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analysis:amplipex:artifacts [2014/01/20 14:12]
ecarmichael created
analysis:amplipex:artifacts [2018/07/07 10:19] (current)
Line 7: Line 7:
 This section addresses visual artifact removal using the FieldTrip toolbox [[http://​fieldtrip.fcdonders.nl/​tutorial/​visual_artifact_rejection|FieldTrip Visual Artifact walkthrough]] This section addresses visual artifact removal using the FieldTrip toolbox [[http://​fieldtrip.fcdonders.nl/​tutorial/​visual_artifact_rejection|FieldTrip Visual Artifact walkthrough]]
  
 +Load the data and define the trials as per [[analysis:​amplipex|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
  
  
 +<code matlab>
 +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
 +</​code>​
  
 +The browser will let you scroll through the trials and use the cursor to highlight a section of the data containing an artifact.
 +{{:​analysis:​amplipex:​artifact_wiki.png?​750|}}
 +
 +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.  ​
 +
 +
 +<code matlab>
 +%% 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
 +</​code>​
 +
 +
 +Now we can visualize the data regions that have been replaced to ensure they have been correctly converted. ​
 +
 +<code matlab>
 +cfg.viewmode ​   = '​vertical';​ % this shows all of the channels vertically
 +ft_databrowser(cfg,​data_trl);​
 +</​code>​
 +
 +From here we can run any further ft analysis.  ​
analysis/amplipex/artifacts.1390245166.txt.gz ยท Last modified: 2018/07/07 10:19 (external edit)