile = bst_report('Save', sFiles);
bst_report('Open', ReportFile);
%bst_report('Export', ReportFile, ExportDir);

end

4

The file type for EEGLAB files is not 'SET' but 'EEG-EEGLAB'.

For writing Brainstorm scripts, always start by generating code that works with the pipeline editor, and then modify only the options you need:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Starting_a_new_script

5

Hello Francois,

I found that the import function doesn't run even using GUI (see the screenshots below).

image
image462×657 14.4 KB

image

So I tried the manual approach by right-clicking on the "Link to raw file" menu, and this worked fine. Am I supposed to have a data.mat file? Or is this a bug?

Sungjin

6

You need to select the files you want to import...

I added a clearer error message when this process is executed without an input file:

7

Hello Francois,

Thanks for your continued support. The problem was file type as you suggested. Since EEGLAB file extension is "set", I put it as a file type in my script. After using GUI, I found that BST treats set as 'EEG-EEGLAB'. After replacing with the correct file type, my script worked fine. Thanks!

Sungjin