Automatic EEG localization and labelling using Revopoint 3D

external/piotr_toolbox/LICENCE.txt

@@ -0,0 +1,26 @@
+Copyright (c) 2012, Piotr Dollar
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met: 
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer. 
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution. 
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation are those
+of the authors and should not be interpreted as representing official policies, 
+either expressed or implied, of the FreeBSD Project.

external/piotr_toolbox/tpsGetWarp.m

@@ -0,0 +1,77 @@
+function [warp,L,LnInv,bendE] = tpsGetWarp( lambda, xsS, ysS, xsD, ysD )
+% Given two sets of corresponding points, calculates warp between them.
+%
+% Uses booksteins PAMI89 method.  Can then apply warp to a new set of
+% points (tpsInterpolate), or even an image (tpsInterpolateIm).
+%  "Principal Warps: Thin-Plate Splines and the Decomposition of
+%  Deformations".  Bookstein.  PAMI 1989.
+%
+% USAGE
+%  [warp,L,LnInv,bendE] = tpsGetWarp( lambda, xsS, ysS, xsD, ysD )
+%
+% INPUTS
+%  lambda      - rigidity of warp (inf means warp becomes affine)
+%  xsS, ysS    - [1xn] correspondence points from source image
+%  xsD, ysD    - [1xn] correspondence points from destination image
+%
+% OUTPUTS
+%  warp        - bookstein warping parameters
+%  L, LnInv    - see bookstein
+%  bendE       - bending energy
+%
+% EXAMPLE - 1
+%  xsS=[0 -1 0 1];  ysS=[1 0 -1 0];  xsD=xsS;  ysD=[3/4 1/4 -5/4 1/4];
+%  warp = tpsGetWarp( 0, xsS, ysS, xsD, ysD );
+%  [gxs, gys] = meshgrid(-1.25:.25:1.25,-1.25:.25:1.25);
+%  tpsInterpolate( warp, gxs, gys, 1 );
+%
+% EXAMPLE - 2
+%  xsS = [3.6929 6.5827 6.7756 4.8189 5.6969];
+%  ysS = [10.3819 8.8386 12.0866 11.2047 10.0748];
+%  xsD = [3.9724 6.6969 6.5394 5.4016 5.7756];
+%  ysD = [6.5354 4.1181 7.2362 6.4528 5.1142];
+%  warp = tpsGetWarp( 0, xsS, ysS, xsD, ysD );
+%  [gxs, gys] = meshgrid(3.5:.25:7, 8.5:.25: 12.5);
+%  tpsInterpolate( warp, gxs, gys, 1 );
+%
+% See also TPSINTERPOLATE, TPSINTERPOLATEIM, TPSRANDOM
+%
+% Piotr's Computer Vision Matlab Toolbox      Version 2.0
+% Copyright 2014 Piotr Dollar.  [pdollar-at-gmail.com]
+% Licensed under the Simplified BSD License [see https://github.com/pdollar/toolbox/blob/master/external/bsd.txt]
+
+dim = size( xsS );
+if( all(size(xsS)~=dim) || all(size(ysS)~=dim) || all(size(xsD)~=dim))
+  error( 'argument sizes do not match' );
+end
+
+% get L
+n = size(xsS,2);
+deltaXs = xsS'*ones(1,n) - ones(n,1) * xsS;
+deltaYs = ysS'*ones(1,n) - ones(n,1) * ysS;
+Rsq = (deltaXs .* deltaXs + deltaYs .* deltaYs);
+Rsq = Rsq+eye(n); K = Rsq .* log( Rsq ); K( isnan(K) )=0;
+K = K + lambda * eye( n );
+P = [ ones(n,1), xsS', ysS' ];
+L = [ K, P; P', zeros(3,3) ];
+LInv = L^(-1);
+LnInv = LInv(1:n,1:n);
+
+% recover W's
+wx = LInv * [xsD 0 0 0]';
+affinex = wx(n+1:n+3);
+wx = wx(1:n);
+wy = LInv * [ysD 0 0 0]';
+affiney = wy(n+1:n+3);
+wy = wy(1:n);
+
+% record warp
+warp.wx = wx; warp.affinex = affinex;
+warp.wy = wy; warp.affiney = affiney;
+warp.xsS = xsS; warp.ysS = ysS;
+warp.xsD = xsD; warp.ysD = ysD;
+
+% get bending energy (without regularization)
+w = [wx'; wy'];
+K = K - lambda * eye( n );
+bendE = trace(w*K*w')/2;

