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Reference

analysis:amplipex:artifacts

## Artifact Removal

A nice artifact detection and removal walkthrough can be found at FieldTrip Artifact Documentation

### Visual Artifact Removal

This section addresses visual artifact removal using the FieldTrip toolbox FieldTrip Visual Artifact walkthrough

Load the data and define the trials as per Loading Amplipex data into fieldtrip. Once this has been done we can begin by setting up our cfg (configuration) structure and using the ft_databrowser function

cfg = data_trl.cfg;
cfg.channel     = 'all';
cfg.trials      = 'all';
cfg.latency     = 'maxperlength';
cfg.method      = 'Summary';
cfg.keepchannel = 'yes';
cfg.metric      = 'var';
cfg.alim        = [];
cfg.coninuous   = 'yes';
cfg.viewmode    = 'vertical'; % this shows all of the channels vertically
cfg = ft_databrowser(cfg,data_trl);
data_trl.cfg = cfg; % rewrite the cfg back into the data set

The browser will let you scroll through the trials and use the cursor to highlight a section of the data containing an artifact.

The selected artifact regions are not altered within the data itself, instead the start and end of each artifact are saved as part of the cfg structure: data_trl.cfg.artfctdef.visual.artifact . So now can change these regions to any value of our choice.

%% Mannual Artifact removal
art_value = 0; %Value to replace the data within artifact regions
artifacts = data_trl.cfg.artfctdef.visual.artifact;
trials = data_trl.cfg.trl;
for iArt = 1:length(artifacts)
for iTrial = 1:length(trials)
if trials(iTrial,1)<= artifacts(iArt,1) && trials(iTrial,2)>= artifacts(iArt,2)
if artifacts(iArt,1)-trials(iTrial,1) ==0
data_trl.trial{1,iTrial}(1:16,(1:artifacts(iArt,2)-trials(iTrial,1)))=art_value;
else
data_trl.trial{1,iTrial}(1:16,(artifacts(iArt,1)-trials(iTrial,1):artifacts(iArt,2)-trials(iTrial,1)))=art_value;
end
end
end
end

Now we can visualize the data regions that have been replaced to ensure they have been correctly converted.

cfg.viewmode    = 'vertical'; % this shows all of the channels vertically
ft_databrowser(cfg,data_trl);

From here we can run any further ft analysis.