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Grouped seeg electrodes #922

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5687dc3
Added IntergroupSpacing field to allow Grouped SEEG intracranial elec…
aarongeller May 20, 2026
f635eea
Added Grouped SEEG functionality to allow SEEG models with 3 groups o…
aarongeller May 20, 2026
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3 changes: 2 additions & 1 deletion toolbox/db/db_template.m
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Original file line number Diff line number Diff line change
Expand Up @@ -734,7 +734,7 @@
case 'intraelectrode'
template = struct(...
'Name', '', ... % Identification
'Type', '', ... % 'SEEG' / 'ECOG'
'Type', '', ... % 'SEEG' / 'Grouped SEEG' / 'ECOG'
'Model', '', ... % String identifying the make and model
'Loc', [], ... % [3xN] positions with all the relevant points (eg. tip and entry)
'Color', [], ... % [1x3] color vector
Expand All @@ -744,6 +744,7 @@
'ContactLength', [], ...
'ElecDiameter', [], ...
'ElecLength', [], ...
'IntergroupSpacing', [], ...
'Visible', 1);

case 'intracontact'
Expand Down
137 changes: 123 additions & 14 deletions toolbox/gui/panel_ieeg.m
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -142,11 +142,13 @@
gui_component('label', jPanelElecOptions, '', 'Type: ');
jButtonGroup = ButtonGroup();
jRadioSeeg = gui_component('radio', jPanelElecOptions, '', 'SEEG', jButtonGroup, '', @(h,ev)ValidateOptions('Type', ev.getSource()));
jRadioGroupedSeeg = gui_component('radio', jPanelElecOptions, '', 'Grouped SEEG', jButtonGroup, '', @(h,ev)ValidateOptions('Type', ev.getSource()));
jRadioEcog = gui_component('radio', jPanelElecOptions, '', 'ECOG', jButtonGroup, '', @(h,ev)ValidateOptions('Type', ev.getSource()));
jRadioEcogMid = gui_component('radio', jPanelElecOptions, '', 'ECOG-mid', jButtonGroup, '', @(h,ev)ValidateOptions('Type', ev.getSource()));
jRadioSeeg.setMargin(java.awt.Insets(0,0,0,0));
jRadioEcog.setMargin(java.awt.Insets(0,0,0,0));
jRadioEcogMid.setMargin(java.awt.Insets(0,0,0,0));
jRadioGroupedSeeg.setMargin(java.awt.Insets(0,0,0,0));
% Electrode model
jPanelModel = gui_river([0,0], [0,0,0,0]);
% Title
Expand Down Expand Up @@ -197,6 +199,11 @@
jLabelElecLength = gui_component('label', jPanelElecOptions, 'br', 'Electrode length: ');
jTextElecLength = gui_component('texttime', jPanelElecOptions, 'tab', '');
jLabelElecLengthUnits = gui_component('label', jPanelElecOptions, '', ' mm');
