Plot cortical surface model.
(VBMEG public function)
[syntax]
vb_plot_cortex(plot_parm,V,F)
vb_plot_cortex(plot_parm,V,F,inf_C)
vb_plot_cortex(plot_parm,V,F,inf_C,J)
vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin)
vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin,Jmax)
vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin,Jmax,ix_area)
[input]
plot_parm: <<struct>> Plotting parameters.
--- fields of plot_parm
LRflag: <<string>> Specifying hemisphere for plotting.
'LR' for both hemishepre
'L' for left hemisphere
'R' for both hemisphere
wmode : <<bool>> If true, absolute value of 'J' is plotted. Otherwise,
raw value of 'J' is plotted.
paint : <<bool>> If true,
cmap : <<int>> Colormap (1: hot, otherwise: jet).
isact : <optional> <<bool>> If true, activity map is superimposed on
cortical surface.
color : <optional> <<vector>>
index : <optional> <<vector>>
area : <optional> <<struct>>
edgecolor : <optional> <<vector>> Color of edges (default: 'none')
--- fields of plot_parm.area
area_file : <<string>> cortical area file(.area.mat)
key : <<cell string>> area key name list.
transparent : = true : area tranceparent plot ON
: = false : area tranceparent plot OFF <<default>>
tranceparent_value : from 0 to 1.0 (0.5 is default).
If you set 0, area will disappear.
clr : <<cell string/3d vector>>
str : <optional> <<cell string>>
Rlabel : <optional> <<double>> Distance between string and area.
---
---
V : <<matrix>> Vertices of cortical surface model.
F : <<matrix>> Faces of cortical surface model.
inf_C : <<vector>> Color of sulcus/gyrus. It should be empty when
plotting folded surface model.
[output]
h: Handle of light.
[example]
% Load inflated standard brain model
[V,F,xx,inf_C] = vb_load_cortex(brainfile,'Inflate');
% Load current and current information
[Jinfo, J] = vb_load_current(currentfile);
% get loaded data index between 80[msec] to 120[msec]
ix = intersect(find(Jinfo.Tmsec>80), find(Jinfo.Tmsec<120));
% Average current between 80msec to 120msec
Jplot = mean(J(:, ix), 2);
% set viewpoint
view([10, -2]);
% plot current on cortical inflate model
plot_parm = vb_set_plot_parm;
vb_plot_cortex(plot_parm,V,F,inf_C,Jplot);
axis equal;
axis off;
[history]
2009-01-26 taku-y
2010-12-27 taku-y
[minor] Not superimpose activity (not invoke patch fnc) if all values
do not exceed threshold.
2012-02-09 taku-y
[enhancement] If isfield(area,'clr'), plor_parm.area{i}.clr is
replaced with a.clr, where a=vb_get_area(area_file,area_key{i}).
2012-03-14 taku-y
[minor] Check color value in a.clr, where
a=vb_get_area(area_file,area_key).
2022-03-14 rhayashi
[enhancement] area transparent valueis added.
