Processing <2009 CRFs; Coordinates no longer mandatory; fix for HUH.

Anthony Boyer · Blandine Chanteloup-Foret · Blandine Chanteloup-Foret · Anthony Boyer
Commit 8883f903a1004005c1a020c9819480a90d049706 1 parent 7550face
Showing 6 changed files with 40 additions and 31 deletions
toolbox/ImaGIN_BadChannel.m
toolbox/ImaGIN_BadChannelQualityControl.m
toolbox/ImaGIN_BipolarMontage.m
toolbox/ImaGIN_CleanEventName.m
toolbox/ImaGIN_Electrode.m
toolbox/ImaGIN_Validate_StimNames.m
--- a/toolbox/ImaGIN_BadChannel.m
View file @8883f90
+++ b/toolbox/ImaGIN_BadChannel.m
View file @8883f90
@@ -246,7 +246,6 @@ if ~exist(figDir, 'dir')
 end
 % close all;
-
 Size = 8;  % Number of channels per screenshot
 n_c  = size(D,1);
 if n_c >= Size
@@ -254,15 +253,17 @@ if n_c >= Size
     for i2 = 1:tmp
         figure(i2);
         set(gcf,'Position',[629 -17 702 1101])
-        for i3 = 1:Size            
-            if intersect(i3+(i2-1)*Size,interIdx) == i3+(i2-1)*Size 
-                    color = 'm'; % Channel doesn't have position and is bad
-            elseif intersect(i3+(i2-1)*Size,NaNbIdx) == i3+(i2-1)*Size  
-                color = 'r'; %Bad channels will be printed in red
+        for i3 = 1:Size  
+            if ~ismember(chanlabels(D,i3+(i2-1)*Size),D.csv_labels)
+                color = 'g'; % Channel was not matched with the .csv
             elseif intersect(i3+(i2-1)*Size,ixNaN) == i3+(i2-1)*Size
-                color = 'b'; %NaN channels will be printed in blue
+                color = 'b'; % Channel was matched, is good, has NaN coordinates            
+            elseif intersect(i3+(i2-1)*Size,interIdx) == i3+(i2-1)*Size 
+                color = 'm'; % Channel was matched, is bad, has NaN coordinates 
+            elseif intersect(i3+(i2-1)*Size,NaNbIdx) == i3+(i2-1)*Size  
+                color = 'r'; % Channel was matched, is bad, has coordinates
             else
-                color = 'k'; %Good channels will be printed in black
+                color = 'k'; % Channel was matched, is good, has coordinates
             end
             subplot(Size,1,i3)
             plot(time(D),D(i3+(i2-1)*Size,:),color);
@@ -284,15 +285,17 @@ if n_c >= Size
     if rmd ~= 0
         figure(tmp + 1)
         set(gcf,'Position',[629 -17 702 1101])
-        for i4 = 1:rmd
-            if intersect(i3+(i2-1)*Size+i4,interIdx)== i3+(i2-1)*Size+i4
-                 color = 'm';
-            elseif intersect(i3+(i2-1)*Size+i4,NaNbIdx)== i3+(i2-1)*Size+i4
-                color = 'r';
+        for i4 = 1:rmd             
+            if ~ismember(chanlabels(D,i3+(i2-1)*Size+i4),D.csv_labels)
+                color = 'g'; % Channel was not matched with the .csv
             elseif intersect(i3+(i2-1)*Size+i4,ixNaN) == i3+(i2-1)*Size+i4
-                color = 'b';
+                color = 'b'; % Channel was matched, is good, has NaN coordinates            
+            elseif intersect(i3+(i2-1)*Size+i4,interIdx) == i3+(i2-1)*Size+i4 
+                color = 'm'; % Channel was matched, is bad, has NaN coordinates 
+            elseif intersect(i3+(i2-1)*Size+i4,NaNbIdx) == i3+(i2-1)*Size+i4  
+                color = 'r'; % Channel was matched, is bad, has coordinates
             else
-                color = 'k';
+                color = 'k'; % Channel was matched, is good, has coordinates
             end
             subplot(rmd,1,i4)
             plot(time(D),D(i3+(i2-1)*Size+i4,:),color);
@@ -312,15 +315,17 @@ else