% Intergroup spacing
jLabelIntergroupSpacing = gui_component('label', jPanelElecOptions, 'br', 'Intergroup spacing: ');
jTextIntergroupSpacing = gui_component('text', jPanelElecOptions, 'tab', '');
jTextIntergroupSpacing.setHorizontalAlignment(jTextNcontacts.RIGHT);
jLabelIntergroupSpacingUnits = gui_component('label', jPanelElecOptions, '', ' mm');
% Set electrode position
jPanelButtons = gui_component('panel');
jCardLayout = java.awt.CardLayout;
Expand Down Expand Up @@ -244,8 +251,12 @@
'jRadioSeeg', jRadioSeeg, ...
'jRadioEcog', jRadioEcog, ...
'jRadioEcogMid', jRadioEcogMid, ...
'jRadioGroupedSeeg', jRadioGroupedSeeg, ...
'jTextNcontacts', jTextNcontacts, ...
'jTextSpacing', jTextSpacing, ...
'jLabelIntergroupSpacing', jLabelIntergroupSpacing, ...
'jTextIntergroupSpacing', jTextIntergroupSpacing, ...
'jLabelIntergroupSpacingUnits', jLabelIntergroupSpacingUnits, ...
'jTextContactDiam', jTextContactDiam, ...
'jLabelContactLength', jLabelContactLength, ...
'jTextContactLength', jTextContactLength, ...
Expand Down Expand Up @@ -292,6 +303,9 @@ function ComboModelChanged_Callback(varargin)
if ~isempty(sModels(iModel).ContactSpacing)
sSelElec(i).ContactSpacing = sModels(iModel).ContactSpacing;
end
if isfield(sModels(iModel), 'IntergroupSpacing') && ~isempty(sModels(iModel).IntergroupSpacing)
sSelElec(i).IntergroupSpacing = sModels(iModel).IntergroupSpacing;
end
if ~isempty(sModels(iModel).ContactDiameter)
sSelElec(i).ContactDiameter = sModels(iModel).ContactDiameter;
end
Expand Down Expand Up @@ -623,6 +637,8 @@ function UpdateModelList(elecType)
switch (elecType)
case 'SEEG'
iMod = find(strcmpi({sModels.Type}, 'SEEG'));
case 'Grouped SEEG'
iMod = find(strcmpi({sModels.Type}, 'Grouped SEEG'));
case {'ECOG', 'ECOG-mid'}
iMod = find(strcmpi({sModels.Type}, 'ECOG'));
end
Expand Down Expand Up @@ -673,13 +689,17 @@ function UpdateElecProperties(isUpdateModelList)
elseif strcmpi(sSelElec(1).Type, 'ECOG-mid')
ctrl.jRadioEcogMid.setSelected(1);
elecType = 'ECOG-mid';
elseif strcmpi(sSelElec(1).Type, 'Grouped SEEG')
ctrl.jRadioGroupedSeeg.setSelected(1);
elecType = 'Grouped SEEG';
else
elecType = [];
end
else
ctrl.jRadioSeeg.setSelected(0);
ctrl.jRadioEcog.setSelected(0);
ctrl.jRadioEcogMid.setSelected(0);
ctrl.jRadioGroupedSeeg.setSelected(0);
elecType = [];
end
% Update list of models
Expand All @@ -695,7 +715,8 @@ function UpdateElecProperties(isUpdateModelList)
end