external/piotr_toolbox/tpsInterpolate.m

@@ -0,0 +1,52 @@
+function [xsR,ysR] = tpsInterpolate( warp, xs, ys, show )
+% Apply warp (obtained by tpsGetWarp) to a set of new points.
+%
+% USAGE
+%  [xsR,ysR] = tpsInterpolate( warp, xs, ys, [show] )
+%
+% INPUTS
+%  warp     - [see tpsGetWarp] bookstein warping parameters
+%  xs, ys   - points to apply warp to
+%  show     - [1] will display results in figure(show)
+%
+% OUTPUTS
+%  xsR, ysR - result of warp applied to xs, ys
+%
+% EXAMPLE
+%
+% See also TPSGETWARP
+%
+% Piotr's Computer Vision Matlab Toolbox      Version 2.0
+% Copyright 2014 Piotr Dollar.  [pdollar-at-gmail.com]
+% Licensed under the Simplified BSD License [see https://github.com/pdollar/toolbox/blob/master/external/bsd.txt]
+
+if( nargin<4 || isempty(show)); show = 1; end
+
+wx = warp.wx; affinex = warp.affinex;
+wy = warp.wy; affiney = warp.affiney;
+xsS = warp.xsS; ysS = warp.ysS;
+xsD = warp.xsD; ysD = warp.ysD;
+
+% interpolate points (xs,ys)
+xsR = f( wx, affinex, xsS, ysS, xs(:)', ys(:)' );
+ysR = f( wy, affiney, xsS, ysS, xs(:)', ys(:)' );
+
+% optionally show points (xsR, ysR)
+if( show )
+  figure(show);
+  subplot(2,1,1); plot( xs, ys, '.', 'color', [0 0 1] );
+  hold('on');  plot( xsS, ysS, '+' );  hold('off');
+  subplot(2,1,2); plot( xsR, ysR, '.' );
+  hold('on');  plot( xsD, ysD, '+' );  hold('off');
+end
+
+function zs = f( w, aff, xsS, ysS, xs, ys )
+% find f(x,y) for xs and ys given W and original points
+n = size(w,1);   ns = size(xs,2);
+delXs = xs'*ones(1,n) - ones(ns,1)*xsS;
+delYs = ys'*ones(1,n) - ones(ns,1)*ysS;
+distSq = (delXs .* delXs + delYs .* delYs);
+distSq = distSq + eye(size(distSq)) + eps;
+U = distSq .* log( distSq ); U( isnan(U) )=0;
+zs = aff(1)*ones(ns,1)+aff(2)*xs'+aff(3)*ys';
+zs = zs + sum((U.*(ones(ns,1)*w')),2);

