| %% Pre-processing pipeline pseudocode | |
| %% Everything run in MATLAB | |
| %% Necessary extensions - eeglab, preppipeline, AMICA, corrmap, CSD | |
| % Preprocessing | |
| read in data | |
| re-reference to average | |
| remove baseline | |
| insert channel locations 'MMN_ElectrodeCoords_MA2.ced)' | |
| High Pass Filter - 'pop_eegfiltnew( EEG, 1, [], [], [0], 0, 0, 0);' | |
| Run preppipeline | |
| intpChans = setxor(1:64, [5 27 38 60]); % which channels to use for interpolation; exclude EOG channels | |
| params = struct('name', [vhdr{1} 'snum' num2str(sx) '.' num2str(nf)], ... | |
| 'lineFrequencies', [60:60:300], ... % Line frequencies to remove | |
| 'referenceChannels', intpChans, ... % Channels to be used for re-referencing | |
| 'evaluationChannels', intpChans, ... % Channels to be used for interpolation | |
| 'rereferencedChannels', [1:64], ... % Channels to be linenoise removed and referenced | |
| 'detrendChannels', [1:64], ... % Channels to detrend | |
| 'lineNoiseChannels', [1:64], ... % Channels to remove line noise from | |
| 'ignoreBoundaryEvents', true, ... % ??? not sure why it doesn't work without | |
| 'detrendType', 'none', ... % Use high pass filter to detrend channels | |
| 'detrendCutoff', 1, ... % High pass filter frequency cut off | |
| 'referenceType', 'robust', ... % Robust reference | |
| 'meanEstimateType', 'median', ... % Use median for robust reference | |
| 'interpolationOrder', 'post-reference', ... % Interpolate channels after robust referencing | |
| 'keepFiltered', true); % Retain filtering? | |
| EEG = prepPipeline(EEG, params); | |
| Low Pass Filter - | |
| pop_eegfiltnew( EEG, [], 50, [], [0], 0, 0, 0); | |
| Epoch to -1.5 - 3 seconds around stimulus using these triggers | |
| [111:114 121:124 211:214 221:224] | |
| Remove large artifacts using pop_autorej | |
| pop_autorej(EEG, 'nogui','on','threshold',500, 'startprob',5,'maxrej',5); | |
| Downsample to 500 Hz | |
| pop_resample( EEG, 500 ); | |
| Run AMICA using the following | |
| [EEG.icaweights, EEG.icasphere, EEG.icamods] = runamica15(EEG.data(:,:), ... | |
| 'max_iter', 10000, 'writestep', 500, 'pcakeep', 42, 'do_reject', 1, ... | |
| 'max_threads', 12, 'rejsig', 4); | |
| Create eeglab 'STUDY' structure | |
| Precompute topography to extract EOG using STUDY | |
| std_precomp(STUDY, ALLEEG, 'components','allcomps','on','recompute','on','scalp','on'); | |
| Find prototypical VEOG artifact and run 'corrmap' to identify all VEOG components | |
| corrmap(STUDY, ALLEEG, indx, 1, 'ics',1,'pl', 'both','clname','VEOG','badcomps','no', 'resetclusters','on'); | |
| Reject epochs by trend and component spectra, exclude for VEOG artifact | |
| pop_rejtrend( EEG, 0, include, size(EEG.times,2), 5, 0.3, 0, 0, 0); | |
| pop_rejspec( EEG, 0, 'elecrange', include ,'threshold',[-50 45;-100 30],'freqlimits',[0 3;20 50],'eegplotcom','','eegplotplotallrej',0,'eegplotreject',0); | |
| EEG.reject.sum = (EEG.reject.icarejfreq + EEG.reject.icarejconst) > 0; | |
| pop_select( EEG, 'notrial', find(EEG.reject.sum)); | |
| Run second round ICA on cleaner data | |
| [EEG.icaweights, EEG.icasphere, EEG.icamods] = runamica15(EEG.data(:,:), ... | |
| 'max_iter', 10000, 'writestep', 500, 'pcakeep', 42, 'do_reject', 1, ... | |
| 'max_threads', 12, 'rejsig', 4); | |
| Identify VEM, HEOG and VEOG artifacts and run corrmap again to identify | |
| Subtract artifacts from EEG | |
| pop_subcomp( EEG, [VEM HEOG VEOG], 0); % Check this | |
| Final clean up - re-baseline correct to 100 ms epoch baseline and remove large noisy epochs | |
| pop_rmbase( EEG, [-100 0]); | |
| pop_eegthresh( EEG, 1, [1:64], -90, 90, -1.5, 3, 0, 1); | |
| Run CSD transformation | |
| Remove eye channels | |
| ConvertLocations | |
| ExtractMontage for CSD | |
| Check Montage (MapMontage(M)) | |
| Set CSD: [G,H] = GetGH(M, 4); | |
| Run CSD: CSD(EEG.data(:,:), G, H, 1.0e-5, 10); | |
| reshape(EEG.CSDdata, size(EEG.data)); | |