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Untitled.m

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+
+%% INFANT Anatomy
+load('C:\BRANELab\matlab_progs\general_progs\EEG_sim\SimSignals_GUI\anatomy\ANATOMY_DEFAULT_BRANELab_EEG_BioSemi_66ch_MRIvolume_1yr_infant.mat');
+
+a=fieldnames(anatomy);
+for k=1:length(a)
+    eval(sprintf('%s = anatomy.%s;',a{k},a{k}))
+end
+save('C:\BRANELab\matlab_progs\general_progs\EEG_sim\SimSignals_GUI\anatomy\ANATOMY_DEFAULT_BRANELab_MEEG_1yr_infant.mat','mri', 'vol', 'elec', 'please_read', 'pial_mesh', 'sens_adult_dewar', 'sens_infant_dewar', 'sens_adult_dewar_supine', 'mesh_hd', 'bnd', 'elec_good', 'chan_idx', 'vol_leadfield', 'mesh_sourcemodel', 'mesh_leadfield', 'leadfield', 'vol2', 'vx_locs', 'eeg_vol_leadfield', 'vol_infant_dewar', 'vol_adult_dewar', 'vol_adult_dewar_supine', 'meg_vol_leadfield', 'vol_eeg');
+
+% adult dewar sitting
+anatomy.sens_adult_dewar.coilori = anatomy.sens_adult_dewar.coilori(1:size(anatomy.sens_adult_dewar.label,1),:);
+anatomy.sens_adult_dewar.coilpos = anatomy.sens_adult_dewar.coilpos(1:size(anatomy.sens_adult_dewar.label,1),:);
+anatomy.sens_adult_dewar.tra     = anatomy.sens_adult_dewar.tra(1:size(anatomy.sens_adult_dewar.label,1),1:size(anatomy.sens_adult_dewar.label,1));
+% adult dewar supine
+anatomy.sens_adult_dewar_supine.coilori = anatomy.sens_adult_dewar_supine.coilori(1:size(anatomy.sens_adult_dewar_supine.label,1),:);
+anatomy.sens_adult_dewar_supine.coilpos = anatomy.sens_adult_dewar_supine.coilpos(1:size(anatomy.sens_adult_dewar_supine.label,1),:);
+anatomy.sens_adult_dewar_supine.tra     = anatomy.sens_adult_dewar_supine.tra(1:size(anatomy.sens_adult_dewar_supine.label,1),1:size(anatomy.sens_adult_dewar_supine.label,1));
+% infant dewar
+anatomy.sens_infant_dewar.coilori = anatomy.sens_infant_dewar.coilori(1:size(anatomy.sens_infant_dewar.label,1),:);
+anatomy.sens_infant_dewar.coilpos = anatomy.sens_infant_dewar.coilpos(1:size(anatomy.sens_infant_dewar.label,1),:);
+anatomy.sens_infant_dewar.tra     = anatomy.sens_infant_dewar.tra(1:size(anatomy.sens_infant_dewar.label,1),1:size(anatomy.sens_infant_dewar.label,1));
+
+
+%% ADULT Anatomy
+sens_adult = anatomy.sens_adult_dewar; % first load in infant anatomy above 
+anatomy2 = load('C:\BRANELab\matlab_progs\general_progs\EEG_sim\SimSignals_GUI\anatomy\ANATOMY_DEFAULT_Biosemi_72ch_Tujillo.mat');
+% % re-aligning sensors to adult dewar <-- but no need to do this because they were already aligned
+% cfg           = [];
+% cfg.method    = 'interactive';
+% cfg.elec    = sens_adult;
+% % cfg.channel      = sens_idx;
+% cfg.headshape = anatomy_adult.scalp.bnd(1);
+% sens_aligned  = ft_electroderealign(cfg,sens_adult);
+anatomy2.sens_adult=sens_adult;
+a=fieldnames(anatomy2);
+for k=1:length(a)
+    eval(sprintf('%s = anatomy2.%s;',a{k},a{k}))