     figure(1)
     set(gcf,'Position',[629 -17 702 1101])
     for i5 = 1:n_c
-        if intersect(i5,interIdx)== i5
-            color = 'm';
-        elseif intersect(i5,NaNbIdx)== i5
-            color = 'r';
-        elseif intersect(i5,ixNaN)== i5
-            color = 'b';
+        if ~ismember(chanlabels(D,i5),D.csv_labels)
+            color = 'g'; % Channel was not matched with the .csv
+        elseif intersect(i5,ixNaN) == i5
+            color = 'b'; % Channel was matched, is good, has NaN coordinates 
+        elseif intersect(i5,interIdx) == i5
+            color = 'm'; % Channel was matched, is bad, has NaN coordinates
+        elseif intersect(i5,NaNbIdx) == i5
+            color = 'r'; % Channel was matched, is bad, has coordinates
         else
-            color = 'k';
-        end
+            color = 'k'; % Channel was matched, is good, has coordinates
+        end         
         subplot(n_c,1,i5)
         plot(time(D),D(i5,:),color);
         ylabel([num2str(i5) ' : ' D.chanlabels{i5}])
--- a/toolbox/ImaGIN_BadChannelQualityControl.m
View file @8883f90
+++ b/toolbox/ImaGIN_BadChannelQualityControl.m
View file @8883f90
@@ -38,7 +38,7 @@ elec= sensors(D,'eeg');  % add channels without positions into bad channels
 pos = elec.elecpos; 
 Sens = elec.label;
 chanLbs = D.chanlabels;
-idxNaN = find(isnan(pos(:,1)));
+idxNaN = [] % find(isnan(pos(:,1))); We now assume channels without coordinates are not bad (CRFs older than 2009 do not have T1pre coordinates)
 if ~isempty(idxNaN)
     bIdx = [bIdx(:);idxNaN(:)];
     bIdx = sort(unique(bIdx));
--- a/toolbox/ImaGIN_BipolarMontage.m
View file @8883f90
+++ b/toolbox/ImaGIN_BipolarMontage.m
View file @8883f90
@@ -51,7 +51,7 @@ for i0=1:size(Filename,1)
     Name=Sensors.label;
     Position=Sensors.elecpos;
     BadChannelsMono=badchannels(D);
-    idxNaN = find(isnan(Position(:,1)));
+    idxNaN = [] % find(isnan(Position(:,1))); We now assume channels without coordinates are not bad (CRFs older than 2009 do not have T1pre coordinates)
     if ~isempty(idxNaN)
         BadChannelsMono = [BadChannelsMono(:);idxNaN(:)];        
     end
@@ -75,7 +75,7 @@ for i0=1:size(Filename,1)
                 end                 
                 label_name_2 = matched_2.label;
                 label_number_2 = matched_2.index;       
-                if strcmp(label_name_1,label_name_2) & str2num(label_number_1)+1 == str2num(label_number_2) & ~(sum(isnan(Position(i1,:))) > 0) & ~(sum(isnan(Position(i2,:))) > 0)
+                if strcmp(label_name_1,label_name_2) & str2num(label_number_1)+1 == str2num(label_number_2) 
                     matched_channels = matched_channels+1;
                     Cpos2full(:,end+1)= mean(Position([i1 i2],:))';
                     Cnamesfull{1,end+1}=[Name{i1} '-' Name{i2}];
--- a/toolbox/ImaGIN_CleanEventName.m
View file @8883f90
+++ b/toolbox/ImaGIN_CleanEventName.m
View file @8883f90
@@ -48,12 +48,14 @@ if KeepEvent == 1 % Navigate all stim events
     noteName(~ismember(double(noteName),['A':'Z' 'a':'z' '_' '.' '''' 'µ' '-' '0':'9'])) ='_';
     noteName = regexprep(noteName,'_+','_'); noteName = regexprep(noteName,'µ','u');
     noteName = strrep(noteName,'usec','us');
+    noteName = strrep(noteName,'sec','us'); % HUH notes
     noteName = regexprep(noteName,'MA','mA'); %OD
     noteName = regexprep(noteName,'Stim_Start_',''); %YUQ notes
     noteName = regexprep(noteName,'Stim_Stop_','');  %YUQ notes