- plot_parm.area.transparent_value
2022-04-26 Y. Takeda
[minor] Added option to set edge color
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function h = vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin,Jmax,ix_area) 0002 % Plot cortical surface model. 0003 % (VBMEG public function) 0004 % 0005 % [syntax] 0006 % vb_plot_cortex(plot_parm,V,F) 0007 % vb_plot_cortex(plot_parm,V,F,inf_C) 0008 % vb_plot_cortex(plot_parm,V,F,inf_C,J) 0009 % vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin) 0010 % vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin,Jmax) 0011 % vb_plot_cortex(plot_parm,V,F,inf_C,J,Jmin,Jmax,ix_area) 0012 % 0013 % [input] 0014 % plot_parm: <<struct>> Plotting parameters. 0015 % --- fields of plot_parm 0016 % LRflag: <<string>> Specifying hemisphere for plotting. 0017 % 'LR' for both hemishepre 0018 % 'L' for left hemisphere 0019 % 'R' for both hemisphere 0020 % wmode : <<bool>> If true, absolute value of 'J' is plotted. Otherwise, 0021 % raw value of 'J' is plotted. 0022 % paint : <<bool>> If true, 0023 % cmap : <<int>> Colormap (1: hot, otherwise: jet). 0024 % isact : <optional> <<bool>> If true, activity map is superimposed on 0025 % cortical surface. 0026 % color : <optional> <<vector>> 0027 % index : <optional> <<vector>> 0028 % area : <optional> <<struct>> 0029 % edgecolor : <optional> <<vector>> Color of edges (default: 'none') 0030 % --- fields of plot_parm.area 0031 % area_file : <<string>> cortical area file(.area.mat) 0032 % key : <<cell string>> area key name list. 0033 % transparent : = true : area tranceparent plot ON 0034 % : = false : area tranceparent plot OFF <<default>> 0035 % tranceparent_value : from 0 to 1.0 (0.5 is default). 0036 % If you set 0, area will disappear. 0037 % clr : <<cell string/3d vector>> 0038 % str : <optional> <<cell string>> 0039 % Rlabel : <optional> <<double>> Distance between string and area. 0040 % --- 0041 % --- 0042 % V : <<matrix>> Vertices of cortical surface model. 0043 % F : <<matrix>> Faces of cortical surface model. 0044 % inf_C : <<vector>> Color of sulcus/gyrus. It should be empty when 0045 % plotting folded surface model. 0046 % 0047 % [output] 0048 % h: Handle of light. 0049 % 0050 % [example] 0051 % % Load inflated standard brain model 0052 % [V,F,xx,inf_C] = vb_load_cortex(brainfile,'Inflate'); 0053 % 0054 % % Load current and current information 0055 % [Jinfo, J] = vb_load_current(currentfile); 0056 % 0057 % % get loaded data index between 80[msec] to 120[msec] 0058 % ix = intersect(find(Jinfo.Tmsec>80), find(Jinfo.Tmsec<120)); 0059 % 0060 % % Average current between 80msec to 120msec 0061 % Jplot = mean(J(:, ix), 2); 0062 % 0063 % % set viewpoint 0064 % view([10, -2]); 0065 % 0066 % % plot current on cortical inflate model 0067 % plot_parm = vb_set_plot_parm; 0068 % vb_plot_cortex(plot_parm,V,F,inf_C,Jplot); 0069 % 0070 % axis equal; 0071 % axis off; 0072 % 0073 % [history] 0074 % 2009-01-26 taku-y 0075 % 2010-12-27 taku-y 0076 % [minor] Not superimpose activity (not invoke patch fnc) if all values 0077 % do not exceed threshold. 0078 % 2012-02-09 taku-y 0079 % [enhancement] If isfield(area,'clr'), plor_parm.area{i}.clr is 0080 % replaced with a.clr, where a=vb_get_area(area_file,area_key{i}). 0081 % 2012-03-14 taku-y 0082 % [minor] Check color value in a.clr, where 0083 % a=vb_get_area(area_file,area_key). 0084 % 2022-03-14 rhayashi 0085 % [enhancement] area transparent valueis added. 