[Eeglablist] visualization of rejmanual timepoints

Tue Feb 21 13:54:10 PST 2023

Thanks Cedric - this makes more sense! :)

Thanks for sharing in the thread. I am sure it’ll be of use to others.

> On Feb 20, 2023, at 2:58 PM, Cedric Cannard <ccannard at protonmail.com> wrote:
> 
> Hi Agatha,
> 
> Sorry about that. This was the code for reconstructed data by ASR. The mask cannot be calculated here with different file lengths, indeed. 
> 
> Here is the code for when data segments are removed (you'll need to run each section separated by %% one by one using ctrl+Enter, to wait for manual rejection to be done before trying to extract the latencies of the bad segments). The most ergonomic is probably to convert this into function. 
> % Make a copy of the dataset
> EEG2 = EEG;
> 
> % Reject bad data manually
> eegplot(EEG2.data,'winlength',15,'srate',EEG2.srate,'spacing',150, ...
>     'command','[TMPEEG, com] = eeg_eegrej(EEG2,eegplot2event(TMPREJ,-1));');
> 
> %% Get latency bounds of the removed segments
> if ~isempty(com)
>     badData = extractBetween(com, ',',')');
>     badData = cellfun(@str2num, badData, 'UniformOutput', false);
>     badData = badData{:};
> else
>     badData = [];
> end
> 
> % Flatten removed segments on EEG2 (dataset copy)
> for iSegment = 1:size(badData,1)
>     EEG2.data(:,badData(iSegment,1):badData(iSegment,2)) = 0;
> end
> 
> % Visualize what you removed (in red)
> vis_artifacts(EEG2,EEG);
> 
> %% If satisfied, remove the bad segments from the original dataset.
> EEG = pop_select(EEG, 'nopoint', badData);
> pop_eegplot(EEG,1,1,1);
> Note: you can adjust window length and scale of the eegplot with the inputs 'winlength' and 'spacing', respectively. For vis_artifacts, you can adjust the scale with +/- key, and scroll to the right with the arrow button at the bottom. 
> 
> I hope this works for you.
> 
> Cedric
> 
> 
> ------- Original Message -------
> On Monday, February 20th, 2023 at 11:39 AM, Agatha Lenartowicz <alenarto at g.ucla.edu> wrote:
> 
>> For documentation purposes - Cedric - the code you provided won’t work (at least with 2022 versions). The mask creation line assumes that EEG.data and EEG2.data are the same size and can be subtracted to uncover the removed timepoints but this is not true. The rejection step modifies the size of the data (by removing windows of data) and thus the operation you provide won’t work.
>> 
>> al.
>> 
>> 
>>> On Jan 24, 2023, at 1:01 PM, Cedric Cannard <ccannard at protonmail.com <mailto:ccannard at protonmail.com>> wrote:
>>> 
>>> Dear Agatha,
>>> 
>>> While I don't know about this previous feature, here is how you can 1) make a copy of your EEG dataset, 2) remove bad portions from that copy, 3) visualize the differences, and 4) remove these segments from original dataset if satisfied. 
>>> 
>>> EEG2 = EEG; % copy
>>> pop_eegplot(EEG2,1,1,1); % plot and remove bad segments manually
>>> vis_artifacts(EEG2,EEG); % compare (removed segments are in red)
>>> mask = sum(abs(EEG.data-EEG2.data),1) > 1e-10; % mask index of bad samples
>>> badData = reshape(find(diff([false mask false])),2,[])'; % reshape for pop_select function
>>> badData(:,2) = badData(:,2)-1; % fix latency
>>> cleanEEG = pop_select(EEG,'nopoint',badData); 
>>> 
>>> Hope this helps,
>>> 
>>> Cedric
>>> 
>>> 
>>> 
>>> ------- Original Message -------
>>> On Monday, January 23rd, 2023 at 10:07 AM, Agatha Lenartowicz <alenarto at g.ucla.edu <mailto:alenarto at g.ucla.edu>> wrote:
>>> 
>>> 
>>>> Hi all.
>>>> 
>>>> It used to be possible to select bad time windows via visual inspection (or otherwise) without actually REJECTing those time points. These would just be saved in EEG.reject.rejmanual. And they could later be viewed and modified.
>>>> 
>>>> In 2022 it looks like this ability to visual inspect rejection-marked epochs has been removed.
>>>> 
>>>> Is that correct? Is there a way to get this functionality back?
>>>> Thanks!
>>>> Agatha
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>> 
>>>> Agatha Lenartowicz, Ph.D.
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>>>> 
>>>> 
>>>> Associate Professor
>>>> Semel Institute for Neuroscience and Human Behavior
>>>> Department of Psychiatry and Biobehavioral Sciences
>>>> Brain Research Institute
>>>> 
>>>> Managing Director Neuroimaging Center for Cognitive Neuroscience
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>>>> 
>>>> 
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>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
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