SEEG: Add infinite homogeneous medium headmodel

toolbox/forward/bst_headmodeler.m

@@ -22,8 +22,13 @@
 %     .EEGMethod:  Method used to compute the forward model for EEG sensors.
 %         - 'eeg_3sphereberg' : EEG forward modeling with a set of 3 concentric spheres (Scalp, Skull, Brain/CSF) 
 %         - 'openmeeg'        : OpenMEEG forward model
-%     .SEEGMethod:    'openmeeg' and 'duneuro'  
-%     .ECOGMethod:    'openmeeg' and 'duneuro' 
+%     .SEEGMethod: Method used to compute the forward model for SEEG sensors.
+%         - 'homogeneous' : Infinite homogeneous medium
+%         - 'openmeeg'    : OpenMEEG forward model
+%         - 'duneuro'     : DUNEuro forward model
+%     .ECOGMethod: Method used to compute the forward model for ECOG sensors.
+%         - 'openmeeg'    : OpenMEEG forward model
+%         - 'duneuro'     : DUNEuro forward model
 %     .NIRSMethod:    'import'
 %
 %     ======= METHODS OPTIONS =============================================
@@ -536,6 +541,13 @@
     Gain(~isnan(Gain_dn)) = Gain_dn(~isnan(Gain_dn));
 end
 
+%% ===== COMPUTE: SEEG INFINITE HOMOGENEOUS MEDIUM HEADMODEL =====
+if strcmp('homogeneous', OPTIONS.SEEGMethod)
+    Gain(iSeeg, :) = bst_seeg_homogeneous(OPTIONS.GridLoc, OPTIONS.Channel(iSeeg), sSurfInner, OPTIONS);
+    strHistory =  [strHistory, ' | ', 'Homogeneous medium (SEEG)', ...
+                               ' | ', sprintf('Conductivity: %1.3f S/m', OPTIONS.Conductivity), ...
+                               ' | ', sprintf('Min dist. betweem SEEG contact and dipoles: %1.3f mm', OPTIONS.MinSeegDipoleDist)];
+end
 
 %% ===== COMPUTE: BRAINSTORM HEADMODELS =====
 Param = [];

toolbox/forward/bst_seeg_homogeneous.m

@@ -0,0 +1,113 @@
+function G = bst_seeg_homogeneous(GridLoc, sChannel, sInnerSkull, Options)
+% bst_seeg_homogeneous: Calculate the electric potential for infinite homogeneous medium
+%
+% USAGE:  G = bst_seeg_homogeneous(GridLoc, sChannel, sInnerSkull, Options)
+%
+% INPUT:
+%    - GridLoc     : Dipole locations (in meters)  [nDipoles x 3]
+%    - sChannel    : Channel structure             [nSensors]
+%    - sInnerSkull : Inner skull surface structure
+%    - Options structure
+%       - Options.Conductivity      : Conductivity (S/m)
+%       - Options.MinSeegDipoleDist : Minimum distance between SEEG and dipoles
+% OUTPUTS:
+%    - G : SEEG forward model gain matrix    [nSensors x (3*nDipoles)]
+%
+% DESCRIPTION:  sEEG single layer forward model
+%     This function computes the voltage potential forward gain matrix for an array of 
+%     sEEG electrodes inside the brain. The conductivity is assumed to be uniform and isotropoic
+%     inside the medium (that is assumed to be infinite).
+%       
+%     For electrodes outside of the brain, the grain is set to 0. 
+% 
+%     Ref: 
+%          + Grova, C., Aiguabella, M., Zelmann, R., Lina, J.-M., Hall, J.A. and Kobayashi, E. (2016), 
+%            Intracranial EEG potentials estimated from MEG sources: A new approach to correlate MEG and iEEG data in epilepsy. 
+%            Hum. Brain Mapp., 37: 1661-1683. https://doi.org/10.1002/hbm.23127
+%   
+%          + Næss, S., Halnes, G., Hagen, E., Hagler Jr, D. J., Dale, A. M., Einevoll, G. T., & Ness, T. V. (2021). 
+%            Biophysically detailed forward modeling of the neural origin of EEG and MEG signals. NeuroImage, 225, 117467.  
+%           
+%                 dot(n_i, u_ij)
+%     V(E_j) = --------------------------
+%              4 * pi * sigma0 * (r_ij)^2
+%
+%     V(E_j) = Electric potential at sensor j
+%     n_i    = Vector, current dipole for source i
+%     u_ij   = Unit vector, oriented from source i to sensor j
+%     sigma0 = Conductivity of infinite homogeneous medium
+%     r_ij   = Euclidean distance between source i and sensor j
+%
+%     Written as matrix multiplication:  V = G * N
+%     V = Electric potential at contacts [nSensors, nTime]
+%     G = Gain matrix                    [nSensors, nDipoles]
+%     N = Dipole activation currents     [nDipoles, nTime]
+%
+
+% @=============================================================================
+% This function is part of the Brainstorm software:
+% https://neuroimage.usc.edu/brainstorm
+% 
+% Copyright (c) University of Southern California & McGill University
+% This software is distributed under the terms of the GNU General Public License
+% as published by the Free Software Foundation. Further details on the GPLv3
+% license can be found at http://www.gnu.org/copyleft/gpl.html.
+% 
+% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
+% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
+% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
+% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
+% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
+%
+% For more information type "brainstorm license" at command prompt.
+% =============================================================================@
+%
+% Authors: Edouard Delaire, 2026
+
+    % Add default options
+    Options = struct_copy_fields(struct('Conductivity', 0.25, 'MinSeegDipoleDist', 3/1000), Options, 1);
+    min_distance = Options.MinSeegDipoleDist;
+    sigma0       = Options.Conductivity;
+
+    NbElectrodes = length(sChannel);
+    NbVertices   = size(GridLoc, 1);
+
+    % Find electrodes that are inside the inner skull
+    SEEG_Loc = [sChannel.Loc]'; 
+    isSEEGInsideSkull   = inpolyhd(SEEG_Loc, sInnerSkull.Vertices, sInnerSkull.Faces);
+
+    % Compute the leadfield
+    bst_progress('start', 'Computing head model', sprintf('Computing head model for %d contacts...', NbElectrodes), 0, NbElectrodes);
+    G = zeros(NbElectrodes , 3*NbVertices);
+    for iContact = 1:NbElectrodes
+        % Ignore contacts outside of the inner skull
+        if ~isSEEGInsideSkull(iContact)
+            continue
+        end
+
+        % Compute unit vectors from SEEG contact to source points (u_j)
+        VectorDipolesToSEEG = SEEG_Loc(iContact, :) - GridLoc;
+        DistanceToDipoles = sqrt(sum(VectorDipolesToSEEG.^2,2));
+        VectorDipolesToSEEG = VectorDipolesToSEEG ./ repmat(DistanceToDipoles, 1, 3);
+
+        % Replace short distance (< 'min_distance') with 'min_distance' to prevent instabilities in the model by too close measurements
+        iShort = find(DistanceToDipoles < min_distance);
+        if ~isempty(iShort)
+            % fprintf(' %d vertex had distance to the cortex smaller than %.2f mm to electrodes %s \n', length(iShort), min_distance*1000, sChannel(iContact).Name);           
+            DistanceToDipoles(iShort) = min_distance;
+        end
+
+        % Compute the leadfield (u_j / (r_j)^2)
+        scaledVector = VectorDipolesToSEEG ./ repmat(DistanceToDipoles.^2, 1, 3); 
+
+        % Organize the matrix as x,y,z
+        G(iContact, :) = reshape(scaledVector', 1, []);
+
+        bst_progress('inc', 1);
+    end
+
+    % Add normalization constant 
+    G = G / (4 * pi * sigma0);
+
+    bst_progress('stop');
+end