toolbox/anatomy/tess_deface.m

@@ -0,0 +1,64 @@
+function [head_surface] = tess_deface(head_surface)
+% TESS_DEFACE: Removing non-essential vertices (bottom half of the subject's face in mesh) to deface the 3D mesh
+%
+% USAGE:  [head_surface] = tess_deface(head_surface);
+%
+% INPUT:
+%     - head_surface:  Brainstorm tesselation structure with fields:
+%         |- Vertices : {[nVertices x 3] double}, in millimeters
+%         |- Faces    : {[nFaces x 3] double}
+%         |- Color    : {[nColors x 3] double}, normalized between 0-1 (optional)
+%
+% OUTPUT:
+%     - head_surface:  Brainstorm tesselation structure with fields:
+%         |- Vertices : {[nVertices x 3] double}, in millimeters
+%         |- Faces    : {[nFaces x 3] double}
+%         |- Color    : {[nColors x 3] double}, normalized between 0-1 (optional)
+%
+% @=============================================================================
+% 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: Yash Shashank Vakilna, 2024
+%          Chinmay Chinara, 2024
+
+% Identify vertices to remove from the surface mesh
+% Spherical coordinates
+[TH,PHI,R] = cart2sph(head_surface.Vertices(:,1), head_surface.Vertices(:,2), head_surface.Vertices(:,3));
+% Flat projection
+R = 1 - PHI ./ pi*2;
+t = (R > 1.1);
+
+% Remove the identified vertices from the surface mesh
+remove = (1:length(t));
+remove = remove(t);
+if ~isempty(remove)
+    [head_surface.Vertices, head_surface.Faces] = tess_remove_vert(head_surface.Vertices, head_surface.Faces, remove);
+    if isfield(head_surface, 'Color')
+        head_surface.Color(remove, :) = [];
+    end
+end
+
+head_surface.VertConn = tess_vertconn(head_surface.Vertices, head_surface.Faces);
+head_surface.VertNormals = tess_normals(head_surface.Vertices, head_surface.Faces, head_surface.VertConn);
+head_surface.Curvature = tess_curvature(head_surface.Vertices, head_surface.VertConn, head_surface.VertNormals, .1);
+[~, head_surface.VertArea] = tess_area(head_surface.Vertices, head_surface.Faces);
+head_surface.SulciMap = tess_sulcimap(head_surface);
+head_surface.Comment = [head_surface.Comment '_defaced'];
+head_surface = bst_history('add', head_surface, 'deface_mesh', 'mesh defaced');
+
+end

toolbox/anatomy/tess_downsize.m

@@ -84,21 +84,27 @@
 
 % Ask for resampling method
 if isempty(Method)
+    % Downsize methods strings
+    methods_str = {['<HTML><B><U>Matlab''s reducepatch:</U></B><BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - Inhomogeneous mesh: large faces at the top of the gyri<BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - Keeps the atlases and the subjects co-registration'], ...
+                   ['<HTML><B>Matlab''s reducepatch + subdivide large faces:</B><BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - The large faces at the top of the gyri are subdivided in three<BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - <U>Deletes</U> the atlases and the subjects co-registration'], ...
+                   ['<HTML><B>iso2mesh/CGAL library:</B><BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - Homogeneous mesh: all the faces have similar sizes<BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - <U>Deletes</U> the atlases and the subject co-registration<BR>' ...
+                    '&nbsp;&nbsp;&nbsp;| - If the downsample looks dark, right-click > Swap faces']};
+        %          ['<HTML><B>iso2mesh/CGAL + project on the original surface:</B><BR>' ...
+        %           '&nbsp;&nbsp;&nbsp;| - Homogeneous mesh but possible <U>topological problems</U><BR>' ...
+        %           '&nbsp;&nbsp;&nbsp;| - <U>Damages</U> the atlases and the subject co-registration']},
+
+    % Show only 'Matlab's reducepatch' method for tess_textured surfaces
+    if ~isempty(regexp(TessFile, 'tess_textured', 'match'))
+        methods_str = methods_str(1); % Inhomogeneous mesh
+    end
     % Ask method
-    ind = java_dialog('radio', 'Select the resampling method:', 'Resample surface', [], ...
-                      {['<HTML><B><U>Matlab''s reducepatch:</U></B><BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - Inhomogeneous mesh: large faces at the top of the gyri<BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - Keeps the atlases and the subjects co-registration'], ...
-                       ['<HTML><B>Matlab''s reducepatch + subdivide large faces:</B><BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - The large faces at the top of the gyri are subdivided in three<BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - <U>Deletes</U> the atlases and the subjects co-registration'], ...
-                       ['<HTML><B>iso2mesh/CGAL library:</B><BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - Homogeneous mesh: all the faces have similar sizes<BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - <U>Deletes</U> the atlases and the subject co-registration<BR>' ...
-                        '&nbsp;&nbsp;&nbsp;| - If the downsample looks dark, right-click > Swap faces']}, 1);
-%                        ['<HTML><B>iso2mesh/CGAL + project on the original surface:</B><BR>' ...
-%                         '&nbsp;&nbsp;&nbsp;| - Homogeneous mesh but possible <U>topological problems</U><BR>' ...
-%                         '&nbsp;&nbsp;&nbsp;| - <U>Damages</U> the atlases and the subject co-registration']}, 1);
+    ind = java_dialog('radio', 'Select the resampling method:', 'Resample surface', [], methods_str, 1);
     if isempty(ind)
         return
     end
@@ -128,6 +134,7 @@
 % Prepare variables
 TessMat.Faces    = double(TessMat.Faces);
 TessMat.Vertices = double(TessMat.Vertices);
+TessMat.Color    = double(TessMat.Color);
 dsFactor = newNbVertices / size(TessMat.Vertices, 1); 
 