% Update control labels
if ~isempty(sSelElec) && strcmpi(sSelElec(1).Type, 'SEEG')
isSeegType = ~isempty(sSelElec) && (strcmpi(sSelElec(1).Type, 'SEEG') || strcmpi(sSelElec(1).Type, 'Grouped SEEG'));
if isSeegType
ctrl.jLabelContactLength.setText('Contact length: ');
ctrl.jLabelElecLength.setVisible(1);
ctrl.jTextElecLength.setVisible(1);
Expand All @@ -710,6 +731,11 @@ function UpdateElecProperties(isUpdateModelList)
ctrl.jLabelElecDiameter.setText('Wire width: ');
ctrl.jLabelElecDiamUnits.setText(' points');
end
% Show Intergroup Spacing only for Grouped SEEG
isGroupedSeeg = ~isempty(sSelElec) && strcmpi(sSelElec(1).Type, 'Grouped SEEG');
ctrl.jLabelIntergroupSpacing.setVisible(isGroupedSeeg);
ctrl.jTextIntergroupSpacing.setVisible(isGroupedSeeg);
ctrl.jLabelIntergroupSpacingUnits.setVisible(isGroupedSeeg);
% Number of contacts
if (length(sSelElec) == 1) || ((length(sSelElec) > 1) && all(cellfun(@(c)isequal(c,sSelElec(1).ContactNumber), {sSelElec.ContactNumber})))
valContacts = sSelElec(1).ContactNumber;
Expand All @@ -722,6 +748,12 @@ function UpdateElecProperties(isUpdateModelList)
else
valSpacing = [];
end
% Intergroup spacing
if isfield(sSelElec, 'IntergroupSpacing') && ((length(sSelElec) == 1) || ((length(sSelElec) > 1) && all(cellfun(@(c)isequal(c,sSelElec(1).IntergroupSpacing), {sSelElec.IntergroupSpacing}))))
valIntergroupSpacing = sSelElec(1).IntergroupSpacing * 1000;
else
valIntergroupSpacing = [];
end
% Contact length
if (length(sSelElec) == 1) || ((length(sSelElec) > 1) && all(cellfun(@(c)isequal(c,sSelElec(1).ContactLength), {sSelElec.ContactLength})))
valContactLength = sSelElec(1).ContactLength * 1000;
Expand All @@ -748,7 +780,8 @@ function UpdateElecProperties(isUpdateModelList)
end
% Update panel
gui_validate_text(ctrl.jTextNcontacts, [], [], {0,1024,1}, 'list', 0, valContacts, @(h,ev)ValidateOptions('ContactNumber', ctrl.jTextNcontacts));
gui_validate_text(ctrl.jTextSpacing, [], [], {0,100,100}, 'optional', 2, valSpacing, @(h,ev)ValidateOptions('ContactSpacing', ctrl.jTextSpacing));
gui_validate_text(ctrl.jTextSpacing, [], [], {0,100,100}, 'optional', 2, valSpacing, @(h,ev)ValidateOptions('ContactSpacing', ctrl.jTextSpacing));
gui_validate_text(ctrl.jTextIntergroupSpacing, [], [], {0,100,100}, 'optional', 2, valIntergroupSpacing, @(h,ev)ValidateOptions('IntergroupSpacing', ctrl.jTextIntergroupSpacing));
gui_validate_text(ctrl.jTextContactLength, [], [], {0,30,100}, 'optional', 2, valContactLength, @(h,ev)ValidateOptions('ContactLength', ctrl.jTextContactLength));
gui_validate_text(ctrl.jTextContactDiam, [], [], {0,20,100}, 'optional', 2, valContactDiam, @(h,ev)ValidateOptions('ContactDiameter', ctrl.jTextContactDiam));
gui_validate_text(ctrl.jTextElecDiameter, [], [], {0,20,100}, 'optional', 2, valElecDiameter, @(h,ev)ValidateOptions('ElecDiameter', ctrl.jTextElecDiameter));
Expand All @@ -758,7 +791,7 @@ function UpdateElecProperties(isUpdateModelList)
colorOn = java.awt.Color(0, 0.8, 0);
colorOff = java.awt.Color(0, 0, 0);
colorNone= java.awt.Color(.4, .4, .4);
if strcmpi(sSelElec(1).Type, 'SEEG')
if strcmpi(sSelElec(1).Type, 'SEEG') || strcmpi(sSelElec(1).Type, 'Grouped SEEG')
ctrl.jCardLayout.show(ctrl.jPanelButtons, 'seeg');
if (size(sSelElec.Loc,2) >= 1)
ctrl.jButtonSeegSet1.setForeground(colorOn);
Expand Down Expand Up @@ -1117,7 +1150,7 @@ function EditElectrodeLabel(varargin)
java_dialog('warning', ['Electrode "' newLabel '" already exists.'], 'Rename selected electrode');
return;
% Check that name do not include a digit
elseif any(ismember(newLabel, '0123456789:;*=?!<>"`&%$()[]{}/\_@ ���������������������������������������������؜����������'))
elseif any(ismember(newLabel, '0123456789:;*=?!<>"`&%$()[]{}/\_@ ���������������������������������������������؜����������'))
java_dialog('warning', 'New electrode name should not include digits, spaces or special characters.', 'Rename selected electrode');
return;
end
Expand Down Expand Up @@ -1219,11 +1252,23 @@ function ValidateOptions(optName, jControl)
elseif strcmpi(optName, 'ContactNumber')
val = round(str2num(jControl.getText()));
% SEEG electrode can have only one dimension, others two dimensions max
if (length(val) >= 2) && strcmpi(sElectrodes(iSelElec).Type, 'SEEG')
if (length(val) >= 2) && (strcmpi(sElectrodes(iSelElec).Type, 'SEEG') || strcmpi(sElectrodes(iSelElec).Type, 'Grouped SEEG'))
val = val(1);
jControl.setText(sprintf('%d', val));
elseif (length(val) >= 3)
val = val(1:2);
end

