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BrainNet.m
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function varargout = BrainNet(varargin)
%BrainNet Viewer, a graph-based brain network mapping tool, by Mingrui Xia
%-----------------------------------------------------------
% Copyright(c) 2019
% Beijing Normal University
% Written by Mingrui Xia
% Mail to Author: <a href="mingruixia@gmail.com">Mingrui Xia</a>
% Version 1.63;
% Create Date 20110906;
% Last edited 20190329
%-----------------------------------------------------------
%
% BrainNet MATLAB code for BrainNet.fig
% BrainNet, by itself, creates a new BrainNet or raises the existing
% singleton*.
%
% H = BrainNet returns the handle to a new BrainNet or the handle to
% the existing singleton*.
%
% BrainNet('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in BrainNet.M with the given input arguments.
%
% BrainNet('Property','Value',...) creates a new BrainNet or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before BrainNet_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to BrainNet_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help BrainNet
% Last Modified by GUIDE v2.5 21-Jun-2019 10:08:41
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @BrainNet_OpeningFcn, ...
'gui_OutputFcn', @BrainNet_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before BrainNet is made visible.
function BrainNet_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to BrainNet (see VARARGIN)
warning off
fprintf('Please cite:\nXia M, Wang J, He Y (2013) BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics. PLoS ONE 8: e68910.\nAn example:\n''The brain networks were visualized with the BrainNet Viewer (http://www.nitrc.org/projects/bnv/) (Xia et al., 2013)''.\n');
% Choose default command line output for BrainNet
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% if exist('BrainNet_Icon.png','file')==2
% newIcon = javax.swing.ImageIcon('BrainNet_Icon.png');
% figFrame = get(handles.NV_fig,'JavaFrame');
% figFrame.setFigureIcon(newIcon);
% end
% movegui(handles.NV_fig,'center');
movegui(hObject,'center');
%opengl software; %% Add by Mingrui, 20140815 enable to fix upside-down text
global FLAG
FLAG.Loadfile=0;
FLAG.EC=0;
FLAG.Rotate=0;
FLAG.EC_change=0;
FLAG.axial=0;
FLAG.sagittal=0;
FLAG.coronal=0;
FLAG.LF=0;
FLAG.MAP=0;
FLAG.IsCalledByCMD = 0;
global EC
EC=[];
EC.bak.color=[1,1,1];
EC.msh.color_type = 1; %Added by Mingrui, 20190521, load color for each vertex; 1 for same; 2 for defined
EC.msh.color=[0.95,0.95,0.95];
EC.msh.color_table = EC.msh.color;
EC.msh.color_table_tmp = EC.msh.color;
EC.msh.alpha=0.3;
EC.msh.doublebrain = 0; %%% Added by Mingrui Xia, 20120717, show two brains in one figure, 0 for one brain, 1 for two brains.
% Added by Mingrui, 20190327, parameters for boundary
EC.msh.boundary = 1;
% 1 for none, 2 for auto, 3 for threshold, and 4 for file
EC.msh.boundary_value = 0;
EC.msh.boundary_color = [0 0 0];
EC.nod.draw=1;
EC.nod.draw_threshold_type=1;
EC.nod.draw_threshold=0;
EC.nod.size=2;
EC.nod.size_size=3;
EC.nod.size_value=1;
EC.nod.size_threshold=0;
EC.nod.size_ratio=1;
EC.nod.color=1;
EC.nod.CM = [[37,89,152]/255;zeros(63,3)];
% Add by Mingrui, 20170317, custom colormap for node
EC.nod.CMt = EC.nod.CM;
EC.nod.cmstring = 'jet(64);';
EC.nod.color_map=1;
% Add by Mingrui, 20170303, fixed range of color mapping
EC.nod.color_map_type = 1; % 1 for auto, 2 for fix
EC.nod.color_map_low = 0;
EC.nod.color_map_high = 1;
EC.nod.color_threshold=0;
EC.nod.CMm=[0.956862745098039,1,0.545098039215686,0,0.247058823529412,0.913725490196078,1,0.803921568627451,0,0.129411764705882,0.611764705882353,1,1,0.298039215686275,0.0117647058823529,0.403921568627451,0.474509803921569,0.376470588235294,0.619607843137255,0,1;
0.262745098039216,0.756862745098039,0.764705882352941,0.737254901960784,0.317647058823529,0.117647058823529,0.596078431372549,0.862745098039216,0.588235294117647,0.588235294117647,0.152941176470588,0.341176470588235,0.921568627450980,0.686274509803922,0.662745098039216,0.227450980392157,0.333333333333333,0.490196078431373,0.619607843137255,0,1;
0.211764705882353,0.0274509803921569,0.290196078431373,0.831372549019608,0.709803921568628,0.388235294117647,0,0.223529411764706,0.533333333333333,0.952941176470588,0.690196078431373,0.133333333333333,0.231372549019608,0.313725490196078,0.956862745098039,0.717647058823529,0.282352941176471,0.545098039215686,0.619607843137255,0,1]';
EC.nod.ModularNumber = [];
% EC.nod.CMm = hsv(64);
% tmp = [];
% for i = 1:8
% tmp = vertcat(tmp,EC.nod.CMm(i:8:64,:));
% % tmp = [tmp,EC.nod.CMm(i:8:256,:)'];
% end
% EC.nod.CMm = tmp;
% clear tmp
EC.lbl=2;
EC.lbl_threshold=0;
EC.lbl_threshold_type=1;
EC.edg.draw=1;
EC.edg.draw_threshold=0;
EC.edg.draw_abs=1;
EC.edg.size=2;
% EC.edg.size_size=0.3;
EC.edg.size_size = 1;
EC.edg.size_value=1;
EC.edg.size_threshold=0;
EC.edg.size_ratio=1;
EC.edg.size_abs=1;
EC.edg.color=1;
% 1 for same
% 2 for colormap
% 3 for threshold
% 4 for distance
% 5 for nodal module
% 6 for custom definition
% Add by Mingrui, 20170303, fixed range of color mapping
EC.edg.color_map_type = 1; % 1 for auto, 2 for fix
EC.edg.color_map_low = 0;
EC.edg.color_map_high = 1;
EC.edg.CM = [[1,0.9,0.73];ones(63,3)*0.38];
% Add by Mingrui 20170317, custom colormap for edge
EC.edg.CMt = EC.edg.CM;
EC.edg.cmstring = 'jet(64);';
EC.edg.color_map=1;
EC.edg.color_threshold=0;
EC.edg.color_distance=0;
EC.edg.color_abs=1;
% Add by Mingrui, 20150120, using custom matrix to define edge color.