+end
+save('C:\BRANELab\matlab_progs\general_progs\EEG_sim\SimSignals_GUI\anatomy\ANATOMY_DEFAULT_MEEG_adult_Tujillo.mat','mri', 'vol', 'elec', 'please_read', 'pial_mesh', 'sens_adult_dewar', 'sens_infant_dewar', 'sens_adult_dewar_supine', 'mesh_hd', 'bnd', 'elec_good', 'chan_idx', 'vol_leadfield', 'mesh_sourcemodel', 'mesh_leadfield', 'leadfield', 'vol2', 'vx_locs', 'eeg_vol_leadfield', 'vol_infant_dewar', 'vol_adult_dewar', 'vol_adult_dewar_supine', 'meg_vol_leadfield', 'vol_eeg');
+
+
+%% Plot anatomy
+figure(1); clf;
+
+% Infant adult dewar supine
+subplot(2,2,1); cla; 
+ft_plot_mesh(anatomy.vol.bnd(3),'facecolor',[1 .6 .4]*.75,'edgecolor',[1 .6 .4]*.85,'facealpha',.4,'edgealpha',.4);
+ft_plot_mesh(anatomy.pial_mesh,'facecolor',[1 1 1]*.8,'edgecolor','none','facealpha',1,'edgealpha',1);
+ft_plot_sens(anatomy.sens_adult_dewar_supine,'label','off', 'chantype','meg','edgecolor','k'); %,'label','off');
+ft_plot_sens(anatomy.elec,'label','off', 'chantype','eeg','facecolor','b','edgecolor','b'); %,'label','off');
+view(-90,0); c=camlight; lighting gouraud; material dull; axis tight; p_axis = [get(gca,'XLim') get(gca,'YLim')];
+
+% Infant adult dewar sitting
+subplot(2,2,2); cla; 
+ft_plot_mesh(anatomy.vol.bnd(3),'facecolor',[1 .6 .4]*.75,'edgecolor',[1 .6 .4]*.85,'facealpha',.4,'edgealpha',.4);
+ft_plot_mesh(anatomy.pial_mesh,'facecolor',[1 1 1]*.8,'edgecolor','none','facealpha',1,'edgealpha',1);
+ft_plot_sens(anatomy.sens_adult_dewar,'label','off', 'chantype','meg','edgecolor','k'); %,'label','off');
+ft_plot_sens(anatomy.elec,'label','off', 'chantype','eeg','facecolor','b','edgecolor','b'); %,'label','off');
+view(-90,0); c=camlight; lighting gouraud; material dull;  axis tight; %axis( p_axis )
+
+% Infant infant dewar
+subplot(2,2,3); cla; 
+ft_plot_mesh(anatomy.vol.bnd(3),'facecolor',[1 .6 .4]*.75,'edgecolor',[1 .6 .4]*.85,'facealpha',.4,'edgealpha',.4);
+ft_plot_mesh(anatomy.pial_mesh,'facecolor',[1 1 1]*.8,'edgecolor','none','facealpha',1,'edgealpha',1);
+ft_plot_sens(anatomy.sens_infant_dewar,'label','off', 'chantype','meg','edgecolor','k'); %,'label','off');
+ft_plot_sens(anatomy.elec,'label','off', 'chantype','eeg','facecolor','b','edgecolor','b'); %,'label','off');
+view(-90,0); c=camlight; lighting gouraud; material dull;  axis( p_axis )
+
+% Adult dewar
+subplot(2,2,4); cla; 
+ft_plot_mesh(anatomy2.scalp.bnd,'facecolor',[1 .6 .4]*.75,'edgecolor',[1 .6 .4]*.85,'facealpha',.4,'edgealpha',.4);
+ft_plot_mesh(anatomy2.pial_mesh,'facecolor',[1 1 1]*.8,'edgecolor','none','facealpha',1,'edgealpha',1);
+ft_plot_sens(anatomy2.sens_adult,'label','off', 'chantype','meg','edgecolor','k'); %,'label','off');
+ft_plot_sens(anatomy2.elec,'label','off', 'chantype','eeg','facecolor','b','edgecolor','b'); %,'label','off');
+view(-90,0); c=camlight; lighting gouraud; material dull;  axis tight
+