     noteName = strrep(noteName,'-','_');  noteName = strrep(noteName,'__','_');
     noteName = strrep(noteName,',','');noteName = strrep(noteName,'_mA_','_');
-    noteName = strrep(noteName,'sec','us');  noteName = strrep(noteName,'_us','us');
+    noteName = strrep(noteName,'sec','us');
+    noteName = strrep(noteName,'_us','us');
     noteName = strrep(noteName,'AA','A'); noteName = strrep(noteName,'_MA_','_'); %some MIL notes
     keepN = ''; noteName = strrep(noteName,'stim','');  noteName = strrep(noteName,'Stim','');
     noteName = strrep(noteName,'TextNote:',''); % for BRN datasets
@@ -93,7 +95,7 @@ if KeepEvent == 1 % Navigate all stim events
                 elseif numel(numbr{2}) == 3
                     if str2double(numbr{2}(1:2)) == str2double(numbr(1)) + 1 || str2double(numbr{2}(1:2)) + 1 == str2double(numbr(1))
                         elecno = strcat(numbr{2}(1:2),'_',numbr{2}(3));
-                        noteName = strrep(noteName,numbr{2},elecno);
+                        noteName = regexprep(noteName,numbr{2},elecno,'once'); % We should replace the first match only
                     elseif str2double(numbr{2}(1)) == str2double(numbr(1)) + 1 || str2double(numbr{2}(1)) + 1 == str2double(numbr(1))
                         elecno = strcat(numbr{2}(1),'_',numbr{2}(2:3));
                         noteName = strrep(noteName,numbr{2},elecno);
--- a/toolbox/ImaGIN_Electrode.m
View file @8883f90
+++ b/toolbox/ImaGIN_Electrode.m
View file @8883f90
@@ -80,7 +80,7 @@ catch
         case '.csv'
             [Name, Position] = readCsv(filename);
             if all(isnan(Position))
-                error('Anatomy not found: possibly patient implanted before 2009. Check implantation scheme!');
+                warning('T1pre coordinates not found: possibly patient implanted before 2009.');
             end
         otherwise 
             disp('ImaGIN> ERROR: Invalid input file type.');
@@ -164,7 +164,9 @@ for i0 = 1:size(t,1)
             chMatchLog{end,2} = Name{iChanPos};
             Sensors.label{i1} = Name{iChanPos};
         else
-            disp(['ImaGIN> WARNING: ' Sensors.label{i1} ' not assigned']);
+            disp(['ImaGIN> WARNING: ' Sensors.label{i1} ' not assigned']);            
+            Sensors.elecpos(i1,:) = NaN;
+            Sensors.chanpos(i1,:) = NaN;
             chNotFound{end+1} = Sensors.label{i1};
         end
     end
--- a/toolbox/ImaGIN_Validate_StimNames.m
View file @8883f90
+++ b/toolbox/ImaGIN_Validate_StimNames.m
View file @8883f90
@@ -115,7 +115,7 @@ for j=1:length(KeepEvent) % Navigate all stim events
     if strcmpi(patientCode(5:end),'MIL');noteName = strrep(noteName,'.0',''); noteName = strrep(noteName,'_MA_','_');end%some MIL notes
     if strcmpi(patientCode(5:end),'REN');noteName = strrep(noteName,'.0','');end%some REN notes   
     if strcmpi(patientCode(5:end),'BIC');noteName = strrep(noteName,'.0','');end%some BIC notes   
-    if strcmpi(patientCode(5:end),'HUH');noteName = strrep(noteName,'.0','');end%some HUH notes 
+    if strcmpi(patientCode(5:end),'HUH');noteName = strrep(noteName,'.0',''); noteName = strrep(noteName,'','u'); end%some HUH notes 
     if strcmpi(patientCode(5:end),'TOU');noteName = strrep(noteName,'.0','');end%some TOU notes
     if strcmpi(patientCode(5:end),'GRE');noteName = strrep(noteName,'.0','');end%some GRE notes
     if strcmpi(patientCode(5:end),'FLO');noteName = strrep(noteName,'.0','');end%some FLO notes