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analysis:amplipex:artifacts [2014/01/20 14:12] ecarmichael created |
analysis:amplipex:artifacts [2018/07/07 10:19] (current) |
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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. |