if strcmpi(sElectrodes(iSelElec).Type, 'Grouped SEEG') && mod(val,3)~=0
bst_error('Invalid value: For grouped SEEG electrode, number of contacts must be evenly divisible by 3.', ...
'Edit Field', 0);
jControl.setText('');
return
else
jControl.setText(sprintf('%d ', val));
end

if (length(val) >= 3)
val = val(1:2);
jControl.setText(sprintf('%d ', val));
end
else
Expand All @@ -1250,7 +1295,7 @@ function ValidateOptions(optName, jControl)
end
% Update the channels types
switch (val)
case 'SEEG'
case {'SEEG', 'Grouped SEEG'}
[GlobalData.DataSet(iDS).Channel(iChan).Type] = deal('SEEG');
case {'ECOG', 'ECOG-mid'}
[GlobalData.DataSet(iDS).Channel(iChan).Type] = deal('ECOG');
Expand Down Expand Up @@ -1457,7 +1502,7 @@ function AddElectrode(newLabel)
java_dialog('warning', ['Electrode "' newLabel '" already exists.'], 'New electrode');
return;
% Check if labels include invalid characters
elseif any(ismember(newLabel, '0123456789:;*=?!<>"`&%$()[]{}/\_@ ���������������������������������������������؜����������'))
elseif any(ismember(newLabel, '0123456789:;*=?!<>"`&%$()[]{}/\_@ ���������������������������������������������؜����������'))
java_dialog('warning', 'New electrode name should not include digits, spaces or special characters.', 'New electrode');
return;
end
Expand Down Expand Up @@ -1904,6 +1949,26 @@ function MergeElectrodes()
sMod(6).ContactNumber = 18;
sModels = [sModels, sMod];

sTemplate = db_template('intraelectrode');
sTemplate.Type = 'Grouped SEEG';
sTemplate.ContactSpacing = 0.0035;
sTemplate.ContactDiameter = 0.0008;
sTemplate.ContactLength = 0.002;
sTemplate.ElecDiameter = 0.0007;
sTemplate.ElecLength = 0.100;
% All models
sMod = repmat(sTemplate, 1, 3);
sMod(1).Model = 'DIXI D08-15BM Microdeep';
sMod(1).ContactNumber = 15;
sMod(1).IntergroupSpacing = 0.007;
sMod(2).Model = 'DIXI D08-15CM Microdeep';
sMod(2).ContactNumber = 15;
sMod(2).IntergroupSpacing = 0.011;
sMod(3).Model = 'DIXI D08-18CM Microdeep';
sMod(3).ContactNumber = 18;
sMod(3).IntergroupSpacing = 0.011;
sModels = [sModels, sMod];

% === AD TECH RD10R ===
% Common values
sTemplate = db_template('intraelectrode');
Expand Down Expand Up @@ -2096,6 +2161,35 @@ function AddElectrodeModel(sNewModel)
sNew.ContactDiameter = str2num(res{5}) ./ 1000;
sNew.ElecDiameter = str2num(res{6}) ./ 1000;
sNew.ElecLength = 0;

% === Grouped SEEG ===
elseif ctrl.jRadioGroupedSeeg.isSelected()
% Ask for all the electrode options
res = java_dialog('input', {...
'Manufacturer and model (SEEG):', ...
'Number of contacts:', ...
'Contact spacing (mm):', ...
'Contact length (mm):', ...
'Contact diameter (mm):', ...
'Electrode diameter (mm):', ...
'Electrode length (mm):', ...
'Intergroup spacing (mm):'}, 'Add new model', [], ...
{'', '', '3.5', '2', '0.8', '0.7', '70', ''});
if isempty(res) || isempty(res{1})
return;
end
% Get all the values
sNew = db_template('intraelectrode');
sNew.Model = res{1};
sNew.Type = 'Grouped SEEG';
sNew.ContactNumber = str2num(res{2});
sNew.ContactSpacing = str2num(res{3}) ./ 1000;
sNew.ContactLength = str2num(res{4}) ./ 1000;
sNew.ContactDiameter = str2num(res{5}) ./ 1000;
sNew.ElecDiameter = str2num(res{6}) ./ 1000;
sNew.ElecLength = str2num(res{7}) ./ 1000;
sNew.IntergroupSpacing = str2num(res{8}) ./ 1000;