0086 % - plot_parm.area.transparent_value 0087 % 2022-04-26 Y. Takeda 0088 % [minor] Added option to set edge color 0089 % 0090 % Copyright (C) 2011, ATR All Rights Reserved. 0091 % License : New BSD License(see VBMEG_LICENSE.txt) 0092 0093 % --- Check input arguments 0094 if nargin<8, ix_area = []; end 0095 if nargin<5, 0096 J = []; 0097 Jmin = []; 0098 Jmax = []; 0099 else 0100 if nargin<7, Jmax = max(abs(J)); end 0101 if nargin<6, Jmin = max(abs(J))*0.1; end 0102 end 0103 if nargin<4, inf_C = []; end; 0104 0105 % color of cortical surface 0106 if isfield(plot_parm,'color') & ~isempty(plot_parm.color) 0107 fclr = plot_parm.color; 0108 else 0109 fclr = [0.8 0.8 0.8]; 0110 end 0111 0112 if ~isfield(plot_parm,'isact'), 0113 plot_parm.isact = true; 0114 end 0115 0116 % Color of edges 0117 if isfield(plot_parm, 'edgecolor') & ~isempty(plot_parm.edgecolor) 0118 edgecolor = plot_parm.edgecolor; 0119 else 0120 edgecolor = 'none'; 0121 end 0122 0123 % Left/Right hemisphere 0124 switch plot_parm.LRflag 0125 case 'L' 0126 F0 = F.F3L; 0127 case 'R' 0128 F0 = F.F3R; 0129 case 'LR' 0130 F0 = F.F3; 0131 end 0132 0133 if isempty(inf_C) 0134 inflate = false; 0135 else 0136 inflate = true; 0137 end 0138 Vshrink = vb_shrink_cortex_for_plot(V, F0, inflate); 0139 0140 % --- Select visible patches 0141 if ~isfield(plot_parm,'index'), index = []; 0142 else index = plot_parm.index; end 0143 if length(index) == 0, FF = F0; 0144 else FF = vb_patch_select2(index,F0,size(V,1)); end 0145 0146 % --- Plot cortical surface 0147 h = gcf; 0148 set(h, 'renderer', 'zbuffer'); 0149 if isempty(inf_C) 0150 % Display patches 0151 patch('Faces',FF,'Vertices',Vshrink,'FaceColor',fclr, ... 0152 'FaceLighting','phong','EdgeColor',edgecolor, ... 0153 'Tag', 'vb_plot_cortex_brain'); 0154 0155 % Light 0156 h = camlight('headlight'); 0157 else 0158 c = repmat(fclr,[length(inf_C) 1]) ... 0159 -0.4*[fclr(1)*inf_C fclr(2)*inf_C fclr(3)*inf_C]; 0160 patch('Faces',FF,'Vertices',Vshrink,'FaceColor','interp',... 0161 'EdgeColor',edgecolor,'FaceVertexCData',c, ... 0162 'Tag', 'vb_plot_cortex_brain'); 0163 h = []; 0164 end 0165 0166 material dull; 0167 hold on; 0168 0169 % --- Superimpose activity 0170 if plot_parm.isact & ~isempty(J), 0171 plot_value(plot_parm,V,F0,J,index,Jmin,Jmax); 0172 end 0173 0174 % --- Superimpose area 0175 if ~isempty(ix_area), 0176 if ~isempty(index), ix_area = intersect(index,ix_area); end 0177 FF = vb_patch_select2(ix_area,F0,size(V,1)); 0178 patch('Faces',FF,'Vertices',V,'FaceColor','b',... 0179 'EdgeColor','none','EraseMode','xor', ... 0180 'FaceAlpha',1); 0181 end 0182 0183 plot_area(plot_parm,V,F0); 0184 0185 0186 % To avoid MATLAB alpha bug(R2014b to R2015b) 0187 if vb_matlab_version('>=', '8.4') && vb_matlab_version('<=', '8.6') 0188 % reset alpha value of brain to 0.99 0189 t = timer('Name', 'vb_plot_cortex', 'StartDelay', 1, ... 0190 'TimerFcn', 'alpha(findobj(gca, ''Tag'', ''vb_plot_cortex_brain''), 0.99);', ... 0191 'ExecutionMode', 'singleshot'); 0192 start(t); 0193 end 0194 0195 return; 0196 0197 % --- Inner function: plot cortical activity 0198 function plot_value(plot_parm,V,F0,J,index,wmin,wmax); 0199 0200 if length(J) == 0 0201 return; 0202 end 0203 0204 % Select vertices 0205 if length(index) == 0 0206 tmp = ones(length(J),1); 0207 else 0208 tmp = zeros(length(J),1); 0209 tmp(index) = 1; 0210 end 0211 0212 % Left/Right hemisphere 0213 tmp2 = zeros(length(J),1); 0214 tmp2(unique(F0(:))) = 1; 0215 0216 tmp = J.