EC.edg.CM_custom = [0.956862745098039,1,0.545098039215686,0,0.247058823529412,0.913725490196078,1,0.803921568627451,0,0.129411764705882,0.611764705882353,1,1,0.298039215686275,0.0117647058823529,0.403921568627451,0.474509803921569,0.376470588235294,0.619607843137255,0,1;
0.262745098039216,0.756862745098039,0.764705882352941,0.737254901960784,0.317647058823529,0.117647058823529,0.596078431372549,0.862745098039216,0.588235294117647,0.588235294117647,0.152941176470588,0.341176470588235,0.921568627450980,0.686274509803922,0.662745098039216,0.227450980392157,0.333333333333333,0.490196078431373,0.619607843137255,0,1;
0.211764705882353,0.0274509803921569,0.290196078431373,0.831372549019608,0.709803921568628,0.388235294117647,0,0.223529411764706,0.533333333333333,0.952941176470588,0.690196078431373,0.133333333333333,0.231372549019608,0.313725490196078,0.956862745098039,0.717647058823529,0.282352941176471,0.545098039215686,0.619607843137255,0,1]';
EC.edg.color_custom_matrix = [];
EC.edg.color_custom_index = [];
EC.edg.interhemiedges = 0; % Add by Mingrui Xia, 20120109, draw inter hemisphere edges.
EC.edg.directed = 0; % Add by Mingrui Xia, 20120621, draw directed network.
% Add by Mingrui, 20140925, dispaly edge by opacity
EC.edg.opacity = 1; % 1 for same opacity, 2 for value mapping
EC.edg.opacity_same = 0.7; % default 0.7 for same
EC.edg.opacity_max = 0.9;
EC.edg.opacity_min = 0.1;
EC.edg.opacity_abs = 1;
EC.img.width=2000;
EC.img.height=1500;
EC.img.dpi=300;
EC.lbl_font.FontName='Arial';
EC.lbl_font.FontWeight='bold';
EC.lbl_font.FontAngle='normal';
EC.lbl_font.FontSize=11;
EC.lbl_font.FontUnits='points';
% Added by Mingrui Xia, 20170919, add option to show label in front.
EC.lbl_front = 0;
EC.lot.view=1;
% 1 for single view
% 2 for full view
% 3 for lateral and medial view
% 4 for lateral, medial and ventral view
% 5 for lateral, medial and dorsal view
EC.lot.view_direction=1;
% Added by Mingrui Xia, 20120806, add custom view for single brain.
EC.lot.view_az = -90;
EC.lot.view_el = 0;
EC.vol.display = [];
EC.vol.pn = [];
EC.vol.px = [];
EC.vol.nn = [];
EC.vol.nx = [];
EC.vol.null=[0.95,0.95,0.95];
EC.vol.CM=ones(1000,3)*0.75;
EC.vol.color_map = 13;
EC.vol.cmstring = 'jet(1000);';
EC.vol.adjustCM = 1;
% Added by Mingrui Xia, 20160407, support annot format
EC.vol.CM_annot = rand(64,3);
% Added by Mingrui Xia, 20140916, add statistic for volume mapping
EC.vol.threshold = 0;
EC.vol.p = 0.05;
EC.vol.clustersize = 0;
EC.vol.rmm = 18;
% Added by Mingrui Xia, 20120726, selection for different mapping algorithm.
% 1 for Nearest Voxel
% 2 for Average Vertex
% 3 for Average Voxel
% 4 for Gaussian
% 5 for Interpolated (default)
% 6 for Maximum Voxel
% 7 for Minimum Voxel
% 8 for Extremum Voxel
% 9 for Most Neighbour Voxel, Added by Mingrui Xia, 20130104
EC.vol.mapalgorithm = 5;
EC.glb.material = 'dull';% Added by Mingrui Xia, 20120316, modify object material, shading, light.
