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05_scripts/ana07_TOPOdiff.m

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%   TopoSurfArea differences for juw_el_table // All participants
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Topography analysis
+% Author: Julius Welzel // University of Oldenburg, 2019
+% Version: 1.0 // 28.02.2019 // Initial setup
+
+% define paths
+PATHIN_ERD =  [MAIN '04_Data\ana04_erd\'];
+PATHIN_RT = [MAIN '04_Data\'];
+PATHIN_EMG = [MAIN '04_Data\ana03_emg\'];
+
+PATHOUT_TOPODIFF = [MAIN '04_Data\ana07_TOPOdiff\'];
+setGlobal(PATHOUT_TOPODIFF);
+
+if ~exist(PATHOUT_TOPODIFF)
+  mkdir(PATHOUT_TOPODIFF);
+end 
+
+list = dir(fullfile([PATHIN_RT 'ana02_clean\*clean*.set']));
+SUBJ = extractBefore({list.name},'_');
+
+load([PATHIN_ERD 'ERD_mue.mat']);
+load([PATHIN_ERD 'cfg_mue.mat']);
+load([PATHIN_EMG 'emg_all.mat']);
+
+% define trails of interest
+ME_trials = [cfg.blck_idx{[1 4],1}];
+MI_trials = [cfg.blck_idx{[2 3],1}];
+
+SUBJ = str2double(SUBJ);
+old = (SUBJ>=80);
+young = (SUBJ<80);
+
+%% Zscore data over all participants only for MI trials
+z_top = zscore(nanmean(m_rERD_trial,3),[],1);
+top_old = mean(z_top(old,:));
+top_young = mean(z_top(young,:));
+
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%                   Extract surface area
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+p_interp = 100; % points to interpolate
+
+% get cartesian coordinates by MIKE X COHEN :D and grid data
+[elocsX,elocsY] = pol2cart(pi/180*[cfg.chanlocs.theta],[cfg.chanlocs.radius]);
+elocsX = elocsX*-1; %swap left/ right
+xlin = linspace(min(elocsX),max(elocsX),p_interp);
+ylin = linspace(min(elocsY),max(elocsY),p_interp);
+[Xgrid, Ygrid] = meshgrid(xlin,ylin);
+
+%% calculate surface area  of topoplot for each trial
+%{
+surf_old = {};
+surf_young = {};
+
+for s = find(young)
+    disp(['SUBJ: ' num2str(SUBJ(s))])
+   for t = MI_trials
+       
+       topo = zscore((m_rERD_trial(s,:,t)));
+       surf_st = griddata(elocsX,elocsY,topo,Xgrid,Ygrid,'cubic');
+       top_thresh = min(min(topo))*0.5;
+       surf_st(surf_st>top_thresh) = NaN;
+       surf_young{end+1} = SurfArea(surf_st,Xgrid,Ygrid);
+       
+   end
+end
+
+for s = find(old)
+    disp(['SUBJ: ' num2str(SUBJ(s))])
+   for t = MI_trials
+       
+       topo = zscore((m_rERD_trial(s,:,t)));
+       surf_st = griddata(elocsX,elocsY,topo,Xgrid,Ygrid,'cubic');
+       top_thresh = min(min(topo))*0.5;
+       surf_st(surf_st>top_thresh) = NaN;
+       surf_old{end+1} = SurfArea(surf_st,Xgrid,Ygrid);
+       
+   end
+end
+%}
+
+
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%                   3D topographies of ERD maps
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Plot topographie interpolated with surface area scatter
+figure
+ax1 = subplot(2,4,[1 2]);
+Z_young = griddata(elocsX,elocsY,top_young,Xgrid,Ygrid,'cubic');
+mesh(Xgrid,Ygrid,Z_young) % interpolate
+colormap(ax1,c_young_map)
+axis tight;hold on;
+plot3(elocsX,elocsY,top_young,'.k','MarkerSize',15)
+title 'Interpolated Topoplot Young'
+hold on
+surf(Xgrid,Ygrid,min(min(Z_young))*0.5*ones(size(Z_young)),'FaceAlpha',0.5,'EdgeColor','none')
+stlwrite('mod_young3D.stl',Xgrid,Ygrid,Z_young*0.2,'FaceColor',c_young) 
+
+ax2 = subplot(2,4,[5 6]);
+Z_old = griddata(elocsX,elocsY,top_old,Xgrid,Ygrid,'cubic');
+mesh(Xgrid,Ygrid,Z_old) % interpolate
+colormap(ax2,c_old_map)
+axis tight;hold on;
+plot3(elocsX,elocsY,top_old,'.k','MarkerSize',15)
+title 'Interpolated Topoplot Old'
+hold on
+surf(Xgrid,Ygrid,min(min(Z_old))*0.5*ones(size(Z_old)),'FaceAlpha',0.5,'EdgeColor','none')
+stlwrite('mod_old3D.stl',Xgrid,Ygrid,Z_old*0.2,'FaceColor',c_old*255) 
+
+x_values = linspace(0,3,length(surf_old));
+subplot(2,4,[3 4 7 8])
+pd = fitdist([surf_old{:}]','normal');
+y = pdf(pd,x_values);