 
@@ -145,6 +152,9 @@
         % Re-order the vertices so that they are in the same order in the output surface
         [I, iSort] = sort(I);
         NewTessMat.Vertices = TessMat.Vertices(I,:);
+        if ~isempty(TessMat.Color)
+            NewTessMat.Color = TessMat.Color(I,:);
+        end
         J = J(iSort);
         % Re-order the vertices in the faces
         iSortFaces(J) = 1:length(J);

toolbox/core/bst_get.m

@@ -3474,9 +3474,11 @@
             'isSimulate',   0, ...
             'Montages',     [...
                 struct('Name',   'No EEG', ...
-                       'Labels', []), ...
+                       'Labels', [], ...
+                       'ChannelFile', []), ...
                 struct('Name',   'Default', ...
-                       'Labels', [])], ...
+                       'Labels', [], ...
+                       'ChannelFile', [])], ...
             'iMontage',     1, ...
             'Version',      '2024'); % Version of the Digitize panel: 'legacy' or '2024'
         argout1 = FillMissingFields(contextName, defPref);
@@ -3633,6 +3635,7 @@
                     {'.gii'},   'GIfTI / World coordinates (*.gii)', 'GII-WORLD'; ...
                     {'.fif'},   'MNE (*.fif)',             'FIF'; ...
                     {'.obj'},   'MNI OBJ (*.obj)',         'MNIOBJ'; ...
+                    {'.obj'},   'Wavefront OBJ (*.obj)',   'WFTOBJ'; ...
                     {'.msh'},   'SimNIBS3/headreco Gmsh4 (*.msh)', 'SIMNIBS3'; ...
                     {'.msh'},   'SimNIBS4/charm Gmsh4 (*.msh)', 'SIMNIBS4'; ...
                     {'.tri'},   'TRI (*.tri)',             'TRI'; ...

toolbox/core/bst_memory.m

@@ -304,6 +304,7 @@
         sSurf.Comment         = surfMat.Comment;
         sSurf.Faces           = double(surfMat.Faces);
         sSurf.Vertices        = double(surfMat.Vertices);
+        sSurf.Color           = double(surfMat.Color);
         sSurf.VertConn        = surfMat.VertConn;
         sSurf.VertNormals     = surfMat.VertNormals;
         [tmp, sSurf.VertArea] = tess_area(surfMat.Vertices, surfMat.Faces);

toolbox/db/db_template.m

@@ -102,6 +102,7 @@
             'Comment',         '', ...
             'Vertices',        [], ...
             'Faces',           [], ...
+            'Color',           [], ...
             'VertConn',        [], ...
             'VertNormals',     [], ...
             'Curvature',       [], ...
@@ -673,6 +674,7 @@
             'Comment',         '', ...
             'Vertices',        [], ...
             'Faces',           [], ...
+            'Color',           [], ...
             'VertConn',        [], ...
             'VertNormals',     [], ...
             'VertArea',        [], ...

toolbox/gui/figure_3d.m

@@ -973,7 +973,7 @@ function FigureMouseWheelCallback(hFig, event, target)
 
