From 2386a15aabdac629c765364fb6427409eba57c41 Mon Sep 17 00:00:00 2001
From: tmedani <takfarinesmedani@live.fr>
Date: Fri, 27 Feb 2026 01:54:47 -0800
Subject: [PATCH 1/2] Handle EEG reference channels in duneuro forward

Detect EEG REF channels and compute reference locations for Duneuro 2019
---
 toolbox/forward/bst_duneuro.m | 52 ++++++++++++++++++++++++++++++++++-
 1 file changed, 51 insertions(+), 1 deletion(-)

diff --git a/toolbox/forward/bst_duneuro.m b/toolbox/forward/bst_duneuro.m
index c537bf3568..c0290aacc6 100644
--- a/toolbox/forward/bst_duneuro.m
+++ b/toolbox/forward/bst_duneuro.m
@@ -48,6 +48,27 @@
 isEcog = strcmpi(cfg.ECOGMethod, 'duneuro') && ~isempty(cfg.iEcog);
 isSeeg = strcmpi(cfg.SEEGMethod, 'duneuro') && ~isempty(cfg.iSeeg);
 
+% Find if EEG Ref exists and find its  position
+iRef = channel_find(cfg.Channel, {'EEG REF'});
+switch length(iRef)
+    case 0 % no reference = > output will be averaged to Avgref        
+        refLoc = [];
+    case 1 % one reference        
+        refLoc = [cfg.Channel(iRef).Loc]';
+    case 2 % two references => ex: linked mastoids       
+        refLoc = [cfg.Channel(iRef).Loc]';
+        % limitation of Duneuro 2019, can not handel multiple ref elec;
+        % Assign by default the first channel, 
+        % will be improved in the DN2026
+        refLoc = refLoc(1,:);
+    otherwise
+        refLoc = [];
+end
+% remove nan value if exist
+refLoc(any(isnan(refLoc), 2), :) = [];
+% if final ref = []; the average ref will be applied by default
+  
+
 % Get the modality
 if ((isEeg || isEcog || isSeeg) && isMeg)
     dnModality = 'meeg';  
@@ -65,6 +86,13 @@
 if (isEeg || isEcog || isSeeg)
     cfg.iEeg = [cfg.iEeg, cfg.iSeeg, cfg.iEcog];
     EegLoc = cat(2, cfg.Channel(cfg.iEeg).Loc);
+    
+    % Add the reference channel
+    % Duneuro 2019 assume the first electrode as the reference, so here we
+    % append it in the first row
+    if ~isempty(refLoc)
+        EegLoc = [refLoc' EegLoc];
+    end
 end
 
 % Get MEG positions/orientations
@@ -544,8 +572,30 @@
 %% ===== READ LEADFIELD ======
 bst_progress('text', 'DUNEuro: Reading leadfield...');
 % EEG
-if (isEeg || isEcog || isSeeg) 
+if (isEeg || isEcog || isSeeg)
     GainEeg = in_duneuro_bin(fullfile(TmpDir, cfg.BstEegLfFile))';
+    % postprocess the gain according to the ref channel
+    if ~isempty(refLoc)
+        switch length(iRef)
+            case 1
+                % Apply the re-referencing to the iRef electrode
+                GainEeg = GainEeg - GainEeg(iRef(1),:);
+                % Remove the iRef row from the Gain matrix
+                GainEeg(iRef(1),:) = [];
+            case 2 % Not supported by this version of Duneuro, will be supported in DN2026 version
+                % Apply the re-referencing using linked masteoids
+                GainEeg = GainEeg - (1/2*GainEeg(iRef(1),:) + 1/2*GainEeg(iRef(2),:));
+                % Remove the iRef row from the Gain matrix
+                GainEeg(iRef(1),:) = [];
+                GainEeg(iRef(2),:) = [];
+            otherwise
+                % Apply the average reference
+                GainEeg = GainEeg - mean(GainEeg);
+        end
+    else
+        % Apply the average reference
+        GainEeg = GainEeg - mean(GainEeg);
+    end
 end
 
 %MEG

From 0359be4f841fdad440c844ddf1002aae2395af7d Mon Sep 17 00:00:00 2001
From: tmedani <takfarinesmedani@live.fr>
Date: Fri, 27 Feb 2026 01:59:09 -0800
Subject: [PATCH 2/2] Simplify EEG reference handling for Duneuro

Adjust re-referencing logic to match Duneuro's assumption that the added channel (1) is the reference.
---
 toolbox/forward/bst_duneuro.m | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/toolbox/forward/bst_duneuro.m b/toolbox/forward/bst_duneuro.m
index c0290aacc6..74f69a1341 100644
--- a/toolbox/forward/bst_duneuro.m
+++ b/toolbox/forward/bst_duneuro.m
@@ -578,18 +578,11 @@
     if ~isempty(refLoc)
         switch length(iRef)
             case 1
-                % Apply the re-referencing to the iRef electrode
-                GainEeg = GainEeg - GainEeg(iRef(1),:);
-                % Remove the iRef row from the Gain matrix
-                GainEeg(iRef(1),:) = [];
-            case 2 % Not supported by this version of Duneuro, will be supported in DN2026 version
-                % Apply the re-referencing using linked masteoids
-                GainEeg = GainEeg - (1/2*GainEeg(iRef(1),:) + 1/2*GainEeg(iRef(2),:));
-                % Remove the iRef row from the Gain matrix
-                GainEeg(iRef(1),:) = [];
-                GainEeg(iRef(2),:) = [];
+                % Remove the added channel, DN assume this is the ref
+                GainEeg(1,:) = [];
             otherwise
-                % Apply the average reference
+                % Apply the average reference (this is not correct as chann1 is assumed to be the ref)
+                % THis will be improved in DN2026 version
                 GainEeg = GainEeg - mean(GainEeg);
         end
     else