Untitled2.m

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+
+
+
+sens_data = h.sim_data.sens_noise_final;
+% sens_data = h.sim_data.sens_sig_data;
+leadfield = h.inv_soln(h.current_inv_soln).leadfield;
+
+vx_idx = h.sim_data.cfg.source.vx_idx; 
+source_ori = h.sim_data.cfg.source.vx_ori; 
+%% conversion factor needed for EEG because Field Trips lead fields appear to be different than in Brainstorm (openmeeg) --> Not sure why this is?
+% adjustment needed by user to get reasonable 150-200 fT for 35-40 nA dipoles in audiotry cortices like in Herdman et al., 2003 NeuroImage dataset
+lf_gain = str2num(h.edit_leadfield_gain.String);
+source_data = project_inverse_SimSignals(sens_data,leadfield,vx_idx,source_ori,lf_gain);
+
+figure(2); clf; plot(squeeze(nanmean(h.sim_data.sig_final,3)),'k','linewidth',2); hold on; plot(squeeze(nanmean(source_data(:,:,:),3)));
+

Untitled3.m

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+
+
+
+
+peak_tfr = h.current_inv_peak_fc_data;
+true_tfr = h.current_inv_true_fc_data;
+act_samps = h.inv_soln(h.current_inv_soln).params.act_samps;
+peak_tfr(abs(peak_tfr)>0)=10;   % values of 10 = significant index; 0 = not significant 
+true_tfr(abs(true_tfr)>0)=5;   % values of 5 = significant index; 0 = not significant 
+
+
+diff_tfr = peak_tfr-true_tfr; 
+hit_tfr = nan(size(diff_tfr)); hit_tfr(diff_tfr==5)=1;
+miss_tfr = nan(size(diff_tfr)); miss_tfr(diff_tfr== -5) = 1;
+fa_tfr = nan(size(diff_tfr)); fa_tfr(diff_tfr== 10) = 1;
+cr_tfr = nan(size(diff_tfr)); cr_tfr(diff_tfr== 0) = 1;
+
+
+num_peak_sig = squeeze(nansum(nansum(peak_tfr(:,:,act_samps),3),1));
+num_true_sig = squeeze(nansum(nansum(true_tfr(:,:,act_samps),3),1));
+
+

WinOnTop.m

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+function wasOnTop = WinOnTop( figureHandle, isOnTop )
+%WINONTOP allows to trigger figure's "Always On Top" state
+%
+%% INPUT ARGUMENTS:
+%
+% # figureHandle - Matlab's figure handle, scalar
+% # isOnTop      - logical scalar or empty array
+%
+%
+%% USAGE:
+%
+% * WinOnTop( hfigure, true );      - switch on  "always on top"
+% * WinOnTop( hfigure, false );     - switch off "always on top"
+% * WinOnTop( hfigure );            - equal to WinOnTop( hfigure,true);
+% * WinOnTop();                     - equal to WinOnTop( gcf, true);
+% * WasOnTop = WinOnTop(...);       - returns boolean value "if figure WAS on top"
+% * isOnTop = WinOnTop(hfigure,[])  - get "if figure is on top" property
+%
+% For Matlab windows, created via `hf=uifigure()` use `uifigureOnTop()`, see: 
+% https://www.mathworks.com/matlabcentral/fileexchange/73134-uifigureontop
+%
+%% LIMITATIONS:
+%
+% * java enabled
+% * figure must be visible
+% * figure's "WindowStyle" should be "normal"
+% * figureHandle should not be casted to double, if using HG2 (R2014b+)
+%
+%
+% Written by Igor
+% [email protected]
+%
+% 2013.06.16 - Initial version
+% 2013.06.27 - removed custom "ishandle_scalar" function call
+% 2015.04.17 - adapted for changes in matlab graphics system (since R2014b)
+% 2016.05.21 - another ishg2() checking mechanism 
+% 2016.09.24 - fixed IsOnTop vs isOnTop bug
+% 2019.10.27 - link for uifigureOnTop; connected to github; renamed to "demo_"
+% 
+% Copyright (c) 2016, Igor
+% All rights reserved.
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions are
+% met:
+% 
+%     * Redistributions of source code must retain the above copyright
+%       notice, this list of conditions and the following disclaimer.
+%     * 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.
+
+
+
+%% Parse Inputs
+
+if ~exist('figureHandle','var'); figureHandle = gcf; end
+
+assert(...
+          isscalar(  figureHandle ) &&...
+          ishandle(  figureHandle ) &&...
+          strcmp(get(figureHandle,'Type'),'figure'),...
+          ...
+          'WinOnTop:Bad_figureHandle_input',...
+          '%s','Provided figureHandle input is not a figure handle'...
+       );
+
+assert(...
+            strcmp('on',get(figureHandle,'Visible')),...
+            'WinOnTop:FigInisible',...
+            '%s','Figure Must be Visible'...
+       );
+
+assert(...
+            strcmp('normal',get(figureHandle,'WindowStyle')),...
+            'WinOnTop:FigWrongWindowStyle',...
+            '%s','WindowStyle Must be Normal'...
+       );
+
+if ~exist('isOnTop','var'); isOnTop=true; end
+
+assert(...
+          islogical( isOnTop ) && ...
+          isscalar(  isOnTop ) || ...
+          isempty(   isOnTop ),  ...
+          ...
+          'WinOnTop:Bad_isOnTop_input',...
+          '%s','Provided isOnTop input is neither boolean, nor empty'...
+      );
+
+
+%% Pre-checks
+
+error(javachk('swing',mfilename)) % Swing components must be available.
+
+
+%% Action
+
+% Flush the Event Queue of Graphic Objects and Update the Figure Window.
+drawnow expose
+
+warnStruct=warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
+jFrame = get(handle(figureHandle),'JavaFrame');
+warning(warnStruct.state,'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
+
+drawnow
+
+
+if ishg2(figureHandle)
+    jFrame_fHGxClient = jFrame.fHG2Client;
+else
+    jFrame_fHGxClient = jFrame.fHG1Client;
+end
+
+
+wasOnTop = jFrame_fHGxClient.getWindow.isAlwaysOnTop;
+
+if ~isempty(isOnTop)
+    jFrame_fHGxClient.getWindow.setAlwaysOnTop(isOnTop);
+end
+
+end
+
+
+function tf = ishg2(figureHandle)
+% There's a detailed discussion, how to check "if using HG2" here:
+% http://www.mathworks.com/matlabcentral/answers/136834-determine-if-using-hg2
+% however, it looks like there's no perfect solution.
+%
+% This approach, suggested by Cris Luengo:
+% http://www.mathworks.com/matlabcentral/answers/136834#answer_156739
+% should work OK, assuming user is NOT passing a figure handle, casted to
+% double, like this:
+%
+%   hf=figure();
+%   WinOnTop(double(hf));
+%
+
+tf = isa(figureHandle,'matlab.ui.Figure');
+
+end

