analysis:amplipex:artifacts
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analysis:amplipex:artifacts [2014/01/20 19:12] ecarmichael created |
analysis:amplipex:artifacts [2018/04/17 15:20] (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. | ||
analysis/amplipex/artifacts.1390245166.txt.gz ยท Last modified: 2018/04/17 15:21 (external edit)
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