EC.glb.material_ka = '0.5';
EC.glb.material_kd = '0.5';
EC.glb.material_ks = '0.5';
EC.glb.shading = 'interp';
EC.glb.lighting = 'phong';
EC.glb.lightdirection = 'right';
EC.glb.render = 'OpenGL'; % Added by Mingrui Xia, 20120413, selection for rendering methods
EC.glb.detail = 3; % Add by Mingrui Xia, 20120413, adjust graph detail
% Add by Mingrui, 20170309, display LR
EC.glb.lr = 1; % 1 for display, 0 for not display
% Added by Mingrui, 20120528, for ROI draw
EC.vol.type = 1; % 1 for volume to surface, 2 for ROI
EC.vol.roi.drawall = 1;
EC.vol.roi.draw = [];
EC.vol.roi.color = hsv(100);
EC.vol.roi.color = [EC.vol.roi.color(1:10:91,:)',EC.vol.roi.color(2:10:92,:)',EC.vol.roi.color(3:10:93,:)',EC.vol.roi.color(4:10:94,:)',EC.vol.roi.color(5:10:95,:)',EC.vol.roi.color(6:10:96,:)',EC.vol.roi.color(7:10:97,:)',EC.vol.roi.color(8:10:98,:)',EC.vol.roi.color(9:10:99,:)',EC.vol.roi.color(10:10:100,:)']';
EC.vol.roi.color = repmat(EC.vol.roi.color,11,1);
EC.vol.roi.colort = EC.vol.roi.color;
% EC.vol.roi.color = ones(2000,3)*0.7;
% EC.vol.roi.colort = EC.vol.roi.color;
EC.vol.roi.smooth = 1;
EC.vol.roi.drawcus = '';
EC.vol.roi.drawt = [];
% Added by Mingrui, 20170317, choice for smooth kernal
EC.vol.roi.smooth_kernal = 1;
% 1 for box
% 2 for Gaussian
global a
if ~isempty(a) && mean(ishandle(a))==1
delete(a);
end
a=[];
global File
File.MF=[];
File.NI=[];
File.NT=[];
File.VF=[];
% if exist('BrainNet_Background.tif','file')==2
% imshow(imread('BrainNet_Background.tif'));
% end
% Modified according to Chris Rorden's suggestion to avoid using addtional image toolbox.
if exist('BrainNet_Background.tif','file')==2 && exist('imshow','file')
imshow(imread('BrainNet_Background.tif'));
end
global OutputText %%% Added by Mingrui Xia, 20120413, give out aal information for selected vertex.
if exist('BrainNet_AAL_Label.mat','file')==2
OutputText.AAL = load('BrainNet_AAL_Label.mat');
else
OutputText.AAL = [];
end
if exist('BrainNet_Brodmann_Label.mat','file')==2 %%% Added by Mingrui Xia, 20120417, give out brodmann information for selected vertex.
OutputText.Brodmann = load('BrainNet_Brodmann_Label.mat');
else
OutputText.Brodmann = [];
end
dcm_obj = datacursormode(hObject);
set(dcm_obj,'UpdateFcn',@BrainNet_Output_txt)
% set(hObject,'toolbar','figure')
% set(gcf,'Renderer','OpenGL');
%set(handles.NV_fig,'position',get(0,'screensize'));
% UIWAIT makes BrainNet wait for user response (see UIRESUME)
% uiwait(handles.NV_fig);
% --- Outputs from this function are returned to the command line.
function varargout = BrainNet_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
%set(handles.NV_axes,'Position',get(handles.NV_fig,'Position'))
% --------------------------------------------------------------------
function NV_m_file_Callback(hObject, eventdata, handles)
% hObject handle to NV_m_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function NV_m_exit_Callback(hObject, eventdata, handles)
% hObject handle to NV_m_exit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global a
if ~isempty(a)
delete(a);
a=[];
end
close(findobj('Tag','NV_fig'));
% --------------------------------------------------------------------
function NV_m_nm_Callback(hObject, eventdata, handles)
% hObject handle to NV_m_nm (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global FLAG
if (isfield(FLAG,'IsCalledByREST') && FLAG.IsCalledByREST==1) || ...