toggle_light_OnOff_Callback.m

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+function toggle_light_OnOff_Callback(varargin)
+global h
+
+axes(h.axes_3D_images); 
+
+if h.toggle_light_OnOff.Value == 0    % off
+    % lighting off;
+    delete(findall(gca,'Type','light'));
+    h.toggle_light_OnOff.ForegroundColor = [1 0 0];  h.toggle_light_OnOff.BackgroundColor = [1 1 1]*.9;
+    h.toggle_light_OnOff.String = 'Light Off';
+
+elseif h.toggle_light_OnOff.Value == 1
+      delete(findall(gca,'Type','light'))
+%     if ~isvalid(h.camlight)
+        h.camlight1 = camlight;
+        h.camlight2 = camlight; % double camlight to make it brighter
+        lighting gouraud; material dull;
+%     end
+    h.toggle_light_OnOff.ForegroundColor = [0 .6 0];  h.toggle_light_OnOff.BackgroundColor = [1 1 1];
+    h.toggle_light_OnOff.String = 'Light On';
+end

toggle_light_OnOff_axes_anatomy.m

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+function toggle_light_OnOff_axes_anatomy(varargin)
+global h
+
+axes(h.axes_anatomy); 
+
+if h.toggle_light_OnOff_anat.Value == 0    % off
+    % lighting off;
+    delete(findall(gca,'Type','light'));
+    h.toggle_light_OnOff_anat.ForegroundColor = [1 0 0];  h.toggle_light_OnOff_anat.BackgroundColor = [1 1 1]*.9;
+    h.toggle_light_OnOff_anat.String = 'Light Off';
+
+elseif h.toggle_light_OnOff_anat.Value == 1
+      delete(findall(gca,'Type','light'))
+%     if ~isvalid(h.camlight)
+        h.camlight1 = camlight;
+        h.camlight2 = camlight; % double camlight to make it brighter
+        lighting gouraud; material dull;
+%     end
+    h.toggle_light_OnOff_anat.ForegroundColor = [0 .6 0];  h.toggle_light_OnOff_anat.BackgroundColor = [1 1 1];
+    h.toggle_light_OnOff_anat.String = 'Light On';
+end

toggle_peak_locs.m

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+function toggle_peak_locs(varargin)
+global h
+
+h.map3D_peak_ori = handle(h.map3D_peak_ori);
+if h.radio_3D_peak_locs.Value == 1
+    h.map3D_peak_locs(1).Visible = 'on'; %h.map3D_peak_locs(2).Visible = 'on';
+    h.map3D_peak_locs(2).Visible = 'on'; %h.map3D_peak_locs(2).Visible = 'on';
+    for v=1:length(h.map3D_peak_ori); h.map3D_peak_ori(v).Visible='on'; end
+elseif h.radio_3D_peak_locs.Value == 0
+    h.map3D_peak_locs(1).Visible = 'off'; %h.map3D_peak_locs(2).Visible = 'off';
+    h.map3D_peak_locs(2).Visible = 'off'; %h.map3D_peak_locs(2).Visible = 'off';
+    for v=1:length(h.map3D_peak_ori); h.map3D_peak_ori(v).Visible='off'; end
+end
+bs_plot_peak_waves;

toggle_true_locs.m

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+function toggle_true_locs(varargin)
+global h
+for v=1:3
+if h.radio_3D_true_locs.Value == 1
+    set(handle(h.map3D_true_locs(1,v)),'Visible','on'); set(handle(h.map3D_true_locs(2,v)),'Visible','on');
+elseif h.radio_3D_true_locs.Value == 0
+    set(handle(h.map3D_true_locs(1,v)),'Visible','off'); set(handle(h.map3D_true_locs(2,v)),'Visible','off');
+end
+end
+bs_plot_peak_waves;