+p1 = plot(x_values,y,'Color',c_old,'LineWidth',2);
+hold on
+scatter([surf_old{:}],x_values,2,c_old)
+hold on
+pd = fitdist([surf_young{:}]','normal');
+y = pdf(pd,x_values);
+p2 = plot(x_values,y,'Color',c_young,'LineWidth',2);
+hold on
+scatter([surf_young{:}],x_values,2,c_young)
+legend([p1 p2],{'OLD','YOUNG'})
+title ({'Surface Area of highest 50% ERD','All trials each group'})
+
+% save_fig(gcf,PATHOUT_TOPODIFF,'surf_area_ERD_st','fontsize',15,'figsize',[0 0 35 25]);
+
+
+%% only 3D topoplots over both groups with topoplot
+c_lines = 10;
+
+figure;
+ax1 = subplot(1,2,1);
+Z_young = griddata(elocsX,elocsY,mean(z_top(young,:)),Xgrid,Ygrid,'cubic');
+mesh(Xgrid,Ygrid,Z_young) % interpolate
+colormap(ax1,c_map)
+axis tight;hold on;    
+plot3(elocsX,elocsY,mean(z_top(young,:)),'.k','MarkerSize',15) %plot electrodes
+title '3D Topoplot Young'
+zlabel 'z-Score'
+set(gca,'YTickLabel',[]);
+set(gca,'XTickLabel',[]);
+hold on
+%intersect lines
+surf(Xgrid,Ygrid,0*ones(size(Z_young)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')
+
+%topoplot
+[~,h] = contourf(Xgrid,Ygrid,Z_young,c_lines);       %# get handle to contourgroup object
+colormap (ax1,c_map)
+%# change the ZData property of the inner patches
+h.ContourZLevel = 1.1*min(min(Z_young));
+
+% OLD 3D PLOT
+ax2 = subplot(1,2,2);
+Z_old = griddata(elocsX,elocsY,mean(z_top(old,:)),Xgrid,Ygrid,'cubic');
+mesh(Xgrid,Ygrid,Z_old) % interpolate
+colormap(ax2,c_map)
+axis tight;hold on;
+plot3(elocsX,elocsY,mean(z_top(old,:)),'.k','MarkerSize',15)
+title '3D Topolot Old'
+zlabel 'z-Score'
+set(gca,'YTickLabel',[]);
+set(gca,'XTickLabel',[]);
+hold on
+%intetsect planes
+surf(Xgrid,Ygrid,0*ones(size(Z_old)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')
+hold on
+
+%topoplot
+[~,h] = contourf(Xgrid,Ygrid,Z_old,c_lines);       %# get handle to contourgroup object
+colormap (ax1,c_map)
+%# change the ZData property of the inner patches
+h.ContourZLevel = 1.1*min(min(Z_old));
+
+% save_fig(gcf,PATHOUT_TOPODIFF,'3D_tops','figtype','.fig')
+
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%                  Calculate area of intersection
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%{
+gd(1).Z= griddata(elocsX,elocsY,mean(z_top(young,:)),Xgrid,Ygrid,'cubic'); %young
+gd(2).Z = griddata(elocsX,elocsY,mean(z_top(old,:)),Xgrid,Ygrid,'cubic'); %old
+group = {'Young','Old'};
+
+plane_sect = linspace(0,-1.2,6);
+
+for g = 1:length(gd)
+    
+    figure
+    for i = 1:length(plane_sect)
+        subplot(2,3,i)
+        mesh(Xgrid,Ygrid,gd(g).Z) % interpolate
+        hold on
+        surf(Xgrid,Ygrid,plane_sect(i)*ones(size(gd(g).Z)),'FaceColor','k','FaceAlpha',0.08,'EdgeColor','none')
+        hold on
+
+        % Take the difference between the two surface heights and find the contour
+        % where that surface is zero.
+        zdiff = gd(g).Z - (plane_sect(i)*ones(size(gd(g).Z)));
+        C = contour(Xgrid, Ygrid, zdiff,[0,0]);
+
+        [a, ca] = cont_area(C,Xgrid,Ygrid,gd(g).Z);
+        % Visualize the line.
+        cl = line(ca.xL, ca.yL, ca.zL, 'Color', 'k', 'LineWidth', 3);
+        title(['Area : ' num2str(a) ' at z = ' num2str(plane_sect(i))])
+    end
+    sgtitle ([group{g} ' participants'])
+    save_fig(gcf,PATHOUT_TOPODIFF,['SurfArea_' group{g}],'figtype','.fig')
+
+end
+%}
+maps_st = zscore(nanmean(m_rERD_trial,3),[],1);
+
+for s = 1:length(SUBJ)
+    if SUBJ(s)<50;c_map = c_y_map;else;c_map = c_o_map;end;
+    area_z_t_avg(s,:) = inter_area(cfg.chanlocs,maps_st(s,:),24,SUBJ(s),PATHOUT_TOPODIFF,c_map);
+end
+
+[m_a_old se_a_old] = mean_SEM(area_z_t_avg(old,:)');
+[m_a_young se_a_young] = mean_SEM(area_z_t_avg(young,:)');
+
+AO = shadedErrorBar(1:24,m_a_old,se_a_old,'lineprops',{'-','Color',c_old,'LineWidth',2})
+hold on
+AY = shadedErrorBar(1:24,m_a_young,se_a_young,'lineprops',{'-','Color',c_young,'LineWidth',2})
+
+