toolbox/forward/panel_headmodel.m

@@ -121,6 +121,7 @@
         jCheckMethodSEEG.setSelected(1);
         % Combobox
         jComboMethodSEEG = gui_component('ComboBox', jPanelMethod, 'tab hfill', [], [], [], @UpdateComment, []);
+        jComboMethodSEEG.addItem(BstListItem('homogeneous', '', 'Homogeneous medium', []));
         jComboMethodSEEG.addItem(BstListItem('openmeeg', '', 'OpenMEEG BEM', []));
         jComboMethodSEEG.addItem(BstListItem('duneuro', '', 'DUNEuro FEM', []));
         jComboMethodSEEG.setSelectedIndex(0);
@@ -437,6 +438,7 @@ function UpdateComment(varargin)
         sMethod.Comment = strrep(sMethod.Comment, 'os_meg',          'Overlapping spheres');
         sMethod.Comment = strrep(sMethod.Comment, 'meg_sphere',      'Single sphere');
         sMethod.Comment = strrep(sMethod.Comment, 'eeg_3sphereberg', '3-shell sphere');
+        sMethod.Comment = strrep(sMethod.Comment, 'homogeneous',     'Homogeneous medium');
         sMethod.Comment = strrep(sMethod.Comment, 'openmeeg',        'OpenMEEG BEM');
         sMethod.Comment = strrep(sMethod.Comment, 'duneuro',         'DUNEuro FEM');
         % Grid type
@@ -446,6 +448,7 @@ function UpdateComment(varargin)
             sMethod.Comment = [sMethod.Comment ' (mixed)'];
         end
     end
+    isHomogeneous = any(strcmpi(allMethods, 'homogeneous'));
     isOpenMEEG = any(strcmpi(allMethods, 'openmeeg'));
     isDuneuro = any(strcmpi(allMethods, 'duneuro'));
     % Get protocol description
@@ -597,6 +600,38 @@ function UpdateComment(varargin)
             bst_error('Please import a cortex surface for this subject.', 'Head model', 0);
             return
         end
+
+        % ===== INFINITE HOMOGENEOUS MEDIUM =====
+        if isHomogeneous
+            % Interactive interface to set the options
+            if OPTIONS.Interactive
+                OPTIONS.Conductivity = [];
+                OPTIONS.MinSeegDipoleDist  = [];
+                % Get options
+                optionsStr = {'Brain conductivity (S/m):','Minimum distance between SEEG and dipoles (mm):'};
+                res = java_dialog('input', optionsStr, 'SEEG head model options', [],  {'0.25','3'});
+                if isempty(res)
+                    return
+                end
+                resDouble = str2double(res);
+                % Validate inputs
+                for iRes = 1 : length(resDouble)
+                    if isnan(resDouble(iRes))
+                        errMessage = sprintf('Invalid input "%s" for option:\n%s', res{iRes}, optionsStr{iRes});
+                        return
+                    end
+                end
+                OPTIONS.Conductivity      = resDouble(1);
+                OPTIONS.MinSeegDipoleDist = resDouble(2)/1000;
+            end
+            % Check that inner skull exists
+            if ~isempty(sSubject.iInnerSkull)
+                OPTIONS.InnerSkullFile = file_fullpath(sSubject.Surface(sSubject.iInnerSkull(1)).FileName);
+            else
+                errMessage = 'No inner skull surface for this subject.';
+                return
+            end
+        end
 
         % ===== OPENMEEG =====
         if isOpenMEEG