(isfield(FLAG,'IsCalledByCMD') && FLAG.IsCalledByCMD==1)
% YAN Chao-Gan 111023. For calling from outside. Edited Mingrui Xia,
% 20121031 add call from commandline
handles.NV_axes=gca(hObject);
end
axes(handles.NV_axes);
cla
global a
if FLAG.Loadfile==0
if exist('BrainNet_background.tif','file')==2
imshow(imread('BrainNet_background.tif'));
end
else
if ~isempty(a) && mean(ishandle(a))==1
delete(a);
end
a=FileView;
end
FLAG.IsCalledByREST = 0;
function NetPrepare
global surf
global EC
switch EC.edg.draw
case 1
[surf.ncyl,surf.cylinder]=Nettrans(surf.net);
% cylinder(:,1:3): node index and value
% cylinder(:,4): size
% cylinder(:,5): color
% cylinder(:,6): opacity
case 2
[surf.ncyl,surf.cylinder]=Nettrans(surf.net,EC.edg.draw_threshold);
end
surf.cylinder(:,4) = surf.cylinder(:,3);
surf.cylinder(:,5) = surf.cylinder(:,3);
surf.cylinder(:,6) = surf.cylinder(:,3);
if EC.edg.size_abs == 1
surf.cylinder(:,4) = abs(surf.cylinder(:,4));
end
switch EC.edg.size
case 1
surf.cylinder(:,4) = EC.edg.size_size;
case 2
switch EC.edg.size_value
case 1
if max(surf.cylinder(:,4)) ~=min(surf.cylinder(:,4))
k = 5.6 /(max(surf.cylinder(:,4))-min(surf.cylinder(:,4)));
b = 6 - k*max(surf.cylinder(:,4));
else
k = 0;
b = 2;
end
surf.cylinder(:,4) = surf.cylinder(:,4) * k + b;
case 2
tmp = surf.cylinder(:,4);
tmp(tmp<0.2) = 0.2;
tmp(tmp>6) = 6;
surf.cylinder(:,4) = tmp;
end
case 3
if EC.edg.size_value == 1
indu = surf.cylinder(:,4) >= EC.edg.size_threshold;
tmp = surf.cylinder(:,4);
tmp2 = tmp(indu);
if max(tmp2) ~= min(tmp2)
k = 5.6 /(max(tmp2)-min(tmp2));
b = 6 - k*max(tmp2);
else
k = 0;
b = 2;
end
tmp2 = tmp2 * k + b;
tmp(indu) = tmp2;
tmp(surf.cylinder(:,4) < EC.edg.size_threshold) = 0.4;
surf.cylinder(:,4) = tmp;
elseif EC.edg.size_value == 2
tmp = surf.cylinder(:,4);
tmp(tmp<EC.edg.size_threshold) = 0.4;
tmp(tmp>6) = 6;
surf.cylinder(:,4) = tmp;
end
end
if EC.edg.color_abs == 1
surf.cylinder(:,5) = abs(surf.cylinder(:,5));
end
switch EC.edg.color
case 1
surf.cylinder(:,5) = 1;
case 2
tmp = surf.cylinder(:,5);
if EC.edg.color_map_type == 1
lowend = min(tmp);
highend = max(tmp);
else
lowend = EC.edg.color_map_low;
highend = EC.edg.color_map_high;
end
if highend~=lowend
k = 63 / (highend - lowend);
b = 64 - k*highend;
else
k = 0;
b = 64;
end
tmp = round(tmp * k + b);
tmp(tmp < 1) = 1;
tmp(tmp > 64) = 64;
surf.cylinder(:,5) = tmp;
case 3
tmp = surf.cylinder(:,5);
tmp2 = tmp;
tmp(tmp2 <= EC.edg.color_threshold) = 64;
tmp(tmp2 > EC.edg.color_threshold) = 1;
surf.cylinder(:,5) = tmp;
case 4
n1 = surf.sphere(surf.cylinder(:,1),1:3);
n2 = surf.sphere(surf.cylinder(:,2),1:3);
length_cyl = sqrt(sum((n1 - n2) .* (n1 - n2), 2));
tmp = length_cyl;
tmp(length_cyl >= EC.edg.color_distance) = 1;
tmp(length_cyl < EC.edg.color_distance) = 64;
surf.cylinder(:,5) = tmp;
case 5
edg_mod = surf.sphere(surf.cylinder(:,1),4);
tmp = surf.sphere(surf.cylinder(:,1),4) - surf.sphere(surf.cylinder(:,2),4);
edg_mod(tmp~=0) = 21;
% Edited by Mingrui, 20150310, fix a bug when module index were not
% noncontinuous.
