Specifying bad segments

Discussions
1

Hello Experts,

I will like to inquire if I can specify the range of segments to exclude from my data. In other words, instead of manually specifying bad segments, is there a way to specify (more like type) a range of the data that is bad.

2

I don't believe this is possible: the range duration can be driven by certain objective properties of the data though, such as amplitude, variance, etc.

3

Thank you. So in other words, I will need to manually specify the bad segment by dragging the slider?

4

To extend @Sylvain's answer. This is not possible through the GUI.

However, it is possible to indicate bad segments as extended events through scripting by adding information to the events structure: https://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers#On_the_hard_drive

The example below shows how to add bad segments to a Link to raw file
The added bad segments are from 1s to 2s and 8s to 10s

%% ===== MANUALLY BAD EXTENDED EVENTS (SEGMENTS) =====
    % Load recording file
    sMat = in_bst_data(sFile.FileName, 'F');
    % Index for new event
    iEvt = length(sMat.F.events) + 1;   
    % "bad_" indicates that it will be considered as bad event
    sMat.F.events(iEvt).label = 'bad_manual';
    % Color for the event in the GUI       
    sMat.F.events(iEvt).color = [0.8, 0, 0]; %RGB
    % Times for extended events
    sMat.F.events(iEvt).times = [1, 8; 2, 10]; % [2 x Nevents], first row = start, second row = end
    % Other required fields
    sMat.F.events(iEvt).epochs  = ones(1, size(sMat.F.events(iEvt).times, 2));  
    sMat.F.events(iEvt).channels = cell(1, size(sMat.F.events(iEvt).times, 2));
    sMat.F.events(iEvt).notes    = cell(1, size(sMat.F.events(iEvt).times, 2)); 
    % Save modified file  
    bst_save(file_fullpath(sFile.FileName), sMat, 'v6', 1);

Note that for considering these extended events as bad, the event label has the string "bad_", as indicated in: Tutorials/BadSegments - Brainstorm

Another example for manually creating events can be found here:

1 Like
5

Thank you for your response
Much appreciated

6

I seem to be having this error when I use the code. Please help

image

7

Could you provide more context about the error and how to reproduce it?

Also, you can find more information regarding scripting in Brainstorm in this tutorial:
Tutorials/Scripting - Brainstorm

8

I just provided the code i wanted to use to apply it in brainstorm. I only changed the portion highlighted in red and tried running it. I got this error

image
image1035×707 44 KB

9

The trouble in the code is that sFiles is not an array structure, but it is a cell array with the file name.

To make the code work, call the functions with the filename:
In lines 12 and 26, substitute sFiles.FileName with sFiles{1}

Keep in mind that:

[The input of the process] can be a cell array of file names (full path, or relative path from the protocol folder), or an array of structures describing the files in the database (returned by a previous call to bst_process).

As described in the scripting tutorial:

10

Thank you
It worked perfectly!