Same changes as for RELAX_Wrapper_beta

Adjusted to provide warning to user if electrode rejections meet or exceed the user set threshold.

RELAX_Wrapper.m

@@ -150,7 +150,7 @@
     % avoid adding temporal dependencies to the data, unlike filtering
     % approaches).
 
-    % de Cheveigné, A., & Arzounian, D. (2018). Robust detrending, rereferencing, outlier detection, and inpainting for multichannel data. NeuroImage, 172, 903-912.
+    % de Cheveigné, A., & Arzounian, D. (2018). Robust detrending, rereferencing, outlier detection, and inpainting for multichannel data. NeuroImage, 172, 903-912.
 
     % Use TESA to apply butterworth filter: 
     EEG = RELAX_filtbutter( EEG, RELAX_cfg.LineNoiseFrequency-3, RELAX_cfg.LineNoiseFrequency+3, 2, 'bandstop' );
@@ -399,7 +399,7 @@
         if isfield(EEG.RELAX, 'eyeblinkmask') % if eyeblinkmask has been created, do the following (thanks to Jane Tan for the suggested bug fix when eyeblinkmask is not created)
             EEG.RELAX=rmfield(EEG.RELAX,'eyeblinkmask'); % remove variables that are no longer necessary
         end
-        EEG.RELAX=rmfield(EEG.RELAX,'ExtremeEpochsToIgnoreInMuscleDetectionStep'); % remove variables that are no longer necessary
+
         EEG.RELAXProcessingRoundThree=EEG.RELAXProcessing; % Record MWF cleaning details from round 3 in EEG file
         RELAXProcessingRoundThree=EEG.RELAXProcessing; % Record MWF cleaning details from round 3 into file for all participants
 
@@ -518,14 +518,14 @@
     end
     if (EEG.RELAXProcessingExtremeRejections.NumberOfMuscleContaminatedChannelsRecomendedToDelete...
             +EEG.RELAXProcessingExtremeRejections.NumberOfExtremeNoiseChannelsRecomendedToDelete...
-            +size(EEG.RELAXProcessingExtremeRejections.PREPBasedChannelToReject,2))...
-            >RELAX_cfg.MaxProportionOfElectrodesThatCanBeDeleted*size(EEG.allchan,2)
-        EEG.RELAX_issues_to_check.ElectrodeRejectionRecommendationsExceededThreshold=...
+            +size(EEG.RELAXProcessingExtremeRejections.PREPBasedChannelToReject,1))...
+            >=RELAX_cfg.MaxProportionOfElectrodesThatCanBeDeleted*size(EEG.allchan,2)
+        EEG.RELAX_issues_to_check.ElectrodeRejectionRecommendationsMetOrExceededThreshold=...
             (EEG.RELAXProcessingExtremeRejections.NumberOfMuscleContaminatedChannelsRecomendedToDelete...
             +EEG.RELAXProcessingExtremeRejections.NumberOfExtremeNoiseChannelsRecomendedToDelete...
-            +size(EEG.RELAXProcessingExtremeRejections.PREPBasedChannelToReject,2));
+            +size(EEG.RELAXProcessingExtremeRejections.PREPBasedChannelToReject,1));
     else
-        EEG.RELAX_issues_to_check.ElectrodeRejectionRecommendationsExceededThreshold=0;
+        EEG.RELAX_issues_to_check.ElectrodeRejectionRecommendationsMetOrExceededThreshold=0;
     end
     if EEG.RELAXProcessingExtremeRejections.ProportionExcludedForExtremeOutlier>0.20
         EEG.RELAX_issues_to_check.HighProportionExcludedAsExtremeOutlier=EEG.RELAXProcessingExtremeRejections.ProportionExcludedForExtremeOutlier;
@@ -633,7 +633,7 @@
 end
 
 set(groot, 'defaultAxesTickLabelInterpreter','none');
-if exist('CleanedMetrics','var')
+if RELAX_cfg.computecleanedmetrics==1
     try
         figure('Name','BlinkAmplitudeRatio','units','normalized','outerposition',[0.05 0.05 0.95 0.95]);
         boxplot(CleanedMetrics.BlinkAmplitudeRatio);
@@ -667,6 +667,15 @@
     warning('You instructed RELAX to clean more files than were in your data folder. Check all your expected files were there?');
 end
 
+if find(RELAX_issues_to_check.ElectrodeRejectionRecommendationsMetOrExceededThreshold>0)>0
+    f = msgbox('Some files met or exceeded the electrode rejection threshold. We recommend visually inspecting the raw and cleaned files where this is the case. Open the "RELAX_issues_to_check" struct in the workspace, and check the third column. Files that exceeded the threshold will show a value above 0. Exclude files where raw data seems irretrievably noisy, or cleaned data still contains excessive noise.'...
+    ,'Some files met or exceeded the electrode rejection threshold');    
+    set(f,'Position',[300,300,450,150]);
+    ah = get( f, 'CurrentAxes' );
+    ch = get( ah, 'Children' );
+    set( ch, 'FontSize', 12 ); %makes text bigger
+end
+
 toc
 %% POTENTIAL IMPROVEMENTS THAT COULD BE MADE:
 % 1) work out a way to threshold horizontal eye movements so the script