tmp = unique(surf.sphere(:,4));
edg_mod2 = ones(size(edg_mod))*21;
for i = 1:length(tmp)
edg_mod2(edg_mod == tmp(i)) = i;
end
surf.cylinder(:,5) = edg_mod2;
case 6
index = sub2ind(size(surf.net),surf.cylinder(:,1),surf.cylinder(:,2));
tmp = EC.edg.color_custom_matrix(index);
tmp2 = zeros(size(tmp));
for i = 1:length(EC.edg.color_custom_index)
tmp2(tmp == EC.edg.color_custom_index(i)) = i;
end
surf.cylinder(:,5) = tmp2;
% if max(tmp) ~=min(tmp)
% k = 63 /(max(tmp)-min(tmp));
% b = 64 - k*max(tmp);
% else
% k = 0;
% b = 64;
% end
% tmp = round(tmp * k + b);
% tmp(tmp < 1) = 1;
% tmp(tmp > 64) = 64;
% surf.cylinder(:,5) = tmp;
end
if EC.edg.opacity_abs == 1
surf.cylinder(:,6) = abs(surf.cylinder(:,6));
end
switch EC.edg.opacity
case 1
surf.cylinder(:,6) = EC.edg.opacity_same;
case 2
tmp = surf.cylinder(:,6);
k = (EC.edg.opacity_max - EC.edg.opacity_min)/(max(tmp)-min(tmp));
b = EC.edg.opacity_max - k*max(tmp);
tmp = tmp * k + b;
tmp(tmp < EC.edg.opacity_min) = EC.edg.opacity_min;
tmp(tmp > EC.edg.opacity_max) = EC.edg.opacity_max;
surf.cylinder(:,6) = tmp;
end
function NodePrepare
global surf
global EC
if EC.nod.color==2
surf.sphere(:,6)=surf.sphere(:,4);
% Modified by Mingrui, 20170303, use only linear mapping, add fixed
% colormap range
% if min(surf.sphere(:,6))<0
% surf.sphere(:,6)=surf.sphere(:,6)-min(surf.sphere(:,6));
% end
% if min(surf.sphere(:,6))<1
% surf.sphere(:,6)=surf.sphere(:,6)+1;
% end
% while max(surf.sphere(:,6))/min(surf.sphere(:,6))>10
% surf.sphere(:,6)=log(surf.sphere(:,6));
% if min(surf.sphere(:,6))<1
% surf.sphere(:,6)=surf.sphere(:,6)+1;
% end
% end
if EC.nod.color_map_type == 1
lowend = min(surf.sphere(:,6));
highend = max(surf.sphere(:,6));
else
lowend = EC.nod.color_map_low;
highend = EC.nod.color_map_high;
end
%Editied by Mingrui, 20181123, fix a bug when the length for inputed
%colormap is not 64
colormap_length = length(EC.nod.CM);
if highend~=lowend
EC.nod.k = (colormap_length-1)/(highend-lowend);
EC.nod.b = colormap_length-EC.nod.k*highend;
else
EC.nod.k=0;
EC.nod.b=1;
end
surf.sphere(:,6)=surf.sphere(:,6)*EC.nod.k+EC.nod.b;
else
surf.sphere(:,6)=surf.sphere(:,4);
end
surf.sphere(:,7) = surf.sphere(:,5); % Edited by Mingrui Xia, 20120702, fix edge length when using fix node size.
switch EC.nod.size
case 1
surf.sphere(:,7) = EC.nod.size_size;
case {2,3}
if EC.nod.size_value == 1
if min(surf.sphere(:,7))<0
surf.sphere(:,7)=surf.sphere(:,7)-min(surf.sphere(:,7));
end
if min(surf.sphere(:,7))<1
surf.sphere(:,7)=surf.sphere(:,7)+1;
end
while max(surf.sphere(:,7))/min(surf.sphere(:,7))>10
surf.sphere(:,7)=log(surf.sphere(:,7));
if min(surf.sphere(:,7))<1
surf.sphere(:,7)=surf.sphere(:,7)+1;
end
end
if max(surf.sphere(:,7))~=min(surf.sphere(:,7))
EC.nod.k=5/(max(surf.sphere(:,7))-min(surf.sphere(:,7)));
EC.nod.b=7-EC.nod.k*max(surf.sphere(:,7));
else
EC.nod.k=0;
EC.nod.b=4;
end
surf.sphere(:,7)=surf.sphere(:,7)*EC.nod.k+EC.nod.b;
end
if EC.nod.size == 3
tmp = surf.sphere(:,7);
tmp(tmp < EC.nod.size_threshold) = 1;
surf.sphere(:,7) = tmp;
end
end
surf.sphere(:,7) = surf.sphere(:,7) * EC.nod.size_ratio;
function fv = ROIPrepare
global EC
global surf
% Added by Mingrui 20140925, draw cluster in statistical files
if ~strcmp(surf.test,'No')
vol_tmp = surf.vol;
vol_tmp(vol_tmp < EC.vol.threshold & vol_tmp > -EC.vol.threshold) = 0;
[L, num] = bwlabeln(vol_tmp,EC.vol.rmm);
vol_tmp2 = zeros(size(vol_tmp));
n = 0;
for x = 1:num
theCurrentCluster = L == x;
if length(find(theCurrentCluster)) >= EC.vol.clustersize
n = n + 1;
vol_tmp2(logical(theCurrentCluster)) = n;
end
end
else
vol_tmp2 = surf.vol;
end
fv = cell(length(EC.vol.roi.draw),1);
for i = 1:length(fv)
vol = vol_tmp2;
vol(vol ~= EC.vol.roi.draw(i)) = 0;
vol(vol == EC.vol.roi.draw(i)) = 1;
if EC.vol.roi.smooth == 1
% vol = smooth3(vol,'gaussian');
if EC.vol.roi.smooth_kernal == 1
vol = smooth3(vol);
else
vol = smooth3(vol,'gaussian');
end
% vol = smooth3(vol);
end
fv{i,1} = isosurface(vol);
while size(fv{i,1}.vertices,1) == 0 %% Added by Mingrui Xia, expand ROI while it is too small
if EC.vol.roi.smooth_kernal == 1
vol = smooth3(vol);
else
vol = smooth3(vol,'gaussian');
end% Modified by Mingrui Xia 20160921, using Gaussian kernel instead of the 'box' kernel
vol(vol>0) = 1;
fv{i,1} = isosurface(vol);
end
coord = fv{i,1}.vertices(:,1);
fv{i,1}.vertices(:,1) = fv{i,1}.vertices(:,2);
fv{i,1}.vertices(:,2) = coord;
fv{i,1}.vertices = fv{i,1}.vertices';
fv{i,1}.vertices(4,:) = 1;
fv{i,1}.vertices = surf.hdr.mat * fv{i,1}.vertices;
fv{i,1}.vertices(4,:) = [];
fv{i,1}.vertices = fv{i,1}.vertices';
clear coord
% if length(find(fv{i,1}.vertices(:,1) < 0)) > length(fv{i,1}.vertices(:,1))/2
% Edited by Mingrui Xia, 20160324, modify the methods for judging if
% the ROI belongs to left or right side.