% === SEEG ===
else
% Ask for all the electrode options
Expand Down Expand Up @@ -2131,6 +2225,10 @@ function AddElectrodeModel(sNewModel)
if any(strcmpi({sModels.Model}, sNew.Model))
bst_error(['Electrode model "' sNew.Model '" is already defined.'], 'Add new model', 0);
return;
elseif strcmp(sNew.Type, 'Grouped SEEG') && mod(sNew.ContactNumber, 3)~=0
bst_error('Invalid value: For grouped SEEG electrode, number of contacts must be evenly divisible by 3.', ...
'Add new model', 0);
return;
% Check that all the values are set
elseif isempty(sNew.ContactNumber) || isempty(sNew.ContactSpacing) || isempty(sNew.ContactDiameter) || isempty(sNew.ContactLength) || isempty(sNew.ElecDiameter) || isempty(sNew.ElecLength)
bst_error('Invalid values.', 'Add new model', 0);
Expand Down Expand Up @@ -2161,7 +2259,7 @@ function RemoveElectrodeModel()
sModelsDefault = GetElectrodeModels('default');
if ismember(sModels(iModel).Model, {sModelsDefault.Model})
java_dialog('warning', [...
'This a Brainstorm default electrode model and cannot deleted.' 10], ...
'This a Brainstorm default electrode model and cannot be deleted.' 10], ...
'Read-only: Default electrode model ');
return
end
Expand Down Expand Up @@ -2747,7 +2845,7 @@ function SeegAutoContactLocalize(Method)
FaceLighting = 'gouraud';

% === SEEG ===
elseif strcmpi(sElec.Type, 'SEEG')
elseif strcmpi(sElec.Type, 'SEEG') || strcmpi(sElec.Type, 'Grouped SEEG')
% If no location available: cannot display
if (size(sElec.Loc,2) < 2)
continue;
Expand Down Expand Up @@ -3123,7 +3221,7 @@ function SeegAutoContactLocalize(Method)
if isImplantation
sChannel = db_template('channeldesc');
switch (sElectrodes(iElec).Type)
case 'SEEG'
case {'SEEG', 'Grouped SEEG'}
sChannel.Type = 'SEEG';
case {'ECOG','ECOG-mid'}
sChannel.Type = 'ECOG';
Expand Down Expand Up @@ -3175,12 +3273,23 @@ function SeegAutoContactLocalize(Method)
linePlot.X = [];
linePlot.Y = [];
linePlot.Z = [];
groupsize = length(iChan)/3;
% Process each contact
for i = 1:length(iChan)
switch (Method)
case 'default'
% Compute the default position of the contact
Channels(iChan(i)).Loc = elecTip + (AllInd(i) - 1) * sElectrodes(iElec).ContactSpacing * orient;
if strcmpi(sElectrodes(iElec).Type, 'Grouped SEEG')
% you need to shave off 1 unit of intragroup spacing for every intergroup gap;
% "ContactSpacing" variable actually includes the contact length so isn't just spacing
intragroup_spacing = sElectrodes(iElec).ContactSpacing - sElectrodes(iElec).ContactLength;
extra_spacing = (sElectrodes(iElec).IntergroupSpacing - intragroup_spacing) ...
* floor((i-1)/groupsize) * orient;
else
extra_spacing = 0;
end
% Compute the default position of the contact
Channels(iChan(i)).Loc = elecTip + extra_spacing + ...
(AllInd(i) - 1) * sElectrodes(iElec).ContactSpacing * orient;
case 'project'
% Project the existing contact on the depth electrode
Channels(iChan(i)).Loc = elecTip + sum(orient .* (Channels(iChan(i)).Loc - elecTip)) .* orient;
Expand Down Expand Up @@ -3481,7 +3590,7 @@ function SetElectrodeLoc(iLoc, jButton)
isImplantation = isImplantationFolder(iDS);
% Update contact positions
% if (~isempty(iChan) || isImplantation) && ...
if ((strcmpi(sSelElec.Type, 'SEEG') && (size(sSelElec.Loc,2) >= 2)) || ...
if (((strcmpi(sSelElec.Type, 'SEEG') || strcmpi(sSelElec.Type, 'Grouped SEEG')) && (size(sSelElec.Loc,2) >= 2)) || ...
(ismember(sSelElec.Type, {'ECOG','ECOG-mid'}) && (length(sSelElec.ContactNumber) == 1) && (size(sSelElec.Loc,2) >= 2)) || ...
(ismember(sSelElec.Type, {'ECOG','ECOG-mid'}) && (size(sSelElec.Loc,2) >= 4)))
% Warnings and checks
Expand Down