*tmp.*tmp2; 0217 ix = find(abs(tmp) >= wmin); 0218 if plot_parm.wmode==1 0219 J = abs(J); 0220 end 0221 0222 % Superimpose activity on cortical surface 0223 if plot_parm.paint==1 0224 h = scatter3(V(ix,1),V(ix,2),V(ix,3),1,J(ix),'.','filled'); 0225 set(h,'MarkerSize',plot_parm.ms); 0226 else 0227 FF = vb_patch_select2(ix,F0,size(V,1)); 0228 if ~isempty(FF), 0229 patch('Faces',FF,'Vertices',V,'FaceColor','interp',... 0230 'FaceVertexCData',J,'EdgeColor','none',... 0231 'FaceLighting','none','FaceAlpha',1); 0232 material dull; 0233 end 0234 end 0235 0236 if plot_parm.wmode==1 0237 caxis([0 wmax]); 0238 else 0239 caxis([-wmax wmax]); 0240 end 0241 0242 if plot_parm.cmap==1 0243 colormap(hot); 0244 else 0245 colormap(jet); 0246 end 0247 0248 return; 0249 0250 % --- Inner function: plot cortical area 0251 function plot_area(plot_parm,V,F0); 0252 0253 if isfield(plot_parm,'area'), 0254 if ~isfield(plot_parm,'index') | isempty(plot_parm.index), 0255 tmp = ones(size(V,1),1); 0256 else 0257 tmp = zeros(size(V,1),1); 0258 tmp(plot_parm.index) = 1; 0259 end 0260 0261 % For compatibility with old format 0262 if isfield(plot_parm,'Rlabel'), 0263 plot_parm.area.Rlabel = plot_parm.Rlabel; 0264 elseif ~isfield(plot_parm.area,'Rlabel'), 0265 plot_parm.area.Rlabel = 1; 0266 end 0267 0268 if isfield(plot_parm,'areafile'), 0269 plot_parm.area.area_file = plot_parm.areafile; 0270 end 0271 0272 % Transparency 0273 if isfield(plot_parm.area,'transparent') & plot_parm.area.transparent, 0274 if isfield(plot_parm.area, 'tranceparent_value') 0275 alpha = plot_parm.area.tranceparent_value; 0276 else 0277 alpha = 0.5; 0278 end 0279 else 0280 alpha = 1.0; 0281 end 0282 0283 % Plot area 0284 area_file = plot_parm.area.area_file; 0285 for i = 1:length(plot_parm.area.key) 0286 Area = vb_get_area(area_file,plot_parm.area.key{i}); 0287 if isfield(Area,'clr'), 0288 clr = Area.clr; 0289 if max(clr)>1 | min(clr)<0, 0290 vb_disp(['Invalid color value of cortical region. area.clr must ' ... 0291 'be in range [0 1], where area = vb_get_area(area_file,' ... 0292 'area_key). Normalized in ' ... 0293 'vb_plot_cortex.']); 0294 clr = abs(clr)./max(abs(clr)); 0295 end 0296 else 0297 Nclr = length(plot_parm.area.clr); 0298 clr = plot_parm.area.clr{1+mod(i-1,Nclr)}; 0299 end 0300 ix = Area.Iextract; 0301 ix = ix(:); 0302 ix = ix(find(ix.*tmp(ix))); % Union 0303 0304 % Dot/Face plot 0305 if plot_parm.paint==1 0306 ix2 = intersect(ix,unique(F0(:))); 0307 plot3(V(ix2,1),V(ix2,2),V(ix2,3),'.',... 0308 'MarkerFaceColor',clr,'MarkerEdgeColor',clr, ... 0309 'MarkerSize',plot_parm.ms); 0310 else 0311 FF = vb_patch_select2(ix,F0,size(V,1)); 0312 patch('Faces',FF,'Vertices',V,... 0313 'FaceColor',clr,'EdgeColor','none', ... 0314 'FaceLighting','gouraud','FaceAlpha',alpha); 0315 end 0316 0317 % Display name of cortical area 0318 if isfield(plot_parm.area,'str') & ... 0319 ~isempty(plot_parm.area.str) & length(FF) > 0, 0320 V0 = mean(V); % Center of cortical model 0321 pos = median(V(ix,:))-V0; 0322 [theta,phi,r] = cart2sph(pos(1),pos(2),pos(3)); 0323 r = plot_parm.area.Rlabel*r; 0324 0325 [x,y,z] = sph2cart(theta,phi,r); 0326 x = x+V0(1); 0327 y = y+V0(2); 0328 z = z+V0(3); 0329 pos = pos+V0; 0330 plot3([pos(1) x],[pos(2) y],[pos(3) z]); 0331 h = text(x,y,z,plot_parm.area.str{i},... 0332 'Interpreter','none','FontSize',plot_parm.fs,... 0333 'HorizontalAlignment','center'); 0334 end 0335 end 0336 end 0337 0338 return;