if (min(fv{i,1}.vertices(:,1)) + max(fv{i,1}.vertices(:,1))) < 0
fv{i,1}.side = 1;
else
fv{i,1}.side = 2;
end
end
function [ncyl,cylinder]=Nettrans(net,t)
% Modified by Mingrui, 20170309, draw two edges for bidirected edges
global EC
global surf
switch EC.edg.draw_abs
case 0
temp=net;
case 1
temp=abs(net);
end
temp = temp - diag(diag(temp));
if nargin == 2
temp(temp < t) = 0;
end
if EC.edg.directed == 0
index = find(triu(temp) ~= 0); % Eddited by Mingrui Xia, 20120702, fix a drawall bug.
% cylinder(:,7) = 1;
else % Add by Mingrui Xia, 20120621, draw directed network.
index = find(temp ~= 0);
%
% temp(temp < t) = 0;
% net_up = triu(temp);
% net_low = tril(temp);
% net_conj = net_low';
% net_conj(net_up == 0) = 0;
% net_conj(net_conj ~= 0) = (net_up(net_conj ~= 0) + net_conj(net_conj ~= 0)) / 2;
% ind = find(net_conj ~= 0);
% cylinder1 = zeros(length(ind),4);
% [cylinder1(:,1),cylinder1(:,2)]=ind2sub(size(net),ind);
% cylinder1(:,3) = net(ind);
% cylinder1(:,7) = 2;
%
% net_conj = net_conj + net_conj';
% temp(net_conj ~= 0) = 0;
% ind = find(temp ~= 0);
% cylinder2 = zeros(length(ind),4);
% [cylinder2(:,2),cylinder2(:,1)]=ind2sub(size(net),ind);
% cylinder2(:,3) = net(ind);
% cylinder2(:,7) = 1;
%
% cylinder = [cylinder1',cylinder2']';
% ncyl = size(cylinder,1);
end
ncyl = length(index);
cylinder = zeros(ncyl,6);
[cylinder(:,1),cylinder(:,2)]=ind2sub(size(net),index);
cylinder(:,3) = net(index);
% Add by Mingrui Xia, 20120109, draw inter hemisphere edges.
if EC.edg.interhemiedges == 1
index = surf.sphere(cylinder(:,1)).*surf.sphere(cylinder(:,2))>0;
cylinder(index,:) = [];
ncyl=size(cylinder,1);
end
function [t,tl,tr,vl,vr,h1,w1,cut,cuv]=CutMesh(surf)
t=size(surf.tri,1);
v=size(surf.coord,2);
tmax=max(surf.tri,[],2);
tmin=min(surf.tri,[],2);
if min(tmin(t/2+1:t))-max(tmax(1:ceil(t/2)))==1
cut=t/2;
cuv=v/2;
else
for i=1:t-1
tmax(i+1)=max(tmax(i+1),tmax(i));
tmin(t-i)=min(tmin(t-i),tmin(t-i+1));
end
cut=min([find((tmin(2:t)-tmax(1:t-1))==1, 1 ) t]); %%% Edited by Mingrui, 20120320, fix a bug.