 %% ===== KEYBOARD CALLBACK =====
 function FigureKeyPressedCallback(hFig, keyEvent)   
-    global GlobalData TimeSliderMutex;
+    global GlobalData TimeSliderMutex Digitize;
     % Prevent multiple executions
     hAxes = findobj(hFig, '-depth', 1, 'Tag', 'Axes3D');
     set([hFig hAxes], 'BusyAction', 'cancel');
@@ -1094,7 +1094,19 @@ function FigureKeyPressedCallback(hFig, keyEvent)
                 case 'a'
                     if ismember('control', keyEvent.Modifier)
                     	ViewAxis(hFig);
-                    end 
+                    end
+                % C : Collect point
+                case 'c'
+                    % for 3DScanner
+                    if gui_brainstorm('isTabVisible', 'Digitize') && strcmpi(Digitize.Type, '3DScanner')
+                        % Get Digitize options
+                        DigitizeOptions = bst_get('DigitizeOptions');
+                        panel_fun = @panel_digitize;
+                        if isfield(DigitizeOptions, 'Version') && strcmpi(DigitizeOptions.Version, '2024')
+                            panel_fun = @panel_digitize_2024;
+                        end
+                        panel_fun('ManualCollect_Callback');
+                    end
                 % CTRL+D : Dock figure
                 case 'd'
                     if ismember('control', keyEvent.Modifier)
@@ -2808,12 +2820,17 @@ function UpdateSurfaceColor(hFig, iTess)
             SulciMap = zeros(TessInfo(iTess).nVertices, 1);
         end
         % Compute RGB values
-        FaceVertexCdata = BlendAnatomyData(SulciMap, ...                                  % Anatomy: Sulci map
-                                           TessInfo(iTess).AnatomyColor([1,end], :), ...  % Anatomy: color
-                                           DataSurf, ...                                  % Data: values map
-                                           TessInfo(iTess).DataLimitValue, ...            % Data: limit value
-                                           TessInfo(iTess).DataAlpha,...                  % Data: transparency
-                                           sColormap);                                    % Colormap
+        if ~isempty(regexp(TessInfo(iTess).SurfaceFile, 'tess_textured', 'match'))
+            FaceVertexCdata = TessInfo(iTess).AnatomyColor(TessInfo(iTess).nVertices+1:end, :);
+        else
+            FaceVertexCdata = BlendAnatomyData(SulciMap, ...                                  % Anatomy: Sulci map
+                                               TessInfo(iTess).AnatomyColor([1,end], :), ...  % Anatomy: color
+                                               DataSurf, ...                                  % Data: values map
+                                               TessInfo(iTess).DataLimitValue, ...            % Data: limit value
+                                               TessInfo(iTess).DataAlpha,...                  % Data: transparency
+                                               sColormap);                                    % Colormap
+        end
+
         % Edge display : on/off
         if ~TessInfo(iTess).SurfShowEdges
             EdgeColor = 'none';

toolbox/gui/gui_brainstorm.m

@@ -147,7 +147,9 @@
             jMenuFile.addSeparator();
         end
         % === DIGITIZE ===  
-        gui_component('MenuItem', jMenuFile, [], 'Digitize', IconLoader.ICON_CHANNEL, [], @(h,ev)bst_call(@panel_digitize, 'Start'), fontSize);
+        jSubMenu = gui_component('Menu', jMenuFile, [], 'Digitize', IconLoader.ICON_CHANNEL,[],[], fontSize);
+            gui_component('MenuItem', jSubMenu, [], 'Digitizer',  IconLoader.ICON_CHANNEL,  [], @(h,ev)bst_call(@panel_digitize, 'Start'), fontSize);
+            gui_component('MenuItem', jSubMenu, [], '3D scanner', IconLoader.ICON_SNAPSHOT, [], @(h,ev)bst_call(@panel_digitize, 'Start', '3DScanner'), fontSize);
         gui_component('MenuItem', jMenuFile, [], 'Batch MRI fiducials', IconLoader.ICON_LOBE, [], @(h,ev)bst_call(@bst_batch_fiducials), fontSize);
         jMenuFile.addSeparator();
         % === QUIT ===