Update automated_pipeline.md

Author: arnodelorme

tutorials/11_Scripting/automated_pipeline.md

@@ -28,7 +28,7 @@ Download the data from [https://openneuro.org/datasets/ds003061/](https://openne
 
 Alternatively, use one of the available [EEGLAB studies](../tutorial_data.html). Note that some of these studies already have their data preprocessed and may not be suitable for automated processing.
 
-Running the pipeline
+Running an ERP pipeline
 ----------------
 
 The pipeline below takes the raw data from all subjects, clean the data, extracts epochs of interest, and plots the grand average ERP.
@@ -51,7 +51,73 @@ pop_editoptions( 'option_storedisk', 1); % only one dataset in memory at a time
 [STUDY, ALLEEG] = pop_importbids(filepath, 'studyName','Oddball', 'subjects', [1:2]); % when using all subjects, one subject is truncated and cause the pipeline to return an error
 
 % remove non-ALLEEG channels (it is also possible to process ALLEEG data with non-ALLEEG data
-ALLEEG = pop_select( ALLEEG,'nochannel',{'EXG1','EXG2','EXG3','EXG4','EXG5','EXG6','EXG7','EXG8', 'GSR1', 'GSR2', 'Erg1', 'Erg2', 'Resp', 'Plet', 'Temp'});
+ALLEEG = pop_select( ALLEEG,'rmchannel',{'EXG1','EXG2','EXG3','EXG4','EXG5','EXG6','EXG7','EXG8', 'GSR1', 'GSR2', 'Erg1', 'Erg2', 'Resp', 'Plet', 'Temp'});
+
+% compute average reference
+ALLEEG = pop_reref( ALLEEG,[]);
+
+% clean data using the clean_rawdata plugin
+ALLEEG = pop_clean_rawdata( ALLEEG,'FlatlineCriterion',5,'ChannelCriterion',0.87, ...
+    'LineNoiseCriterion',4,'Highpass',[0.25 0.75] ,'BurstCriterion',20, ...
+    'WindowCriterion',0.25,'BurstRejection','on','Distance','Euclidian', ...
+    'WindowCriterionTolerances',[-Inf 7] ,'fusechanrej',1);
+
+% recompute average reference interpolating missing channels (and removing
+% them again after average reference - STUDY functions handle them automatically)
+ALLEEG = pop_reref( ALLEEG,[],'interpchan',[]);
+
+% run ICA reducing the dimention by 1 to account for average reference 
+plugin_askinstall('picard', 'picard', 1); % install Picard plugin
+ALLEEG = pop_runica(ALLEEG, 'icatype','picard','concatcond','on','options',{'pca',-1});
+
+% run ICLabel and flag artifactual components
+ALLEEG = pop_iclabel(ALLEEG, 'default');
+ALLEEG = pop_icflag( ALLEEG,[NaN NaN;0.9 1;0.9 1;NaN NaN;NaN NaN;NaN NaN;NaN NaN]);
+
+% extract data epochs
+% this is not necessary if you have resting state data or eyes open
+% eyes closed data, you need to define the design in the STUDY
+ALLEEG = pop_epoch( ALLEEG,{'oddball_with_reponse','standard'},[-1 2] ,'epochinfo','yes');
+ALLEEG = eeg_checkset( ALLEEG );
+
+% create STUDY design
+STUDY = std_maketrialinfo(STUDY, ALLEEG);
+STUDY = std_makedesign(STUDY, ALLEEG, 1, 'name','STUDY.design 1','delfiles','off', ...
+    'defaultdesign','off','variable1','type','values1',{'oddball_with_reponse','standard'},...
+    'vartype1','categorical','subjselect', STUDY.subject);
+
+% precompute ERPs at the STUDY level
+[STUDY, ALLEEG] = std_precomp(STUDY, ALLEEG, {},'savetrials','on','rmicacomps','on','interp','on','recompute','on','spec','on');
+
+% plot ERPS
+STUDY = pop_erpparams(STUDY, 'topotime',350);
+chanlocs = eeg_mergelocs(ALLEEG.chanlocs); % get all channels from all datasets
+STUDY = std_specplot(STUDY,ALLEEG,'channels', {chanlocs.labels}, 'design', 1);
+
+% revert default option
+pop_editoptions( 'option_storedisk', 0);
+```
+
+Running an spectral pipeline
+----------------
+
+The pipeline below takes the raw data from all subjects, clean the data, extracts epochs of interest, and plots the spectrum to compare conditions. It is very similar to the ERP pipeline above.
+
+```matlab
+% check folder
+eeglab;
+if ~exist('task-P300_events.json', 'file')
+    error('Download the data from https://openneuro.org/datasets/ds003061/ and go to the downloaded folder');
+else
+    filepath = fileparts(which('task-P300_events.json'));
+end
+
+% import data
+pop_editoptions( 'option_storedisk', 1); % only one dataset in memory at a time
+[STUDY, ALLEEG] = pop_importbids(filepath, 'studyName','Oddball', 'subjects', [1:2]); % when using all subjects, one subject is truncated and cause the pipeline to return an error
+
+% remove non-ALLEEG channels (it is also possible to process ALLEEG data with non-ALLEEG data
+ALLEEG = pop_select( ALLEEG,'rmchannel',{'EXG1','EXG2','EXG3','EXG4','EXG5','EXG6','EXG7','EXG8', 'GSR1', 'GSR2', 'Erg1', 'Erg2', 'Resp', 'Plet', 'Temp'});
 
 % compute average reference
 ALLEEG = pop_reref( ALLEEG,[]);