cuv=tmax(cut);
end
tl=1:cut;
tr=(cut+1):t;
vl=1:cuv;
vr=(cuv+1):v;
h=0.39;
r=max(surf.coord,[],2)-min(surf.coord,[],2);
w1=h/r(2)*r(1)*3/4;
h1=h/r(2)*r(1);
function w1=NoMeshPage(surf)
h=0.39;
r=max(surf.sphere,[],1)-min(surf.sphere,[],1)*2;
w1=h/r(2)*r(1)*3/4;
function Viewer=GenerateView8(h1,w1)
Viewer(1,:)=[0.055,0.62,0.2925,0.4,-90,0];
Viewer(2,:)=[0.3,0.58,0.4,0.39,0,90];
Viewer(3,:)=[0.6525,0.62,0.2925,0.4,90,0];
Viewer(4,:)=[0.055,0.29,0.2925,0.4,90,0];
Viewer(5,:)=[0.3,0.18,0.4,0.39,0,-90];
Viewer(6,:)=[0.6525,0.29,0.2925,0.4,-90,0];
Viewer(7,:)=[0.055,0.02,w1,h1,180,0];
Viewer(8,:)=[0.945-w1,0.02,w1,h1,0,0];
function Viewer=GenerateView6(w1)
% Viewer(1,:)=[0.05,0.58,0.34,0.4,-90,0];
% Viewer(2,:)=[0.4,0.58,0.2,0.39,0,90];
% Viewer(3,:)=[0.61,0.58,0.34,0.4,180,0];
% Viewer(4,:)=[0.05,0.15,0.34,0.4,90,0];
% Viewer(5,:)=[0.4,0.15,0.2,0.39,0,-90];
% Viewer(6,:)=[0.61,0.15,0.34,0.4,0,0];
Viewer(1,:)=[0.055,0.58,0.2925,0.4,-90,0];
Viewer(2,:)=[0.35,0.58,0.3,0.39,0,90];
Viewer(3,:)=[0.6525,0.6,0.25,0.33,180,0];
Viewer(4,:)=[0.055,0.15,0.2925,0.4,90,0];
Viewer(5,:)=[0.35,0.15,0.3,0.39,0,-90];
Viewer(6,:)=[0.6525,0.17,0.25,0.33,0,0];
function Viewer=GenerateView4
% YAN Chao-Gan 111023 Added. For Medium View (4 views)
Viewer(1,:)=[0.045,0.45,0.4387,0.6,-90,0];
Viewer(2,:)=[0.52,0.45,0.4387,0.6,90,0];
Viewer(3,:)=[0.045,-0.01,0.4387,0.6,90,0];
Viewer(4,:)=[0.52,-0.01,0.4387,0.6,-90,0];
function Viewer=GenerateView4v
% Lijie Huang 130221 Added. For Medium View (4 views) and 2 Ventral Views
Viewer(1,:)=[0.045,0.6,0.4387,0.36,-90,0];
Viewer(2,:)=[0.52,0.6,0.4387,0.36,90,0];
Viewer(3,:)=[0.045,0.23,0.4387,0.36,90,0];
Viewer(4,:)=[0.52,0.23,0.4387,0.36,-90,0];
Viewer(5,:)=[0.045,0.03,0.4387,0.18,-90,-90];
Viewer(6,:)=[0.52,0.03,0.4387,0.18,90,-90];
function Viewer = GenerateView5
% Added by Mingrui, 20170309, add layout for lateral, medial and dorsal view
Viewer(1,:) = [0.055,0.5,0.2925,0.4,-90,0];
Viewer(2,:) = [0.3,0.29,0.4,0.39,0,90];
Viewer(3,:) = [0.6525,0.5,0.2925,0.4,90,0];
Viewer(4,:) = [0.055,0.145,0.2925,0.4,90,0];
Viewer(5,:) = [0.6525,0.145,0.2925,0.4,-90,0];
function Surfmatrix=GenertateSurfM8(surf,tl,tr,vl,vr,cuv)
global EC
Surfmatrix.tri{1}=surf.tri(tl,:);
Surfmatrix.tri{2}=surf.tri;
Surfmatrix.tri{3}=surf.tri(tr,:)-cuv;
Surfmatrix.tri{4}=surf.tri(tl,:);
Surfmatrix.tri{5}=surf.tri;
Surfmatrix.tri{6}=surf.tri(tr,:)-cuv;
Surfmatrix.tri{7}=surf.tri;
Surfmatrix.tri{8}=surf.tri;
Surfmatrix.coord{1}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{2}=[surf.coord(1,:)',surf.coord(2,:)',surf.coord(3,:)'];
Surfmatrix.coord{3}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{4}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{5}=[surf.coord(1,:)',surf.coord(2,:)',surf.coord(3,:)'];
Surfmatrix.coord{6}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{7}=[surf.coord(1,:)',surf.coord(2,:)',surf.coord(3,:)'];
Surfmatrix.coord{8}=[surf.coord(1,:)',surf.coord(2,:)',surf.coord(3,:)'];
if isfield(surf,'T')
Surfmatrix.T{1}=surf.T(vl);
Surfmatrix.T{2}=surf.T;
Surfmatrix.T{3}=surf.T(vr);
Surfmatrix.T{4}=surf.T(vl);
Surfmatrix.T{5}=surf.T;
Surfmatrix.T{6}=surf.T(vr);
Surfmatrix.T{7}=surf.T;
Surfmatrix.T{8}=surf.T;
end
if isfield(surf,'boundary_value')
Surfmatrix.boundary_value{1}=surf.boundary_value(vl);
Surfmatrix.boundary_value{2}=surf.boundary_value;
Surfmatrix.boundary_value{3}=surf.boundary_value(vr);
Surfmatrix.boundary_value{4}=surf.boundary_value(vl);
Surfmatrix.boundary_value{5}=surf.boundary_value;
Surfmatrix.boundary_value{6}=surf.boundary_value(vr);
Surfmatrix.boundary_value{7}=surf.boundary_value;
Surfmatrix.boundary_value{8}=surf.boundary_value;
end
if EC.msh.color_type == 2
Surfmatrix.color_table{1} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{2} = EC.msh.color_table;
Surfmatrix.color_table{3} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{4} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{5} = EC.msh.color_table;
Surfmatrix.color_table{6} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{7} = EC.msh.color_table;
Surfmatrix.color_table{8} = EC.msh.color_table;
end
function Surfmatrix=GenertateSurfM4(surf,tl,tr,vl,vr,cuv)
% YAN Chao-Gan 111023 Added. For Medium View (4 views)
global EC
Surfmatrix.tri{1}=surf.tri(tl,:);
Surfmatrix.tri{2}=surf.tri(tr,:)-cuv;
Surfmatrix.tri{3}=surf.tri(tl,:);
Surfmatrix.tri{4}=surf.tri(tr,:)-cuv;
Surfmatrix.coord{1}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{2}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{3}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{4}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
if isfield(surf,'T')
Surfmatrix.T{1}=surf.T(vl);
Surfmatrix.T{2}=surf.T(vr);
Surfmatrix.T{3}=surf.T(vl);
Surfmatrix.T{4}=surf.T(vr);
end
if isfield(surf,'boundary_value')
Surfmatrix.boundary_value{1}=surf.boundary_value(vl);
Surfmatrix.boundary_value{2}=surf.boundary_value(vr);
Surfmatrix.boundary_value{3}=surf.boundary_value(vl);
Surfmatrix.boundary_value{4}=surf.boundary_value(vr);
end
if EC.msh.color_type == 2
Surfmatrix.color_table{1} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{2} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{3} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{4} = EC.msh.color_table(vr,:);
end
function Surfmatrix=GenertateSurfM4v(surf,tl,tr,vl,vr,cuv)
% Lijie Huang 130221 Added. For Medium View (4 views) and 2 ventral views
global EC
Surfmatrix.tri{1}=surf.tri(tl,:);
Surfmatrix.tri{2}=surf.tri(tr,:)-cuv;
Surfmatrix.tri{3}=surf.tri(tl,:);
Surfmatrix.tri{4}=surf.tri(tr,:)-cuv;
Surfmatrix.tri{5}=surf.tri(tl,:);
Surfmatrix.tri{6}=surf.tri(tr,:)-cuv;
Surfmatrix.coord{1}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{2}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{3}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{4}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{5}=[surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{6}=[surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
if isfield(surf,'T')
Surfmatrix.T{1}=surf.T(vl);
Surfmatrix.T{2}=surf.T(vr);
Surfmatrix.T{3}=surf.T(vl);
Surfmatrix.T{4}=surf.T(vr);
Surfmatrix.T{5}=surf.T(vl);
Surfmatrix.T{6}=surf.T(vr);
end
if isfield(surf,'boundary_value')
Surfmatrix.boundary_value{1}=surf.boundary_value(vl);
Surfmatrix.boundary_value{2}=surf.boundary_value(vr);
Surfmatrix.boundary_value{3}=surf.boundary_value(vl);
Surfmatrix.boundary_value{4}=surf.boundary_value(vr);
Surfmatrix.boundary_value{5}=surf.boundary_value(vl);
Surfmatrix.boundary_value{6}=surf.boundary_value(vr);
end
if EC.msh.color_type == 2
Surfmatrix.color_table{1} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{2} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{3} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{4} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{5} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{6} = EC.msh.color_table(vr,:);
end
function Surfmatrix = GenertateSurfM5(surf,tl,tr,vl,vr,cuv)
% Added by Mingrui, 20170309, add layout for lateral, medial and dorsal view
global EC
Surfmatrix.tri{1} = surf.tri(tl,:);
Surfmatrix.tri{2} = surf.tri;
Surfmatrix.tri{3} = surf.tri(tr,:)-cuv;
Surfmatrix.tri{4} = surf.tri(tl,:);
Surfmatrix.tri{5} = surf.tri(tr,:)-cuv;
Surfmatrix.coord{1} = [surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{2} = [surf.coord(1,:)',surf.coord(2,:)',surf.coord(3,:)'];
Surfmatrix.coord{3} = [surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
Surfmatrix.coord{4} = [surf.coord(1,vl)',surf.coord(2,vl)',surf.coord(3,vl)'];
Surfmatrix.coord{5} = [surf.coord(1,vr)',surf.coord(2,vr)',surf.coord(3,vr)'];
if isfield(surf,'T')
Surfmatrix.T{1} = surf.T(vl);
Surfmatrix.T{2} = surf.T;
Surfmatrix.T{3} = surf.T(vr);
Surfmatrix.T{4} = surf.T(vl);
Surfmatrix.T{5} = surf.T(vr);
end
if isfield(surf,'boundary_value')
Surfmatrix.boundary_value{1}=surf.boundary_value(vl);
Surfmatrix.boundary_value{2}=surf.boundary_value;
Surfmatrix.boundary_value{3}=surf.boundary_value(vr);
Surfmatrix.boundary_value{4}=surf.boundary_value(vl);
Surfmatrix.boundary_value{5}=surf.boundary_value(vr);
end
if EC.msh.color_type == 2
Surfmatrix.color_table{1} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{2} = EC.msh.color_table;
Surfmatrix.color_table{3} = EC.msh.color_table(vr,:);
Surfmatrix.color_table{4} = EC.msh.color_table(vl,:);
Surfmatrix.color_table{5} = EC.msh.color_table(vr,:);
end
function a=PlotMesh4(Viewer,Surfmatrix,alpha)
% Mingrui Xia 111026 Added. For Medium View (4 views)
global EC
global cam
a=zeros(1,4);
for i=1:4
a(i)=axes('position',Viewer(i,1:4));